Insect identification - Is this a bedbug?

Unfortunately, you're the first I've seen on here actually to have a bed bug.
See  this picture  from University of Kentucky for comparison:

Here is one moving (more footage & info here):

Below is a picture from Bed-Bugs-Handbook.com demonstrating the relative size and appearance of 6 different life (molt) stages:

From Left to Right: Nymphs to adults both before (top row) and after (bottom row) feeding and becoming engorged with blood.

General Info:
Bed bugs are parasitic insects of the cimicid family that feed exclusively on blood. Cimex lectularius (or the common bed bug) is the most well known species as it is the one that feeds primarilly on human hosts and infests human dwellings. These insects often dwell in beds, couches or other upholstered furniture, and they are also known to live in cracks and crevices in walls, behind wallpaper and wood paneling, or under carpeting (Krueger 2000).
They usually feed nocturnally, and in the absence of allergic rashes from their bites, their presence can go unnoticed. The first signs of a bed bug infestation are often the bed bugs themselves or small dark stains bed bugs can leave behind.

See this EPA page for more information about locating bed bugs in a potential infestation.

Description
From University of Florida:

The adult bed bug is a broadly flattened, ovoid insect with greatly reduced wings (Schuh and Slater 1995). The leathery, reduced fore wings (hemelytra) are broader than they are long, with a somewhat rectangular appearance. The sides of the pronotum are covered with short, stiff hairs (Furman and Catts 1970). Before feeding, bed bugs are usually brown in color and range from 6 to 9.5 mm in length. After feeding, the body is swollen and red in color (USDA 1976).

Nymphs and larvae are smaller than adults, with late-stage nymphs being about 4.5mm long. (see here for size ranges). However, only adult females can lay eggs (see here and here for sexing tips). Their small (~1/10") white eggs are laid in clusters in mattresses, furniture, or in cracks in the wall, baseboard, or floorboards. (See here for more egg info).
Do you have a problem?
From Wikipedia:

Certain signs and symptoms suggest the presence of bed bugs; finding the adult insects confirms the diagnosis.

However, other than being a nuisance (e.g., having a "gross" factor + some skin conditions such as rashes), bed bugs have not been known to transmit dangerous human diseases (e.g., see Dolling 1991 and Kolb et al. 2009)
What to do:
Below, are a number of reputable and useful resources for handling and ridding yourself of bed bug infestations:

Bed Bugs: Get Them Out and Keep Them Out (U.S. EPA)

How to Treat Bed Bug Bites and Find the Pest (U.S. pest control company Terminix)

Bed Bugs: How to Get Rid of Bedbugs (pest-control company Orkin)

Finally, a quick search for "bed bug" on this site as well as visiting this reddit page can provide info for a myriad of species that are often mistaken to be bed bugs (e.g., carpet beetle larvae, psocids, fleas, ticks, etc.). Again, unfortunately, you're the (un)lucky winner and do in fact have a definitive specimen.

Citations:

Dolling W.R. 1991. The Hemiptera. Oxford University Press, New York, New York.

Kolb, Adam, Glen R. Needham, Kimberly M. Neyman, & Whitney A. High. (2009). "Bedbugs". Dermatologic Therapy. 22 (4): 347–52. doi:10.1111/j.1529-8019.2009.01246.x. PMID 19580578.

Krueger L. 2000. Don't get bitten by the resurgence of bed bugs. Pest Control 68: 58-64.


evolution and mutation of microrganisms against medicines?

A few throughts about this: Microorganisms have a short life span but they replicate very fast with a short generation time. So this create vast amounts of "offsprings" with some mutations naturally occurring. Due to this large numbers the chance of developing resistances is much higher than for slowly replicating species.

This is especially true, when the selection pressure is high, as this is the case when you treat with drugs which usually kill these microbes efficiently. When people are not taking these drugs (antibiotics for example) according to the necessary scheme, the concentration of the drug in the body is lower than necessary to kill of all microorganisms. This leads to the survival of microorganisms which are a bit adapted to survive the drug and so on.

The real problem are people who are not following their treatment regime necessary and thus causing resistancies. A case for this is tuberculosis. Regarding taking medication: Always take them when necessary and leave them out when not. A simple cold for example can not be treated antibiotics since it is viral, the secondary middle ear infection usually can.


holding an object is usually a task that requires visual and mechanical processing (i.e. what the object looks like (i.e. what material does it seem to be made of, what is your former experience with that material, how heavy does it feel) and muscle memory.
according to the physiological definition of a reflex:

Reflex, in biology, an action consisting of comparatively simple segments of behaviour that usually occur as direct and immediate responses to particular stimuli uniquely correlated with them.

according to this same source, innate reflexes such as walking, blinking and swallowing require skeletal muscles but are still considered reflexes despite the fact that for some of these tasks (such as walking and standing) we do not know from birth (meaning reflexes can be taught and unlearned/lost).
There are other reflexes such as intestinal smooth muscle contractions etc... that we are usually completely unaware of and are controlled by the central nervous system (CNS) unconsciously.
The response to pain is also a reflex; the thermal/mechanical neural sensors in your arm (for example) send the information to your spine which directly sends a signal to your muscles to contract in order to avoid/release the object.
the palmar grasp reflex is one of many reflexes babies have that they do not need to be taught. Adults usually unteach these reflexes as some of them are not as frequently necessary in later stages of life. Newborn apes for one use the palmar grasp reflex to hold on to their mothers (it is possible that is where that reflex came from from an evolutionary standpoint).
consider that all reflexes are caused by cues that your nervous system senses and responds to. Some of these reflexes can be controlled and others not and may vary depending on your environment. A famous example of this is the pavlov's dog experiment which proved that you could also be conditioned to respond to a certain stimulus. In your case, seeing or feeling the cup is supposed to provide a stimulus to your brain reminding you that you are holding an object that requires a specific mechanical maneuver which you have learnt over time.


Interpreting qPCR curves: how to find Ct value in my case?

The software is correct. $C_t$ values are chosen to be sufficiently above background. As you can see, the background level is very different for two of the curves, so you can't use the same signal threshold for determining their $C_t$.


Why hasn't there been a serious effort to develop an anti-inflammatory that blocks the responsible genes?

Your question is very complex, so for now I'll focus on a few points and answer these first:

  Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.

You are right that all of these options to block genes exist for laboratory or research purposes. Using them on humans as medicine is a lot more complex in a lot of ways though. One main factor I'm not going to discuss much is the cost of all these techniques - which generally a lot more compared to making a simple chemical drug.

Blocking translation
This is a almost a standard experiment for research labs and can usually be done quite specifically (without side effect on most other genes). In oder to achieve a transient (short lasing) effect you usually use RNA knockdown: The introduction of small RNAs, that specifically target the mRNA of the gene you want to knock down, into a given cell with stop transcription in that cells. There are two problems with using this in patients: 1) transformation efficiency: you need to bring RNA into to the cells, which is not a very efficient process. You'll need even higher doses of the stuff to get a strong enough effect in the immune cells you want to target, since it's very hard to specifically target them. 2) The transformation process itself requires either potentially toxic chemicals or viruses to get the RNA into cells, both of which a costly to make and no one wants to take them unless they have to. Taken together this makes RNA knockdown a very bad drug / treatment strategy.

Blocking transcription
The only way to block transcription of a gene permanently is gene editing - which you really don't want to as a short term treatment against inflammation. To make it work transiently you'd have to bring proteins into the cell that bind to and block the genes you want to suppress - inactive transcription factors would do the trick. One (almost minor) problem is that they wouldn't be very specific, so you'd get lots of side effects. The bigger problem is that it's very hard the get a lot of proteins into cells. You'd need large scale transformation and there are many problems with that, which I discussed above.

Stopping the protein/product from exiting its cell
This is an interesting idea, which might actually work - given a few additional years of research. It's probably not possible to this specifically, so you'd generally block the release of proteins from cells. However if you find a drug that only lasts for a few hours it might work. One important caveat is, that the same (or at least a very similar) mechanism is used, when synapses release neurotransmitters - which you definitely do not want to mess with.

There seems to be active research in this area

Blocking its receptor / blocking intermediates

This strategy is very viable in the immune system, where many soluble factors like cytokines with respective receptors are important. Blocking of receptors or soluble proteins can be done by antibodies and there are many people working on this, some antibodies are already licensed by the FDA as drugs for humans. In most cases these are however intended for use in cancer or other more severe diseases, as all of these are immensely expensive.

  Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.

You do not want to this. Inflammation is an important process that keeps your body healthy and permanently disabling it would basically make you immune deficient, which is not a good thing.

  The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.

Biochemical 3D printing will likely never be a thing. It's possible to print e.g. organs with cells, but printing proteins requires molecular construction and it's unlikely we're ever ging to find a system that's better than what nature came up with during a few million years of evolution.
In general though technological advancements should decrease the cost of all these strategies.


How to get phased haplotype from vcf file?

You should be able reformat BAM files to VCF files with PGDSpider.

I find using specific softwares for this type data formatting tends to be error prone and not practical when having a large number of files to reformat, so I personally like to simply read about the format standard and write the code to reformat myself but that's very much a matter of personal preference.


What sample sizes are ideal for carrying out Bayesian Skyline Plots?

I found a PLOS one article that might help. In this they used similar numbers you're planning to use (if i get your question and the article's data right).

  The influence of the sampling scheme was investigated by drawing 40 samples in three different ways: 1) all 40 samples from a single deme, 2) 4 samples from each of 10 demes and 3) one sample from each of the 40 demes in the structured population. These correspond respectively to the local, pooled and scattered

(taken from the above linked article)

So depending on your sampling scenario your 30 samples seems to okay.

Also this is a link for the BEAST FAQ that might be helpful.


Is hair made of protein or dead cells or both?

I found the answer while trying to write the question. Hopefully this helps others

  We usually say that hair is “made” of a protein called keratin—that’s a bit of a simplification. As hairs become part of the shaft, they undergo a process called keratinization, in which they become filled with keratin. So, technically, instead of being made up of pure keratin, hair is made up of dead cells that are filled with and surrounded by keratin.

Source

I'd say some visualisation would be helpful, please add a new answer or propose edits to this answer


The existence of membrane potential is just that: as long as they are alive, cells try to keep their cytosol different from the outside soup, mainly by expelling sodium ions. There is a longer story, with cells pumping other ions in or out, or leaking ions due to the imbalance, but resting membrane potential really revolves around sodium. There is an imbalance in sodium across the membrane, and that makes sodium naturally try to balance out, by trying to leak back in.

I am sure you have heard about the famous sodium/potassium ATPase. It expels sodium ions, while letting in fewer positive ions. It is just the most studied way the cells are going about making sure their innards poorer in cations, that is, negatively charged when compared to their environment.

All these pumps are ATP-dependent, and you would know ATP is the main energy store. So as long as cells live and make ATP, they can maintain this difference between their innards and the environment. Once they die, ATP is gone, pumps stop, and there is no sodium disequilibrium - no membrane potential.

Diffusion potential is an artificial concept that we use in order to make sense of the membrane. We imagine a membrane that opposes sodium movement alone, and we calculate how hard will it be (how much energy must be spent) to keep the asymmetry of low sodium inside - higher sodium outside, were a hole punched in the semipermeable membrane. Luckily, we can use some physics and maths, and figure that this energy is dependent of the ratio of sodium concentrations ([Na]in divided by [Na]out). For typical cells, there are 150 mM Na outside and 15 mM Na inside a cell; physics tells us it will take 62 milli-electronvolts to hold a Na ion out once some hole is found.

If you don't provide those 62 meV and you don't close the doors for leaking, sodium ions will fly in. And that is indeed what happens in depolarization, when sodium gets a chance to move.

These electronvolts are a unit of energy, or work. We can think of a few ways of performing this work on a Na ion that tries to leak in: heat the cell until ions stop caring about direction of movement, hold the outside Na in some tight  chemical structure etc. But the simplest way is to apply an electric field. If you add to the concentration imbalance a 62 mV electrical difference in electrical potential, you stopped the flow of sodium either way. Get a bit less than 62 mV, and the Na ions will carry on their old ways and try to no avail to leak into the cell. Get a bit above 62 mV, and the flow of sodium will be force in the opposite way. Stay on 62 mV and you achieve equilibrium potential: neither direction will have the upper hand.

The picture is way more complex once you factor in the other ions, but the facts are:

resting and action potentials are voltages one can measure across membranes, quite often during cells' lives
diffusion potentials are part of an abstract model
equilibrium potential is something one could impose on a cell - not something that you'd find in natural frequently, yet not plain fiction.


Organisms that use more than the 20+2 commonly occurring amino acids?

At this point in time it appears that no known organisms use amino acids beyond the standard repertoire of the 20+2 common amino acids (the +2 being selanocysteine and pyrrolysine) to construct proteins directly from the ribosome. The extensive review provided by Ann Rev Genetics 2017 mentions only selanocysteine and pyrrolysine, and no other amino acids beyond that.


With respect to the giraffe claim, this article seems relevant:

D. M. Henderson, D. Naish, Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis, J Theoretical Biology 265 (2010) 151-159.

It cites several non-"random person on the internet" claims that giraffes cannot swim:

  It is generally thought that giraffes cannot swim, but relevant
  observations are few. Shortridge (1934) and Goodwin (1954) state that
  giraffes were poor waders and unable to swim. Crandall (1964)
  discussed a case where a captive giraffe escaped from a carrying
  crate, ran to the end of a jetty, and fell into the water. The animal
  reportedly sank without making any attempt to swim. MacClintock (1973,
  p. 54) stated ‘Giraffes cannot swim. Rivers are barriers they do not
  cross’. Wood (1982, p. 20) noted that ‘Because of its extraordinarily
  anatomical shape the giraffe is one of the very few mammals that
  cannot swim – even in an emergency! Deep rivers are an impassable
  barrier to them, and they will avoid large expanses of water like the
  plague’.

They then go on to show that a model giraffe could plausibly swim, writing: "For practical and ethical reasons we are unable to use live giraffes..."

They conclude:

  In summary, the results and speculations of this study show that it is
  not impossible that a giraffe could propel itself in water, but in
  terms of energy efficiency relative to that of the horse, it would
  appear that the costs of aquatic locomotion might be too high. It is
  reasonable to expect that giraffes would be hesitant to enter water
  knowing that they would be at a decided disadvantage compared to being
  on solid ground.


Species Identification: large shiny black beetle, Detroit USA

You found a stag beetle (family Lucanidae).

Although the males are much more readily recognized with their large "stag antler" shaped mandibles, these species are often sexually dimorphic with females having much smaller mandibles (e.g., see here). However, in some species the males' mandibles are likewise diminished and not stag shaped.

According to the Wikipedia page:

  Currently, the only means of identification of world species is the illustrated text by Mizunuma, T. and S. Nagai. 1994. The Lucanid Beetles of the World. Mushi-sha, Tokyo. 337 pp. based on the work Catalogue illustré des lucanides du globe in Encyclopédie Entomologique (series A 27: 1-223) by Robert Didier and Eugene Seguy.

So without this guide (and without known dimensions of your specimen), an exact identification will be very difficult.

However, your species looks very similar to a male specimen of Lucanus placidus.

Additional pictures (such as the one below) can be found here.

According to Wikipedia, L placidus is 22–35 mm long, has two or more teeth on its jaws and has dark femora. The species is sometimes found in soil and it does live in Michigan:

We can rule out Lucanus capreolus because the color is wrong:

  [L. capreolus is] dark reddish brown in color with a smooth, shiny elytra; [their] femora are orange-brown.


How does kissing burst a person's ear drum?

"The kiss reduced pressure in the mouth, pulled the eardrum out and caused the breakdown of the ear"

All you really need to understand the mechanism given this statement is anatomy: the nasal cavity and ears are connected through the https://en.wikipedia.org/wiki/Eustachian_tube so pressure changes in the mouth can be communicated to the ears. A typical individual would experience this when having the ears 'pop' in response to changes in outside pressure due to elevation or swimming underwater.

  is there any kind of anatomical disposition that would make the woman more susceptible to this happening

Although I have not conducted a survey with a sufficient sample size, I don't believe most peoples' passionate kissing involves forming a mouth-to-mouth seal and then sucking/inhaling forcefully to create enough of a vacuum to damage someones' eardrum. It seems that the anatomical disposition most likely to make a woman or man more susceptible to this happening is having a kissing partner with this unorthodox approach. As commenter @kmm points out, you would also need to seal the nose, so having a partner who plugs your nose during kissing or having nasal congestion would also be necessary.

With 7 billion+ humans, though, there is a large enough sample that statistically rare events occur all the time, in part because there is also a near-infinite set of possible rare events.


Here is an educated guess: firstly the typical dental anesthetic is lidocaine which tastes very bitter. Secondly, a bitter taste if often misclassified as sour. Thirdly, sensory thresholds (the amount of a compound required to detect its taste) is temperature dependent and lower at cooler temperatures. In other words, I assume that drinking cold water made you able to detect small remaining traces of bitter lidocaine that were too small to detect at warmer temperatures, and that you misclassified as sour.

Wei, Y., Nedley, M. P., Bhaduri, S. B., Bredzinski, X., & Boddu, S. H. (2015). Masking the bitter taste of injectable lidocaine HCl formulation for dental procedures. AAPS PharmSciTech, 16(2), 455-465.

https://www.sensorysociety.org/knowledge/sspwiki/Pages/Sour-Bitter%20Confusion.aspx

McBurney, D. H., Collings, V. B., & Glanz, L. M. (1973). Temperature dependence of human taste responses. Physiology & Behavior, 11(1), 89-94.


Forced breathing, a.k.a hyperventilation, causes hypertonic dehydration.

According to Greger and Windhorst, Comprehensive Human Physiology (2014):

  Loss of more water than NaCl leads to hypertonic dehydration and hypernatremia. In this condition the intracellular volume is marked decreased, whereas the extracellular volume is less compromised. Possible causes of hypertonic dehydration include excessive loss of hypotonic fluid (e.g., sweat) or hyperventilation.

Therefore, the decrease of the size of red blood cells is due to the dehydration following hyperventilation.

Source:

Greger, R. and Windhorst, U. (2014). Comprehensive Human Physiology. Berlin: Springer Berlin.


Insects were the first animals to conquer land. Vertebrates followed later. So there may not have been an absence of a food supply. Also, the ability to leap to land for safety to avoid a predator is useful if said predator cannot follow. similar in manner to flying fish.


Does an increase in cancer cell traction forces increase metastasis of the cancer cells?

You have pointed out in your question that two different research groups have differing conclusions about your question.  The answer is not known which is why they are studying it.

Their differing results probably turn on how cell traction force is defined and the experimental system used to measure it.  It may not even be consistently ture - for example metastasis via the lymphatic system may be mediated by different properties than metastasis through the bloodstream or local tissue invasion.


How can a non-mutagenic agent be carcinogenic?
An agent that causes overexpression of oncogenes or inhibition of tumor suppressors, would be carcinogenic but not mutagenic.
HPV, for instance, produces proteins that cause inactivation and degradation of tumor suppressors, p53 and pRb[1].
Regarding alcohol. As you guessed, alcohol is metabolized to form acetaldehyde which is mutagenic as well as carcinogenic. Moreover, alcohol metabolism can lead to production of ROS which can also be mutagenic. Overall, alcohol is considered a potential carcinogen by IARC due to the observed effects. These classifications are not based on molecular mechanisms.
More recently, a study by Riva et al (2020) has found that only three out of the twenty carcinogens they tested had a mutagenic effect.
Thus, to conclude, not all carcinogens are mutagens.

Reference:
 [1] IARC Working Group on the Evaluation of Carcinogenic Risk to Humans. Human Papillomaviruses. Lyon (FR): International Agency for Research on Cancer; 2007. (IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, No. 90.) 4, Molecular Mechanisms of HPV-induced Carcinogenesis.


There is both a set "list" of agents, but more importantly, a set of properties that an organism needs to be in order to be truly worrisome.

First, the list:

The CDC classifies agents into one of three categories, Class A, B, or C.

Class A: These are organisms that are hard to control, highly transmissible, and lethal:

Anthrax (Bacillus anthracis)
Botulism (Clostridium botulinum toxin)
Plague (Yersinia pestis)
Smallpox (variola major)
Tularemia (Francisella tularensis)
Viral hemorrhagic fevers (filoviruses [e.g., Ebola, Marburg] and arenaviruses [e.g., Lassa, Machupo])

Class B: These are organisms that are fairly easy to disseminate, make people sick but don't necessarily have high mortality rates, and may be difficult to detect.

Brucellosis (Brucella species)
Epsilon toxin of Clostridium perfringens
Food safety threats (e.g., Salmonella species, Escherichia coli O157:H7, Shigella)
Glanders (Burkholderia mallei)
Melioidosis (Burkholderia pseudomallei)
Psittacosis (Chlamydia psittaci)
Q fever (Coxiella burnetii)
Ricin toxin from Ricinus communis (castor beans)
Staphylococcal enterotoxin B
Typhus fever (Rickettsia prowazekii)
Viral encephalitis (alphaviruses [e.g., Venezuelan equine encephalitis, eastern equine encephalitis, western equine encephalitis])
Water safety threats (e.g., Vibrio cholerae, Cryptosporidium parvum)

And finally, Class C, which are emerging threats that may be dangerous if engineered largely due to their novelty and their potential lethality/transmissability. The CDC uses examples like Nipah virus and hantavirus.

So that's the list of what the CDC thinks is a big deal. You'll note influenza isn't even on there. I'd argue that any given novel influenza strain belongs in Class C, and likely not Class A because, while potentially both transmissible and virulent, a known vaccine exists and simply needs to be formulated.

In terms of properties for an organism, I'd suggest the following, in no particular order (it likely depends on what said organism is meant to do):

Highly virulent: The disease needs to be able to cause human disease, with high rates of both morbidity and mortality.
Highly transmissible: Unless the goal is to cause a "one off" incident, the disease needs to be able to establish a productive chain of human-to-human infections. Humans can't be a dead-end host. Ideally, this needs to be direct human to human transmission, rather than a vector born disease like West Nile.
Stable and amenable to engineering. It needs to be something that's easy to culture and grow in large numbers. This one often gets overlooked somewhat, but despite the fact that its now somewhat commonplace, bioengineering isn't exactly easy.
Not amenable to treatment. The organism needs to not be easily treatable - broad spectrum antibiotics, existing vaccine stock, etc. mean that the normal public health infrastructure can address, or at least mitigate, an attack. For an attack to be truly effective, it needs to swamp existing infrastructure, and one way to do that is to necessitate intensive, unusual care in hospitals and out of the ordinary action on the part of public health officials.


How do NSAID's work and what are the differnces between COX-1 and COX-2?

NSAIDs work by inhibiting COX-1 and/or COX-2. These are the key enzymes in prostaglandin biosynthesis. Prostaglandins act as messenger molecules in the process of inflammation and therefore can cause pain and other inflammatory symptoms. Source

COX-1 is normally present in different tissues of the human body and is for example important for maintaining the stomach lining. By contrast COX-2 mediated prostaglandin synthesis is only induced by injuries and inflammation. The analgesic effect of NSAIDs is therefore mainly based on the inhibition of COX-2.

There are to different classes of NSAIDs, non-selective (aspirin, naproxen, ibuprofen, ...) and COX-2 selective (celecoxib, parecoxib, ...-coxib). Due to the different roles of COX-1 and COX-2 these different drug classes have different adverse effects and differ in their analgesic effect depending on the dose. E.g. use of aspirin can lead to ulcers of the stomach or duodenum while COX-2 selective drugs do not cause gastric problems (but others).


Are coronaviruses gaining an evolutionary advantage?

It is not a coincidence, but it doesn't have to do with sudden evolutionary changes, rather with human behavior.
The three viruses you mention are zoonotic — they can infect different species, including humans.
Increased development of formerly untouched lands is bringing people into contact with animals (and existing, but formerly unknown zoonotic pathogens) in greater numbers.
Humans bring the virus back to concentrated human populations — cities, say — either being infected themselves, or bringing back infected animals for consumption. This increases the opportunities for further spread.
With the help of global leadership that is corrupt, incompetent, or antiscience, the multiplier effect of repeated infections in cities turns a small pool of cases into a pandemic. Rinse and repeat.

The risk of emerging infectious diseases such as COVID-19 from animals is on the rise, in large part because of our environmental footprint and the blurring between the natural and the built environments. Increasingly, humans, livestock and wildlife are interacting in new and unexpected ways, bringing new species – and their resident infections – together with unpredictable results.
Climate change is accelerating the loss of animal habitats and the ways humans change the land. Cutting down old-growth and rain forests, which harbour a rich biodiversity of life, to create agricultural or pastoral land potentially brings people and livestock in closer contact with previously isolated populations of bats, and other animals harbouring previously unencountered disease. In turn, biodiversity loss threatens natural food sources which means animals seek other sources of food found where people live. As climate change causes large disasters like floods and drought, human food sources are also lost, and growing food insecurity pushes people to further encroach on animal habitats, increasing animal contact and contributing to the trade in wildlife.
The speed and magnitude of environmental change has implications for future epidemics and pandemics. The first few cases of COVID-19 have been traced back to a ‘wet market’ that contained wild animals sold for food or medicines. Such markets can be ideal environments for zoonotic spread as the unusual mixing of animals (which is not common in the wild) can provide opportunities for viruses to jump between species, and potentially then to people.

Development isn't just loosing coronavirus — there are other pathogens that have been loosed by encroaching on their natural reservoirs:

We invade tropical forests and other wild landscapes, which harbor so many species of animals and plants — and within those creatures, so many unknown viruses. We cut the trees; we kill the animals or cage them and send them to markets. We disrupt ecosystems, and we shake viruses loose from their natural hosts. When that happens, they need a new host. Often, we are it.
The list of such viruses emerging into humans sounds like a grim drumbeat: Machupo, Bolivia, 1961; Marburg, Germany, 1967; Ebola, Zaire and Sudan, 1976; H.I.V., recognized in New York and California, 1981; a form of Hanta (now known as Sin Nombre), southwestern United States, 1993; Hendra, Australia, 1994; bird flu, Hong Kong, 1997; Nipah, Malaysia, 1998; West Nile, New York, 1999; SARS, China, 2002-3; MERS, Saudi Arabia, 2012; Ebola again, West Africa, 2014. And that’s just a selection. Now we have nCoV-2019, the latest thump on the drum.

The three viruses you mention are serious. MERS and SARS have high fatality rates. The third (SARS-CoV-2) is highly contagious. These attributes disrupt everyday life.
But the aforementioned and other viruses are also serious for similar reasons. Zika, for instance, can cause life-altering birth defects, has been known about for decades, and human-caused climate change has been enabling it to spread to more densely-populated areas.
Evolution — natural selection — takes place over thousands to millions of years. Human behavior has changed the earth only within a few hundred years, much of it in the last century or so.


Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two 20 bp segments of each 40mer.


This question has been asked in different forums and many of the answers say that there is no nociception in insects. This book, however claims that Drosophila do have heat induced nociception and is mediated by TRPA ion channels. Also, there is a gene called painless whose mutation causes loss of nociception.


Why are (some) cats attracted by bleach?

I can't give a definite answer, and there's nothing in the literature about this specifically, but perhaps some relevant information and a suggested behavioural experiment will help.

Background
Firstly, I assume you are talking about sodium hypochlorite (which is usually what people mean by bleach)? If so, there are several compounds your cat could be reacting to. Chlorine is an obvious candidate, which is released as sodium hypochlorite decomposes in solution. Additionally, bleach can react with various organic materials to release a variety of volatile organic compounds (VOCs), which your cat might be able to smell. In addition to also releasing chlorine gas, the same suite of VOCs are released when the chlorine in chlorinated tap water reacts with organic contaminants (Odabasi, 2008). The VOCs include chloroform and carbon tetrachloride.

Next, cats are known to exhibit modified behaviour in response to a variety of compounds. Some are suspected pheromone components of cat urine, such as felinine (Hendriks et al, 1995) and its breakdown products, such as MMB (Miyazaki et. al, 2006).

Some cats also react to externally-produced compounds with a particular response called the 'catnip response', which involves rubbing the face on the ground or other objects, shaking the head, rolling, etc. (Tucker & Tucker, 1988). Not all cats exhibit the response, around 50-50% do, and susceptibility is genetic and heritable. Some sources eliciting the catnip response include:

nepetalactone released from catnip (Nepeta cataria)
actinidine released from valerian (Valeriana officinalis)
essential oil of Actinidia macrosperma (Zhao et al., 2006)
the compounds epinepetalactone, dihydronepetalactone, isodihydronepetalactone, neonepetalactone, iridomyrmecin, boschnialactone, onikulactone, boschniakine, actinidiolide and dihydroactinidiolide (Tucker & Tucker, 1988)

In general all the catnip response elicitors share a two-ring structure, which is not to my knowledge shared by any of the volatiles given off by bleach.

A possible experiment
So, two obvious possibilities (regarding what type of behavioural response is being elicited) are that either:

your cat is interpreting the volatile as a pheremone and therefore as some sort of sexual or territorial signal, or
it is showing the catnip response

As a first experiment, you could check whether your cat (and any others you can get hold of - in an ethical way) respond to bleach and/or to catnip. If the cats do not exhibit the catnip response to catnip, they aren't exhibiting it in response to bleach, and thus some other explanation is more likely.

As a second experiment, you could make a detailed observation of the precise behaviour shown in response to bleach. Compare it to that exhibited when the cats encounter catnip (depending on the outcome of the first experiment) and when they are oestrous (if female) or encounter an oestrous female (if male). You could also compare to the response to the urine of other (male and female, familiar and unfamiliar) cats.

An experiment you shouldn't do
If you wanted to find out which chemical your cat is responding to, you could allow your cat to sniff pure chlorine which hasn't encountered organic contaminants, as well as chloroform, and carbon tetrachloride. However, all three of those compounds are extremely dangerous and could easily kill you or your cat, so please don't.

I general, I would caution against exposing your cat to bleach, because it can induce serious health effects depending on dose and mode of exposure, ranging from asthma to third-degree burns to carcinogenesis. If they are attracted to it, that is a good reason to keep it away from them to prevent them ingesting it, which is more harmful than inhaling the fumes.

I can't comment on whether the behaviour is acquired as result of domestication, but that too could be tested by comparing the reaction of a large sample of wild cats (!).

References

Hendriks, Wouter H., Paul J. Moughan, Michael F. Tarttelin, and Anthony D. Woolhouse. “Felinine: a Urinary Amino Acid of Felidae.” Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 112, no. 4 (December 1995): 581–588.
Miyazaki, Masao, Tetsuro Yamashita, Yusuke Suzuki, Yoshihiro Saito, Satoshi Soeta, Hideharu Taira, and Akemi Suzuki. “A Major Urinary Protein of the Domestic Cat Regulates the Production of Felinine, a Putative Pheromone Precursor.” Chemistry & Biology 13, no. 10 (October 1, 2006): 1071–1079.
Odabasi, Mustafa. “Halogenated Volatile Organic Compounds from the Use of Chlorine-Bleach-Containing Household Products.” Environ. Sci. Technol. 42, no. 5 (2008): 1445–1451.
Tucker, Arthur, and Sharon Tucker. “Catnip and the Catnip Response.” Economic Botany 42, no. 2 (1988): 214–231.
Zhao, Yun-peng, Xiao-yun Wang, Zhi-can Wang, Yin Lu, Cheng-xin Fu, and Shao-yuan Chen. “Essential Oil of Actinidia Macrosperma, a Catnip Response Kiwi Endemic to China.” Journal of Zhejiang University. Science. B 7, no. 9 (September 2006): 708–712.


What kind of "size" does SDS-PAGE separate by?

The protocol for SDS-PAGE uses a solution of sodium dodecyl sulfate (SDS, also known as lauryl sulfate) to solubilize and linearize folded protein molecules and give them a negative charge that is approximately proportional to the length (and more or less to the mass) of the protein, depending on its sequence. Some sequences may bind the SDS more readily, while others may not, so the relationship between charge and mass/length is not perfect.

The linearized (and often reduced, typically with DTT or β-mercaptoethanol) protein solution is separated by polyacrylamide gel electrophoresis (PAGE), wherein the negatively-charged protein(s) migrate though the pores in a gel due to an electrical field applied across the gel. Smaller proteins run faster, and are visualized (by many different methods) nearer to the bottom of the gel, whereas larger proteins are closer to the top. Typically, a standard molecular weight marker is run alongside the samples of interest so that approximate molecular mass can be gauged. A number of situations may cause the samples to not migrate exactly according to their calculated molecular mass, including high levels of glycosylation, phosphorylation, or other post-translational modifications, as well as variable binding to the SDS as discussed above.


What is this strange mantis-like coral reef dwelling creature?

The specimen is indeed a mantis shrimp (to be specific, a peacock mantis shrimp).

These predators have highly sophisticated vision and, depending on the species, either spearlike limbs or clubs that move so fast the water can't keep up, causing dangerous cavitational effects that can even break glass.


Would tinnitus be explained by perpetually-bent/opened hairs in the cochlea?

What you're describing would likely cause hearing loss, which could later result in tinnitus, but not by the mechanism you describe.
Hair cells transduce sound via remarkably fragile connections between stereocilia. The channels are closed until tension pulls the channels open (see Fettiplace 2011 for a review that covers pretty much all of sound transduction including a detailed description of the tip links and channels involved). Disconnection would result in the channels being perpetually closed, not perpetually open.
Anything like the trauma you describe would irreversibly damage the tip links and sound transmission would fail. There are mechanisms in the ear to prevent this sort of damage, but for sufficiently loud sounds the damage is not avoidable.
@AliceD has another excellent answer on tinnitus specifically here for more realistic mechanisms proposed for tinnitus: What is the mechanism behind tinnitus?. These are all centrally derived in some way. In short, the absence of proper input to the auditory processing parts of the brain results in compensation that induces an illusory perception. Similar sensations are experienced in other parts of the body as well, such as phantom limb.

Fettiplace, R. (2011). Hair cell transduction, tuning, and synaptic transmission in the mammalian cochlea. Comprehensive Physiology, 7(4), 1197-1227.


How to supply oxygen to a culture vessel?

Gases are supplied to culture vessels by design. Flasks, for example, may have filtered caps that allow gas in, or microplates with lids that have enough room under the lid to allow a gas exchange interface with the culture medium. Of course with these traditional culture vessels you need to make careful consideration about fill volume, since the gases won't penetrate 100% through the culture medium.

In the case of your paper they cut a large hole in the side of the cup and plugged it with cotton, then fed a small plastic tube through into the cup. They attach a gas line and feed oxygen through the tube. The cotton plug is where the gas will escape back out without letting contaminants in, as the cotton plug acts as a filter. The system seems to have no other outlet, so it makes sense.

In order to control a gas flow rate, you need a regulator of some sort to act as an output control.


When has an organism evolved enough to be called a new species?

I think LuketheDuke's answer is an oversimplification of the biological species concept (possibly resulting from the dictionary having a poor definition). The definition he gives is one of many which are in current use, and is made redundant by many types of organism.

It is important to recognise that because reproduction is not the same process in all organisms, genetic differentiation between individuals occurs in different ways for different groups.

Let's take the definition given in LuketheDuke's answer...

  The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but are not able to breed with members of another species.

Under this definition, lions and tigers (see ligers and tiglons, which are sterile hybrids between the two) would be considered one species, as would donkeys and horses (see mules and hinnys, again sterile hybrids). There are hundreds of other examples of pairs of animal species which can hybridise to produce sterile offspring.

However, these animal hybrids usually only take place with human intervention, by delibrate breeding efforts. Thus we could extend the previous definition to include them...

  The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but do not breed freely with members of another species in the wild.

That last part takes care of the ligers and tiglons. But what if we consider plants? Under the definition I just gave, most grasses (around 11,000 species) would have to be considered as one species. In the wild, most grasses will freely pollinate related species and produce hybrid seed, which germinates. You might then think we could just modify the definition to specify that the offspring must be fertile (i.e. able to reproduce with one another)...

  The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but do not breed freely with members of another species in the wild to produce fertile progeny.

Unfortunately, the situation is still more complicated (we've barely started!). Often wild hybridisation events between plants lead to healthy, fertile offspring. In fact common wheat (Triticum aestivum) is a natural hybrid between three related species of grass. The offspring are able to breed freely with one another.

Perhaps we could account for this by taking into account whether the populations usually interbreed, and whether they form distinct populations...

  The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of populations or meta-populations of related individuals that resemble one another, are able to breed among themselves, but do tend not to breed freely with members of another species in the wild to produce fertile progeny.

This accounts for the grasses, but it still leaves a messy area when you have a hybridisation which establishes - until the hybrid population is segregated away from the parent populations it is unclear whether they still count as the same species.

We could probably live with this situation, except for the fact that bacteria refuse to conform to it at all. Bacteria of the same species, or even very different species, can freely transfer genes from one to the other in conjugation, which combined with fission can result in perfectly replicable hybrids. This is such a common occurence that it breaks even the 'tend to' part of the previous definition, and members of a population can be doing this almost constantly, which negates the segregation requirement.

Richard Dawkins had a go at defining around this, by stating that...

  two organisms are conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides

This partly gets around the bacterial problem and means that bacteria which result from conjugation are a new species. Unfortunately under this definition we might as well not ever bother trying to classify bacteria as billions of new species would be created every day - something which the medical profession might have something to say about. This definition would also mean that those with genetic diseases like trisomy 21 are not human. The final nail in the coffin of this attempt is that there are many species, including frogs and plants, which are very certainly considered a single species by taxonomists but which have some variety in the presence of small accessory chromosomes, which occur in different combinations between individuals.

Let's consider one last option. We now live in the era of genomics where data about genomes of thousands of organisms is accumulating rapidly. We could try to use that data to build a species definition based upon similarity at the nucleotide level. This is often used for bacteria, by considering organisms with less than 97% nucleotide similarity to be different species.

The major point I've been trying to make, though, is that species is not a natural concept. Humans need to be able to classify organisms in order to be able to structure our knowledge about them and make it accessible to people trying to link ideas together. But the natural world doesn't care about our definitions. Ultimately the species concept is different for different groups of organisms and will continue to change over time as our analytical methods and the requirements of our knowledge change. Note that I've deliberately skipped over many historical species concept ideas.

The direct answer to your horse question is "it depends how you want to define a horse".


Neuronal membrane resting potential for large cells

In a typical neuron at rest, potassium is high inside the cell and low outside, with the opposite true for sodium. The membrane is mostly permeable to potassium. Let's ignore the other ions.

The resting potential in this situation will be something like -70 mV. Rest means that the net current flow is zero; however, there is still current: potassium is flowing out of the cell and sodium is flowing in. Therefore, if we turn off the sodium-potassium pump, over time, the concentration gradients will slowly equalize.

The authors are making an assumption that the current is roughly a function of membrane surface area: more membrane = more current. However, the "reservoir" of concentration imbalance is a function of volume: a bigger cell has more total potassium ions than a smaller cell.

Therefore, in a large cell, if the membrane potential is mostly driven by the concentration gradient, and it takes a long time for the concentration inside to equalize with the outside because the current is small relative to the volume, the membrane potential will only change slowly if you use a toxin to stop the sodium-potassium pump.

I don't think the authors are really intending to say anything special about large cells versus small ones, they are just setting up some assumptions under which their argument about the resting potential is going to be most evident. This is a bit like in a physics textbook where you read something like "assume a uniform spherical baseball."

The claim they are making: "the membrane potential is because of the concentration gradient, not the action of the pump itself" is true for all cellular membranes, not just in large cells. This particular piece of evidence they are referring to, however, is going to be most obvious in a large cell. That's all.

If you tried to do this experiment in a very small cell by turning off the pumps and watching the membrane potential, you might erroneously conclude that the pump was responsible for the membrane potential, but this would be a false conclusion caused by the concentration gradient equalizing too quickly. Instead you should test it in a big cell to see the effect more clearly.

In my personal opinion, this is not the best evidence to explain this feature, but it's a hard concept for many people to grasp and I suspect the authors of your text approach it in several different ways to find one that sticks.


Do animals have different taste preferences within the same species?

Yes. Intra-species variation in food preferences has been observed in

Rabbits (Bilko et al. 1994)
Copepods (Rieber 1982; Berghe and Bergmans 1981)
C. elegans (Abada et al. 2009)
Earthworms (Bonkowski 2000)
Butterflies (Jermy et al. 1968)
Beetles (Sarker et al. 2013)

I am sure most pet owners will find the existence of this variation quite intuitive. No too cats have the same food preferences.

Why such variation exist?

I can think of several possible (non-exclusive and non-exhaustive) reasons for why such variation exist?

Individuals compete. If preferences vary, it allow specialisation (inspired from @John's comment)
Phenotypic variance (whether genetic, environmental or other) is not necessarily maintained by some kind of balancing selection. You may observe purely neutral variation in preferences.
Genetic variance can explain variance in food needs and therefore it is good that preference can be plastic
Same as above but for environmental reason. Say, an individual may have different need based on its environment.
One must learn to recognize good food. There might be a tradition among family of liking specific types of food.


Is the Hypothalamus part of the Central Nervous System or Endocrine System

CNS refers to the brain and spinal cord. Its a very general term. Hypothalamus is part of the CNS structure but its unique in a sense that it secretes many chemicals into the bloodstream like glands hence part of the endocrine system! so they are both correct!


Is there an association between environmental and mutational robustness?

Hansen (2006) says (middle of page 140):

  A link between genetic and environmental robustness is plausible, because genetic en environmental disturbances may often affect the same functional pathways in the organism, and ny increase in the robustness of a pathway leads to both genetic and environmental canalization. Evidence for a correlation between environmental and genetic robustness has been fund in studies of RNA folding (Ancel & Fontana 2000), in the effects of heat-shock proteins (Stearns et al. 1995).

He also cites Rifkin et al. (2005) who also showed evidence for this correlation. Finally Hansen cites Dworkin (2005) who did not find this link.

Hansen does not cite any theoretical paper and does not offer clear arguments of why this link exist but it is the best I could find


Leonardo's answer:

Animal study on sheep - here.

where

  [L]ymphatic flow in sheep, and
  the range being very heterogeneous (virtually no flow at the lower
  bound). I would agree that, in general, this is a very heterogeneous
  effect subject to many chemical (hydration, osmotic balance, blood
  pressure modifying drugs) and physical (cardiovascular tone, posture,
  activity level) factors.


How does symbiogenesis explain reproduction of organelles along with the cell?

I'm not sure about all organelles but mitochondria and chloroplasts are commonly used examples of independent devision in eukaryotic cells. They have independent DNA that forms separate mitotic spindles during division. Similar mechanisms likely existed for other organelles originally but the genetic material may have eventually been combined with the nuclear DNA for simplicity. This is a very simplified explanation but I think addresses the basic question.


Would constant light or fading light be registered as more wakefulness promoting by the Supra Chiasmatic Nucleus?

There is no light adaptation (such as Arrestin-mediated light adaptation http://www.sciencedirect.com/science/article/pii/S0896627303003908) or other negative feedback loop that attenuates melanopsin that I have ever heard of. Rodents in constant light lose behavioural circadian rhythmicity (http://www.ncbi.nlm.nih.gov/pubmed/23714074), which could technically be due to some sort of long-term depression of melanopsin-mediated signaling, but I have always hypothesized that the rhythm disruption comes from aberrant Period gene expression in the SCN due to constant light signals stimulating its transcription via retinohypothalamic tract->SCN->cAMP->PKA activation->CREB phosphorylation->PER transcription. This paper shows the rescue of rhythms in  in VIP knockout animals using constant light (http://www.nature.com/articles/srep14044), suggesting melanopsin signaling remains intact. They also claim that light may be providing tonic input to the SCN, so they are thinking melanopsin is still intact.

In terms of light influencing the brain? That sounds very vague, as light influences the brain in many ways. How would you want to delineate light input via the visual pathway from circadian light input via the RHT? Light can produce an image on your eye, and the higher thought representation of that image could evoke an emotion or an arousal state. This would be wholly different than a circadian effect.


Does mechanotransduction of cells play a role in the biocompatibility of titanium?

First off, AOZ has a wonderful page about titanium alloy uses in medical applications you should read and that most of my info is coming from:

Suitability of Titanium for Implant Purposes

I think you're having a couple of easy to correct misconceptions. First, titanium alloys are used for medical implants and replacements because they're lightweight, stronger by tensile strength than steel and judged to be completely inert and immune to corrosion by all body fluids and tissue, and is thus wholly biocompatible. It's also non-magnetic, meaning you can even go through an MRI machine with it! The range of alloys that we're able to produce is also key to the widespread use of titanium in medical applications as different alloys can serve their purpose as anything from hip joints to jaw reconstruction bases to spinal fusion devices based on their composition.

But cells don't exactly "stretch on it" and in fact in many operations additional material is used to ensure that the host body is able to function with the implant. This includes the use of polymethyl methacrylate bone cement to ensure that implant joints stay in place, and the use of roughened bioactive surfaces (hydroxyapatite) to stimulate the integration of the bone and surrounding tissue onto the implant.

As far as mechanotransduction goes, the problem is that it covers an extremely wide range of topics so ascribing it only one definition can quickly cause issues between studies. I usually go off of Nature's definitions for these kinds of things, which in this case says that "Mechanotransduction refers to the processes through which cells sense and respond to mechanical stimuli by converting them to biochemical signals that elicit specific cellular responses" (1). If you peek at the studies highlighted on google scholar for mechanotransduction you can see that the range of work is extreme and that's why ascribing the term one specific meaning at this point is unrealistic.


When looking at skulls from early hominids, how do we know their language creation abilities?

If there are no vocal chords left

The hyoid bone, which is part of the voice box, does fossilize -- at least occasionally -- and can be used to partially reconstruct the larynx capabilities, so this premise is wrong.

  We now report the discovery of a well-preserved human hyoid bone from Middle Palaeolithic layers of Kebara Cave, Mount Carmel, Israel, dating from about 60,000 years BP. The bone is almost identical in size and shape to the hyoid of present-day populations, suggesting that there has been little or no change in the visceral skeleton (including the hyoid, middle ear ossicles, and inferentially the larynx) during the past 60,000 years of human evolution.

--A Middle Palaeolithic human hyoid bone

  The Dikika australopithecine hyoid body proportions are chimpanzeelike.  ... The Kebara hyoid dimensions (body alone, and articulated body and greater horns) are almost all within the observed range for human hyoids. Discriminant functions clearly distinguish human from African ape hyoids and classify the Kebara 2 hyoid as human  ...  the expanded bulla characteristic of the African ape and australopithecine hyoid body is therefore interpreted as reflecting the presence of such a laryngeal air sac extension. Its absence in the human, Neanderthal, and H. heidelbergensis (Atapuerca SH) hyoids implicates the loss of the laryngeal air sacs as a derived Neanderthal and modern human trait ...

--Comparative Morphology of the Hominin and African Ape Hyoid Bone, a Possible Marker of the Evolution of Speech

  Modelling of the potential acoustic capability of Neanderthal VTs [vocal tracts] was carried out by Lieberman et al. [24,25] based on their three-dimensional reconstruction of the La Chapelle-aux-Saints fossil ... A different approach to Neanderthal VT reconstruction was taken by Boë et al. [41] who maintained that the Neanderthal larynx and hyoid bone sat lower in the VT than in Lieberman's reconstruction ... In this paper, we report a new study of the speech potential of Neanderthals, based on reconstructions of the positions of the hyoid and tongue root

--Articulatory capacity of Neanderthals, a very recent and human-like fossil hominin

  The description of a Neanderthal hyoid from Kebara Cave (Israel) in 1989 fuelled scientific debate on the evolution of speech and complex language. Gross anatomy of the Kebara 2 hyoid differs little from that of modern humans. ... Because internal architecture reflects the loadings to which a bone is routinely subjected, our findings are consistent with a capacity for speech in the Neanderthals.

--Micro-biomechanics of the Kebara 2 hyoid and its implications for speech in Neanderthals.

As well as larynx reconstruction and anatomic evidence, researchers have other lines of evidence about speech capabilities in Neanderthals and other non-modern humans, such as the genetics (especially the gene FOXP2).


How is receptor production (recycling) regulated?

So, what is causing the higher degradation than usual? Is it the lack of the materials required to produce the receptor?

Lack of materials is almost never the reason. Receptor turnover is actively controlled by different mechanisms. Ubiquitylation is one of the common mechanisms. Ubiquitylated receptors are internalized; these internalized receptors can later on be sent back to the membrane (recycled) or be degraded depending on the conditions.

Receptor downregulation can also happen by stopping their production either at the level of transcription or translation (For an example see this).


What is the reproductive success of a biting mosquito?

The amount (percentage) of eggs to mature varies greatly and depends on many factors and off course varies by season.

The correct (but not really satisfying) answer is that from every 100 eggs, between 0 and 100 eggs will mature. On average, this number is greater than 1 (otherwise the species would go extinct), and much smaller than 100 (otherwise the world would drown in mosquitoes). Because the question doesn't include the complete lifecycle, it is not exactly 1, but greater than 1.

Some explanation
Mosquitoes lay eggs in water, and the larvae are easy prey for predatory invertebrates (larvae of dragonflies, beetles etc.) and fish. Many mosquito species choose small, isolated waters (like small pools and plant-pots) where there is likely to be little predation. This however carries a risk: these waters often dry out (reproductive succes 0%), offer little resources (reproductive succes low) and offer no shelter against an unforseen predator (reproductive succes low). If they choose wisely however, reproductive succes can be very high. Because of this large variation, an average number is really not so informative.


Are there emotions that motivate pattern completion? If so, where in the brain are they located?

This "tension" is actually called anticipation in neurobiology and related fields. Whole purpose of this is to get higher reward. This is generally happens because of dopamine release. Many musicians have utilized this 'anticipation' technique in their compositions. Famous example is Led Zeppelin's stairways to heaven in which audience is 'anticipating' third part of song where Page's guitar in high tempo. Anatomically distinct dopamine release happens during anticipation and one will experience of peak emotion to music. You can read this paper for experiments related to this. This paper's introduction has given reference to many of such research papers. Go through it's references.


What has caused life to choose this unfathomably tiny subset of all possible proteins?

The answer is chance or, even better, contingency.

About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the scaffolds and functionalities have been. It is true that protein-based life could be evolved somewhere else, and it is true that the overall sequence space evolved somewhere else would be different from the one evolved on this planet. However, I would expect to find almost the same palette of biochemical reactions that we have discovered on our proteins.

I would suggest reading the work of P.L. Luisi here. He makes really good points on this issue.

A new paper just came out, I think it is a nice addendum to this answer.


How is the sequenced genome of a person useful to him in practice, now?

A human genome sequence can uncover large deletions and insertions in the genome and would give the genotypes of both common and private (rare to very rare) small polymorphisms (e.g. SNPs) and SSRs (simple sequence repeats). From this information, one can learn about some curiosity traits (say, sensing asparagus metabolites in the urine, slow or fast twitch muscles, curly vs not curly hair) and, more importantly, about disease risk. Ancestry and family relationships can also be learned as in, for example, a half-sibling relationship.

As many diseases are polygenic with numerous loci each making small contributions to the variance, it becomes very difficult to fully describe the level of increased or decreased risk. In other words, we don't yet know all the players and so assessing their contribution to risk of disease can't be done with complete confidence. To further compound this problem are both epistasis and gene-environment interactions. Epistasis is a gene-gene (gene-gene-gene, etc) interaction, such that genes A and B separately make no contribution to the phenotype (disease risk), but do so in combination - say in ab/ab individuals. A gene-environment interaction can be described as when an allele associates with increased risk only when an environmental factor (e.g., exercise, fat in the diet, sun exposure, oxygen tension (altitude), etc), passes a certain threshold.

Still, the most powerful predictor of disease risk, onset and progression is family history. A genome sequence approaches that history (half your genome is from your mother and half from your father, of course), but remains fairly uninterpretable in terms of complex traits. You may carry a couple variants posing increased risk for heart disease, but what about the other hundred or so loci that also make small contributions to this affliction? Sure, if we knew exactly what those other hundred were and how much they each contribute and if they interact with each other or the environment. An incomplete picture emerges.

With rare diseases and altered genomes (say in cancer compared to normal) great strides are being made to either identify the small number of defective genes (rare diseases) or the commandeered pathways exploited for uncontrolled growth (cancer). In this regard, much can be learned and will have quicker, but still measurable in years, applications to the clinic.


Quick answer is yeah, the G is the "reference allele" as you put it.  The greater than symbol is acting as an arrow, ie, G goes to C, that is, G is replaced with C.

Actually you get a pretty clear indication of that if you look down a line it two where it mentions the frequency:

  C=0.000419 (104/247982, GnomAD_exome)
  C=0.000494 (62/125568, TOPMED)
  C=0.000538 (62/115296, ExAC)

The C frequency is way too low to be the "normal" allele.  It's rather the substitution which results in a missense variant. You can see more specific stats by clicking on the frequency button.  In this case they basically just say that in all studied populations the G variant is by far the most common.


How Would I Isolate and Amplify a Viral Enzyme?

Each virus would contain extremely low amounts of enzyme (probably a few individual molecules, at best); collecting and concentrating enough viruses to extract a significant amount of enzyme would be long and difficult, if at all possible.

The usual strategy in research laboratories is to clone the nucleic acid sequence coding for this protein (either by direct amplification from an HIV-infected cell, or by synthesizing a piece of DNA in vitro) and integrate it in an expression vector, that is, a larger piece of DNA, usually circular, suitable for integration in a host cell (human, or even bacterial) and carrying the sequences necessary for persistence and gene expression. This way you can produce thousands of copies of the enzyme you are interested in in each cell, and you can then purify a significant amount of integrase to study it.

To make purification easier, it is common practice to add to the gene a sequence coding for a "purification tag", that is, a few extra amino acids that have special properties that make the final protein easier to purify. Stretches of 6-8 histidine residues are very commonly used. The assumption is that the protein carrying this tag will have an activity similar to the natural enzyme, after purification.


Although it can't be said definitively because of the picture quality, these are actually very likely maple trees. It's possible that they are either Red Maple (Acer rubrum) or sycamore maple (Acer pseudoplatanus) trees in spring leafout.

Source

Evidence:

The branches have an opposite arrangement. Very few tree are opposite (see MADHORSE)
The Rhode Island Wild Plant Society claims that red maple is abundant on the northern part of the island.
The Virginia Cooperative Extension provides an incomplete but detailed list of trees that can tolerate salt spray.

Two maples, Acer psudoplatanus and Acer campestre, (which are tolerant of salt spray) are both present as an exotic plant in that region of the country (see BONAP range map 1 and 2)
The Prudence Island flora mentions that A. pseudoplatanus is a common escaped cultivar on the island.

I'm leaning toward Red maple because of the red leaves appearing -- this is more typical of A. rubrum compared to the often more yellowish spring leaves of A. pseudoplatanus.

Note: The salt spray and windy environment will cause these trees (and most vegetation along a coastline) to develop "strange" (often gnarly) tree shapes.


At which point does a cell switch its function?

As MattDMo suggested there are so much possibilities. I would recommend to take a look at this information:

Cellular differentiation wiki
The Cell: A Molecular Approach. 2nd edition (NCBI)

I will summarize some points, however note that this will not include every aspect.
Every cell contains the same genome (same DNA), so what can make these cells to differ so much form each other (e.g. neurons vs muscle cells). As noted in the Wikipedia article:

  Since each cell, regardless of cell type, possesses the same genome,
  determination of cell type must occur at the level of gene expression

I added this figure just to give a representation of the hierarchy.
However probably you already knew this because you were asking about the mechanism of how these cells can become different from their parent cells.
I will provide two important examples (again notice that this is just a simple summary):

first let's talk about Cytoplasmic determinants

  Cytoplasmic determinants are special molecules which play a very
  important role during oocyte maturation, in the female's ovary (wiki)

the cytoplasmic determinants are molecules such as mRNA or proteins which are e.g. unequally distributed in the egg cell, which means that if this cell devides one half will get other proteins(e.g. transcription factors(TF)) and mRNA than the other half. Different TFs --> different gene expression --> different proteins --> different cells.
Secondly we have induction which is really important in cell differentiation:

  frequently we find that cells become different from one another as a
  result of inductive signals coming either from other cells or from
  their external environment (source)

These two (induction and Cytoplasmic determinants) are important to determine the fates of cells(we also have gastrulation, HOX genes, etc). But how does the induction and the cytoplasmic determinants cause a change in gene expression? The same is true for this, there are a lot of different ways how this can happen (see gene silencing):

Genomic Imprinting
Paramutation
Transposon silencing (or Histone Modifications)
Transgene silencing
Position effect
RNA-directed DNA methylation

I can write pages of Cellular differentiation because this question is really broad. So I will advice you to read the following articles:

Differential gene expression and development
The process of differentiation
Cellular differentiation


The feeling of cold from mints is caused by menthol. Menthol affects the TRPM8 receptor on skin and also in the mouth. TRPM8 is also a general cold receptor: so if you are in contact with menthol the receptor reacts just like when you are exposed to cold (Bautista et al., 2007).

The receptor is strongly activated at temperatures below 26 degrees Celsius (Bautista et al., 2007). Drinking water is usually colder than that. So if you ate mints and drink cold water afterwards, the receptor response is even stronger.


I think almost everything is correct except for the last part.
The reason one may easily overlook that part is that we inherit the complete 22 molecules from our mother who inherited the whole 2.35 * 10^10 molecules from her grandmother zygote. Grandma gave the whole thing to her daughter and that that number was distributed in all the cells in mom's body, which is 22 per cell. These 22 lipid molecules would be inherited by us from our mom, so the answer seems to be 22 logically.
This can be understood easily as given below:
2.35*10^10 -> From granny to mommy
22 -> From mommy to us
Hope this made sense... Thanks!


Where can I find a list of common enzyme cofactors and/or co-enzymes?

Check this out. This resource lists organic cofactors and the associated enzymes.
See the wikipedia page also.

Many metals also serve as prosthetic groups in enzymes. They include- Magnesium, Manganese, Iron, Cobalt, Nickel, Copper, Zinc, Molybdenum.

FeS clusters are also an important part in many important enzymes in mitochondria and plastids.


I can't tell how big your spider is. :( But I agree, it's probably not a wolf spider. (The fourth pair of legs is the longest in the wolf spider

I think it might be a fishing spider (Dolomedes tenebrosus). They do hang out in man made structures and are the most common fishing spiders found.

  Fishing spiders are similar to the larger wolf spiders in size, shape, and coloration. Species in the genus Dolomedes are called fishing spiders because most live near water and have been reported to catch small fishes and aquatic insects from the water as they walk on the surface. The species Dolomedes tenebrosus is more frequently associated with wooded areas (it would be more accurately classified as a tree-dwelling spider) and is a common household invader in these locations. It occurs from New England and Canada south to Florida and Texas.

The stripes on the legs are characteristic, the shape and size ratio of the thorax and abdomen are right, and they are smaller than their giant cousins that catch minnows (!). The coloration on the abdomen can vary. The females are 1.5 to 2.6 cm *about an inch) in length; males are smaller. The legs of both male and female are banded with alternating brown/black, scalloped rings on the femurs and reddish-brown/black rings on the tibia. Seeing an eye pattern and/or a good side view would help.


Book recommendations for evolutionary models

You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes.

In my first class of evolutionary biology I had this textbook: Futuyama, Evolution I think it gives a good start to the field and offers a good overview of the difference subfields.

If you think you already know enough about the concepts selection, genetic drift, molecular evolution, etc… and you want a book that provides mathematical formulations of evolution, then you might want to have a look into the field of population genetics. On this post you'll find some book-recommendations

If you are particularly interested into molecular evolution, I'd suggest: Yang, Computational molecular evolution

Maybe you are particularly interested into the statistical methodology used in DNA annotation or in phylogeny. Then…. I don't know! It's not quite my field!


Does Lucid Dreaming decrease the regenerative effect of sleep?

It's possible that they do, depending on the intensity of the dream and the amount of brain activity.

For example, if the dreamer is thinking too much or is having a dream that's way too intense, the brain activity goes up and they're not as rested.  However, lucid dreaming can be good for sleep if the dreamer creates a more relaxed dream.  This can possibly be better for the sleeper, especially if they're someone who experiences nightmares every night.

Basically, it just depends on what you're dreaming about.  The calmer and more relaxing the dream is, the better.

Source:
-www.world-of-lucid-dreaming.com


How do T-cells determine which cells they've already inspected?

Your question spans two activities of T-cells that are related to each other: migration and activation. T-cells that usually stay in lymphoid organs migrate to non-lymphoid organs with different mechanisms for each T-cell subtype. When migrated to non-lymphoid organ, the T-cells move through the organ looking for infected cells.

Migration

As you can see in the image below, there are many mechanisms for moving T-cells across the endothelial layer.

The main idea for all three mechanisms is that the tethering of the T-cell to the endothelial layer is weak. Because of the weak interaction, the blood flow causes the T-cell to move across the endothelial layer while still being attached to the endothelial layer. This is known as rolling. Other stimuli (usually chemokines) such as CCL21, CCL25, or ICAM 1 are needed to induce T-cell to migrate across the endothelial layer. This is important because these chemokines are expressed where there is inflammation. For example, there is a correlation between CCL25 level in the gut and inflammation in the area.

T-cells express α4β7 integrin or CCR7 that bind T-cell to the endothelial layer. Central memory T-cells and naive T-cells express CCR7 and CD62L and thus reside preferentially within the secondary lymphoid organs. Effector memory T-cells bind to gut endothelium with α4β7 integrin, CCR9, and LFA-1.

CCL21 is expressed by both stromal cells of lymph node paracortex and endothelium of lymphatic vessels to assist migration of activated dendritic cells and naive and central memory T-cells to lymph node respectively. Dendritic cells are professional antigen-presenting cells (APCs) that migrate to lymph node where it can interact with T-cells more efficiently.

T-cell activation

One important concept to take away from T-cell activation is that there needs to be direct contact between MHC complex and T-cell receptor (TCR).

T-cells that have moved into the lymph node interact with dendritic cells, which have high MHC complex concentration on their cell surface. This leads to subsequent activation of the T-cell leading to release of cytokines such as IL-2 leading to proliferation of activated T-cells.

The activated T-cells now are able to freely move across the endothelial layer of non-lymphoid organs to infiltrate and look for infected sites. (Naive T-cells enter endothelial layer of non-lymphoid organs as well but this is chemokine independent nad thus not a reaction to inflammation).

Sources:

Difference between naive T-cells and memory T-cells: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782715/

Dendritic cell's role in immune response: http://lab.rockefeller.edu/steinman/dendritic_intro/immuneResponse

Memory vs naive T-cell migration:
http://www.nature.com/icb/journal/v86/n3/full/7100132a.html

Dendritic cell and role of CCL21:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078419/

Naive T-cell non-lymphoid organ infiltration: http://onlinelibrary.wiley.com/doi/10.1002/eji.200535539/full

CCL25 and inflammation relation:
http://www.sciencedirect.com/science/article/pii/S0896841116300014


What determines whether a regulatory T cell suppresses a naive T cell binding the same antigen-presenting cell?

There a strong implication for a feedback loop mechanism for IL-2.

If a Treg is bound to an APC, it downregulates IL-2. It will then require exogenous IL-2 to be maintained. This IL-2 comes from a nearby naive T cell which is also binding a self-antigen. When that happens it upregulated IL-2. When it upregulates IL-2 and dumps it to all nearby cells which are then taken up by the nearby Treg. That causes Treg to continue its normal function by suppressing all nearby cells. It's an IL-2 negative feedback loop. It's all about proximity. What you are suggesting is not feasible since T cells recognise APC cells by MHC class II which are loaded by phagocytosis, meaning that the self-antigen has to be taken from outside of the cell. That means the APC would have to engulf two different self-antigens and displayed them on separate MHC class II which I guess is probably possible...

Check out this paper and figure 2:

http://www.cell.com/cell/pdf/S0092-8674(08)00624-7.pdf


This is an excellent question, I have been training people to culture cells for about 12 years and students have a hard time grasping this and appreciating the importance etc.

What cells are usually experiencing during pipetting is analogous to a crowd of people trying to fit through the doorway of a building. Shearing during pipetting  is certainly a legitimate concern in cell culture. You will notice its negative effect on viability most explicitly when pipetting cells in freezing
 medium (containing DMSO) following a thaw. Until their DMSO concentration drops their membranes are weaker & more fluid. That's why you pipette the frozen cells drop-wise to the fresh medium, to be especially gentle at this point.

Prokaryotic cells such as the above mentioned TOP10 cells are treated with Calcium chloride and glycerol which has essentially the same effect on their walls and membranes. Hence pipetting should be delicately performed after thawing these cells as well.

With that being said, if you compare the sensitivity of prokaryotic and eukaryotic cells to shearing, eukaryotic cells are profoundly more sensitive.

For individuals using competent bacteria for sub-cloning and other routine uses, killing a small percentage of of your cells is not that important. However if you are using the transformation to generate cDNA libraries it's very important that you have a titer sufficiently representing the transcriptome the library is composed of.

In these instances using a more premium competent cell, adhering to correct temperatures and minimizing pipetting is essential. This is why many are taught to swirl the DNA the with the competent cells, rather than the harsher alternative: pipetting up-and-down.

The four most important factors that contribute to cellular shearing are, and in order form most to least contributory:

Diameter of the bore in the pipette tip, the smaller the more shearing.
Speed at which the suspension is passing through the opening of the tip. The faster the more damaging.
Size and rigidity of the cell. Larger cells are more prone to damage.  Cells with a murein wall are less prone to damage.
Concentration of cells. Cultures that are more concentrated are more prone to damage.

Because the make up if the cell itself is so influential on the amount of damage, and because of the enormous variety of cells; designing a representative experiment to assess damage would be very difficult and  laborious.

Finally,  the variety of tips and seriologicals is also enormous. However if one were to attempt to assess this it could be done:

Choose a representative variety of cell lines, choose a representative variety of pipettes. One would probably want to use a robotic pipette to be able to  evaluate incrementally assigned speeds and pressures. Look at different culture concentrations,  phases of the growth curve, time between pipetting and analysis, distance between the exiting fluid and the culture etc, etc.

I think a very successful analysis method would be using propidium iodide and FACS.

After your experiment which will cost a lot of time and $, I think you will find common sense rules: keep pipetting to a minimum and use wider tips whenever possible.


When lactose is present in a cell, some of it is enzymatically converted by $\beta$-galactosidase from the $\beta(1,4)$ linkage (typical of lactose) to the $\beta(1,6)$ glycosidic linkage (becoming allolactose). Allolactose and other analogues can then bind LacI to induce the appropriate conformational change and unbind the lac operator (one such review here).

Why does allolactose act as a signal of lactose presence instead of just lactose? From the perspective of the lac operon, there is no operational difference between lactose and allolactose -- either way one molecule binds LacI and cannot be metabolized while bound. The full paradox is explained by Edgel and summarized by well-known biochemistry textbook author and scientist, Larry Moran, on his personal blog. The short version is that neither allolactose nor lactose are the intended substrates for $\beta$-gal and instead a different sugar entirely is the "natural" inducer and substrate.

Juers DH, Matthews BW, Huber RE. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci. 2012 1792-807.
Egel R. The 'lac' operon: an irrelevant paradox? Trends Genet. 1988 Feb;4(2):31.


Firstly, is important to remember that protein structures are dynamic due to the torsion angles between the N-terminal and C-terminal bonds. There are different conformations to expose different sequences to the outside of the protein to react/catalyze. So there is no one perfect conformation for a protein in a biological system.

The best models we have are taken through x-ray crystallography of the crystalized protein structure. This static portrayal of the protein may be inaccurate, because the biological system will expose the protein to different hydrophobic/hydrophilic interactions than the affect of the protein to itself.

Anfinsen's experiments were able to definitively prove the a proteins structure is coded by its amino acid sequence. To answer your question, this sequence is primarily responsible for a protein's core structure formation.

It is still incredibly difficult to predict the structure of a protein using its amino acid sequence. The tertiary structure is a product of salt bridges, hydrogen bonds, hydrophobic forces  and polar attractive forces within the molecule  (disregarding a proteins possible quaternary structure ). Scientists  (from what I believe is Yale, but I may be incorrect), have been trying to find a pattern using computing software for years. As of right now, we cannot purely use amino acid sequence to determine a protein's dynamic structure.

Loops and coils on the outside of proteins because they tend to compose of polar or charged amino acids. Hydrophobic amino acids tend to get pushed towards the center of the protein structure. This occurs because polar residues do not affect affect the entropy of water molecules as much as the nonpolar residues (in the system).

Many deletions/insertions occur during specific transition states that the protein is in. Enzymes actually target specific conformations of a protein that best produces the P product. See image:


Are mutations accumulating far faster than selected out?

Welcome to Biology.SE

Is the rate at which new mutations occurring higher than the rate at which alleles fix today in humans?

Human populations are exploding! Genetic diversity within a population is a function of the effective size of its population. As the population expansion in human is extremely recent, we ought to expect that our genetic diversity is much lower than what would be expected from our population size and structure. Therefore, yes, genetic diversity is currently increasing, or in other words, more mutations appear than there are alleles that fixed.

Is the genome deteriorating?

I am not sure what you mean by "the genome is deteriorating" but the answer to "Is the genome deteriorating?" is likely no!

Actually, larger populations tend to suffer from less drift load and as such our mean fitness would rather be increasing. However, given the population size, I doubt that would make such an important difference.

On the other hand, medicine is greatly affecting our environment and is reducing the strength of purifying selection. As a consequence, modern populations would eventually be less fit than our ancestors if placed in the environment experienced by our ancestor (that is an environment with little to no medicine). But this will not be true in our current environment.

Prerequisite to understand the answer

This answer felt quite introductory but it actually contains all the following concepts:

Allele
Allele fixation
Genetic drift
Effective population size
Population structure
Drift load
Purifying selection
Genetic diversity (typically defined as the expected heterozygosity)
Effective population size
Environment (and even niche construction)

If any of the above concept is unclear to you (and I very much suspect that at least the term "drift load" will be new to you), then you might want to start with an intro course to evolutionary biology and population genetics.


I would strongly recommend benchling https://benchling.com

This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently started using it and I am really impressed with the technical support they offer: you can chat with them and they would reply within minutes. Also, if there is a feature you would like to have implemented they would definitely consider it. Benchling is free, open source and you might be even able to code up some features yourself.


How to build a phylogenetic tree without an outgroup?

Most classic phylogeny reconstruction algorithms root the tree a posteriori, based on the outgroup chosen by the user. The tree is actually inferred and internally represented without root.

Therefore, if you use a program that asks you an outgroup, it is likely that you can just choose an arbitrary one and later "de-root" the obtained tree.


Evidence against aging caused by loss of information in genome and epigenome in humans?

By loss of genome, I think he is referring to the shortening of telomeres. This
study compares the length of telomeres of human epidermal cells. The authors report that over time, the telomeres do shorten. They also report on the rate of loss of around 32 base pairs per year. Thus there is loss of some genomic information over the age of an individual.
However, the loss of epigenomic information is trickier. The primary reason for it being some regions of the genome have been shown to lose DNA methylation marks whereas others gain it. However, leaving that aside, there is comprehensive proof that DNA methylation changes with age. This study on female peripheral leukocytes shows that approximately 350 regions (known as CpG islands) which are differentially methylated with age. Of these 350, 250 loci become hypermethylated i.e. methylation increases with age while the opposite happens for the remaining 150 loci.


How can I make legal mature female Cannabis plants to Flower in home during March (springtime)?

Keep the plants in dark night for 12 h , 13h then 14h per night.
Keep the plants well fertilized with lower N , higher P and K.
Keep well watered with a dry period in between watering.
Keep the plants protected until the plants are ready to flower.


When is voltage generated across a membrane?

The main thing the sodium/potassium pump does is to move sodium and potassium ions, Na+ and K+. It technically generates a bit of charge separation in doing this, but you can ignore it for now.

What is important is that because of the operation of this pump, you now have two sides of membrane with different ion concentrations. One side is high in sodium ions (outside the cell), the other side is high in potassium ions (inside the cell).

So far, that doesn't really do anything electrical, but it does take a lot of energy to get this arrangement: the whole time, the pump is moving sodium ions to where sodium ions are high, and moving potassium ions to where potassium ions are high. Moving things against their concentration gradient costs energy. The sodium/potassium pump gets this energy from ATP.

Now, imagine you open some pores in the membrane (we call them leak channels), that are a particular size that only lets potassium ions through. The sodium ions can't move, but the potassium ions can. A few potassium ions move over to the high sodium side, down the concentration gradient for potassium. This doesn't take any energy, it just happens passively. It also doesn't involve very many ions, just a few, so the concentrations don't change much.

However, potassium ions have charge! These are positive charges, flowing out of the cell: that makes the inside more negative.

Also, because they are positively charged, potassium ions would tend to move towards more negatively charged spaces. So, as the inside of the cell gets more negative, potassium won't leave as quickly. There is an equilibrium, where the forces pulling potassium ions out to where potassium concentration is low equals the forces pulling potassium ions in to where the voltage is negative.

The voltage where this equilibrium occurs is called the resting membrane potential, and for many cells is somewhere between -100 and -40 millivolts: that's the voltage generated across the membrane, indirectly, by the sodium/potassium pump.

Purves' Neuroscience is a good general reference textbook for this sort of thing. The Goldman equation is a mathematical way to figure out what the voltage will be if you know the concentrations and permeability.


Can living cells be imaged with electron microscopy?

While it may not be possible yet to image live cells with EM, it is possible to image live animals. For one example, Ishigaki et al. (2012) imaged live ticks (Haemaphysalis flava) with scanning electron microscopy. They could even see the ticks moving their legs inside the microscope for about 1 min after they went in the chamber. The ticks were still alive after they were removed from the vacuum inside the microscope. Half of those exposed to the vacuum and the electron beam died within the next two days, but the rest remained alive for at least two more weeks. Apparently, ticks that were only put inside the vacuum all survived just fine. It was only when they were blasted with the high-energy electron beam that their chances of dying increased.

Live ticks in SEM
Notice that the scale bars in panels B-F should be in $\mu m$, not $mm$

This is not the first study to succeed in imaging live organisms with electron microscopy; that was Pease et al. in 1966. It appears that in some insects the ionizing beam induces the polymerization of "extracellular substances" into a thin (~5 $\mu$m) membrane that acts as a protective "nano-suit" (Takaku et al. 2013). Takaku et al. (2013) could induce the formation of a similarly protective thin membrane by using polysorbate 20, a broadly used surfactant. Artificially inducing the formation of similar "nano-suits" may be a more promising way to image live cells with electron microscopy rather than relying on quantum mechanical measurements. Takaku et al. (2013) even go as far as to speculate that the natural formation of similar "nano-suits" may have acted as a protective shield for prokaryotic extremophiles that could have invaded the earth during early evolution (panspermia hypothesis).

References

 - Ishigaki Y, Nakamura Y, Oikawa Y, Yano Y, Kuwabata S, Nakagawa H, et
   al. (2012). Observation of Live Ticks (Haemaphysalis flava) by
   Scanning Electron Microscopy under High Vacuum Pressure. PLoS ONE
   7(3): e32676. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032676
 - Pease, R.F.W., Hayes, T.L., Camp, A.S. and Amer, N.M., (1966). Electron microscopy of living insects. Science, 154(3753):
   1185-1186. http://science.sciencemag.org/content/154/3753/1185
 - Takaku Y., Suzuki H., Ohta I., IshiiD., Muranaka Y., Shimomura M., and HariyamaT. (2013). A thin polymer membrane, nano-suit, enhancing
   survival across the continuum between air and high vacuum
   PNAS 110 (19): 7631-7635. 10.1073/pnas.1221341110


First of all I find quorum sensing to be generally facinating, so I'm happy to see the topic brought up here.

Dr. Bassler has many papers on the subject, but I think one of the most relevant ones to this question is here.

Regarding your question, you have the right idea, but you're missing the point of her comment.  The Western shows a more dramatic difference in cqsA- bacteria because they are not inhibiting themseleves (as you suggested).  Thus the lower concentrations have much higher levels of the toxin produced because the only CAI-1 being provided is the synthetic one.  This makes the ramp up in administered CAI-1 seem more drastic because you start at a higher level.

I hope that makes since, if I can find an open writes version of the Western, I'll come back and give further analysis on it.

Regarding @AlanBoyd 's comments, V. cholerae is different because it seeks to create an acute infection, not a persistent one.  Cholera toxin is what causes the majority of diarrhea and virulence from cholera.  V. cholera produces the toxin until it's inhibited by ether auto-inducer (which should be after the pt already has massive diarrhea), then it switches to produce enzymes which detach it from the gut.  The pt still has diarrhea at this point, cholera just doesn't need to make any more toxin for it to continue.  To do so would probably waste energy, and not help the bacteria make it back to a water supply.


It was a simple search. You could have easily searched for glucose oxidase in KEGG, and you would have got this reaction.

In fact if you had clicked the link for glucunolactone's compound page, you would have got a list of many different reactions that convert glucose to glucunolactone.

You can even click the arrow which opens the KEGG-ORTHOLOGY page. You can find a field called RN in the section called "Other DBs". The links corresponding to this field would give you the exact reactions, that the pathway uses.