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Breakthrough in solid-state storage innovates how biological materials are stored and handled
Scientists have developed a novel method for storing biological materials such as RNA and proteins in a solid-state. The storage in solid-state resembles the form of a pill or a tablet, which dissolves in water for on-demand use. The innovation provides a new way to overcome current limitations in the storage and handling of products derived from living cells used for a variety of health care and scientific research purposes.
Biological materials that are frequently used in developing new medicines and diagnostic testing tools such as mRNA, enzymes, and antibodies are highly sensitive to changing ambient conditions during storage, transportation, and handling. When they are not stored and handled properly, they can degrade or become inactive. The result is a fundamental limitation to access in resource-limited and underserved communities.
For example, the Pfizer COVID vaccine rollout was limited in speed and breadth due the need for deep freezers for storage and transport. More broadly, even when refrigeration infrastructure is present, failures occurred in over 10% of cases, resulting in over $35 billion in losses annually according to IQVIA Institute for Human Data Science.
To overcome some of the key limitations, researchers at California Polytechnic State University (Cal Poly) in San Luis Obispo, CA, have developed the new method for storing biological materials with vast potential for use by the scientific and medical communities.
When most of us open our medicine cabinets, we find pharmaceutical drugs stored in forms such as liquids, powders packaged in capsules, pills and tablets. Pharmaceuticals have proven that each form plays an important role in how the medication is stored and used.
Apart from a few exceptions, biological materials such as medications, are currently limited to being stored as frozen or refrigerated liquids and freeze-dried powders. The absence of a tablet-like form has limited the field, often making it challenging to reach the locations and users where they are needed.
"Just as tablets have changed the way we take medications, the solid-state storage platform opens new possibilities for how we handle and use biological materials, unlocking the potential for existing therapies and emerging biotechnologies," said Dr. Javin Oza, associate professor in chemistry and biochemistry, who led the research on the new storage platform.
Most biological materials require storage as liquids which are frozen in deep freezers for the duration of their shelf life. As a society, we accomplish this through a complex and integrated system of refrigerators and freezers, known as the cold-chain. In recent years, many research teams, including the group at Cal Poly have made progress in freeze-drying biological materials, which has improved the way they are stored and handled, but the use of freeze-drying remains limited.
The solid-state storage of biologics represents the next big step because tablets provide unique advantages to better preserve the material they encapsulate. For example, the innovation allows researchers to be able to package biological materials into tablets that can be stored on a shelf at room temperature, and added to water to be dissolved for on-demand use. In addition to ensuring the stability and activity of the biological materials, solid-state storage has been developed to ensure that tablets quickly disintegrate and dissolve into water.
"Our innovation makes storing and using biologics as easy as an Alka-Seltzer tablet, just drop it into water, mix, and it's ready to go," Oza added.
As a test case for the solid-state storage platform's ability to support a complex mixture of biologics, the team demonstrated that the cell's machinery capable of decoding genetic information into making RNA and proteins can be stored in a solid-state. When added to water, the machinery reactivates to decode genetic information as if it were still within the cell. The team also went a step further to demonstrate that emerging biotechnology tools such as CRISPR can be activated after storage in a solid-state.
The team's results demonstrate potential for a wide range of applications. The ability to store biologics at room temperature and activate them on demand could be useful for delivering therapeutics to remote locations where the cold-chain is unavailable. For instance, one could envision portable, on-demand production of vaccines to remote locations. The platform could also be used for diagnostic testing of anything from COVID-19 screening to testing wastewater contaminants, simply by changing the composition of the tablets. For utilization in the field, the solid-state storage has the added benefit of being simple to use, reducing the need for specialty training of technicians, further improving access at the point of need.
Further improvements to the platform will be needed to suit specific use cases. The researchers anticipate that additional modifications such as coatings could help the solid-state storage be more suitable for withstanding extreme environments such as heat, humidity, and chemicals. Additionally, continued improvements in treatments and coatings to the solid-state biologics could lead to biological medication tablets that can be taken orally rather than through injections. If successful, medications such as insulin and Humira (immunosuppressive treatment for arthritis) could someday be taken orally rather than through injections, improving the quality of life for millions of people.
Since the field of biotechnology is growing rapidly, the potential impacts extend beyond health care, and into biomanufacturing, education, and research. The innovation is also likely to impact the way biologics are transported around the globe and into space for the on-demand production of life-saving therapies.
More information: August W. Brookwell et al, Development of Solid-State Storage for Cell-Free Expression Systems, ACS Synthetic Biology (2023). DOI: 10.1021/acssynbio.3c00111
Journal information: ACS Synthetic Biology
Provided by California Polytechnic State University | Biology |
Scientists lure Burmese pythons using radio telemetry during mating/breeding season
University of Florida wildlife scientists are scouting for Burmese pythons in the Everglades by using previously captured pythons to lure, locate and learn how the invasive species is thriving in the Everglades.
This latest effort is a large-scale python removal scout program led by UF/IFAS scientists in collaboration with the United States Geological Survey (USGS), Fort Collins Science Center, South Florida Water Management District (SFWMD) and the Florida Fish and Wildlife Conservation Commission (FWC).
Researchers are using pythons captured by SFWMD's Python Elimination Program and FWC's Python Action Team to study python biology further as they leverage radio telemetry technology during the species mating and breeding seasons to remove pythons.
"Our study links python ecology with removal efforts," said Melissa Miller, project lead and research assistant scientist specializing in invasion biology at UF/IFAS Fort Lauderdale Research and Education Center. "This allows for long-term, in-depth research projects, which are critical to understanding cryptic, long-lived species such Burmese pythons, all while continuing to find and remove pythons from the Everglades."
Adult male and female pythons, provided by the water management district's Python Elimination Program and FWC's Python Action Team, are implanted with tracking devices and released into Everglades Francis S. Taylor Wildlife Management Area.
As pythons form mating aggregations consisting of multiple male suitors lured by a female, tracking them during their breeding season can increase the number of snakes removed. The tracked males can help scientists locate female pythons capable of producing up to 100 eggs, which can be captured and removed. Sex pheromones secreted by tracked females lure males naturally and female pythons can provide important life history information concerning reproduction and survivorship that can be used to help estimate the number of pythons in the Everglades.
The tracking devices will lead researchers to the snakes, allowing them to record behavior and document reproductive data such as nesting sites, clutch size, hatchlings and how many survive.
The project will help inform management efforts by increasing our understanding of how pythons use a predominant habitat type—sawgrass marsh interspersed with tree islands—within the Everglades.
The team has started tracking eight adult pythons, which will provide data on habitat use and python abundance that will help natural resource managers evaluate control efforts, said Miller, who is also affiliated with the UF/IFAS Croc Docs.
"As administering a python radiotelemetry project in the Everglades requires many resources, the project will also assess innovative tools to reduce those resources while allowing for increased data collection," Miller said.
The program launch coincides with the release of a paper last month which takes a deep dive into what scientists have learned over decades about the python invasion. 'Burmese pythons in Florida: A synthesis of biology, impacts, and management tools,' led by the USGS Wetland and Aquatic Research Center, is a collaboration among several federal and state agencies, non-governmental organizations and academic institutions, including UF/IFAS.
The paper showcases years of research, control efforts and the challenges associated with management of the Burmese python in Florida.
Miller, along with UF/IFAS wildlife ecology and conservation faculty Christina Romagosa and Frank Mazzotti who collectively have more than 40 years of experience studying large reptile invasions in Florida—contributed their findings to the manuscript.
"Years of research by UF/IFAS faculty have added to our knowledge of python biology, impacts and management, including identifying native wildlife at risk of predation by pythons, and impacts of pythons through introduction of emerging pathogens and parasites," said Miller.
The research has further increased our understanding of pythons' ability to withstand cold temperatures, identified how they use habitats within biologically sensitive areas, and explored methods to increase python detection and removal.
Florida is a hotspot for invasive species, with over 500 nonnative species reported, according to FWC.
"Once a nonnative species becomes established in the wild (meaning reproducing), it is often too late to eradicate; and as is the case with Burmese pythons, natural resource managers must focus on containment and long-term management which is costly on resources and impacts to native ecosystems," said Miller.
For this reason, the UF/IFAS Croc Docs reminds Florida residents and visitors to report sightings of invasive species immediately on EddMapS, the IveGot1 smartphone app or call 1-888-Ive-Got1 to prevent establishment and to protect the Everglades ecosystem.
To reduce the number of nonnative species released into the wild, the Florida Fish and Wildlife Conservation Commission's Exotic Pet Amnesty Program provides owners the opportunity to surrender pets for any reason at any time, even if those pets are regulated in Florida.
The research is published in the journal NeoBiota.
More information: Jacquelyn C. Guzy et al, Burmese pythons in Florida: A synthesis of biology, impacts, and management tools, NeoBiota (2023). DOI: 10.3897/neobiota.80.90439 | Biology |
Fetuses favor patterns of light that resemble faces over those without face-like features, a new study suggests. The study, published last week in Current Biology, is the first to test visual processing in babies before birth.
The findings suggest that a preference for faces starts even before a baby has ever seen a face. And they run counter to the idea that babies like faces simply because that’s what they see first.
Gaining a better understanding of how face processing develops could help scientists better understand atypical development, including in the case of autism, says lead researcher Vincent Reid, professor of psychology at Lancaster University in the United Kingdom.
“It could be that somebody’s early elements of visual processing are somehow not constructed correctly, which could then lead on to other forms of visual problems that you see in autism,” Reid says.
The work also has practical implications. Some children with autism avoid looking at people’s eyes and show an unusually weak brain response to images of faces. Scientists could look at the preferences of babies at high risk of autism while they are still in the womb.
“In principle, it could lead to the discovery of a very early developmental marker for risk for developing autism,” says Ralph Adolphs, professor of psychology and neuroscience at the California Institute of Technology, who was not involved with the study. Such a marker could help parents and clinicians decide on the best early therapies, he says.
Bright spot:
From the first hours of life, babies prefer to look at faces over other stimuli. But their vision is blurry at birth, so they don’t see the details of a face, just its general outline. Until several years ago, scientists thought the uterus was a dark environment. But the uterus is now thought to transmit light in amounts that a fetus can see.
In the new study, researchers used lasers to shine three bright dots through the uterine wall in 39 women in their third trimester of pregnancy. In one configuration, the dots formed an inverted triangle resembling two eyes and a mouth. In the other, the dots formed a triangle with one dot at the top and two at the bottom.
Reid and his team showed each fetus both dot patterns five times, moving the light across each woman’s abdomen for five seconds. They recorded the fetus’ reaction using 4-D ultrasound, which streams a video of 3-D scans. Fetuses were more than twice as likely to turn their heads toward the face-like pattern as toward the simple triangle.
The ability to track the visual response of a fetus represents “a methodological advance,” says Mark Johnson, director of the Centre for Brain and Cognitive Development at Birkbeck, University of London, who was not involved in the study. “It was known for quite a long time that we can study the auditory system of the fetus, see how they respond to speech and music, but it was assumed there was no point doing similar things with the visual system.”
The study also offers a way to extend work on infant vision to fetal development. It shows, Reid says, that “the fetus does not passively process the environment but actively responds to the environment.”
The researchers plan to extend the study to other areas of perception and cognition in fetuses. For example, they say, they would like to explore whether the fetus can discriminate between different numbers of dots.
Further Reading:
- Doubt Greets Reports of Suramin’s Promise for Treating Autism
- Parents’ Interactions with Infants May Alleviate Autism Features
- New Tools Strengthen Old Link Between Autism, Mitochondria
- Autism in Motion | Biology |
A new grant will allow Rochester researchers to leverage bacteria and nanomaterials to mimic photosynthesis and produce clean-burning hydrogen fuel.
As the world faces an increasing demand for clean and sustainable energy sources, scientists are turning to the power of photosynthesis for inspiration. With the goal of developing new, environmentally friendly techniques to produce clean-burning hydrogen fuel, a team of researchers at the University of Rochester is embarking on a groundbreaking project to mimic the natural process of photosynthesis using bacteria to deliver electrons to a nanocrystal semiconductor photocatalyst.
By leveraging the unique properties of both microorganisms and nanomaterials, the project has the potential to replace current approaches that derive hydrogen from fossil fuels, revolutionizing the way hydrogen fuel is produced and unlocking a powerful source of renewable energy.
The Rochester team, led by Kara Bren, the Richard S. Eisenberg Professor in Chemistry, along with Todd Krauss, a professor of chemistry; Anne S. Meyer, an associate professor of biology; and Andrew White, an associate professor of chemical engineering, received a nearly $2 million, three-year grant from the US Department of Energy (DOE) to create their “living bio-nano system” to produce solar hydrogen.
“Hydrogen is definitely a fuel of high interest for the DOE right now,” Bren says. “If we can figure out a way to efficiently extract hydrogen from water, this could lead to an incredible amount of growth in clean energy.”
Why is hydrogen a promising fuel source?
Hydrogen is “an ideal fuel,” Bren says, “because it’s environmentally-friendly and a carbon-free alternative to fossil fuels.”
Hydrogen is the most abundant element in the universe and can be produced from a variety of sources, including water, natural gas, and biomass.
Unlike fossil fuels, which produce greenhouse gases and other pollutants, when hydrogen is burned, the only byproduct is water vapor. Hydrogen fuel also has a high energy density, which means it contains a lot of energy per unit of weight. It can be used in a variety of applications, including fuel cells, and can be made on both small and large scales, making it feasible for everything from home use to industrial manufacturing.
Why is hydrogen fuel difficult to produce?
Despite hydrogen’s abundance, there is virtually no pure hydrogen on Earth; it is almost always bound to other elements, such as carbon or oxygen, in compounds like hydrocarbons and water. To use hydrogen as a fuel source, it must be extracted from these compounds.
Scientists have historically extracted hydrogen either from fossil fuels, or, more recently, from water. To achieve the latter, there is a major push to employ artificial photosynthesis.
During natural photosynthesis, plants absorb sunlight, which they use to power chemical reactions to convert carbon dioxide and water into glucose and oxygen. In essence, light energy is converted into chemical energy that fuels the organism.
Similarly, artificial photosynthesis is a process of converting an abundant feedstock and sunlight into a chemical fuel, such as producing hydrogen gas from water. Systems that mimic photosynthesis require three components: a light absorber, a catalyst to make the fuel, and a source of electrons. These systems are typically submerged in water, and a light source provides energy to the light absorber. The energy allows the catalyst to combine the provided electrons together with protons from the surrounding water to produce hydrogen gas.
Most of the current systems, however, rely on fossil fuels during the production process or don’t have an efficient way to transfer electrons.
“The way hydrogen fuel is produced now effectively makes it a fossil fuel,” Bren says. “We want to get hydrogen from water in a light-driven reaction so we have a truly clean fuel—and do so in a way that we don’t use fossil fuels in the process.”
What makes the Rochester system unique?
Krauss’s group and Bren’s group have been working for about a decade to develop an efficient system that employs artificial photosynthesis and utilizes semiconductor nanocrystals for light absorbers and catalysts. Semiconductor nanocrystals are tiny crystals made of semiconducting materials. Due to their small size—they are composed of only a few hundred to a few thousand atoms—they have unique properties, which can be easily tuned. Krauss’s lab has made major advances in developing efficient quantum dots, one type of semiconductor nanocrystal.
“Our role in the project is centered on making the nanoparticles that absorb light, and then conducting measurements of the rates of charge transfer in the system,” Krauss says. “This will help us figure out how to eventually scale the system and also make it more efficient.”
Another challenge the researchers faced was figuring out a source of electrons and efficiently transferring the electrons from the electron donor to the nanocrystal. Other systems have used ascorbic acid, commonly known as vitamin C, to deliver electrons back to the system. While vitamin C might seem inexpensive, “you need a source of electrons that is almost free or the system becomes too expensive,” Krauss says.
In a paper published in PNAS, Krauss and Bren demonstrate an unlikely electron donor: bacteria. They found that Shewanella oneidensis, bacteria first gathered from Lake Oneida in upstate New York, offers an effectively free, yet efficient, way to provide electrons to their system.
While other labs have combined nanostructures and bacteria, “all of those efforts are taking electrons from the nanocrystals and putting them into the bacteria, then using the bacterial machinery to prepare fuels,” Bren says. “As far as we know, ours is the first case to go the opposite way and use the bacteria as an electron source to a nanocrystal catalyst.”
What makes bacteria an efficient electron donor?
When bacteria grow under anaerobic conditions—conditions without oxygen—they respire cellular substances as fuel, releasing electrons in the process. Shewanella oneidensis can take electrons generated by its own internal metabolism and donate them to the external catalyst.
“This technique is really promising because it can produce hydrogen energy efficiently while relying only upon sustainable sources for electrons and energy,” says Meyer, whose lab has previously worked with Shewanella oneidensis to produce materials with unique properties. In this project, her lab is designing and creating new strains of Shewanella that will have enhanced abilities to transfer electrons. They will apply their pioneering 3D printing techniques to print living material that can incorporate quantum dots.
“By combining our engineered Shewanella bacteria together with the photocatalyst developed by the Bren and Krauss labs, we will be able to create physically robust, long-lived materials that will make the hydrogen production reaction faster and more efficient,” Meyer says.
Because the system is so complex, White’s lab will use machine learning and artificial intelligence techniques to determine which factors and variables could be changed to optimize the system; for instance, predicting which 3D-printed geometries will be the most likely to produce hydrogen more efficiently.
Pursuing both basic and applied science
While the ultimate goal is to develop a better system for producing hydrogen fuel, Bren is also committed to understanding the basic science behind the project.
“For example,” she says, “how can we most effectively get the electrons from the bacteria to the quantum dots? How do nanomaterials and microorganisms work together?”
Bren envisions that, in the future, individual homes could potentially have vats and underground tanks to harness the power of the sun and produce and store small batches of hydrogen, allowing people to power their homes and cars with inexpensive, clean-burning fuel. Bren notes there are currently trains, buses, and cars powered by hydrogen fuel cells but almost all the hydrogen that is available to power these systems comes from fossil fuels.
“The technology’s out there,” she says, “but until the hydrogen’s coming from water in a light-driven reaction—without using fossil fuels—it isn’t really helping the environment.”
Read more
By harnessing the power of metals, Rochester researchers are making the material an ever more viable replacement for silicon in solar cells and detectors.
Graphene is a revolutionary nanomaterial, the discovery of which led to a Nobel Prize. By mixing graphite with bacteria, Rochester scientists are making graphene easier and more environmentally friendly to produce.
Rochester researchers led by Todd Krauss, a professor of chemistry, are joining a major US Department of Energy-funded initiative to advance quantum science and technology.
Category: Science & Technology | Biology |
Scientists have created an AI system capable of generating artificial enzymes from scratch. In laboratory tests, some of these enzymes worked as well as those found in nature, even when their artificially generated amino acid sequences diverged significantly from any known natural protein.
The experiment demonstrates that natural language processing, though developed to read and write language text, can learn at least some of the underlying principles of biology. Salesforce Research developed the AI program, called ProGen, which uses next-token prediction to assemble amino acid sequences into artificial proteins.
Scientists said the new technology could become more powerful than directed evolution, a Nobel-prize-winning protein design technology, and will energize the 50-year-old field of protein engineering by speeding the development of new proteins that can be used for almost anything from therapeutics to degrading plastic.
Programs like ProGen Can Design Proteins From Scratch
Users Input Control Tag
A user enters a control tag, which can be a protein type such as lysozome, into the ProGen AI model.
ProGen AI Model
The ProGen AI model uses the tag to assemble amino acid sequences into artificial proteins.
Output of Proteins
These new artificial proteins can be used for almost anything from therapeutics to degrading plastic.
“The artificial designs perform much better than designs that were inspired by the evolutionary process,” said James Fraser, PhD, professor of bioengineering and therapeutic sciences at the UCSF School of Pharmacy, and an author of the work, which was published Jan. 26, in Nature Biotechnology. A previous version of the paper has been available on the preprint server BiorXiv since July 2021, where it garnered several dozen citations before being published in a peer-reviewed journal.
“The language model is learning aspects of evolution, but it’s different than the normal evolutionary process,” Fraser said. “We now have the ability to tune the generation of these properties for specific effects. For example, an enzyme that’s incredibly thermostable or likes acidic environments or won’t interact with other proteins.”
To create the model, scientists simply fed the amino acid sequences of 280 million different proteins of all kinds into the machine learning model and let it digest the information for a couple of weeks. Then, they fine-tuned the model by priming it with 56,000 sequences from five lysozyme families, along with some contextual information about these proteins.
The model quickly generated a million sequences, and the research team selected 100 to test based on how closely they resembled the sequences of natural proteins as well how naturalistic the AI proteins’ underlying amino acid “grammar” and “semantics” were.
Out of this first batch of 100 proteins, which were screened in vitro by Tierra Biosciences, the team made five artificial proteins to test in cells and compared their activity to an enzyme found in the whites of chicken eggs, known as hen egg white lysozyme (HEWL). Similar lysozymes are found in human tears, saliva and milk, where they defend against bacteria and fungi.
Two of the artificial enzymes were able to break down the cell walls of bacteria with activity comparable to HEWL, yet their sequences were only about 18% identical to one another. The two sequences were about 90% and 70% identical to any known protein.
Just one mutation in a natural protein can make it stop working, but in a different round of screening, the team found that the AI-generated enzymes showed activity even when as little as 31.4% of their sequence resembled any known natural protein.
The AI was even able to learn how the enzymes should be shaped, simply from studying the raw sequence data. Measured with X-ray crystallography, the atomic structures of the artificial proteins looked just as they should, although the sequences were like nothing seen before.
Salesforce Research developed ProGen in 2020, based on a kind of natural language programming their researchers originally developed to generate English language text.
They knew from their previous work that the AI system could teach itself grammar and the meaning of words, along with other underlying rules that make writing well-composed.
“When you train sequence-based models with lots of data, they are really powerful in learning structure and rules,” said Nikhil Naik, PhD, director of AI research at Salesforce Research, and the senior author of the paper. “They learn what words can co-occur, and also compositionality.”
With proteins, the design choices were almost limitless. Lysozymes are small as proteins go, with up to about 300 amino acids. But with 20 possible amino acids, there are an enormous number (20300) of possible combinations. That’s greater than taking all the humans who lived throughout time, multiplied by the number of grains of sand on Earth, multiplied by the number of atoms in the universe.
Given the limitless possibilities, it’s remarkable that the model can so easily generate working enzymes.
“The capability to generate functional proteins from scratch out-of-the-box demonstrates we are entering into a new era of protein design,” said Ali Madani, PhD, founder of Profluent Bio, former research scientist at Salesforce Research, and the paper’s first author. “This is a versatile new tool available to protein engineers, and we’re looking forward to seeing the therapeutic applications.”
Please see the paper for a complete author and funding list. A comprehensive codebase for the methods described in the paper is publicly available. | Biology |
Living in a greener environment has an impact on the composition of oligosaccharides in mother's breastmilk, which in turn may affect the infant’s health. A study conducted at the University of Turku showed that greater diversity and proportion of green environments in the residential area were associated with increased diversity in the composition of the oligosaccharides in breastmilk. A new study conducted at the Departments of Biology and Public Health at University of Turku examined the association between the residential green environment and the individual oligosaccharide profile in the mother’s breastmilk. Oligosaccharides are sugar molecules that are the most common component in breastmilk after lactose and fat. So far, approximately 200 oligosaccharides have been discovered and they form a very versatile group of different kinds of complex structures. The oligosaccharides in breastmilk can protect the infant from harmful microbes and reduce the risk of developing allergies and diseases. The oligosaccharides are also closely connected to the immune system and gut microbiota which also have an impact the infant’s health. “Earlier studies have shown that genetic and biological factors, such as mother’s obesity, can change the oligosaccharide composition in breastmilk. Our aim was to study how green living environments affect the composition of oligosaccharides in breastmilk, as greener environments have been found to have a beneficial impact on immunity and reduce the risk of disease in children,” says Docent Mirkka Lahdenperä from the Department of Biology at the University of Turku. Closer Connection to Nature May Affect Child's Health via Breastmilk Approximately 800 mothers participated in the longitudinal follow-up study, the STEPS Study, that started at the University of Turku in 2007. The breastmilk samples were collected when the infants were three months old, after which the oligosaccharide composition was analysed at the Bode Lab at the University of California San Diego. The residential green environments were measured at the time the child was born around the homes of the families with measures of greenness, diversity of vegetation, and naturalness index, i.e. how much human impact and intervention there has been in the residential area. The results were independent of the education level, occupation, marital status and health of the children’s parents as well as the socio-economic disadvantage in the residential area. The study showed that the diversity of oligosaccharides increases and the composition of several individual oligosaccharides changes when the mother’s residential area includes more green environments. “This could indicate that increased everyday contacts with nature could be beneficial for breastfeeding mothers and their children as the oligosaccharide composition of breastmilk would become more diverse. The results imply that breastfeeding could have a mediating role between residential green environments and health in infancy,” says Lahdenperä and continues: “The results highlight the importance of understanding the biological pathways that can impact health and lead to the development of different diseases starting from infancy.” The research was funded by the Academy of Finland and Juho Vainio Foundation as well as the Hospital District of Southwest Finland. > The research article was published in the journal Scientific Reports Support science and research | Biology |
Sign up for CNN’s Wonder Theory science newsletter. Explore the universe with news on fascinating discoveries, scientific advancements and more. CNN — From a deer’s elaborate branching antlers to the fiddler crab’s oversize claw, the animal kingdom is full of flashy features used in combat to help secure a mate. A team of researchers announced last week that it has found the earliest known evidence of sexual combat in the form of a trident-headed trilobite that scuttled the seafloor 400 million years ago. Trilobites were one of the earliest arthropods, the group of invertebrates containing insects, spiders, lobsters, crabs and other organisms with exoskeletons, segmented bodies and jointed limbs. These pill bug-like sea creatures first emerged 521 million years ago and died out 252 million years ago in the mass extinction that gave way to the dinosaurs. There were over 22,000 species of trilobite, some reaching lengths of more than 2 feet, but the type that caught the eye of paleontologist Alan Gishlick was more modest in size, around 2 to 3 inches. He recalls seeing specimens of Walliserops at fossil trade shows and marveling at the trident-shaped protrusion branching off the trilobites’ heads. “That’s the type of structure that has to have a function. You don’t put that much biological energy into something that doesn’t do something,” said Gishlick, an associate professor of paleontology at Bloomsburg University of Pennsylvania. Researchers have proposed various uses for these forking protrusions, including defense, hunting and attracting mates. In a paper published January 17 in the scientific journal Proceedings of the National Academy of Sciences, Gishlick and coauthor Richard Fortey delved into these hypotheses, ruling out the trident as a means of defense or a hunting tool based on how the trilobite would have been able to move it. The trident wouldn’t be of much use against predators attacking from above or behind, and while it could have been used to spear prey, the trilobite would then be stuck with its meal just out of reach. What made the most sense to Gishlick and Fortey, a paleontologist at the Natural History Museum in London, was that Walliserops used the trident to fight among each other. Their thinking was bolstered by an unusual specimen of Walliserops with a deformed trident bearing four prongs instead of the usual three. If the trident was a vital part of day-to-day survival, they reasoned, then the trilobite probably wouldn’t have lasted for long with a malformed one. Bolstered with the evidence for Walliserops’ trident being used to win mates, the researchers turned to the closest analogue they could find in the modern world. “The structure reminds me a heck of a lot of beetle horns,” Gishlick said. The researchers used a technique called landmark-based geometric morphometrics, which Gishlick described as a means of comparing complex shapes in a statistically robust way, to analyze the surface-level similarity of trilobite tridents and horns of rhinoceros beetles. They found that the trilobite tridents’ shape had a lot in common with the horns of beetles that flip their dueling partners in a “shoveling” motion, as opposed to other species whose horns are better for fencing or grasping. Gishlick said he believes that, like in beetles, trilobites’ tridents were “sexual weapons” used by males sparring to win mates. “This is the earliest known structure that we can point to and say, ‘Yeah, I’m pretty sure that this is an animal weapon used in reproductive competition,’ ” he said. Furthermore, Gishlick explained: “Generally, organisms that are involved in interspecific combat over mates are highly dimorphic” — varying in appearance from one sex to the other — “because only one does the competition, and generally in the animal world that’s the male.” Growing features such as big combat-ready horns requires a lot of energy, and female animals already have to expend lots of it to produce eggs. If the trilobites’ tridents are the first evidence of sexual weapons, then they could also be the earliest known evidence of sexual dimorphism. There’s one problem with this hypothesis, however: Scientists have no definitive means of telling which Walliserops are male and which are female, and no trident-less Walliserops have been discovered. That might be due to bias by fossil collectors, who Gishlick said often prioritize bigger, flashier specimens, or because the females might be labeled as entirely different species. “This to me makes it very clear that you better be looking for females,” Gishlick said. Erin McCullough, an assistant professor of biology at Clark University in Massachusetts, said she agrees with the researchers’ conclusion that the trilobite tridents were likely used for interspecies combat. However, she’s not sold on their argument that this was a trait only possessed by males. “In general, if there’s going to be an extravagant trait that’s used for fighting for mates, usually, it’s the males that have the extravagant trait, but biology is fun because there’s always exceptions — female reindeer have antlers,” said McCullough, who was not involved with the study (but whose beetle analyses Gishlick and Fortey drew upon for their work). “If they are arguing that these are male weapons that are used to gain access to females, it would have been a stronger story to me if they had evidence that the females don’t have weapons.” Kate Golembiewski is a freelance science writer based in Chicago who geeks out about zoology, thermodynamics and death. She hosts the comedy talk show “A Scientist Walks Into a Bar.” | Biology |
Introduction
Does an unseen force lurk within genetics? Biologists have made enormous strides over the past 100 years in understanding the role of the millions of parcels that convey our genetic information — DNA, RNA and proteins. But they have also learned about undetectable interactions between these biochemical agents, hiding in their midst like ghosts in the machine, complicating our quest to learn the secrets of life, one gene at a time. These interactions all fit under the umbrella of “epistasis” — not exactly a new idea in biology, but one whose influence and importance are only now being fully appreciated.
Geneticist Daniel Weinreich and colleagues suggested that epistasis is akin to the “surprise” at the effects of mutations when they combine, given what we know about them individually. Whenever a life form’s observable attributes differ from what the DNA would lead you to expect, epistasis may be to blame. Imagine that you know of two hypothetical mutations associated with a flower stem that’s ordinarily 40 centimeters long: Mutation A is associated with a long stem (say, 50 centimeters), and mutation B confers a short stem (30 centimeters). You might expect the mutations to cancel each other out, leaving a flower with a normal-length stem. Or perhaps the combination of mutations adds their independent lengths together, resulting in an extra-long stem (80 centimeters). But instead they end up producing an extra-short stem (10 centimeters). Geneticists would say that there is a nonlinear relationship between the effects of mutations A and B, which gives you the surprising outcome. This is a signature of epistasis.
The flower-stem example represents one of the simplest cases of epistasis, where the nonlinear interaction manifests between two genes or mutations. And there are cases in nature that aren’t so different from this hypothetical one (such as the pigmentation of pigeons, where three genes are responsible). But what about the rest of nature? The human genome, at last count, has roughly 20,000 genes. The genome of the domestic apple (Malus domestica) has over 57,000. All these different genes mean many possible epistatic interactions.
Epistasis can even occur in viruses, which often have relatively tiny genomes, many with fewer than a dozen genes. For example, the HIV virus can develop mutations that make it drug resistant. But these mutations can depend profoundly on the genetic background of the specific form of HIV. To identify the key mutations, you need to know what other mutations are in its genome. With this emphasis on context, epistasis modifies the grammar and logic of molecular biology: It would be easier if “mutations for drug resistance” really were just mutations for drug resistance, no matter what.
This is, in a way, a familiar idea. For example, I teach students in my evolutionary theory course that master chefs are experts at understanding and predicting epistatic effects. The specific challenge of cooking dishes with sophisticated recipes, or of being able to improvise new ones on the fly, is in understanding that ingredients can interact in surprising ways. And so there’s a long tradition of fields that address why the whole can be more than — or at least different from — the sum of its parts.
Indeed, the first references to epistasis came shortly after the rediscovery of Gregor Mendel’s experiments at the turn of the 20th century, which established our modern ideas of heredity and genes. Despite the Mendelian assumption that genes and mutations often act independently in crafting traits, scientists soon observed several counterexamples. In 1909, William Bateson introduced the word epistasis — from the Greek for “standing upon” — while trying to explain the repressive effects of some mutations on the effects of others.
But while the concept was developed long ago, it has taken almost a century for the idea of epistasis to rise to prominence. Partly that’s because it makes things harder for biologists. Its focus on genetic context means that there can be no “gene for mutant powers,” as in our favorite comic books — there is only a “gene that confers mutant powers when in a genome of a certain kind, and/or in the presence of other gene variants 1, 2 or 2,578 (perhaps in a specific combination).” That hypothetical comic book isn’t easy to read or write.
Some biologists remain so opposed to the idea that they don’t believe it’s worthwhile to focus on epistasis. They might object on technical grounds, saying, “Sure, it’s real, but single genes and mutations still matter!” These folks aren’t lying. We know of thousands of single genes or mutations that have a reliably large effect, across many experiments, independent (we think) of the genetic context. That is, there are many important genetic stories to tell without epistasis. Sometimes there are no ghosts.
But part of the opposition can also be charitably characterized as philosophical. This school says that if we can only know how a gene’s mutation works in the apple genome by understanding how it depends on the other 56,999 genes, then that introduces an astronomical number of possibilities — too many to test rigorously. To put it differently, a full embrace of epistasis can feel almost nihilistic. Predicting how genes will work might be tricky, but we can’t set the bar so high that it requires knowing everything about every gene (and mutation). Such a reality would make many of our efforts hopelessly messy. Alas, the only reasonable response to this objection is a common one in science: It is not nature’s job to make itself easy to study, or to submit to our assumptions. Life is complex. We must let it be.
Thankfully, modern breakthroughs in the study of epistasis have worked to partly demystify it. For example, in 2017 the statistician Lorin Crawford and colleagues pioneered a method (known as MAPIT) to measure epistatic interactions between mutations in large sets of data spanning a species’ entire genome — effectively plotting and measuring possible epistatic effects among existing genes and mutations in large genomes. Approaches like this allow us to identify and measure how these ghosts manifest across the genome, helping us understand where human traits come from, including those associated with disease risk.
Other breakthroughs live at the level of proteins: New methods allow us to measure thousands of variants of a single protein, allowing us to see how epistasis manifests in important proteins, such as in the virus that causes Covid-19.
Further, a new idea called global epistasis suggests that the ghost might not be so ghostly. With our hypothetical flower-stem mutations A and B, a global epistasis approach would suggest that the effects of adding mutation B to any genome (whether or not it contains mutation A) will follow a set pattern. Perhaps mutation B acts like a negative amplifier of other mutations, and when in the presence of a mutation that confers a long stem, it reverses the effect. These kinds of patterns have already been observed in several systems independently. How widespread this global epistasis is, and to which systems it applies, is still the object of current research. But it is exciting to know that there might be a way to predict the surprise.
The “ghost in the machine” metaphor was originally used to discuss the mind-body duality problem, the distinction between the nonphysical mind and the mechanical body it controls. It has often been invoked to describe the fear that we might not be building what we think we are — whether it’s increasingly intelligent machines or our understanding of subtly interacting genetic codes. And indeed, bioengineering is where epistasis might cause us the most trouble. Anyone who wants to engineer new livestock (or designer babies) with desirable traits, one mutation at a time, will need to contend with the constant specter of unforeseen consequences — to say nothing of the enormous ethical issues.
These ghosts make the work of geneticists that much more challenging, true. But they also make the biological world that much more fantastic. | Biology |
One of the major benefits of certain artificial intelligence models is that they can speed up menial or time-consuming tasks —- and not just to whip up terrible "art" based on a brief text input. University of Leeds researchers have unveiled a neural network that they claim can map an outline of a large iceberg in just 0.01 seconds.
Scientists are able to track the locations of large icebergs manually. After all, one that was included in this study was the size of Singapore when it broke off from Antarctica a decade ago. But it's not feasible to manually track changes in icebergs' area and thickness — or how much water and nutrients they're releasing into seas.
"Giant icebergs are important components of the Antarctic environment," Anne Braakmann-Folgmann, lead author of a paper on the neural network, told the European Space Agency. "They impact ocean physics, chemistry, biology and, of course, maritime operations. Therefore, it is crucial to locate icebergs and monitor their extent, to quantify how much meltwater they release into the ocean.”
Until now, manual mapping has proven to be more accurate than automated approaches, but it can take a human analyst several minutes to outline a single iceberg. That can rapidly become a time- and labor-intensive process when multiple icebergs are concerned.
The researchers trained an algorithm called U-net using imagery captured by the ESA's Copernicus Sentinel-1 Earth-monitoring satellites. The algorithm was tested on seven icebergs. The smallest had an area roughly the same as Bern, Switzerland and the largest had approximately the same area as Hong Kong.
With 99 percent accuracy, the new model is said to surpass previous attempts at automation, which often struggled to tell the difference between icebergs and sea ice and other features. It's also 10,000 times faster than humans at mapping icebergs.
"Being able to map iceberg extent automatically with enhanced speed and accuracy will enable us to observe changes in iceberg area for several giant icebergs more easily and paves the way for an operational application," Dr. Braakmann-Folgmann said. | Biology |
The quickly changing coronavirus has spawned yet another super contagious omicron mutant that’s worrying scientists as it gains ground in India and pops up in numerous other countries, including the United States.Scientists say the variant – called BA.2.75 – may be able to spread rapidly and get around immunity from vaccines and previous infection. It’s unclear whether it could cause more serious disease than other omicron variants, including the globally prominent BA.5.“It’s still really early on for us to draw too many conclusions,” said Matthew Binnicker, director of clinical virology at the Mayo Clinic in Rochester, Minnesota. “But it does look like, especially in India, the rates of transmission are showing kind of that exponential increase.” Whether it will outcompete BA.5, he said, is yet to be determined.Still, the fact that it has already been detected in many parts of the world even with lower levels of viral surveillance “is an early indication it is spreading,” said Shishi Luo, head of infectious diseases for Helix, a company that supplies viral sequencing information to the U.S. Centers for Disease Control and Prevention.The latest mutant has been spotted in several distant states in India, and appears to be spreading faster than other variants there, said Lipi Thukral, a scientist at the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology in New Delhi. It’s also been detected in about 10 other countries, including Australia, Germany, the United Kingdom and Canada. Two cases were recently identified on the West Coast of the U.S., and Helix identified a third U.S. case last week.Fueling experts’ concerns are a large number of mutations separating this new variant from omicron predecessors. Some of those mutations are in areas that relate to the spike protein and could allow the virus to bind onto cells more efficiently, Binnicker said.Another concern is that the genetic tweaks may make it easier for the virus to skirt past antibodies — protective proteins made by the body in response to a vaccine or infection from an earlier variant.But experts say vaccines and boosters are still the best defense against severe COVID-19. In the fall it’s likely the U.S. will see updated formulations of the vaccine being developed that target more recent omicron strains.“Some may say, ‘Well, vaccination and boosting hasn’t prevented people from getting infected.’ And, yes, that is true,” he said. “But what we have seen is that the rates of people ending up in the hospital and dying have significantly decreased. As more people have been vaccinated, boosted or naturally infected, we are starting to see the background levels of immunity worldwide creep up.”It may take several weeks to get a sense of whether the latest omicron mutant may affect the trajectory of the pandemic. Meanwhile Dr. Gagandeep Kang, who studies viruses at India’s Christian Medical College in Vellore, said the growing concern over the variant underlines the need for more sustained efforts to track and trace viruses that combine genetic efforts with real world information about who is getting sick and how badly. “It is important that surveillance isn’t a start-stop strategy,” she said.Luo said BA.2.75 is another reminder that the coronavirus is continually evolving – and spreading.“We would like to return to pre-pandemic life, but we still need to be careful,” she said. " We need to accept that we’re now living with a higher level of risk than we used to.” | Biology |
Scientists in Australia have discovered a new species of shark with bizarre, human-like molars that it uses to smash down on prey.
The new species, named painted hornshark (Heterodontus marshallae), is part of the order Heterodontiformes, which are classified by their unique body shape and small horns that protrude from above their eyes.
"This order of sharks resembles fossils of long extinct sharks due to similar morphology, including spines. But we know now they’re not closely related," Helen O’Neill, a fish biologist at the Australian National Fish Collection (ANFC) part of the Australian government agency CSIRO, said in a statement.
The newly described species is only found in the waters of northwest Australia, roughly 410 to 751 feet (125 to 229 meters) below the surface, according to a study published July 12 in the journal Diversity.
They have several rows of teeth and an extremely large jaw relative to their skull, which enables them to snack on creatures like molluscs and crustaceans.
"The teeth of all of the hornshark species are very similar to each other, but hornsharks as a group have very different teeth to most other sharks. [They] have grasping teeth near front and large molar-like teeth as you move back along the jaw," Will White, a senior curator of the ANFC and co-author on the study, told Live Science in an email. "This group has evolved to crush heavy shelled prey utilising its molar-like teeth."
In November 2022, the researchers were surveying seabed habitats in Gascoyne Marine Park in Western Australia when they caught an adult male H. marshallae that was about 1.75 feet (53 centimeters) long when measured from the tip of its snout to its tail fin.
"Compared to other Australian hornsharks, this species has a distinctive striped pattern," White said. "This pattern is very similar to the Zebra hornshark and was previously thought to be the same species."
However, zebra hornsharks (H. zebra) are found in shallower waters and normally live near Indonesia or Japan, while H. marshallae prefer the deeper ocean surrounding Australia's coast. Prior to the 2022 expedition, the researchers had examined six specimens and an egg casing of what would later be identified as H. marshallae from museum collections around Australia, and they were in the process of classifying this new species when they stumbled upon the living male.
“We have a female specimen in our collection, but the one we collected during the voyage is a male," O’Neill, who was also a co-author on the study, said in the statement. "We prefer to use males for shark holotypes because they have claspers, which are external reproductive organs that can vary between species and help us tell them apart."
Researchers last described a shark species from the order Heterodontiformes in 2005, and scientists are skeptical that they will find any more of these underwater predators, White said.
"This order of sharks and very distinctive in their large head, crests above eyes and spines in front of dorsal fins," he said. "My gut feeling is that we would have seen specimens of such a distinct species since they are mostly shallow water… where exploration has been substantial in most places. I could just as easily be wrong though."
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Kiley Price is a Live Science staff writer based in New York City. Her work has appeared in National Geographic, Slate, Mongabay and more. She holds a bachelor's degree from Wake Forest University, where she studied biology and journalism, and is pursuing a master's degree at New York University's Science, Health and Environmental Reporting Program. | Biology |
Sign up for CNN’s Wonder Theory science newsletter. Explore the universe with news on fascinating discoveries, scientific advancements and more. CNN — Sometime during the Cretaceous Period, 120 million years ago, a dinosaur wolfed down its last meal — a small mammal the size of a mouse. And it’s still there. A researcher with a sharp eye spotted the mammal’s foot preserved inside the guts of a fossilized Microraptor zhaoianus, a feathered therapod less than a meter (3 feet) long. “At first, I couldn’t believe it. There was a tiny rodent-like mammal foot about a centimeter (0.4 inch) long perfectly preserved inside a Microraptor skeleton,” said Hans Larsson, a professor of biology at McGill University’s Redpath Museum in Montreal. Larsson came across the fossil while visiting museum collections in China. “These finds are the only solid evidence we have about the food consumption of these long extinct animals — and they are exceptionally rare,” Larsson said in a news release. The research, which was published in the Journal of Vertebrate Paleontology on December 20, said this was only the 21st known example of a fossilized dinosaur with its last meal preserved. It’s rarer still to find that a mammal was on the menu; there’s only one other such example currently in the fossil record. “We already know of Microraptor specimens preserved with parts of fish, a bird, and a lizard in their bellies. This new find adds a small mammal to their diet, suggesting these dinosaurs were opportunistic and not picky eaters,” Larsson, a coauthor of the study, said in a statement. “Knowing that Microraptor was a generalist carnivore puts a new perspective on how ancient ecosystems may have worked and a possible insight into the success of these small, feathered dinosaurs,” he explained. Generalist predators, like foxes and crows, are important stabilizers in today’s ecosystems because they can feed on several species, the news release said. According to the research, the Microraptor is the first known example of a generalist carnivore in a dinosaur era. It was possible that other dinosaurs from the therapod family, which included the Tyrannosaurus rex, might also have shared a similarly unfussy diet, the study said. The Microraptor fossil was discovered in the rich fossil deposits in Liaoning in northeastern China in the early 2000s. The specimen, which features plumage on its arm wings and legs, was one of the first feathered dinosaurs to be unearthed. “While this mammal would absolutely not have been a human ancestor, we can look back at some of our ancient relatives being a meal for hungry dinosaurs,” said study coauthor Dr. David Hone, a reader in zoology at Queen Mary University of London, in a statement. “This study paints a picture of a fascinating moment in time — one of the first record(s) of a dinosaur eating a mammal — even if it isn’t quite as frightening as anything in ‘Jurassic Park.’” | Biology |
Finding the genes that help kingfishers dive without hurting their brains
If you've ever belly-flopped into a pool, then you know: water can be surprisingly hard if you hit it at the wrong angle. But many species of kingfishers dive headfirst into water to catch their fishy prey. In a new study in the journal Communications Biology, researchers compared the DNA of 30 different kingfisher species to zero in on the genes that might help explain the birds' diet and ability to dive without sustaining brain damage.
The type of diving that kingfishers do—what researchers call "plunge-diving"—is an aeronautic feat. "It's a high-speed dive from air to water, and it's done by very few bird species," says Chad Eliason, a research scientist at the Field Museum in Chicago and the study's first author. But it's a behavior that's potentially risky.
"For kingfishers to dive headfirst the way they do, they must have evolved other traits to keep them from hurting their brains," says Shannon Hackett, associate curator of birds at the Field Museum and the study's senior author.
Not all kingfishers actually fish—many species of these birds eat land-dwelling prey like insects, lizards, and even other kingfishers. Previously, co-authors Jenna McCollough and Michael Andersen, researchers from the University of New Mexico, led the team in using DNA to show that the groups of kingfishers that eat fish aren't each others' closest relatives within the kingfisher family tree. That means that kingfishers evolved their fishy diets—and the diving abilities to procure them—a number of separate times, rather than all evolving from one common fish-eating ancestor.
"The fact that there are so many transitions to diving is what makes this group both fascinating and powerful, from a scientific research perspective," says Hackett. "If a trait evolves a multitude of different times independently, that means you have power to find an overarching explanation for why that is."
For this study, the researchers—including co-authors Lauren Mellenthin currently at Yale University, who was an undergraduate intern at Field Museum at the time this research was conducted; Taylor Hains at the University of Chicago and Field Museum; Stacy Pirro at Iridian Genomes; and Michael Anderson and Jenna McCullough at the University of New Mexico—examined the DNA of 30 species of kingfishers, both fish-eating and not.
"To get all the kingfisher DNA, we used specimens in the Field Museum's collections," says Eliason, who works in the Field's Grainger Bioinformatics Center and Negaunee Integrative Research Center. "When our scientists do fieldwork, they take tissue samples from the bird specimens they collect, like pieces of muscle or liver. Those tissue samples are stored at the Field Museum, frozen in liquid nitrogen, to preserve the DNA."
In the Field's Pritzker DNA Laboratory, the researchers began the process of sequencing full genomes for each of the species, generating the entire genetic code of each bird. From there, they used software to compare the billions of base pairs making up these genomes to look for genetic variations that the diving kingfishers have in common.
The scientists found that the fish-eating birds had several modified genes associated with diet and brain structure. For instance, they found mutations in the birds' AGT gene, which has been associated with dietary flexibility in other species, and the MAPT gene, which codes for tau proteins that relate to feeding behavior.
Tau proteins help stabilize tiny structures inside the brain, but the accumulation of too many tau proteins can be a bad thing. In humans, traumatic brain injuries and Alzheimer's disease are associated with a buildup of tau.
"I learned a lot about tau protein when I was the concussion manager of my son's hockey team," says Hackett. "I started to wonder, why don't kingfishers die because their brains turn to mush? There's gotta be something they're doing that protects them from the negative influences of repeatedly landing on their heads on the water's surface."
Hackett suspects that tau proteins may be something of a double-edged sword. "The same genes that keep your neurons in your brain in all nice and ordered are the things that fail when you get repeated concussions if you're a football player or if you get Alzheimer's," she says. "My guess is there's some sort of strong selective pressure on those proteins to protect the birds' brains in some way."
Now that these correlated genomic variations have been identified, says Hackett, "The next question is, what do the mutations in these birds' genes do to the proteins that are being produced? What shape changes are there? What is going on to compensate in a brain for the concussive forces?"
"Now, we know which of the underlying genes are shifting that help create the differences that we see across the kingfisher family," says Eliason. "But now that we know which genes to look at, it created more mysteries. That's how science works."
In addition to a better understanding of kingfisher genetics and potential implications for understanding brain injuries, Hackett says that this study is important because it highlights the value of museum collections.
"One of the specimens we got DNA from in this study is thirty years old. At the time it was collected, we couldn't do anywhere near the kind of analyses we can do today—we couldn't even do some of this stuff five years ago," says Hackett. "It traces back to the ability of individual specimens to tell new stories through time. And who knows what we'll be able to learn from these specimens in the future? That's why I love museum collections."
More information: Chad Eliason et al, Genomic signatures of convergent shifts to plunge-diving behavior in birds, Communications Biology (2023).
Journal information: Communications Biology
Provided by Field Museum | Biology |
Study: Rising rainfall, not temperatures, threaten giraffe survival
Giraffes in the East African savannahs are adapting surprisingly well to the rising temperatures caused by climate change. However, they are threatened by increasingly heavy rainfall, as researchers from the University of Zurich and Pennsylvania State University have shown.
Climate change is expected to cause widespread decline in wildlife populations worldwide. But little was previously known about the combined effects of climate change and human activity on the survival rates not only of giraffes, but of any large African herbivore species.
Now researchers from the University of Zurich and Pennsylvania State University have concluded a decade-long study—the largest to date—of a giraffe population in the Tarangire region of Tanzania. The research is published in the journal Biodiversity and Conservation. The study area spanned more than a thousand square kilometers, including areas inside and outside protected areas. Contrary to expectations, higher temperatures were found to positively affect adult giraffe survival, while rainier wet seasons negatively impacted adult and calf survival.
First exploration into the effects of climate variation on giraffe survival
Led by Monica Bond, a postdoctoral research associate in the Department of Evolutionary Biology and Environmental Studies at the University of Zurich, the research team quantified the effects of local anomalies of temperature, rainfall and vegetation greenness on the probability of survival of the giraffes. They also explored whether climate had a greater effect on giraffes that were also impacted by human activity at the edges of the protected reserves.
"Studying the effects of climate and human pressures on a long-lived and slow-breeding animal like a giraffe requires monitoring their populations over a lengthy time period and over a large area, enough to capture both climate variation and any immediate or delayed effects on survival," said Bond. The team obtained nearly two decades of data on local rainfall, vegetation greenness and temperature during Tanzania's short rains, long rains and dry season, and then followed the fates of 2,385 individually recognized giraffes of all ages and sexes over the final eight years of the two-decade period.
Surprising effects of temperature on giraffe survival
The team had predicted that higher temperatures would hurt adult giraffes because their very large body size might make them overheat, but in fact they found that higher temperatures positively affected adult giraffe survival. "The giraffe has several physical features that help it to keep cool, like a long neck and legs for evaporative heat loss, specialized nasal cavities, an intricate network of arteries that supply blood to the brain, and spot patches which radiate heat," noted Derek Lee, associate research professor of biology at Pennsylvania State University and senior author of the study.
However, Lee also pointed out that "temperatures during our study period may not have exceeded the tolerable thermal range for giraffes, and an extreme heat wave in the future might reveal a threshold above which these massive animals might be harmed."
Heavy rains may increase parasites while reducing nutritional value of vegetation
Survival of giraffe adults and calves was reduced during rainier wet seasons, which the researchers attributed to a possible increase in parasites and disease. A previous study in the Tarangire region showed giraffe gastrointestinal parasite intensity was higher during the rainy seasons than the dry season, and heavy flooding has caused severe outbreaks of diseases known to cause mortality in giraffes, such as Rift Valley fever virus and anthrax. The current study also found higher vegetation greenness reduced adult giraffe survival, potentially because faster leaf growth reduces nutrient quality in giraffe food.
Human pressure place additional stress on already declining populations
Climate effects were exacerbated by the giraffes' proximity to the edge of protected reserves, but not during every season. "Our findings indicate that giraffes living near the peripheries of the protected areas are most vulnerable during heavy short rains. These conditions likely heighten disease risks associated with livestock, and muddy terrain hampers anti-poaching patrols, leading to increased threats to giraffe survival," said Arpat Ozgul, University of Zurich professor and study author.
The team concluded that projected climate changes in East Africa, including heavier rainfall during the short rains, will likely threaten the existence of giraffes in one of Earth's most important landscapes for large mammals, indicating the need for effective land-use planning and anti-poaching to improve giraffes' resilience to the coming changes.
More information: Monica L. Bond et al, Effect of local climate anomalies on giraffe survival, Biodiversity and Conservation (2023). DOI: 10.1007/s10531-023-02645-4
Journal information: Biodiversity and Conservation
Provided by University of Zurich | Biology |
The Food and Drug Administration on Friday announced the fast-tracked approval of an Alzheimer’s drug that modestly slows the brain-robbing disease to those with mild impairment.The drug, Leqembi, is the first that’s been convincingly shown to slow the decline in memory and thinking that defines Alzheimer’s by targeting the disease's underlying biology. The FDA approved it for patients with Alzheimer's, specifically those with mild or early-stage disease.The approval came after clinical trials that showed the drug slows cognitive decline but also carries the risk of brain swelling and bleeding.ALZHEIMER'S EXPERIMENTAL DRUG MAY SLOW PROGRESSION OF DISEASE, BUT THERE ARE RISKS: EXPERTS A doctor points to PET scan results that are part of a study on Alzheimer's disease at a hospital in Washington. On Friday, the FDA approved an Alzheimer’s drug that modestly slows the brain-robbing disease. (AP Newsroom)"Alzheimer’s disease immeasurably incapacitates the lives of those who suffer from it and has devastating effects on their loved ones," said Billy Dunn, M.D., director of the Office of Neuroscience in the FDA’s Center for Drug Evaluation and Research. "This treatment option is the latest therapy to target and affect the underlying disease process of Alzheimer’s, instead of only treating the symptoms of the disease."Leqembi was developed by Japan's Eisai and its U.S. partner Biogen. Eisai is pricing the drug at $26,500 annually per patient.Eisai executives said they have already spent months discussing their drug's data with Medicare officials. Coverage isn't expected until after the FDA confirms the drug's benefit, likely later this year.The FDA approval came through its accelerated pathway, a shortcut that allows drugs to be launched based on early results. Despite the approval, the pathway has come under criticism. The Biogen Inc., headquarters is shown March 11, 2020, in Cambridge, Massachusetts. (AP Photo/Steven Senne, File)A congressional report released last week found that the FDA's approval of another Alzheimer's drug called Aduhelm — also from Biogen and Eisai — was "rife with irregularities," including a number of meetings with drug company staffers that went undocumented.About 13% of patients in Eisai’s study had swelling of the brain and 17% had small brain bleeds, side effects seen with earlier amyloid-targeting medications. In most cases, those problems didn’t cause symptoms, which can include dizziness and vision problems.Also, several Leqembi users died while taking the drug, including two who were on blood-thinning medications. Eisai has said the deaths can’t be attributed to the drug. The FDA label warns doctors to use caution if they prescribe Leqembi to patients on blood thinners.More than 6.5 million Americans age 65 or older are living with dementia due to Alzheimer's, according to the Alzheimer’s Association.CLICK HERE TO GET THE FOX NEWS APP The Associated Press contributed to this report. | Biology |
This year, Australia’s Great Barrier Reef was hit by another mass bleaching. Scientists say the reef isn’t dying, but it also isn’t thriving. With only about 100 of the 3,000 individual reefs actively monitored, there’s still much to learn. In November, the Great Reef Census—a citizen project led by Earth Hour co-founder Andy Ridley and supported by local tourism operators and their guests—will move into its third year of mapping the entire 1,400-mile reef, resulting in critical knowledge to safeguard its future. Visitors can also learn about traditional reef management from Dreamtime Dive & Snorkel’s Indigenous sea rangers, or aboard Reef Magic, a newly launched sustainably powered pontoon (using 18 solar panels and three wind turbines). Its team of Indigenous guides interweave Aboriginal storytelling with Western science, while an onboard marine-biology lab conducts research. Guests can swim, snorkel, scuba dive, or just lounge in the sun. Scientist Katie Chartrand dives at Moore Reef as part of the Great Reef Census along the Great Barrier Reef, Australia. Christian Miller—Courtesy Citizens of the Great Barrier Reef Other new attractions include Townsville’s Museum of Underwater Art and the Lady Musgrave Pontoon. Pent-up demand for travel to Australia prompted United Airlines to add new nonstop, year-round transpacific service between San Francisco and Brisbane, beginning in October. Contact us at [email protected]. | Biology |
University of Wyoming researchers' study of how microscopic creatures called tardigrades survive extreme conditions has led to a major breakthrough that could eventually make life-saving treatments available to people where refrigeration isn't possible.
Thomas Boothby, an assistant professor of molecular biology, and colleagues have shown that natural and engineered versions of tardigrade proteins can be used to stabilize an important pharmaceutical used to treat people with hemophilia and other conditions without the need for refrigeration -- even amid high temperatures and other difficult conditions. The findings are detailed today (Monday) in Scientific Reports, an online, open access journal from the publishers of Nature.
The pharmaceutical, human blood clotting Factor VIII, is an essential therapeutic used to treat genetic disease and instances of extreme bleeding. Despite being critical and effective in treating patients in these circumstances, Factor VIII has a serious shortcoming, in that it is inherently unstable. Without stabilization within a precise temperature range, Factor VIII will break down.
"In underdeveloped regions, during natural disasters, during space flight or on the battlefield, access to refrigerators and freezers, as well as ample electricity to run this infrastructure, can be in short supply. This often means that people who need access to Factor VIII do not get it," Boothby says. "Our work provides a proof of principle that we can stabilize Factor VIII, and likely many other pharmaceuticals, in a stable, dry state at room or even elevated temperatures using proteins from tardigrades -- and, thus, provide critical live-saving medicine to everyone everywhere."
Measuring less than half a millimeter long, tardigrades -- also known as water bears -- can survive being completely dried out; being frozen to just above absolute zero (about minus 458 degrees Fahrenheit, when all molecular motion stops); heated to more than 300 degrees Fahrenheit; irradiated several thousand times beyond what a human could withstand; and even survive the vacuum of outer space. They are able to do so, in part, by manufacturing a sugar called trehalose and a protein called CAHS D.
According to the research paper, Boothby and his colleagues fine-tuned the biophysical properties of both trehalose and CAHS D to stabilize Factor VIII, noting that CAHS D is most suitable for the treatment. The stabilization allows Factor VIII to be available in austere conditions without refrigeration, including repeated dehydration/rehydration, extreme heat and long-term dry storage.
The researchers believe the same thing can be done with other biologics -- pharmaceuticals containing or derived from living organisms -- such as vaccines, antibodies, stem cells, blood and blood products.
"This study shows that dry preservation methods can be effective in protecting biologics, offering a convenient, logistically simple and economically viable means of stabilizing life-saving medicines," Boothby says. "This will be beneficial not only for global health initiatives in remote or developing parts of the world, but also for fostering a safe and productive space economy, which will be reliant on new technologies that break our dependence on refrigeration for the storage of medicine, food and other biomolecules."
Boothby and other researchers hope that their discoveries can be applied to address other societal and global health issues as well, including water scarcity. For example, their work might lead to better ways of generating engineered crops that can cope with harsh environments.
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Cells with XX or XY chromosomes provide researchers with a new tool to study how differences in sex chromosomes can influence health and developmentThis image depicts a karyotype, or chromosomal profile, created by performing a chromosomal analysis on a sample of human peripheral blood, revealing the full complement of 46 chromosomes, or 23 pairs. Credit: CDC/Dr. LaineMost people have two sex chromosomes, either two X’s or an X and a Y, which give rise to female or male biological attributes on a spectrum. Studies suggest these chromosomes also have much broader effects, contributing to processes that include immune system function, neuronal development, disease susceptibility and reactions to drugs. But scrutinizing the specific role of X and Y chromosomes is challenging. With current tools, it is difficult to disentangle the effects of genes versus hormones, for example. Now scientists have devised a tool that could overcome this obstacle—by generating XX and XY cells from a single person for the first time. This unique set of cells could help researchers tackle long-standing questions about how sex chromosomes affect disease and the role they play in early development. “This is a really cool set of cell lines,” says Barbara Stranger, a professor of pharmacology at Northwestern University, who was not involved in this study. “We’ve had cell lines from males and females before, but the fact that they’re coming from same person with just the same sex chromosome difference—it’s a big step.” Benjamin Reubinoff, a professor of obstetrics and gynecology at the Hadassah Medical Center in Israel, and his team began the project to overcome barriers facing investigations of sex differences in humans. Currently there are two major ones, according to Reubinoff: the difficulty of separating chromosomal and hormonal effects and the inability to pinpoint the effects of X and Y chromosomes while ruling out contributions from the rest of a person’s genetic makeup. “The main reason for doing this study was the lack of a good model to study differences between males and females in humans,” Reubinoff says. “There have been animal models, but a model in humans was not available.” To create such a model, Reubinoff, his former M.D. and Ph.D. student Ithai Waldhorn and their colleagues first obtained white blood cells previously collected from a person with Klinefelter syndrome, a condition in which male individuals are born with an extra X chromosome. The cells came from the repositories of the Coriell Institute for Medical Research, where people donate samples for use in a wide range of biomedical research projects. The donor had a rare “mosaic” form of the condition, in which some of their cells had three sex chromosomes (XXY), some had two X chromosomes, and some had one X and one Y. The researchers reprogrammed all three cell types into induced pluripotent stem cells, which have the capacity to self-renew and to develop into neurons, muscle cells or other cell types. Ultimately the team generated XX and XY cells that—apart from their sex chromosomes—were genetically identical. The researchers then conducted a series of experiments replicating findings from prior studies with other models. For example, they confirmed previously reported differences in genes that were turned on in XX or XY cells. They also coaxed their stem cells to develop into immature versions of neurons and found evidence of previously reported sex differences in early neural development. “It was reassuring to see that the model really shows differences between the sexes that were reported from other systems,” Reubinoff says. The findings were published last month in Stem Cell Reports. “This is a very well-designed study that validates the notion that sex differences start early in development—and that they depend on the sex chromosomes because that’s the only thing that can account for those differences,” says Nora Engel, a professor of cancer and cell biology at Temple University, who was not involved in this work. In the past, researchers have probed the effects of sex chromosomes in animals using the “four core genotypes” mouse model, which includes modifying a gene called Y(Sry). This region of the Y chromosome contains instructions for developing testes, and the changes create animals with XX chromosomes and testes or XY chromosomes and ovaries. Animals with the same sex organs but different chromosomes enable scientists to isolate the effects of sex chromosomes from the effects of sex hormones, which are secreted by the reproductive organs. The mouse model was transformative for the field of sex difference research, Stranger says. Being able to move this research into humans “is really neat,” she adds. “I think this is going to open up avenues for new research,” says Jessica Abbott, a senior lecturer in eukaryote evolutionary genetics at Lund University in Sweden, who was not involved in this research. Abbott notes that it will be important to derive XX and XY stem cells from another person to see how much variation there is between people—which will help determine how generalizable findings from these cells are to the broader population. Cells, of course, cannot model the entire human body or interactions between organs—at least not yet. But Reubinoff notes that with the development of new techniques such as microfluidic “body-on-a-chip” systems that model the connections between cells from different organs, scientists may be able to address a broader array of research questions in the future. For now, Reubinoff is excited about the experiments that will be possible with the stem cells alone. “You have a tool that you can, at least theoretically, use [indefinitely to] generate any cell type and develop models for various types of diseases,” he says. “The model we developed opens wide horizons.ABOUT THE AUTHOR(S)Diana Kwon is a freelance journalist who covers health and the life sciences. She is based in Berlin. Follow Kwon on Twitter @DianaMKwon Credit: Nick Higgins | Biology |
A diverse set of species, from snails to algae to amoebas, make programmable DNA-cutting enzymes called Fanzors — and a new study from scientists at MIT’s McGovern Institute for Brain Research has identified thousands of them. Fanzors are RNA-guided enzymes that can be programmed to cut DNA at specific sites, much like the bacterial enzymes that power the widely used gene-editing system known as CRISPR. The newly recognized diversity of natural Fanzor enzymes, reported Sept. 27 in the journal Science Advances, gives scientists an extensive set of programmable enzymes that might be adapted into new tools for research or medicine.
“RNA-guided biology is what lets you make programmable tools that are really easy to use. So the more we can find, the better,” says McGovern Fellow Omar Abudayyeh, who led the research with McGovern Fellow Jonathan Gootenberg.
CRISPR, an ancient bacterial defense system, has made it clear how useful RNA-guided enzymes can be when they are adapted for use in the lab. CRISPR-based genome editing tools developed by MIT professor and McGovern investigator Feng Zhang, Abudayyeh, Gootenberg, and others have changed the way scientists modify DNA, accelerating research and enabling the development of many experimental gene therapies.
Researchers have since uncovered other RNA-guide enzymes throughout the bacterial world, many with features that make them valuable in the lab. The discovery of Fanzors, whose ability to cut DNA in an RNA-guided manner was reported by Zhang’s group earlier this year, opens a new frontier of RNA-guided biology. Fanzors were the first such enzymes to be found in eukaryotic organisms — a wide group of lifeforms, including plants, animals, and fungi, defined by the membrane-bound nucleus that holds each cell’s genetic material. (Bacteria, which lack nuclei, belong to a group known as prokaryotes.)
“People have been searching for interesting tools in prokaryotic systems for a long time, and I think that that has been incredibly fruitful,” says Gootenberg. “Eukaryotic systems are really just a whole new kind of playground to work in.”
One hope, Abudayyeh and Gootenberg say, is that enzymes that naturally evolved in eukaryotic organisms might be better suited to function safely and efficiently in the cells of other eukaryotic organisms, including humans. Zhang’s group has shown that Fanzor enzymes can be engineered to precisely cut specific DNA sequences in human cells. In the new work, Abudayyeh and Gootenberg discovered that some Fanzors can target DNA sequences in human cells even without optimization. “The fact that they work quite efficiently in mammalian cells was really fantastic to see,” Gootenberg says.
Prior to the current study, hundreds of Fanzors had been found among eukaryotic organisms. Through an extensive search of genetic databases led by lab member Justin Lim, Gootenberg and Abudayyeh’s team has now expanded the known diversity of these enzymes by an order of magnitude.
Among the more than 3,600 Fanzors that the team found in eukaryotes and the viruses that infect them, the researchers were able to identify five different families of the enzymes. By comparing these enzymes’ precise makeup, they found evidence of a long evolutionary history.
Fanzors likely evolved from RNA-guided DNA-cutting bacterial enzymes called TnpBs. In fact, it was Fanzors’ genetic similarities to these bacterial enzymes that first caught the attention of both Zhang’s group and Gootenberg and Abudayyeh’s team.
The evolutionary connections that Gootenberg and Abudayyeh traced suggest that these bacterial predecessors of Fanzors probably entered eukaryotic cells, initiating their evolution, more than once. Some were likely transmitted by viruses, while others may have been introduced by symbiotic bacteria. The research also suggests that after they were taken up by eukaryotes, the enzymes evolved features suited to their new environment, such as a signal that allows them to enter a cell nucleus, where they have access to DNA.
Through genetic and biochemical experiments led by biological engineering graduate student Kaiyi Jiang, the team determined that Fanzors have evolved a DNA-cutting active site that is distinct from that of their bacterial predecessors. This seems to allow the enzyme to cut its target sequence more precisely the ancestors of TnpB, when targeted to a sequence of DNA in a test tube, become activated and cut other sequences in the tube; Fanzors lack this promiscuous activity. When they used an RNA guide to direct the enzymes to cut specific sites in the genome of human cells, they found that certain Fanzors were able to cut these target sequences with about 10 to 20 percent efficiency.
With further research, Abudayyeh and Gootenberg hope that a variety of sophisticated genome editing tools can be developed from Fanzors. “It’s a new platform, and they have many capabilities,” says Gootenberg.
“Opening up the whole eukaryotic world to these types of RNA-guided systems is going to give us a lot to work on,” Abudayyeh adds. | Biology |
Biologists have produced a strain of yeast whose genome is more than 50% synthetic DNA. Standard brewer’s yeast (Saccharomyces cerevisiae) stores its genetic blueprint across 16 chromosomes. In the new strain, 6.5 of those chromosomes were edited and synthesized in the laboratory — and an extra one was stitched together from edited bits of the yeast’s genetic code.
The feat is the latest milestone for a group of labs, called the Sc2.0 consortium, that has been trying to create a strain of yeast with a fully synthetic genome for 15 years. A package of papers published today in Cell1,2 and Cell Genomics3 describes the team’s accomplishment, how it made the new strain and other tests it performed on the yeast genome.
Some viruses and bacteria have already been engineered to have entirely synthetic genomes, but they have all had simple genetic structures — the bacterium Escherichia coli, for example, has just one chromosome. They have also had a simple inner configuration: the bacteria, for instance, have been prokaryotes, which means they are single cells, without a nucleus to hold their chromosomes. If the Sc2.0 group, which includes researchers from labs in Asia, Europe, North America and Oceania, can achieve its goal, its engineered yeast will be the first eukaryote with a fully synthetic genome. (Eukaryotes are organisms with cells that store their genetic material in a nucleus, and include humans, plants and animals.)
The Sc2.0 team hopes to manipulate its synthetic brewer’s yeast so that it can one day produce drugs and fuels, rather than beer. But the quest has other benefits, says Jef Boeke, a synthetic biologist at New York University in New York City and the leader of the project. By tweaking the organism without interfering with its survival, “we learn a lot about the biology of yeast”, he says.
Nili Ostrov, chief scientific officer at Cultivarium, a non-profit firm in Watertown, Massachusetts, that develops tools for bioengineers, says that Sc2.0 is “pushing the boundaries of what we can engineer in biology”. Historically, genetic engineers have focused on modifying individual genes in organisms. Now, biologists can see what happens when they re-engineer entire chromosomes. “This allows you to ask questions you couldn’t ask before,” Ostrov says. In the process, the project is developing methods that could advance biological engineering, she says.
Rewriting the genome
One of Sc2.0’s main goals is to eliminate potential sources of instability in the yeast genome. One such source is large stretches of repetitive DNA that don’t code for anything, but that can recombine with each other through natural processes, causing major structural changes in the genome. The synthetic biologists want to have complete control of their engineered yeast, so the team combed through S. cerevisiae’s genome with computer programmes to find highly repetitive regions — and then deleted them. These sequences are effectively “genome parasites”, Boeke says.
Another change the researchers made to reduce instabilities was to remove from the chromosomes all DNA segments that encode transfer RNA, and to relocate them into an entirely synthetic ‘neochromosome’2. Transfer RNAs (tRNAs) are crucial to a cell’s functioning — they ferry amino acids to an apparatus that uses the molecules to make proteins. But the DNA sequences that code for them “are hotspots for instability”, Boeke says. So moving them into their own new chromosome, designed for greater stability, was a way for the team to bring the synthetic yeast under greater control, and probe the limits of biology.
To bring the 7.5 synthetic chromosomes together into a single cell, the team made strains of yeast that each contained one of the edited chromosomes, along with the natural versions of the other 15. Then they bred two of the strains and selected for offspring that contained two different edited chromosomes. Those strains were then bred to add another edited chromosome, and so on.
Even with all the big changes in the chromosomes, the cells that ended up with the 7.5 chromosomes survived and could replicate, Boeke says.
Although the process of making the cells was time-consuming, what really slowed things down is debugging, Boeke says. Researchers first had to test whether each yeast cell with a new synthetic chromosome in it was viable — meaning it could survive and function normally — then fix any problems by tweaking the genetic code1. When two or more synthetic chromosomes are inside the same cell, this can lead to new bugs that must be fixed, so the debugging problem becomes more complex as the process proceeds.
The Sc2.0 project is allowing scientists to test questions that were previously impossible, Ostrov says — for instance, “What happens when you introduce chromosomes that weren’t there before?”
Boeke says the team is now plugging away at replacing the remaining natural chromosomes with entirely synthetic ones, adding new chromosomes one at a time and then debugging the ever more complex system. “It will take a lot of doing it all over again,” he says. | Biology |
Q&A: Researchers track new invasive insect, the elm zigzag sawfly
A new invasive insect, the elm zigzag sawfly, has arrived in North Carolina. This sawfly, Aproceros leucopoda, is native to East Asia, was first seen in the U.S. in 2021, and it has been detected in five eastern states so far. The insect feeds on the leaves of elm trees, but long-term impacts on tree health and the best ways to manage the insect's spread are still unknown, according to a North Carolina State University forest health researcher.
The elm zigzag sawfly was identified in North Carolina last year, according to a new paper tracking the insect's spread, published in the Journal of Integrated Pest Management.
"This is a very new invasive species first found in Canada in 2020 and in the U.S. in Virginia in 2021," said the study's first author Kelly Oten, assistant professor of forest health at NC State. "In 2022, four additional states confirmed it. It happened very quickly. This paper was our effort to document the very first stages of the invasion, and let people know where it is, and what we know about its biology and management so far."
The Abstract spoke to Oten about the spread of the elm zigzag sawfly, and what researchers know about it.
The Abstract: How quickly has elm zigzag sawfly spread?
Kelly Oten: We aren't sure how quickly it's spreading, but we are detecting it in a lot of places in a short period of time. It's been detected from New York to North Carolina, but we only have it in one spot in N.C. so far. I am working with the U.S. Forest Service to get a lot of states involved in surveying, as we suspect it is in a lot more places that we don't know about.
TA: How did it get here?
Oten: A lot of invasive species are hitchhikers. Someone could have moved live elm trees with the sawfly on them or its cocoon could have attached to an inanimate object that was moved overseas.
TA: When was it discovered in N.C.?
Oten: Last August, a homeowner in North Carolina called the N.C. Forest Service because their large, mature American elm trees were severely defoliated. After they investigated, I also got called in.
We found thousands of sawflies, and trees nearly completely defoliated. All of the badly defoliated trees leafed out well this spring, but they're getting attacked again. Usually defoliation doesn't harm a tree unless it happens over and over again. If they are getting defoliated year after year, we have to consider the impact on the trees' health.
TA: What do you know about the threat of the insect to elm trees?
Oten: We have 210 million elm trees in North Carolina forests, and this does not include urban trees. Historically, elm trees were a very prized street tree. However, an invasive disease, Dutch elm disease, came through and decimated the vast majority of our elms in the mid-1900s. Ironically, a lot of towns and municipalities replaced them with ash trees, and then we saw the same thing happen with the emerald ash borer invasion.
It's too early to tell right now how damaging elm zigzag sawfly will be to elms. The majority of trees have very minor defoliation. You probably wouldn't even know something was happening to the tree until you got up close. However, we have seen severely defoliated trees, too, and if this happens year after year, it might stress or weaken a tree or potentially cause dieback and even death. We just don't have enough information yet.
TA: Is there any way to manage the insect?
Oten: Right now, we are doing research looking at the life cycle of elm zigzag sawfly in North Carolina so we know when to monitor, and when to time treatments. We also have an insecticide trial in place. We don't think that is a suitable strategy for forest settings, but we're studying it to see if individual homeowners could use it to protect landscape elm trees from defoliation.
We also looked at natural enemies of the elm zigzag sawfly. We're already seeing some insects that could be helping to control elm zigzag sawfly like ladybugs and assassin bugs.
TA: What should the public know and do about this?
Oten: Our recommendation for the public right now is to not freak out. We don't think this is going to be a tree killer, so people don't need to start cutting down their elms. We do ask that if people see the defoliation pattern on elm trees, to call it into their county extension agent or the N.C. Forest Service. It's pretty easy to recognize. The insect got its name because it makes a very characteristic zigzag pattern in the leaves as it feeds.
TA: How many more new invasive insects do you expect to see?
Oten: We detected two new invasive species last year. Before that, we went nine years in North Carolina without a new one since the emerald ash borer was detected in 2013. Invasive species aren't going to go away; they're a byproduct of global commerce and travel. It's also a lesson to make sure we diversify our plantings—whether that be in reforestation efforts or in urban plantings—so we don't have a canopy that's predominately one tree type, and we don't lose everything if a new invasive is introduced that attacks it.
Hopefully, we will get better at predicting and detecting new non-native species, and improving sanitation methods when we ship things. All of these can help us reduce introductions and damage from invasive species.
More information: Kelly L F Oten et al, First records of elm zigzag sawfly (Hymenoptera: Argidae) in the United States, Journal of Integrated Pest Management (2023). DOI: 10.1093/jipm/pmad009
Provided by North Carolina State University | Biology |
Irvine, Calif., April 20, 2023 — Scientists at the University of California, Irvine have made a remarkable discovery about cellophane bees – their microbiomes are some of the most fermentative known from the insect world. These bees, which are named for their use of cellophane-like materials to line their subterranean nests, are known for their fascinating behaviors and their important ecological roles as pollinators. Now, researchers have uncovered another aspect of their biology that makes them even more intriguing.
According to a study published in Frontiers in Microbiology, cellophane bees “brew” a liquid food for their offspring, held in chambers called brood cells. The microbiome of these brood cells is dominated by lactobacilli bacteria, which are known for their role in fermenting foods like yogurt, sauerkraut and sourdough bread. The researchers found that these bacteria are highly active in the food provisions of cellophane bees, where they likely play an important role as a source of nutrients for developing larvae.
“This discovery is quite remarkable,” said Tobin Hammer, assistant professor of ecology & evolutionary biology and lead author. “We know that lactobacilli are important for fermentation of food, but finding wild bees that use them essentially the same way was really surprising. Most of the 20,000 species of bees get their nutrition from nectar and pollen, but for these cellophane bees, we suspect that lactobacilli are also really important. They have effectively evolved from herbivores into omnivores.”The study also found that the food provisions of cellophane bees have much higher bacterial biomass compared to other bee species, matching the unusually fermentative smell that emanates from their brood cells. These uniquely rich, lactobacilli-dominated microbreweries of cellophane bees could have important implications for the health of the bees, as well as for the ecology of the ecosystems in which they live.
“It was intriguing to find that cellophane bees use a strategy called ‘spontaneous fermentation,’ which is how certain fermented foods like sauerkraut are made. Rather than passing on starter cultures from generation to generation, they use wild strains of lactobacilli that are ubiquitous in flowers,” said Hammer. “It suggests that fermentation-based symbioses like this one can evolve without domestication. What makes these bees special is that they’ve figured out how to create a favorable environment in which lactobacilli can grow really well.”
This study highlights the importance of studying the microbiomes of insects, which are often overlooked in favor of more familiar animals like birds and mammals, despite playing an enormous role in ecosystems the world over. By understanding the complex interactions between microbes and their insect hosts, scientists can gain new insights into the biology of these important animals and the ecosystems that they inhabit.
This study was a collaboration between researchers at Cornell University, the Smithsonian Tropical Research Institute, UC Riverside, Colorado State University and the University of Arizona. The National Science Foundation, the U.S. Department of Agriculture and the Simons Foundation provided support.
About UCI’s Brilliant Future campaign: Publicly launched on Oct. 4, 2019, the Brilliant Future campaign aims to raise awareness and support for UCI. By engaging 75,000 alumni and garnering $2 billion in philanthropic investment, UCI seeks to reach new heights of excellence in student success, health and wellness, research and more. The School of Biological Sciences plays a vital role in the success of the campaign. Learn more by visiting https://brilliantfuture.uci.edu/school-of-biological-sciences/.
About the University of California, Irvine: Founded in 1965, UCI is a member of the prestigious Association of American Universities and is ranked among the nation’s top 10 public universities by U.S. News & World Report. The campus has produced five Nobel laureates and is known for its academic achievement, premier research, innovation and anteater mascot. Led by Chancellor Howard Gillman, UCI has more than 36,000 students and offers 224 degree programs. It’s located in one of the world’s safest and most economically vibrant communities and is Orange County’s second-largest employer, contributing $7 billion annually to the local economy and $8 billion statewide. For more on UCI, visit www.uci.edu.
Media access: Radio programs/stations may, for a fee, use an on-campus ISDN line to interview UCI faculty and experts, subject to availability and university approval. For more UCI news, visit news.uci.edu. Additional resources for journalists may be found at communications.uci.edu/for-journalists. | Biology |
Rebel Neurons Fuel Appetite in Obesity
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Our appetites should normally be linked to the levels of energy stored in our body, increasing when we need additional fuel. Nevertheless, excessive eating behavior fuels obesity. Researchers have identified a subset of brain cells that intensify appetite when an extended energy surplus is present in the body – for example, high levels of body fat in obesity. The findings, published in the journal Cell Metabolism by a team from the Garvan Institute of Medical Research, offer a fresh perspective on obesity and could pave the way for innovative anti-obesity treatments.
Over one in ten adults globally are obese. This figure is drastically increased in Western countries – as of 2020, over four in ten adult Americans were obese. This is a significant health concern due to obesity’s links with long-term health conditions like diabetes and heart disease. The origins of obesity are complex, but the condition primarily stems from an excessive accumulation of fat tissue in the body and is influenced by dietary habits and exercise levels.
How the brain regulates body weight
Our appetite is a complex system regulated by a network of different molecules throughout the brain and body. The current study focused on one of these molecules, NPY (neuropeptide Y). "Our brain has intricate mechanisms that sense how much energy is stored in our body and adjust our appetite accordingly. One way it does this is through the molecule NPY," explained
Professor Herbert Herzog, a visiting scientist at the Garvan Institute and the study’s senior author. “When the energy we consume falls short of the energy we spend, our brain produces higher levels of NPY. When our energy intake exceeds our expenditure, NPY levels drop and we feel less hungry. However, when there is a prolonged energy surplus, such as excess body fat in obesity, NPY continues to drive appetite even at low levels. We wanted to understand why,” Herzog added.
Herzog and his colleagues investigated cells in the brains of mice that release NPY. A significant chunk of these neurons – around one in six of the population – did not shut down NPY production even under obese conditions.
This chunk of rebel neurons was sufficient to drive appetite and even resulted in further changes in brain biology. “These cells did not only produce NPY, but also sensitized other parts of the brain to produce additional receptors or 'docking stations' for the molecule – supercharging appetite even further," Herzog said.
A “vicious cycle”
Herzog called this process a “vicious cycle” where the body’s careful metabolic balance between its energy input and stores is knocked out of balance, influencing the development of obesity.
“Our brain is wired to resist energy deficiency or weight loss, as it sees this as a threat to our survival and kickstarts mechanisms that increase our appetite so that we seek out food. As we found now, this even occurs when we have excess energy stored in the body,” Herzog added.
The researchers hope to use this initial finding as a launchpad for exploring interventions for obesity that might be able to block the hypersensitive NPY receptors.
“Our study addresses a long-standing question about how appetite is controlled in obesity and has the potential to take the development of therapy into a new direction,” Herzog concluded.
Reference: Qi Y, Lee NJ, Ip CK, et al. Agrp-negative arcuate NPY neurons drive feeding under positive energy balance via altering leptin responsiveness in POMC neurons. Cell Metabolism. 2023;0(0). doi:10.1016/j.cmet.2023.04.020
This article is a rework of a press release issued by the Garvan Institute of Medical Research. Material has been edited for length and content. | Biology |
Friend or foe? Study reveals evolution of controversial human gut microbe
Blastocystis is one of the most common microbes found in our guts but its role in human health is poorly understood. Blastocystis infection can lead to diarrhea, nausea, weight loss and fatigue, yet the microbe's presence is also considered by some as a sign of a healthy gut.
"One in six people on the planet have it and we don't know if it can hurt you or not. Probably we should know how this thing works," says Joel Dacks, professor of infectious diseases in the Faculty of Medicine & Dentistry and co-lead on new research published in Current Biology that seeks to illuminate the evolutionary biology of Blastocystis.
"We understand that the gut microbiome is an incredible modulator of human health. When it is healthy it seems to be quite protective, but when it's dysregulated it causes all manner of problems," says Dacks, who is also an adjunct professor of biological sciences in the Faculty of Science.
Dacks co-led an international research team along with Anastasios Tsaousis, principal investigator of the Laboratory of Molecular and Evolutionary Parasitology in the School of Biosciences at the University of Kent in the U.K., seeking to understand how and why Blastocystis seems to be following an evolutionary path toward thriving in the oxygen-free environment of our guts—a path similar to that already taken by other parasites, such as those that cause vaginitis, amebic dysentery and beaver fever.
"They've all gone through this process, so by studying the different parasites independently, kind of like a historian, you can understand if there is something in common," Dacks explains. "What are the greater forces? How does the shift happen? What happens to the cells and the genomes?
"Parasites are interesting because they're important to human health—and also because they're wonderfully weird."
Important and weird
Blastocystis is a eukaryote, or cell with a nucleus, much like those found in human bodies and plants. It is a member of the Stramenopila, a group of organisms that includes algae, kelp and the water mold Phytophthora infestans, which caused the Irish Potato Famine. Stramenopila are descended from organisms that have specialized hair-like structures on their flagella that help them move around in liquid, although Blastocystis no longer has any. It looks more like a tennis ball under a microscope. Blastocystis is transmitted from person to person through contact with infected feces or contaminated water.
To study the evolution of Blastocystis, the team compared it with its very close relative, Proteromonas lacertae, which lives in the guts of reptiles and still has many of the cellular features of the Stramenopila group, and by so doing were able to reveal several important discoveries.
For example, only three genes had previously been proposed as being responsible for flagella. By comparing the gene sequences of the two related microbes, the team identified nearly 40 genes that could possibly play a role. These can now be narrowed down in future studies by deactivating them out one at a time.
"We were able to open up an avenue of investigation into a fundamental structure in these organisms that have massive global impact, such as diatoms, which are responsible for about 30% of the oxygen production on the planet, or mycetes, which are still serious crop pathogens," Dacks says.
In general, the researchers found Blastocystis has lost many of the genes from its common ancestor with Proteromonaslacertae as it has specialized to live in the human intestine. Another function both microbes had been thought to have lost over time is that of peroxisomes, parts of a cell involved with metabolism.
As expected, the team found no traces of peroxisomes in Blastocystis; however, by developing antibodies to test for them, they did uncover traces of peroxisomes in P. lacertae. Again, this is a discovery that will need further investigation to be better understood, says Dacks.
"As far as we're aware, this is the most reduced form of this organelle that has ever been reported," he says. "This looks like a missing link in the degenerative evolutionary process. Now the question is whether there are other organisms out there that show something similar."
Still more to learn
The research team also uncovered new evidence of evolutionary changes in the two microbes' membrane trafficking systems, which allow cells to move fuel, waste and other cargo in, around and out of the cell, much like a mail sorting system. This is the Dacks' lab's area of specialty, and he suggests the new information may help scientists understand how Blastocystis takes up material from its human host.
Dacks notes there is still much more to be learned about Blastocystis and its impact on human health. He points out that at least 12 subtypes of the microbe have now been identified in humans.
"It's possible that some of them are making people sick and some of them aren't, but we've been calling them the same thing," he says. "The other possibility is that under some conditions it's fine, but when you stress the environment, then it can cause disease."
This effect is much like what happens to ocean coral, where symbiotic algae are healthy for the coral until ocean temperatures rise and changes to the algae result in coral bleaching and ultimately death, Dacks explains.
More information: Kristína Záhonová et al, Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis, Current Biology (2023). DOI: 10.1016/j.cub.2023.05.025
Journal information: Current Biology
Provided by University of Alberta | Biology |
Transgender athletes could be banned from track and field next, as World Athletics president Sebastian Coe backs FINA’s ruling as being ‘in the best interests of sport’ because ‘biology trumps gender’FINA voted that trans women who 'experienced any part of male puberty' can no longer enter female eventsWorld Athletics will re-examine transgender guidelines at the end of the yearThe governing body could follow FINA's decision as President Seb Coe spoke in support of the hardline approachCoe insisted fairness for females in athletics will always come ahead of inclusionHe backed FINA, insisting swimming's governing body is working in the interest of its sport Published: 12:01 EDT, 20 June 2022 | Updated: 17:24 EDT, 20 June 2022 World Athletics will re-examine their transgender guidelines at the end of the year after Sebastian Coe spoke in support of the hardline approach adopted by swimming’s governing body.In the past week, FINA has voted that trans women who 'experienced any part of male puberty' can no longer enter female events - a marked departure from the prevailing stances of Olympic sports.While World Athletics rules say a transgender athlete can compete if she has a testosterone level below 5 nmol/L continuously for a period of at least 12 months – six months longer than stipulated by their regulations around athletes with differences of sexual development (DSD) - Coe has been emphatic in his belief that ‘biology trumps gender’. His point of view is bolstered by testosterone research around the DSD issue in track and field, which was challenged in the lengthy case with Caster Semenya. In giving his opinion on FINA’s position, Coe said: ‘We see an international federation asserting its primacy in setting rules, regulations and policies that are in the best interest of its sport. This is as it should be. 'We have always believed, and repeated constantly, that biology trumps gender and we will continue to review our regulations in line with this.’ Seb Coe has been emphatic in his belief that ‘biology trumps gender’ and World Athletics will re-examine their transgender guidelines at the end of the year Testosterone research around the DSD issue was challenged in the lengthy case with Caster SemenyaWhen asked if WA would adopt a similar stance, Coe added: ‘We have always said our regulations in this area are a living document, specific to our sport and we will follow the science. FINA (pictured president Husain Al Musallam) voted that trans women who 'experienced any part of male puberty' can no longer enter female events'We continue to study, research and contribute to the growing body of evidence that testosterone is a key determinator in performance and have scheduled a discussion on our DSD and Transgender regulations with our council at the end of the year.’Coe insisted that on his watch fairness for females in athletics will always come ahead of inclusion.He said: ‘My responsibility is to protect the integrity of women’s sport and we take that very seriously, and if it means that we have to make adjustments to protocols going forward, we will. 'And I’ve always made it clear: if we ever get pushed into a corner to that point where we’re making a judgement about fairness or inclusion, I will always fall down on the side of fairness.‘You have to and that’s my responsibility. Of course, it’s a societal issue. If one of my colleagues here in my team suddenly becomes transgender, it doesn’t make a difference to me. They will continue to do the same job with skill and aplomb in exactly the way they were before they made that transition. This is not possible in sport. It is fundamental to performance and integrity and that, for me, is the big, big difference.’Coe indicated some organisations could fear taking a hardline stance against inclusivity for fear of crippling legal challenges. Coe said some organisations could oppose taking a hardline stance for fear of legal challenges University of Pennsylvania trans athlete Lia Thomas prepares for the 500m freestyle at the NCAA Swimming and Diving Championships in MarchHe said: ‘We’ve spent $1,000,000 (on legal fees related to DSD). We’re not Fifa but we’re not bereft. But there are other sports that are genuinely fearful that, if they go down that road, they’ll bankrupt themselves defending this. So it’s not that easy for us to just sit there and say, “Well, some sports are sort of tiptoeing around it”.‘The reality of it is it’s quite an outlay and they’ve also got limited data and research.‘The International Olympic Committee created the framework, which said that nobody should be making these decisions unless you’ve got 10 years of longitudinal study.‘Well we have. I doubt whether, on transgender, anybody in sport has got 10 years of longitudinal study – they just haven’t.’ Advertisement | Biology |
Hip phantom images: In CT slices of a hip phantom, no optimal keV setting could be found to effectively reduce metal artefacts. Adding iterative metal artefact reduction (iMAR) strongly reduced the base artefact level for all energies. (Courtesy: J A Anhaus et al Phys. Med. Biol. 10.1088/1361-6560/ac71f0)
Metal implants in the body, such as hip replacements or dental fillings, are a major source of artefacts in CT images. Clinically available methods reduce these metal artefacts – up to a point.
Iterative metal artefact reduction (iMAR) decreases the influence of metal during image reconstruction by interpolating between boundaries of metal in a tissue-normalized sinogram. However, iMAR doesn’t incorporate spectral information, so some anatomic information is lost. A second technique, virtual monoenergetic imaging (VMI), combines multiple spectra from a dual-energy CT acquisition.
New photon-counting CT systems inherently provide spectral information without requiring a dual-energy acquisition and offer better spatial resolution, improved contrast-to-noise ratio and lower radiation dose than conventional energy-integrating detectors. The first photon-counting CT system, the NAEOTOM Alpha from Siemens Healthineers, received CE certification and 510(k) FDA clearance in 2021.
Julian Anhaus, a third-year PhD student in the CT Physics department at Siemens Healthineers in Germany, is investigating different approaches for metal artefact reduction on these systems. He and his PhD research advisors, Christian Hofmann, a global CT technology manager at Siemens Healthineers, and Andreas Mahnken, a professor at Philipps-Universität Marburg, recently studied some of the possibilities for metal artefact reduction on the NAEOTOM Alpha, publishing their findings in Physics in Medicine & Biology.
“Of course, clinicians must make their own experiences with different protocols and consequentially spectra and other scan parameters, patients and implant types, but this work can be used as an orientation and guideline for clinicians on how to tune their clinical protocols on the NAEOTOM Alpha when performing scans on patients with metal to provide best possible images for the patient’s diagnosis or care,” Anhaus says.
VMI plus iMAR reduces artefacts from high-Z metals
Anhaus tested iMAR and VMI on the NAEOTOM Alpha using anthropomorphic phantoms for different body regions and a tissue characterization phantom. He reconstructed images with and without iMAR and computed VMIs in 10 keV steps from 40 to 190 keV.
Virtual monoenergetic imaging: For spine implants, a clear optimal energy setting was observed at which metal artefacts were minimized. (Courtesy: J A Anhaus et al Phys. Med. Biol. 10.1088/1361-6560/ac71f0)
Results were mixed – Anhaus found that VMI could reduce metal artefacts in metals with low atomic numbers and low penetration lengths, such as those used in spinal implants. But for cases with large metal implants and materials with high atomic numbers, such as those used in dental fillings or in the hip head, he could only reduce artefacts by applying iMAR after VMI.
“The inherent spectral information, which is one of the main benefits of recent [photon-counting detector CT] systems, can be utilized to reduce metal artefacts without iMAR. Unfortunately, this only applies to certain metal and implant types,” Anhaus summarizes. “In most implant types, the utilization of spectral information reduces the base artefact level, but iMAR is still required to provide metal artefact-free CT images.”
Anhaus says that this study only scratches the surface of metal artefact reduction options for the NAEOTOM Alpha and other photon-counting CT systems. Read more Deep learning transforms standard CT scans towards spectral images “There are many thrilling methods which can be enabled through the photon-counting detector system and carried over to [metal artefact reduction] applications,” he says.
He and Hofmann emphasize that this study is not intended to compare image quality and artefact reduction potential between photon-counting CT and conventional energy-integrating detector CT systems that require dual-energy CT acquisition for VMI. A comprehensive comparison is part of their future work. | Biology |
DURHAM, N.C. -- Some animals are quick-change artists. Take the hogfish, a pointy-snouted reef fish that can go from pearly white to mottled brown to reddish in a matter of milliseconds as it adjusts to shifting conditions on the ocean floor.
Scientists have long suspected that animals with quick-changing colors don’t just rely on their eyes to tune their appearance to their surroundings -- they also sense light with their skin. But exactly how “skin vision” works remains a mystery.
Now, genetic analysis of hogfish reveals new evidence to explain how they do it. In a new study, Duke University researchers show that hogfish skin senses light differently from eyes.
The results suggest that light-sensing evolved separately in the two tissues, said Lori Schweikert, a postdoctoral scholar with Sönke Johnsen, biology professor at Duke.
With “dermal photoreception,” as it is called, the skin doesn’t enable animals to perceive details like they do with their eyes, Schweikert said. But it may be sensitive to changes in brightness or wavelength, such as moving shadows cast by approaching predators, or light fluctuations associated with different times of day.
Schweikert, Johnsen and Duke postdoctoral associate Bob Fitak focused on the hogfish, or Lachnolaimus maximus, which spends its time in shallow waters and coral reefs in the western Atlantic Ocean, from Nova Scotia to northern South America. It can make its skin whitish to blend in with the sandy bottom of the ocean floor and hide from predators or ambush prey. Or it can take on a bright, contrasting pattern to look threatening or attract a mate.
The key to these makeovers are special pigment-containing cells called chromatophores, which, when activated by light, can spread their pigments out or bunch them up to change the skin’s overall color or pattern.
The researchers took pieces of skin and retina from a single female hogfish caught off the Florida Keys and analyzed all of its gene readouts, or RNA transcripts, to see which genes were switched on in each tissue.
Previous studies of other color-changing animals including cuttlefish and octopuses suggest the same molecular pathway that detects light in eyes may have been co-opted to sense light in the skin.
But Schweikert and colleagues found that hogfish skin works differently. Almost none of the genes involved in light detection in the hogfish’s eyes were activated in the skin. Instead, the data suggest that hogfish skin relies on an alternative molecular pathway to sense light, a chain reaction involving a molecule called cyclic AMP.
Just how the hogfish’s “skin vision” supplements input from the eyes to monitor light in their surroundings and bring about a color change remains unclear, Schweikert said. Light-sensing skin could provide information about conditions beyond the animal’s field of view, or outside the range of wavelengths that the eye can pick up.
Together with previous studies, “the results suggest that fish have found a new way to ‘see’ with their skin and change color quickly,” Schweikert said.
This research was supported by a Charles W. Hargitt Research Fellowship and the Duke Biology Department. The study appears online and will be published in a forthcoming issue of the Journal of Comparative Physiology A.
CITATION: "De Novo Transcriptomics Reveal Distinct Phototransduction Signaling Components in the Retina and Skin of a Color-Changing Vertebrate, the Hogfish (Lachnolaimus Maximus)," Lorian E. Schweikert, Robert R. Fitak and Sönke Johnsen. Journal of Comparative Physiology A, February 28, 2018. https://doi.org/10.1007/s00359-018-1254-4 | Biology |
The explosion in text-to-image AI models like OpenAI’s DALL-E 2—programs trained to generate pictures of almost anything you ask for—has sent ripples through the creative industries, from fashion to filmmaking, by providing weird and wonderful images on demand. The same technology behind these programs is also making a splash in biotech labs, which have started using this type of generative AI, known as a diffusion model, to conjure up designs for new types of protein never seen in nature. Today, two labs separately announced programs that use diffusion models to generate designs for novel proteins with more precision than ever before. Generate Biomedicines, a Boston-based startup, revealed a program called Chroma, which the company describes as the “DALL-E 2 of biology.” At the same time, a team at the University of Washington led by biologist David Baker has built a similar program called RoseTTAFold Diffusion. In a preprint paper posted online today, Baker and his colleagues show that their model can generate precise designs for novel proteins that can then be brought to life in the lab. “We’re generating proteins with really no similarity to existing ones,” says Brian Trippe, one of the co-developers of RoseTTAFold. These protein generators can be directed to produce designs for proteins with specific properties, such as shape or size or function. In effect, this makes it possible to come up with new proteins to do particular jobs on demand. Researchers hope that this will eventually lead to the development of new and more effective drugs. “We can discover in minutes what took evolution millions of years,” says Gevorg Grigoryan, CTO of Generate Biomedicines. “What is notable about this work is the generation of proteins according to desired constraints,” says Ava Amini, a biophysicist at Microsoft Research in Cambridge, Massachusetts. Symmetrical protein structures generated by ChromaGENERATE BIOMEDICINES Proteins are the fundamental building blocks of living systems. In animals, they digest food, contract muscles, detect light, drive the immune system, and so much more. When people get sick, proteins play a part. Proteins are thus prime targets for drugs. And many of today’s newest drugs are protein based themselves. “Nature uses proteins for essentially everything,” says Grigoryan. “The promise that offers for therapeutic interventions is really immense.” But drug designers currently have to draw on an ingredient list made up of natural proteins. The goal of protein generation is to extend that list with a nearly infinite pool of computer-designed ones. Computational techniques for designing proteins are not new. But previous approaches have been slow and not great at designing large proteins or protein complexes—molecular machines made up of multiple proteins coupled together. And such proteins are often crucial for treating diseases. A protein structure generated by RoseTTAFold Diffusion (left) and the same structure created in the lab (right)IAN C HAYDON / UW INSTITUTE FOR PROTEIN DESIGN The two programs announced today are also not the first use of diffusion models for protein generation. A handful of studies in the last few months from Amini and others have shown that diffusion models are a promising technique, but these were proof-of-concept prototypes. Chroma and RoseTTAFold Diffusion build on this work and are the first full-fledged programs that can produce precise designs for a wide variety of proteins. Namrata Anand, who co-developed one of the first diffusion models for protein generation in May 2022, thinks the big significance of Chroma and RoseTTAFold Diffusion is that they have taken the technique and supersized it, training on more data and more computers. “It may be fair to say that this is more like DALL-E because of how they’ve scaled things up,” she says. Diffusion models are neural networks trained to remove “noise”—random perturbations added to data—from their input. Given a random mess of pixels, a diffusion model will try to turn it into a recognizable image. In Chroma, noise is added by unraveling the amino acid chains that a protein is made from. Given a random clump of these chains, Chroma tries to put them together to form a protein. Guided by specified constraints on what the result should look like, Chroma can generate novel proteins with specific properties. Baker’s team takes a different approach, though the end results are similar. Its diffusion model starts with an even more scrambled structure. Another key difference is that RoseTTAFold Diffusion uses information about how the pieces of a protein fit together provided by a separate neural network trained to predict protein structure (as DeepMind’s AlphaFold does). This guides the overall generative process. Generate Biomedicines and Baker’s team both show off an impressive array of results. They are able to generate proteins with multiple degrees of symmetry, including proteins that are circular, triangular, or hexagonal. To illustrate the versatility of their program, Generate Biomedicines generated proteins shaped like the 26 letters of the Latin alphabet and the numerals 0 to 10. Both teams can also generate pieces of proteins, matching new parts to existing structures. Most of these demonstrated structures would serve no purpose in practice. But because a protein’s function is determined by its shape, being able to generate different structures on demand is crucial. Generating strange designs on a computer is one thing. But the goal is to turn these designs into real proteins. To test whether Chroma produced designs that could be made, Generate Biomedicines took the sequences for some of its designs—the amino acid strings that make up the protein—and ran them through another AI program. They found that 55% of them would be predicted to fold into the structure generated by Chroma, which suggests that these are designs for viable proteins. Baker’s team ran a similar test. But Baker and his colleagues have gone a lot further than Generate Biomedicines in evaluating their model. They have created some of RoseTTAFold Diffusion’s designs in their lab. (Generate Biomedicines says that it is also doing lab tests but is not yet ready to share results.) “This is more than just proof of concept,” says Trippe. “We’re actually using this to make really great proteins.” A protein structure generated by RoseTTAFold Diffusion that binds to the SARS-CoV-2 spike proteinIAN C HAYDON / UW INSTITUTE FOR PROTEIN DESIGN For Baker, the headline result is the generation of a new protein that attaches to the parathyroid hormone, which controls calcium levels in the blood. “We basically gave the model the hormone and nothing else and told it to make a protein that binds to it,” he says. When they tested the novel protein in the lab, they found that it attached to the hormone more tightly than anything that could have been generated using other computational methods—and more tightly than existing drugs. “It came up with this protein design out of thin air,” says Baker. Grigoryan acknowledges that inventing new proteins is just the first step of many. We’re a drug company, he says. “At the end of the day what matters is whether we can make medicines that work or not.” Protein based drugs need to be manufactured in large numbers, then tested in the lab and finally in humans. This can take years. But he thinks that his company and others will find ways to speed up those steps as well. “The rate of scientific progress comes in fits and starts,” says Baker. “But right now we're in the middle of what can only be called a technological revolution.” | Biology |
Introduction
Just as people in different places seem to operate at different rhythms, so too do different species. They age at their own rates: Some, like the fruit fly, race to adulthood so they can reproduce before their ephemeral food source disappears, while creatures like humans mature slowly over decades, in part because building a large, complex brain requires it. And at the very beginning of an embryo’s life, small tweaks in the timing of when and how different tissues develop can dramatically alter an organism’s form — a mechanism that evolution exploits in creating new species. However, what sets the tempo of an organism’s growth has remained a mystery.
“Our knowledge of what controls developmental timing has really lagged behind other areas in developmental biology,” said Margarete Diaz Cuadros, who leads research focused on developmental tempo at Massachusetts General Hospital in Boston.
Developmental biologists have had tremendous success in identifying networks of regulatory genes that talk to one another — cascading systems of feedback loops that turn genes on or off at exactly the right time and place to build, say, an eye or a leg. But the highly conserved similarity in these gene networks among species contrasts with huge differences in developmental timing. Mice and humans, for example, use the same sets of genes to create neurons and build spines. Yet the brain and spine of a mouse turn out quite differently than those of a human because the timing of when those genes are active is different, and it’s unclear why that’s so.
“Gene regulation does not seem to explain everything about developmental timing,” said Pierre Vanderhaeghen, who studies the evolution and development of the brain at KU Leuven in Belgium. “Now, this is a bit provocative because in a way, in biology, everything should be explained by gene regulation, directly or indirectly.”
New explanations for what makes life tick are emerging from innovations — like advances in stem cell culture and the availability of tools to manipulate metabolism, initially developed to study cancer — that now allow researchers to chart, and toy with, the pace of development of early embryos and tissues in greater detail. In a string of papers over the past few years, including one key publication in June, several research teams have independently converged on intriguing connections between the tempo of development, the pace of biochemical reactions, and the overall metabolic rate of an organism.
Their findings point to a common metronome: the mitochondria, which may be the timekeeper of the cell, setting the rhythm for a variety of developmental and biochemical processes that create and maintain life.
A Neuron Keeps Time
More than a decade ago, Vanderhaeghen did an experiment that laid the foundation for modern studies about how developmental tempo is kept. The neurobiologist was in his Belgian lab growing stem cells in petri dishes and observing how long they took to mature from cellular blank slates to full-fledged neurons connecting and communicating with others. He thought he might find clues to the origin and evolution of the human brain by comparing these mouse and human stem cells primed to become neurons.
The first thing he noticed was that mouse stem cells differentiated into mature brain cells in about a week — more quickly than human stem cells, which took their time growing over three to four months.
Introduction
But would those cells develop the same way in a growing brain rather than in an isolated dish? To find out, he transplanted a mouse neuron into a live mouse brain. The cell followed the same timeline as the neurons of the host mouse, differentiating after about one week. Then he tried the same thing with a human neuron, implanting it into a mouse brain. To his amazement, the human neuron kept its own time. It took nearly a year to mature despite its rodential environment.
“That provided us a first important answer, which is that whatever the timing mechanism is, a lot of it seems to be in the neurons themselves,” Vanderhaeghen said. “Even if you take the cells out of the petri dish and put them in another organism, they will still keep their own timeline.”
Still, virtually nothing was known about the underlying cellular mechanism until a couple of years ago.
Vanderhaeghen started thinking about where the building blocks of a neuron come from. “To make neurons, it’s like building a super complicated building,” he said. “You need some good logistics.” Cells need not only energy but a source of raw materials to grow and divide.
He suspected that mitochondria might provision these building blocks. The organelles are key to a cell’s growth and metabolism. They produce energy, earning them the nickname “the powerhouse of the cell,” and they also produce metabolites essential for constructing amino acids and nucleotides and for regulating gene expression.
The classic view of mitochondria is that they don’t change over a cell’s life span. “They’re just this nice, picturesque little sausage in the cell, and they provide energy,” Vanderhaeghen said. But when he and Ryohei Iwata, a postdoctoral scholar in his lab, looked more closely at developing neurons, they saw that mitochondria need time to develop as well.
Introduction
Young neurons, they reported in Science, had few mitochondria, and the ones they had were fragmented and generated little energy. Then, as the neurons matured, the mitochondria grew in number, size and metabolic activity. What’s more, the changes occurred faster in mice than in humans. Essentially, the system scaled: The maturation of mitochondria stayed in sync with the maturation of neurons in both species.
The discovery struck Vanderhaeghen and Iwata as important. And it made them wonder if mitochondria could be the quiet drumbeat driving the vast differences in developmental tempo among species.
How to Grow a Spine
One of the classic models for studying the tempo of embryonic development is the patterning of the spine. All vertebrates have a spine composed of a string of vertebral segments, but species vary in their number and size. A natural question therefore arises about the developmental mechanisms that give rise to this essential vertebrate feature and its many variations throughout the animal kingdom.
In 1997, the developmental biologist Olivier Pourquié, now at Harvard Medical School, first uncovered a molecular oscillator called a segmentation clock that drives the mechanism that patterns the vertebrate spine. Working with chicken embryos, his research team identified the key players that are rhythmically expressed during the formation of each vertebral segment in embryonic tissue. The segmentation clock triggers oscillations of gene expression, causing cells to fluctuate in their responsiveness to a wavefront signal that moves from head to tail. When the wavefront encounters responsive cells, a segment forms. In this way, the clock-and-wavefront mechanism controls the periodic organization of the spine.
The genes that orchestrate the segmentation clock are conserved across species. However, the clock period — the time between two peaks in an oscillation — is not. For many years, developmental geneticists were at a loss to explain this: They didn’t have the genetic tools to manipulate the clock precisely in a growing embryo. So, around 2008, Pourquié started to develop methods to better dissect the mechanism in the lab.
At that time, “it sounded like total science fiction,” he said. But the idea became more plausible over the following decade, as Pourquié’s lab and others around the world learned to culture embryonic stem cells and even build organoids — like a retina, gut or mini-brain — in a dish.
Pourquié and Diaz Cuadros, then his graduate student, found a way to reproduce the clock in mouse and human stem cells. In early experiments, they observed that the clock period runs about two hours in mice, whereas it takes about five hours to complete an oscillation in human cells. It was the first time anyone had identified the segmentation clock period in humans.
Other labs also saw the potential of these advances in stem cell biology to tackle long-standing questions about developmental timing. In 2020, two research groups — one led by Miki Ebisuya at the European Molecular Biology Laboratory in Barcelona and the other by James Briscoe at the Francis Crick Institute in London — independently discovered that basic molecular processes in the cell stay on beat with the pace of development. They published studies side by side in Science.
Ebisuya’s team wanted to understand differences in the rate of molecular reactions — gene expression and protein degradation — that drive each clock cycle. They found that both processes worked twice as fast in mouse cells as in human ones.
Briscoe looked instead at the early development of the spinal cord. Like the segmentation clock cycle, the neuron differentiation process — including the expression of gene sequences and the breakdown of proteins — was proportionally stretched out in humans compared to mice. “It takes two to three times longer to get to the same stage of development using human embryonic stem cells,” Briscoe said.
It was as if, inside of each cell, a metronome was ticking away. With each swing of the pendulum, a variety of cellular processes — gene expression, protein degradation, cell differentiation and embryonic development — all kept pace and stayed on time.
Introduction
But was this a general rule for all vertebrates, beyond mice and humans? To find out, Ebisuya’s graduate student Jorge Lázaro created a “stem cell zoo,” home to cells from a variety of mammals: mice, rabbits, cattle, rhinoceroses, humans and marmosets. When he reproduced the segmentation clock of each species, he saw that the speed of biochemical reactions stayed in rhythm with the segmentation clock period in every one.
What’s more, the clock tempos did not scale with the animals’ size. Rhinoceros cells oscillated more quickly than human cells, while marmoset cells had the slowest oscillations of all, slower even than those of mouse cells.
The findings, published in Cell Stem Cell in June, suggested that the speed of biochemical reactions could be a universal mechanism for regulating developmental time.
They also pushed the bounds of an important but overlooked aspect of the central dogma of molecular biology. “We’re talking about transcription, translation and protein stability,” Diaz-Cuadros said. Everyone had thought that they were the same in all mammalian or vertebrate species, “but now what we’re saying is that the speed of the central dogma is species-specific, and I think that is quite fascinating.”
Make or Break a Protein
The clock, then, must stem from a mechanism that sets the pace of biochemical reactions across species. Teresa Rayon wanted to uncover its origins when she watched motor neurons differentiate in her London laboratory, where she studied under Briscoe.
She genetically engineered developing mouse and human neurons to express fluorescent protein, which glows brightly when excited by a laser at the right wavelength. Then she watched the introduced proteins as they degraded. To her surprise, the very same fluorescent proteins came apart more quickly in mouse cells than in human cells, keeping time with the neurons’ development. That suggested to her that something in the intracellular environment set the tempo of degradation.
Introduction
“If you were to ask a biologist, ‘How do you determine the stability of a protein?’ they would tell you that it’s down to the sequence,” said Rayon, who now leads her own lab at the Babraham Institute in Cambridge, England. “However, we found that that’s actually not the case. We think that it might be the machinery that is degrading the proteins that might be playing a role.”
But she and her group were looking in only a single cell type. If cell types in various tissues develop at different rates, would their proteins degrade at different rates, too?
Michael Dorrity at the European Molecular Biology Laboratory in Heidelberg was digging into that question by thinking about how temperature affects development. Many animals, from insects to fish, develop faster when reared at higher temperatures. Intriguingly, he observed that in zebra fish embryos raised in a warm environment, the developmental tempo of some cell types accelerated faster than that of others.
In a preprint he posted last year, he homed in on an explanation involving the machinery that makes and degrades proteins. Some cell types require a greater volume or more complex proteins than others. As a result, some cell types are chronically “putting a load on these protein quality control mechanisms,” he said. When the temperature rises, they don’t have the capacity to keep up with the higher protein needs, and so their internal clock fails to speed up and keep pace.
In that sense, organisms don’t maintain a single unified clock, but have many clocks for many tissues and cell types. Evolutionarily speaking, this is not a bug but a feature: When tissues develop out of sync with one another, body parts can grow at different rates — which can lead to the evolution of diverse organisms or even new species.
Introduction
So far, these mechanisms across systems and scales — in the developing embryo’s segmentation clock, in a single developing neuron, and in more fundamental protein machinery — have all continued to beat in time.
“Pretty much everything we looked at so far is scaling,” Pourquié said, “which means that there is a global command for all these processes.”
The Tick-Tock of Metabolism
What could this upstream control system be? Pourquié and Diaz Cuadros pondered which system could potentially affect a variety of cellular processes — and they landed on metabolism, driven by mitochondria. Mitochondria produce ATP, the energy currency of the cell, as well as a host of metabolites essential for building proteins and DNA, regulating the genome, and performing other critical processes.
To test that idea, they devised genetic and pharmacological methods to speed up and then slow down the metabolic rates of their stem cells. If mitochondria were indeed setting the cellular tempo, they expected to see their experiments alter the rhythm of the segmentation clock.
When they slowed metabolism in human cells, the segmentation clock slowed too: Its period stretched from five to seven hours, and the rate of protein synthesis slowed as well. And when they sped metabolism up, the clock’s oscillations accelerated, too.
It was as if they had discovered the tuning knob of the cell’s internal metronome, which let them accelerate or decelerate the tempo of embryonic development. “It’s not differences in the gene regulatory architecture that explains these differences in timing,” Pourquié said. The findings were published in Nature earlier this year.
This metabolic tuning knob wasn’t limited to the developing embryo. Iwata and Vanderhaeghen, meanwhile, figured out how to use drugs and genetics to toy with the metabolic tempo of maturing neurons — a process that, unlike that of the segmentation clock, which runs for only a couple of days, takes many weeks or months. When mouse neurons were compelled to generate energy more slowly, the neurons matured more slowly, too. Conversely, by pharmacologically shifting human neurons toward a faster pathway, the researchers could accelerate their maturation. The findings were published in Science in January.
To Vanderhaeghen, the conclusion of their experiments is clear: “Metabolic rate is driving developmental timing.”
Yet, even if metabolism is the upstream regulator of all other cellular processes, those differences must come back to genetic regulation. It’s possible that mitochondria influence the timing of the expression of developmental genes or those involved in the machinery for making, maintaining and recycling proteins.
One possibility, Vanderhaeghen speculated, is that metabolites from the mitochondria are essential to the process that condenses or expands folded DNA in genomes so that it can be transcribed to build proteins. Maybe, he suggested, those metabolites limit the rate of transcription and globally set the pace at which gene regulatory networks are turned on and off. That’s just one idea, however, that needs experimental unpacking.
There is also the question of what makes mitochondria tick in the first place. Diaz Cuadros thinks that the answer must lie in DNA: “Somewhere in their genome, there has to be a sequence difference between mouse and human that is encoding that difference in developmental rate.”
“We still have no idea where that difference is,” she said. “We’re unfortunately still very far from that.”
Finding that answer may take time, and like the mitochondrial clock, scientific progress proceeds at a tempo all its own. | Biology |
Often referred to as the "powerhouses of the cell," mitochondria are well known for their role as energy suppliers, but these organelles are also critical for maintaining our overall health.Mitochondrial stress is associated with aging and age-related diseases, including neurodegeneration, but there has been a limited understanding of the molecular mechanisms behind this mitochondrial stress signaling. Now, a study by Scripps Research scientists has revealed an important step in this process.
The new study, published August 7, 2023, in the journal Nature Structural & Molecular Biology, shows how a mitochondrial protein structure is necessary to activate the cell's integrated stress response (ISR) -- a critical pathway that helps our cells maintain health. The researchers believe this mitochondrial structure, made up of a protein called DELE1, could serve as a target for future therapeutics for age-related diseases.
"Understanding the molecular details of this signaling pathway could help us potentially develop treatments for a range of diseases, such as neurodegenerative diseases, cancer and heart disease," says first author Jie Yang, PhD, a postdoctoral fellow in the lab of Gabriel Lander at Scripps Research.
In order to maintain cellular function and health, mitochondria must continually sense and respond to stressors, such as viral infections and iron deficiency. However, their ability to do so decreases as people age.
"Just like every other part of our body, mitochondria age and become slightly less productive," says co-author Kelsey Baron, a graduate student in the lab of Luke Wiseman at Scripps Research. "When you have this loss of mitochondrial productivity, your cells don't have as much energy to fight different stressors, and many people believe that is a major trigger of neurodegeneration."
One method by which mitochondria deal with stress is by activating the ISR. Prior studies have shown that the DELE1 protein is involved in activating this integrated stress response, but before now, little was known about the protein's molecular structure. Characterizing DELE1's structure is a key step towards understanding and treating diseases associated with mitochondrial stress.
The researchers focused on a fragment of DELE1 -- the C terminus -- that is known to be actively involved in initiating the ISR. When they isolated this fragment, they were surprised to find that it was much heavier than expected, which suggested that multiple copies of the protein fragment were binding together. Using electron microscopy, the team showed that this protein complex (or oligomer) was a highly symmetrical cylinder composed of eight identical fragments -- in other words, an octamer.
"It was completely unexpected that it was forming this much larger, oligomeric structure," says study co-senior author Gabriel Lander, PhD, professor in the Department of Integrative Structural and Computational Biology at Scripps Research. "It's kind of like two four-legged spiders whose legs are intertwined to form this flexible cylindrical structure."
The researchers captured more than 12,000 electron microscope images of the octamer and then used algorithms to produce a three-dimensional structural model. Then, by looking at the positions of different amino acids (the building blocks of proteins) within the structure, they were able to identify which amino acids are involved in binding and assembling the octamer.
To test whether this oligomerization of DELE1 is required to activate the ISR, the researchers then introduced mutations into some of the key amino acids, which would disrupt the ability of DELE1 to bind together. When they cultured cells that contained this mutated, un-oligomerizable version of DELE1, the cells were unable to activate the ISR -- suggesting that oligomerization is critical to activating this stress signaling pathway.
The next step is to find ways to use this structural information to manipulate these pathways -- notably in different diseases and disorders, the researchers say.
"Knowing that this oligomerization step is a potential site of regulation gives us a platform for potential drug development," says co-senior author Luke Wiseman, PhD, professor in the Department of Molecular medicine at Scripps Research. "We think that targeting this pathway has potential for improving outcomes in a variety of different disorders."
As well as Jie Yang, Kelsey Baron, Luke Wiseman, and Gabriel Lander, authors of the study "DELE1 oligomerization promotes integrated stress response activation," include Daniel E. Pride, Anette Schneemann, Wenqian Chen, and Albert S. Song of Scripps Research; and Xiaoyan Guo, Giovanni Aviles and Martin Kampmann of the University of California, San Francisco.
This study was funded by the National Institutes of Health (grants NS095892 and NS125674 and fellowship F31AG071162) and the Olson-King Endowed Skaggs Fellowship from Scripps Research.
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A new study published in Science Advances today provides evidence that large-scale, offshore, and fully-protected marine areas (MPAs) protect biodiversity without negatively impacting fishing and food security.
Washington, D.C. (May 31, 2023)—In the first-ever “before and after” assessment of the impact of establishing Mexico’s Revillagigedo National Park on the fishing industry, a team of US and Mexican researchers found that Mexico’s industrial fishing sector did not incur economic losses five years after the park’s creation despite a full ban on fishing activity within the MPA.
Established in 2017, the “Galápagos of Mexico” is the world’s 13th-largest MPA, and one of the few where all damaging human activities, including fishing, are banned to help marine populations recover. Home to one of the world’s largest aggregations of sharks and manta rays, as well as tuna, humpback whales and five species of sea turtles, it also shelters more than 300 species of fish, of which 36 are not found anywhere else in the ocean. At the time, the Mexican industrial fishing lobby opposed the creation of the National Park, arguing that it would impact their catches and increase their costs.
“Worldwide, the fishing industry has blocked the establishment of the marine protected areas we urgently need to reverse the human-caused global depletion of sea life. This study uses satellite tracking of fishing vessels and artificial intelligence (AI) to show that the fishing industry’s concerns are unfounded,” said Enric Sala, Explorer in Residence at National Geographic Society, the founder of Pristine Seas and a study co-author. “Even the largest of MPAs, which safeguard entire ecosystems, home to thousands of species of marine creatures, do not impact the handful of fish species that the fishing industry seeks out. The larger the MPA, the larger the benefits.”
Methodology
The study, conducted by a team of researchers from the Mexican Center for Marine Biodiversity, UC San Diego’s Scripps Institution of Oceanography, the Institute of Americas’ Gulf of California Marine Program, and the National Geographic Society, analyzes the behavior and productivity of the Mexican industrial fishing sector before and five years after the implementation of the largest fully protected MPA in North America, the Revillagigedo National Park.
Using data from satellite tracking, fish catches from the Mexican Fisheries Commission, and new AI tools from the Allen Institute for AI’s Skylight platform, the experts set out to determine whether the creation of the MPA reduced fishing within the protected area, whether fishing catches were affected and if the creation of the MPA displaced fishing onto a larger area, resulting in an overall negative impact on marine biodiversity.
“The use of satellite tracking devices and AI monitoring platforms was critical to show compliance from the fishing industry and for the MPA managers’ to monitor the protected area,” said Dr. Fabio Favoretto, postdoctoral scholar at Scripps Institution of Oceanography and lead author of the study.
The satellite data analyzed by Favoretto came from government-mandated GPS devices installed on some 2,000 fishing vessels. By reviewing the open source data, they were able to identify movement of fishing vessels to see if fishing behaviors or maneuvers were performed. The team then employed machine-learning enabled techniques to identify patterns associated with vessels.
They found that the Revillagigedo National Park has had no negative effect on the Mexican industrial fleet’s catches, nor did it increase the area used for fishing that would drive fishing vessels to venture further to catch fish. Skylight revealed only a few isolated cases of illegal fishing within the MPA after 2017, highlighting the effectiveness of technology in helping those monitoring and protecting the 147,000 square kilometers of waters included within the park’s boundary.
The study results refute the Mexican fishing industry’s argument that the park would cause a potential loss of 20% of their tuna and other pelagic catches and provide proof that large, fully-protected MPAs can contribute to a more sustainable and equitable use of the ocean, without major economic repercussions on the fishing industry.
“The findings of this study are consistent with what experts have recorded in other Pacific marine protected areas,” said Octavio Aburto, co-author and professor of marine biology at Scripps Institution of Oceanography. “Any argument to the contrary were just assumptions — this study provides the data to show that negative impacts to fishing do not exist. We hope the results can open a discussion to work together with the fishing industry to protect biodiversity and improve fish stocks.”
Safeguarding Biodiversity
The findings are released at a time when countries debate how to implement the global goal to protect and conserve at least 30% of the ocean by 2030, which is enshrined in a landmark agreement reached at the UN Global Biodiversity Conference (COP15) in December 2022. Just last month, United Nations members agreed on a legally-binding instrument to protect biodiversity in the high seas — the international waters beyond national jurisdictions.
“The clock is ticking until 2030,” Sala said. “If the world is serious about protecting the natural world — our life support system — we need to drastically increase ocean protection. Right now, less than 8% of the ocean is somewhat protected, and only 3% is fully protected from fishing and other damaging activities. Millions of species, including humans, who rely on the ocean for oxygen, food, mitigation of global warming, medicine and more depend on us to act.”
Threatened by human activities like overfishing, the ocean’s rich stockpile of biodiversity is rapidly declining, posing risks to food security, health and the environment. By rapidly establishing marine protected areas in strategic ocean areas, the world can collectively safeguard more than 80% of the habitats of endangered species, up from a current coverage of less than 2%.
Amid these debates, the study provides empirical evidence that large-scale MPAs in countries’ Exclusive Economic Zones can contribute to global conservation goals without compromising fisheries’ interests or a nation’s ability to ensure food security.
Shoring up the Fishing Industry
The study refutes a long-held view promoted by the industrial fishing lobby that ocean protection harms fisheries, and opens up new opportunities to revive the industry just as it is suffering from a recession due to overfishing and the impacts of global warming.
“Some argue that closing areas to fishing hurts fishing interests. But the worst enemy of fishing is overfishing and bad management — not protected areas,” Dr. Sala said.
The study will enrich ongoing discussions taking place in Mexico and beyond as Catalina López-Sagástegui, co-author and a researcher at the Institute of Americas, said: “Access to data and technology is improving our collective understanding of marine ecosystems health, which allows us to design and implement MPAs that help restore the health and resilience of marine ecosystems, benefiting fisheries in the long term.”
Dr. Reniel Cabral, Senior Lecturer at James Cook University in Australia, who wasn’t involved in this study, added: “It’s simple: When overfishing and other damaging activities cease, marine life bounces back. After protections are put in place, the diversity and abundance of marine life increase over time, with measurable recovery occurring in as little as three years. Target species and large predators come back, and entire ecosystems are restored within MPAs. With time, the ocean can heal itself and again provide services to humankind.”
Dr. Sala said: “MPAs are the most effective tool we have for protecting the health and diversity of our oceans. We need to expand and strengthen protected areas to ensure that our oceans can continue to provide food, jobs and other vital benefits for future generations. Our study helps to dispel the myth put forward by the industrial fishing lobby that MPAs harm them.”
This study was funded by Oceans 5 and the Patrick J. McGovern Foundation.
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About Pristine Seas
Pristine Seas works with Indigenous and local communities, governments, and other partners to help protect vital places in the ocean using a unique combination of research, community engagement, policy work, and strategic communications and media. Since 2008, our program has conducted 38 expeditions around the world and helped establish 26 marine reserves, spanning more than 6.5 million square kilometers of ocean. | Biology |
Plasma-structural coloring: A new colorful approach to an inkless future
New developments for achieving structural coloring through plasma irradiation of graphite can reduce the reliance upon harmful color dyes. Colors achieved by plasma irradiation are completely erasable and can be manipulated using time exposed to the plasma irradiation, intensity of the irradiation and the thickness of the graphite layer applied.
The application of plasma-structural coloring aims to lessen the environmental toll typical adverse dyes have and combat them with the technology surrounding structural colors. Structural colors look different than how we perceive colors dyed by pigment, because structural colors are based on viewing how the light scatters when reflected, giving an iridescent quality to the observed colors. In nature, this type of coloring can be seen in peacock feathers and some insects like beetles.
Many inks used for coloring, whether it is on paper or textiles, are bad for the health of the environment. The process of making dyes along with the volatile compounds comprising the dyes are major pollutants, and a sustainable solution is in order. This solution may be seen by way of structural coloring through plasma irradiation.
"We called this technique 'plasma structural coloring'. The method is an entirely new technique that changes the color of the penciling part on a paper by plasma irradiation. The technique is an environmentally friendly coloring method and can be applied to various activities, such as study and art," said Hiroshi Moriwaki, professor in the Department of Applied Biology at Shinshu University.
The new finding was published in ACS Applied Materials & Interfaces.
"Structural colors" are colors that are viewed by the human eye due to the interference of light reflected off the surface of a nanostructured material, such as the graphite from a pencil. The study looked into how plasma irradiation can manipulate the appearance of color by testing materials, plasma intensity and time needed to alter the color.
In the new study, the structural colors and coloring using plasma irradiation were put to the test. They showed some promise: graphite on paper was successfully changed into blue, yellow, and red corresponding to the length of exposure to the plasma irradiation. The colors were also found to be angle-independent, so no matter which way the colors were viewed, the color observed was fixed.
"We would like to make readers understand that we have developed a simple method for the formation of structural colors at low cost and in a short time. We believe this method can contribute to the achievement of a sustainable society," Moriwaki said.
Another benefit to structural colors is their stability: they don't degrade or fade through chemical reactions like other dyes might. Increasing the durability of colors will yield higher-quality work without the concern of fading in the future. This is of particular use in the art world, where many works have to be shielded from light to preserve the intensity of the colors and quality of the piece.
"The ultimate goal is to spread the method of coloring pencil writing by the plasma irradiation. For that purpose, it is important to develop a simple and easy-to-use small plasma device suitable for this method. In addition, we think it would be interesting if an artist could create paintings colored only with structural colors," Moriwaki said.
The next step in perfecting the plasma-structural coloring process is to reduce the variability in the colors through the process. Additionally, the most effective tools are currently a specific type of pencil with high-graphite content, so finding a way to make the process available on a broader spectrum of tools may also be useful for future studies. Making the device simple and cost-effective will broaden the use of this product too, further reducing the need for harmful dyes amongst artists and other people who frequently use colored ink in their craft.
More information: Hiroshi Moriwaki et al, "Plasma-Structural Coloring" of Penciling on a Paper, ACS Applied Materials & Interfaces (2023). DOI: 10.1021/acsami.2c19642
Provided by Shinshu University | Biology |
Malformations in heart, eyes and nervous system: Nano-plastics disrupt growth
Nano-plastics cause malformations. Meiru Wang, researcher at the Institute of Biology Leiden, looked at the extreme effects polystyrene nano-particles could have, using chicken embryos as a model. Her results were quite alarming. Especially as nano-particles are everywhere. In the air, floating through our seas and rivers, in cosmetics and shampoos, and now researchers are even investigating whether they can be used in human medicines.
‘We see malformations in the nervous system, heart, eyes and other parts of the face,’ Wang says. ‘We used a high concentration of polystyrene particles, that would normally not be present in an organism. But it shows what nano-plastics can do in extreme cases on very young embryos. And it also gives us guidelines on what can happen less severely in the developmental stage.’ The results are now published in the leading journal Environment International.
Nano-plastics target stem cells
Nano-plastics target the embryonic neural crest cells, Wang found. These stem cells are formed very early in all vertebrates at the beginning of their existence. The neural crest cells start in what will be the spinal cord, and migrate to create part of the nervous system. They also form parts of several important organs, such as the arteries, heart and face.
‘When you know the mechanism, everything else falls into place.’
However, when nano-particles surround the neural crest cells, the migration of those cells is disrupted. This results in growth disturbances. Michael Richardson, supervisor of Wang: ‘When you know the mechanism, everything else falls into place. We think they stick to the neural crest cells, which causes the cells to die. Neural crest cells are sticky, so nano-particles can adhere to them and thereby disrupt organs that depend on these cells for their development. I like the metaphor of making dough. When making bread, for example, you put flour on it to make it not sticky anymore. However, in this case, it ruins the migration of the neural crest cells.’
Finding mechanisms with 3D reconstructions, X-rays and expertise
The research project involved multiple research centers in Leiden and abroad including CML, whose new director, Martina Vijver, is Wang’s supervisor. ‘Because nanoplastics are so small, it is impossible to see them using conventional microscopes. That is what makes it difficult to research. We can only see them when they are fluorescently tagged,’ Richardson explained. ‘Collaboration was the way to go, as this type of research can’t be done as a one-man band.’
The researcher continues: ‘At Naturalis Biodiversity Center in Leiden, Martin Rücklin and Bertie Joan van Heuven were able to make 3D reconstructions of the embryos, so we could clearly see the malformations. And with the high-resolution synchrotron Switzerland, we could see what happens in the heart. Experienced researchers from the LUMC helped define what we see.’
One step forwards
Wang is very happy with her research, even with its worrying results. ‘Everything is a question mark in research, and you get the chance to fill in the gaps. I have many great supervisors and colleagues, who encourage me and make me braver. This research is only one step to see what are the ultimate effects of nano-plastics in our environment. And especially as people are now looking into using them in human medicines, we believe that we should take care before these drastic effects are seen in humans.’
Read the publication
Wang, M., Rücklin, M., Poelmann, R. E., de Mooij, C. L., Fokkema, M., Lamers, G. E., ... & Richardson, M. K. (2023). Nanoplastics causes extensive congenital malformations during embryonic development by passively targeting neural crest cells. Environment International, 107865. https://doi.org/10.1016/j.envint.2023.107865 | Biology |
Deblina Sarkar makes little machines, for which she has big dreams. The machines are so little, in fact, that they can humbly inhabit living cells. And her dreams are so big, they may one day save your mind.
Sarkar is a nanotechnologist and assistant professor at MIT. She develops ultratiny electronic devices, some smaller than a mote of dust, that she hopes will one day enter the brain. She’s also a fan of Kung Fu movies and likes to dance her own twist on bharata natya, a classical Indian dance form. Occasionally she goes hiking with her graduate students, once taking them as far as Yellowstone. Building camaraderie is vital, Sarkar says. But “I’m probably working day and night on my research,” she confesses. “There is an urgent problem at hand.”
That problem is Alzheimer’s disease, Parkinson’s disease and other neurological afflictions that assault the minds of millions of people worldwide. Sarkar’s solution: Employ minute machines to detect and reverse these disorders.
“She was always interested in applying … electronics to biological systems,” says collaborator and bioengineering researcher Samir Mitragotri of Harvard University, who has known Sarkar for about a decade and was on her thesis committee. She envisions using her tools to “transform how people are conducting biology,” he says, “bridging the worlds.”
A focus on nanoelectronics
Born in Kolkata, India, Sarkar credits both of her parents as early inspirations. Her boldness as a researcher comes from her mother, who as a young woman defied social norms in her village by working to fund her own education and speaking out against the dowry system. Meanwhile, Sarkar’s father sparked her fascination for engineering.
At the age of 15, he abandoned his dreams of becoming an engineer to find other jobs; he needed to support his parents and the rest of his family after his father, an Indian freedom fighter, was shot in the leg and could no longer work. Still, Sarkar recalls her father finding time for his passion, fashioning devices to make home life more convenient. These included an electricity-free washing machine and vehicles that could freight hefty loads down local byroads to their house.
“That got me very, very interested in science and technology,” Sarkar says. “Engineering specifically.”
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After earning a bachelor’s degree in electrical engineering from the Indian Institute of Technology Dhanbad, Sarkar moved to California to study nanoelectronics at the University of California, Santa Barbara. There, she tested new ways to create nanodevices that could reduce the amount of power consumed by computers and other everyday electronics.
One standout device Sarkar developed during her graduate work was a transistor that reduced the amount of power lost as heat by 90 percent compared with some of today’s most common silicon transistors (SN: 3/18/22). For the breakthrough, UC Santa Barbara awarded Sarkar’s Ph.D. dissertation the Lancaster Award for its impact in advancing math, physical sciences and engineering.
When tech meets the body
Along the way, Sarkar became fascinated with the brain, which she calls “the lowest energy computer.” A project imaging amyloid-beta plaques as a postdoc at MIT opened the door to fusing her dual interests, and she stayed on as an assistant professor to found the Nano-Cybernetic Biotrek group. Her group develops nanodevices that can interface with living cells, and “neuromorphic” computing devices, which have architectures inspired by the human brain and nervous system.
So far, the group’s most innovative device may be the Cell Rover, a flat antenna that could monitor processes inside cells. For a study reported in 2022, Sarkar and her colleagues used magnetic fields to finesse a Cell Rover, roughly the size of a tardigrade, into a mature frog egg cell. The team demonstrated that when stimulated by a magnetic field created by an alternating current, molecules in the nanodevice vibrated at frequencies safe for living cells. Using a wire coil receiver, the researchers were able to detect how those vibrations affected the device’s own magnetic field, thus showing it could communicate with the outside world. Cell Rovers could be outfitted with films that latch onto and detect select proteins or other biomolecules.
Sarkar envisions using the device to spot misfolded proteins in the brain that may be early signs of Alzheimer’s disease. Today, memory loss is the only way to know a living person has Alzheimer’s, but by then, the damage is irreversible, Sarkar says. Cell Rovers could also be paired with nanodevices that harvest energy from and electrically stimulate cells, opening the door for new types of brain electrodes and subcellular pacemakers. Or fleets of remotely controlled devices could replace invasive surgeries — detecting a small tumor growing in the brain, for example, and maybe even killing it.
She’s essentially establishing a new field of science, at the intersection of nanoelectronics and biology, Mitragotri says. “There are many opportunities for the future.”
One day, Sarkar hopes to insert nanodevices between human neurons to boost the computing speed of the fleshy processor already in our skulls. Our brains are remarkable, she says, but “we could be better than what we are.” | Biology |
In the last decade, archaeologists have discovered evidence that foxes may have been kept as pets thousands of years ago—or, at the very least, tolerated to hang around human settlements.OffEnglishTo learn more about the relationship between foxes and our ancestors, I spoke with an archaeologist and a zoologist about the latest scientific findings and what they mean for our understanding of animal domestication in human history.Fox burialsThe most recent study of archaeological burial sites where both foxes and humans were found has taken place in Spain. The site belonged to an agricultural society, one growing barley and legumes and taking care of livestock like sheep and cattle.Researchers from several institutes and universities analyzed bones collected at the burial site. They studied the isotopes found in the collagen preserved in the bones, which can provide insights into the diets of individuals. In human bones, we can learn about the diet of an adult in the last five to 10 years of life. In young adult dogs, the diet data spans from six months to three years.The first significant finding was how many fox bones the researchers found, explained by Aurora Grandal-d’Anglade, the lead researcher and a senior lecturer at the University of A Coruña.G/O Media may get a commission“The fox was already a striking finding, since in the Can Roqueta burials there were only domestic animals,” she said. “Later, when collaborating with researchers from other sites, they saw that there were more cases, and this was a key to consider that the foxes had a special value.”The results show that the foxes had a diet similar to some of the humans and dogs. This suggests a higher level of interaction than previously assumed between these societies and foxes 4.000 years ago.Moreover, the team found something surprising: One of the four foxes, the one with the most human-like diet (large amounts of vegetable protein), had healed broken bones. The way in which the bones were healed is compatible with the immobilization of the fractured bones, presumably by humans. “The healed fracture in the fox’s paw was a finding that caught the attention of the team working at Can Roqueta from the moment of the excavation,” Grandal-d’Anglade said. “When I came to collaborate with the zooarchaeologists with the isotopic analyses, we predicted for the fox an isotopic signature somewhat different from that of a wild carnivore, but it turned out to be more special than expected.”In addition to finding similarities between foxes’ diets and that of humans and their dogs, the researchers found that, in the case of the injured fox, its diet contained an important amount of vegetable protein. This diet is similar to that of young dogs at the site, rich in cereals. This could indicate that the fox was being fed by humans, at least for a time before the its death. However, the isotopic signature is not specific enough to verify this.Although studying a much older burial, approximately 15,000 years old, a similar study in Germany and Switzerland also found differences between the diets of foxes surrounding human settlements and wild foxes. In that study, however, the fox diet was still quite distinct from that of humans, indicating a commensal relationship, where foxes would obtain food scraps from humans, one way or another.Around the same time, approximately 13,000 years ago in the Levant, a careful burial was performed: the burial of a human with a fox. Both their bones were treated with red ochre (treatment not given to the other bones found at the burial site), indicating some sort of significance of the fox in contrast to the other animals. Moreover, the burial was later re-opened, and the bones were taken elsewhere, but the human and the fox were kept together through these different burials.This study, published 10 years ago, analyzed the burial site’s composition. Notably, the date of this unique human-fox burial pre-dates the appearance of domesticated dogs in the region. Of course, figuring out the social meanings of a human society that existed thousands of years ago is a complex task. However, it is not hard to imagine that, at some point in time, foxes may have been seen as analogues to dogs and of some potential usefulness to keep around.Adaptable animalsAs remarked by Kat Black, an adjunct biology instructor at Radford University who has studied foxes living in and around human areas, foxes are very adaptable.“As opportunistic omnivores, foxes have a highly flexible diet, and can capitalize on anthropogenic food resources such as scraps from unsecured garbage bins, compost piles, pet food, etc,” Black explained. “They can also take advantage of high densities of prey species, such as mice and rats. Unlike some species that require large areas of old-growth forest or pristine wetlands to thrive, red foxes will readily use a wide variety of habitat types and seem to particularly like edge habitats and areas where several different habitat types occur in close proximity.”Whether foxes in the past were just living near human settlements or were purposefully kept (or allowed) around them, urban foxes are a phenomenon for which we can find analogues in more recent times.Records of foxes around urban areas are present in both the 19th and 20th centuries. Records of urban foxes are found both in areas where they are native and where they have been introduced: Melbourne in the 1940s, suburban Stockholm in the 1960s, and Brussels in the early 1970s, for examples.Usually, these urban foxes were not broadly welcomed. As Black explained, living next to foxes is not necessarily easy.“For people, red foxes can become a nuisance when their activities interfere with human ideals,” she said. “Knocking over trash cans, raiding gardens, denning under porches and sheds, and defecating in yards is normal red fox behavior, but not everyone is willing to tolerate such unruly neighbors. People may also have concerns about fox impacts on human and pet health and safety. Fox attacks on people, dogs, and cats are rare, but foxes can carry rabies and other diseases that can be transmitted to people and the pets they care about.”However, there are records of foxes being tamed and kept as pets. In Finland, a country with many records of foxes living in or around urban centers, there are also reports of some of the tamer urban foxes being captured and then kept as pets. For example, in 1921, a fox was caught in the Turku city barracks and was kept as a pet.Time to revisit old digging sitesIt is not hard to imagine how similar situations may have occurred throughout history when someone decided to keep a fox as a pet (or maybe wanted their fur after they grew up). But unfortunately, there is still much we don’t know.To answer the question of why our ancestors did not domesticate foxes the way they did dogs, we still have a long way to go. It is possible, however, that some of the critical remains have already been unburied, waiting to be analyzed with new techniques and an open mind, noted Grandal-d’Anglade.“It is quite possible that the skeletal remains of foxes that may have been found in archaeological contexts have been directly classified as the remains of hunted animals without considering other hypotheses. The idea that the fox was simply a wild animal is prevalent among archaeologists, but in my opinion, it is a preconceived idea,” she said. “If only domestic animals are included in funerary structures, the presence of a fox may indicate a close relationship with the buried human.... But when approaching an archaeological context, it is necessary to pay attention to various kinds of evidence. We studied the diet of these foxes and found it to be like that of dogs, and even similar to that of children. Hence our suggestion that these foxes were not entirely wild animals. Perhaps if we review more sites from this point of view, we could find similar cases. “Maria Gatta is an ecologist and science writer with a passion for the relationships between plants, animals, and humans. She is also a biology consultant for video game companies. Follow her on Twitter: @M_Gatta | Biology |
When driving through a rainstorm, traction is key. If your tires lack sufficient tread, your vehicle will slip and slide and you won't have the grip needed to maneuver safely. When torrential rains hit nearshore, shallow water ecosystems, sea urchins experience a similar challenge. Heavy precipitation can alter the concentration of salt in the ocean waters causing lower salinity levels. Even a slight change in salinity can affect the ability of sea urchins to securely attach their tube feet to their surroundings -- like tires gripping the road. This becomes a matter of life and death for the small spiny creatures, as they rely on their adhesive structures to move in the wave-battered rocky area near the seashore.
Syracuse University biologists co-authored a study exploring how sea urchin adhesive abilities are affected by differing levels of water salinity.
The survival of sea urchins is vital for maintaining balance within marine ecosystems. Sea urchins are responsible for grazing around 45% of algae on coral reefs. Without sea urchins, coral reefs can become overgrown with macroalgae, which can limit the growth of corals. With the importance of coral reefs for coastal protection and preservation of biodiversity, it is critical to safeguard the sea urchin population.
As global climate change causes weather extremes ranging from heat waves and droughts to heavy rains and flooding, the large amounts of freshwater pouring into nearshore ecosystems are altering habitats. A team of biologists, led by Austin Garner, assistant professor in the College of Arts and Sciences' Department of Biology, studied the impacts of low salinity and how it alters sea urchins' ability to grip and move within their habitat. Garner, who is a member of Syracuse University's BioInspired Institute, studies how animals attach to surfaces in variable environments from the perspective of both the life and physical sciences.
The team's study, recently published in the Journal of Experimental Biology, sought to understand how sea urchin populations will be affected by future extreme climatic events.
"While many marine animals can regulate the amount of water and salts in their bodies, sea urchins are not as effective at this," says Garner. "As a result, they tend to be restricted to a narrow range of salinity levels. Torrential precipitation can cause massive amounts of freshwater to be dumped into the ocean along the coastline causing rapid reductions in the concentration of salt in seawater."
The group's research was conducted at the University of Washington's Friday Harbor Laboratories (FHL). The study's lead author, Andrew Moura, who is a graduate student in Garner's lab at Syracuse, traveled to FHL along with Garner and researchers from Villanova University to conduct experiments with live green sea urchins. They worked alongside former FHL postdoctoral scholar Carla Narvaez, who is now an assistant professor of biology at Rhode Island College, and Villanova University professors Alyssa Stark and Michael Russell.
At FHL, the researchers separated sea urchins into 10 groups based on differing salinity levels within each tank, from normal to very low salt content. Among each group, they tested metrics including righting response (the ability for sea urchins to flip themselves over), locomotion (speed from one point to another) and adhesion (force at which their tube feet detach from a surface). In Garner's lab at Syracuse, he and Moura completed data analysis to compare each metric.
The team found that sea urchin righting response, movement, and adhesive ability were all negatively impacted by low salinity conditions. Interestingly, though, sea urchin adhesive ability was not severely impacted until very low salinity levels, indicating that sea urchins may be able to remain attached in challenging nearshore environmental conditions even though activities that require greater coordination of tube feet (righting and movement) may not be possible.
"When we see this decrease in performance under very low salinity, we might start seeing shifts in where sea urchins might be living as a consequence of their inability to remain stuck in certain areas that experience low salinity," explains Moura. "That could change how much sea urchin grazing is happening and could have profound ecosystem effects."
Their work provides critical data that enhances researchers' ability to predict how important animals like sea urchins will fare in a changing world. The adhesion principles Garner and his team are exploring could also come in handy for human-designed adhesive materials -- work that aligns with the Syracuse University BioInspired Institute's mission of addressing global challenges through innovative research.
"If we can learn the fundamental principles and molecular mechanisms that allow sea urchins to secrete a permanent adhesive and use it for temporary attachment, we could harness that power into the design challenges or our adhesives today," says Garner. "Imagine being able to have an adhesive that is otherwise permanent, but then you add another component, and it breaks it down and you can go stick it again somewhere else. It's a perfect example of how biology can be used to enhance the everyday products around us."
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How male mosquitoes compensate for having only one X chromosome
The research group of Dr. Claudia Keller Valsecchi (Institute of Molecular Biology, Mainz, Germany) and their collaborators have discovered the master regulator responsible for balancing the expression of X chromosome genes between males and females in the malaria mosquito.
This discovery helps scientists to better understand the evolution of the epigenetic mechanisms responsible for equalizing gene expression between the sexes. The findings may contribute to the development of new ways to prevent the spread of malaria. The research was published in the journal Nature.
Most people would agree that mosquitoes are among the most annoying species on the planet. They keep us up all night with their whining, whirring wings, all while seeking a way to bite us and suck our blood. Yet mosquitoes are more than just a nuisance—they can also carry a whole host of serious, sometimes deadly diseases.
One of the most dangerous diseases that mosquitoes can carry is malaria, a disease that affects millions of people and causes hundreds of thousands of deaths every year, primarily in African countries. Malaria is caused by Plasmodium parasites, which are spread through mosquito bites—specifically those of marsh mosquitoes (Anopheles).
Importantly, only female mosquitoes bite, as they need the nutrients from blood to produce eggs. Scientists are therefore interested in understanding the mechanisms responsible for the molecular differences between male and female mosquitoes, as it could help us develop new ways to combat malaria.
Just like humans, the sex of a mosquito is determined by the sex chromosomes: females have two X chromosomes (XX), while males have an X and a Y chromosome (XY). This can be problematic, as males have only half the number of X chromosome genes as females, and hence would have only half the amount of proteins from the X chromosome. To compensate for this, there must be a way to increase the expression of X chromosome genes in males. However, no one knew what this mechanism could be in mosquitoes.
Agata Kalita from Claudia's group, who is the first author of the study, spearheaded the research. The team collaborated with the groups of Dr. M. Felicia Basilicata (Mainz University Medical Center), Dr. Eric Marois (University of Strasbourg, France) and Prof. Franjo Weissing (University of Groningen, The Netherlands).
Together, the researchers discovered that the protein SOA (sex chromosome activation) is the key regulator that balances X chromosome gene expression in male mosquitoes. They found that SOA works by binding to X chromosome genes and increasing their expression, but only in males. Female mosquitoes, on the other hand, only produce a small amount of very short, non-functional SOA.
Agata comments, "Balancing gene expression on sex chromosomes is essential for development in some species. However, others do not have such a mechanism at all. Unexpectedly, we discovered that in mosquitoes, balancing X chromosome expression by SOA is not necessary for development, but it does give males a head start.
"This is an important clue as to how the mechanisms that balance gene expression on sex chromosomes may have evolved in the first place."
M. Felicia Basilicata, a joint senior author, adds, "Understanding the molecular principles acting on sex chromosomes will help us to understand differences between males and females in various human pathologies."
The groups' findings mark a major step forward in our understanding of how gene expression is balanced on the sex chromosomes. The researchers speculate that genetically manipulating genes that exclusively affect one sex could be a useful strategy for reducing the number of blood-sucking female mosquitoes, which would be a huge boon in the fight against malaria.
More information: Agata Izabela Kalita et al, The sex-specific factor SOA controls dosage compensation in Anopheles mosquitos, Nature (2023). DOI: 10.1038/s41586-023-06641-0
Journal information: Nature
Provided by Johannes Gutenberg University Mainz | Biology |
Timing matters Predicted equivalent dose distributions (EQDRT) for time intervals of 0 hr and 4 h between radiotherapy and hyperthermia in an example thermoradiotherapy case. (Courtesy: CC BY 4.0/H P Kok et al Int. J. Radiat. Oncol. Biol. Phys. 10.1016/j.ijrobp.2022.10.023)
Thermoradiotherapy is a cancer treatment in which hyperthermia – heating the tumour to above body temperature – is used to enhance the efficacy of radiotherapy. The amount of this enhancement is expressed as EQDRT, the equivalent radiation dose needed to achieve the same therapeutic effect without heating.
Clinical trials have shown that this approach can substantially improve treatment outcomes in several tumour types, without increasing normal tissue toxicity. Previous studies also demonstrated that both the achieved temperature and the time interval between radiotherapy and hyperthermia impact the clinical outcome.
To understand this process in more detail and help optimize treatments, researchers at Amsterdam UMC have used biological modelling to investigate the impact of maximum temperature and time interval on EQDRT. Describing their findings in the International Journal of Radiation Oncology Biology Physics, they report that both high temperatures and short time intervals are essential to maximize therapeutic enhancement.
Biological model To perform thermoradiotherapy, clinicians use a radiofrequency or microwave device to apply heat to the tumour once or twice a week, either before or after a radiotherapy session. Tumour temperature is kept below 45°C to prevent heating normal tissue, but sometimes unwanted (and painful) hot spots can occur, which limit the maximum tolerable power level that can be used during a hyperthermia treatment.
First author Petra Kok and colleagues developed software to model the biological effects of radiotherapy plus hyperthermia in terms of equivalent dose distributions. The model, which accounts for DNA-repair inhibition by hyperthermia, as well as direct heat-induced cytotoxicity, enables evaluation of the quality of combined treatment plans using standard dose–volume histograms.
To obtain basic insight into the impact of hyperthermia parameters, the team first calculated the enhancement of a standard 23 × 2 Gy dose distribution by homogeneous temperatures of between 37 and 43 °C, for time intervals between 0 and 4 h.
The model showed that EQDRT increased significantly with both increasing temperature and decreasing time interval. For a 1 h time interval, for example, it predicted an EQDRT increase of 2–15 Gy for temperatures from 39 to 43°C. These findings emphasize the importance of achieving the highest tolerable tumour temperature to optimize clinical outcome.
The impact of time interval was most pronounced at higher temperatures (above 41°C). At a typical hyperthermic temperature of 41.5°C, an EQDRT increase of about 10 Gy was achieved with a 0 h time interval. This decreased to around 4 Gy enhancement with a 4 h interval, indicating that as the time interval increases, a higher temperature is needed to realize the same effect.
Clinical cases
Next, the researchers evaluated realistic treatment scenarios based on inhomogeneous temperature distributions and clinical radiotherapy plans. They calculated the EQDRT for 10 patients with locally advanced cervical cancer. All patients had received 23 × 2 Gy volumetric-modulated arc therapy (VMAT), with hyperthermia applied weekly during the treatment course.
As seen with the uniform temperatures, EQDRT was largest for the smallest time interval. When hyperthermia was applied immediately before or after radiotherapy (0 h time interval), the mean EQDRT to 95% of the volume (D95%) was 51.7 Gy – a gain of 6.3 Gy over radiation alone. Increasing the time interval to 4 h reduced this gain to 2.2 Gy.
The model predicted that most of the dose enhancement is lost within the first hour. For clinical use, therefore, the time between radiotherapy and hyperthermia delivery should be as short as possible – ideally by patients receiving both treatments in the same hospital. The team note that while the order of the two treatments is not clinically relevant, as it takes time to heat up the tumour, applying hyperthermia first could enable significantly shorter time intervals, even close to 0 h.
Finally, the researchers modelled the impact of achieving slightly lower tumour temperatures than planned, due to the occurrence of treatment-limiting hot spots. The effect on EQDRT was most pronounced for a short time interval between radiotherapy and hyperthermia. For a 1°C lower temperature and a 0 h time interval, for example, the mean predicted EQDRT(D95%) decreased by 1.8 Gy (from 51.7 to 49.9 Gy); for a 4 h interval, the decrease was about 0.7 Gy. Read more Radiotherapy is more effective in warmed-up tumours In cases where no hot spots appear, it may be possible to increase the output power and reach a higher temperature than planned. Once again, the benefit of achieving a higher temperature was greatest for shorter time intervals, with the exact gain dependent upon the actual temperatures reached.
“Biological modelling provides relevant insight into the relationship between treatment parameters and expected EQDRT,” Kok and colleagues conclude. “Both high temperatures and short time intervals are essential to maximize EQDRT. | Biology |
It may be possible to predict whether a person's lung cancer could return after surgery by zooming in on the seemingly healthy tissue near their tumors, a lab study suggests.
Lung cancer is the leading cause of cancer deaths in the U.S. One of the most common types is lung adenocarcinoma, which arises in the cells that line the air sacs of the lungs. The usual treatment for the early stages of this disease, before the cancer has spread, is surgery to remove the tumor. However, even when caught at this early stage, cancers like adenocarcinoma return 30% of the time, and so far there has been no accurate way to predict whether this will occur.
In the new study, published Wednesday (Nov. 8) in the journal Nature Communications, scientists analyzed tissue samples from 143 men and women with early-stage lung adenocarcinoma. They found that the activity of genes, specifically those involved in inflammation, in the healthy lung tissue adjacent to tumor cells was able to more accurately indicate whether a patient's cancer returned within five years of surgery than the corresponding gene expression in tumor cells.
The new research was conducted only in the lab, in isolated tissue samples. However, the researchers hope the findings could eventually be used to flag patients at high risk of relapse and ensure that they receive additional care.
"If you determine that the patient is at high risk, then you can do two things: monitor them more frequently, or even — but this of course requires a clinical trial — think of potential therapies in addition to surgery," co-senior study author Aristotelis Tsirigos, a cancer biologist at New York University Langone Health, told Live Science. For instance, some immunotherapies, which help the body's cells detect and attack tumors, are already being trialed in early stage lung cancer, he said.
In the laboratory study, the scientists focused on the transcriptome, meaning all the RNA molecules in the tissues they sampled. RNA shuttles instructions for how to build proteins from a cell's DNA to its protein-making factories. In addition, the team gathered information on whether a patient's disease returned after surgery to retrospectively predict their risk of recurrence using artificial intelligence.
Overall, the authors found that analyzing RNA from healthy lung tissue accurately predicted cancer recurrence 83% of the time, compared with 63% for tumor cell RNA.
The authors also discovered that the RNA for inflammatory proteins, such as tumor necrosis factor-α (TNF-α) and interferon-gamma (IFN‐γ), were the strongest predictors of recurrence. In a separate part of the study, the authors found that the same group of inflammatory proteins were also associated with poorer outcomes for patients with other types of cancer, such as breast and kidney cancer. They deduced this using data from The Cancer Genome Atlas, a collection of cancer tissue samples collected from more than 11,000 patients in the U.S. over 12 years.
Before this research can be tested in clinical trials, further studies are needed to understand exactly what activates these inflammatory genes in healthy tissue and how this can forecast recurrence, Tsirigos said.
Tsirigos theorized that, because the inflammatory RNA signatures were seen in both immune cells and non-immune cells, perhaps immune cells were actually detecting tumor cells hidden in the seemingly healthy tissue, or maybe the inflammation they triggered destabilized otherwise healthy cells and pushed them to turn cancerous. For now, though, these are just ideas.
In the meantime, even if a specific therapy for high-risk patients is not discovered down the line, it is possible that these inflammatory signatures could still be a valuable diagnostic tool for doctors, Tsirigos said.
This article is for informational purposes only and is not meant to offer medical advice.
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Emily is a health news writer based in London, United Kingdom. She holds a bachelor's degree in biology from Durham University and a master's degree in clinical and therapeutic neuroscience from Oxford University. She has worked in science communication, medical writing and as a local news reporter while undertaking journalism training. In 2018, she was named one of MHP Communications' 30 journalists to watch under 30. ([email protected]) | Biology |
Scientists warn that the Amazon is approaching a tipping point beyond which it would begin to transition from a lush tropical forest into a dry, degraded savanna. This point may be reached when 25% of the forest is lost.In a newly released report, the Monitoring of the Andean Amazon Project (MAAP) estimates that 13.2% of the original Amazon forest biome has been lost due to deforestation and other causes.However, when the map is divided into thirds, it shows that 31% of the eastern Amazon has been lost. Moisture cycles through the forest from east to west, creating up to half of all rainfall across the Amazon. The 31% figure is critical, the report says, “because the tipping point will likely be triggered in the east.”Experts say the upcoming elections in Brazil could have dramatic consequences for the Amazon, and to avert the tipping point we must lower emissions, undertake ambitious reforestation projects, and build an economy based on the standing forest. Granting and honoring Indigenous land tenure and protected areas are also key strategies. Scientists warn that the Amazon is hurtling toward a tipping point, beyond which it would begin to transition from lush tropical forest into a dry, degraded savanna, unable to support the immense diversity of life that call the world’s largest rainforest home.
This change could be triggered when 25% of the forest has been lost under current climate pressures, scientists estimate. So how close are we to the tipping point? To answer that question, we need to know how much of the original Amazon forest biome has been lost.
“Surprisingly, we did not find any actual definitive studies that answered this question directly,” Matt Finer, senior research specialist and director of the Monitoring of the Andean Amazon Project (MAAP), a U.S.-based nonprofit, told Mongabay. So, about three years ago, MAAP set out to do exactly that.
In a newly released report, MAAP estimates that 13.2% of the original Amazon forest biome has been lost due to deforestation and other causes. This equates to more than 85 million hectares (211 million acres), an area about one-tenth the size of the United States or China.
Map showing total forest loss in the original Amazon forest biome. An estimate 13.2% has been lost due to deforestation and other causes. Data from Amazon Conservation Association and MAAP.
The original Amazon biome forest prior to European colonization: more than 647 million hectares (1.6 billion acres). Data from Amazon Conservation Association and MAAP.
To arrive at this number, MAAP first had to create a map of the original Amazon biome, prior to European colonization, and then overlay the total historical forest loss. The researchers combined data from the University of Maryland, Brazil’s national space research institute (INPE), ArcGis satellite images, Planet mosaics, Google Earth Engine Landsat images, and official government data for several countries. They made modifications such as converting deforested areas and historic dam reservoirs to original forest to reconstruct the biome.
The MAAP highlights another critical number. When divided into thirds, the map shows that 31% of the eastern Amazon is gone. “This finding is critical,” the report says, “because the tipping point will likely be triggered in the east.” Tree loss in the east is significant because moisture cycles through the forest from east to west, creating up to 50% of all rainfall across the Amazon.
“Water for the Amazon is coming from the [Atlantic] ocean,” Finer said. “You see the map and all of a sudden realize, this is a whole different ballgame.”
Total Amazon forest loss. Vertical lines indicate the Amazon split into thirds; 31% of the eastern Amazon has been lost to deforestation and other causes. Data from Amazon Conservation Association and MAAP.
The Amazon Rainforest gets up to half of its rain from moisture recycling. The sun warms the surface waters of the Atlantic Ocean and causes vapor to rise and form clouds. These clouds carry rain to the eastern Amazon. The forest absorbs the rain and then releases water vapor back into the atmosphere through transpiration. This water vapor from eastern forests is carried by winds to the west, and forms the Amazon’s “flying rivers,” which rain down in the west. Thus, deforestation in the east may have a more detrimental effect on the whole system.
“Deforestation is not created equal when you’re talking about the tipping point,” Finer said. “The real number to pay attention to is this 31%.”
Another recent study found that for every three trees that die due to drought in the Amazon Rainforest, a fourth tree, even if it’s not directly affected by drought, will also die. With fewer trees in the east to recycle moisture due to drought and deforestation, the rest of the Amazon becomes drier. “The lack of moisture recycling in some parts of the forest can be propagated downwind … resulting in approximately one-third of all tipping events,” the paper says.
This map shows the atmospheric moisture recycling network, overlayed atop the MAAP deforestation map. Arrows represent the direction of moisture flow from the Atlantic Ocean across the Amazon. Moisture data from Wunderling et al. (2022).
The drought-deforestation feedback loop in the Amazon. Image from Staal et al. (2020).
When it was first conceived, the tipping point concept was thought of as an abrupt ecosystem change, “but it is now believed that the shift could happen gradually,” over the course of 30 to 50 years, the MAAP report says.
Rather than thinking of the Amazon Rainforest as “one big tipping element that will vanish from Earth past a certain threshold,” it’s helpful to note that some regions are much more vulnerable to tipping than other regions, Nico Wunderling, a researcher at the Potsdam Institute for Climate Impact Research, who was not involved in the MAAP report, told Mongabay.
The southern region of the Amazon, Wunderling and colleagues found, is most vulnerable. Here, deforestation is at its most extreme along the notorious “arc of deforestation” being carved into the rainforest by cattle ranching and agriculture.
“I don’t think there’s a point beyond which the whole Amazon collapses,” Daniel Nepstad, president of the Earth Innovation Institute, told Mongabay in a 2019 interview. “It is all a question of how frequent and intense those really severe droughts are.”
The first signs of more permanent drying and more severe droughts in the rainforest are already showing, scientists warn. Plant species adapted to wet conditions are starting to die, and satellite images show a decrease in water vapor over parts of the rainforest that are far from the arc of deforestation.
“Not only is the dry season lengthier, but also it’s drier, with less rainfall, and 2-3° [Celsius, or 3.6-5.4° Fahrenheit] warmer,” Carlos Nobre, one of Brazil’s top climate scientists and a researcher at the University of São Paulo who reviewed the MAAP report, told Mongabay in a phone call. Droughts, such as those experienced in the Amazon in 2005 and 2010, he said, “could become the norm.”
“The risk of the tipping point is very real,” Nobre said.
Greenpeace Brazil flew over the southern Amazonas and northern Rondônia states in Brazil to monitor deforestation and forest fires in the Amazon in July 2022. Shown here are fires in Apuí, Amazonas state. © Christian Braga / Greenpeace
Understory forest fires may start on farms or in pastures but can escape into standing forests when conditions are dry. Fire-damaged trees eventually die, providing fuel and making the forest more vulnerable to future fires. Image by Sérgio Vale/Amazônia Real.
Deforestation and fires in the Amazon have soared under the administration of Brazil’s current president, Jair Bolsonaro, who has adopted policies that undermine Brazil’s various environmental protection and monitoring agencies. Under Bolsonaro, the Brazilian Amazon has lost an area of forest larger than Belgium and recorded its highest deforestation rate in 15 years.
In the Amazon, fires aren’t naturally occurring, but rather are set after deforestation to clear the land for cattle ranching and soy farming. In 2021, more than 44,000 hectares (109,000 acres) burned in Brazil alone. A 2021 study found that the Brazilian Amazon is emitting more carbon than it captures, mostly due to fires.
“If you’re thinking a tipping point for the Amazon [is when] it becomes a carbon source, this [southern] region is at a tipping point,” Luciana Gatti, a researcher at INPE, the national space research institute, and lead author of the 2021 study, told Mongabay. “My question is, if we stop now with fires and deforestation and start the very important repair process for forests, could we reverse the picture?”
“We really have to ramp down [forest] clearing, start fighting fires and ramp up recovery,” Nepstad told Mongabay in 2019. “We have everything we need to know to act now, urgently, to prevent a large-scale fire and drought driven dieback.”
Stepping back from the precipice of tipping will require nations to change the monoculture agribusiness models of cattle and soy, undertake ambitious reforestation projects, and raise the quality of life for people who live in Amazonian cities by building an economy based on the standing forest, Nobre and the late Thomas Lovejoy, a prominent and influential conservation biologist who worked with MAAP in the early stages of this report, said in a 2019 editorial published in Science.
Nobre noted that a drier Amazon is caused both by deforestation and climate change, so reducing emissions in order to meet the Paris Agreement goal of keeping warming below 1.5°C is also crucial to averting disaster in the Amazon and beyond.
Former president and poll front-runner Luiz Inácio Lula da Silva rallies his supporters in Belo Horizonte, the Minas Gerais state capital, in August. Experts say the upcoming October election could have important consequences for the fate of the Amazon. Image courtesy of Ricardo Stuckert.
Shown here are members of La Guardia Patrol started by Alexandra Narvaez (third from left) who led an Indigenous movement to protect her ancestral territory from gold mining. Indigenous territories, such as that of the Cofán of Sinangoe in northern Ecuador, are important strongholds for biodiversity. Image courtesy of Goldman Environmental Prize.
“There is also the more positive side of this story,” Adriane Esquivel Muelbert an expert in Amazon forest change at the University of Birmingham, told Mongabay in an email. “Some large areas of the Amazon are still very wet and not suffering from the increase in aridity. [I]f we control deforestation now we can avoid the Amazon tipping point.”
Protected areas and Indigenous territories are important strongholds for safeguarding the remaining Amazon Rainforest and meeting climate goals. Most of the deforestation and fires in the Amazon over the past five years have taken place outside of these key land-use designations, highlighting the importance of granting and honoring Indigenous land tenure and protected status.
Upcoming elections in Brazil could also have dramatic consequences for the fate of the Amazon, experts say. “The re-election of a [Bolsonaro] government that incentivizes deforestation can accelerate the Amazon tipping point drastically,” Muelbert said. “The election of former president Lula, currently the leading figure at the polls, is promising to bring deforestation rates down again in the Brazilian Amazon…hopefully moving the trajectory of Amazonian forests away from the tipping point.” Lula’s policies once helped to reduce annual deforestation by 82%, to the lowest rate since satellite monitoring began.
Ultimately, no one can predict how rapidly the forest will change past the tipping point, Lovejoy told Mongabay in 2019.“Will it be a long slide, or will the kinds of changes that are already being seen start happening with greater magnitude? … Let’s not find out by tipping it.”
Citations:
Finer, M., & Mamani, N. (2022). Amazon tipping point — Where are we? (164) Retrieved from MAAP website: https://www.maaproject.org/2022/amazon-tipping-point/
Lovejoy, T. E., & Nobre, C. (2018). Amazon tipping point. Science Advances, 4(2), eaat2340. doi:10.1126/sciadv.aat2340
Wunderling, N., Staal, A., Sakschewski, B., Hirota, M., Tuinenburg, O. A., Donges, J. F., … Winkelmann, R. (2022). Recurrent droughts increase risk of cascading tipping events by outpacing adaptive capacities in the Amazon rainforest. Proceedings of the National Academy of Sciences, 119(32), e2120777119. doi:10.1073/pnas.2120777119
Gatti, L. V., Basso, L. S., Miller, J. B., Gloor, M., Gatti Domingues, L., Cassol, H. L., … Neves, R. A. (2021). Amazonia as a carbon source linked to deforestation and climate change. Nature, 595(7867), 388-393. doi:10.1038/s41586-021-03629-6
Lovejoy, T. E., & Nobre, C. (2019). Amazon tipping point: Last chance for action. Science Advances, 5(12), eaba2949. doi:10.1126/sciadv.aba2949
Esquivel-Muelbert, A., Baker, T. R., Dexter, K. G., Lewis, S. L., Brienen, R. J., Feldpausch, T. R., … Phillips, O. L. (2019). Compositional response of Amazon forests to climate change. Global Change Biology, 25(1), 39-56. doi:10.1111/gcb.14413
Barkhordarian, A., Saatchi, S. S., Behrangi, A., Loikith, P. C., & Mechoso, C. R. (2019). A recent systematic increase in vapor pressure deficit over tropical South America. Scientific Reports, 9(1), 15331. doi:10.1038/s41598-019-51857-8
Vargas Zeppetello, L. R., Raftery, A. E., & Battisti, D. S. (2022). Probabilistic projections of increased heat stress driven by climate change. Communications Earth & Environment, 3(1), 183. doi:10.1038/s43247-022-00524-4
Song, X. P., Hansen, M. C., Potapov, P., Adusei, B., Pickering, J., Adami, M., … Tyukavina, A. (2021). Massive soybean expansion in South America since 2000 and implications for conservation. Nature Sustainability. doi:10.1038/s41893-021-00729-z
Staal, A., Flores, B. M., Aguiar, A. P. D., Bosmans, J. H., Fetzer, I., & Tuinenburg, O. A. (2020). Feedback between drought and deforestation in the Amazon. Environmental Research Letters, 15(4), 044024. doi:10.1088/1748-9326/ab738e
Banner image: Total Amazon forest loss. Vertical lines indicate the Amazon split into thirds; 31% of the eastern Amazon has been lost to deforestation and other causes. Data from Amazon Conservation Association and MAAP.
Liz Kimbrough is a staff writer for Mongabay. Find her on Twitter: @lizkimbrough_
FEEDBACK: Use this form to send a message to the author of this post. If you want to post a public comment, you can do that at the bottom of the page. Article published by Amazon Biodiversity, Amazon Conservation, Amazon Destruction, Amazon Drought, Amazon Rainforest, Biodiversity, Climate Change, Climate Change And Biodiversity, Climate Change And Extreme Weather, Climate Change And Forests, Deforestation, Drought, Environment, Environmental Law, Environmental Policy, Environmental Politics, Featured, Forests, Governance, Government, Impact Of Climate Change, Indigenous Communities, Indigenous Peoples, Indigenous Rights, Politics, Rainforest Conservation, Rainforests, Saving The Amazon, Threats To Rainforests, Threats To The Amazon, Trees, Tropical Forests, Weather Print | Biology |
How cells are influenced by their environment as tissues grow
How does an embryo develop? How do children grow, wounds heal or cancer spread? All of this has to do with the growth of body tissue. One of the major research interests of ETH Professor Viola Vogel and her senior assistant Mario C. Benn is to understand this growth in detail. In their quest, they have departed from well-trodden research paths.
For a long time, biology was about studying cells and the biochemistry of the metabolic processes within them, often regardless of their natural environment. Vogel and Benn, by contrast, are focusing on the extracellular matrix (ECM), a fibrous structure that surrounds body cells. This matrix is produced by the cells themselves and is a major component of all tissue.
There are many different interactions between body cells and this fibrous matrix. In recent years, research has increasingly shown that not all of these interactions are exclusively biochemical. In fact, some are mechanical or physical. For example, cells are capable of sensing mechanical stimuli from this extracellular matrix.
Together with their team of researchers, Vogel and Benn have now been able to replicate tissue growth in vitro and study this process in detail. "Our results underline the importance of the interactions between cells and the extracellular matrix," Benn says. In time, he hopes to make medical use of these findings—to prevent wound-healing disorders, for example, or in the therapy of cancer and connective-tissue diseases.
Cell transformation
Their study, now published in Science Advances, focused on two cell types: fibroblasts and myofibroblasts. Each of them is important for human tissue functionality, and each one can change into the other. Fibroblasts are found in the connective tissue of our organs, where they ensure that the extracellular matrix is continuously renewed and remains healthy. If an injury occurs or tissue growth is required, the fibroblasts transform into myofibroblasts, which play a key role in healing wounds and the growth of new tissue. Myofibroblasts not only produce large amounts of ECM but are also strong enough, for example, to pull together tissue in wounds.
"When it comes to wound healing, myofibroblasts are our friends," Benn says. Once their work is done, however, it is important that these myofibroblasts change back into the less active fibroblasts. If not, this can lead to fibrosis—the excessive formation of scar tissue. Myofibroblasts are also found in cancer tissue. For many cancers, high levels of these cells is associated with a poor prognosis.
Three-dimensional matrix
Some things are known about the biochemical processes that take place when myofibroblasts revert to fibroblasts. Yet little research has been done to explain how the ECM influences this cellular transformation. "With conventional cell-culture methods, the cells grow flat across the culture dish. This leads to the formation of an unnaturally planar ECM," Vogel explains. "And anyway, research up to now has generally ignored the ECM. But studying cells without the extracellular matrix is a bit like studying the behavior of spiders without their web."
The method used by Vogel and Benn is quite different. It was originally developed at the Max Planck Institute of Colloids and Interfaces in Potsdam and has now been refined by the ETH scientists. They use a silicone scaffold, coated with specific proteins, that has microscopic triangular-shaped clefts and sits in a tissue culture medium. Over a two-week period, new tissue forms in these clefts, together with a more natural ECM. Growth begins at the apex, progressively filling the cleft as the tissue grows.
The researchers observed how myofibroblasts are always located precisely at the growth front—i.e., in the area of the tissue that is being newly formed. They were also able to show how myofibroblasts in this area form new ECM—initially in a provisional and then in a more stable form—before converting back into fibroblasts. "The processes are similar to those that take place in human subcutaneous tissue during the late phase of wound healing," Benn says.
The researchers were also able to show that rapidly changing ECM is one of the triggers for the reversion of myofibroblasts to fibroblasts. Moreover, this reversion is promoted when a certain type of ECM fiber—fibronectin—changes from a stretched to a relaxed state. It seems likely that similar interactive processes occur during wound healing.
The researchers then purposely interfered with the cell transition using various agents that change the composition or structure of the extracellular matrix. In this way, they were able to replicate what occurs with pathologies such as fibrosis or cancer—namely, that instead of reverting to fibroblasts as in healthy tissue, the myofibroblasts are stabilized by the extracellular matrix.
Future mechano-medicine
The researchers hope that such miniature tissue cultures will help them decipher further details of the interaction between human cells and their extracellular matrix. This will not only avoid animal testing, which otherwise is often necessary in biomedical research; it is also a method that in future could be used to test candidate substances during drug development. "These applications and research questions are low-hanging fruit," Benn explains. "If we can understand how myofibroblasts and fibroblasts change into one another, and control that process, then we can also make major progress with conditions such as wound-healing disorders, fibrosis and cancer."
Benn and Vogel also refer to a future field called mechano-medicine. This term describes the medical application of findings from the field of mechanobiology: the study of how cells can sense and process mechanical signals. In other words, mechano-medicine aims to apply the insights gained from mechanobiology to medical practice.
In time, the researchers hope to use mechano-medicine in the development of new diagnostic methods for the early detection of fibrotic tissue. "With many conditions, including pulmonary fibrosis, successful treatment depends on early detection," Benn says.
Current screening methods are unable to detect myofibroblasts in lung tissue with any great accuracy. Benn now hopes that further study of the extracellular matrix will reveal biomarkers that enable earlier and easier detection of fibrosis and similar connective-tissue diseases.
More information: Mario C. Benn et al, How the mechanobiology orchestrates the iterative and reciprocal ECM-cell cross-talk that drives microtissue growth, Science Advances (2023). DOI: 10.1126/sciadv.add9275
Journal information: Science Advances
Provided by ETH Zurich | Biology |
Some organisms, such as tardigrades, rotifers, and nematodes, can survive harsh conditions by entering a dormant state known as "cryptobiosis." In 2018, researchers from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia found two roundworms (nematode) species in the Siberian Permafrost. Radiocarbon dating indicated that the nematode individuals have remained in cryptobiosis since the late Pleistocene, about 46,000 years ago. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne, all located in Germany, used genome sequencing, assembly, and phylogenetic analysis and found that the permafrost nematode belongs to a previously undescribed species, Panagrolaimus kolymaensis. They showed that the biochemical mechanisms employed by Panagrolaimus kolymaensis to survive desiccation and freezing under laboratory conditions are similar to those of a life-cycle stage in the important biological model Caenorhabditis elegans.
When Anastasia Shatilovich at the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia revived two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, she and her colleagues were beyond excited. After thawing the worms in the lab, a radiocarbon analysis of plant material from the burrow revealed that these frozen deposits, 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, the research group of Teymuras Kurzchalia at the MPI-CBG (Teymuras Kurzchalia is now retired) was already addressing the question of how larval stages of the nematode Caenorhabditis elegans survive extreme conditions. When the team heard about the permafrost nematodes, they immediately reached out for a collaboration with Anastasia Shatilovich.
Vamshidhar Gade, a doctoral student at that time in the research group of Teymuras Kurzchalia, started to work with the permafrost nematodes. "What molecular and metabolic pathways these cryptobiotic organisms use and how long they would be able to suspend life are not fully understood," he says. Vamshidhar is now working at the ETH in Zurich, Switzerland.
The researchers in Dresden conducted a high-quality genome assembly of one of the permafrost nematodes in collaboration with Eugene Myers, Director Emeritus and research group leader at the MPI-CBG, the DRESDEN-concept Genome Center, and the research group of Michael Hiller, research group leader at that time at the MPI-CBG and now Professor of Comparative Genomics at the LOEWE-TBG and the Senckenberg Society for Nature Research. Despite having DNA barcoding sequences and microscopic pictures, it was difficult to determine whether the permafrost worm was a new species or not. Philipp Schiffer, research group leader at the Institute of Zoology, co-lead of the incipient Biodiversity Genomics Center Cologne (BioC2) at the University of Cologne, and expert in biodiversity genomics research, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Using phylogenomic analysis, he and his team were able to define the roundworm as a novel species, and the team decided to call it "Panagrolaimus kolymaensis." In recognition of the Kolyma River region from which it originated, the nematode was given the Latin name Kolymaensis.
By comparing the genome of Panagrolaimus kolymaensis with that of the model nematode Caenorhabditis elegans, the researchers in Cologne identified genes that both species have in common and that are involved in cryptobiosis. To their surprise, most of the genes necessary for entering cryptobiosis in Caenorhabditis elegans so-called Dauer larvae were also present in Panagrolaimus kolymaensis. The research team next evaluated Panagrolaimus kolymaensis's ability to survive and discovered that mild dehydration exposure before freezing helped the worms prepare for cryptobiosis and increased survival at -80 degrees Celsius. At a biochemical level, both species produced a sugar called trehalose when mildly dehydrated in the lab, possibly enabling them to endure freezing and intense dehydration. Caenorhabditis elegans larvae also benefited from this treatment, surviving for 480 days at -80 degrees Celsius without suffering any declines in viability or reproduction following thawing.
According to Vamshidhar Gade and Temo Kurzhchalia, "Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods."
"Our findings are essential for understanding evolutionary processes because generation times can range from days to millennia and because the long-term survival of a species' individuals can result in the re-emergence of lineages that would otherwise have gone extinct," concludes Philipp Schiffer, one of the authors who oversaw the study. Eugene Myers adds: "P. kolymaensis's highly contiguous genome will make it possible to compare this feature to those of other Panagrolaimus species whose genomes are presently being sequenced by Schiffer's team and colleagues." Philipp Schiffer is convinced that "studying the adaptation of species to such extreme environments by analyzing their genomes will allow us to develop better conservation strategies in the face of global warming.." Teymuras Kurzchalia says: "This study extends the longest reported cryptobiosis in nematodes by tens of thousands of years."
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A lack of sleep and reduced physical activity during pregnancy are linked to risk of preterm birth, according to new research led by the Stanford School of Medicine.
In the study, which will publish online Sept. 28 in npj Digital Medicine, the researchers collected data from devices worn by more than 1,000 women throughout pregnancy. With a machine learning algorithm, the scientists sifted through participants' activity information to detect fine-grained changes in sleep and physical activity patterns.
"We showed that an artificial intelligence algorithm can build a 'clock' of physical activity and sleep during pregnancy, and can tell how far along a patient's pregnancy is," said senior study author Nima Aghaeepour, PhD, an associate professor of anesthesiology, perioperative and pain medicine and of pediatrics at Stanford Medicine. Normal pregnancy is characterized by progressive changes in sleep and physical activity as the pregnancy advances, he said. "But some patients don't follow that clock." When patients' sleep and activity levels don't change on a typical trajectory, the study showed, it',s a warning sign for premature birth, he added.
The study's lead author is Neal Ravindra, PhD, a former postdoctoral scholar at Stanford Medicine.
As the pregnancies progressed, sleep typically became more disrupted, and women became less physically active, the study showed. However, some women's sleep and activity patterns changed on an accelerated timeline relative to how far along they were in their pregnancies. These individuals were more likely to deliver early, the study found.
"The people who look 'very pregnant' to the AI algorithm -- but are not -- end up being at significantly increased risk of preterm birth," Aghaeepour said.
A struggle to prevent early deliveries
Premature birth, when a baby is born 3 or more weeks early, affects 10.5% of births in the United States; these rates are higher in some other parts of the world. Premature newborns can suffer many medical complications, including diseases of the eyes, lungs, brain and digestive system. Prematurity is the leading cause of death for children under age 5 around the world.
Research has identified a variety of risk factors for premature delivery, including greater levels of inflammation in the pregnant person, specific immune-system changes, African American race, higher levels of stress, history of having a preterm birth and certain types of bacteria in the mother's microbiome.
But doctors still can't reliably determine which pregnancies are at risk for premature delivery. Even when they know a mom is at risk -- because she's previously had a premature delivery, for example -- they still don't have great treatments to extend the pregnancy closer to the due date. Developing medications that could do this would be complex, in part because of ethical concerns regarding testing drugs that might harm the fetus.
If researchers can identify sleep and activity patterns that lower prematurity risk, they can design interventions to help expectant mothers adopt better sleep and exercise habits, a potentially low-risk way of reducing preterm births, Aghaeepour said.
Focusing on at-risk moms
The Stanford Medicine team collaborated with scientists at Washington University in St. Louis, who collected the sleep and physical activity data from 1,083 pregnant women treated there. More than half of the cohort (706 participants) were Black. In the United States, the rate of premature birth is about 50% higher in Black women than in white women.
"Our patient population experiences a lot of adversity, and our preterm birth rates are much higher than at Stanford," said study coauthor Sarah England, PhD, professor of obstetrics and gynecology at Washington University School of Medicine in St. Louis. The study participants included women experiencing a variety of stressors linked with higher rates of preterm birth, such as racism, low socioeconomic status and living in areas with higher crime rates, England said, adding that it is important for studies of preterm birth to include populations with the greatest need. "Typically, Black women and women of color have not been included in many large cohort studies," she said.
The participants wore actigraphy devices similar to smartwatches to collect once-a-minute measurements of physical activity and light exposure starting in the first trimester of pregnancy and continuing until their babies were born. The researchers also had data from participants' electronic medical records on gestational age, or how far along each pregnancy was; maternal medical conditions such as high blood pressure, diabetes, heart disease and depression; pregnancy complications such as preeclampsia and infections; and information about the birth, including duration of the pregnancy, the baby's birth weight and newborn medical complications.
With the movement and light exposure data, the research team developed a machine learning model of activity and sleep during pregnancy. The model shows that patterns of sleep and physical activity change over the course of pregnancy, which generally is associated with more sleep disruption and less physical activity as pregnancy progresses.
"Anecdotally, lots of women will say, 'Of course!'" said study coauthor Erik Herzog, PhD, professor of biology at Washington University in St. Louis, adding that, for example, women experience more sleep disruptions as the baby gets larger and more active. "But, surprisingly, the literature has not had a real consensus about what exactly happens to sleep in pregnancy," he said. Using imprecise methods to measure sleep habits, such as questionnaires, has not provided adequate answers.
The researchers were surprised at how strongly deviations from the normal pattern of sleep and physical activity could predict preterm birth. If the machine-learning model classified a woman as sleeping better and being more physically active than usual for her stage of pregnancy, this was linked with a 48% reduction in risk for preterm delivery. Conversely, if the model classified a woman as sleeping worse and being less physically active than usual for her stage of pregnancy, her risk for preterm delivery was 44% higher than for pregnant women with typical sleep and activity patterns.
Strong clues for preventing prematurity
"This is exciting preliminary data," Aghaeepour said. The results suggest that scientists should run studies to test whether tracking and modifying pregnant women's sleep or physical activity could their lower prematurity risk, he said, adding, "It's telling us where to go for future interventions."
The circadian clock regulates several other biological pathways implicated in premature birth, such as those regulating inflammation and the immune response, the scientists said. They plan to test whether improving sleep and physical activity in pregnancy could modify other key pathways, such as those controlling inflammation.
"Our feeling is that if we look at this overarching regulator, we may be able to control individual systems that lead to preterm birth," England said.
Although the findings are at an early stage, and more work is needed to understand their implications for preventing prematurity, there's little risk in advising pregnant women to maintain good sleep habits now, she added. For instance, women should try to maintain consistent bedtimes and wake-up times, get enough sleep, and get some natural light during the day to help regulate their body clock.
"I tell everyone who is pregnant, 'I hope you keep a regular sleep schedule,'" England said.
"If we can use sleep and physical activity to modulate biology in the right direction, it could be a great intervention for reducing the rate of preterm birth," Aghaeepour added.
The study was funded by the National Institutes of Health (grants R35GM138353, R01HD105256, P01HD106414, 1R01HL139844, 19PABHI34580007, R61NS114926, R01AG058417 and P30AG066515), the American Heart Association, the Burroughs Wellcome Fund, the March of Dimes, the Robertson Foundation, the Bill and Melinda Gates Foundation, and the Alfred E. Mann Family Foundation.
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Three nasal spritzes, now in advanced trials, could trigger stronger immunity than shots in the arm Credit: Dzmitry Kliapitski/Alamy Stock Photo The relentless evolution of the COVID-causing coronavirus has taken a bit of the shine off the vaccines developed during the first year of the pandemic. Versions of the virus that now dominate circulation—Omicron and its subvariants—are more transmissible and adept at evading the body’s immune defenses than its original form. The current shots to the arm can still prevent serious illness, but their ability to ward off infection completely has been diminished. And part of the reason may be the location of the jabs, which some scientists now want to change. To block infections entirely, scientists want to deliver inoculations to the site where the virus first makes contact: the nose. People could simply spray the vaccines up their nostrils at home, making the preparation much easier to administer. There are eight of these nasal vaccines in clinical development now and three in phase 3 clinical trials, where they are being tested in large groups of people. But making these vaccines has proven to be slow going because of the challenges of creating formulations for this unfamiliar route that are both safe and effective. What could be most important about nasal vaccines is their ability to awaken a powerful bodily defender known as mucosal immunity, something largely untapped by the standard shots. The mucosal system relies on specialized cells and antibodies within the mucus-rich lining of the nose and other parts of our airways, as well as the gut. These elements move fast and arrive first, stopping the virus, SARS-CoV-2, before it can create a deep infection. “We are dealing with a different threat than we were in 2020,” says Akiko Iwasaki, an immunologist at Yale University. “If we want to contain the spread of the virus, the only way to do that is through mucosal immunity.” Iwasaki is leading one of several research groups in the U.S. and elsewhere that are working on nasal vaccines. Some of the sprays encapsulate the coronavirus’ spike proteins—the prominent molecule that the virus uses to bind to human cells—into tiny droplets that can be puffed into the sinuses. Others add the gene for the spike to harmless versions of common viruses, such as adenoviruses, and use the defanged virus to deliver the gene into nasal tissue. Still others rely on synthetically bioengineered SARS-CoV-2 converted into a weakened form known as a live attenuated vaccine. The more familiar shots in the arm create a type of immune response known as systemic immunity, which produces what are called immunoglobulin G (IgG) antibodies. They circulate throughout the bloodstream and patrol for the virus. Nasal sprays assemble a separate set of antibodies known as immunoglobulin A (IgA). These populate the spongy mucosal tissues of the nose, mouth and throat, where the COVID-causing coronavirus first lands. Iwasaki likens mucosal vaccines to putting a guard at the front door, as opposed to waiting until the invader is already inside to attack. While conventional injectable vaccines are generally poor at inducing protective mucosal immunity, nasal vaccines have been shown to do a good job of triggering both mucosal and systemic responses. Last year researchers at the National Institutes of Health conducted a side-by-side comparison of intranasal and intramuscular delivery of the Oxford-AstraZeneca vaccine. They found that hamsters that had received the vaccine through the nose had higher levels of antibodies against SARS-CoV-2 in their blood than those who received it through the muscle. The University of Oxford is now testing intranasal vaccination in a phase 1 trial, which will assess the safety of the vaccine in a small number of people. Developing a nasal vaccine is tricky, however, because scientists know relatively little about the machinations of mucosal immunity. “While the human immune system is a black box, the mucosal immune system is probably the blackest of the black boxes,” says epidemiologist Wayne Koff, CEO and founder of the Human Vaccines Project, a public-private partnership aimed at accelerating vaccine development. What scientists do know is making them tread cautiously. Because of the nose’s proximity to the brain, substances squirted up the nasal passages could raise the risk of neurological complications. In the early 2000s, a nasal flu vaccine licensed and used in Switzerland was linked to Bell’s palsy, a temporary facial paralysis. “Since then, people have become a little bit nervous about a nasal vaccine,” Iwasaki says. And although a spray seems like an easier delivery method than a shot, in practice, that is not the case. With intramuscular injections, a needle delivers the vaccine ingredients directly into the muscle, where they quickly encounter resident immune cells. Sprays, in contrast, must make their way into the nasal cavity without being sneezed out. Then those ingredients have to breach a thick barrier gel of mucus and activate the immune cells locked within. Not all do. One company, Altimmune, stopped development of its COVID nasal vaccine AdCOVID after disappointing early trial results. Weakened or attenuated viruses can get through the barrier to infect cells, so some vaccine developers are turning to them. Two companies, Meissa Vaccines and Codagenix, have used synthetic biology to build an attenuated version of the novel coronavirus containing hundreds of genetic changes that drastically reduce its ability to replicate. In a recent news release, the Codagenix team reported promising results of their vaccine, CoviLiv, in a phase 1 trial. The spray induced a strong immune response against proteins shared by different variants of SARS-CoV-2, including the recent Omicron subvariant BA.2. That is because the vaccine trains the immune system to recognize all the viral proteins, not just the spike. Presenting all components of the virus makes the vaccine less vulnerable to the whims of evolution that might alter a few proteins beyond recognition. “The beauty of live attenuated vaccines is that they can provide broad long-term immunity in a very resistant context,” says J. Robert Coleman, a virologist and the company’s co-founder. CoviLiv is moving on to advanced testing in people as part of the World Health Organization–sponsored Solidarity Trial Vaccines, a giant randomized controlled trial of several new COVID vaccines. For each of the candidates that have made it into clinical trials, there are several more in preclinical development. In research with mice at Yale, Iwasaki has devised a nasal spray that works as a booster to the standard intramuscular shot. The strategy, which she calls “Prime and Spike,” starts with an injection of an mRNA or other COVID vaccine based on the spike protein, and this triggers an initial immune response. Then researchers spray a mix with similar spike proteins directly into the nose, converting that first reaction into mucosal immunity. In a preprint study not yet published in a peer-reviewed scientific journal, her team found that their one-two-punch protected mice from severe COVID while also significantly reducing the amount of SARS-CoV-2 in the nose and lungs. When the researchers added spike proteins from the coronavirus that created a global outbreak in 2003—SARS-CoV-1—to their spray, they found that it induced a broad spectrum of antibodies. The combination has the potential to defend against new coronavirus strains or variants “There is a big push for a universal coronavirus vaccine,“ Iwasaki says. “We can get there, and as a bonus we can provide mucosal immunity.” She has licensed the technology to Xanadu Bio, a company she co-founded, and is currently seeking funding to launch human trials. With no needles or syringes, nasal inoculations could reach a lot more people, and that could prove to be a big advantage. Koff, however, thinks the real deciding factor will be whether tests prove these vaccines stop infections and illness, and those results will be more important than ease of use. “At the end of the day, efficacy is going to trump everything,” he says.ABOUT THE AUTHOR(S)Marla Broadfoot is a freelance science writer who lives in Wendell, N.C. She has a Ph.D. in genetics and molecular biology. Credit: Nick Higgins | Biology |
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An unusual animal with canine teeth similar to those of a saber-toothed cat and the wide-set eyes of a cow lived in South America some 5 million years ago.
In order to successfully hunt prey and survive, the “marsupial sabertooth,” called Thylacosmilus atrox, adapted to view the world in a unique way, according to new research, because its canine teeth that jutted downward from its mouth were so large that their roots wrapped over the top of its skull.
“They weren’t just large; they were ever-growing, to such an extent that the roots of the canines continued over the tops of their skulls,” said lead study author Charlène Gaillard, a doctoral student at the Argentine Institute of Nivology, Glaciology and Environmental Sciences in Mendoza, Argentina, in a statement accompanying the release of new research on the Thylacosmiluss.
The study, describing findings based on analysis of the animal’s skull, published Tuesday in the journal Communications Biology.
Researchers think the Thylacosmilus was a hypercarnivore — an animal with a diet that was about 75% meat — similar to lions. But unlike most predators with forward-facing eyes and full 3D vision to help them pursue prey, the creature had eyes on the side of its head like a horse.
The position of the animal’s large canines meant there was no room for the animal to have eyes on the front of its face. Eyes don’t remain in the fossil record, but eye sockets in skulls can help researchers determine more about the visual physiology of extinct creatures.
Visual depth perception
Gaillard used 3D virtual reconstruction and CT scanning to analyze a Thylacosmilus skull and compare it with that of other mammals, especially carnivores.
She determined that Thylacosmilus’ eye sockets were more vertically oriented than other comparable animals to achieve depth perception.
“Thylacosmilus had a panoramic-like vision,” she said. “One way to imagine it would be when you take a picture of a panoramic view with your cell phone. … The resulting image is a wide-angled view of the landscape, but single elements of the landscape are harder to separate and focus on.”
About 70% of its visual field could overlap, enough to make it a successful predator, said study coauthor Analia M. Forasiepi, a researcher at the National Scientific and Technical Research Council, or CONICET, the Argentine science and research agency.
Analysis of Thylacosmilus’ skeleton, combined with the researchers’ understanding of its vision, showed that the animal wasn’t capable of high-speed pursuit of prey. The ancient marsupial relative resembled predatorial big cats and weighed about 220 pounds (100 kilograms). However, Thylacosmilus was more likely the animal would “lie in ambush, blend in with the scenery and wait for a likely prey item to come along,” said study coauthor Ross D.E. MacPhee, a senior curator of mammalogy at the American Museum of Natural History in New York City, in a statement.
With a prey animal in sight — and range, Thylacosmilus’ massive canines would have been able to strike a death blow by plunging into its target.
Skull adaptations
Apart from the unusual adaptation to accommodate for hulking teeth, a Thylacosmilus skull also featured a bone structure that closed off its eye sockets from the side to prevent deformation and excessive bulging while eating, since its eyeballs were so close to the chewing muscles.
Researchers believe the Thylacosmilus went extinct as environmental changes altered the landscape of South America 3 million years ago, causing prey to become scarce, MacPhee said. Thylacosmilus followed suit, and once it disappeared, saber-toothed cats from North America moved south to take their place as predators. (For comparison, these saber-toothed cats, such as Smilodon, that lived across North America went extinct just 11,000 years ago.)
Studying Thylacosmilus has created more questions than answers, such as why it was the only animal to have teeth of such a size that required skull adaptations.
“It might have made predation easier in some unknown way,” Gaillard said. “The canines of Thylacosmilus did not wear down, like the incisors of rodents. Instead, they just seem to have continued growing at the root, eventually extending almost to the rear of the skull.”
Researchers want to explore how the animal may have used other senses to help it hunt for prey.
“One thing is clear: Thylacosmilus was not a freak of nature … in its time and place it managed, apparently quite admirably, to survive as an ambush predator,” Forasiepi said. “We may view it as an anomaly because it doesn’t fit within our preconceived categories of what a proper mammalian carnivore should look like, but evolution makes its own rules.” | Biology |
Humans bite back by deactivating mosquito sperm
New UC Riverside research makes it likely that proteins responsible for activating mosquito sperm can be shut down, preventing them from swimming to or fertilizing eggs.
The study could help control populations of Culex, the common house mosquito that transmits brain-swelling encephalitis and West Nile Virus.
"During mating, mosquitoes couple tail to tail, and the males transfer sperm into the female reproductive tract. It can be stored there awhile, but it still has to get from point A to point B to complete fertilization," said Cathy Thaler, UCR cell biologist and the study's first author.
Key to completing that journey are the specialized proteins secreted during ejaculation that activate the sperm flagella, or 'tails,' that power their movement.
"Without these proteins, the sperm cannot penetrate the eggs. They'll remain immotile, and will eventually just degrade," said Richard Cardullo, UCR biology professor and corresponding author of the new study.
The study, detailed in the journal PLOS ONE, details a full portrait of all the proteins in the insect's sperm, allowing researchers to find the specific ones that maintain the quality of the sperm while they're inactive, and that also activate them to swim.
To get this detailed information the research team worked with a team of graduate and undergraduate students who isolated as many as 200 male mosquitoes from a larger population. They then extracted enough sperm from the tiny reproductive tracts for mass spectrometry equipment to detect and identify the proteins.
Previously, the team determined that sperm need calcium upon entering a reproductive tract to power forward motion. "Now we can look in the completed protein profile we've created, find the calcium channel proteins, and design experiments to target these channels," Cardullo said.
This kind of protein profiling offers a path toward controlling mosquitoes that is more environmentally friendly than other methods that can have unintended, toxic effects. "We've given up on spraying pesticides all over, because that kills everything, good insects and bad, and harms other animals," Thaler said.
"Our work sets the foundation for a form of biological control, which most would agree is preferable," Cardullo added.
The operative word is control, rather than eradicate. Even though immobilizing the sperm would be 100% effective for the treated mosquitoes, it is not possible or desirable to kill all mosquitoes. This technology would change the proportion of fertile to infertile males in a given mosquito population, rather than wiping them all out.
"Mosquitoes are the deadliest animals on Earth. But as much as people hate them, most ecologists would oppose a plan to completely eradicate them. They play an important role in the food chain for fish and other animals," Cardullo said.
The team is hoping that information about sperm motility regulators in Culex will also apply to other species of mosquitoes. As climate change intensifies, a lot of other mosquitoes, such as those that carry malaria, are moving into the Northern Hemisphere.
Additionally, learning more about Culex sperm motility may have implications for improving fertility in humans.
Cardullo has long studied mammalian sperm, in the hopes of developing a male contraceptive. Just as important as preventing unwanted pregnancies, however, is the effort to help couples conceive. Human fertility rates have been falling for years, in part due to environmental factors. A better understanding of sperm could help overcome some of these factors.
"Many cells have flagella, or tails, including human respiratory cells as well as cells in our guts," Cardullo said. "What we learn in one system, such as mosquitoes, can translate to others."
More information: Catherine D. Thaler et al, Using the Culex pipiens sperm proteome to identify elements essential for mosquito reproduction, PLOS ONE (2023). DOI: 10.1371/journal.pone.0280013
Journal information: PLoS ONE
Provided by University of California - Riverside | Biology |
No beast on Earth is tougher than the tiny tardigrade. It can survive being frozen at -272° Celsius, being exposed to the vacuum of outer space and even being blasted with 500 times the dose of X-rays that would kill a human. In other words, the creature can endure conditions that don’t even exist on Earth. This otherworldly resilience, combined with their endearing looks, has made tardigrades a favorite of animal lovers. But beyond that, researchers are looking to the microscopic animals, about the size of a dust mite, to learn how to prepare humans and crops to handle the rigors of space travel. Sign Up For the Latest from Science News Headlines and summaries of the latest Science News articles, delivered to your inbox The tardigrade’s indestructibility stems from its adaptations to its environment — which may seem surprising, since it lives in seemingly cushy places, like the cool, wet clumps of moss that dot a garden wall. In homage to such habitats, along with a pudgy appearance, some people call tardigrades water bears or, adorably, moss piglets. But it turns out that a tardigrade’s damp, mossy home can dry out many times each year. Drying is pretty catastrophic for most living things. It damages cells in some of the same ways that freezing, vacuum and radiation do. For one thing, drying leads to high levels of peroxides and other reactive oxygen species. These toxic molecules chisel a cell’s DNA into short fragments — just as radiation does. Drying also causes cell membranes to wrinkle and crack. And it can lead delicate proteins to unfold, rendering them as useless as crumpled paper airplanes. Tardigrades have evolved special strategies for dealing with these kinds of damage. As a tardigrade dries out, its cells create long, crisscrossing proteins (shown) that cushion and protect the cells’ membranes.M. Yagi-Utsumi et al/Scientific Reports 2021 As a tardigrade dries out, its cells gush out several strange proteins that are unlike anything found in other animals. In water, the proteins are floppy and shapeless. But as water disappears, the proteins self-assemble into long, crisscrossing fibers that fill the cell’s interior. Like Styrofoam packing peanuts, the fibers support the cell’s membranes and proteins, preventing them from breaking or unfolding. At least two species of tardigrade also produce another protein found in no other animal on Earth. This protein, dubbed Dsup, short for “damage suppressor,” binds to DNA and may physically shield it from reactive forms of oxygen. Emulating tardigrades could one day help humans colonize outer space. Food crops, yeast and insects could be engineered to produce tardigrade proteins, allowing these organisms to grow more efficiently on spacecraft where levels of radiation are elevated compared with on Earth. Scientists have already inserted the gene for the Dsup protein into human cells in the lab. Many of those modified cells survived levels of X-rays or peroxide chemicals that kill ordinary cells (SN: 11/9/19, p. 13). And when inserted into tobacco plants — an experimental model for food crops — the gene for Dsup seemed to protect the plants from exposure to a DNA-damaging chemical called ethyl methanesulfonate. Plants with the extra gene grew more quickly than those without it. Plants with Dsup also incurred less DNA damage when exposed to ultraviolet radiation. Microscopic tardigrades can withstand the freezing cold, desiccation and extreme levels of radiation thanks to unique molecular adaptations.VIDEOLOGIA/ISTOCK/GETTY IMAGES PLUS Tardigrades’ “packing peanut” proteins show early signs of being protective for humans. When modified to produce those proteins, human cells became resistant to camptothecin, a cell-killing chemotherapy agent, researchers reported in the March 18 ACS Synthetic Biology. The tardigrade proteins did this by inhibiting apoptosis, a cellular self-destruct program that is often triggered by exposure to harmful chemicals or radiation. So if humans ever succeed in reaching the stars, they may accomplish this feat, in part, by standing on the shoulders of the tiny eight-legged endurance specialists in your backyard. | Biology |
Breaking news: T.rex had baboon-like numbers of neurons! I never really had an interest in dinosaurs - until I started paying attention to the intersection of growth and life history, energy use, and numbers of brain neurons. How could those creatures possibly get so big? Then, just some months ago a former collaborator published the database that was missing to complete what I had started (and that we were supposed to complete together, but that's another story): the numbers of neurons in the brains of plenty more bird species, and also the other non-avian sauropsids, a.k.a. "reptiles" - though we're not supposed to use that word anymore... and I noticed that I probably had EVERYTHING that I needed, right there, to estimate what dinosaur brains were made of. So I dropped everything else that I was doing to give myself a crash course in dinosaur biology and evolution. I like to think that my beer hour companions, Jon Kaas and Ken Catania, were amused by the regular updates on my discoveries over the months that ensued.There was only one catch: first I needed to convince myself of whether dinosaur brains could have abided by the scaling rules of endothermic sauropsids (the birds) or, instead, by the scaling rules of ectothermic sauropsids (the aforementioned "reptiles"). Trouble was, maybe they were in-between - "mesotherms", as a study published in Science in 2014 suggested: warm-ish, neither here nor there, in an undefinable mathematical chasm. Crap. Me standing next to a life-size cast of Sue The T. rex (the one in the Chicago Field Museum) during a visit in 2017 to the Stone Age Institute, Indiana. The thing in my hands is an also life-sized copy of Sue's endocast. It's laughed at for being tiny compared to her body - but it's actually baboon brain-sized, and so perfectly sufficient to hold baboon-like numbers of neurons in the telencephalon! Copyright of the author. Use authorized if accompanied by a link to this page. But it turned out that respecting dinosaur diversity, that is, not treating them all as the same, quickly showed that the "mesotherms" denomination was a mathematical fantasy, akin to throwing apples and oranges in a blender and deducing, from the mixed juice, that there is such a thing in the world as the mixed fruit. Looking at the relationship between estimated brain and body size, theropod dinosaurs (which includes T. rex and all other bipedal carnivorans) scaled just like modern ostriches and emus and chickens still do, which confirms several inferences by other researchers that they were endotherms already. Conversely, most of the big quadrupeds with data available scaled instead like modern ectothermic sauropsids still do, so they were probably ectotherms. Apples and oranges. Not mesotherms.Which was great, because that meant that I could use the scaling rules that apply to ostriches/emus/chickens and similar birds today (which arose from ancestors that were contemporary and thus true cousins to T. rex) and use the estimated brain size of T. rex and other dinosaurs to calculate their numbers of neurons. The verdict: they were the PRIMATES of their time. Alosaurus had as many neurons in the telencephalon as a monkey; T. rex had as many as a modern baboon.Which is, frankly, terrifying. Plus, with that many neurons and what I've learned about how life history scales with those, not body mass, I could also predict that dinosaurs took about 5 years to reach sexual maturity, and had a maximum longevity predicted at 40 years, just like a baboon - enough to learn to use and craft tools and build and transmit a culture. Even worse: a dinosaur that had developed the cheat of predigesting food before putting it in their mouths COULD, in theory, have evolved to have as many neurons as... humans did, in the 2-3 million years since our ancestors started processing food, first with tools, then with fire.I'll never look at dinosaurs the same way again. Also: Thank you, asteroid hit of 65 million years ago :) The video above summarizes the paper, which you can find here, published in The Journal of Comparative Neurology (which - full disclosure - I now edit, BUT the submission was of course handled by a different editor). Reference: | Biology |
Watch hammerhead sharks get their hammer
For weeks, you’d be hard pressed to tell if the rapidly growing animal was going to become a chicken, a fish, a frog, or even a human.
Then out of nowhere: the hammer.
In an unprecedented look at perhaps the strangest, most captivating animals in the ocean, University of Florida scientists have documented how hammerhead sharks stretch and distort their skulls into their namesake hammer-like shape.
“This is a look at how monsters form,” said Gareth Fraser, a UF professor of biology who supervised the new study. “This is an insight into the development of a wonder of nature that we haven’t seen before and may not be able to see again.”
In a series of striking pictures, the study reveals how, roughly halfway through gestation, two-inch-long bonnethead shark embryos suddenly widen their heads. The growing skull pushes out their still-growing eyes at unnatural-looking angles. In the following weeks, the front of the hammer rounds out as it pushes backward toward the gills, creating the final shovel-like shape.
A couple months later, the fully-formed, foot-long shark is born.
Fraser and his graduate student Steven Byrum led the work to document in careful detail the development of bonnetheads, the smallest hammerhead shark species. Bonnetheads are abundant in the Gulf of Mexico and the Atlantic Ocean and spend time near shore, making them relatively easy to study.
But this detailed look at hammerhead development had previously escaped scientists. Most fish, and many sharks, lay eggs that can be easily collected and examined back at the lab. Hammerheads give birth to live young, which makes it exceedingly difficult to watch embryos develop. Many species are endangered, prohibiting the harvesting of sharks to study their young.
Fraser’s team made the most of existing specimens. Through their collaborators, they gained access to embryos that were preserved from bonnetheads caught during other biological studies. No additional sharks were harmed to complete the study.
Because of the difficulty of studying hammerheads, the scientists say that such a close look at their development may never happen again.
“It’s the perfect qualities of the bonnethead that allowed us do it with this species,” said Byrum. “This was a unique opportunity we may not be able to get for very much longer with bonnetheads and may not be able to get in any other species of hammerhead.”
Byrum and Fraser worked with Gavin Naylor, director of the Florida Program for Shark Research at the Florida Museum of Natural History, and scientists from the South Carolina Department of Natural Resources and Florida State University to publish their findings Sept. 28 in the journal Developmental Dynamics.
The documentation sets up future experiments to determine how hammerheads control their head shape and why they evolved their unusual features, which are thought to amplify their field of vision and ability to detect electrical movements of prey. | Biology |
Understanding nitrogen metabolism could revolutionize tuberculosis treatment
Development of new drugs to effectively target the bacterium that causes tuberculosis (TB) could be one step closer following an important discovery from the University of Surrey.
The Surrey study used a technology called fluxomics to reveal important information about how cells process nitrogen, which could help us better understand how harmful bacteria survive and cause disease. These findings have significant implications for studying the behavior and impact of pathogenic bacteria on human health.
In the most comprehensive study of its kind, the research team from Surrey conducted a study on the bacterium that causes tuberculosis, called Mycobacterium tuberculosis (Mtb). They wanted to understand how nitrogen is processed within Mtb cells, which is essential for the bacterium's survival. Surprisingly, previous studies had mostly examined the role of carbon in Mtb's survival, leaving the role of nitrogen poorly understood.
Dr. Khushboo Borah Slater, co-author of the study and research fellow from the University of Surrey, said, "Drug resistance is a major problem affecting tuberculosis treatment. New drugs are urgently needed to tackle the growing threat of this infectious disease and finding out more about how nitrogen is metabolized within cells could help us achieve this. Using drugs to target the nitrogen metabolism could be a novel way to disrupt how the bacterium survives, multiplies and spreads inside the human host cell."
Using the new fluxomic tool, Bayesian 13C15N-metabolic flux analysis, developed at Surrey and with Forschungszentrum Jülich, researchers were, for the first time, able to track both carbon and nitrogen atoms within Mtb cells. Following rigorous statistical assessment of all carbon and nitrogen biochemical reactions within the bacterium, researchers were able to identify the crucial role the amino acid glutamate plays within the nitrogen metabolism in Mtb, providing the important target for new drug development.
Professor Johnjoe McFadden, co-author of the study from the University of Surrey, added, "Understanding the Mtb's nitrogen metabolism will help to develop drugs to tackle TB. Specifically creating drugs that target the amino acid glutamate could disrupt the nitrogen metabolism and curb the spread of the disease.
"The technology we developed will play a key role in learning more about the carbon and nitrogen metabolisms in any living organisms and could pave the way for more effective drug treatments being created for other human diseases."
This study was published in the journal Molecular Systems Biology and was conducted in partnership with Forschungszentrum Jülich, Germany.
More information: Khushboo Borah Slater et al, One‐shot 13 C 15 N ‐metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux, Molecular Systems Biology (2023). DOI: 10.15252/msb.202211099
Journal information: Molecular Systems Biology
Provided by University of Surrey | Biology |
CNN — It was only a matter of time before human-caused climate change and pollution reached even the most isolated continent on the planet. As global temperature rises, Antarctica’s pristine landscape is already changing, and new research shows most of the region’s plant and animal species – including its iconic penguins – are in trouble. The study published Thursday in the journal PLOS Biology found that 65% of Antarctica’s native species, emperor penguins top among them, will likely disappear by the end of the century if the world continues its business-as-usual ways and fails to rein in planet-warming fossil fuel emissions. The study also showed that the current conservation efforts in Antarctica are not working on the rapidly changing continent. Researchers concluded implementing an extra layer of cost-effective strategies, which they lay out in the study, could save up to 84% of Antarctica’s vulnerable biodiversity. “Antarctica is not really contributing to climate change; there’s not a large-scale number of people living there, so the greatest threat to the continent is coming from outside the continent,” Jasmine Lee, lead author of the study, told CNN. “We really need global action on climate change, as well as some more local and regional conservation efforts, to give Antarctic species the best chance of surviving into the future.” Antarctica’s geographic isolation has long protected the continent from the worsening impacts of the climate crisis and other environmental disasters that plague the rest of the world, such as wildfires, flooding, and drought. Scientists have already observed significant changes in its northern counterpart, the Arctic, which is warming four times faster than the rest of the planet. But the impacts of climate change are just starting to emerge in Antarctica. Recent data, for example, suggests Antarctica’s sea ice is dropping more rapidly now than decades prior. Thursday’s study shows that disappearing sea ice threatens several species of marine seabirds, like emperor and Adélie penguins, that rely on the ice from April through December to nest their little ones. If the ice melts earlier or freezes later in the season, as a result of rising temperatures, penguins struggle to complete their reproductive cycle. “These iconic species, like emperor penguins and Adélie penguins, are at risk and it’s really sad to think that Antarctica is one of the last great wildernesses on the planet and human impacts are being seen and felt there,” Lee said. “It’s just incredibly sad to think that we could drive those kinds of species towards extinction.” Human presence and activity are also increasing in the region. The study shows that scientific expeditions and infrastructure are expanding, while annual tourist numbers have skyrocketed more than eight-fold since the 1990s. A separate study from earlier this year showed that increasing human presence in the region is causing more snow melt. Scientists found black carbon – the dark, dusty pollution that comes from burning fossil fuels – settling in locations where people spend a lot of time. Even the tiniest amount of this pollutant can have a significant impact on melting. While the threat to Antarctica’s species and its ecosystem are increasingly well-documented, they aren’t as widely understood among policymakers, Lee said. And finding the funds for conservation can be challenging. But the study lays out several measures that are actually cost-effective, with an estimated cost of $1.92 billion over the next 83 years, or around $23 million per year – a fraction of the global economy. These strategies include minimizing and managing human activity, transport and new infrastructure, as well as protecting native species while also controlling non-native species and diseases that enter the region. It also includes a focus on external policies, like achieving the broader international climate goals under the 2015 Paris Agreement, which aim to reduce planet-warming emissions and stave off a dire rise in global temperature. “The benefits of doing something about climate change is good for human health, livelihood and also the economy,” Lee said. “The incentive is there, but it’s just finding that initial investment, and it just depends on priorities.” Cassandra Brooks, an assistant professor at the University of Colorado Boulder who has done extensive research on marine animals in Antarctica, said that the study is “timely and important” to draw attention to how critically threatened Antarctic biodiversity is. “This study builds on previous work showing the urgency with which policymakers need to take action on climate change, if there is any chance of safeguarding Antarctic biodiversity,” Brooks, who is not involved with the study, told CNN. It “makes crystal clear that current conservation strategies are insufficient at doing anything beyond supporting the decline of biodiversity.” The latest research comes days after negotiators at the UN biodiversity summit in Montreal reached a landmark agreement to better protect the planet’s vital ecosystems, including a pledge to protect 30% of land and oceans by 2030. With the climate crisis now the most pervasive threat to Antarctic biodiversity, Lee said influencing global policy is needed more than ever to save one of Earth’s vast, pristine biomes. “This is just the tip of the iceberg,” Lee said. “We’re at this huge turning point now not just for Antarctica, but globally, when it comes to climate. We’ve got the opportunity to stop it and if we don’t do something now, then the impacts are going to be much, much worse than what they could be.” | Biology |
Mushrooms and possibly all fungi have the ability to cool down by “sweating” away water, a new study reveals.
It’s not yet clear why fungi might want to stay cool. However, the discovery sheds light on a potentially fundamental aspect of fungal biology and may even have implications for human health.
“It is, to me, a very interesting … unexplained phenomenon,” said Dr. Arturo Casadevall, a microbiologist at Johns Hopkins University and one of the study authors on the new paper, published last month in PNAS.
Lead author Radamés Cordero, who is also a microbiologist at Johns Hopkins, used an infrared camera to snap pictures of mushrooms in the woods. Infrared cameras can visualize the relative temperatures of each object in a photo, and Cordero noticed something odd: The mushrooms seemed to be colder than their surroundings.
Scientists had previously observed that mushrooms tend to be colder than their environments. But Casadevall said he had never heard of the phenomenon, so the team decided to find out if this cooling effect applied to all fungi.
In addition to photographing wild mushrooms, the researchers grew and photographed different types of fungi in the lab and found the same effect — the fungi were colder than their surroundings. This was even the case with their culture of Cryomyces antarcticus, a fungus that grows in Antarctica.
The fungi seem to cool down through evapotranspiration of water from their surface — meaning, essentially, they sweat. Think about coming out of the shower, Casadevall told Live Science. When you’re covered in water, you feel cold because some of the water on your skin is evaporating, taking heat with it.
The team then created a sort of mushroom-powered air conditioner. They put mushrooms — Agaricus bisporus, commonly sold in supermarkets as portobello and white mushrooms, among other names — into a styrofoam box with a hole on each side. A fan was placed outside one of the holes, and they put this “MycoCooler” into a larger container and turned the fan on to circulate air over the mushrooms.
After 40 minutes, the air in the larger container had dropped from about 100 degrees Fahrenheit (37.8 degrees Celsius) down to about 82 F (27.8 C). The mushrooms had lowered the temperature through evaporative cooling, using up heat in the air to convert liquid water into gas.
The scientists are still unsure why fungi might want to keep cool.
In their paper, the authors speculate that it might have something to do with creating optimal conditions for spore formation, or it may help fungi spread their spores — by altering the temperature, they might be causing tiny winds that can blow the spores around.
It’s also possible that this phenomenon is due to something else entirely. For example, evapotranspiration also increases humidity, and when asked if it’s possible that the fungi are trying to keep humid, and the cooling is simply a by-product, Casadevall said it was conceivable.
Understanding the reason behind this cooling phenomenon in mushrooms and other fungi could help us understand how fungi interact with their environment and other organisms — ourselves included. Fungal diseases are estimated to kill more than 1.5 million people per year, many of them immunocompromised people.
At the moment, however, people also have some protection from fungal infections as we're warm-blooded, and fungi don’t grow very well at our body temperature, Casadevall said.
But with climate change, fungi could start to adapt to warmer temperatures — potentially enabling them to more easily infect humans. If we understand why a fungus might prefer cooler temperatures, it might be able to help us inhibit fungal infections, Casadevall said.
But so far, this new discovery likely poses more questions than answers. “I think that if we could understand why — why do they want to be a bit colder than the environment?, we're going to learn a lot.” Casadevall said.
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Ethan Freedman is a science and nature journalist based in New York City, reporting on climate, ecology, the future and the built environment. He went to Tufts University, where he majored in biology and environmental studies, and has a master's degree in science journalism from New York University. | Biology |
I first held a violin in my late forties. Placing it under my chin, I let go an impious expletive, astonished by the instrument’s connection to mammalian evolution. In my ignorance, I had not realized that violinists not only tuck instruments against their necks, but they also gently press them against their lower jawbones. Twenty‑five years of teaching biology primed me, or perhaps produced a strange bias in me, to experience holding the instrument as a zoological wonder. Under the jaw, only skin covers the bone. The fleshiness of our cheeks and the chewing muscle of the jaw start higher, leaving the bottom edge open. Sound flows through air, of course, but waves also stream from the violin’s body, through the chin rest, directly to the jawbone and thence into our skull and inner ears.Music from an instrument pressed into our jaw: These sounds take us directly back to the dawn of mammalian hearing and beyond. Violinists and violists transport their bodies—and listeners along with them—into the deep past of our identity as mammals, an atavistic recapitulation of evolution.The first vertebrate animals to crawl onto land were relatives of the modern lungfish. Over 30 million years, starting 375 million years ago, these animals turned fleshy fins into limbs with digits and air‑sucking bladders into lungs. In water, the inner ear and the lateral line system on fish’s skin detected pressure waves and the motion of water molecules. But on land the lateral line system was useless. Sound waves in air bounced off the solid bodies of animals, instead of flowing into them as they did underwater. In water, these animals were immersed in sound. On land, they were mostly deaf. Mostly deaf, but not totally. The first land vertebrates inherited from their fishy forebears inner ears, fluid‑filled sacs or tubes filled with sensitive hair cells for balance and hearing. Unlike the elongate, coiled tubes in our inner ears, these early versions were stubby and populated only with cells sensitive to low‑frequency sounds. Loud sounds in air—the growl of thunder or crash of a falling tree—would have been powerful enough to penetrate the skull and stimulate the inner ear. Quieter sounds—footfalls, wind‑stirred tree movements, the motions of companions—arrived not in air, but up from the ground, through bone. The jaws and finlike legs of these first terrestrial vertebrates served as bony pathways from the outside world to the inner ear.One bone became particularly useful as a hearing device, the hyomandibular bone, a strut that, in fish, controls the gills and gill flaps. In the first land vertebrates, the bone jutted downward, toward the ground, and ran upward deep into the head, connecting to the bony capsule around the ear. Over time, freed from its role as a regulator of gills, the hyomandibula took on a new role as a conduit for sound, evolving into the stapes, the middle ear bone now found in all land vertebrates (save for a few frogs that secondarily lost the stapes). At first, the stapes was a stout shaft, both conveying groundborne vibrations to the ear and strengthening the skull. Later, it connected to the newly evolved eardrum and became a slender rod. We now hear, in part, with the help of a repurposed fish gill bone.After the evolution of the stapes, innovations in hearing unfolded independently in multiple vertebrate groups, each taking its own path, but all using some form of eardrum and middle ear bones to transmit sounds in air to the fluid‑filled inner ear. The amphibians, turtles, lizards, and birds each came up with their own arrangements, all using the stapes as a single middle ear bone. Mammals took a more elaborate route. Two bones from the lower jaw migrated to the middle ear and joined the stapes, forming a chain of three bones. This triplet of middle ear bones gives mammals sensitive hearing compared with many other land vertebrates, especially in the high frequencies. For early mammals, palm‑sized creatures living 200 million to 100 million years ago, a sensitivity to high‑pitched sounds would have revealed the presence of singing crickets and the rustles of other small prey, giving them an advantage in the search for food. But before this, in the 150 million years between their emergence onto land and their evolution of the mammalian middle ear, our ancestors remained deaf to the sounds of insects and other high frequencies, just as we, today, cannot hear the calls and songs of “ultrasonic” bats, mice, and singing insects. | Biology |
For the past 2,200 years, Andean condors (Vultur gryphus), among the largest known flying birds in the world, have been nesting — and pooping — at a cliffside grotto in northern Patagonia, Argentina. Now researchers are studying the massive pile of guano to learn more about the threatened species and how it has adapted to its environment over time.
To study the doughnut-shaped poop mound, which measures roughly 10 feet (3 meters) in diameter, researchers carved it like a pie, removing a single 10-inch-deep (25 centimeters) slice of excrement. Thanks to the deposit's location inside the grotto, the preserved poo had been well protected from wind and rain, allowing it to amass for thousands of years, according to a study published May 3 in the journal Proceedings of the Royal Society B (opens in new tab).
"By looking at the different layers, we could go back in time," lead study author Matthew Duda (opens in new tab), a graduate student of biology at Queen's University in Kingston, Ontario, told Live Science. "We carbon dated [the pile] to figure out the nest's age, which is over 2,000 years old."
By examining the preserved poo, the team discovered how the condors' diets had evolved over time.
"Condors are scavengers, and at one time they would fly along the shores and eat carcasses of whales and native species such as llamas and alpacas," Duda said. "But as livestock like sheep and cattle were introduced into South America [by Europeans], their diets changed along with it. We saw a complete shift from before to what is currently most abundant for them to eat."
Unfortunately, this shift also meant the condors are ingesting more lead, which Duda attributed to "lead shot being used to kill vermin, which the condors would then eat." These toxic metals were then excreted by the birds.
"We saw that the concentration of lead was significantly higher now than in the past," Duda said.
This is particularly concerning since Andean condors are on the Red List of Threatened Species monitored by the International Union for Conservation of Nature (opens in new tab), and their numbers continue to dwindle with only about 6,700 adults still living in the wild.
The researchers also noticed that for one 1,000-year stretch of time, roughly between 650 and 1,650 years ago, the condors more or less abandoned the site, resulting in the guano accumulation dropping drastically from approximately 3 cubic feet (0.08 cubic m) per year to 0.11 cubic feet (0.003 cubic m) per year. They think that increased volcanic activity forced the condors to leave, according to the study.
"We measured an increase in sulfur and sodium, which are both associated with volcanic activity," said Duda, who suspects that as volcanic ash blanketed the surrounding vegetation, herbivores were forced to leave in search of new food resources, causing the condors to take flight too.
The researchers plan to study other Andean condor deposits in the region to determine "baseline conditions" for the sites, eventually applying their methods to other threatened bird species, including oilbirds (Steatornis caripensis) (opens in new tab), a nocturnal fruit-eating bird that uses echolocation to navigate.
"It is clear that quality breeding sites are critical for this species' survival," the study authors wrote in their paper. "To support effective conservation efforts, nesting and roosting sites need extensive protection."
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Jennifer Nalewicki is a Salt Lake City-based journalist whose work has been featured in The New York Times, Smithsonian Magazine, Scientific American, Popular Mechanics and more. She covers several science topics from planet Earth to paleontology and archaeology to health and culture. Prior to freelancing, Jennifer held an Editor role at Time Inc. Jennifer has a bachelor's degree in Journalism from The University of Texas at Austin. | Biology |
A research vessel off the coast of the Galapagos Islands recently spotted a rarely seen, ghostly squid with weak, sucker-less tentacles floating in the deep, marking only the second time this elusive species has ever been filmed alive.
Researchers from the Schmidt Ocean Institute, in collaboration with the Charles Darwin Foundation and Parque Nacional Galápagos, spotted the ethereal cephalopod, dubbed Grimalditeuthis bonplandi, using a remotely operated vehicle (ROV) during an expedition to hydrothermal vents.
G. bonplandi can grow up to 10 inches (25 centimeters) in length. These squid have fragile bodies and are slow swimmers. According to the Schmidt Ocean Institute, the species inhabits depths of 660 to 5,000 feet (200 to 1,500 meters). Although believed to exist worldwide, the squid are rarely encountered — until 2005, scientists had only studied dead specimens that came from the stomach contents of sperm whales (Physeter macrocephalus).
Unlike other squid, G. bonplandi has feeding tentacles with no suckers. Other cephalopods whip and thrash, grabbing their prey with their tentacles and trapping them with their suckers, but G. bonplandi is thought to be a graceful feeder that undulates its tentacles to lure small shrimp and other crustaceans.
Early research collected from dead specimens made it clear that this squid lacked muscle in its tentacles. In 2005, scientists spotted the creature in the Monterey Canyon off central California and recorded its strange behavior for 22 minutes. At that time, the creature stayed still, as if stunned. Only the ends of its tentacles waved and fluttered. This behavior led scientists to speculate how the animal captures its prey. It could be mimicking the movement of a small fish or worm, luring creatures by resembling their prey — a method called aggressive mimicry, which is common in other cephalopods. However, with the limited video observations and infrequent encounters, this is uncertain.
There is still much to learn about these mysterious creatures, but ROVs have made it possible to capture illuminating footage to inform new theories until the next live sighting.
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Elise studied marine biology at the University of Portsmouth in the U.K. She has worked as a freelance journalist focusing on the aquatic realm. Elise is working with Live Science through Future Academy, a program to train future journalists on best practices in the field. | Biology |
The key to a successful sleight-of-hand magic trick is how well a magician manipulates the audience's perception, especially of manual movements, since that is crucial to how we anticipate another's actions. To learn more about how humans experience such misdirection, researchers in the UK performed simple magic tricks for three species of monkeys to see if they could be fooled. They found that only those species with at least partially opposable thumbs were fooled, suggesting that having similar anatomy (and therefore biomechanical ability) plays a vital role in the illusion. They described their results in a new paper published in the journal Current Biology.
“Magicians use intricate techniques to mislead the observer into experiencing the impossible," said co-author Elias Garcia-Pelegrin, who practices magic and conducted this research while completing his PhD at the University of Cambridge. "It is a great way to study blind spots in attention and perception. By investigating how species of primates experience magic, we can understand more about the evolutionary roots of cognitive shortcomings that leave us exposed to the cunning of magicians. In this case, whether having the manual capability to produce an action, such as holding an item between finger and thumb, is necessary for predicting the effects of that action in others.”
The researchers focused on three species with different hand anatomies and associated biomechanical abilities: yellow-breasted capuchin monkeys, Humboldt's squirrel monkeys, and common marmosets. For instance, capuchins are known for their manual dexterity, due in part to the fact that they can individually control their fingers. So they can perform a scissor grip (holding an object between the sides of two fingers), as well as a precision grip (bringing the thumb to the index or middle finger). They can even probe, pinch, or enclose an object with both hands, much like humans, and use stone tools to crack nuts.
Squirrel monkeys aren't nearly as dexterous by comparison, but they have been known to use simple tools occasionally. They have hinge-like joints that limit thumb rotation, so the thumbs aren't fully opposable. But they can still touch the side of the index of middle finger (though not the pads). Marmosets, on the other hand, evolved for vertical movement like climbing tree trunks, and opposable thumbs would not be an advantage for that, so they don't have them. They have rigid thumbs instead. Per the authors, marmosets climb by spreading their five digits as wide as possible to increase the surface area, flexing all the digits simultaneously to dig in with their claws. They use a combination of power grips and scissor grips to manipulate objects. | Biology |
In recent years, steady progress has been achieved in the field of brain-computer interfaces. Devices have been tested and utilized by paralyzed patients to reliably move robotic arms or computer cursors with great dependability. Although such technologies can substantially enhance disabled individuals' freedom, at the moment there are no reliable methods of communication for those who are unable to talk.However, researchers from the Netherlands and Germany have made great strides in that area as they developed a system that can instantly convert thoughts in the brain into speech with the clever use of machine learning. The scientists were able to get an epilepsy patient with depth electrodes in her brain to utter words she only thought of in her head. The team published their findings in the highly regarded scientific journal Communications Biology.Dr. Pieter Kubben from the Dutch Maastricht University Medical Center explained in an interview that a wide range of tests was performed on epilepsy patients that were monitored at the Kempenhaeghe expertise center for epilepsy. These patients already had depth electrodes in their brains and agreed to partake in this study while on observation for epilepsy research. Thus, they were hitting two birds with one stone, so to speak.Converting brain activity into speechOne particular series of tests focused on speech. First, a patient had to read aloud a selection of texts, after which a computer distilled the relationship between spoken words and brain activity using machine learning. Finally, the system could generate audio directly from measured brain activity, even when the patient only imagined the words without speaking them out loud. Christian Herff, the study's lead author, stated that the data models derived from brain activity from ordinary speech also work for imagined speech.This extraordinary breakthrough is a significant step forward in the conception of a speech neuroprosthesis. It would allow those with severe speech problems caused by brain injury to participate in the program to speak again.The current feasibility research was based on 100 different words. The researchers are now increasing their experiments with the aim of getting patients to convert entire sentences made up in the brain to speech.For a more detailed overview of the study, be sure to check out the paper listed below.Sources and further reading:Real-time synthesis of imagined speech processes from minimally invasive recordings of neural activity (communications biology)Machine learningMaastricht UMC | Biology |
A world-first holistic framework for assessing the mental and psychological wellbeing of wild animals has been developed by UTS Chancellor's Postdoctoral Research Fellow Dr Andrea Harvey, a veterinarian and animal welfare scientist in the TD School at the University of Technology Sydney.
The significance of the study lies in its potential to revolutionise conservation efforts. Instead of focusing solely on population numbers and reproductive success, the research explores the quality of life experienced by wild animals.
This shift in perspective could provide crucial early warning signals about species challenges and population declines, leading to more effective conservation strategies.
"While research on the welfare of domestic and farm animals has been considerable, including indicators of emotional states such as stress, pain and fear, my aim is to bridge the gap by examining the individual lives, feelings and mental experiences of wild animals," Dr Harvey said.
"A deeper understanding of the wellbeing of wild animal populations can not only enhance conservation efforts, but also provide an indication of the state of the natural environment and its recognised links to human health and wellbeing."
The study, which was part of Andrea's PhD research at the UTS Centre for Compassionate Conservation, focuses on brumbies -- free-roaming wild horses -- from Australia's alpine regions, however the framework is widely applicable for evaluating many wildlife species.
Dr Harvey chose brumbies as horse welfare has been studied in domestic environments, providing a bridge to wild animals. The paper, Mental Experiences in Wild Animals: Scientifically Validating Measurable Welfare Indicators in Free-Roaming Horses, was recently published in Animals.
Her comprehensive conceptual framework, called the '10 Stage Protocol', includes physical and behavioural indicators for both negative and positive mental experiences in wild animals.
"If you have a dog, you know their usual routine, what they like, and how they behave in certain circumstances. You know if they're happy, sad, or distressed, so this research is shifting that understanding to wild animals.
"We can never be certain what's going through an animal's mind and exactly what they're feeling. It's also an area that scientists have traditionally shied away from. However, we know mental experiences arise from physical states, and we can directly measure these states.
"Nutrition, the physical environment, health, and behavioural interactions all provide clues to the mental experience of animals. This includes negative states such as thirst, hunger, heat and cold discomfort, pain, fatigue, anxiety and fear and positive ones such as satiety, exercising agency, physical vitality and positive social interactions."
This holistic approach brings together different areas of scientific knowledge, including neuroscience, behaviour, and neuroethology -- the study of the neural basis of an animal's natural behaviour -- to interpret the data collected and gain insights into wellbeing.
Dr Harvey is currently collaborating with researchers studying Australian water birds, such as the straw-necked ibis and pelicans. These birds serve as indicators of water quality and wetland health, which could inform management decisions in the Murray Darling Basin.
The welfare of koalas, which have been declared endangered in NSW, is also under scrutiny. Previous koala research has focused primarily on survival and disease. Dr Harvey's research aims to evaluate overall koala wellbeing to inform policy decisions around conservation and habitat protection.
Dr Harvey is also working with other researchers studying the welfare of kangaroos and dingoes at a field station in southern Queensland, focusing on the predator-prey relationship, and the impact of climate change and drought recovery.
Each species presents unique challenges, such as identifying individuals, evaluating mental experiences in large populations, and considering different environments and habitats.
Dr Harvey acknowledges the challenges of studying the mental experiences of wild animals compared to domesticated ones. The absence of close human relationships with individual animals and the difficulty in observing them for extended periods pose significant hurdles.
However, innovative methods like remote camera traps have proven valuable in collecting fine-detail data on wild animal behaviour, including body posture and facial expressions.
Dr Harvey's ground-breaking research holds immense potential in transforming the field of conservation biology, by shedding light on the mental experiences of wild and endangered animals.
"Welfare assessments need to be part of all wildlife monitoring, and ultimately all environmental policy decision making, which needs to take into account not just individual species, but also interactions between different species, and their ecosystems."
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Neuroscience tool's structure may lead to next gen versions
In order to more fully understand how diseases arise in the brain, scientists must unravel the intricate way neurons relay messages (either chemical or electrical) along a complex web of nerve cells. One way is by using a tool called DREADDs, which stands for Designer Receptors Activated by Designer Drugs.
When introduced to a nerve cell or neuron, DREADDs acts like a specialized lock that only works when a key—in the form of a synthetic designer drug—fits into that lock. DREADDs can enable researchers to turn specific cell functions on or off to examine groups of neurons in circuits more precisely. (see Animations)
Now, a University of Maryland School of Medicine researcher and his colleagues at the University of North Carolina Chapel Hill (UNC) have unveiled the structure of these DREADDs that will pave the way for creating the next generation of these tools. This step ultimately will bring them closer to an elusive goal—understanding the underpinnings of brain disorders, such as schizophrenia, substance abuse, epilepsy, and Alzheimer's, in order to develop more effective drugs to treat them.
The research team published their findings in a recent issue of Nature.
"These findings provide atomic clarity into the nature of DREADD receptors bound to their drugs, resulting from the culmination of all these technologies converging at the right place and right time," said study author Jonathan Fay, Ph.D., Assistant Professor of Biochemistry and Molecular Biology at UMSOM. "This knowledge will allow this tool to be further refined and optimized. We were previously limited in how to upgrade their designs because we didn't fully understand how they worked at the structural level."
Hundreds of labs around the world now use the DREADD tool, which was developed at UNC. Scientists there designed these receptor proteins to react only to uniquely designed drugs that are pharmacologically inert because they only bind to the DREADD protein receptor.
For this new study, researchers used a newer imaging technology, known as cryogenic electron microscopy, to determine the molecular structure of DREADD receptors with the drugs. This process flash-freezes the DREADDs in a way that does not form traditional ice crystals, but instead creates a sort of slurry that allows some movement in the molecules. This technique allowed researchers to determine the DREADD's structure when other older molecular imaging methods failed. The researchers observed inhibitory (turning off cell functions) or stimulatory (turning on cell functions) DREADD receptors bound to each of two different designer drugs.
The researchers also compared the structure of the natural brain receptor from which DREADDs originated to see how it differed from DREADDs. The original brain receptor, found in the cell membrane of neurons, traditionally binds to a molecule involved in learning and memory. By changing two of the natural receptor's building blocks, the engineered DREADD receptor binds better to its own laboratory-designed drugs rather than to the original memory molecule—a process they visualized through their experiments.
"With this imaging technique, we could see that the genetic changes in the DREADDs opened up the space where the memory molecule normally binds, allowing the new designer drugs to slip in. We could see that shape of the space changed as well, contributing to why the new drugs fit better," said Dr. Fay.
The class of receptors from which DREADDs originated are often the intended targets of many therapeutics. However, various drugs bind to several kinds of receptors or activate others in unintended ways. The result might be a beneficial effect, but also can result in side effects.
"Because of the precise way in which these designer drugs in DREADDs bind so specifically, it is likely possible that researchers will one day eventually develop targeted therapies for many of these other similar receptors without the cross-reactivity and unpleasant side effects," said UMSOM Dean Mark T. Gladwin, MD, Vice President for Medical Affairs, University of Maryland, Baltimore, and the John Z. and Akiko K. Bowers Distinguished Professor.
Although the microscopy-related part of this study occurred at UNC, UMSOM also has high-tech structural biology capabilities in their Center for Biomolecular Therapeutics (CBT), where researchers determine the structures of the human body's proteins to better develop new drugs to treat a variety of diseases. Dr. Fay plans to use CBT's facilities to analyze the structure of other brain receptors, as well as to continue his collaboration with UNC on potential DREADD 2.0 versions.
A major focus of UMSOM's research, as evidenced by the launch of the University of Maryland-Medicine Institute for Neuroscience Discovery (UM-MIND) in late 2022 includes neuroscience and brain-related diseases. Dr. Fay's work directly contributes towards these institutional priorities.
More information: Shicheng Zhang et al, Molecular basis for selective activation of DREADD-based chemogenetics, Nature (2022). DOI: 10.1038/s41586-022-05489-0 | Biology |
Irvine, Calif., Oct. 4, 2022 — A discovery about how some visually impaired adults could start to see offers a new vision of the brain’s possibilities. The finding that the adult brain has the potential to partially recover from inherited blindness comes from a collaboration between researchers in the University of California, Irvine School of Biological Sciences and the School of Medicine. Their paper appears in Current Biology.
The team was examining treatment for Leber congenital amaurosis, known as LCA. The term refers to a group of inherited retinal diseases distinguished by severe visual impairment at birth. The condition, which stems from mutations in any of over two dozen genes, causes degeneration or dysfunction in the retina’s photoreceptors.
Administering chemical compounds that target the retina, called synthetic retinoids, can restore a notable amount of vision in children with LCA. The UCI team wanted to find out if the treatment could make a difference for adults who have the condition.
“Frankly, we were blown away by how much the treatment rescued brain circuits involved in vision,” said Sunil Gandhi, professor of neurobiology and behavior and the corresponding author. Gandhi is a fellow of UCI’s Center for the Neurobiology of Learning and Memory and a member of the Center for Translational Vision Research. “Seeing involves more than intact and functioning retinae. It starts in the eye, which sends signals throughout the brain. It’s in the central circuits of the brain where visual perception actually arises.” Until now, scientists believed that the brain must receive those signals in childhood so that central circuits could wire themselves correctly.
Working with rodent models of LCA, the collaborators were surprised by what they found. “The central visual pathway signaling was significantly restored in adults, especially the circuits that deal with information coming from both eyes,” Gandhi said. “Immediately after the treatment, the signals coming from the opposite-side eye, which is the dominant pathway in the mouse, activated two times more neurons in the brain. What was even more mind-blowing was that the signals coming from the same-side eye pathway activated five-fold more neurons in the brain after the treatment and this impressive effect was long-lasting. The restoration of visual function at the level of the brain was much greater than expected from the improvements we saw at the level of the retinae. The fact that this treatment works so well in the central visual pathway in adulthood supports a new concept, which is that there is latent potential for vision that is just waiting to be triggered.”
The finding opens exciting research possibilities. “Whenever you have a discovery that breaks with your expectations about the possibility for the brain to adapt and rewire, it teaches you a broader concept,” Gandhi said. “This new paradigm could aid in the development of retinoid therapies to more completely rescue the central visual pathway of adults with this condition.”
Gandhi and first author Carey Huh, PhD, who initiated the project, teamed with the School of Medicine Department of Ophthalmology Chair and Distinguished Professor Krzysztof Palczewski. Palczewski, director of the Center for Translational Vision Research, is renowned for his work on retinoids and the visual cycle. School of Medicine Physiology and Biophysics Associate Professor Philip Kiser, an expert on visual cycle biochemistry, helped lead the group. Kiser, who holds a joint appointment in ophthalmology, is a member, Center for Translational Vision Research.
The research was funded by the National Institutes of Health, the Department of Veterans Affairs and the Research to Prevent Blindness foundation.
About the University of California, Irvine: Founded in 1965, UCI is a member of the prestigious Association of American Universities and is ranked among the nation’s top 10 public universities by U.S. News & World Report. The campus has produced five Nobel laureates and is known for its academic achievement, premier research, innovation and anteater mascot. Led by Chancellor Howard Gillman, UCI has more than 36,000 students and offers 224 degree programs. It’s located in one of the world’s safest and most economically vibrant communities and is Orange County’s second-largest employer, contributing $7 billion annually to the local economy and $8 billion statewide. For more on UCI, visit www.uci.edu.
Media access: Radio programs/stations may, for a fee, use an on-campus ISDN line to interview UCI faculty and experts, subject to availability and university approval. For more UCI news, visit news.uci.edu. Additional resources for journalists may be found at communications.uci.edu/for-journalists. Tweet Share 0 Reddit +1 LinkedIn 0 Email | Biology |
Experts discover how zebra stripes work to thwart horsefly attacks
Researchers at the University of Bristol have found why zebra fur is thinly striped and sharply outlined.
Their findings, published Feb. 17 in the Journal of Experimental Biology, reveal that stark black-white distinctions and small dark patches are particularly effective in thwarting horsefly attack. These characteristics specifically eliminate the outline of large monochrome dark patches that are attractive to horseflies at close distances.
The team theorizes that the thin back stripes serve to minimize the size of local features on a zebra that are appealing to the biting flies.
The research was led by Professor Tim Caro and Dr. Martin How, both from the University of Bristol's School of Biological Sciences.
Prof. Caro explained, "We knew that horseflies are averse to landing on striped objects—a number of studies have now shown this, but it is not clear which aspects of stripes they find aversive.
"Is it the thinness of the stripes? The contrast of black and white? The polarized signal that can be given off objects? So we set out to explore these issues using different patterned cloths draped over horses and filmed incoming horseflies."
The team found that tabanid horseflies are attracted to large dark objects in their environment but less to dark broken patterns. All-gray coats were associated with by far the most landings, followed by coats with large black triangles placed in different positions, then small checkerboard patterns in no particular order. In another experiment, they found contrasting stripes attracted few flies whereas more homogeneous stripes were more attractive.
Professor Caro added, "This suggests that any hoofed animal that reduces its overall dark outline against the sky will benefit in terms of reduced ectoparasite attack."
The team found little evidence for other issues that they tested, namely polarization or optical illusions confusing accurate landings such as the so-called "wagon-wheel effect" or "the barber-pole effect."
Now the team want to determine why natural selection has driven striping in equids—the horse family—but not other hoofed animals.
Professor Caro added, "We know that zebra pelage—fur—is short, enabling horsefly mouthparts to reach the skin and blood capillaries below, which may make them particularly susceptible to fly annoyance, but more important, perhaps, is that the diseases that they carry are fatal to the horse family but less so to ungulates. This needs investigation."
More information: Tim Caro et al, Why don't horseflies land on zebras?, Journal of Experimental Biology (2023). DOI: 10.1242/jeb.244778 | Biology |
Editor’s Note: The views expressed in this commentary are solely those of the writers. CNN is showcasing the work of The Conversation, a collaboration between journalists and academics to provide news analysis and commentary. The content is produced solely by The Conversation. The Conversation — It’s a hair condition that has frustrated parents for decades, now scientists believe they have found the genes responsible for “uncombable hair syndrome”. Yes, it really is a thing. Uncombable hair syndrome is more than just difficult hair. As its name suggests, it’s hair that sticks out at all angles, making it almost impossible to tame let alone comb. It usually starts in children between the ages of three months and 12 years and is characterized by straw blond or silvery blond frizzy hair. It’s usually wavy, dry and brittle and, thanks to its appearance, it’s sometimes called spun glass hair, pili trianguli et canaliculi or cheveux incoiffables. READ MORE: The secret information hidden in your hair Boris Johnson or Albert Einstein might spring to mind, but while those high-profile men are famous for their unruly locks, with very few cases of uncombable hair syndrome in the world, it’s highly unlikely they have or had the condition. Besides, the condition tends to improve or even disappear by adulthood. There hasn’t been much research on this rare condition, which first appeared in published articles in the 1970s. Since then, fewer than 70 publications have appeared, most being case reports. One of the more recent studies involving 11 children with uncombable hair was performed by geneticists at the University of Bonn, Germany. They found that the condition seemed to be explained by mutations in three genes that code for well-known proteins in the hair follicle. However, since that study was widely reported by the press, more families with kids with this condition came forward and now the same scientists have repeated the genetics with over 100 children. They have confirmed that in 76 of these children, the cause is linked to mutations in the PADI3 gene as well as the involvement of two other genes, all three of which code for important proteins involved in hair-fiber formation. READ MORE: A huge history of big hair bows Human variation in appearance, including in hair, is a result of the many small variations in our genes in the global population. When a mutation happens in a gene, sometimes it leads to a change in the function of the protein. If that protein is in the hair follicle, it’s more than likely that the hair will look different. So this can be brown, blond, curly, thick, straight, red or even bald. There are a few well-known inherited variations in hair fibre shape and curl, but rarely are these linked to any serious illness. Interestingly, often the proteins that are affected are in the inner root sheath: three layers of the hair follicle that help put the shape into the hair fiber. We also know that uncombable hair is a “recessive” genetic characteristic. In other words, both parents must be carriers of the mutated gene, although they may not have it themselves. Then, if their child inherits one copy of the affected gene from each parent, they will have the syndrome. So why study such genetic hair disorders? This type of genetic study generates enough information such that parents can now request a genetic test that may help allay any concerns about other rare conditions that can affect the hair. READ MORE: Beauty still trumps brains in too many workplaces From the scientific perspective, it also helps the hair biology research community understand more about normal hair growth and the importance of different proteins for controlling hair shape and appearance. For example, we can now explain why changes to PADI3 might alter hair shape by finding out more about how it works in the follicle. Hair is one of the most culturally distinctive and personal attributes. Its style, shape, color and indeed absence is something everyone thinks about every day. A huge hair-care industry has developed over the last century to help us all manage our hair. So when a rare condition leads to such a fascinating yet impossible to manage change in hair, it is easy to appreciate why scientists want to understand how it happens and to help the families with affected children understand it better too. READ MORE: How we discovered the genetic origin of the ‘monobrow’ and other hair traits Gill Westgate is a business development manager at the University of Bradford’s Faculty of Life Sciences Republished under a Creative Commons license from The Conversation. | Biology |
A new study shows that bats evolved to avoid cancer and the data may uncover how humans can treat or prevent viruses as well as cancer.
A rapid evolution in bats, the only winged mammal, may account for their “extraordinary” ability to both host and survive infections and even to avoid cancer—and that success is in their genes.
Bats are exceptional among mammals for not only their ability to fly but also their long lives, low cancer rates, and robust immune systems.
The ability of bats to tolerate viral infections may stem from unusual features of their innate immune response—and these characteristics may have implications for human health.
For example, by better understanding the mechanisms of the bat immune system that allow bats to tolerate viral infections, researchers may be better able to prevent disease outbreaks from animals to people.
Comparative genomic analyses of bats and cancer-susceptible mammals may eventually provide new information on the causes of cancer and the links between cancer and immunity. Studies of bats and other organisms complement studies based on mouse models; mice are more amenable than bats to experimental manipulation but exhibit fewer characteristics with implications for human disease.
In a paper published in Genome Biology and Evolution by Oxford University Press
this week, researchers used the Oxford Nanopore Technologies long-read platform, and bat samples collected with help from the American Museum of Natural History in Belize, to sequence the genomes of two bat species—the Jamaican fruit bat and the Mesoamerican mustached bat.
The researchers at of Cold Spring Harbor Laboratory in New York carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals.
They found genetic adaptations in six DNA repair-related proteins and 46 proteins in bats that were cancer-related, meaning that researchers have previously found such proteins suppress cancer.
Notably, the study found these altered cancer-related genes were enriched more than two-fold in the bat group compared to other mammals.
“By generating these new bat genomes and comparing them to other mammals we continue to find extraordinary new adaptations in antiviral and anticancer genes,” said the paper’s lead author, Armin Scheben.
“These investigations are the first step towards translating research on the unique biology of bats into insights relevant to understanding and treating aging and diseases, such as cancer, in humans.”
Founded in 1890 and home to eight Nobel Prize winners, the not-for-profit Cold Spring Harbor Laboratory furthers biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Additional funding came from National Institutes of Health and Simons Center for Quantitative Biology.
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Under the right conditions, researchers say, some crop yields could increase by 50 percent or more. Gary J Weathers/Getty Images This past summer, a widespread drought across the United States lowered crop yields by as much as one-third as corn, wheat, barley and other plants suffered from too much heat and too little water. It’s a scenario that will likely become more common as climate change makes much of the world a hotter, drier place. Scientists are trying to teach old crops some new tricks that will let them flourish in these harsher conditions—turning to secrets that reside in plants like pineapples, orchids and agaves. These and certain other plants have hacked photosynthesis in ways that allow them to thrive when it’s hot and dry, and even to withstand blistering periods of drought. Many orchids, for example, live in nooks and crannies of trees where their only water comes in sporadic bouts of rain, while others, like agaves, thrive in the rocky soils of desert grasslands. If scientists could engineer crop plants like rice and wheat to be more like these heat-tolerant species, crops could be grown in lands that can’t be farmed right now. Under the right conditions, researchers say, some crop yields could increase by 50 percent or more. The work is still years from being done, but it could be vital. Climate change is predicted to cause more droughts and make farmland less productive. At the same time, the number of people the world needs to feed will increase to 10 billion from 8 billion by the end of the century. “It is getting more and more apparent that climate change is going to be a big challenge,” says Xiaohan Yang, a plant molecular biologist at Oak Ridge National Laboratory in Tennessee. “These plants are a natural solution to mitigate climate change.” The trouble with photosynthesis Traditionally, crop improvements have come from targeting traits like the size of the plant, its resistance to pests or the length of its growing season. But in recent years, scientists have been targeting photosynthesis, the process by which plants grow that ultimately fuels almost all life on Earth. Photosynthesis uses sunlight, water and carbon dioxide to make sugars and other molecules plants need. But in dry or hot environments, the dual requirements for water and carbon dioxide present a dilemma: To let carbon dioxide in, plants must keep open small pores on their leaves. But those same pores also let water vapor out. When it’s hot and dry, that can lead to deadly water loss, inefficient photosynthesis or both. Many plants that are adapted to dry environments have water-saving traits, including fleshy leaves. Orchids, pineapple, agave (shown above) and sedum are among the plants that have also tweaked the process of photosynthesis such that water loss is minimized. Wolfgang Kaehler/LightRocket via Getty Images Photosynthesis happens in two main stages, however, and that provides an opening for scientists to work with. In the first part of photosynthesis, called the “light reactions,” the plant captures photons from the sun. The main point of this stage is to create energy-storing molecules that will fuel reactions in the next step. It’s akin to filling up a tank of gasoline so you can be at the ready. The second stage of the process, the “dark reactions,” doesn’t require light. An enzyme called rubisco grabs carbon dioxide that has entered the leaf and attaches it to a molecule known as RuBP. The sunlight’s energy that was captured and stored earlier is used to fuel reactions that create a simple sugar from the carbon. The plant can use the sugars to make more complex molecules. This version of photosynthesis is how 85 percent of all plants do things, including most trees and most major food crops—rice, wheat, soybeans and more. Such plants are referred to as C3 plants because they make a three-carbon molecule in one of the first steps of photosynthesis. Although only the first part of photosynthesis requires light, in most plants both parts of the process—including grabbing CO2—happen at the same time, while the sun is shining. If it gets hot, the pores in the leaf either remain open and lose water, or close and shut off access to CO2 in the air. If the pores close, the concentration of CO2 inside the leaf drops, so there’s less CO2 for photosynthesis. Worse still, it can really gum up the works—because the enzyme rubisco starts grabbing oxygen instead. This kicks off a wasteful process called photorespiration, during which the plant has to throw out some of the carbon it’s painstakingly collected. Photorespiration can cut the efficiency of fixing carbon by 40 percent, stunting the plants. Photosynthesis happens in two main stages, but only one requires light. The light-dependent reactions (left) generate high-energy molecules that fuel the second stage, the dark reactions (right), in which carbon dioxide is converted into sugars. In many plants, both sets of reactions are carried out during the day. But some plants do the dark reactions only at night, collecting carbon dioxide when it is relatively cool out, which helps prevent water loss from leaves. Plants have figured out two slightly different ways to get around the problem, and scientists are hoping to exploit both of them. Some plants use a process called Crassulacean acid metabolism, or CAM: They take in CO2 during the night, while it’s relatively cool, and concentrate and store it until it can be used during the day to make sugars. Other plants—known as C4 plants—concentrate and store carbon dioxide in specialized cells, thus avoiding the wasteful photorespiration. In both cases, these plants have separated the part of photosynthesis that captures carbon dioxide from the air from the part of the process where rubisco grabs the CO2 and begins the process of turning it into a sugar. CAM plants separate the processes according to time of day, and C4 plants separate them physically in different parts of the plant. The adaptations help plants in two different ways. In the first place, they save water, letting the plant make do with less. Just as important, by limiting the wasteful effects of photorespiration, they let the plants grow bigger from the same amount of nutrients. The CAM strategy CAM got its name from Crassulaceae, the family of succulent plants in which it was first observed. The strategy with its extra step evolved starting some 20 million years ago. CAM plants open the pores in their leaves, called stomata, at night, when it’s relatively cool. Then, instead of using rubisco, the CO2-grabbing enzyme that C3 plants rely on, CAM plants use an enzyme called PEP (or phosphoenolpyruvate) to capture CO2. Unlike rubisco, PEP is very specific to CO2 and won’t take hold of oxygen. The plant then converts the CO2 to a chemical called malate and tucks it away for the night in a cellular closet called a vacuole. When the sun comes up, CAM plants can close their stomata to conserve water, because they’ve already got carbon stashed away in the vacuole. That carbon can now be converted back to CO2 and used by rubisco to build the molecules the plant needs. The carbon dioxide that’s needed for photosynthesis enters plants via pores on their leaves. Most plants use C3 photosynthesis (left) in which the enzyme rubisco (orange) grabs carbon dioxide and sends it down the photosynthesis assembly line. But water can escape from the same pores that let in the CO2. Some plants get around this by keeping their pores closed during the heat of the day. These CAM plants (middle) employ a different enzyme, PEP carboxylase (pink), to grab the carbon dioxide. It’s converted to a storable form, malate, and then turned back into carbon dioxide and passed on to rubisco during the day. A third strategy, C4 (right), keeps rubisco away from the plant pores and surrounded by carbon dioxide for efficiency's sake. Rubisco does its job in separate leaf cells, the bundle sheath cells. Many scientists think CAM is a promising target for engineering. Because CAM evolved independently many times in many different plants, there shouldn’t be a fundamental barrier to inducing the process in non-CAM plants, Katharina Schiller and Andrea Bräutigam write in the 2021 Annual Review of Plant Biology. In fact, CAM seems to rely on enzymes and other molecular machinery that are already found in C3 plants—they just use them in different ways at different times. That suggests it’s possible to repurpose already existing genes in normal plants to make them CAM plants. CAM’s complexities But that is easier said than done. To make a CAM plant, researchers would have to create biochemical pathways not only to make malate at night, but also to transport malate around the cell and then release the CO2 when the time is right. For now, scientists are still working to understand CAM well enough to control it. That has been painstaking work over many decades, and there are still unanswered questions. Much of today’s knowledge comes from studying the common ice plant (Mesembryanthemum crystallinum), which is able to switch from C3 metabolism to CAM. By studying the differences in the two metabolisms, scientists have been able to figure out many of the processes that have to kick in to make CAM work. And the devil is in the details. For instance, scientists had identified 13 enzymes and regulatory proteins that seemed to be involved in storing CO2 in the form of malate and then getting it back out again. To better understand the role of each of them, plant molecular biologist John C. Cushman of the University of Nevada, Reno, and his colleagues inserted the genes for each one into a non-CAM plant called mouse-ear cress (Arabidopsis thaliana, the lab rat of plant science). Then they measured how much of a difference each gene made. They also measured where in the cells the regulatory proteins and enzymes were put to work. Most of the genes involved in malate production would increase malate at least a little bit when turned on one at a time. And most of the ones involved in switching malate back to CO2 would decrease it, the team reported in 2019 in Frontiers in Plant Science. The effects of drought, seen here in a 2013 photo of a Texas soybean field, have become all too common as the climate warms. USDA photo by Bob Nichols via Flickr under CC BY 2.0 Cushman and colleagues have also focused on another feature of CAM plants: the thickness of their leaves. Many CAM plants have thick, fleshy leaves, a trait called succulence that helps them retain and store water (think of a cactus stem, or the leaves of a jade plant or orchid). The trait appears to be important, since succulence seems to make CAM more efficient, helping the leaf retain the stored CO2. Using genes from wine grapes that cause the fruit to become fleshy and ripen, the researchers have increased the succulence of mouse-ear cress, creating leaves that store more water than normal. With so many complicated mechanisms to be coordinated, there’s still a lot of work to do. Schiller and Bräutigam point out that it’s not enough to know what genes need to be turned on to get production of particular enzymes. The genes also need to be turned on in the right places and at the right times, and produce the right amount of proteins. “I would say, within five years, we should have a pretty good idea whether this is going to work or not,” Cushman says. Yang, at Oak Ridge National Laboratory, is optimistic that CAM engineering can work because evolution has come up with the same solution many times independently. Given enough time and effort, he says, synthetic biology and genome editing will be able to replicate the process. How corn does it Another approach to keeping photosynthesis humming along efficiently even when it’s hot and dry is to engineer C4 traits into C3 plants. Many of our cereal crops are already C4 plants, including corn, sugar cane and sorghum, and evidence suggests that the trait has evolved independently upwards of 60 times. (C4 is named after a characteristic four-carbon molecule produced by the plants during photosynthesis, compared with the three-carbon molecule produced by C3 plants.) Rubisco, the enzyme that grabs carbon dioxide during photosynthesis, will sometimes grab oxygen instead, gumming up the photosynthesis assembly line. C4 plants (right) prevent this by keeping rubisco sequestered in bundle sheath cells, the blue, wreath-like rings at the center of the leaves in this simplified diagram. In ordinary C3 plants (left) rubisco is found in mesophyll cells and is the first enzyme to grab carbon that enters the leaf. C4 plants also convert CO2 to storage-friendly malate before sending it down the assembly line to make sugars. And C4 plants have evolved a particular leaf anatomy: They pack two types of leaf cells—mesophyll cells and bundle sheath cells—in concentric circles. Carbon dioxide enters the mesophyll cells, as it does with C3 plants. But in C4 plants, the enzyme rubisco is sequestered only in the bundle sheath cells. This arrangement keeps the enzyme surrounded by CO2 and away from oxygen, thus minimizing wasteful photorespiration. The pores of C4 plants don’t do the open-only-at-night trick, and the plants are generally less water-efficient than CAM plants, although still twice as efficient as C3 plants. Their big advantage is that by sequestering rubisco in the bundle sheath cells, they cut down on photorespiration. If rice was turned into a C4 plant, “Models predict that yield could increase by 50 percent; water use efficiency would be hugely improved, as would nitrogen use efficiency,” says Jane Langdale, a geneticist at the University of Oxford in the U.K. who leads the C4 Rice Project, a long-running effort of several research groups funded by the Bill and Melinda Gates Foundation. Two years ago, researchers with the project introduced five genes from corn into a rice plant. These five, they figured, were the minimum number necessary for the basic reactions: Get the CO2 turned into malate and then back into CO2 again. All of the genes yielded the proteins they were intended to, and the rice plants suffered no harm. What’s more, the altered rice did create malate. But it did not convert the malate back into CO2, and researchers are still trying to figure out why. “That’s the major focus of what’s being looked at, at the moment,” Langdale says. Still, the work was enough to convince Langdale and her colleagues that they can get portions of C4 metabolism working in rice. At a minimum, they would be happy to have C4 photosynthesis working alongside C3 photosynthesis. CAM vs. C4 throwdown Although the C4 and CAM approaches share similarities, they have different strengths and weaknesses. CAM is relatively simpler, since you don’t have to arrange the leaf cells in the special C4 way. And because many existing plants have both C3 and CAM characteristics, there’s reason to think that even partial CAM pathways will be a benefit to plants, Cushman says. On top of that, CAM is more water-efficient. On the other hand, C4 is more likely to create big gains in crop yields while also increasing water use efficiency compared to C3 plants, Langdale says. “CAM has never evolved to increase yield, or biomass. CAM has evolved as a survival mechanism under severe stress conditions,” she says. “So I don’t think you'd ever want to put CAM in to increase yield. But you may want to engineer CAM to use in marginal lands, for example.” It’s even possible that you could do both: engineer CAM traits into C4 plants like corn to make them even more efficient at using water, Cushman says. In both cases, it’s not clear yet whether commercial crop plants are possible. Yang says that it’s evident CAM can be engineered into C3 plants, but it remains to be seen whether useful crops will result. If they can, he estimates it will be about 10 years before they are available. “First step is, can we do it? I think yes,” he says. “But then can we optimize it? … That’s the next question.” The C4 Rice Project, for its part, gathered momentum in 2006 with the understanding that it would be a long-term effort requiring a lot of basic research. According to the original timeline, it’s not until 2039 that the project expects to hand a working C4 rice plant to commercial breeders. In the current phase, the researchers are trying to create a prototype of rice that displays basic C4 characteristics, and it’s likely to be four or five years more before they know for sure whether C4 rice will work. They need to figure out how to get the plant to change malate back into CO2, and they would like to be able to increase the size of cells around the veins in the leaf as a step toward specialized bundle sheath cells, among other things. “It’s really hard to predict. We feel like we’re sort of on the bleeding edge of the technology development all the time,” Langdale says. “And so what that means is, we take two steps forward, one step back, two steps forward, one step back—which is part of the excitement, but also part of the frustration.”Knowable Magazine is an independent journalistic endeavor from Annual Reviews. Botany Climate Change Farming Food Food Science Genetics Plants Sustainability Recommended Videos | Biology |
Image source, OceanXImage caption, The reef is mostly made of hard red algae, providing an attractive habitat for marine life such as this moray eelScientists say a unique reef habitat near the mouth of the Amazon river is under threat from plans to drill for oil. The reef was discovered in 2016, and researchers say it could contain many unknown species of medicinal or scientific value.The Amazon reef is unusual because it lies in deep water, and is sometimes hidden by the muddy waters flowing into the sea from the world's largest river.Its depth - up to 220m (725ft) and the strong currents in the area mean that it has been little studied since it was discovered."It's a very wide area, there are things that we don't know yet," says César Cordeiro, a professor at the Center for Biosciences and Biotechnology at the University of Northern Rio de Janeiro."There are species that may be appearing only in that area and nowhere else in the world."One is a sponge currently being studied at the University of São Paulo, which has shown signs of possessing anti-cancer properties."There is great potential for economic gain with the study and protection of these systems," says Rodrigo Leão de Moura, professor at the Institute of Biology at the University of Rio de Janeiro and the leading scientist involved in the reef's discovery."Of course, we have this immediate need for cheap energy, but how much does this sacrifice a future based on biotechnology?"The scientists worry that plans by the Brazilian oil company Petrobras to drill for oil close to the reef could cause an oil leak that would devastate the ecosystem.Petrobras is planning this month to carry out a test to learn more about how oil would be dispersed in the case of a leak. If that satisfies Brazil's environmental protection agency, Ibama, exploration wells could follow soon afterwards, 160km (100 miles)from the shore, but much closer to the reef.Brazilian Environment Minister Joaquim Leite - a member of the outgoing government appointed by President Jair Bolsonaro - has said it is possible to explore for oil there and protect the environment, but Prof Moura has doubts."This area has one of the strongest currents on the planet and a tidal range that can be greater than 10m (33ft). These are environmental conditions that challenge any engineering work, making it very risky," he says.Many reefs occur in shallow water, where the sun provides abundant energy for corals to grow.This one is different. It is deeper and gloomier, and is mainly composed of hard red algae capable of carrying out photosynthesis - the process by which plants turn sunlight, water and CO2 into carbohydrates and oxygen - in low-light conditions."They are red algae that use light in a more filtered way - they use the blue spectrum of light," says Prof Moura.Image source, PceanXImage caption, The reef is deep and lies below murky water flowing out of the AmazonThe algae are hard because they contain a chalk-like substance in their cell walls, and this allows large solid structures to grow over time. The reef is thought to cover an area of 56,000 sq km (22,000 sq miles) and to shelter many different sponges, some corals, and at least 70 species of fish, shrimp, and lobster. These in turn provide a source of food and income for thousands of families on the Brazilian coast, some of whom are also concerned about Petrobras's plans.Fisherwoman Darcirene Garcia worries that the disturbance created by the oil company's ships will drive fish away: "They will go further out, and in our small boats we will not be able to go after them."An oil spill that hit the coast of northern Brazil in 2019 also casts a long shadow. Tons of thick black crude began washing up at a thousand locations, and brought the tourism industry to a halt. Overnight the biggest market for locally caught fish disappeared. Other buyers stopped buying too, for fear of contamination, so sales fell by 80% or 90% says Carlos Pinto, of the seaworkers' union, Confrem.Image source, Getty ImagesImage caption, Oil washed up along Brazil's northern coast in 2019Darcirene Garcia took part in a meeting with Petrobras on 8 November, along with other members of the fishing community in Brazil's most northerly town, Oiapoque."It seemed to be ready-made answers," she says. "Whatever we asked, their answer was always: 'It is too far from the coast.' At the end of the meeting, the fishermen shouted together, saying that they were against the drilling, but they didn't say anything." Petrobras says it is holding meetings with communities that could be affected by the project, in order to "clarify doubts and expectations".Oil discoveries along the coast of countries to the north-east - Suriname and Guyana - have heightened expectations of important oil reserves off the Brazilian coast.Petrobras signalled on 1 December that Brazil's northern coast would be a priority over the next five years, attracting half of the company's $6bn exploration budget over this period. But it is unknown whether the incoming government of President Luiz Inácio Lula da Silva will back the plan to drill near the reef.His party's spokesperson on the environment has indicated her opposition, but the last time Lula was in government he relied on the revenue from oil finds in the Santos Basin south of Rio de Janeiro to fund social programmes.Image source, Rede Abrolhos, F Moraes and R MouraImage caption, The reef helps to ensure an abundance of fish on Brazil's north coastProfessors Rodrigo Moura and César Cordeiro see the reef's biodiversity as one of its main benefits, but also point out others. One is that it provides a more sustainable source of income than many other local industries."If people cannot fish, they will have to find another source of income, and what is there in the Amazon to do?" Prof Moura asks. "Hunting, deforestation, opening of pastures, migration to forest areas?"Another is that it operates as a carbon sink. The hard cell walls of the algae contain calcium carbonate, Prof Cordeiro points out, thus helping to remove carbon from the atmosphere for an indefinite period. | Biology |
In the fight against warming, a formidable ally hides just beneath our feet. Toby Kiers, evolutionary biologist, taking soil samples beneath one of the oldest trees in the world. Climate correspondent Somini Sengupta and photographer Tomás Munita reported from Chile on scientists building a global atlas of underground fungal networks. July 27, 2022 — Toby Kiers took long strides across the spongy forest floor, felt the adrenaline rush in her veins and stopped at the spot she had traveled so far to reach. Into the ground went a hollow metal cylinder. Out came a scoop of soil. Dr. Kiers stuck her nose into the dirt, inhaled its scent, imagined what secrets it contained to help us live on a hotter planet. “What’s under here?” she asked. “What mysteries are we going to unveil?” The soil was deposited into a clear plastic bag, then labeled with the coordinates of this exact location on Earth. Dr. Kiers, 45, an evolutionary biologist based at the Free University of Amsterdam, is on a novel mission. She is probing a vast and poorly understood universe of underground fungi that can be vital, in her view, in the era of climate change. Some species of fungi can store exceptional levels of carbon underground, keeping it out of the air and preventing it from heating up the Earth’s atmosphere. Others help plants survive brutal droughts or fight off pests. There are those especially good at feeding nutrients to crops, reducing the need for chemical fertilizers. In short, they are what she called “levers” to address the hazards of a warming climate. Dr. Kiers, right, mapping an area for soil sampling with Merlin Sheldrake. Dr. Kiers and Dr. Sheldrake inspecting fungus. Yet they remain a mystery. Dr. Kiers wants to know which fungi species are where, what they do, and which should be immediately protected. In short, she wants to create an atlas of all that which we cannot see. And all that is right under our feet. “It’s seeing Earth’s metabolism,” she said. “Who is there? What is their function? Right now, we are concerned so heavily on the overground, we are literally missing half the picture.” By one estimate, 5 billion tons of carbon flow from plants to mycorrhizal fungi annually. Without help from the fungi, that carbon would likely stay in the atmosphere as carbon dioxide, the powerful greenhouse gas that is heating the planet and fueling dangerous weather. “Keeping this fungal network protected is paramount as we face climate change,” Dr. Kiers said. In addition, the biodiversity of underground fungi is a huge factor in soil health, which is crucial to the world’s ability to feed itself as the planet warms. Specific knowledge of the power of these networks, said Tim G. Benton, a biologist at Leeds University who isn’t involved in Dr. Kiers’s work, is “very patchy.” “More information would be very valuable,” he said. Yet so little is known about fungi that they are not even counted in the Convention on Biodiversity, the global treaty aimed at protecting nature. That treaty is aimed at plants and animals. Fungi are neither. They make up a separate kingdom of life altogether. Underground, mycorrhizal fungi are crucial trading partners. Trees crave the nutrients they offer. Fungi gobble up the carbon that trees provide in return. To understand this kingdom, fungi aficionados argue, is to see the natural world differently — less as a collection of individual species, with humans dominating them all, and more as a web of organisms dealing with crises together. The origin of life Fungi made the world as we know it. As some of the first life forms on the planet, they consumed minerals locked in rocks, creating what we now know as soil. Without them, there would be no plants on land, and therefore, no animals. No us. Dr. Kiers’s expedition to southern Chile aims to fill in some of the gaps in knowledge about fungi, specifically the mycorrhizal fungi that live symbiotically with plant roots and drive carbon into the soil. That is what gives them such an urgent role on a hotter planet. “Mycorrhizal networks,” Dr. Kiers said, “are a major global carbon sink.” The expedition was shaped by Big Data. With the help of scientists in Switzerland, an algorithm had crunched all kinds of above-ground information — temperature, soil moisture, types of trees — and predicted where in the world Dr. Kiers might find high and low levels of underground fungal biodiversity. Then it offered coordinates, as if to say, “Go here, take a soil sample, see if I’m right.” For their first expedition, in Chile, the researchers arrived at each location, pinpointed by the algorithm, drew a grid 30 by 30 meters, collected spoonfuls of soil, bagged it and sent it to a local lab for genetic analysis. “Once we know who’s there, we can see what they’re good at,” Dr. Kiers said. Her partner on this expedition was Giuliana Furci, a Chilean environmentalist who, as the head of the Fungi Foundation, an advocacy group, successfully lobbied to include fungi for protection under Chilean environmental law. Also on the expedition was the biologist and writer Merlin Sheldrake and his musician brother, Cosmo, who stuck microphones into the earth to record the sounds underground. Sometimes he captured the noise of gurgling liquids or the scratching, marching busywork of invisible organisms. Other times, just the thud of the researchers’ boots nearby. Cosmo Sheldrake, seated, shared a recording. Giuliana Furci, in red, smelled the soil. They scooped soil from under a volcano, crisscrossed pine and eucalyptus plantations, bushwhacked through brambles, climbed up rocks jutting into the Pacific, coaxed homeowners to let them onto their properties to take a bit of dirt. They rescued an injured parrot one day and a lost hiker on another. Sometimes, the algorithm led them to peaceful places, where Dr. Sheldrake said the “zen factor” was high. Other times, not so much. One day, they walked into a rainforest full of leeches. Every day, they smelled the soil they sampled, declared their verdicts. Ms. Furci: “Peppery.” Dr. Kiers: “Kind of pondish.” Dr. Sheldrake: “Bit farty.” Each sample, representing one square kilometer of land, would be used to identify the genetic properties of fungal species that were storing particularly high levels of carbon in the dirt, or which species might help trees adapt to drought. Dr. Kiers said she aimed to collect 10,000 samples over 18 months. Mushroom whisperer “Volva. Volva!” Ms. Furci yelled in excitement. In her hand she held a thing that looked like an egg cup from which a mushroom had emerged, pale and cloudy like milk — a volva. “A native amanita,” she said, smiling. “Look at the volva. Volva. With an O.” Mushrooms are the above-ground avatars of the fungi kingdom, but they represent a fraction of the fungal web underground. Ms. Furci spots them everywhere. Concealed on the forest floor, wrapped around fallen twigs, attached like luminescent clams on branches. You have to be there in the brief window of time when they are visible. “All mushrooms are magic,” she said. There’s just a brief window of time when mushrooms are visible. “All mushrooms are magic,” Ms. Furci said. Ms. Furci was born and raised in England, where her mother, a political dissident, lived in exile during the dictatorship of Augusto Pinochet. She came to Chile when her mother returned home, and, a few years later, had what she calls “an encounter.” She saw a striking, rust-orange mushroom in a forest (she later learned it was part of the gymnopilus family) and wanted to know more. An obsession began. Since then, Ms. Furci has written guidebooks on fungi and named unnamed species (a pitch-black mushroom with white scales she called “galactica”). She has helped persuade the International Union for the Conservation of Nature to include fungi as a category to protect, alongside flora and fauna. When asked what fungi do, or how they behave, Ms. Furci became visibly annoyed. Their vast biodiversity is not only under-explored, she said, they are misunderstood. They are thought to be just one thing, but they are not. “A morel and a button mushroom are as closely related as a flea and an elephant,” she said. In the course of a day, she identified nine different mushrooms. One resembled a hamburger bun top. Another, a witch’s hat. The colors ranged from vanilla to deep raspberry to the speckled back of a fawn. By the end of a brief trek, she had scooped up two fistfuls of lactarius deliciosus, which grew abundantly alongside the pine trees planted there to harvest timber, one of Chile’s main exports. Without this fungi, Ms. Furci pointed out, pines wouldn’t survive. For dinner that night, the lactarius were sautéed in butter. An old tree’s oldest friends Dr. Kiers grew up in small towns in Connecticut and Maine. Her parents sent her out with her sister to collect morels in summer. The underground became her passion. She studied biology at Bowdoin College, worked at a research station in Panama and earned her doctorate at the University of California, Davis. She co-founded a nonprofit advocacy group, the Society for the Protection of Underground Networks. One Thursday afternoon recently, Dr. Kiers walked through a dark, gnarly rainforest with a fellow underground fungus scholar, César Marín, from the Universidad Santo Tomás in Chile. How many did you sample so far, Dr. Marín asked. “Fifteen,” Dr. Kiers said. Far fewer than she had hoped to. “It always happens,” Dr. Marín replied. “I knew you’d understand,” said Dr. Kiers. Taking soil samples is time-consuming, tedious work. Drive for hours. Walk for hours. Bushwhack. Squish around in bogs. Gather a spoonful of dirt. Do it all again. They were walking in an extraordinary place. A very old, very slow-growing rainforest, this section of the forest potentially holds some of the largest and oldest stores of carbon on Earth. It is home to one of the oldest trees on Earth, a massive Fitzroya, or alerce in Spanish, estimated to be at least 3,500 years old, known here as the great-grandfather alerce. Dr. Kiers said the data they collect here will signal which mycorrhizal fungi species are doing the work of sequestering so much carbon underground. Soil sampling beneath the ancient tree. Cosmo Sheldrake Fungi are sensitive to human activity. Chemical fertilizers diminish their volume and diversity. Logging destroys them. Climate change is the latest stressor, which is why Dr. Marín was keen for Dr. Kiers to sample the same three plots he had tested seven years ago. He wanted to know if the megadrought that has been melting Chile’s glaciers over the past few years has also changed the mycorrhizal networks underground. Fungi have helped trees adapt on a millennial scale. They could be crucial to helping trees adapt in the climate crisis. “In difficult times, organisms find new symbiotic relationships in order to expand their reach,” said Dr. Sheldrake, the biologist. “Crisis is the crucible of new relationships.” They walked briskly. Fern fanned out in the understory, along with canelo trees, bamboo, and tall, slender alerce, for which this park is named. Dr. Kiers approached the great-grandfather tree in silence. She took off her hiking boots, walked gently around the fragile roots. Cosmo Sheldrake took out a pennywhistle and played. The tree stood 30 meters tall. Its craggy trunk was half dead. Hundreds of fungal species are associated with its root system, Dr. Marín said. Being near it, Dr. Kiers said, felt “dizzying.” “Wouldn’t you want to know about this healthy partnership that’s lasted 5,000 years through so many changes?” she said. It was clearly a rhetorical question. A mushroom rises from the forest floor. Roots rise from shallow soil. On the last Friday evening of their weeklong expedition, they hiked to a rocky outcropping on the coast. “Zen factor is high,” Dr. Sheldrake said. An otter played in the water. The sun shone golden on the lapping waves. Some of the boulders were dotted with lichen the color of marigold. As they have for millennia, Dr. Sheldrake observed, fungi were eating rock. By the end of this one-week outing, they had collected 30 bags of soil. Nearby, over the next several weeks, Dr. Marín’s team would gather 64 more. It’s a drop in the bucket, considering the thousands needed to construct the global map they envision. This week, Dr. Kiers is on the other side of the world, in the Apennines, the mountain range in Italy. North of the place she planned to collect samples, a glacier has collapsed. Wildfires rage nearby. “This is a race against time,” she said in an email. “We are nervous these fungal communities are disappearing before we can even document who is there.” | Biology |
Just a few swabs from a handful of leaves can say a lot about what animals are roaming in the area.
Two dozen leaf swabs from plants in Uganda’s Kibale National Park revealed a stunningly accurate genetic picture of the park’s vertebrate diversity, researchers report in the Aug. 21 Current Biology. The swabs picked up environmental DNA, or eDNA, shed from 52 animals, 30 of which could be identified to the species level. The quick and easy technique is a potentially revolutionary way to monitor biodiversity.
“The fact that they could just swab a few leaves like that and get that many species is really kind of cool and remarkable,” says Julie Lockwood, a biologist at Rutgers University in New Brunswick, N.J., who was not involved with the study.
While we often picture DNA sitting safe and snug inside of cells, the truth is that particles of the genetic material are loose all over the environment. This eDNA often collects in “pools” in bodies of water or on surfaces like tree bark. Finding and analyzing eDNA can reveal what species are in an area — even those that are hard to spot.
Jan Gogarten, a biologist at the University of Greifswald in Germany, wanted to compare his eDNA source — flies that pick up DNA from dead animals and feces — with that of biologist Christina Lynggaard, who collects eDNA from the air (SN: 1/18/22). The two set out to compare their respective techniques in Kibale, but setting up the necessary air filters was time-consuming, so after collecting his flies, Gogarten decided to swab some nearby leaves while he waited.
“It was not something that we had planned before,” says Lynggaard, of the University of Copenhagen.
All the swabbing in the study, done across three areas of the park, took 72 minutes in total—an average of three minutes per swab. For comparison, Lynggaard ran air filters to collect eDNA for a minimum of 30 minutes each in a prior study, not including time to set up and clean the apparatus. The researchers then brought the swabs back to Denmark for analysis.
The eDNA turned up many charismatic birds and mammals that are known to live in the park, including the great blue turaco (Corythaeola cristata) and the African bush elephant (Loxodonta africana), but there were a few surprises too.
Colin Chapman, another collaborator on the project and a biologist at Vancouver Island University in Nanaimo, Canada, “has been working in the forest for 30-something years,” Gogarten says, “and he had bird species on the list that he hadn’t seen before,” but have been spotted in the park by others. “There’s a lot out there that we just don’t see” that can be revealed with eDNA.
What’s more, the swabs are more convenient to travel with compared with other sampling devices. Lockwood, for example, samples eDNA from plant surfaces using paint rollers. With the smaller swabs, she says, “you can just use established forensic techniques to save the swabs and get them out of the field and take them back to the lab.”
With biodiversity declining in many areas around the globe, sampling eDNA using techniques like leaf swabs “allows us a revolutionary step forward in our ability to document those changes and respond to them,” Lockwood says (SN: 9/4/20). “There’s not one tool for gathering the eDNA and processing everything that works in every case. So the more tools we have, the better off we are.”
Gogarten and Lynggaard hope that others will take their swabbing technique and run with it. Because the method “can be used by nonscientists,” Lynggaard says, “people interested in citizen science could … help researchers fight this biodiversity loss that we’re having worldwide.”
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For example, schoolchildren armed with swabs, Gogarten says, could sample leaves in their backyards and produce a picture of their own area’s biodiversity. | Biology |
Reference
A recent study by Japanese researchers, published online in Microbiology Spectrum on 6 July 2023, has now provided the answer. By using primary B cells from healthy donors instead of cell lines, the team uncovered the genetic machinery responsible for inducing growth transformation following EBV infection. Explaining the rationale behind the study, principal investigator Prof. Takayuki Murata commented, “Insights from EBV research that uses cell lines has been limited, because cell lines are already in an immortalized state. To overcome this roadblock, we used primary B cells from healthy donors and then infected them with EBV. This allowed us to monitor the step-by-step growth transformation of B cells and analyze the mechanisms involved.”
The first step involved the careful observation of primary B cells infected with wild-type EBV using electron microscopy and immunostaining. As early as two days after infection, the morphology of B cells showed significant alterations. An enlargement of the nucleolus (a region within the nucleus that produces ribosomes, the cell’s protein-producing machinery) was observed, along with an increase in the number of nucleoli. Interestingly, nucleolar enlargement was followed by an enlargement of both—the nuclei and the cells.
To understand the transcriptional changes that occurred in infected B cells, RNA sequencing was performed. “Among the genes showing significantly altered expression levels, one named IMPDH2 stood out, as it had previously been linked to similar morphological changes in glioblastoma (another type of cancer). Careful analysis showed that the levels of the IMPDH2 peaked two days after infection—coinciding with the timing of nucleolar enlargement. This suggested that we were on the right path,” explained Dr. Atsuko Sugimoto from Fujita Health University School of Medicine, who was also a part of the research team.
Interestingly, changes such as IMPDH2 induction and nucleolar enlargement could be seen when primary B cells were activated using inflammatory signals, even in the absence of EBV infection. Finally, the inhibition of IMPDH2 using silencer RNAs and the drug mycophenolic acid (MPA) prevented the growth transformation of primary B cells after EBV infection, producing smaller nucleoli, nuclei, and cells. This confirmed that IMPDH2 induction played a key role in the growth transformation of EBV-infected B cells.
The next step involved understanding how EBV activates IMPDH2 expression. Three key viral genes—EBNA2 and LMP1—were tested because of their known role in EBV-induced B cell transformation. Interestingly, when EBV lacking EBNA2 was used for infection, IMPDH2 induction following primary EBV infection was blocked. This effect was not observed with LMP1 knockout. “This very clearly demonstrated that EBV induces IMPDH2 expression via EBNA2
-dependent mechanisms. In addition, cellular transcription factor MYC was also involved in the IMPDH2 induction,” clarified Dr. Sugimoto.
With several key pieces of evidence on their plate, the researchers finally set out to find the final piece of the puzzle. To highlight the clinical significance of their findings, they examined whether the drug mycophenolate mofetil (MMF) could prevent B cell transformation and PTLD. Prof. Murata elaborated, “Like MPA, which we tested in the earlier part of our study, MMF is an IMPDH2 inhibitor. More importantly, MMF is already a clinically approved immunosuppressant. That is why it was useful to test if it could be applied for the clinical prevention of PTLD.” As expected, the administration of MMF in a pre-clinical mouse xenograft model led to improved survival and reduced splenomegaly (enlargement of the spleen, indicating reduced B cell proliferation). These observations confirmed that the use of MMF can inhibit PTLD development.
This study is the first to demonstrate that IMPDH2 activation and nucleolar hypertrophy are essential for EBV-induced B cell transformation and that IMPDH2 inhibition can suppress PTLD. It could lead to the adoption of MMF as an agent for the prevention of EBV-positive PTLD, providing significant relief to transplant patients.
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About Fujita Health University
Fujita Health University is a private university situated in Toyoake, Aichi, Japan. It was founded in 1964 and houses one of the largest teaching university hospitals in Japan in terms of the number of beds. With over 900 faculty members, the university is committed to providing various academic opportunities to students internationally. Fujita Health University has been ranked eighth among all universities and second among all private universities in Japan in the 2020 Times Higher Education (THE) World University Rankings. THE University Impact Rankings 2019 visualized university initiatives for sustainable development goals (SDGs). For the “good health and well-being” SDG, Fujita Health University was ranked second among all universities and number one among private universities in Japan. The university became the first Japanese university to host the "THE Asia Universities Summit" in June 2021. The university’s founding philosophy is “Our creativity for the people (DOKUSOU-ICHIRI),” which reflects the belief that, as with the university’s alumni and alumnae, current students also unlock their future by leveraging their creativity.
About Professor Takayuki Murata from Fujita Health University
Prof. Takayuki Murata is a Professor at the Department of Virology, Fujita Health University School of Medicine, Japan. He completed his PhD in Medical Sciences from Nagoya University. He is a leading expert in the fields of virology and tumor biology research, with a focus on the Epstein-Barr virus, Hepatitis B virus, and SARS-CoV-2. He is a member of the American Society for Microbiology and the Fujita Medical Society. In his long and illustrious scientific career, he published more than 100 studies and received several prestigious research grants.
Funding information
This work was supported by grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (20H03493 to H.K.), the Japan Society for the Promotion of Science (22K10520, 21J40038 to A.S.), the Japan Agency for Medical Research and Development (JP20wm0325012 to T.M., T.W., Y.O., Y.S., and H.K. as well as JP21wm0325042 to A.S., Y.S., H.K., and T.M.), the Takeda Science Foundation (to T.M.), a Nihon Shinyaku Research Grant (to A.S. and T.M), and the Chemo-Sero-Therapeutic Research Institute (to H.K.).
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Sex is a tricky business, evolutionarily speaking. One problem is that sexually reproducing organisms must suffer the considerable faff of securing a mate (for the males of some species, the struggle to do so can be fatal). Another is that the mixing of two genomes into one offspring means that, per child, each parent gets only half its genes into the next generation rather than the full complement.
The fact that it is nonetheless widespread suggests that sex must have big advantages, too. One concerns genetic variety. In asexually reproducing species, the only source of variation is mutation. Sex, by contrast, produces genetically unique individuals every time. That may increase the chance that at least some survive a disease, or a change in environmental conditions, that prematurely kills the others.
Some animals, though, like to have things both ways. American crocodiles, for example, usually reproduce sexually. But in a paper published in Biology Letters on June 7th, a team led by Warren Booth, an entomologist at Virginia Polytechnic Institute and State University, show that this is not always true. It seems that female crocodiles can, under some conditions, reproduce via “parthenogenesis”—the production of fertile eggs without the involvement of a male.
The female crocodile in Dr Booth’s paper lives in a Costa Rican reptile park. Now 18 years old, she was obtained by the park at the age of two, and has been kept by herself ever since. The park staff were therefore surprised when, in 2018, she laid a clutch of 14 eggs. When workers examined the eggs—by holding them in front of a bright light, giving a murky view of the contents—seven appeared to be fertile.
Intrigued, the park incubated the fertile eggs. None hatched. Six contained embryos that had died early in their development. But one contained a fully developed crocodile fetus that was almost ready to hatch. The mother, it seemed, had given parthenogenetic reproduction a go, and very nearly succeeded.
Parthenogenesis is fairly common. Some insects, scorpions and worms, among others, are known to do it. But it was thought to be rare among vertebrates. That assumption, though, is changing. In the 1950s turkey farmers discovered that some of their hens had laid viable eggs despite never having had access to males. Lizards and snakes were added to the list in the 1960s and 1990s respectively. In 2021 researchers monitoring the critically endangered California condor noticed that some of the birds lacked genes from the males that were supposed to be their fathers.
Crocodiles are the newest members of the vertebrate-parthenogenesis club. Its growing membership raises questions about just how widespread the ability might turn out to be. Despite their differences crocodiles, lizards, snakes and birds (which are descended from dinosaurs) are all members of the clade Reptilia. The evolutionary distance between those species suggests the ability is an ancient one. Might that mean that other members of Reptilia—turtles, for example, or chameleons—could have it too?
© 2023 The Economist Newspaper Limited. All rights reserved.
From The Economist, published under licence. The original content can be found on https://www.economist.com/science-and-technology/2023/06/07/reproduction-without-sex-is-more-common-than-scientists-thought | Biology |
Hyenas inherit power from mothers, but it's a privilege they pay dearly for, finds 30-year study
In some monarchies, inherited power offers a ladder that can be ascended to absolute authority—be it through diplomacy, ruthlessness, or the passing of time. But in hyena monarchies, inherited power is a slippery downward slide. A study from the Max Planck Institute of Animal Behavior examined hyena societies over three decades. They found that the process by which hyenas inherit rank from their mothers—known as maternal inheritance—corrodes the social status of individuals.
According to the study, now published in the journal Philosophical Transactions of the Royal Society B: Biological Sciences, every member of a hyena clan, except the highest-ranking queen, suffers downward mobility across their lifetime.
"It paints a pretty bleak picture of hyena societies," says Eli Strauss, a scientist at Max Planck Institute of Animal Behavior and sole author on the paper. "No matter what position you inherit, the only way is down."
Fair or not, hyenas haven't earned a reputation for regality, yet their societies bear a striking resemblance to human monarchies. Hyena clans are arranged in a linear dominance hierarchy, and offspring inherit their rank below their mother through a monarchy-like process. At the top of the hierarchy is the highest-ranked female—the queen—followed by her young, and then all other females with their young.
A hyena's place in the hierarchy matters a lot. "A lower rank means you have less access to food, you have to travel more to hunt, you are harassed more, you even have less time nursing your babies," says Strauss, who also holds a position at Michigan State University. For Strauss, the raised stakes in turn raised a fascinating question. If hyenas inherit their positions from their mothers, can they break rank and change status? Or, is the quality of a hyena's life pre-destined from birth?
To find out, Strauss tapped a remarkable database from the Mara Hyena Project, which has been studying spotted hyenas in the Maasai Mara National Reserve in Kenya since the late 1980s. Analyzing three decades of data on hyena behavior from four social groups, Strauss discovered that hyenas could indeed move up and down in the hierarchy over time, but they slid down much more often than jumping up. "You wouldn't think this downward mobility was happening if you were just observing the animals in the wild, because the process happens over many years," he says. "It's only by taking an intergenerational view that you realize that a daughter born to the alpha queen has suffered a significant downturn in status throughout the course of her life."
But what was causing the persistent downward trajectory? By digging into the life histories of all individuals, Strauss found that hyenas descended in rank most often because another hyena had joined or left the group. In other words, through simple demographic turnover. "It's tempting to imagine the intrigue and machinations of Game of Thrones, where animals are plotting to overthrow each other," he says. "But in hyena societies, an individual's power is passively eroded as other clan members are born or die."
Drawing on methods used to study social mobility in human societies, Strauss then created computer simulated hyena societies, where he could turn off various aspects of their biology. This allowed him to pinpoint the specific societal rules that were driving the unusual pattern. The simulation pointed to two sources: the monarchy-like inheritance of hyena societies and the fact that higher-ranking females also give birth to more offspring. These combined traits mean that new group members are not being added randomly.
"They are constantly being added to the top of the hierarchy, under the dominant females, which pushes all other individuals down over time," says Strauss. Of note, only the queen escaped this fate of slow decline in status over time, because it's not possible for anyone to inherit a position above her.
The work demonstrates how societal features can have an outsize influence on individuals, sometimes usurping an animal's own agency in altering the course of its life. Says Strauss, "It seems that no matter what a hyena does, they are going to experience a decline in rank over time. It's hard to fathom that they navigate lives in which everybody, but the queen, suffers a loss in quality. Clearly, they do succeed, so the next question is how."
More information: Eli D. Strauss, Demographic turnover can be a leading driver of hierarchy dynamics, and social inheritance modifies its effects, Philosophical Transactions of the Royal Society B: Biological Sciences (2023). DOI: 10.1098/rstb.2022.0308
Provided by Max Planck Society | Biology |
By Paul Jepson and Richard Ladl - University of OxfordWWF’s Living Planet report highlights a 58% decline in the abundance of 3,706 animal species since 1970, reinforcing the fear that humanity is bringing about a sixth mass extinction.The roots of this fear stretch back more than a century, when a series of well-publicised extinctions provided incontrovertible evidence that human actions could wipe out other life forms, even superabundant ones such as the passenger pigeon. These extinctions had a profound influence, and saving species has been a fundamental tenet of conservation ever since.What is less widely appreciated is that contemporary usage of the term extinction encompasses a wide variety of meanings and applications, each with a distinct role in conservation advocacy. In a 2008 paper we classified several different types of “extinctions” to better understand the rhetorical power of each, and to ask whether they reinforce or undermine conservation communication. Here’s an updated version of our list:True extinction is well summarised by the IUCN definition that there is “no reasonable doubt that the last individual [of the species] has died”. This category includes many iconic species such as the dodo, passenger pigeon, great auk and Steller’s sea cow. Here, extinction only refers to species that we know of: if not, how could the fate of a last individual be ascertained? Ecological extinction is where a species only survives in zoos and private collections. The Scimitar oryx, Spix’s macaw and the pheasant-like Alagoas currasow all fall into this category and are classed by the IUCN as “extinct in the wild”.Local extinction refers to when a species has been wiped out from part of its range. The beaver is a good example. Once common, it had been hunted to extinction in the UK by the 16th century but many people are now working to bring them back.Wallacean extinction is named after Alfred Russel Wallace, a contemporary of Charles Darwin who independently developed a theory of natural selection. It refers to species that are erroneously classed as extinct due to our ignorance of where they actually live – that is, species that are “lost” rather than extinct. The most famous example is the coelacanth, which was classed as an extinct fossil fish until a living specimen was found in 1938 off the east coast of South Africa. These rediscoveries are a continued source of hope for people trying to find animals like the Tasmanian tiger or the ivory-billed woodpecker. Linnaean extinctions, named after Carl Linnaeus who invented the system of scientific species names, involve the large discrepancy between the number of species described and the likely number out there. Here, extinctions are extrapolated from the rate of habitat loss for known and undiscovered species. This type of extinction underpins widely used estimates of tens of thousands of extinctions per year.Lazarus extinction refers to cases where there is still hope of resurrection because DNA of extinct species lives on in domestic breeds and a “replica” species could be recreated though back breeding. De-domestication is a component of European rewilding. Herds of wild cattle resembling the extinct Auroch in looks and ecology are being established in natural areas in the Netherlands, Portugal, Spain, Croatia, the Czech Republic and Romania. Closely related to Lazarus extinctions is the concept of de-extinction, the idea that advances in synthetic biology will eventually allow us to extract DNA from the preserved remains of extinct species and insert them into the eggs of surrogate animals. An elephant with mammoth-like traits may well be born within the next 20 years.Some ‘extinctions’ have more impact than others“Extinction is forever” was a rallying cry of the conservation movement during the 1960s and 1970s. Images of gorillas, tigers and rhino made extinction feel real and meaningful and reminded people of the sense of collective loss and remorse they would feel if these species died out.Fast forward several decades, and individual species no longer have such an impact. In September 2016, for instance, the death of the last Rabb’s fringed-limbed tree frog passed with little media comment.Since the 1990s conservation rhetoric has focused on the zoomed-out, planetary-scale Linnaean extinctions. Conservation International’s extinction clock presents the end of a species as a routine and impersonal event happening every 20 minutes. Why should one extinction be newsworthy if more than 26,000 are happening each year?Nevertheless, it was the spectre of mass extinctions that grabbed the attention of policymakers. While they may not have shed any tears for an individual tree frog species, they rightly feared the loss of economically-valuable ecosystem services. Governments responded with a massive and systematic expansion of protected areas internationally. However, the impact of “sixth mass extinctions” and other doom and gloom rhetoric may be on the wane, especially since the 2007 global economic crisis.A different tack might be needed: one that repersonalises extinction and balances stories of loss with stories of hope. This could be achieved by bringing local and Lazarus extinctions to the fore. Both of these can be tied to reintroduction projects that offer an optimistic sense that humanity can make amends for the ills it has inflicted on other life forms.We need to match reports of alarming declines in species with reports analysing places where populations can be restored. The idea that “extinction” is in some cases reversible certainly supports the new practice of ecosystem restoration. If conservation is to regain the initiative it needs to both protect what’s left, and restore what is lost.Source: The Conversation | Biology |
With a huge body, sharp claws, and dagger-like teeth, Tyrannosaurus rex would not have relied on looks to kill. But research suggests its eyes may have contributed to its bone-crushing bite.A study has proposed the keyhole-shaped eye sockets of T rex may have helped to disperse stress across the skull of the fearsome predator as it chomped on its prey.“They really had specialised eye socket shapes, which helped them deal with high bite forces,” said Dr Stephan Lautenschlager, a vertebrate palaeontologist at the University of Birmingham and author of the study.But, he added, the benefit to skull stability may have come at a cost, noting the T rex had relatively small eyes for the size of its skull.While Lautenschlager said that did not mean the T rex had bad eyesight, he said large eyes were associated with sharper sight.“There’s a bit of a trade-off between better vision, larger eyes, but higher stresses in the skull because of [a circular eye socket],” he said. Writing in the journal Communications Biology, Lautenschlager analysed the shape of the eye socket, or orbit, of 410 species that lived between 252m and 66m years ago, including dinosaurs, pterosaurs and the ancestors of crocodiles.His results reveal that while most of the species had circular eye sockets, some had orbits that resembled a keyhole or a figure-of-eight.“About two-thirds or three-quarters have the typical circular orbit and then the rest are deviating from that and doing something more extreme or more fancy,” said Lautenschlager.Lautenschlager notes the keyhole or figure-of-eight orbits were generally found among meat-eaters with large skulls, in particular big carnivorous theropod dinosaurs such as Tyrannosaurus rex.“There are a few groups within the theropods which have switched diet and adapted to a plant-eating or herbivorous diet. And those again have circular orbits,” said Lautenschlager. “So [orbit shape is] very closely linked to diet and size.”Lautenschlager used a series of computer models to explore the ramifications of the different eye socket shapes, finding that a circular orbit is associated with greater deformation of the bones around the eye socket during biting, and that key-hole or figure-of-eight shaped orbits helped to distribute stresses across the skull so they were not concentrated at one point.The study also proposes that circular orbits might limit the space for jaw muscles, and hence their volume, with Lautenschlager noting that could affect overall bite force.Lautenschlager said it was likely the non-circular eye sockets and high bite forces evolved in parallel.“Interestingly, you see that in juvenile T rex, they still have the perfectly circular or nearly circular orbits, because they didn’t produce that high bite forces presumably, or had slightly different diet, or different prey repertoire,” Lautenschlager added.Prof Steve Brusatte, a palaeontologist and T rex expert at the University of Edinburgh, who was not involved in the work, welcomed the study.“When you peer into the eyes of a T rex skull, the eye socket looks a little bit funny, kind of like a keyhole. And it seems small for an animal with a head the size of a bathtub,” he said.“This innovative new study shows that the eyes of T rex were shaped not only by the need for keen vision, but also by the need to bite strongly,” said Brusatte.“As weird as it seems, the eyes of T rex actually helped make it one of the strongest biters in Earth history.” | Biology |
About a decade ago, scientists observing clonal raider ants spotted something strange: Although the species is known to be queenless, a few ants were posing as queens of the colony, lording over their hardworking counterparts. These wannabe queens had wing stubs, as well as giant eyes and ovaries.
Researchers had long assumed that these "workerless social parasite" ants, which depend on other workers for survival, acquired these traits one by one, through a series of mutations. But now, scientists have discovered that a single mutation of a "supergene" can turn regular clonal raider ants (Ooceraea biroi) workers into lazy queenlike parasites.
"This was a shocking discovery," Waring "Buck" Trible (opens in new tab), an entomologist, John Harvard Distinguished Science Fellow and the lead author of the study in which the findings were published, told Live Science in an email. "The clonal raider ant is a queenless ant species, and no winged female adults have been observed in this species previously."
The pseudo queens are born with wings that they shed as adults, but they retain visible scars. They are the same size as worker ants, but their general indifference to labor such as brood care, foraging and nest defense makes them stand out in the colony.
The researchers isolated the parasites and found that their offspring also had wings, suggesting that the queenlike traits were genetic. They ran analyses to confirm this observation and discovered a mutation in a "supergene" on chromosome 13.
This single mutation may be the switch that turned clonal raider ants from the "wild type" usually found in nature into a mutant variant of the same species.
"That's actually really surprising, given that the parasites differ from the wild types in so many traits, including morphology [a segmented thorax], anatomy, and even behavior," Daniel Kronauer (opens in new tab), an associate professor and head of the Laboratory of Social Evolution and Behavior at The Rockefeller University in New York City, told Live Science in an email.
"What we describe here is a mutant strain that is extremely closely related to its wild type ancestors. So it's not really a different species, but maybe what could be considered an intermediate form," Kronauer added.
The researchers noted that the wannabe queens laid twice as many eggs as regular clonal raider ants. They can't let their numbers grow too big, however, because they need the workers. "When they become too common they run into problems," Kronauer said. The parasites catch their bulky wings on their pupal skin when molting, and if there aren't enough workers around to help untangle them, many of them die.
The sweet spot seems to be when the parasites make up around a quarter of the colony, according to the study, published Feb. 28 in the journal Current Biology (opens in new tab). When the wannabe queens' proportion was higher, their survival rates plummeted.
While some species of exclusively social parasite ant queens exist in the wild, the clonal raider ant is the first documented to have evolved wannabes within its own species.
"I was very surprised to find these ants," Kronauer said. "Social parasites are typically very rare, and can only be found in a few colonies of the host species. But the crazy thing in this case is that the parasites must have arisen within the host colony via a mutation, rather than having infiltrated the colony from outside, which is the case with social parasites in the wild." | Biology |
Researchers identify underused strategy for recovering endangered species
During a recent review of the U.S. Fish and Wildlife Service's recovery plans for more than 200 endangered and threatened vertebrate species in the United States, Michigan State University researchers made an interesting discovery.
They found that two-thirds of these species could benefit from a gene-boosting diversity strategy known as genetic rescue. Surprisingly, just three of these plans to support species recovery currently use this approach. The paper was published in the Journal of Heredity.
Genetic rescue is an increase in population size caused by the movement of new genetic material from one population to another. This can happen through either human-assisted intervention or natural migration. As a conservation tool, this strategy can increase the genetic diversity of small, isolated populations and help them recover from inbreeding.
"These small, isolated populations are becoming more frequent, fragmented and in trouble," said Sarah Fitzpatrick, an associate professor in the Department of Integrative Biology in the College of Natural Science and a W.K. Kellogg Biological Station faculty member. "They might benefit from some human-assisted migration to help infuse deteriorating populations with more genetic variation, which can help them respond to changes in the environment as well."
Translocating, or the act of moving individuals from one place to another, is a common practice that has most often been used outside the context of genetic rescue.
"This is pretty common in fish management," said Cinnamon Mittan-Moreau, an MSU Ecology, Evolution and Behavior Presidential Postdoctoral Fellow based at KBS. "Managers have been moving animals and plants around for more than a century, just not with the intention of increasing genetic variation."
The good news is that, in many cases, the logistics of carrying out these translocations have already been overcome, and so the time is ripe for more attempts at genetic rescue. Despite this, however, this strategy continues to be left out of species recovery plans.
"We found that over two-thirds of the 222 species we evaluated would be good candidates for consideration of genetic rescue," said Fitzpatrick. "And yet, we found only three examples of implementation of genetic rescue. As genomic resources become available for more species, we hope to see increased incorporation of genetic information in recovery planning, including informed translocation actions for the purpose of genetic rescue."
Along with Fitzpatrick and Mittan-Moreau, co-authors on this study include post-doctoral researcher Jessica Judson and former laboratory manager Madison Miller.
"There's a lot of opportunity for this to help, but we don't see it very often," said Mittan-Moreau. "No one had done this full review to see if this could be considered more often for endangered species plans."
More information: Sarah W Fitzpatrick et al, Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States, Journal of Heredity (2023). DOI: 10.1093/jhered/esad002
Journal information: Journal of Heredity
Provided by Michigan State University | Biology |
A man developed an "extensive" infection that caused his hands to swell after being bitten by a stray cat that was carrying an unknown species of bacteria, a new case report reveals.
The 48-year-old went to an emergency department in the U.K. because of painful swelling that developed in both his hands eight hours after he'd been bitten multiple times by a stray cat.
After washing and dressing his wounds, doctors gave him antibiotics and a booster dose of the tetanus vaccine to protect against infection by Clostridium tetani bacteria, which can cause painful muscle spasms, seizures and potentially death.
A day later, the patient returned to hospital as the infection had spread deep into the tissue of his left little finger, right middle finger and both his forearms, which had grown red and even-more swollen. He had signs of cellulitis, a bacterial infection in the deep layers of the skin, and tenosynovitis, a condition in which the protective, fluid-filled tissue layer around the tendon becomes inflamed.
Doctors administered several antibiotic drugs into the patient's veins, and they removed damaged tissue from his infection sites and washed out the remaining wounds. After that, the man was given oral antibiotics to take for five days and fully recovered.
Scientists analyzed tissue taken from the patient to find out what caused the infection. At first, scientists struggled to identify bacteria in the sample, probably because of the previous antibiotic treatment. They did, however, notice some Staphylococcus epidermidis that had been growing on the man's right middle finger, and a "Streptococcus-like organism" they couldn't initially identify. The mystery bacterium didn't match any genetic records of known bacterial species, but the team determined that it belonged to the genus Globicatella.
Globicatella bacteria are small microbes that resemble the more commonly known Streptococcus genus, which includes the Group A Streptococcus bacteria that can cause strep throat, scarlet fever and "flesh-eating infections." Until now, scientists only knew two species of Globicatella: G. sanguinis — which can infect humans and cause blood, heart, central nervous system and urinary tract infections — and G. sulfidifaciens, which so far has been found to infect only animals, such as pigs, cows and sheep.
The newly identified microbe's genome bacteria differed from that of G. sanguinis and G. sulfidifaciens by around 20%, which indicated it was "a distinct and previously undescribed species." Importantly, the newfound species responded well to many antibiotics, including some that other Globicatella bacteria have shown resistance to in the past, such as cefotaxime and penicillin.
In the U.S., 1% of emergency department visits are caused by dog or cat bites, with our feline friends being responsible for 15% of these visits. "Cats are major reservoirs of zoonotic infections," the case report authors wrote. "Their long, sharp teeth predispose to deep-tissue bite injuries and direct inoculation of feline saliva gives high risk for secondary infection."
Bites may become infected with bacteria that live in the cat's mouth, such as Pasteurella and Streptococcus species. Cat bites, like those from other domestic animals, can also cause rabies and tetanus infections. The Centers for Disease Control and Prevention (CDC) advises that anyone who is bitten or scratched by an animal should immediately clean the wound for at least 20 minutes with soap and running water then seek medical attention.
The authors of the new case report published their findings June 14 in the CDC journal Emerging Infectious Diseases.
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Emily is a health news writer based in London, United Kingdom. She holds a bachelor's degree in biology from Durham University and a master's degree in clinical and therapeutic neuroscience from Oxford University. She has worked in science communication, medical writing and as a local news reporter while undertaking journalism training. In 2018, she was named one of MHP Communications' 30 journalists to watch under 30. ([email protected]) | Biology |
Newly discovered deep-sea enzyme breaks down PET plastic
Plastic pollution is increasingly affecting the health of coasts and oceans. One well-known problem is plastic bottles made from polyethylene terephthalate, or PET.
A new study involving scientists from Professor Ruth Schmitz-Streit's research group at Kiel University has shown for the first time, using microorganisms from the deep sea, that polymers such as PET are continuously degraded by an enzyme. Researchers from the University of Hamburg and the Heinrich-Heine-University Düsseldorf played a major role in the microbiological study.
The results fundamentally expand the knowledge of PET-degrading enzymes, the underlying mechanism and the evolutionary understanding of the diversity of putative PET-degrading enzymes throughout the global ocean. The research team published the results in the journal Communications Chemistry, where they discuss both biotechnological applications and the high relevance for biogeochemical processes in the ocean and on land.
The study highlights a special feature of the PET-degrading enzyme. "In our study, we have discovered a new genetic resource from deep-sea organisms belonging to the archaea," says Professor Ruth Schmitz-Streit, head of the Molecular Biology of Microorganisms working group at the Institute of General Microbiology (IfAM) and member of the research priority area Kiel Marine Science (KMS) at Kiel University. Until now, about 80 different PET-degrading enzymes were known, most of which were found in bacteria or fungi.
"Our data contribute to a better understanding of the ecological role of deep-sea archaea and the possible degradation of PET waste in the sea," says the microbiologist.
The new enzyme: PET46
Using a metagenomic approach, the research team has identified and biochemically described the PET-degrading enzyme PET46 from a non-cultured deep-sea microorganism for the first time. This involved identifying the gene from a deep-sea sample based on similarities to known sequences, synthesizing the corresponding coding gene, producing the protein in the bacterium Escherichia coli and then studying it biochemically and structurally.
PET46 has many unusual properties and adds to the scaffold diversity of PET-active enzymes. Structurally, the enzyme differs significantly from those previously discovered. For example, it has the ability to degrade both very long-chain PET molecules, known as polymers, and short-chain PET molecules, known as oligomers, which means that degradation can be continuous.
Among other things, PET46 uses a completely different mechanism for substrate binding than previously known PET-degrading enzymes. The researchers describe an unusual 'lid' of 45 amino acids above the enzyme's active center as crucial for binding. In other PET enzymes, aromatic amino acids close to the active site are typical.
Promising biotechnology applications
At the molecular level, PET46 is very similar to another enzyme, ferulic acid esterase. This degrades the natural polymer lignin in plant cell walls by breaking down lignin polymers to release sugars from woody plant parts. Lignin and PET have many structural similarities, so the PET-degrading enzymes found in nature may be important for composting wood in forest soils, for example.
The biochemical properties of PET46 therefore make it a very interesting enzyme both for marine and terrestrial plastics and for biotechnology. Compared to the best-characterized PET-degrading enzymes from bacteria and composting plants, PET46 is more efficient at 70° Celsius than these reference enzymes at their respective optimum temperatures.
The research was carried out as part of the PLASTISEA project, coordinated by Professor Ute Hentschel Humeida of the GEOMAR Helmholtz Center for Ocean Research in Kiel. First author Dr. Jennifer Chow from the University of Hamburg and first author Dr. Pablo Pérez-Garcia, who works as a research assistant in Schmitz-Streit's group, contributed equally to the study.
More information: Pablo Perez-Garcia et al, An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate, Communications Chemistry (2023). DOI: 10.1038/s42004-023-00998-z
Journal information: Communications Chemistry
Provided by Christian-Albrechts-Universität zu Kiel | Biology |
Researchers at a Florida university say a small but feisty species of carpet shark with an extraordinary ability to walk on land is evolving to better survive warming seas and the climate crisis.The epaulette shark, commonly found on shallow reefs of Australia and New Guinea, can walk for up to 30 meters on dry land using paddle shaped fins, and survive hypoxia – a deficiency of oxygen – for up to two hours.The Florida Atlantic University (FAU) biologists, and their research partners in Australia, say these remarkable abilities enable the reef-dwelling sharks to survive increasingly hostile environments as conditions change.“Such locomotor traits may not only be key to survival but also may be related to their sustained physiological performance under challenging environmental conditions, including those associated with climate change,” the study, published in the integrative and comparative biology journal, says.“Findings to date suggest that this species has adaptations to tolerate some, but perhaps not all, of the challenging conditions predicted for the 21st century.”Marianne Porter, professor of biomechanics at FAU’s department of biological sciences, said the sharks are able to slow and fast walk, as well as swim, giving them an exceptional ability to cross land to reach more favorable environments that other species did not possess.“You might not think of beautiful, tropical beaches as harsh but in reality tidepools and coral reef environments are pretty harsh, subjected to warm temperatures when the tide is out and a lot of changes, a lot of things happening when the tide comes in and goes out,” she said.“These little sharks can move from tidepool to tidepool, allowing them to access new pools to forage for food, or tidepools with better oxygenated water.“Our collaborators in Australia have found they are able to withstand climate change conditions very well. These sharks are great models in starting to look at how these changing conditions may affect vertebrates in general, and other species, and can help us reflect what we might see in future oceans.”Epaulettes are not the only shark species known to have ambulatory abilities. In 2013, researchers in Indonesia discovered a species that uses its fins to “walk” along the ocean floor, foraging for small fish and crustaceans.A 2020 study by researchers at the University of Queensland and international partners, meanwhile, found at least nine species of shark used fins to walk in shallow water.What sets epaulettes apart, however, is their tolerance of hypoxia for a prolonged period and ability to not only survive being on land, but to be able to walk distances up to 30 times its body length.“Their ability to move around and walk from one place to another is really very important,” Porter said.The researchers noted that it gave the sharks better agility to evade predators, and reach areas with more plentiful food and less competition for it. | Biology |
We have all experienced the frustration of trying to hold a conversation in a loud pub or restaurant. Now researchers have shown that dolphins may face a similar scenario, showing that they “shout” to each other when faced with background noise.The findings revealed that a noisy environment makes it harder for dolphins to communicate and cooperate on tasks, adding to concern about the impact of human noise pollution on marine life.“In a very noisy pub we find ourselves increasing the volume of our voice,” said Pernille Sørensen, a graduate student at the University of Bristol and first author of the research, published in the journal Current Biology. “Dolphins respond in a similar way – they’re trying to compensate but there are some miscommunications.”Dolphins are social, intelligent animals, relying on clicks and whistles to communicate and using echolocation to hunt and navigate. So noise generated from human activity such as drilling and shipping has a potentially harmful impact on the health of marine populations.The latest study involved a pair of dolphins, Delta and Reese, and looked at how their ability to cooperate was affected by background noise. The dolphins were required to work together to both press their own underwater button placed at either end of a lagoon within one second of each other – a task that some humans would struggle to coordinate. They were released from a starting point during each trial, and in some trials, one of the dolphins was held back for five to 10 seconds. This meant that the dolphins had to rely solely on vocal communication to coordinate the button press.When increasing levels of noise were played from an underwater speaker, both dolphins compensated by changing the volume and length of their calls to coordinate the button press. Nevertheless, they could not entirely compensate. From the lowest to highest levels of noise, the dolphins’ success rate dropped from 85% to 62.5%, according to the research.The dolphins also changed their body language, reorienting themselves to face each other more frequently at higher noise levels and swimming across the lagoon to be closer to each other.The highest noise levels were comparable with what are sometimes experienced in marine environments as a result of shipping and drilling.“Despite their attempts to compensate, despite being highly motivated and the fact that they know this cooperative task so well, the noise still impaired their ability to successfully coordinate,” said Sørensen.Sound travels 4.5 times faster through water than through air, meaning many marine organisms have evolved to rely on sounds to provide important cues to navigate, forage for food, avoid predators and enable communication. Invertebrates and fish hear sounds at low frequency, while cetaceans (dolphins and whales) can hear very high frequencies, up to 200Hz and also use active sonar to detect objects, including prey. Humpback whales, singing at a low frequency, can be heard up to 16,000 kilometres away.But during recent decades, the underwater soundscape has radically changed from one that featured mostly natural sounds to one in which some regions are dominated by human noise pollution, from shipping traffic, seismic exploration, oil drilling and offshore windfarms. The increase in background noise has been linked to strandings, decompression sickness and behavioural changes.“Those same reasons that make sound so advantageous for animals to use also make them susceptible to disturbance from noise in the environment,” said Sørensen.In September 2020, Australia experienced the largest whale stranding recorded in history in which 450 pilot whales were found washed up on the west coast of Tasmania, most of which had to be euthanised due to their low chance of survival. Some linked the mass stranding to underwater noise pollution.Another recent study found that when narwhals are exposed to seismic air guns, used for surveying in the oil and gas industry, they immediately begin diving to escape from the noise. These high-intensity dives use much more energy than normal and put the marine mammals’ health at risk, scientists said.Sørensen said there had been some positive attempts to address the issue, such as the use of bubblenet structures around construction sites to muffle sounds. Some noises, such as ships engines, are more difficult to avoid, but the overall impact could be mitigated by better understanding how noise affects marine life and taking this into account. “Maybe there are times of the year that it is better not to be in a certain area,” said Sørensen. “So you could reduce traffic at certain times and increase it at others.” | Biology |
Humans retain an understanding of gestures made by other great apes even though we no longer use them ourselves, according to a new study by researchers at the University of St Andrews.
People playing an online game correctly identified more than half of the gestures made by chimpanzees and bonobos in a pioneering experiment run by Dr Kirsty Graham and Dr Catherine Hobaiter from the School of Psychology and Neuroscience. The study is published today (Tuesday 24 January) in open access journal PLOS Biology.
A total of 5,500 people took part in the experiment, viewing short videos of the ten most common gestures used by chimpanzees and bonobos. Asked to select the meaning of the gesture from four possible answers, participants performed significantly better than expected by chance, correctly interpreting the meaning of chimpanzee and bonobo gestures more than 50 per cent of the time. When the participants were provided with additional information on the context of the communication, it only had a very small effect on success, suggesting that humans can correctly identify ape gesture meanings from the gestures themselves.
The results suggest that although humans no longer use these gestures, we may have retained an understanding of this ancestral communication system.
Video playback experiments have traditionally been used to test language comprehension in non-human primates, but this study reversed the paradigm to assess humans’ abilities to understand the gestures of their closest living relatives for the first time.
Dr Graham said: “All great apes use gestures, but humans are so gestural – using gestures while we speak and sign, learning new gestures, pantomiming etc – that it’s really hard to pick out shared great ape gestures just by observing people. By showing participants videos of common great ape gestures instead, we found that people can understand these gestures, suggesting that they may form part of an evolutionarily ancient, shared gesture vocabulary across all great ape species, including us.”
This research builds on decades of painstaking work during which the scientists have carefully recorded and studied the meanings of the almost 100 different gestures that apes use to navigate their day-to-day social lives. It was only after the gestures and what they mean were established in the apes’ own communication that scientists could ask the question of whether humans might still be able to decode these gestures.
Dr Hobaiter said: “On one hand it’s really incredible that we’re able to do this – Kirsty and I have spent years living in the forest with chimpanzees and bonobos and working hard to study their communication. But it turns out that perhaps we didn’t need to! We can decode these gestures almost instinctively. It’s a useful reminder that we are also great apes! And that, even though today modern humans have language, we’ve kept some understanding of our shared ancestral system of ape communication.”
It remains unclear whether humans’ ability to understand specific great ape gestures is inherited, or whether humans and other great apes share an ability to interpret meaningful signals because of their general intelligence, physical resemblance, and similar social goals.
Although data is no longer being collected, you can still take an online quiz version of the experiment and test your own ability to interpret the gestures of your ancestors. The quiz is hosted by mixed methods behavioural research platform Gorilla. The paper ‘Towards a great ape dictionary: Inexperienced humans understand common nonhuman ape gestures’ is published in PLOS Biology and is available online.
Image 1 Caption: The online experiment could be completed on a laptop or tablet. A little cartoon showed participants what gesture they were looking for in the video and half of participants were told what the apes were doing. Credit: Kirsty E Graham. (CC-BY 4.0)
Image 2 Caption: Chimpanzees use lots of different gestures to communicate, like this “reach” which they usually use to ask for food. Participants selected the right meaning for the reach gesture and were overall able to understand ape gestures. Credit Catherine Hobaiter (CC-BY 4.0)
Issued by the University of St Andrews Communications Office. Category Research | Biology |
Though humans’ nearly hairless bodies stick out like a cowlick among other primates, our nakedness isn’t unique in the world of mammals. Dolphins and whales are naked, says biological anthropologist Tina Lasisi of the University of Southern California in Los Angeles. There are naked mole-rats. “Elephants, depending on how you look at them, are kind of naked,” she says. “But we’re the only weirdos that are naked except for our head.” Our species traded off much of our body hair for more sweat glands, an evolutionary adaptation that helps us regulate body heat more efficiently. But what about another uniquely human feature? We’re the only animals known to express tightly curled hair, like that seen in many people of African descent. Lasisi wants to know why and how it came to be. Backstory For decades, traits that have been associated with racial categories, such as skin pigmentation and hair texture, have gone understudied or ignored among anthropologists, Lasisi says. Much of the study of human biological variation was deserted after the post–World War II backlash against eugenics, a racist field birthed from the idea that humankind could be improved if those deemed to have desirable traits were selectively allowed to reproduce. Since then, research on human variation has largely focused instead on traits that are not overtly racialized, such as lactose intolerance and adaptations to high altitudes. But studying all forms of human variation is crucial to understanding our species’s evolution, Lasisi says. Studying variation in a way that normalizes rather than dampens or paints differences in a bad light is key not only to righting anthropology’s harmful legacy, but also ethical, socially responsible and sound science, she says. Sign Up For the Latest from Science News Headlines and summaries of the latest Science News articles, delivered to your inbox Lasisi discovered biological anthropology as an undergraduate student at the University of Cambridge. As a Black person who spent many of her formative years among white people in the Netherlands, she was always aware of skin color. She vividly remembers learning that human skin pigmentation evolved as an adaptation to ultraviolet radiation — research pioneered by anthropologist Nina Jablonski of Penn State, who would later become Lasisi’s primary adviser. “It’s like a lightbulb went off in my head,” Lasisi says, and it made her wonder, “What else out there can be explained by evolution?” Her interest in the origins of curly hair grew in part as an effort to understand her own locks. “Research is me-search,” Lasisi says. But when she first began, there wasn’t much science to comb through, and methodologies for measuring hair texture were either unreliable or inefficient. Standout research As part of her Ph.D. research, Lasisi worked with a team of anthropologists, thermal engineers and physiologists to study how curly hair might have given our bipedal ancestors a leg up in the hot and dry African savanna. The team placed a variety of wigs made of human hair onto heat-sensing models and measured heat transfer in different environments. In dry settings, curly hair, especially tightly curled hair, protected the scalp from solar radiation while releasing more heat from the head than straight hair. Lasisi speculates that the larger amount of air space within curly hair is what does the trick. To underpin her efforts and support future hair research, Lasisi developed an improved and standardized way of measuring hair curvature and cross-sectional shape. The technique involves segmenting, washing and taking pictures of hair strands and then running the images through an open-source computer program that she created. Measuring these characteristics on a continuous spectrum (much like we do height, for instance), she argues, is a better way of studying hair texture than the long-standing practice of classifying hair into discrete categories, such as straight, wavy or curly. Such discrete categories are not standardized among experts and can become subjective, she says. They also obscure the immense variation that exists, even on a single person’s head, and especially among curly hair. Cloudy categories Hair with similar curvatures can be perceived as straight, wavy or curly, as seen in this figure that compares the self-reported hair texture of 140 people of European and African ancestry with the actual curvature of their hair samples. Self-reported hair texture vs. measured curvature T. Lasisi et al/Scientific Reports 2021T. Lasisi et al/Scientific Reports 2021 Lasisi is doing highly technical work that hasn’t been part of the conversation, says Robin Nelson, a biological anthropologist at Arizona State University in Tempe. “Before Tina, very few people were working on hair texture in the same way.” Lasisi will bring this experience to the University of Michigan in Ann Arbor as an assistant professor in 2023, where she’ll continue her studies on human variation. Reaching out Lasisi wants everyone to be included in conversations about what makes humans human. She has appeared on the podcast Getting Curious with Jonathan Van Ness (of Queer Eye fame). She also hosts a PBS digital show on human evolutionary biology called Why Am I Like This?, which she helps conceptualize and write. What’s more, Lasisi has cultivated a community of curious science seekers on Twitter, Instagram and TikTok. Through short-form videos marked by her signature wit and humor, such as her “Melanin March” series or “Darwin’s greatest hits against white supremacy,” Lasisi educates thousands of followers on human variation, how to talk about race and ethnicity from an anthropological perspective, and much more. She even gives prospective anthropologists career tips and behind-the-scenes glimpses of life in academia. Two-way discussions let her learn from her audience, which she calls her “little focus groups.” In a series of videos on TikTok, Tina Lasisi introduces viewers to melanin, its different types and what it’s got to do with squid ink, mushrooms and watermelons. Lasisi hopes her research and outreach will inspire and provide a helpful framework for more nuanced discussions about race, ethnicity, ancestry and human diversity — and that her visibility as a Black anthropologist will encourage other people of color to ask questions that are important to them. “I want to put enough information out there in the world, and [have] enough people out there in the world who have a grasp of that information,” she says, “so that we can see human variation for the beautiful, magnificent, complex thing that it is.” Want to nominate someone for the next SN 10 list? Send their name, affiliation and a few sentences about them and their work to [email protected]. | Biology |
Home News Science & Astronomy An artist's impression of a comet flying through space trailed by twin streams of gas and dust. (Image credit: Shutterstock) (opens in new tab)A bizarre, volcanic comet has violently erupted, spewing out more than 1 million tons of gas, ice and the "potential building blocks of life" into the solar system. The volatile comet, known as 29P/Schwassmann-Wachmann (29P), is around 37 miles (60 kilometers) wide and takes around 14.9 years to orbit the sun. 29P is believed to be the most volcanically active comet in the solar system. It is one of around 100 comets, known as "centaurs," that have been pushed from the Kuiper Belt — a ring of icy comets that lurk beyond Neptune — into a closer orbit around the sun between those of Jupiter and Neptune, according to NASA (opens in new tab).On Nov. 22, an amateur astronomer named Patrick Wiggins noticed that 29P had drastically increased in brightness, according to Spaceweather.com (opens in new tab). Subsequent observations made by other astronomers revealed that this spike in luminosity was the result of a massive volcanic eruption — the second largest seen on 29P in the last 12 years, according to the British Astronomical Association (opens in new tab) (BAA). The largest eruption during this time was a huge outburst in September 2021 (opens in new tab). Related: Watch the biggest-ever comet outburst spray dust across the cosmos An eruption of this size is "pretty rare," Cai Stoddard-Jones (opens in new tab), a doctoral candidate at Cardiff University in the U.K. who took a follow-up image of 29P's eruption, told Live Scence. "It's [also] difficult to say why this one is so big."The explosion was followed by two smaller outbursts on Nov. 27 and Nov. 29, according to BAA.Unlike volcanoes on Earth, which eject scalding-hot magma and ash from the mantle, 29P spits out extremely cold gases and ice from its core. This unusual type of volcanic activity is known as cryovolcanism, or "cold volcanism." Cryovolcanic bodies, which include a handful of other comets and moons in the solar system such as Saturn's Enceladus, Jupiter's Europa and Neptune's Triton, have a surface crust surrounding a mainly solid icy core, Richard Miles (opens in new tab), a BAA astronomer who has studied 29P, told Live Science. Over time, radiation from the sun can cause the comets' icy interiors to sublime from solid to gas, which causes a buildup of pressure beneath the crust. When radiation from the sun also weakens the crust, that pressure causes the outer shell to crack, and cryomagma shoots out into space. An infrared image of the coma and tail of comet 29P captured by the Spitzer Space Telescope after an eruption on Dec. 8 2003. (Image credit: NASA/Spitzer Space Telescope ) (opens in new tab)The cryomagma from comets like 29P is mainly composed of carbon monoxide and nitrogen gas, as well as some icy solids and liquid hydrocarbons, which "may have provided some of the raw materials from which life originated on Earth," NASA representatives wrote.The ejecta from the most recent eruption of 29P stretched up to 34,800 miles (56,000 km) away from the comet and is traveling at speeds of up to 805 mph (1,295 kph), according to BAA. The plume "probably comprised more than one million tons of ejecta," Miles added.Photographs of the erupting comet also show that the plume formed an irregular Pac-Man-like shape, which suggests the eruption originated from a single point or region on the comet's surface, according to Spaceweather.com. These observations back up previous research that suggests 29P's eruptions are linked to its rotation. Miles and Stoddard-Jones believe that the comet's slower rotation causes solar radiation to absorb more unevenly on the comet, triggering the eruptions. So far eruptions from the comet tend to match up with its 57-day rotation period, the researchers said. Related: Volcanic eruptions on the moon happened much more recently than we thoughtResearchers also suspect that 29P's most explosive eruptions follow a cycle based on its orbit around the sun. A number of large eruptions were detected between 2008 and 2010, and now two massive explosions have occurred within the last two years, Miles said. It is therefore likely that there will be least one more major eruption from 29P by the end of 2023, he added.The roughly circular orbit of 29P (in white) around the sun. (Image credit: NASA/JPL Small-Body Database Browser) (opens in new tab)However, it is less clear how this longer eruption cycle is occurring, because unlike most other comets, which get closer to the sun during a specific period of their orbits, 29P has a largely circular orbit, meaning it never gets much closer to the sun than its average distance, Stoddard-Jones said. 29P has largely been ignored by the astronomical community since its discovery in 1927, but as new evidence emerges about its unusual volcanic activity it is starting to be taken more seriously, Miles said. "Clearly there is something new to be discovered in studying 29P."The James Webb Space Telescope is scheduled to take a closer look at 29P early next year, he added. Join our Space Forums to keep talking space on the latest missions, night sky and more! And if you have a news tip, correction or comment, let us know at: [email protected].
Harry is a U.K.-based staff writer at Live Science. He studied Marine Biology at the University of Exeter (Penryn campus) and after graduating started his own blog site "Marine Madness," which he continues to run with other ocean enthusiasts. He is also interested in evolution, climate change, robots, space exploration, environmental conservation and anything that's been fossilized. When not at work he can be found watching sci-fi films, playing old Pokemon games or running (probably slower than he'd like). | Biology |
Some 230 million years ago, massive dolphinlike reptiles called ichthyosaurs gathered to breed in safe waters — just like many modern whales do. That’s the conclusion that researchers arrived at after studying a mysterious ichthyosaur graveyard in Berlin-Ichthyosaur State Park in Nevada. The park is home to the world’s richest assemblage of fossils of Shonisaurus popularis, one of the largest ichthyosaurs ever discovered (SN: 8/19/02). “This is something we see in modern marine vertebrates — gray whales make [the] trek to Baja California every year” to breed, says Randall Irmis, a paleontologist at the National History Museum of Utah in Salt Lake City. The sheltered, warm water offers safety for the whales (SN: 1/19/80). Science News headlines, in your inbox Headlines and summaries of the latest Science News articles, delivered to your email inbox every Friday. The new finding, described December 19 in Current Biology, shows that this behavior “goes back at least 230 million years,” Irmis says. “It really connects the past to the present in a big way.” The idea of birthing areas for ichthyosaurs has been proposed previously, and is even well-known enough to often be incorporated into artists’ renderings of the creatures, says Erin Maxwell, a paleontologist at the State Museum of Natural History in Stuttgart, Germany, who wasn’t involved in the new research. But, she says, this study “is the first to support these speculations with data.” Nevada’s ichthyosaur fossil trove has been a puzzle to paleontologists for decades. One curiosity is the many ichthyosaur fossils clustered in what’s now the park, but about 230 million years ago, was part of a tropical sea. Another oddity is that the site seems as if it were almost entirely populated by giant, 14-meter-long adult S. popularis. And then there’s the tantalizing question of what caused the deaths. Scientists have previously suggested that the reptiles, which could be roughly the length of a school bus when grown, had congregated together for some unknown reason before something caused their mortality en masse. Several pockets, or quarries, of specimens are scattered across the park. All told, Irmis and colleagues identified at least 112 ichthyosaur individuals in these quarries, including at one site where park officials had left previously discovered bones half-encased in the rock for public viewing. That death snapshot meant that scientists could examine how the fossils were arranged relative to one another, perhaps offering insight into the reptiles’ behavior, says Neil Kelley, a paleontologist at Vanderbilt University in Nashville. Kelley, Irmis and colleagues used digital cameras and a laser scanner to collect hundreds of measurements of the bone bed with the half-buried reptiles, combining the data into a 3-D model of the site. The team also studied the sizes and shapes of bones from across the park, including some now in museum collections. And the researchers analyzed the chemical makeup of the surrounding rocks and pored over older photographs and field notes. Fossilized bones from at least seven ichthyosaurs (each highlighted with a different color) are shown in this 3-D model of a fossil bed in Nevada.Smithsonian These scraps of evidence helped the researchers begin to understand what they were looking at — and potentially solve at least one long-standing mystery: what brought these creatures together. Though almost all of the park’s Shonisaurus skeletons are fully-grown adults, the site does have a few very tiny ichthyosaur remains, the scientists found. Using micro-computed tomography, a 3-D imaging technique that uses X-rays to see inside the fossils, the researchers discovered that some tiny bones were those of embryonic and newborn Shonisaurus. From astronomy to zoology Subscribe to Science News to satisfy your omnivorous appetite for universal knowledge. The finding led the team to conclude that the site was a birthing ground. That could explain why there were so many of the same creatures in the same place alongside newborns, the researchers say. The site also seems to have been a birthing ground for Shonisaurus for a long time. Rather than all the quarries dating to roughly the same time, different ones are separated by at least hundreds of thousands of years, the researchers found. As for what killed the reptiles, “we don’t know,” Irmis says. Among the hypotheses for a mass mortality event were harmful algal blooms or large-scale volcanic activity. But the new rock chemistry data eliminated those events as culprits. Some of the animals in each quarry could have still died en masse. Having the creatures grouped in one place to breed may have left the reptiles vulnerable to a sudden catastrophic event that buried them in sediment, such as an undersea landslide. But the fossil finds might also represent “just normal mortality over time,” Irmis says, given how the creatures seem to have come to the site again and again. | Biology |
Psilocybin, the main psychoactive ingredient in magic mushrooms, could be a promising new treatment option for anorexia, early clinical tests have shown.
In a small trial, 10 women with the eating disorder received a single dose of psilocybin, while supported by a therapist, and tolerated the drug's short-term effects while not experiencing any serious side effects. Most patients reported a positive experience with the drug, reporting that their quality of life improved and that they felt more optimistic. Four participants had entered remission from their symptoms after three months.
The findings, published Monday (July 24) in the journal Nature Medicine, will need to be replicated in larger trials to confirm that psilocybin can effectively relieve anorexia's core symptoms, the study authors noted. However, with no currently approved medications for anorexia on the market, these initial results could signal hope for a new treatment option for this potentially deadly illness.
New treatments "urgently need to be developed," as anorexia nervosa "has the highest mortality of any psychiatric disorder and is notoriously costly and challenging to treat and recover from," Rebecca Park, an associate professor in the University of Oxford Department of Psychiatry who was not involved in the research, told Live Science in an email.
Anorexia nervosa is a serious mental illness in which people become obsessed with their body weight and image, restrict their food intake and sometimes exercise excessively to induce weight loss. The condition is notoriously difficult to treat, with half of patients hospitalized for the disorder experiencing relapse within a year of discharge. Despite affecting up to 4% of women and 0.3% of men — with cases among men likely being underestimated, as with other eating disorders — the condition has no approved medications available.
The hallucinogen psilocybin has already shown promise as a treatment for other mental health conditions, such as depression, alcohol use disorder and obsessive-compulsive disorder. It is believed to work by switching on receptors in the brain that normally react to the "feel-good" hormone serotonin — also called 5-HT2a— whose function can be reduced in patients with anorexia.
In this first-of-its-kind trial, scientists sought to determine whether psilocybin could be a safe and well-tolerated treatment for the disorder. They gave 10 women, ages 18 to 40, one 25-milligram dose of synthetic psilocybin while providing them with psychological support from trained therapists.
Following treatment, 90% of the group reported that they had a more positive outlook on life, with 80% rating the experience as one of their "top five most meaningful of life" and 70% feeling that their general quality of life improved. Although most participants reported these positive experiences, only four entered remission after three months, meaning their characteristic eating disorder symptoms, such as weight concerns, fell to baseline levels experienced by the general population.
So what might have driven this improvement in symptoms?
"While speculative," Dr. Walter Kaye, senior author and professor of psychiatry at the University of California, San Diego, told Live Science in an email, "it is possible that psilocybin administration may reverse altered serotonin function in anorexia nervosa and help patients develop a new perspective on their symptoms and behaviors."
The authors noted limitations of the study — namely, that it "lacked gender, racial and cultural diversity," as all 10 patients were women, and nine self-identified as "white." The exploratory study also lacked a control group of participants who took a placebo rather than psilocybin.
Although these are "important preliminary positive findings," Park stressed that psilocybin "remains an experimental treatment" and more data is needed before the psychedelic can be approved for use in anorexia.
Future research should include larger groups of patients and people whose symptoms vary in severity, as well as test different psilocybin dosages. Studies should also explore further how psilocybin may be helping to relieve eating disorder symptoms, she noted.
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Emily is a health news writer based in London, United Kingdom. She holds a bachelor's degree in biology from Durham University and a master's degree in clinical and therapeutic neuroscience from Oxford University. She has worked in science communication, medical writing and as a local news reporter while undertaking journalism training. In 2018, she was named one of MHP Communications' 30 journalists to watch under 30. ([email protected]) | Biology |
The search for functional natural compounds that can improve age-related cognitive decline has recently emerged as an important research focus to promote healthy aging. Trigonelline (TG), a plant alkaloid found in coffee, as well as in fenugreek seed and radish, was anticipated to possess cognitive enhancement properties.
In this study, researchers led by the University of Tsukuba investigated the effects of TG on memory and spatial learning (acquiring, retaining, structuring, and applying information related to the surrounding physical environment) from both a cognitive and molecular biology perspective in an integrated manner using a senescence-accelerated mouse prone 8 (SAMP8) model.
Following oral administration of TG to SAMP8 mice for 30 days, the Morris water maze test indicated a significant improvement in spatial learning and memory performance compared with SAMP8 mice that did not receive TG. Next, the researchers performed whole-genome transcriptomic analysis of the hippocampus to explore the underlying molecular mechanisms. They found that signaling pathways related to nervous system development, mitochondrial function, ATP synthesis, inflammation, autophagy, and neurotransmitter release were significantly modulated in the TG group.
Furthermore, the research team found that TG suppressed neuroinflammation by negatively regulating signaling factor Traf6-mediated activation of the transcription factor NF-κB. Additionally, quantitative protein analysis confirmed that the levels of inflammatory cytokines TNF-α and IL-6 were significantly decreased and the levels of neurotransmitters dopamine, noradrenaline, and serotonin were significantly increased in the hippocampus. These findings suggest the efficacy of TG in preventing and improving age-related spatial learning memory impairment.
This work was supported by DyDo DRINCO and Japan Science and Technology Agency (JST grant number JPMJPF2017)
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African trypanosomes mapped for the first time to understand evolution and potential treatments
A parasite which has devastating impacts on agriculture and human health is the first pathogen to have its proteins located and mapped within its cells—providing clues to their function and helping to identify potential drug targets.
African trypanosomes are parasites transmitted by tsetse flies that cause sleeping sickness in humans (presenting as fever, anemia and, in serious cases, death) and a similar disease celled nagana in cattle. These parasites have made large areas of Africa unsuitable for livestock production, costing rural farmers up to ~3.7 billion pounds each year in lost revenue.
For the first time ever, scientists have developed a detailed "protein atlas" of a pathogen—a kind of biological map that locates proteins in cells. They conducted the research on Trypanosoma brucei (T. brucei), helping to understand where proteins are within its cells, providing functional insights that may ultimately help treat parasite infections.
The benefits of this ground-breaking research by the Universities of Warwick, Oxford and Oxford Brookes do not stop there. In mapping the proteins within T. brucei, scientists now understand more about its evolutionary cell biology. Like humans, T. brucei are eukaryotes—meaning their cells have a nucleus. However, T. brucei evolved in a very divergent way to human cells. Exploring protein mapping sheds light on how it evolved to be so different.
Samuel Dean, Assistant Professor of parasitology at the University of Warwick, said, "In this study, we genetically modified trypanosome parasites to make proteins attached to a green fluorescent dye. This helped to show exactly where its proteins are within the cell. Using this information, we are able to understand more about what these proteins might be doing. Up until now 50% of the proteins in T. brucei had unknown functions.
"This has significant impacts on our understanding of pathogen evolution and provides functional clues for thousands of otherwise uncharacterized proteins. This will help further investigations and may help to inform on new treatments for these terrible diseases."
Professor Keith Matthews, expert in parasite biology at the University of Edinburgh, added, "This important resource will be of immense long-term value to researchers focused on these devastating pathogens, but also helps to understand the protein function and evolution of all nucleated cells, including our own."
University of Ghana senior lecturer, Theresa Manful Gwira, who is Head of Research Training at the West African Centre for Cell Biology of Infectious Pathogens, added, "This is a very important work, and a powerful resource that will be useful to many researchers including African scientists that work on the devastating African trypanosomiasis, thus contributing to a better understanding of the parasite biology."
The research is published in the journal Nature Microbiology.
More information: Karen Billington et al, Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei, Nature Microbiology (2023). DOI: 10.1038/s41564-022-01295-6
Journal information: Nature Microbiology
Provided by University of Warwick | Biology |
The drug-resistant fungus Candida auris (C. auris) was only discovered some 15 years ago but is already one of the world's most feared hospital microbes.
If it gets inside the body, the yeast-type fungus can affect the bloodstream, the nervous system and several internal organs. The World Health Organization (WHO) estimates that its mortality rate ranges from 30% to 53% of patients affected by an invasive infection.
What is more worrisome is that the fungus has proven to be resistant to the most common types of antifungal drugs. Some strains are resistant to all of the medicines we have, says BBC's health correspondent James Gallagher.
According to the US Centers for Disease Control and Prevention (CDC), there have been outbreaks in more than 30 countries. A 2020 review from case reports from those nations found almost 4,750 cases globally between 2009 and 2019.
The CDC said new data showed the fungus has "spread at an alarming rate in US healthcare facilities" in 2020 and 2021. Clinical cases in the country trebled - from 476 in 2019 to 1,471 in 2021.
Also, a 2019 study by an international team of researchers suggested that rising temperatures linked to climate change may have played a role in the rising number of Candida auris infections.
Here is everything you need to know about this deadly superbug.
What is Candida auris?
Candida auris (C. auris) is a yeast, a family of fungus which contains species pretty helpful to humans in activities such as bread-making and beer-brewing, but which also features species that cause infections in humans.
One example is the very common Candida albicans, which causes thrush but also may trigger more severe infections.
C. auris was first discovered in the ear canal of a patient at the Tokyo Metropolitan Geriatric Hospital in 2009, which inspired its name (auris is Latin for ear).
Most of the time, Candida yeasts live on our skin without causing problems, but they can cause infections if we are unwell or they get into the wrong place, like the bloodstream or the lungs.
What sort of illness does it cause?
C. auris most frequently causes bloodstream infections, but it can also affect the respiratory system, the central nervous system and internal organs, as well as the skin.
These infections are usually quite serious.
The fungus is often resistant to the usual drugs, which makes infections difficult to treat.
"The biggest problem with this fungus is its resistance to the drugs we have," said Dr Tina Joshi, associate professor in Molecular Biology at the University of Plymouth, in the UK.
"But another issue is that identifying a C. auris infection is quite difficult and it can easily be mistaken for other fungi, leading to the wrong treatment."
This means that the patient might be ill for longer, or get worse before accessing the appropriate treatment.
How does it spread?
Transmission is mainly through contaminated surfaces in hospitals. It sticks to intravenous lines and blood pressure cuffs. It's really hard to clean off, according to Dr Neil Stone, leading fungal expert at the Hospital for Tropical Diseases, University College London.
The solution is often to close off entire wards.
"It is the most worrying fungi and we ignore it at our peril," Dr Stone said.
"It could shut down entire healthcare systems."
In a statement issued on 20 March, the CDC said new data showed that the fungus has "spread at an alarming rate" in the US.
Should I be worried about getting an infection?
It is unlikely that you will pick up a C. auris infection going about your daily life.
However, the risk is higher if you are in a hospital for a long time or if you are in a nursing home, and patients who are in intensive care are much more likely to get a C. auris infection, according to the CDC.
The risk of picking up an infection is also higher if you have been on antibiotics a lot, because the drugs also destroy good bacteria that can stop C. auris getting in.
Why is C. auris resistant to the usual drugs?
Resistance to the common antifungal drugs, like fluconazole, has been seen in the majority of C. auris strains.
This means that these drugs do not work on C. auris. Because of this, less common antifungal drugs have been used to treat infections, but C. auris has now developed resistance to these, too.
DNA evidence shows that the antifungal resistance genes in C. auris are very similar to those found in the very common C. albicans.
This suggests that the resistance genes may have passed from one species to the other.
How can climate change be responsible for the high numbers of infections?
A 2019 study, published by the journal mBio from the American Society for Microbiology, suggested that the reason C. auris infections have become so common may be because this species has been forced to live at higher temperatures because of climate change.
Most fungi prefer the cooler temperatures found in soil. But, as global temperatures have risen, C. auris has been forced to adapt to higher temperatures.
This may have made it easier for the fungus to thrive in the human body, which is warm at 36C to 37C.
What can be done to control the number of infections?
A better understanding of who is most at risk of contracting a C. auris infection is the first step towards reducing the number of infections.
"We are behind the curve in what concerns the study of fungi," Dr Joshi said.
"I am not surprised at all we are now having to catch-up with it."
Healthcare professionals need to know that people who spend long periods of time in hospitals or nursing homes or those who have a weakened immune system are at higher risk.
Not all hospitals identify C. auris in the same way. They are sometimes mistaken for other fungal infections, like thrush, and the wrong treatment is given.
Improving diagnosis will help to identify patients with C. auris earlier, which will mean that the right treatment is given - preventing the spread of infection to other patients.
But above all, infection prevention efforts need to be improved, said Dr Joshi.
"The main measure is infection prevention and control, because we have already seen how difficult it is to tackle what it does to patients."
"Hospitals need to be on top of disinfecting and cleaning."
Is this the only nasty fungus around?
Not quite. In its first-ever list of fungal "priority pathogens", published last October, the WHO named no less than 19 fungi that represent a great threat to public health.
C. auris was one of four fungi to appear in the "critical priority" group, being described by the WHO as "intrinsically resistant to most available antifungal medicines".
This article has been adapted from material produced by Lena Ciric and James Gallagher. | Biology |
Rice University bioengineer Jerzy Szablowski has won a prestigious Young Faculty Award from the Defense Advanced Research Projects Agency (DARPA) to identify nongenetic drugs that can temporarily enhance the human body’s resilience to extreme cold exposure.
Jerzy Szablowski (Photo by Jeff Fitlow/Rice University)Szablowski, an assistant professor of bioengineering at Rice’s George R. Brown School of Engineering, plans to deploy a new screening method to find drugs capable of enhancing the cold adaptation response of brown adipose tissue (BAT), or brown fat, which regulates body temperature by breaking down blood sugar and other fat molecules in a process known as thermogenesis. The human body’s response to cold involves two types of thermogenesis. “One involves shivering, which all of us have experienced,” Szablowski explained. “If you are getting ill and you are developing a fever, you begin to shiver, and that shivering raises your body temperature. The problem is that you lose dexterity and it is really unpleasant. “The other type of thermogenesis involves BAT, which is capable of generating heat through a chemical reaction,” he said. “Nonshivering thermogenesis kicks in sooner but is not as efficient, so it cannot generate quite as much heat, at least not in humans.” Through the DARPA award, Szablowski will work with Miao-Hsueh Chen, an associate professor of pediatric nutrition at Baylor College of Medicine and an expert on BAT, to enhance nonshivering thermogenesis. A drug that boosts BAT response could help first responders treat victims of hypothermia and even lower the cost of arctic exploration. “If you have a drug that makes brown fat more active, then instead of having to spend weeks and weeks adapting to cold, you can perform better within hours,” he said. Szablowski said the new screening method could also be applied to optimize the development of drugs to treat diseases and infections, a process that is currently both cost- and time-consuming. Drug development involves multiple stages, each of which requires specific resources and expertise. “First, you have to understand the biology of the disease or physiological process, and then find a site to intervene, like a protein or a process in the cell that you can target with a drug,” said Szablowski, who is a core faculty member in the Rice Neuroengineering Initiative. “This is where this project comes in. The main innovation of this screening method is that it is mechanism-agnostic, meaning that we might not need to fully understand the disease or physiological process before developing mitigation strategies. “Simply put, it would allow us to screen a very large number of drugs,” he said. -30- Packard Foundation backs Rice bioengineer:https://news.rice.edu/news/2021/packard-foundation-backs-rice-bioengineer Brain-to-brain communication demo receives DARPA funding:https://eceweb.rice.edu/news/brain-brain-communication-demo-receives-darpa-funding 'Smart' wound-healing patch: DARPA awards $22 million grant:https://news.rice.edu/news/2020/smart-wound-healing-patch-darpa-awards-22-million-grant Links: Laboratory for Noninvasive Neuroengineering (Szablowski lab):https://www.szablowskilab.org/ This release can be found online at news.rice.edu. Follow Rice News and Media Relations via Twitter @RiceUNews. Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation’s top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 4,240 undergraduates and 3,972 graduate students, Rice’s undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 1 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger’s Personal Finance. | Biology |
LAWRENCE, Kan. — Around 14 million tons of plastic end up in the ocean every year. But that is not the only water source where plastic represents a significant intrusion.
“We found microplastics in every lake we sampled,” said Ted Harris, associate research professor for the Kansas Biological Survey & Center for Ecological Research at the University of Kansas.
“Some of these lakes you think of as clear, beautiful vacation spots. But we discovered such places to be perfect examples of the link between plastics and humans.”
Harris is one of 79 researchers belonging to the international Global Lake Ecological Observatory Network (GLEON), which examines processes and phenomena occurring in freshwater environments. Their new paper, titled “Plastic debris in lakes and reservoirs,” reveals that concentrations of plastic found in freshwater environments are actually higher than those found in so-called “garbage patches” in the ocean. The article is published in Nature.
For his role, Harris teamed with Rebecca Kessler, his former student and recent KU graduate, to test two Kansas lakes (Clinton and Perry) and the Cross Reservoir at the KU Field Station.
“That entailed us going out, tolling a net with tiny little holes in it, dragging it for about two minutes, then collecting those samples of microplastics and sending them off to (the lead researchers),” Kessler said.
The research project was designed and coordinated by the Inland Water Ecology and Management research group of the University of Milano-Bicocca, Italy (headed by Barbara Leoni and Veronica Nava). The team sampled surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes. It detected plastic debris in all studied lakes and reservoirs.
“This paper essentially shows the more humans, the more plastics,” Harris said. “Places like Clinton Lake are relatively low in microplastics because — while there are many animals and trees — there aren’t a lot of humans, relative to somewhere like Lake Tahoe where people are living all around it. Some of these lakes are seemingly pristine and beautiful, yet that’s where the microplastics come from.”
Harris said that many of the plastics are from something as outwardly innocuous as T-shirts.
“The simple act of people getting in swimming and having clothing that has microplastic fibers in it leads to microplastics getting everywhere,” he said.
The GLEON study cites two types of water bodies studied that are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas; and those with elevated deposition areas, long water retention times and high levels of anthropogenic influence.
“When we started the study, I didn’t know a lot about microplastics versus large plastics,” Harris said.
“When this paper says ‘concentrations as much or worse than the garbage patch,’ you always think of the big bottles and stuff, but you’re not thinking of all that smaller stuff. You don’t see a huge garbage patch in Lake Tahoe, yet it’s one of the most impacted lakes when it comes to microplastics. Those are plastics you can’t really see with the naked eye, and then you get underneath a scope at 40,000x, and you see these little jagged pieces and other particles that are the same size as algae or even smaller.”
Part of Harris and Kessler’s enthusiasm for taking part in this project was to highlight a region of the U.S. that is often overlooked.
“In this study, there’s one dot in the middle of the country, and that’s our sample,” he said. “In Iowa, Missouri and Colorado, there’s this huge swath of area that has water bodies, but we often don’t get them into those massive global studies. So it was really important for me to put Kansas on the map to see and contextualize what these differences are in our lakes.”
Harris has worked at KU since 2013, where his research focuses on aquatic ecology. Kessler graduated KU in 2022 with a degree in ecology, evolutionary & organismal biology.
“The biggest takeaway from our study is that microplastics can be found in all lakes,” Kessler said. “Obviously, there are different concentrations. But they are literally everywhere. And the biggest contributing factor to these microplastics is human interaction with the lakes.”
Top photo: Rebecca Kessler samples water for microplastics in Clinton Lake, Lawrence. Photo by Ted Harris.
Journal
Nature
Method of Research
Survey
Subject of Research
Not applicable
Article Title
Plastic debris in lakes and reservoirs
Article Publication Date
13-Jul-2023 | Biology |
With technology evolving quickly, it is not surprising that we are in a spiral of transition, making through daily changes. On the one hand, AIs like Chat GPT and GPT 4 are making a mark, and blockchain is encrypting at its best. On the other side, here are these future technologies that will make a difference. The ones mentioned below are currently under development, going through various laboratory experiments. Yet they are already making some big revelations. So continue with your reading task to better understand the situation ahead.
4D Printing
4D printing involves developing complex 3D structures that adapt to different forms or shapes under various environmental stimuli. Some researchers think of 4D printing as an extension of the 3D printing ability. The exclusive unique shape change capability involved in the process makes all the difference, a type of active origami. An object printed using 4D technology has those extra details, making it capable of changing shape or adhering to new situations. This also makes the material fit for self-repair and adequate environmental adaptivity.
Owing to the incredibility of the technology, researchers are always working towards implementing 4D printing technology in their works across biomedical and engineering fields. Especially they think of the particular right choice for cardiovascular implants. The 4D printing technology can be used to create adaptable and programmable prostheses. That facilitates the right typology for target tissue implantation.
Genomics
Genomics, or gene technology as it is known, is an interdisciplinary field of Biology focusing on manipulating and understanding genomes and DNAs in living organisms. The researchers try new experiments, editing the pre-existing genes to find alternatives and better variations of a pre-habituated system. The resolutions to queries that once seemed part of science fiction are now real, trying to help humans with a better life. All because of the advanced studies on Genomics.
If you are wondering about a proper application area of gene technology, then the production of vaccines can be a complete output with factual evidence. Also, in the future, researchers are working towards eradicating genetic diseases like cancer and aim to produce vaccines against the same.
Moreover, gene therapy sometimes includes inserting RNA or DNA into the cells as a precaution against diseases that are not treatable with medicines. This is only done for somatic cells, which cannot be passed from one person to another. Making alterations to human genes is banned as per rules and regulations.
Quantum Microscopy
The third in the list of future technologies that will make a difference is quantum microscopy. It integrates quantum technology into a conventional microscope. A quantum microscope can detangle the quantum phenomena, measuring the proportions of photons, electrons, and other particles at an atomic scale.
Other microscopes have laser or light to view transparent or semi-transparent materials. In the process, some of the matter does get destroyed, making it difficult for the researchers to analyze. A quantum microscope, on the other hand, offers a clear overview of the material under the lens.
Though powerful, the entire idea is still under process, and scientists are always working towards developing modernized versions of quantum computers that they can use for further research. Recently, researchers from the University of Melbourne and (SQC)/UNSW Sydney have developed a solid-state quantum microscope that can be used to analyze and monitor the wave functions of atomic qubits within silicon. Such innovations, on rounds, elaborate on how the world is moving towards a pathway of next-generation technologies.
Xenotransplantation
In general, we share the world with other living creatures, right? From the food chain to living habits, there are multiple ways that humans are dependent on other creatures living around them. Likewise, Xenotransplantation is just a step ahead, signifying the procedure of implementing, transplanting, and infusing humans with tissues, cells, or organs from an animal source. At present, Xenotransplantation is a rare case scenario. Part of future technologies that will make a difference. But the time ahead shows adequate potential for the topic to revolutionize the entire mode of surgery.
Till now, there have been two reported cases of Xenotransplantation, where the procedure involved inserting a pig’s heart into that of a human. One lived only a few months out of the two patients, and the other is under observation.
This type of surgery is a risky thing so far. One cannot straightaway put a pig’s heart into a human. Certain genes are first disqualified from the pig’s heart and replaced with human genes related to immunity and excess heart tissue growth prevention.
So that is all listing out the future technologies that will make a difference. The ones mentioned here are still in their early stage, and only time can reveal the best part of them. | Biology |
They say that elephants never forget, but what about other animals? A recent study in Current Biology reveals that trained bats remember their training after several years of life in the wild. This study moves scientists one step closer to understanding the complexities of animal memory in nature.Wild Animals and MemoryMemory plays a vital part in survival for many animals. Between apes, bears or bees, animals need to remember how to navigate home, how to find food and water and how to interact with other creatures. Sometimes, it could mean the difference between life and death. A strong memory can also remind animals of faraway sources of food and water and help them adapt to climate change and habitat reductions. “Trying to figure out how animals use learning and memory is one way to figure out how they’re going to make it in a life full of change,” says May Dixon, a postdoctoral student at Ohio State University who led the recent study for the Smithsonian Tropical Research Institute, in a press release. Though the study identifies approximately 40 other investigations into the memory abilities of bats, birds and many other creatures, much of this research focuses only on animals in captivity. “There are relatively few studies of long-term memory in wild animals, and we don’t have systematic understanding of long-term memories in nature yet,” Dixon says. And that’s a problem for biologists, since animals think and behave differently in captivity than they do in the wild. “You can’t necessarily extrapolate from the wealth of data we have on animals in the lab to what they’re facing in the wild, where there are many more things they have to remember,” says study co-author Gerald Carter, a professor in Ohio State University’s Department of Evolution, Ecology and Organismal Biology, in a press release. “The brain is different in the wild versus captivity.” Measuring MemoryTo address this imbalance, the researchers focused their attention on 50-or-so frog-eating bats (fringe-lipped bats) from the wild. Researchers captured these bats and introduced them to the sound of their preferred prey. They then rewarded the bats for flying toward the sound with a taste of food. Slowly they substituted the frog sounds for an unassociated ringtone, and the researchers continued to reward the wild bats whenever they flew toward the tone. The researchers not only trained the bats to respond to ringtones; they also trained them to differentiate between ringtones. Some were associated with rewards and some ringtones were not. When they demonstrated that they could consistently distinguish between the tones, responding only to the rewarded sounds and ignoring the unrewarded one, the researchers released the bats once again into wild within their native habitat in Central and South America. Researchers later recaptured eight of the bats and subjected them to the same tests after a period of one to four years in nature. They found that every one of the eight bats responded to the ringtones and six of the eight took the food reward (though several did struggle to distinguish between the rewarded and unrewarded tones from several years prior). “I was surprised,” Dixon says in a press release. “Four years strikes me as a long time to hold on to a sound that you might never hear again.”While all eight of the recaptured bats responded to the ringtones, bats without any previous training tended to ignore the tones. Ultimately, these findings aid scientists in understanding the scope and purpose of wild animals’ memory abilities. “We want to figure out when these skills are actually going to help animals,” Dixon says in a press release. | Biology |
In 1961, American architect Irving Geis received an unusual commission: he was to draw by hand the first protein structure revealed through X-rays. It was myoglobin, which is responsible for oxygenating muscles and for giving flesh its red color. It is a sort of necklace with 153 pearls, which folds into eight tangled helices. It took Geis six months to draw it, but his effort succeeded in awakening worldwide fascination with this invisible inner world. Now, science has progressed. Last year, the Google-owned artificial intelligence company DeepMind managed to accurately predict the structure of over 200 million proteins, that is, almost all known proteins. Spanish bioinformatician Iñigo Barrio helped organize that chaos, grouping them by similar shapes. His work reveals surprising data. Humans possess 13 unique structures, which do not appear in any other living beings. Acidobacterium bacterium, a ubiquitous bacterium in soil, has nearly 1,900 unique forms.
A living being’s DNA holds the recipes for making proteins, the basic building blocks of life. Humans have some 30,000 different types, which are responsible for essential functions such as generating energy, providing support and defending the organism against viruses. They are large and complex molecules; some are simple shapes — spheres, cylinders, rings, stars, spirals and even swastikas — and others are unimaginable structures, like hemoglobin, which transports oxygen through the blood from the lungs to the rest of the body. It has thousands of carbon, hydrogen, nitrogen, oxygen, sulfur and iron atoms. Hemoglobin’s formula is C₂₉₅₂H₄₆₆₄N₈₁₂O₈₃₂S₈Fe₄.
Barrio studied this welter at the European Bioinformatics Institute in Hinxton, England. The researcher and his colleagues fine-tuned a new algorithm, called Foldseek Cluster, which can identify similar patterns among the proteins. Barrio used the tool with the AlphaFold database of 215 million proteins. The team has identified 2.3 million types of structures, over 700,000 of them unknown. Understanding a protein’s structure is essential to understanding its function and it could potentially help to design new drugs. The researchers published their findings on Wednesday in the journal Nature.
“There is almost always a relationship between the structure of a protein and its function. Almost always. In biology, you should never say always,” says Barrio, who recently joined the Wellcome Sanger Institute, also in Hinxton, very close to Cambridge. His work has succeeded in linking proteins of known function with unexplored ones. “If proteins A and B have a very similar structure, you can infer that they will have a similar function,” the researcher explains. His work is reminiscent of an archaeologist extracting mysterious prehistoric tools from the subsoil. “If you discover something in the shape of a beak, you can intuit that it is used for chopping, but there are exceptions. A fork and a comb look very similar, but they are not used for the same thing,” he observes.
The AlphaFold database includes predictions developed by DeepMind and the European Bioinformatics Institute, part of the European Molecular Biology Laboratory, an organization with over 1,800 employees at sites in Spain, France, Germany, Italy and the United Kingdom. Analysis of the 215 million proteins suggests that most of the structures appeared very early on in the evolution of living beings, in the common ancestor of animals and plants or even earlier. Only 4% of the configurations appear to be specific to a single species.
“Humans have 13 protein groups with unique structures,” Barrio explains. That figure contrasts with those of the five organisms with the most unique three-dimensional shapes: the bacteria Acidobacteria bacterium, Escherichia coli and Chloroflexi bacterium, the Asian spider Araneus ventricosus and the Pharaoh cuttlefish, with between 1,400 and 1,900 unique structures each. “We tend to see evolution as a linear process, but it’s more like a tree. We are at the end of a branch, but bacteria have continued to evolve on their own branches. There are bacteria [that are] newer than us,” the bioinformatician explains. “Moreover, developing a new structure for a new problem is not always the best way to evolve. Often, structures are recycled. There are proteins in the human species that possibly have a different function than the one they had in our ancestors,” Barrio says.
The British company DeepMind boasts that its artificial intelligence system achieves 95% accuracy. However, nine of the 13 uniquely human structures are based on predictions with high uncertainty; according to Barrio, that might be because they are particularly disorganized conformations. The remaining four are VPS53, which is involved in transport within cells; U54, a herpes virus protein integrated into the human genome; annexins, which are involved in crossing cell membranes; and a fourth little-studied protein that may be more of a simple fragment. The 30,000 types of human proteins are grouped into some 9,000 structures.
Another of the study’s lead authors, Portuguese bioinformatician Pedro Beltrao, highlights the finding of human proteins involved in the immune system that are very similar to other bacterial proteins of unknown function. “This suggests that proteins involved in the immune system could have an ancient evolutionary origin, which we share with bacterial species. If true, this could transform what we know about immunity,” Beltrao, of the Swiss Federal Institute of Technology in Zurich, Switzerland, said in a statement.
Biologist Júlia Domingo considers the new research, in which she did not participate, “very necessary.” She explains that “we are entering a new era of massive data, and we need new tools to process, analyze and use it at high speed. Along with other colleagues at the Center for Genomic Regulation (CRG) in Barcelona, Spain, Domingo developed a method to identify the hidden buttons that change the function of proteins. Domingo says that structure is not enough to accomplish that task. “Other layers of functionality are involved, such as energies and affinity for other proteins,” she notes.
It took architect Irving Geis six months to draw myoglobin in 1961. The British chemist who provided him with the data, John Kendrew, won the 1962 Nobel Prize in Chemistry for reading that first structure with X-rays. The possibilities that artificial intelligence and new algorithms open up now are unimaginable, as Iñigo Barrio explains. “With previous methods, we would have needed 10 years to do this work. It took us five days,” he says.
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New way to count microbes speeds research, cuts waste, could lead to new antibiotics
University of Colorado Boulder researchers have developed a new way of counting microorganisms that works as much as 36 times faster than conventional methods, cuts plastic use more than 15-fold, and substantially decreases the cost and carbon footprint of biomedical research.
The technique, described in the journal Nature Microbiology, could revolutionize the way microbiology experiments are conducted around the world, allowing clinicians to diagnose and treat infections faster and researchers to test potential new antibiotics in a fraction of the time.
The invention comes as concern about antibiotic resistance grows worldwide, with drug-resistant bugs contributing to nearly 5 million deaths globally in 2019.
"We are in the middle of a silent pandemic of antimicrobial resistance and there is an urgent need to speed up the discovery of new antibiotics," said senior author Anushree Chatterjee, associate professor of chemical and biological engineering at CU Boulder. "We believe this new method can do that, and much more."
A new way to fill the pipeline
Since 1938, microbiologists have used a simple method, the colony-forming unit (CFU) assay, for counting bacterial cells in a sample. They start by diluting the sample down into eight to 10 different concentrations, put drops from each into petri dishes filled with bacteria food, wait hours or days for individual colonies to form, and count them. If they are testing a new molecule to see how well it can kill bacteria, they add that in to see how many bacteria survive.
The process is notoriously laborious and wasteful, often taking hours to assess a small sample and producing mounds of discarded plastic.
Because it takes so long and costs so much, researchers must be choosy about which potential new drugs or combinations they test, so they're discouraged from taking chances, Chatterjee said.
This high-cost, low-profit equation has led pharmaceutical companies to steer away from developing new antibiotics.
"We are basically out of antibiotics," said Chatterjee, noting that many widely circulating pathogens—including Staphylococcus aureas (staph) and Neisseria gonorrhoeae (gonorrhea)—are now resistant to most drugs designed to treat them.
"In order to have a sustainable pipeline of new options, we have to fundamentally change the way discovery is done," Chatterjee said.
Math instead of plastic
The new method, known as Geometric Viability Assay (GVA), replaces the arduous multi-step process of manual dilutions with a one-step process, informed by simple geometry and math.
"We are using the same kinds of math that can help students estimate the number of M&M's in a jar," said first author Christian Meyer, a postdoctoral fellow in the departments of Molecular, Cellular and Developmental Biology and Chemical and Biological Engineering. "Instead of counting all the M&M's individually, a clever student might count the bottom layer and then multiply by the height."
Similarly, instead of manually dividing the samples into numerous subsamples to make counting colonies easier, GVA counts colonies in one place, inside a portion of the cone of a single pipette tip, and then uses multiplication to calculate total concentration.
To do this, scientists embed the samples into a gel inside the cone, in which colonies form. When it's time to count, they can use various techniques—including ones that involve taking a picture or using a paper ruler—to accurately measure samples with anywhere from one to 1 billion microbes.
"It involves no mathematics that a high-school calculus student couldn't perform," said Meyer. But it could have a big impact.
Faster, cheaper, greener
In laboratory tests measuring common bacteria like Escherichia coli (E. coli) and Salmonella enterica, the researchers found that while preparing 96 samples took three hours by classical methods, GVA took 5 minutes—a 36-fold time savings. Even when compared to a more modern method involving robotics, GVA was still nine times faster and used one-tenth the plastic.
Using GVA, a single researcher could accurately measure the microbial concentration of 1,200 samples in a single day, the study found.
Ultimately, Chatterjee believes the method could also enable doctors to diagnose infection and find the right antibiotic for that infection faster.
"Instead of someone being in the hospital for three days while they figure out what that particular bug is sensitive to, we could potentially someday know overnight what the right antibiotic might be," she said, noting that more research is needed to advance to the clinical stage. Meyer invented the technique with Joel Kralj, a former assistant professor in the BioFrontiers Institute. The two are working with Venture Partners and have filed a provisional patent.
The research team has also created a website, and are now working to develop a smartphone version that scientists and the general public can use.
"Someone wise once said that the correct punctuation for a scientific advance is not an exclamation mark, but a semicolon," said Meyer. "In that spirit, while we are thrilled to be part of reinventing a core technique of microbiology, we are most excited for what will come next."
More information: Christian T. Meyer et al, A high-throughput and low-waste viability assay for microbes, Nature Microbiology (2023). DOI: 10.1038/s41564-023-01513-9
Journal information: Nature Microbiology
Provided by University of Colorado at Boulder | Biology |
Researchers understand the structure of brains and have mapped them out in some detail, but they still don't know exactly how they process data — for that, a detailed "circuit map" of the brain is needed.
Now, scientists have created just such a map for the most advanced creature yet: a fruit fly larva. Called a connectome, it diagrams the insect's 3016 neurons and 548,000 synapses, Neuroscience News has reported. The map will help researchers study better understand how the brains of both insects and animals control behavior, learning, body functions and more. The work may even inspired improved AI networks.
"Up until this point, we’ve not seen the structure of any brain except of the roundworm C. elegans, the tadpole of a low chordate, and the larva of a marine annelid, all of which have several hundred neurons," said professor Marta Zlatic from the MRC Laboratory of Molecular Biology. "This means neuroscience has been mostly operating without circuit maps. Without knowing the structure of a brain, we’re guessing on the way computations are implemented. But now, we can start gaining a mechanistic understanding of how the brain works."
To build the map, the team scanned thousands of slices from the larva's brain with an electron microscope, then integrated those into a detailed map, annotating all the neural connections. From there, they used computational tools to identify likely information flow pathways and types of "circuit motifs" in the insect's brain. They even noticed that some structural features closely resembled state-of-the-art deep learning architecture.
Scientists have made detailed maps of the brain of a fruit fly, which is far more complex than a fruit fly larva. However, these maps don't include all the detailed connections required to have a true circuit map of their brains.
As a next step, the team will investigate the structures used for behavioural functions like learning and decision making, and examine connectome activity while the insect does specific activities. And while a fruit fly larva is a simple insect, the researchers expect to see similar patterns in other animals. "In the same way that genes are conserved across the animal kingdom, I think that the basic circuit motifs that implement these fundamental behaviours will also be conserved," said Zlatic. | Biology |
Fuzzy, long-legged spiders may attack their prey with an ingeniously gruesome tactic — by covering them in toxic digestive fluids.
Unlike most other spiders, feather-legged lace weavers (Uloborus plumipes) don't have venom-producing glands or a way to inject their prey with toxins through their fangs. Instead, these spiders seem to produce neurotoxins in their gut, which may help explain their unusual hunting strategy of dousing their victims in fluids from their digestive system, researchers have discovered. The findings were posted as a non-peer-reviewed preprint on BioRxiv on June 28.
"It really looks like there's something in these digestive fluids that kill the prey,” which could be the toxins found in this study, co-author Giulia Zancolli, an evolutionary biologist at the University of Lausanne in Switzerland, told Live Science.
When most spiders trap an insect in their web, they inject it with venom from their fangs to paralyze it. They then cover each bite with digestive fluids to help break the insect down before consuming it.
But spiders in the Uloboridae family, such as feather-legged lace weavers, wrap their victims in a copious amount of silk — sometimes more than hundreds of feet of it — before covering them in fluids and eating them.
While scientists already knew about this unusual behavior, they weren't exactly sure how the victims actually died, the new paper said.
To investigate, Zancolli and her colleagues extracted RNA — a cousin to DNA — from different parts of feather-legged lace weavers. RNA can contain instructions for cells on how to make different materials, so by extracting RNA from different areas of the spiders' bodies, the researchers could see what kinds of compounds the animals were producing and where they were being produced. The researchers then looked at the structure of each of those compounds to determine whether they were likely to be toxic.
The team didn't find many potential toxins near the spiders' heads, nor did they find many in their silk. But they did find RNA for multiple potential toxins in the midgut gland (an organ that produces digestive fluids) — indicating that the digestive fluid may be toxic. In addition, the team found no evidence of venom glands or a typical venom-delivery system through the fangs.
The team didn't actually examine what was in the digestive fluid itself. But Zancolli noted that in another recent study, scientists did find toxins in an Uloborus digestive system.
This discovery could show that while spiders in the Uloboridae family may not be able to inject venom through their fangs, they may still be using toxins — in a unique, vomit-y way.
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Ethan Freedman is a science and nature journalist based in New York City, reporting on climate, ecology, the future and the built environment. He went to Tufts University, where he majored in biology and environmental studies, and has a master's degree in science journalism from New York University. | Biology |
People demand rights for the unemployed during the Great Depression in 1931 in front of the US Capitol.Credit: Alamy The worst recession in US history shaped how well people would age — before they were even born. Researchers have found1 that the cells of people who were conceived during the Great Depression, which lasted from 1929 to 1939 and, at its height, saw about 25% of the US workforce unemployed, show signs of accelerated ageing. ‘Inflammation clock’ can reveal body’s biological age The study authors measured these changes in the cells’ epigenome — the collection of chemical markers attached to DNA that determines when, where and by how much genes are expressed in each cell. And they think the pattern of markers that they uncovered could be linked to higher rates of both chronic illness and death.The work, published on 8 November in the Proceedings of the National Academy of Sciences1, adds to a cache of studies indicating that exposure to hardship such as stress and starvation during the earliest stages of development can shape human health for decades. The findings highlight how social programmes designed to help pregnant people could be a tool for fighting health disparities in children, says co-author Lauren Schmitz, an economist at the University of Wisconsin–Madison.Although the study is far from the first to link big historical events to changes in the epigenome, the fact that the signal appears in data collected from people in their seventies and eighties is “mind-blowing”, says Patrick Allard, an environmental epigeneticist at the University of California, Los Angeles.“It’s definitely something that will make its way into the textbooks,” he says.Epigenetic alterationsIn the earliest stages of development, an embryo is a packet of potential, containing genetic instructions to build the molecular components of the body. Over time, however, cells add and remove chemical modifiers known as epigenetic tags to their DNA, and these shape how those cells and their descendants execute the instructions. The tags are influenced by a variety of factors, including hormones, diet and people’s environment. Poverty linked to epigenetic changes and mental illness The alterations made during this key window can last a lifetime. In 2008, researchers found2 that people conceived during a famine in the Netherlands at the end of the Second World War had different epigenetic markers compared with siblings born outside this time frame. Those born during the famine had higher rates of metabolic illness later in life, leading scientists to suspect that their exposure to malnutrition during early development permanently shaped how their bodies processed food3.Since then, a slew of animal studies have linked early exposure to pollutants, stress and poor diet to a wide variety of epigenetic alterations that can shape everything from hair colour to brain development4,5. But only a handful of studies have succeeded in finding these trends in humans, says Ainash Childebayeva, a biological anthropologist at the Max Plank Institute for Evolutionary Anthropology in Leipzig, Germany.This is partly because subjecting people to harmful events such as famines to see how gene expression is shaped would be unethical. Instead, scientists have to look back on major historical events to determine whether those events affected people’s biology later in life. The Great Depression and its aftermath offered Schmitz and a colleague one such opportunity. Poverty shrinks brains from birth By comparing markers of ageing in around 800 people who were born throughout the 1930s, the team observed that those born in US states hit hardest by the recession — where unemployment and wage reductions were highest — have a pattern of markers that make their cells look older than they should. The impact was diminished in people who were born in states that fared better during the 1930s.The cells could have altered the epigenetic tags during early childhood or later in life. But the results suggest that some sort of biological foundation was laid before birth for children of the Great Depression that affected how they would age, epigenetically, later in life.It’s not clear whether diet, stress or some other factor drove the accelerated ageing, and without being able to go back in time and tease apart those effects, it will be hard to pin down the biological mechanisms behind the signal, Childebayeva says. Nonetheless, “these kinds of studies are really important because they highlight how early development matters for health and disease outcomes later in life”, she says.Science and societyAlthough both health care for pregnant people and economic theory have evolved since the 1930s, Schmitz thinks that studies such as this one can shed light on societal issues today. For instance, earlier this year, the US Supreme Court revoked the federal right to an abortion. Decades of research have shown that people who are denied abortions are more likely to experience financial hardship after an unwanted pregnancy than are those who can access abortions.“What we see from this study is that socio-economic structural inequalities that make it difficult for women to access the care they need might have long-term consequences,” Schmitz says. With social inequality on the rise around the world, the findings also highlight how paid parental leave, welfare payments and other policies and programmes can help to blunt health disparities in the future.“What we experience in those first nine months may affect us our entire lives,” Schmitz says. “I think we as a society can agree that experiencing a recession before you’re even born shouldn’t affect how long you live.” ReferencesSchmitz, L. L. & Duque, V. Proc. Natl Acad. Sci. USA 119, e2208530119 (2022).Article PubMed Google Scholar Heijmans, B. T. et al. Proc. Natl Acad. Sci. USA 105, 17046–17049 (2008).Article PubMed Google Scholar Tobi, E. W. et al. Nature Commun. 5, 5592 (2014).Article PubMed Google Scholar Dolinoy, D. C. Nutr. Rev. 66, S7–S11 (2008).Article PubMed Google Scholar Stankiewicz, A. M. et al. Brain Res. Bull. 98, 76–92 (2013).Article PubMed Google Scholar Download references | Biology |
Bangkok — Scientists have developed human embryo-like structures without using sperm, an egg or fertilization, offering hope for research onand birth defects but also raising fresh ethical concerns.
Earlier this year, several labs around the world released pre-print studies that had not been peer-reviewed, describing their development of early human embryo-like structures. Now one group's research has been published in the peer-reviewed journal Nature, describing how they coaxed humanto self-organize into a model resembling an early embryo.
The research was welcomed by some scientists as an "impressive" advance that could help unlock secrets about the precarious early stages of pregnancies, when failure is most common.
The work will however renew debate on the need for clearer ethical rules on development of lab-grown human embryo models.
The researchers, led by Palestinian scientist Jacob Hanna at the Weizmann Institute in Israel, harnessed the, which can become any kind of cell. They produced embryo models up to 14 days old, which is the legal limit for human embryo lab research in many countries, and the point at which organs like the brain begin to develop.
The researchers say their work differs from those of other teams because it uses chemically rather than genetically modified embryonic stem cells and produces models more like real human embryos, complete with yolk sac and amniotic cavity.
These similarities could make the models more useful for research into conditions like miscarriage, birth defects and infertility, said James Briscoe of Britain's Francis Crick Institute.
The model "seems to produce all of the different types of cells that form tissues at this early stage of development," said Briscoe, principal group leader and associate research director at the biomedical research charity.
The research "is a step towards opening a window on the period of human development where many pregnancies fail and which has been really difficult to study up until now."
Both the researchers and scientists not involved in the work emphasized that the models should not be considered human embryos.
The structure "highly resembles, but (is) not identical, to the in utero situation," the research notes.
The success rate on generating the models was also low, with the stem cells organizing correctly just a small percentage of the time.
Still, "in contrast to similar studies published earlier this year, these embryo-like structures contained most of the cell types found in developing embryos," said Darius Widera, an expert in stem cell biology at the U.K.'s University of Reading.
The research and other recent work shows "that models of human embryos are getting more sophisticated and closer to events that occur during normal development."
That highlights "that a robust regulatory framework is more needed than ever before," he added.
In Britain, Cambridge University has begun developing the country's first governance framework for stem cell-based human embryo models.
British law prohibits the culturing of human embryos in labs beyond the 14-day mark, but because the structures derived from stem cells are formed artifically, they are not explicitly covered by existing regulations.
Still, most researchers have adopted voluntary limits on their work at this stage.
The Weizmann Institute research did not develop its models beyond 14 days and does not involve transferring the models into a human or animal womb.
for more features. | Biology |
Researchers reveal how our muscle cells deteriorate with age, hampering recovery from injury
Researchers have revealed how muscle cells become impaired as we get older, impacting their ability to regenerate and recover after an injury.
A team at Nottingham Trent University analysed the full set of more than 11,000 gene transcripts inside muscle cells, finding that the ‘development pathways’ – the different ways in which genes work together to regenerate muscle – become weakened in aged cells.
The study may help to shed some light on why muscle damage take longer to recover from as we age.
The researchers developed a new approach to examine muscle cells in vitro in the laboratory to enable them to observe the different molecular mechanisms that drive muscle ageing.
They were able to study muscle cells from donors, chemically injuring cells after they had been donated and isolated, then assessing how they heal and regenerate back to their pre-injury baseline levels
Looking at cell lines derived from a 20 and 68-year-old donor, there were distinct differences in the development pathways of the younger and older cells, the researchers found.
While younger muscle cells fully recovered from the injury, the team found that in older cells the pathways linked to muscle development and regeneration were all ‘downregulated’.
This means that the genes are expressing less of what they need to, leaving the cells no longer able to perform in the way they should.
This contributes to reduced regeneration capacity leading to thinner, less robust ‘myotubes’ – a type of cell that can fully develop into a muscle fibre.
Muscle regeneration is a complex and finely balanced biological process and is known to deteriorate with ageing, leading to the decline of musculoskeletal health and in some cases metabolic and genetic diseases.
“This goes some way towards explaining why muscle injures may take longer to recover as we get older,” said lead researcher Dr Lívia Santos, an expert in musculoskeletal biology in Nottingham Trent University’s School of Science and Technology.
She said: “We know that healthy muscle regenerates after we’ve had an injury, but ageing impairs that regeneration potential and recovery gets harder the older we get. What we’ve observed, in terms of what happens inside the cells, helps us to better understand why we don’t heal as well or as quickly in older age.
“The pathways that control cell processes and development work differently in older cells and are downregulated, meaning regeneration is impacted the older we get. If we can understand these pathways, however, we could potentially identify new therapies and interventions to mitigate the problem.”
Janelle Tarum, another researcher on the study, said: “We’ve been able to develop a new approach to assess muscle regeneration which involves a state-of-the-art technique called RNA-sequencing.
“There’s a very clear reduced regeneration capacity and weakened recovery of aged cells and we have been able to further understand the factors underlying this impairment.
“Our work enables us to examine muscle cell regeneration across the lifespan and this in turn could be key for future drug discovery for disease related to muscle ageing.”
The study, which also involved Manchester Metropolitan University, Liverpool John Moores University is published in the Journal of Tissue Engineering and Regenerative Medicine.
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Notes for editors
Nottingham Trent University (NTU) received the Queen’s Anniversary Prize for Higher and Further Education in 2021 for cultural heritage science research. It is the second time that NTU has been bestowed the honour of receiving a Queen’s Anniversary Prize for its research, the first being in 2015 for leading-edge research on the safety and security of global citizens.
The Research Excellence Framework (2021) classed 83% of NTU’s research activity as either world-leading or internationally excellent. 86% of NTU’s research impact was assessed to be either world-leading or internationally excellent.
NTU was awarded The Times and The Sunday Times Modern University of the Year 2023 and ranked University of the Year in the Whatuni Student Choice Awards 2023. It was awarded Outstanding Support for Students 2020 (Times Higher Education Awards), University of the Year 2019 (Guardian University Awards, UK Social Mobility Awards), Modern University of the Year 2018 (Times and Sunday Times Good University Guide) and University of the Year 2017 (Times Higher Education Awards).
NTU is the 5th largest UK institution by student numbers, with approximately 40,000 students and more than 4,400 staff located across five campuses. It has an international student population of 7,000 and an NTU community representing over 160 countries.
Since 2000, NTU has invested £570 million in tools, technology, buildings and facilities.
NTU is in the UK’s top 10 for number of applications and ranked first for accepted offers (2021 UCAS UG acceptance data). It is also among the UK’s top five recruiters of students from disadvantaged backgrounds and was the first UK university to sign the Social Mobility Pledge.
NTU is ranked 2nd most sustainable university in the world in the 2022 UI Green Metric University World Rankings (out of more than 900 participating universities).
Researchers reveal how our muscle cells deteriorate with age, hampering recovery from injury
- Subject area: Sciences including sport sciences
- Category: Press office; Research; School of Science and Technology | Biology |
Killer whales are mama’s boys. A son will trail after his mother, grabbing bits of fish and other food, throughout his life, even as his sisters grow up and have calves of their own. This neediness comes at a significant cost to mom, who forgoes having additional children to look after her boy, according to a new study.
“This hasn’t really been looked at before,” says Eva Stredulinsky, an aquatic biologist at Fisheries and Oceans Canada who was not involved with the work. Researchers knew mother whales take good care of their sons, she says, but the new study “provides the first definitive description of what this support costs mothers.”
Michael Weiss has observed the mother-son bond firsthand in killer whale groups off the Pacific coast of North America. “It’s kind of wild,” says the behavioral ecologist at the University of Exeter and the Center for Whale Research in Washington state. These animals live for decades, yet even fully grown males “act like little kids around their mom, rolling around and swimming right beside and behind her like they’re still calves.”
Weiss wanted to know whether these high-maintenance offspring come at a cost—specifically, whether they hurt a mother’s ability to raise more children. He and colleagues sifted through 40 years’ worth of data on three Pacific pods, social groups typically consisting of a couple dozen, maternally related killer whales that travel and hunt fish together. Sure enough, the team found a “huge effect,” Weiss says. In a given year, mothers of sons were less than half as likely to have another calf as were childless females or mothers of daughters. Strikingly, the result was independent of the son’s age, the team reports today in Current Biology. In other words, both a 3-year-old son and an 18-year-old son lower their mom’s chances of having more children, Weiss says.
The team’s findings are convincing and unusual, says Janet Mann, a behavioral ecologist at Georgetown University who was not involved in the work. “You’d think that a big killer whale male would be able to take care of himself.”
The researchers suggest mom’s favoritism toward her boys evolved because of the particular social structure of these pods. When a daughter reproduces, her calves stay in the same group as her and her mom and therefore compete with the rest for food and attention. By contrast, a son doesn’t bring more mouths into the group—he mates with females in passing pods who then go on to raise offspring in their own social units.
His kids are thus “someone else’s problem,” Weiss explains. So, it makes sense for mom to invest more energy in him than in his sisters if she wants as many grandchildren as possible with the least competition.
The team didn’t establish exactly how sons prevented their mothers from having more offspring. But a female who shares a significant amount of her food with a demanding child might lack the energy to bring up anyone else, Weiss speculates. This could be a particular problem in the pods Weiss studies, which feed on Chinook salmon. These fish are now scarce where the whales live, so moms may well be going hungry, making them too weak to raise more calves.
Mann agrees this is one possible explanation for the data, but she says the research leaves many open questions. She notes that the evolutionary costs and benefits of raising sons might change as a mother approaches and passes menopause—killer whales are one of only a handful of species, including humans, known to do so—at about 40 years old, years or even decades before she dies. This is something that the team didn’t fully explore.
Mann adds it’s unlikely that sons in pods that feed on other sorts of prey are quite so dependent on their mothers. A bulky body might slow males down when darting about for salmon, but it could be an advantage when hunting larger marine animals such as seals. She says it would be interesting to study these other killer whale populations to see whether the mothers are similarly self-sacrificing.
Weiss says he hopes to do this kind of comparison across populations, and in different species of whales. In the meantime, killer whales remain an extreme example of parental care across the animal kingdom. In other animals, he says, “at some point, you just stop relying on your mom as much.” | Biology |
Climate Change Is Putting Larger Fish at Risk
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As the old proverb goes, “there’s always a bigger fish.” But will that hold for much longer?
According to a new paper examining drought-induced fish deaths in the Netherlands, climate change is disproportionately impacting larger and older fish, which are struggling to adapt as our waters become warmer and more deoxygenated. The research was published in the journal Environmental Biology of Fishes.
Studying at-risk groups
Previous scientific research has established that there is an inter-species correlation between a fish’s body size and its sensitivity to hypoxia and thermal stress. However, it is less clear whether this trend holds within a species as well.
To make matters more complex, experimental studies and fisheries management literature can sometimes contradict each other, making it particularly challenging for researchers to draw fixed conclusions about which fish might be most at risk under certain conditions.
“There is usually a discrepancy between the interpretation by the authors of some laboratory studies versus fieldwork experience when it comes to explaining whether and why larger fish are more vulnerable than smaller fish to warming and deoxygenated waters,” said Daniel Pauly, co-author of the new study and principal investigator of the Sea Around Us initiative.
“Resolving this discrepancy is urgently needed, as rapid climate change increases periods of drought and extreme heat worldwide and we need to understand the tolerance of fishes of different sizes to these events.”
A poorer metabolism is putting large fish at risk
In search of a broader explanation to explain this question, the researchers behind this new study conducted a thorough literature review, searching for collected data on three phenomena: sensitivity to hypoxia and high temperatures; aquatic surface breathing and the size-related scaling of anaerobic metabolism in fish.
This was combined with data that had been collected on three fish kills that occurred in the summers of 2020 and 2022 in Brabant, a region in the south of the Netherlands. The extreme heat during these seasons caused surface water levels to fall to record lows, prompting interventions to save the surviving fish. During the rescue of these fish, the numbers and size of the fish were recorded.
“In 30 of the 35 species assessed in the different studies and field manuals that we reviewed, larger fish were explicitly reported as having less tolerance to oxygen-depleted and warm waters,” said Johannes Müller, lead author of the paper and a lecturer at Leiden University. “In the case of the fish kills in the Netherlands, we confirmed that lack of oxygen and heat stress affected larger fish more drastically than juveniles, particularly pike, perch and tench.”
The researchers determined that the smaller gill size to body mass ratio of larger fish is the most likely reason why they are disproportionately impacted by warming waters.
Under normal conditions, a smaller ratio would only impact a fish’s growth rate. But when temperatures get higher, a fish’s oxygen demand will also increase. At the same time, the amounts of available oxygen in the water will start to decrease, increasing the strain.
Smaller and younger fish, with a larger gill surface-to-body mass ratio and thus a more favorable “aerobic scope” – referring to an animal’s capacity to increase its aerobic metabolic rate above normal maintenance levels – are physiologically better primed to deal with these additional stressors.
“Larger individuals, in the course of fish kills, often resort to sucking better-oxygenated surface waters and relying on metabolic mechanisms that do not require oxygen, which allow them to survive for a little bit longer, but these resources are not endless,” Pauly explained. “The accelerated metabolism caused by heat and its higher oxygen demand eventually kill the larger fish.”
What does this mean in a warming world?
As climate change continues to cause episodes of extreme weather, including drought and extreme heat, it is important that scientists are able to model the effects that this could have on fish populations properly.
The researchers believe that their findings could help to shed some light on why fish in some regions are not reaching their full potential. For example, large fish in colder environments are already close to their limits in terms of supplying their bodies with sufficient oxygen. These animals will find it even more difficult to deal with higher temperatures and critical levels of oxygen.
“This is why in colder places that have been warming up, some fish are not reaching anymore the maximum sizes that would be possible for their species,” said co-author Niels Houben, a consultant at the sports fishing association Sportvisserij Zuidwest Nederland.
Reference: Müller J, Houben N, Pauly D. On being the wrong size, or the role of body mass in fish kills and hypoxia exposure. Environ Biol Fish. 2023;106(7):1651-1667. doi:10.1007/s10641-023-01442-w
This article is a rework of a press release issued by the Sea Around Us initiative. Material has been edited for length and content. | Biology |
Researchers from the University of Florida and the Seattle Aquarium are exploring 100 meters underwater in the Pacific Northwest this summer to learn more about mysterious ghost sharks, one of the strangest beasts from the depths of the ocean.
Using remotely operated underwater vehicles, or ROVs, the scientists searched for nesting grounds of the Pacific spotted ratfish, Hydrolagus colliei, a ghostlike fish that lurks on the ocean floor.
“We know very little about these elusive relatives of sharks and even less about their spawning habits and embryonic development,” said Gareth Fraser, an assistant professor of biology at UF, before leaving for the expedition. “We will deploy ROVs to try to find where these ghost sharks lay their eggs.”
Related to sharks and rays but separated by nearly 400 million years of evolution, ghost sharks — formally called chimaeras — are one of the most enigmatic and understudied group of fishes, Fraser said. They typically live in deep waters, which is why scientists don’t know much about them. However, there are a few places in the world, including in the Salish Sea along the coast of Washington, where chimaeras will come into more shallow waters to breed and feed, especially during the summer months.
“If we can locate their embryos, we can begin to learn about the developmental processes that lead to some weird morphologies, or biological characteristics, unique to these fishes,” Fraser said.
For example, chimaeras have big round eyes like a rabbit that allow them to see as they creep in the dark hunting for food. They have ever-growing tooth plates like a rodent, which is why they are often called ratfish. While shark skin is covered in teeth, chimaeras have no teeth on their skin, and the males have a giant bulb on their forehead called a tenaculum that grows spiky teeth that look like shark teeth.
“We think they use this head clasper like a second ‘jaw’ on their head to bite down and attach to the female during copulation,” Fraser explained. “Ghost sharks are a very strange group of shark relatives whose biology makes them a bit other-worldly. When we get a chance to find these obscure fish where they feed and breed, we have to go for it.”
Fraser and others across the globe have had success in the last year with deep-water trawling projects locating adult ghost sharks, but studying older fish doesn’t shed much light on their developmental processes. This summer’s underwater search for the ghost shark nesting areas is the first of its kind for this species.
“We found a lot of different stages of the fish last year, from newly hatched babies to fully mature adults, so this year, we’re going back to find their nursery grounds,” Fraser said.
The ghost shark exploration project is supported through funds from a National Science Foundation grant focused on skin teeth of sharks and Fraser’s UF start-up grant. The team hopes to uncover secrets about origins of teeth, which could help them learn more about how to regrow human teeth.
The four-day expedition began June 11 in Seattle, with the team on a pier operating the ROV, which is essentially an underwater drone, that traveled about 10 meters deep in search of the ghost shark nesting sites.
In the coming weeks, the team will deploy the ROV about 100 meters deep from a boat in Elliot Bay in Puget Sound, and other sites around the San Juan Islands. Covered in cameras that will deliver 360-degree views, the ROV will capture images designed to create a virtual reality scene of the depths of the ocean for scientists once they are back in the lab.
“This will take us to the waters off Washington state, so that we can swim with these ghost sharks virtually and get an up-close, panoramic view of their environment,” Fraser said.
Karly Cohen, a UF biology postdoctoral fellow in the Fraser Lab who originally located the potential ghost shark nursing sites, said their project is an excellent opportunity to help strengthen conservation efforts.
“It’s important to learn about these understudied deep-water fish and their reproductive strategies,” she said. “Ultimately, we want to protect this really charismatic species.” | Biology |
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