What is two-start or zigzag model of 30 nm chromatin fibre?

From the MB Info Wiki you linked:

  In the one-start solenoid model, bent linker DNA sequentially connects each nucleosome cores, creating a structure where nucleosomes follow each other along the same helical path [4, 7]. Alternatively, in the two-start zigzag model, straight linker DNA connects two opposing nucleosome cores, creating the opposing rows of nucleosomes that form so called “two-start��? helix.

This means that in the one-start model each nucleosome is connected to the one adjacent to it, and this is a continuous cycle. Meaning that it is more like a phone chord.

The Zig-Zag model instead proposes that each nucleosome is connected to the nucleosome approximately opposite to it (parallel), and is a pattern that is continuous through out the chromatin fiber. This is more complicated to understand but imagine it being more like lacing on a shoe.It goes from a hole on one side to a hole on the other side parallel to it but not in the same plane as itself.

To move to the third nucleosome (and pack as tightly as possible) instead of it being directly below the 1st one it is slightly off to the side and not exactly parallel to the 2nd nucleosome.

However the 4rth nucleosome will be exactly parallel to the 3rd, and thus the same amount of degrees off-center from the 2nd nucleosome as the 3rd nucleosome is to the 1st, maintaining the pattern.

This forms a more 3-D tubular strucuture than an actual shoelace on a shoe would (which is more flat like a plane but serves for visual cue).

A 2D step-by-step representation of this would be like the image below:

Here is a model of final figure I made to help explain this:

In the MBI figure each "Green" nucleosome is connected to an opposite slighty lower "Purple" nucleosome and that purple one is connected to yet another green one that is slightly off center to the first green nucleosome:

In Theory (Not sure if correct):
This may mean that when this fiber "unwraps" it would act less like a spring coming undone(where the whole structure would start to unravel due to how it's linked) and instead each sequential nucleosome being pulled away from the fiber after the one its connected to has moved and experiences full tension.

For the ZigZag model imagine you take a piece of paper and fold it many times as if it were an accordion. Then hold the paper folded up in one hand. Take your opposite hand and pull the paper from one end slowly unfolding it. You'll notice that each fold comes out sequentially while the rest of the structure stays intact until the fold before it flattens out so the tension can pull it. At least that is what would happen in my mind. I could be totally off base.


A vaccine isn't antibodies.  It's bits of virus or microbe that elicits a response from the immune system, the most important component being the creation of specific memory cells which are ready to react if the real invader is introduced.


Can birds suddenly suspend in the air in one position?

Doing a stationary flight is called hovering (as @kmm said in the comments).

With head wind

When there is a (relatively important) head wind, many birds are able to perform stationary flights. However, in the bird's referential the flight is not stationary. It is typically common to see that for see birds.

True hovering

In absence of head wind, most birds aren't able to hover. There are a few exceptions. Hummingbirds hover while feeding on nectar. Some birds of prey are able to hover (they do so for hunting purposes) such as the common kestrel for example. While fishing, the pied kingfisher is famous for its hovering behaviour.

Anatomy and metabolic cost

Generally speaking, hovering requires flapping its wings very fast and is therefore energetically very costly. From wikipedia

  Most birds that hover have high aspect ratio wings that are suited to low speed flying. One major exception to this are the hummingbirds, which are the most accomplished hoverers of all the birds. Hummingbird flight is different from other bird flight in that the wing is extended throughout the whole stroke, the stroke being a symmetrical figure of eight, with the wing producing lift on both the up- and down-stroke. Some hummingbirds can beat their wings 52 times a second, though others do so less frequently.

Videos

Here are some videos of birds hovering:

Hummingbird hovering
Common kestrel hovering
pied kingfisher hovering


Answers in comments are correct. The tail effect of hypnotic drugs combined to opiates given for pain relief will make you feel really tired just after surgery.

But if you are referring to a more long-term effect, such as feeling tired for several days after surgery, then several factors combine:

psychological stress
physical deconditioning: inpatients usually do not move much. And even a few days of immobility will have a huge impact on your physical abilities. That is why in modern medicine, every effort is made to make the patient move as quickly as possible. Intensive physical therapy, readaptation therapy, and fast-track pathways are a result of this effort.
physical stress: undergoing surgery is a physical effort. Your body needs to accommodate for large shifts in volemia, positive pressure ventilation, reaction to pain (which still takes place during anesthesia), etc. The physical abilities of the patient are evaluated by the anesthesiologist for that reason, using MET effort units (often measured in number of flights of stairs you can climb without stopping). People with angina pectoris or diagnosed atherosclerosis can also be submitted to an ergometric test (cycling) or stress echocardiography/scintigraphy to evaluate if their heart can tolerate the physical stress of surgery.


Why is second pKa value of phosphoric acid different across different sources?

Someone will probably come along and move this to "chemistry", but here goes anyway.

The answer is: it depends upon how you measure it.

See:

  Jungas, RL (2006) Best literature values for the pK of carbonic and phosphoric acid under physiological conditions. Analytical Biochemistry 349 1-15

The author states that   "..the best value for the true thermodynamic second dissociation constant of phosphoric acid in pure water at 38°C is 7.180, rounded to the nearest 0.005."

He then goes on to re-analyse the data reported in:

  Cohn, EJ (1927) The activity coefficients of the ions in certain phosphate solutions: a contribution to the theory of buffer action. J Am Chem. Soc. 49 173-193

and concludes that under physiological conditions of ionic strength and pH the best estimate is 6.795.


Was it by chance?

Yes, sometimes, Penicillin was discovered by chance (and good observation), see http://www.nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html.

  I know some where accidents, but how are the majority found, testing lots of chemicals on your target?

Other important classes, like tetracyclines, were discovered by screening of soil samples for antibacterial activity (The history of the tetracyclines
). At that time it was not known what is the target of tetracycline, it was only observed that it was able to inhibit bacterial growth.
A synthetic antibiotic, nalidixic acid, was discovered as an impurity in the synthesis of another pharmaceutical agent and later became the template for other important antibiotics like ciprofloxacin. (Origins of the Quinolone Class of Antibacterials)

  I imagine now we would have the capability to quickly identify structures and molecules unique to pathogens and be able to model them on a computer, and generate suitable proteins or other compounds that can interfere with their bonding/properties to damage the pathogen?

In theory, yes, but from computer simulation to a drug there is a long, bumpy road. Most bacteria have a cell wall (with either one or two membranes, see here for a detailed discussion), so drugs need to penetrate this barrier before reaching their target. Even if they do so, they must also preferably inhibit bacterial enzymes but leave human enzymes active. This is especially complicated for targets, like DNA replication, protein synthesis, etc. which evolved early in evolution and are common to bacteria and humans. Some antibacterial drugs target tiny differences between humans bacteria, for some like Gentamicin it works well, for others like Chloramphenicol the side effects are dose-limiting. Here is a good blog entry on this topic: Antibiotics not as easy as theysay, look at the blog for other excellent comments on drug discovery and antibiotics).

For something like a 70s ribosome in a pathogen, what is the process of being able to understand its structure, its shape, etc? How much effort does it take to model onto a computer? Or instead a single protein (as a 70s ribosome will be more complex), how long does it take to model a new protein?

To quote Wikipedia:

  "Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. [..] The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins."

To get a computer model of the structure for a single protein where a similar protein is known, it takes a few hours. But to validate this model, i.e. showing that the hypothetical structures matches the real structure, it takes months of human work. You can imagine how much work it is for 31 proteins. In addition tiny deviations in the model, may cause your predictions to give false positive or negative hits (i.e. your computer model predicts that inactive compounds bind to the target or real inhibitors don't do anything to the target).

The traditional approach, finding compounds which kill bacteria or inhibit their growth, is much more promising since one might discover novel targets in bacteria and microorganisms came up with dozens of ways of killing their competition. One new approach is to cultivate bacteria which cannot be cultivated with traditional methods and screen them for antibacterial compounds, e.g. as described in this summary of this research article

Some more good reads on this topic:

The role of serendipity in drug discovery
A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future


Is there a correlation between total neurons and intelligence?

There are an estimated 100 billion neurons within the human brain. In general a minor variation in the number of neurons should not effect individuals too much, however when there is a more significant loss, such as brain injury or in some forms of dementia cognitive abilities do decline. So in this sense yes the number of neurons does relate to intelligence. However this variation is not what accounts for general variation of intelligence in the population.


Carbon Monoxide and High-Oxygen-Affinity Varieties of Hemoglobin

My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?

Yes. To put out a few other facts from the Stritch School of Medicine:

CO has 250 times the affinity for hemoglobin than O2
Hb becomes 100% saturated with CO at PCO = 0.6 mm Hg
Hb becomes 100% saturated with O2 at PO2 = 600 mm Hg

What does that mean? Well, that means that when the partial pressure of CO is 1mmHg, you're well and truly dead. So if the bar headed goose could survive in an environment more than 1% CO its hemoglobin would have to bind to molecular oxygen very, very tightly below 1mmHg. If this was true you would expect their binding curve to reach a high % of O2 saturation below a partial pressure of 1mmHg. Does it exhibit that?

Nope. At 1mmHg (remember, CO has 100% binding at 0.6mmHg) the bar headed goose hemoglobin's saturation is less than 2%. In fact, they're pretty similar to humans:

Is this casual glance conclusive? Well... Not entirely. I couldn't find any carbon monoxide data for the bar headed goose, but to overcome the 250x higher affinity for CO the goose's hemoglobin would have to be very, very different from that of humans while still exhibiting a similar binding curve. I've not received the education to determine if that's possible or how it would occur, but it is a very remote possibility.

Erring on the side of "most likely", however, I think it's safe to say that given a room filled with 1% CO you'd end up eventually killing anything that relied on hemoglobin to move necessary oxygen to tissues.


Why is there extreme itching when we touch a hairy caterpillar? What are ways to stop itching?

It would seem that you're referring to caterpillars that have urticating hairs, such as the goldtail moth caterpillar.

Erebidae similis

  .. when we touch those hairs we get extreme itching on that area i want to know why we got that itching?

In this case, the itching sensation is the effect of a hair-specific, soluble protein known as Thaumetopoein. According to this publication, in where they studied the urticating hairs of the Thaumetopoea pityocampa moth caterpillar when applied to guinea-pig skin:

  The hairs are hollow inside with sloping spikes toward the distal end. There are no holes or pores on the hair and the irritating factor can only be obtained by crushing the hair. This suggests that when stinging occurs the hair is broken in the skin and the substance [Thaumetopoein] is released.

More information about this immunological reaction begins on page 5 (numbered 350).

  And if one has got itching how to remove it?

Remove all caterpillar hairs by first using tweezers to extract any embedded hairs, then the sticky side of tape to remove surface resting hairs. Do not use your bare hands, as this will only spread the caterpillar hairs.
Rinse the affected area with warm water & soap.
Apply some kind of hydrocortisone cream.

Poison.org - Caterpillar Stings


What does differential consumption mean?

Second, differential consumption of plant growth forms can enforce changes in the composition of vegetation and thereby alter the type and arrangement of fuel.

This sentence means that herbivores eat more of certain plant growth forms than others. "Differential consumption" just means "different consumption." This can be important in the context of fire risk because herbivores will tend to not eat certain types of plant biomass, such as full-grown trees, but will eat new growth, grasses, etc (therefore the total amount of fuel by type is different).


Can a protein falling below a threshold trigger another response?

Of course, that is possible. I'll give a simple example. If your protein (X) is an inhibitor of the other protein (Y), then when X falls, Y will rise. This would not really be "thresholded".

There are many mechanisms that can lead to thresholding which include co-operativity (in the action of X) and positive feedbacks. How these mechanisms work would be a different question altogether. (A quick read would be this wikipedia article).


Yes. Samples for SDS-PAGE are mixed with a loading buffer containing SDS (final concentration of SDS is usually 2%). Generally, the SDS will disrupt protein-protein interactions, even before boiling. Reducing agent (usually DTT or b-mercaptoethanol) is added to disrupt disulfide bonds.
See diagram here.

There are, however, exceptions. Some protein complexes/multimers are resistant to SDS until boiling, and some even maintain interactions after boiling. Some examples: Xia et al 2007, Kubista et al 2004, Grigorian et al 2009.


When glucose production is low, the brain begins using ketoacids as energy... how does that work?

Human body is a glucose driven machine which intake carbohydrates and converts to glucose. Energy is yielded from the glucose and glucose is stored as glycogen. When the carbohydrate intake is somehow reduced then body will shift its mechanism and uses the fatty acids to produce energy. Liver synthesis ketones from fatty acids in our diet or from body fat. Ketones(acetoacetate and acetone) are released into the blood, which is absorbed by the brain and synthesis energy from it through their mitochondria.

  The brain gets a portion of its energy from ketone bodies when glucose
  is less available (e.g., during fasting, strenuous exercise, low
  carbohydrate, ketogenic diet and in neonates). In the event of low
  blood glucose, most other tissues have additional energy sources
  besides ketone bodies (such as fatty acids), but the brain has an
  obligatory requirement for some glucose. After the diet has been
  changed to lower blood glucose for 3 days, the brain gets 25% of its
  energy from ketone bodies.After about 4 days, this goes up to 70%
  (during the initial stages the brain does not burn ketones, since they
  are an important substrate for lipid synthesis in the brain).
  Furthermore, ketones produced from omega-3 fatty acids may reduce
  cognitive deterioration in old age.
  Reference

When the body starts using the fatty acids for energy production, one problem arises in the brain and that is the blood-brain barrier( barrier that separates the circulating blood from the brain extracellular fluid in the central nervous system )Brain cannot use long chain fatty acids because they cannot cross the blood-brain barrier due to their bondage with albumin. As ketones are medium chain fatty acids which can effectively cross the barrier. So brain uses the ketones for energy production by a process called as ketosis. The ketone bodies are then incorporated into acetyl-CoA and used in the citric acid cycle.

  The citric acid cycle – also known as the tricarboxylic acid (TCA)
  cycle or the Krebs cycle – is a series of chemical reactions used by
  all aerobic organisms to generate energy through the oxidation of
  acetate derived from carbohydrates, fats and proteins into carbon
  dioxide and chemical energy in the form of adenosine triphosphate
  (ATP).
  Reference

Metabolic pathways to produce energy


Using decoy proteins to treat viral illness

This is indeed a reputable strategy (#1,2,4) for rapid response to novel pathogens.  See https://phys.org/news/2020-01-scientists-decoy-molecule-neutralizes-arenaviruses.html and the open access article it cites https://www.nature.com/articles/s41467-019-13924-6

In the case of coronavirus, however, there is an issue (your #3) in that ACE2 is an enzyme that catalyzes the breakdown of a circulating hormone, angiotensin II, which is responsible for maintaining high (or normal) blood pressure.  So the "bait" used would have to be at least somewhat altered from this.  You would probably have to take into account how it affected other protein interactions such as with integrin beta 1 ... (see articles like https://europepmc.org/article/MED/14754895 ) to avoid getting caught up in speculation, it makes sense that a neutralizing protein might be made from part of ACE2 just as a neutralizing monoclonal antibody could be made, but you still have to have something specific before you can test for safety and efficacy.


Pangolin scales are certainly not retained from fish. Pangolins are within the clade Pholidota (Tree of Life page for Eutheria) and their nearest relatives are anteaters, sloths, and armadillos.

According to the University of California Museum of Paleontology, similarities between pangolin and armadillos are the results of convergent evolution. So the pangolin scales are a new feature that arose somewhere on the lineage leading to pangolins.


Can Nanodiscs be used to study membrane energetics?

Nanodiscs are very powerful technology for membrane protein invented in Stephen Sligar's lab at the University of Illinois.
A nanodisc is composed of a membrane protein, lipids and two monomers of a "scaffold protein". The most used scaffold protein is an N-terminal truncation of apolipoprotein A-1 (apoA-1), which is the primary protein component of high-density lipoprotein (HDL) particles. But because the size of the scaffold protein defines the size of the nanodisc, membrane proteins with different size could require different type of scaffold protein.

The reconstitution of a membrane protein into a lipid disc is a self assembled process. The reaction consists in mixing the membrane protein solubilised in detergent with lipids (that can be chosen according to the protein) and the scaffold protein. Removal of the detergent (using for example Bio-Beads™ SM-2 Resin) starts the self assembled process and the nanodiscs are created.

Nanodiscs provide an environment where membrane proteins are stable and compatible with aqueous environments in a native-like phospholipid bilayer. The aquesous environment makes membrane proteins compatible with analytical methods that have primarily been limited to investigating soluble proteins. The lipidic environment, that can be chosen and optimised, keeps the membrane protein stable, monodisperse and active. The stoichiometry of the protein can also be controlled.
Compared to nanodiscs, liposome are large, unstable and difficult to prepare with precisely controlled size and stoichiometry.

Several membrane proteins have now been reconstitued into nanodiscs and used for different type of studies, for example for studying ligand affinities  and kinetics, for NMR, for studying protein association state, signalling properties, and ion channels (http://molsense.com/applications/trubind-at-work/ion-channel-inhibitors/).

http://www.sciencedirect.com/science/article/pii/S0014579309007960


Is water released when a phosphodiester bond is made between two nucleotides during DNA replication?

No, nucleophillic attack by the activated 3'-hydroxyl on the α-phosphate of the incoming nucleoside triphosphate results in the formation of a new phosphodiester bond and release of pyrophosphate (PPi), which is subsequently hydrolyzed.

[image source]


We can't really say for sure, because we have insufficient information about this. We can't trace every step of evolution through fossils. We can make educated guesses for most stages of evolutionary history, but they remain guesses.

Please note: Most of what we find in the fossil record are species that are not directly our ancestors, but rather branched off our evolutionary line and then went extinct. Those fossils can still give a good indication as to what the morphological features of our common ancestor were. And a lot of this is guesswork with some evidence behind it.

Going "down" the timeline of humans, we roughly encounter these steps:

Homo

The genus Homo: appeared roughly three million years ago, includes species such as Homo erectus and Homo habilis. Fossils of Homo habilis point to a height of around 100 to 135 centimeters, fossils of Homo erectus are closer in size to modern humans with 145 to 185 centimeters. The rest of the Homo genus was smaller than modern humans (Homo heidelbergensis/rudolfensis/neanderthalis)

Australopithecus

The fossils from Australopithecus are around 3 to 4 million years old, the most famous is probably "Lucy", a member of Australopithecus afarensis. Since members of all Australopithecus species appear to be smaller than humans (afarensis: 100-150 centimeters, africanus: 115 to 140 centimeters, etc.), it is likely that our common ancestor was smaller than modern humans. (Our ancestors likely were Australopithecus, we just don't know which species)

Apes

The split between the line leading to modern humans and the line leading to modern chimpanzees occured somewhere around 4 to 7 million years ago. The clade is called Hominini. The split between those and the line leading to modern gorillas occured around 8 to 19 million years ago (yes, the dates are getting fuzzier). A fossil coming close to this ancestor may be Nakalipithecus nakayamai, however, we only have a fossil jaw from that species.

Going back, we get to the split between modern-day humans/chimpanzees/gorillas and modern-day orang-utans. This is the "ape" family, Hominidae. The largest ape that we know of, Gigantopithecus, that grew to about 3 meters, is classified as an orang-utan. Note that this is not a direct ancestor of humans. Even if our ancestors were larger than modern humans at this point it's unlikely that we are talking about anything larger than a big gorilla.

Primates

Going a bit in the reverse order here: The first true primates evolved around 55 million years ago. Fossils from that time are about the size of squirrels. Humans are "old world monkeys" who first appeared around 40 million years ago - the fossils from that clade we know, for example Apidium or Aegyptopithecus are a bit larger, some as large as a dog.

Primate-like mammals

The first primate-like mammals, called Plesiadapiformes appeared around 60 million years ago. We don't know all that much about them, but the most famous Purgatorius was the size of a rat or mouse.

Mammals / placenta mammals

Going back even further, things become even murkier, but early mammals were small. Placentalia, placental mammals appeared around 90 million years ago. They were small, arboreal (tree-dwelling) animals. Early mammals appeared around 160 million years ago and fossils we have from that time place them around the size of a shrew.

Now, is it possible that there were larger mammals in there somewhere, that then "shrunk" again? Sure. Just unlikely.

Therapsid

Therapsis are mammals and their ancestors, evolved around 275 million years ago. The most well-known fossils from around then are Tetraceratops insignis. All we have from it is a skull of about 9 centimeters size.

Synapsid

Synapsis are making things complicated. As you mentioned in a comment, there were some really big synapsids. According to the Tree of Life project:

  Early synapsids were moderately large (body length between 50 cm and 3 m)

Tetrapods

Tetrapods is the name for the clade that encompasses what we now call amphibians, reptiles and mammals - those animals appeared around 380 million years ago. An example of an early fossil from that time is Dendrerpeton, which was up to 1 meter in length.

Vertebrata

Synapsids are vertebrates. Vertebrates first appeared more than 450 million years ago. The time period following that, the Silurian, is called the "age of fishes".  Those fish could get really large, some of their jaws being over one meter wide. That's really all the information I could find.

Chordates

Taking another big step back, vertebrates are chordates, a group that first appeared in the Cambrian, somewhere around 550 million years ago. Early fossils are mostly small, for example Pikaia is about 5 centimeters large. Yannanozoon lividum is around 3 centimeters.

Before chordates

Before chordates, we really don't know all that much, the fossil record is poor because the structures that usually fossilize hadn't even evolved yet. For example, Hiemalora is around 3 centimeters in diameter. Whether it is our ancestor, we have no idea.

And before that come the first multicellular animals, the first animals, the first eukyrotes, and the archae,...

In summary

In summary, while we can only make guesses, the history of animal size from unicellular organisms to us probably wasn't spectacular. We go from very small (pre-Cambrian), to small (Cambrian), large or small (fish and synapsids), around 1 meter-ish (tetrapods), smaller again (early mammals, mammals), a bit larger (primates), again a bit larger (apes), and then to "human-sized".


Corrupted chromosome will be in any cell of body if zygote was corrupted?

The terms 'corrupted chromosome' and 'corrupted zygote' are very unusual and quite loaded. Mutations occur all the time (of the order of 1-10 mutations per individual per generation in humans, Drake et al. 1998) and it is unclear how big a mutation needs to be so that you talk about "corruption".

But in any case, yes, the egg will copy itself via mitosis to create the whole body. As such any mutation (whether a small substitution or a chromosomal duplication) present in the egg will be transmitted to all the daughter cells and will therefore be found in the entire body. Note that many of the changes in chromosome numbers lead to unviable zygotes and the baby never develop fully.

Note that during mitosis, sister chromatids are being separated and therefore the number of chromosome copy should not matter much in the general case.


What is the role of TATA box in transcriptional regulation?

TATA box serves as a binding site for the TATA-binding protein (TBP; and its associated factors, together comprising the TFIID).

TATA-box is one of the basic promoters present in many genes and therefore TBP is a general transcription factor i.e. TATA-box and TBP do not have specific roles. TATA-box is like a minimal promoter.


First we will take a look at the lines of resistance of a carrot. There are three

  The skin - The first line of resistance is the outer membrane or skin of the carrot and chemical compounds that are normally present
  there. Two antifungal polyacetylenes, falcarinol and falcarindiol, and
  an isocoumarin, 6-methoxymellein, are present in small amounts in a
  normal carrot and present the first barrier in undamaged carrots.

  Post Harvest - If during harvest or post harvest handling this barrier is broken, the surface is punctured, scraped or sliced,
  microorganisms may begin to grow. The carrot at this point begins a
  wound healing process by accumulating suberin, a complex
  polysaccharide, at the wound site. Along with suberin, lignin is also
  accumulated. Suberisation is complete within 48 hours after wounding,
  and lignification is complete within 168 hours of wounding..

  Phytoalexin barrier - The last and most important line of resistance is the phytoalexin barrier. Phytoalexins are chemicals
  produced by plants that impart disease resistance in response to
  mechanical injury, physiological stimuli or infection. Scopoletin, a
  coumarin,and para-hydroxy benzoic acid, a phenol, are apparently early
  arrivals on the scene but later disappear (reference).

There are three enemies of carrot storage: wilt, re-growth and rot.

Some reasons for carrots rotting faster:

Many fruits and vegetables start to produce ethylene gas when they start to ripen. Some foods are extremely sensitive to ethylene gas which makes them rot faster (reference). I am guessing that you keep different vegetables close together. Maybe if you stored carrots separately, it might make them last a bit longer.

  Major post-harvest losses in carrots are due to Sclerotinia rot,
  Botrytis rot, Bacterial soft rot (Erwinia) and Sour rot (Geotrichum).
  Of these, Sclerotinia rot is the most prevalent.The Sclerotinia fungus
  infects the carrot roots in the field through the crown. During
  storage, the Sclerotinia fungus produces a white, cottony mycelium
  which covers the roots. Infected roots are usually soft and watery (reference).

There would definitely be more reasons but I am guessing that these are the major contributors to it rotting faster.


The Integrated Taxonomic Information System (ITIS) is maintained regularly by a consortium of North American governmental agencies, and will give you a list of all the classes, orders, families or genera in any of seven kingdoms they recognize. It might be biased towards North American taxa, but it might be quicker to get a list from then rather than extracting them from Wikipedia.

To help you further, user Rozenn Keribin used an awk script to summarize the number of families per phylum at https://justpaste.it/163c6.

Phylum:  Myxozoa -- 4
Phylum:  Chordata -- 1049
Phylum:  Echinodermata -- 139
Phylum:  Hemichordata -- 7
Phylum:  Xenacoelomorpha -- 9
Phylum:  Chaetognatha -- 9
Phylum:  Arthropoda -- 2504
Phylum:  Kinorhyncha -- 10
Phylum:  Loricifera -- 2
Phylum:  Nematoda -- 192
Phylum:  Nematomorpha -- 3
Phylum:  Onychophora -- 2
Phylum:  Priapulida -- 3
Phylum:  Tardigrada -- 20
Phylum:  Annelida -- 142
Phylum:  Brachiopoda -- 21
Phylum:  Bryozoa -- 133
Phylum:  Kamptozoa -- 5
Phylum:  Mollusca -- 581
Phylum:  Nemertea -- 20
Phylum:  Phoronida -- 0
Phylum:  Sipuncula -- 6
Phylum:  Acanthocephala -- 26
Phylum:  Gastrotricha -- 13
Phylum:  Gnathostomulida -- 12
Phylum:  Micrognathozoa -- 1
Phylum:  Orthonectida -- 2
Phylum:  Platyhelminthes -- 321
Phylum:  Rhombozoa -- 3
Phylum:  Rotifera -- 34
Phylum:  Cnidaria -- 269
Phylum:  Ctenophora -- 19
Phylum:  Placozoa -- 0
Phylum:  Porifera -- 142
Total -- 5703


Check out the excellent Wikimedia picture of the carbon cycle:

All the numbers are in billions of tons of carbon: white = stored, yellow = natural flux, red = human contribution. Notice that the deep ocean stores much more accessible carbon than any other carbon cycle source, and is only surpassed by the lithosphere* in overall quantity of carbon stored on the planet. Some is stored by algae/sea plants, but the vast majority is stored as dissolved CO2.

*The lithosphere (crust and upper mantle) is not involved in the carbon cycle, and is therefore not shown in the above image.


How does the MET gene work and what happens when the promoter region gets mutated?

HGF is the ligand for Met, which is a membrane receptor involved in multiple transduction pathways. Gene ID 4233 we're looking at a single gene product for MET.

If we're just reading through the wikipedia page for c-Met, when HGF binds to Met, it activates the tyrosine kinase activity of Met. Met recruits Gab1, and this complex mediates interactions with Ras, P13K, ß-catenin.. not just pathways associated w/ Autism, but also associated with invasive growth cancers. An interesting note about the C allele, it's associated with decreased Met transcription. Quoting a recent article,

  The present morphological and functional studies have revealed a highly novel mechanism conferred by MET receptor signaling, which we show serves a pleiotrophic role in controlling both neuronal and spine morphology, and the time course of glutamatergic synapse maturation on CA1 hippocampal neurons. Such findings are consistent with the possibility that mistimed maturation of glutamatergic synapses underlie aberrant function of neural circuits that are enriched in MET during development.

Source

So the critical results from the same study showed that when Met got knocked down or deleted, we saw maturation of neural tissue. So now, if i'm thinking about Met and HGF, your article notes that HGF is decreased in autism brains. If we (1) need HGF for Met function, and (2) ASD may be attributed to decreased Met function, and (3) the C allele decreases Met levels, we're basically looking at a system that's modulating for ASD.


When is strict sterile technique necessary? Cloning vs. protein expression

For most plasmid preparation, strict sterile technique is not necessary. The antibiotics in the media will select for bacteria which carry a resistant plasmid, so you don't usually have to worry about other organisms getting in.

However, when you're using several types of plasmid, you do need to be careful to avoid cross-contamination, because each plasmid is resistant, so bacteria transformed with plasmid A will live just fine on plasmid B's plate. When plating your cells, be sure to pass your cell spreader through a flame. It doesn't have to be an official Bunsen burner, I used an alcohol burner just fine.

If you make a big bottle of media and use small aliquots at a time, then the bottle should only be opened inside the hood.


What Proteins Are Universal To All Life Forms?

This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement:

  All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick genetics overview).
  The 23 universal proteins perform fundamental cellular activities, such as DNA replication and the translation of DNA into proteins, and are crucial to the survival of all known life-forms—from the smallest microbes to blue whales.

The article is referring to a paper published in Nature in 2010.

http://www.ncbi.nlm.nih.gov/pubmed/20463738

This paper uses a set of 23 proteins to test the idea that certain genes arose only once.

  The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution27. The conserved proteins in this data set were identified based on significant sequence similarity using BLAST searches, and they have consequently been postulated to be orthologues.

There is no suggestion that there are only 23 such proteins, it's just that the author chose this subset to test his ideas.

And here they are:

  alanyl-tRNA synthetase, aspartyl-tRNA synthetase, glutamyl-tRNA synthetase, histidyl-tRNA synthetase, isoleucyl-tRNA synthetase, leucyl-tRNA synthetase, methionyl-tRNA synthetase, phenylalanyl-tRNA synthetase β subunit, threonyl-tRNA synthetase, valyl-tRNA synthetase, initiation factor 2, elongation factor G, elongation factor Tu, ribosomal protein L2, ribosomal protein S5, ribosomal protein S8, ribosomal protein S11, aminopeptidase P, DNA-directed RNA polymerase β chain, DNA topoisomerase I, DNA polymerase III γ subunit, signal recognition particle protein and rRNA dimethylase


Is there a strong reason to be sceptical about the "cured HIV patient" being reported by mainstream media?

Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.

The mother's T-cells are in the fetus anyways (15/18 Fetal lymph nodes contained T-reg cells). If the mother is infected and left untreated (as was the case with the Mississippi child), then the viral load is going to be high. The chances of it passing to the fetus are going to be high as a result.

  Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is "cured".

"Flawed" is the wrong word. The argument is built into the tests. The child was functionally cured - which means below detectable levels instead of "completely nonexistent within the body." Yes, it's entirely possible that the HIV is hiding somewhere in the body and could make a reappearance, but at the moment it's not showing any significant titer in the blood.

I don't think there's been a test developed that can assess the entire body to find the lone viral capsid left.

However - that isn't to say that the "cure" has been found. So far it's a single person cured this way. One. That makes it a case study, not a therapy, treatment, vaccine, or even reasonable assessment that it's possible to do again.


For humans, our blood and other tissues have a salinity which is less than that of sea water. The osmolarity of blood is 275-299mOsm/L, while the osmolarity of seawater is ~1000 mOsm/L.

The major reason we need to drink and excrete (sweat, breath and urine) water is to rid the system of waste- i.e. water soluble chemicals or heat we do not need.  The kidneys do a lot of this work and they need a reasonable osmotic potential to help them.

The osmotic potential is the tendency of molecules, for instance salts, to diffuse from one reservoir of liquid to another.  The kidneys burn metabolic energy (food) to create a slightly higher concentration of waste chemicals into the bladder/urine.  Other organs will fail or also work to maintain a local salt concentration (e.g. any nerve cell which depends on Na+/K+ concentrations to transmit their signals.  But the kidneys are the gatekeepers of salinity in the body.  They work hardest (and can get injured) when there is more salt in the water we drink. If you drink sea water you will quickly find your kidneys overworked and not really functioning.

That's why salt water will tend to make you thirsty (if you can drink any at all). Most people will gag when they drink even a little sea water, much less a glassful.

Sea mammals actually eat their fresh water. They rely on the fluid they get from fish to keep their salt balance.  Its true that some animals like fish and molluscs etc have adapted other means of keeping their salt balance in check.  Its just also true that its a lot of work to keep this ability and when animals move away from the oceans, they quickly lose that ability.


Is there any alternative to cryopreserve cell lines without -80 freezer?

A tank of liquid nitrogen is not just an alternative, but a much better substitute, IMHO. The problem of gradually cooling inside a isopropanol container can be overcome by using a box full of dry ice (-79°C as I recall).


Explanation of protocol in DNA extraction experiment

The DNA solution has a fixed volume (e.g., 0.1 mL). To a suitable test tube is added 0.2 mL of buffer-saturated phenol. After closing the test tube the mixture is mixed well, typically using a vortex mixer, but possibly by careful, repeated inversion. The aqueous phase and the organic phase are barely miscible. The tube is centrifuged to speed up the equilibration, and concentrate the denatured protein at the interface. After centrifugation the aqueous layer is carefully removed to a fresh test tube.

That is one organic extraction. This is repeated with a fresh aliquot of buffer-saturated phenol (another 0.2 mL). Then the aqueous phase is decanted again and extracted with 0.2 mL of CHCl3.

According to the recipe you provided, the buffer-saturated phenol was purchased from a vendor (Sigma-Aldrich Chemicals, of St. Louis, Missouri, USA), so you can look up the ingredients and composition on their online catalogue (no doubt).

The buffer recipe you provided is the proteinase K digestion buffer. It is typically performed at an elevated temperature.

This protocol is designed to isolate DNA from the nuclei of hair cells. Fully half of the contents of a eukaryotic nucleus are chromosomal proteins, by mass, so the proteinase K digestion step not only breaks open the hair cells, but also helps to remove all of the unwanted, contaminating cellular and nuclear proteins.


Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

In general transcription activators are transcription factors. These are very different in eukaryotes although some families share similar domains (e.g. two component signalization). I recommend you read through these two chapters to get a more complete overview on the differences.

https://www.ncbi.nlm.nih.gov/books/NBK21683/

https://www.ncbi.nlm.nih.gov/books/NBK21572/


Species that murder their own counterparts when put in captivity

Some individuals kill their own offspring (https://en.wikipedia.org/wiki/Infanticide) or eat their offspring (https://en.wikipedia.org/wiki/Filial_cannibalism) or their own siblings (https://en.wikipedia.org/wiki/Siblicide).  See this article about siblicide and fratricide in bacteria:  https://www.webmedcentral.com/article_view/4804.

Other conflict and killing between members of a population occurs in many species, including humans (https://en.wikipedia.org/wiki/Homicide), mice (https://sci-hub.tw/10.1111/j.1469-185X.1991.tb01147.x), and other primates (https://www.sciencedirect.com/science/article/pii/S0140175082920632).

Search "intraspecific killing" on Google or Google Scholar.

See also a similar question here:  Why social animals attack odd members of their own group?


When does histone synthesis occur in relation to DNA replication?

Yes, they have to. But that is just half of the story.

The (canonical) histones which are used in DNA replication are synthesized at the beginning of the S phase, and subsequently transported into the nucleus. Studies have shown that newly synthesized DNA is immediately packed into nucleosomes. Thus, it is necessary that these structures are available prior to (or at least just in time with) the replication.

However, there are different models on how the histones are inserted into new DNA. One model assumes that old and new nucleosomes are both incorporated into newly synthesized DNA after the replication fork. Others assume a semi-conservative approach where the old histones are disassembled into their subunits and then mixed together with the newly synthesized ones. For example, there is a model that proposes that the parental H2A/H2B and the H3/H4 dimers disassociate, while another assumes a disassociation of the H3/H4 dimers as well.

Figure: Nucleosome synthesis models for DNA replication

References

a Angélique Galvani and Christophe Thiriet (2013). Replicating – DNA in the Refractory Chromatin Environment, The Mechanisms of DNA Replication, Dr. David Stuart (Ed.), InTech, DOI: 10.5772/52656. Available from: https://www.intechopen.com/books/the-mechanisms-of-dna-replication/replicating-dna-in-the-refractory-chromatin-environment


There are several hypotheses about the evolution of dominance. It is important first of all, to note that empirical observations show that beneficial alleles tend to be more dominant than detrimental alleles. Among the two main hypotheses to explain the evolution of dominance, one has been formulated by Ronald Fisher and one by Sewall Wright.

Fisher's hypothesis

According to Fisher's hypothesis, between two equally beneficial alleles, if one is more dominant than the other than it's heterozygote carrier will have higher fitness. In consequence, beneficial alleles evolve to become more dominant while detrimental alleles evolve to be recessive (so that they can hide from selection in heterozygotes).

Wright's hypothesis

According to Wright's hypothesis, beneficial alleles are more dominant because of the kinetic of biochemical reactions. The rate of a biochemical reaction is a function of the concentration in the substrates of interest. The function is called "Michaelis-Menten function" after the name of the authors. The Michaelis-Menten function looks like this:

Think about a knock-out mutation. Such mutation will decrease by half the concentration of protein the gene in question produce in heterozygotes. Imagine, the concentration of proteins in the wildtype homozygote was 3 (see above graph). The rate of reaction of this homozygote is therefore about 3. The heterozygote would have a concentration of 1.5 and the rate of the reaction is therefore about 2.5-2.75. Assuming that the rate of this biochemical reaction is directly related to fitness, then a the locus of interest, benefical alleles are necessarily dominant and detrimental alleles are necessarily recessive. Selection for dominance is not involved in Wirght's model.

Is Fisher's or Wright's hypothesis correct?

Current state of the art is to consider Wright's model to be correct and Fisher's model to be wrong. In reality, the truth probably lies somewhere in between these two extremes. Note also that some other alternative explanations may exist in the literature but Wright and Fisher original hypotheses are by far the most considered hypotheses for the evolution of dominance. During my undergrad, I remember a speaker (but I forgot his name, sorry!) who showed that some alleles actually have some domain that are directly responsible for decreasing the expression of the other allele on the sister chromosome suggesting that Fisher's hypothesis might sometime be a good explanation as well.


I am normally reluctant to cite Wikipedia articles, however, the one for Sequential or Serial Passaging explains it quite nicely.

In short:

  In microbiology, sequential or serial passaging refers to the process
  of growing bacteria or viruses in iterations. In essence this means
  that a virus or a strain of bacteria will be isolated and allowed to
  grow for a period of time. After the sample has grown for some time,
  part of it will be transferred to a new environment and allowed to
  grow for the same period of time.This process will be repeated as many
  times as desired. The final product is studied, often in comparison with the original virus or bacterial strain to see whether it has evolved or any other changes have occurred.


List authors (scientists) by various attribute

I don't think that you can do this systematically in Web of Science but you can do it in an exploratory way.

Initial search: Topic - "population genetics" + Address - UK

sort by Times cited is probably more useful than the default (newest to oldest)

open Authors in sidebar - this is a list of the top 100 names
can refine to the top 10, or whatever

For example consider Brian Charlesworth:

Open an item with his name in the author list (he has some single author items)
Click on the link of his name to see his papers
Click on Create citation report to see charts of published items per year and citations per year

It may be that you know all this.


Why do the brains of cocaine-users shrink faster than the brains of non-cocaine users?

The mechanism of action of cocaine is dependent on pre-existing dopamine production and secretion. Normally, secreted dopamine is cleared from the synapse via the dopamine transporter (DAT) located on presynaptic dopaminergic terminals. Cocaine inhibits
this reuptake of dopamine, increasing it's duration of action on post-synaptic dopamine receptors. Thus, cocaine's effect depends on neuronal dopamine production. Without intrinsic dopamine, cocaine would have no effect. This is actual not exactly true though because cocaine also inhibits serotonin and norepinepherine reuptake transporters as well but the same argument applies to those neurotransmitters as well.

The overall effect of cocaine on the nervous system is extremely complex as it prolongs the action of dopamine, serotonin and norepinephrine wherever those reuptake transporters are present. There is a particularly high density of DAT in the basal ganglia and nucleus accumbens. What these areas of the brain normally do is under intense study and debate. The accumbens may play a role in goal directed behavior and incentive salience, which is the attribution of value to various actions or objects in the environment. This is what naturally guides us to perform one action over another. The simplistic view is that cocaine "highjacks" this system such that cocaine itself acquires greater incentive salience than natural reinforcers such as food, sex, money etc.

Getting back to the original question regarding why cocaine causes brain atrophy. This appears to be a finding quoted from a paper by the original inquirer. It is not obvious to me what the mechanism of this atrophy would be. I suggest you look at the discussion section of the paper from which that abstract was quoted to see what the authors suggest. However, to my knowledge, such atrophy has not been widely discussed in the cocaine literature but I could be wrong.

For further information see Sulzer. 2011. How Addictive Drugs Disrupt Presynaptic Dopamine Neurotransmission.


Do mosquitoes allow for DNA transfer between unrelated species?

In general foreign materials may be transferred from one organism to another in a mosquito, as is obviously the case with malaria, but for DNA to make it from inside the cells of one organism to inside the cells of another organism is exceedingly rare. In general DNAses and RNAses are present anywhere around living cells so when DNA is released it is quickly chewed up into useless fragments. Most likely this happens readily inside the digestive tract of a mosqito (Evolutionarily this makes sense as it would be extremely bad if a mosquito started absorbing genes from any of the organisms it was feeding off of!). Furthermore, DNA is an enormous charged molecule and does not easily pass through a cellular membrane. In a laboratory setting, DNA may be transferred into organisms with the help of electroporation or "gene guns" but this requires large amounts of identical genes to be effectively forced into cells, and even then, efficiencies of gene transfer are low. In short, no, it would be effectively impossible for a gene to be transferred from one organism to another by a mosquito. However, if a virus gets transferred by the mosquito...


In a vertebrate chimera, are particular organs homogenous genetically?

Chimerism (or genetic mosaicism if the cells come from the same zygote) is possible in the same organ or tissue. I don't think you will see a homogeneous distribution of the chimeric tissue because the tissue in any vertebrate organ is rarely homogeneous to begin with. Microchimerism may occur in a small number of cells. That's about all I know.


Cells take up external material in the process pf phagocytosis. This involves creating a vesicle from plasma membrane that will contain the external material. The vesicle enters the cytoplasm where it is called (early) endosome. The cellular membrane components of this endosome are recycled and gave back to the plasma membrane. The endosome pH decreases and it is now called late endosome.

Meanwhile, peptides (which will form the future hydrolases) are produced in the ribosomes of the endoplasmic reticulum and mannose 6-phosphate is added to these peptides. They are further transported to the Golgi apparatus which "packs" them into lysosomal vesicles.

The lysosomal vesicles fuse with a late endosome and due to the acidic medium of the endosome, the peptides dissociate from mannose 6-phosphate. This process turns the late endosome into a mature lysosome that is capable to digest material taken up via endocytosis.

  My book wrote: lysosomes are formed from ER or golgibodies.

ER and Golgi help supply the enzymes to endosomes, thus turning them into lysosomes.

References:

Wikipedia contributors, "Lysosome," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Lysosome&oldid=635272974 (accessed November 30, 2014).
Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Lysosomes. Available from: http://www.ncbi.nlm.nih.gov/books/NBK9953/


What is the impact of the invasiveness of the European Starling in North America?

First, for the record, I do not know the North American Starling situation well. However, I know of one study (Koenig, 2003) that failed to find strong effects of Starlings on other cavity nesters (i.e. looking at effects from cavity competition). When trying to control for other effects, only one species was potentially negatively effected by Starlings.

Starlings cause quite large economic effects though (Linz et al, 2007), and it wouldn't surprise me if this is the main reason for the control measures. The paper refers to a previous study which estimates that Starlings cause crop damage costs of \$800 million/year as well as \$800 million/year in health costs, due to disease transmission to livestock and humans (both figures from Pimentel et al., 2000).

So my feeling, based on a couple papers and some quick searches, is that the ecological impacts are uncertain (or to a large extent unknown) but that the economic impacts are quite large. Given the North American population sizes of European Starlings it would however surprise me a lot if there weren't any ecological effects on other species (negative and positive). These issues are hard to study though, especially without long-term data of high quality.


What determines whether I will have any dream or not?

According to the DreamResearch.net of UCSC, typically, we dream up to 10 times a night (sometimes more, sometimes less), and it is likely that on those nights when you feel that you have not dreamt, you may have forgotten the dream.

Dream amnesia is very common, where we forget most of the dreams (an any instances of sleep walking etc), this article Dreaming: A Neurocognitive Approach has more of the study.


Do any fish have to hold their urine in deep water?

In a salty environment there is the risk of loosing water by osmosis.
There are different strategies to prevent this.
One of them is to hold the salts of the urine (not the urine itself) by reuptaking them from the kidney.
The resulting high internal salt concentration prevents the water loss.

This strategy is used by Sharks and rays/ skates, they take up urea and TMAO from the kidneys. Those metabolites are highly concentrated in their blood, which makes them unhealthy to eat, when fresh. However, after fermenting they are edible: Hakarl is an icelandic dish of fermented shark. The linked Wikipedia-Article gives more details about the topic.

I guess your friend was referring to this phenomenon, but his memory was a bit imprecise.


Is DNA mutation locally energetically stabilizing the DNA molecule

a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system

Why do you think that? Because it’s an endothermic reaction?

Consider that mutations don’t happen “just like that” (at least to my knowledge) –they are triggered by external energy influx from things like reactive oxygen species or ionising radiation. So yes, they cost energy but that energy doesn’t come energetically unstable chemical bonds; it is supplemented from external sources.

So it’s not necessarily true that mutations produce lower-energy chemical bonds.


Evolution, What would the first plants have been like?

You can have a look to the most basal branches and you may get a pretty good idea of what those early plants looked like.

What we call plants is what we call plantae or Archaeplastida in Latin. This clade contains the red algae and the green algae. Within the green algae are the land plants. In the land plants are the embryophyta which contain all what you think of when talking about plants. Below are a bunch of pictures so that you can get an idea of what the basal branches look like.

(Basal Plantae) Red algae

(Basal Green Algae) Green Algae

(Basal embryophyta) Green Algae > Embryophyta > Hornworts

(Basal embryophyta) Green Algae > Embryophyta > Mosses

You can explore the tree of life by yourself by going on tolweb.org. You can try to find the apple tree, the ladybug of the human by clicking on the links. It is fun and it is good to learn a bit how the tree of life looks like.


why and how multi allele gets reported during variant calling in vcf?

In your example the 4th column contains the reference allel on the given position. It is not said, that your sample has this. The 5th column contains all alternative alleles found on the given position.

Which alleles are present in your sample is given in the last column by 1/2. This means you have one allel with the first value in the 5th column and one allele with the second value given in the 5th column. You see, that your sample has exactly alleles, but none of them is the reference. This would be indicated by a 0.


What does the hominin phylogenetic tree look like?

Gonzalez-Jose et al. (2008) published the following cladograms, based on two analyses (parsimony versus maximum likelihood). The table shows the legend. The interesting case of Homo floriensis, among others are not included, likely because of their recent discoveries and limitations of the study cited.

Reference
- Gonzalez-Jose et al. Nature (2008); 453 775-79


How many Type II restrictions enzymes are currently available (commercially)

The Restriction Enzymes section at Biocompare is likely not comprehensive, but short of contacting every single molecular biology company and merging all their inventories into a master list, it's probably the best you can do on short notice. They currently list 289 uniquely-named enzymes, but I'm not enough of an expert to say how many are similar in activity/recognition sequence, or whether they might also be known by other names not currently listed. For your purposes, however, it'd probably be enough to tell your students that there are on the order of 300 common commercially-available enzymes. Hope this helps.


Does SARS-CoV-2 kill its host cell or not?

The answer is yes, as there is no indication that SARS-COV-2 is an exception to the rule.
Cp., for instance: SARS-CoV-2 triggers inflammatory responses and cell death through caspase-8 activation,   Shufen Li, Yulan Zhang, Zhenqiong Guan, Huiling Li, Meidi Ye, Xi Ch https://www.nature.com/articles/s41392-020-00334-0
On exceptions to the rule cp., for instance
V. Kaminskyy, B. Zhivotovsky, To kill or be killed: how viruses interact with the cell death machinery
https://pubmed.ncbi.nlm.nih.gov/20433575/
In my opinion, only in the context you cited your question seems a still open one:
https://www.sciencemag.org/news/2020/12/coronavirus-may-sometimes-slip-its-genetic-material-human-chromosomes-what-does-mean
"... Baltimore says. “It is also not clear if, in people, the cells that harbor the reverse transcripts stay around for a long time or they die.”
However, this statement does not contradict the general rule that cells infected by viruses finally die.
There is always, as cited, some "staying around" - otherwise the immunogenic mechanism of presenting antigen would not exist.
As for retro viruses, host cells might divide, thereby multiplying the integrated genome of the virus, so one might speak of "no dying" as in such case the cell is still able to divide. However, that should be seen as only "staying around" for a very much longer time, as every infected cell will sooner or later become the retro viruses' friendly host - if that cell hasn't died before  because of other reasons:-) Still, if CoV-2 were a retro virus the answer to question had to be "no" - but it is not, CoV is no retro virus.
Refering to integration by LINE elements: this is different from retro viruses and it might be an open question, see the text passage cited, if the integration as a  coincidental and irregular  one (that should be current common belief)  does interfere with viral replication of CoV-19. In the study cited it is suggested that the RNA of the virus that has been retrotranscribed and integrated into the host's DNA is being read and transcribed to viral RNA. Interestingly, at that point  the study speaks of viral "chimeric RNA" being detected,  not viral proteins that maybe have not been searched for. The study also speaks of antigen that has been transcribed and translated from retro-integrated RNA may still be presented (on MHC) to immune cells. The latter possibility might be ruled out if viral proteins or peptides have not been found - in that case it is much more probable that the expression of viral genes has stopped the host from producing virions which is in line with a known strategy of "restriction" (e.g. by small or large interfering RNA).
In other words: to me it is highly probable that the reading of integrated viral RNA is   a mechanism of "restriction" in  a wider sense in that by activating the transposon after integration  the cell activities that would help the invading virus to replicate are being halted which different from o known defence mechanisms in bacteria/procaryotes leads to cell death probably by apoptosis, but maybe by necrosis.
This indeed seems coherent to "cytokine storm" as a reaction to SARS-Covid not of the adaptive but the innate immune systems that tries to clear up dead cells.
Another argument pro cell death  is the fact that - maybe contrary to common belief - it does not seem a seldom and random event that viral RNS becomes integrated as the study's outcome apparently is a  "first hit - success". To my mind, the  - disputable -  fact that there are no viruses that infect cells of the germ-line with the exception of certain retro(!)-viruses, cp.  https://en.wikipedia.org/wiki/Endogenous_retrovirus, https://www.sciencedirect.com/science/article/pii/S0014579300016069, https://www.sciencedaily.com/releases/2019/10/191010113231.htm  can be reconciled with and thus corroborates my opinion that integration of viral genes as transposons a. is no rare event and  b. leads to cell death in eucaryotes because, otherwise, the  integration of transposons the activation of which leads to apoptotic processes in stem cells  might put the indivual if not the host species at risk.
In my opinion it is a possibility that the LINE insertion is part of a yet rather unknown  "restriction process" of certain infected cells  that interferes with viral replication. The study found viral RNA transcribed from DNA that had been successfully integrated into cell's genome. The RNA found in samples might be some "interfering RNA" of some mechanism of "restriction".  If this is correct, it seems a possibility that  cells stays alive with viral genes integrated and - refering to maybe the gist of your question - divide and multiply, in an attempt to replace other cells who were not successful with this restriction strategy. Moreover, those successful restrictive cells might (seems like a paradox) NOT  present antigen to cytotoxic T-cells, and not get killed by those. However, I think this is highly unlikely. Much more coherent with findings of chimeric RNA is some induction of cell death by expression of integrated viral genes. It is known that active transposons can interact with genes they transpose to, leading to heritable disease (in eukaryotes). That should be - next to adaptive immune system defence -   another way infected cells die altruistically, in order to stop the progression of viral invasion.
In any case, the answer is: yes, cells infected by SARS-CoV-2 die.
Still, it is a possibility that "successful restriction" (integrated RNA becomes interfering RNA) leads to destruction of the virus, as this seems to be a known defence outcome in the bacterial world. However, the findings - RNA detected outside cells  - suggest that apoptosis or necrosis is the way to die for human cells infected by CoV-19.
Hint:  In any case, the fact that killer cells of the immune system lead to apoptosis of infected cells does not imply that a cell would survive an infection (if it were not for the killing by killer cells).


How Behind is the Human Mind (Latency of the Senses)

There is a huge amount research into this subject. It is vast and nebulous as such I cannot give you an overall picture of this. I can however illustrate some of the complexities to this.

Firstly I would say that what you mean by human perception is extremely complex, there are different modalities of perception. For example in terms of a visual stimulus, we may simply perceive its basic shape, outline, colour, whether or not it is moving. We then may also perceive higher levels of information such as the function of the object. Similarly there are different aspects to other stimuli.

These different components of perception are transmitted by different neurons leading to the brain and then processed by different areas of the brain suited to specific tasks and then are integrated together to give us a conscious idea of what the object is.

Therefore when measuring the latency of human perception you would first have to decide what exactly you mean by this?

The other aspect is that a lot of study has occurred in this area as we are aware that perception can be altered by states of illness (for example audio evoked responses in schizophrenia, or visual evoke responses in multiple sclerosis). The perception of pain is yet another huge area of study.

Again this is such a vast area of research that I wouldn't really know where to point you to. However for a entertaining read on how perception can change in neurology I would recommend reading the books of Oliver Sacks, in particularly "The Man Mistook His Wife for a Hat" and an "Anthropologist on Mars".

I am sorry I haven't provided you with more detail but good luck in reading around this subject. If you are more specific about what perceptions, (e.g. perception of faces, perception of danger etc..) then maybe you will receive more specific answers.


The difference in flame diameter between a Bunsen and Meker (or Fisher) burner really isn't that much, so I'm not sure how much larger the sterile field would be. On the other hand, Fisher burners can be tuned to be much hotter than standard Bunsen burners, so that may impact the size of the field as well. But, at the same time, they use more fuel, so you have to think of that as an additional cost.
If you're just sterilizing inoculating needles/loops, flask necks, etc., a Bunsen is perfectly fine. However, if you're trying to create a larger "sterile" field, there are too many variables to make a definitive recommendation. Are you setting up in an area with relatively little airflow, or are there cross-breezes? How large of a field do you actually need - what is the area where you'll be working with open containers of sterile media?
All in all, to be safest, you'd probably want the Fisher burner, but I don't know what the cost differential is and what your budget is. If you're careful with media manipulation and have a good still area to work in, a Bunsen should be fine, though.


Many articles focus on the pro-oxidant function of iron (and globins in particular). It makes sense that levels may be higher in the CNS due to their role in respiration, which is increased secondary to the “absolute requirement” for glucose facilitated by constitutive GLUT3 expression. So perhaps ferritin is increased to maintain supply for neuroglobin synthesis?

Another thing to consider, Ferroportin1 (FPN1) (iron export protein) is expressed at relatively low levels in the brain when compared to i.a. bone marrow (HPA 2018). You could hypothesise that increased storage is required as a result of decreased transport. But I would look at expression of import proteins; TFR, DMT1, and ZIP 8/14, as that could very quickly throw this theory off.

References:

The Human Protein Atlas (HPA) 2018, SLC40A1, The Human Protein Atlas, 11 September 2018, www.proteinatlas.org


Can 'human' become a genus due to space colonization?

The concept you are referring to is speciation and it has been well studied in a wide variety of different natural organisms. I suppose here we are talking about the biological species concept.
The overall answer is yes it is possible, but critically depends on a few different factors. The reality of speciation in the wild is very complex, but these are some things to consider:
Genetic isolation
If two groups, such as your Martian colony and humans on earth isolate from one another, then for speciation to occur, there needs to be a significant level of genetic differentiation between them. This means substantial differences in the kinds of genetic variants found at positions along the genome.
Genetic differences are eroded by post-isolation gene flow – in your example, that might mean a spaceship flying back to Earth with Martian colonists, who then have offspring with people on Earth.
Although there is plenty of evidence that speciation with gene flow can occur, the general rule of thumb is that increased gene flow means a longer divergence time is required to fully speciate.
In nature, this is often caused by some kind of geographic barrier to gene flow, such as mountains or rivers forming, but it can also be caused by morphological differences, such as variation in sexual appendages. Of course, in our example, this barrier to gene-flow would be the large and difficult to traverse distance between the Earth and Mars.
Divergence time
You alluded to some kind of separation time, and you are right to be talking on the scale of millions of years. Speciation can occur extremely quickly; in Lake Tanganyika cichlids, it has occurred probably within the last 15,000 years. Humans have created whole new species of crops, such as maize, within the past 10,000 years. There is even evidence of some fish speciating in 3000 generations.
However speciation is often a much longer process. For example humans and chimps were thought to speciate in 4.5 millions years.
Of course, there is an interaction with several other factors. All other things being equal, less post-isolation gene flows results in a shorter time to speciation and vice versa. Stronger selective pressure between the different environments leads to a more rapid accumulation of genetic differences.
As Konrad Rudolph correctly points out, divergence time is strongly related to generation time, with all other things being equal, a shorter generation time, results in faster speciation.
Selection pressures & differing environments
I think the last main factor governing speciation is how different the Martian colonists environment was from that on Earth.
Different environments can lead to natural selection occurring in opposing directions in the two populations, leading to ecological speciation. Speciation can proceed without differing environments, where neutral drift in allele frequencies can eventually cause speciation, but this will be a long process.
Speciation will occur much more rapidly if there is a start difference in environment and selection pressures between the two groups.
So in conclusion, given enough time, genetic isolation and differential selection pressures (or some combination of the above), it is plausible that a new species of human could form. However, given the time-scales required, it seems a bit unlikely to me.
EDIT
I think it is worth pointing out what @Jaquez said in the comments. If current terrestrial humans split from an extraterrestrial source to form another species, it would be named as another species within the Homo, such as Homo extraterrestrialis, for example. The addition of a new species does not move the group Homo up to become an e.g. Tribe or Family.


How does it make sense to speak of heritability of qualitative traits?

The concept of heritability is a concept coming from quantitative genetics. It only applies to quantitative traits. This does not mean that the trait must be continuous. Discrete traits (such as the number of eyes for example) are quantitative traits.

For boolean traits, it is common to set one outcome to 0 and the other to 1. Which outcome is set to which value does not matter as it won't affect the variance. To take your example of homosexuality, one would classify all individuals as homosexual or heterosexual (with not in between or other variants) and set homosexual to 0 and heterosexual to 1 (or vice-versa) and compute the heritability from there.

As far as I know, for non-boolean nominal traits, the concept of heritability is undefined.


How much energy is used to construct a pound of fat tissue?

A rough answer to a rough question

According to a study conducted in the 1960s, human adipose tissue, on average, contained (per 100g wet weight) 87g fat, 2g protein, 2g sodium and potassium and 10g water. (Nothing else was measured.) This suggests that approx. 3% of adipose tissue is solids other than triglyceride.

The figure quoted is presumably the energy yield for the complete oxidation of triglyceride. The energy yield for the complete oxidation of the non-triglyceride solids in adipose tissue  — the appropriate, if hypothetical, comparison would be less than that for triglyceride, which is much more chemically reduced, so the yield for the oxidation of non-triglyceride might be approx. 1–2% that of triglyceride.

The energy needed to bio-synthesize any organic compound (triglyceride, carboyhdrate or protein) is more than is obtained from it by oxidation because a negative free energy change is needed to drive reactions. Hence, as regards the relatively constant (slowly turning-over) portion of the adipose tissue, the cost would be higher — perhaps 2–3% of that quoted produced by oxidizing the triglyceride.

The problem with this question

Some people say that there is no such thing as a stupid question. Nevertheless, there are questions that are formulated as if their answer will establish solve some problem, when in fact it will not because the premise on which it is based is false.

In this case a comparison is made between the triglyceride and non-triglyceride content of adipose tissue with the implication being that the latter should be assessed in the creation of the former:

  “Those fat cells, and connective tissue took energy to assemble as
  well. How much energy is used to create a pound of fat tissue?”

As already mentioned, it is invalid to make a numerical comparison between the energy required to synthesize one compound with that released by the oxidation of another compound, as it costs more to synthesize a compound than is released by its oxidation.

However, quantitatively more fundamentally wrong is the implication that the one-time synthesis of the structural components of the cell should be costed into the repeated oxidation of triglyceride in that cell. How many grams of triglyceride are synthesised per gram of cell structural material during the lifetime of a cell? Very many, I should imagine if the cells turn over much more slowly than the lipid they contain.

It would be more pertinent (assuming that you are interested in such things) to ask what the cost is in terms of the energy used by whatever muscles are used by the lungs to breath in the oxygen needed to oxidize the fat, and the energy used by the heart muscle to pump the blood containing the oxygen to the fat cells so that it can be oxidized.

Finally, it is naïve to think of the energy cost of maintaining a fat cell in terms of the synthesis of its structural components. Other metabolic processes are continually occurring that require energy even in fat cells.

No doubt it would be possible to perform a calculation that took all these things into account (although what would you start with “from scratch” — ingested carbohydrate or carbon dioxide and water?). Personally, I am happy to accept that the system makes a profit and interest myself with the details of how it operates and adjusts to different circumstances.


Can catecholamines degrade back into tyrosine, or, is synthesis irreversible? (in human body)

A glance at the relevant BioCyc entry tells us that each reaction in the catecholamine biosynthesis pathway is irreversible. The standard free energy change of each reaction—again from BioCyc—is given below.

\begin{array} {|r|r|}
\hline
\text{Reaction} & \Delta _r G' ^{\circ} \text{ in kcal mol}^{-1}\\
\hline
\text{Tyrosine hydroxylation} & -93.0 \\
\hline
\text{Decarboxylation of DOPA} & -3.09
\\
\hline
\text{Hydroxylation of dopamine} & -67.9
\\
\hline
\text{Norepinephrine to epinephrine} & -10.5
\\
\hline
\end{array}

Note that all the free energy changes are negative, i.e. all reactions are irreversible under physiologic circumstances. (For the last one, there is a simple explanation: S–adenosylmethionine is a powerful methylator [1].)

Another aspect is worth a mention. Under physiologic conditions, the reversibility of a reaction depends not only on the free energy changes involved, but also on what happens to the reactants and products. A large supply of reactants, or rapid removal of reaction products, can make the reaction physiologically irreversible. Applying this principle to the catecholamine biosynthesis pathway:

A steady supply of oxygen is available from the atmosphere—this drives the tyrosine and dopamine hydroxylation reactions in the forward direction.
The dihydrobiopterin produced by tyrosine hydroxylase is scavenged by reduction to tetrahydrobiopterin, which further takes part in the tyrosine hydroxylase reaction [1].
The carbon dioxide produced by DOPA decarboxylase is exhaled out.

This further adds to irreversibility.

Of course, as mentioned by @user1136 in the comments, it is theoretically possible to have a "reverse" pathway by coupling to ATP hydrolysis. However, I could not find any such pathway in database searches.

Summary: To the best of my knowledge, humans cannot convert catecholamines back to tyrosine.

Reference

Nelson DL, Cox MM. Lehninger principles of biochemistry. 6th ed. New York: WH Freeman and Company; c2013. Chapter 18, Amino acid oxidation and the production of urea; p 695–730.


Tool for translating chomosome, index numbers to sequence information

You can write a small script to do that. Basically you just have to print a string from position-x to position-y. Explaining how to do that is not really on-topic here.

From available tools you can use getfasta from the bedtools package. This requires a BED file, or a GTF file  as an input. The three column format as in your question will also work but usually the orientation (+/-) is also important to fetch the right sequence; otherwise all sequences would be fetched from the + strand only. GTF format is a bit different: the three columns in your question would be the first fourth and fifth column in the GTF. Seventh column holds the orientation.

bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

(or):

getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

There is another one called gffread which comes with the tophat package.

gffread takes a GTF/GFF file as an input and gives you a fasta file of sequences corresponding to the positions listed in the GTF file. The third column (feature) should be exon or transcript as this tool was actually designed to extract transcript sequences.

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf


Broad question. Summary:

The innate immune system processes everything. When it senses that something is dangerous it tells the adaptive immune system, that is T and B cells, that this thing I'm holding is dangerous (via coreceptors and cytokines).

T and B cells that are specific for this dangerous protein (or sometimes non-protein) are activated.

Ideally T and B cells that react to self proteins are deleted. These are from central tolerance mechanisms when the cells are developing (T and B cells are tested against self proteins; if they react they die) and in the periphery (once they're mature) by them only getting activated by the innate immune system and other mechanisms. There's also T regs which regulate the immune system by preventing any cells that react to self proteins from being activated.

Autoimmune disorders are caused by a break down of these mechanisms.


Basic question about symbiosis( or about kinds of symbiosis)

I see that there exists some confusion over the meaning of Symbiosis itself [in reference to the comments and answer(s)].

Your question/ query seeking information about "some type of Symbiosis" that harms one organism without affecting the other in any form is very much legitimate.

Amensalism (as responded by Sanjukta) is indeed the answer, but saying that "No. There seems to be no intimate association (symbiosis) that does not benefit any partner" is suggesting that Amensalism is not Symbiosis (which is not true).

Amensalism is one of the types of symbiotic associations only (Symbiosis is nothing but 'Living Together' of two / more organisms - which may or may not benefit/ harm either or both or none of the parties involved in the association).

Point to be taken is that, Symbiotic relation refers to the members of two different species (i.e., two populations) engaging in interaction and the interaction can be of any type (Amensalism is just another Symbiotic association).

Edit:
If one looks into the Etymology of the word, Symbiosis, he/she should be able to decipher the meaning of Symbiosis:

One may support the argument using latest updation of Encyclopedia of Evolutionary Biology (Amensalism=Symbiosis) and the classical example of Walnut tree (which tends to kill or inhibit the growth of shrubs that grow around its roots) may be cited. Their growth is inhibited,  but their niche still remains the same. More importantly, the Honeybee - wasp relationship (a long term one) is best fit for Symbiotic Ammensalism.

So, Mutualism, Commensalism, Amensalism, are all Symbiotic Relations.

References:

Miami College of Arts and Sciences, Department of Biotechnology Lecture Notes

Wiki Link about Biological Interactions


What's the mechanism behind 'losing heat through your extremities'?

Your extremities lose heat at a faster rate than the rest of your body because they have higher surface area per unit volume. Heat exchange happens at surfaces, so if you have more surface, you transfer heat more quickly. Imagine you have a sphere of water with 1L volume, and a long cylinder of water, also 1L, lets say 1cm wide, the sphere will hold heat longer because it has less surface area per unit volume.

Why does losing heat through extremities cool the rest of your body? Because of your blood. As blood runs through your core, it takes heat from surrounding tissues. The blood carries that heat to the extremities, where cooler tissues pull it away from the blood. It's kind of like how the coolant in your car takes heat from the engine block to the radiator.

When it is very cold, your body will reduce blood flow to the extremities to save heat, making your fingers vulnerable to frostbite. However, it cannot stop bloodflow, those tissues still need oxygen, so you still lose some heat.


pH affects the structure of all macromolecules that compose bacteria, and indeed all cells.

Here's a shortlist of examples:

Lipids

Lipids are hydrolyzed by extreme pH levels. They undergo chemical reactions and fall apart into constituent molecules, which may be toxic. The membrane is made of lipids; if it is disrupted, the cell ceases to exist.

Nucleic acids

At low pH, RNA and DNA hydrolyze - bonds are broken between individual bases (phosphodiester bonds) and nitrogen bases break off from the (deoxy)ribose groups. Structures and hydrogen bonding (necessary for DNA replication or transcription of genes) are impaired.

In alkaline conditions, DNA typically denatures but remains intact. Structures and hybrogen bonding are still strongly impaired though.

Protein

Low or high pH environments affect ionization of amino-acid functional group ionization. This affects hydrogen bonding in such a way as to denature the molecule, because it adopts very different conformations. This of course renders the protein or enzyme non-functional, and may cause it to aggregate or become cytotoxic. If any one of the hundreds of essential enzymes fails to function correctly, a bacterium will die.

Potentials across membranes

Changes in pH have drastic effects on proton concentrations both in and outside the bacterium. Respiration depends on a concentration gradient of protons. Low or high pH will make it difficult for cells to establish a potential (different in concentration across a membrane). This gradient must be upkept for a bacterium like E.coli to generate energy, and it's difficult if protons are being neutralized or are in sheer excess!

Any one of these is enough to have a bactericidal or bacteriostatic effect! This is also why cells that do live in slightly alkaline or acidic environments have to specialize, and they have narrow windows of pH that they can survive under, because they have to compensate so much to counteract the protonation or lack-thereof in their environments.


Conductance is the inverse of resistance, and measures how much of a given substance flows throught a channel. In this context, it means how many calcium ions enter the cell in a period of time.

There are at least two ways potassium channels may prevent the calcium to enter in the cell.

1) Potassium intake by ion channels decrease the membrane potential, restoring it to its rest state. Since many calcium channels are voltage-dependent, a reduction of the membrane potential would close them, effectively decreasing the calcium conductance.

2) Potassium channels may be coupled to different signaling pathways (i.e. G proteins), wich may affect indirectly other calcium channels.

In the case of opioid receptors it seems to be the first mechanism. With potassium channels open, the neuron is less likely to be activated, because it needs higher stimulation to reach the action potential. Calcium channels open in neurons mainly during action potential events (althought they may exist other calcium channels that open in other conditions, i. e in response to hormones or neuromodulators).


Do humans have the hyaloid canal, after all?

Yes, humans do have the hyaloid canal.

Schematic diagram of the human eye (reference)

For function and other information, please refer to this journal article.


Lost Ability to Regenerate Body Parts during the Transition from Amphibians to Mammals

Regeneration of limbs in amphibians is an adaptation where new limbs are generated by dedifferentiated cells. This process is tightly linked to the embryonic program which, in most animal cells, is a difficult program to access once terminal differentiation has occurred (but it's possible, e.g. induced pluripotent stem cells).

Of note, amphibians have a unique life cycle that includes metamorphosis. It is thought that organisms with more diverse stages in their development may have increased potential for regeneration. Mammals, after birth, do pass through multiple stages of development, but these stages are largely continuous.

So the quick answer is: mammalian limbs are made up of terminally differentiated cells (and specialized stem cells) with high barriers of reprogramming. They're difficult to reprogram because there hasn't been strong selective pressure to do so. Limb regeneration might seem like a great adaptation, but it doesn't seem to be that important for the success of mammals. Additionally, selection for "maintaining a full set of functional limbs" could evolve many different ways. For example, primates may have evolved behaviors or reinforced anatomy that reduces their risk of injuring a limb. Also, larger animals are probably less likely to have limbs removed just given their size. And if they do, it may have little effect on their reproductive fitness. A legless amphibian probably finds few, if any, mates.

Yun Gates, and Brock. Regulation of p53 is critical for vertebrate limb regeneration, PNAS 2013


Arabidopsis thaliana RCSB active site gene mutant

I can tell you generally how to go about it.

Go to table S2 from the paper and download the spreadsheet.  You can search RCSB for each gene symbol. There are 2400 individual genes and there are probably over 1000 alias genes, so that's a lot of searching.  You can do this en masse by using a python script and a library like BioPython, or you can put each symbol into the search box at RCSB.org and see if a structure comes up.

You can and should look over that table for phenotypes you think you can actually work with.  Many of the phenotypes in the paper might require a microscope or a good deal of experience with arabidopsis.  E.g. "Embryo defective; Preglobular / Globular" what does that mean?  You can also write the authors for advice but they might be too busy to get back to you.

Cutting down your search like this before you do it would be very helpful.  The number of genes with both an accessible phenotype and a structure will probably be a relatively small list (50?).

Relatively few arabidopsis protein structures are solved, so you will have to do homology modeling - aligning any protein structure sequence(s) you find with the A. thaliana sequence, and deciding where the active site or disruptive mutation would be in the plant gene.

Example: CHY1(CoA Ester Hydrolase) must be solved - searching for "CoA Ester Hydrolase" at rcsb I find a three structures.  the human structure 2DQZ has a lot of annotation associated with it.  This class of enzymes has been studied for a while, so the active site probably has been studied.  A pubmed search should give a lead on where the active site research has been done.  using BLAST to align the structures to the arabidopsis gene or to all other CoA Ester Hydrolases would be an important step to take too.

Hope this helps.


How many diseases can be linked to disruption in the microbiome of a human?

It is an open question and an active area of research. You will not be able to get a definitive answer to your question of number, as each new discovery will add to the total.

As for repopulating, we have not even determined all of the strains of microbes that populate us, many are very difficult to culture in vitro, and we do not know of all the functions for each species, so we do not have a clear picture of which need to be there, which don't, and whether or not some species work together to provide us with a benefit. For certain conditions such as Irritable Bowel Syndrome, one of the treatments that has been tried is fecal transplant.

Do a literature search for recent reviews. Nature Reviews tend to do detailed reviews, especially on topics as in the news as the Human Microbiome. That is probably the best first place to start. Then you can start to drill down into the reference papers that are cited in the review. That will generally give you a good state of play in the field.


What causes the bright flash of light when poking my eye?

Short answer
Pressure phosphenes are believed to be induced by stretch-induced activation of retinal ganglion cells.

Background
Flashes of light (phosphenes) due to pressure on the eye ball are referred to as pressure phosphenes. Based on an electrophysiological study (Grüsser et al., 1989), eyeball indentation presumably tangentially stretches the retina locally, which variably depolarizes horizontal cells. This in turn depolarizes ON-bipolar ganglion cells, while hyperpolarizing OFF-bipolars. Some ON-center neurons also seem to respond to the removal of the deformation. Bipolar cells connect to the retinal ganglion cells. These ganglion cells carry visual information from the retina via their axons in the optic nerve to the brain. Hence, to answer your question: yes, pressure phosphenes are related to activity in the optic nerve.

Reference
- Grüsser et al., Vis Res (1989); 29(2): 181–94


Why does spiral or annular thickening occur in water conducting plant vessels?

Non uniform lignification of xylem vessels is beneficial to a plant in that it enables growth. It is at the unlignified parts of plants that growth occurs since fully lignified tissues are dead and so can not grow. Spiral and annular thickening allows for vessels to elongate and thus allows tissues to expand without breaking the vessel walls.

Water cannot just go on flowing from plant cells because they are not lignified, plant cells have cellulose cell walls and cell membranes which prevent water loss. In addition, water in the xylem is not under pressure so I do not think water would be able to flow out of the xylem vessels except in cases where water is forced to move to adjacent phloem tissues by osmosis during phloem translocation.


Is Valerian extract a diuretic or an antidiuretic?

There is one study that I can find that has been cited in the medical literature that examines individuals taking valerian extract for generalized anxiety disorder. In this paper, there do not appear to be any claims that valerian has any diuretic or anti-diuretic properties. However, that's not to say that those properties don't exist. Additionally, there is no indication that the extract is associated with hyponatremia or hypernatremia, which are two other signs of disorders affecting salt/water balance. Overall, it sounds like if there is a diuretic or anti-diuretic effect of valerian, it is not well-described (yet).


Reference sequence for defining single nucleotide polymorphisms

I don't see your point. If we take e.g. the definition from Wikipedia:

SNP "is a DNA sequence variation occurring when a Single Nucleotide ... in the genome ... differs between members of a biological species or paired chromosomes",

there is no place for reference genome. SNP is just a variable position with (commonly) two alternatives in individuals of the same species. In whole-genome sequencing projects some SNPs can be discovered (namely those which are in heterozygous state), but definitely not all.

One can investigate SNPs and/or use them as genetic markers irrespective of the availability of the reference genome. That's the way one does it for non-model organisms - e.g. utilizing RAD Seq: you discover SNPs simultaneously with genotyping.


How exactly are petri dishes used (e.g. in medicine)?

I think the petri dishes you are referring to are also called agar plates. Agar is a 'growth medium' for microorganisms. It provides the nutrients that the microorganisms need to survive. It can also contain main other 'things', such as antibiotics or pH color change indicators. There are many types of agar, for example, tryptic soy agar is used to grow E. coli. I think the oven you are referring to is called an incubator. Incubators provide the atmosphere, particularly temperature, needed for the organisms to grow. There are many types of incubators. Some microorganisms actually cannot grow in oxygen rich environments, and some only grow at specific temperatures. These organisms must be incubated under their preferred conditions in order for them to grow.

And yes, a lot can be learned from simply looking at the agar with the organisms on it. What exactly can be learned depends on the growth medium (agar or other medium).

To summarize, petri-dishes are just the plastic dishes that contain growth medium. And incubators are usually refrigerator looking things that provide the proper temperature for the organisms to grow. The goal is generally to mimic the natural environment of the organism, but as I stated, scientists often add many other things to the environment for experimental and diagnostic purposes.

Here is a list of common agars used in bacteriology http://learn.chm.msu.edu/vibl/content/differential/


Transpiring and panting are ways to regulate body temperature. When sweat evaporates, it cools the skin, and panting releases heat through the mouth. Horses, humans and even plants transpire for this reason, while dogs and birds pant. But how do cats release heat?
In fact, cats sweat through their paws. It appears that a cat after it has been frightened may leave wet pawprints on the floor. Although it's all over the internet, I couldn't find a convincing picture and as a cat lover, I've never noticed this phenomenon. That aside, cat's paws have little surface area, and cannot provide much cooling power. Instead, felines have other, more effective strategies to adjust their core temperature. Like dogs, they often sprawl out on cool surfaces (Fig. 1), or they seek out the shade on hot days. They also tend to sleep a lot, which reduces core temperature and is preferable of being very active in hot times in terms of body temperature (Fig. 2).

Fig. 1. Sprawling cat. source: Columbian blogs

Fig. 2. Cats in the shade. source: Cat memes
Source
- Indiana Public Media


Why is it so important to avoid infection of lacerations to the scalp?

Deep lacerations of the scalp that penetrate the fourth layer (area of loose connective tissue) have an increased risk of infection. This is because pus and blood spread easily within it. This can easily pass into the cranial cavity along the emissary veins Therefore, infection can spread from the scalp to the meninges and could lead to meningitis.