text:
Where do biologists get information about mouse genes?
From this article https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract
“We created transgenic mice that overexpress human catalase localized in the peroxisome, nucleus, or mitochondria (MCAT).”
How exactly do such changes occur step by step? Those. how did they find which genes needed to be changed in order to get the result in overexpression of catalase and in mitochondria?
I am new to biology, and although I understand, for example, how CRISPR works, it’s not clear where people get such data "this gene in the mouse is responsible for the expression of catalase in mitochondria. "Where to find such data?

When looking at the scientific literature, it's often helpful to looks at the Methods section to figure out how people did specific things. Unfortunately some journals aren't great about making the methods obvious, but for your paper it is accessible here: https://science.sciencemag.org/content/sci/suppl/2005/06/23/1106653.DC1/Schriner.SOM.pdf. Look at the section **Generation of Transgenic Mice **.

Hi Potion and welcome to Biology Stack Exchange and biology in general!
To answer your questions, these changes do not occur. The authors of the publication have engineered "new" genes (also called transgenes in this context).
They have done so by fusion a portion of a of another gene (also called domain) to the beginning or the end of the sequence of the catalase gene. If your gene of interest is localized to a given organelle (for example mitochondria), you can also swap the domain which is responsible for the targeting to this particular organelle with one from a different gene you know goes for let's say peroxisomes.
If you want to know more details for this particular work I encourage you to check the supplementary material here: https://science.sciencemag.org/content/sci/suppl/2005/06/23/1106653.DC1/Schriner.SOM.pdf
Hope that helps!


text:
Oxygen uptake with gills from water vs lungs from atmosphere
The concentration of oxygen in water tends to be around 6.5-8 mg/L. In the atmosphere, it is 21%, one liter of air weighs roughly 1.25 gram, so, oxygen concentration is 0.25 g/L or 250 mg/L. So, lungs can access 50x higher concentration of oxygen than gills can. This suggests, sort of, that maximum oxygen uptake possible should have a significant increase when lungs evolved. Is that trend observed and a topic that is often talked about?

The assumption in the question was corroborated by this article here, and is correct. The downvote is unnecessary, it is a valid question, and was easily answered with strong scientific consensus.

As a precondition for the coevolution of eurythermy and life with high energy turnover, oxygen availability had to be maximized and the
  capacity of oxygen supply mechanisms selected high (Fig. 2). Such
  preconditions were met with atmospheric oxygen levels always above a
  minimum of 13%–15% during animal evolution (Fig. 4). Moreover, such
  preconditions were most ideally met in terrestrial environments since
  breathing air rather than water implies a reduction by one order of
  magnitude in the energy cost of ventilation at 30–35 times higher
  levels of ambient oxygen and about 103 times lower viscosity of the
  respiratory medium. However, new and largely different ventilatory
  systems had to be developed in air (lungs instead of gills in
  vertebrates) in most cases (except for terrestrial crabs) to exploit
  the excess amount of oxygen. At the same time, thermal conductivity in
  air is more than 20 times less and specific heat about four times less
  than in water, reflecting that thermal buffering is much less in the
  968 H. O. Po¨rtner terrestrial than in the aquatic environment. As a
  consequence, temperature changes occur on shorter timescales and at
  larger amplitudes in terrestrial than in aquatic environments.
  Therefore, terrestrial organisms at the same latitude are likely to
  experience much larger temperature fluctuations than aquatic
  organisms. Opposite to the marine realm, where temperature
  oscillations are less in polar and tropical than in temperate areas,
  those in air increase at high, especially Northern, latitudes, as
  estimated for mainland locations in the Americas (Gaston and Chown
  1999). According to these considerations, extreme stenotherms
  comparable to Antarctic marine species are highly unlikely to exist in
  (cold) terrestrial environments. Eurytherms will predominate instead.

Pörtner, H. O. (2004). Climate Variability and the Energetic Pathways of Evolution: The Origin of Endothermy in Mammals and Birds. Physiological and Biochemical Zoology, 77(6), 959–981. https://doi.org/10.1086/423742

A mammal would have to breathe 800 times more volume to throughput the same weight of medium, so, in a given time, the fish puts through more oxygen than the land animal.
Considering salmon and tuna and sea iguanas and turtles, reptiles aren't more active than fish, and air is inefficient to lift against, so sharks and mammals move at around the same speed. Great white sharks and humans have the same hemoglobin concentrations, 14g/l.
We can also compare a great white shark and a killer whale, a tuna and a wolf.
Yes the maximum available oxygen is higher on land, although the limiting factor for energy throughput can be measured through food consumption and metabolism temperature:
Dolphins consume 4-10% of their bodyweight per day
Tuna consume 5-15% of their bodyweight per day.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
Do floating plants on a quiet body of water significantly affect the evaporation?
A situation such as a pond where a plant like duck weed covers essentially all visible surface water  : Is evaporation slowed or stopped ?

To what degree are you or are you not interested in including the plants' evapotranspiration rate into the evaporation rate of the pond water? In other words, are you more interested in the net change of water level or in the specific mechanism of surface evaporation from the pond surface?

Actually I am interested in heat loss . I cover the pond with Styrofoam panels in cold ( air below 50 F) weather. The Koi don't care but I have tropicals in it; Danios .They have tolerated water temp. down to 50 F  . I want to avoid putting on the panels for an occasional cold night.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Could old-style "inoculation" be used against COVID-19?
Before the first vaccination was invented, for smallpox, there already was a technique called inoculation or https://en.wikipedia.org/wiki/Variolation. Unlike vaccination where dead or modified viruses are introduced to the immune system without causing an illness, in those old-style innoculations, people were infected with real live smallpox viruses, but not through the normal infection mechanism (the mucus membranes) but through scratches in the skin. Apparently when the virus arrives in the "wrong" organ, it can't cause as much damage quickly, but still the immune system gets a chance to prepare antibodies for it - so at the end the individual does get sick, but it's a much milder version and not as deadly.
Could we do something similar for COVID-19, i.e., deliberately infect at-risk individuals in locations far away from the pulmonary system (e.g., scratches in the skin) hoping such innoculation will indeed cause disease but a milder and less deadly version?
Is there any reason, besides the ethical questions of how to test this approach, why such an approach might not work? (again, "work" here means reducing the morbidity rate. It will not reduce the number of people sick, unlike a proper vaccine - it should just reduce the number of critically ill and most importantly, the death rate).

SE Biology is concerned with the mechanisms of biological processes, and questions are generally answered by people with biological rather than medical or epidemiological expertise. Although I understand your concern about the coronavirus outbreak, your question asks for subjective view on a proposal for combating the disease. Such questions are off-topic here. I advise you to consult more appropriate reputable sources for such information, some of which are listed here.

My question is not about epidemiology - the spread of viruses - it is about viruses, the human immune system and the (now considered antiquated) concept of inoculation. I think all are biological concepts, and not "subjective" in any sense, nor "medical" (the question was not about how to treat a certain person given his symptoms).


text:
Reliability of SARS-CoV-2 tests - false negatives
This is about the entire process from sample collection through transportation to lab processing and assessment. In Canada, we are seeing about one COVID-19 test in 10 produce a positive result. Can we be confident that the number of false negatives is negligible? There have been reports of issues potentially occurring at every step which could result in a false negative, from failed collection of the sample to degradation of the sample in transit, to perhaps process or reagent issues in the lab.
Also, is there any possibility of the virus mutating in such a way that what makes it COVID-19 from a public health point of view remains the same but its genetic identity changes enough to no longer be recognized by the existing tests?
Is the testing process from end to end reliable enough that we can trust the reported result be it positive or negative?

SE Biology is a question and answer site — not a discussion site or a site for floating ideas. It is concerned with the mechanisms of biological processes, not medical or social aspects of biology. For one of these reasons I think  that your question on the coronavirus outbreak is off-topic here. Question of a medical nature might be on-topic at SE Medical Sciences. Otherwise you are advised to consult more appropriate reputable sources for such information, some of which are listed here.

Also, is there any possibility of the virus mutating in such a way that what makes it COVID-19 from a public health point of view remains the same but its genetic identity changes enough to no longer be recognized by the existing tests?

That's unlikely. These assays look for several specific regions of the viral genome under high selection pressure (i.e., highly conserved) to make a clinical diagnosis (such as orf1ab, N, and S genes, ref. https://www.thermofisher.com/us/en/home/clinical/clinical-genomics/pathogen-detection-solutions/coronavirus-2019-ncov/genetic-analysis/taqpath-rt-pcr-covid-19-kit.html and https://www.fda.gov/media/136286/download for examples), with the aim to minimize test error from off-target effects (varieties of genomic mutations, ref. https://en.m.wikipedia.org/wiki/Off-target_genome_editing) and misidentification with other respiratory viruses.
I can't speak to the other questions in your question with numerical error rates of tests, except to say that controls, procedures, and better PCR primers can be used to increase sensitivity, to get a true positive (ref. https://en.m.wikipedia.org/wiki/Sensitivity_and_specificity). Sensitivity is a real issue for test kits in Russia, where one must have high viral counts (and likely be very ill) in order for a test to give a positive diagnosis (ref. https://abcnews.go.com/International/russia-reporting-covid-19-cases-cover/story?id=69717763)

According to PCR News, the Russian test is based on the same method used by other countries.
But the Russian test, PCR News wrote, only detects the virus when there are over 100,000 copies of it per milliliter in a sample. That is far more than in other countries’ tests. A test in use in the U.S., for example, will pick up the virus with just 6,250 copies.
“That would mean it’s about 10-16 times less sensitive than what’s available in the U.S.,” Carmen Wiley, president of the American Association of Clinical Chemistry, told ABC News by a phone. At such a level, she said there was a risk the Russians were missing cases, in particular where people were asymptomatic.

From a public health standpoint, I suspect diagnosis of sick people is less useful than diagnosis of asymptomatic carriers who feel fine but are shedding virus everywhere. You want a test to let you quickly tell positive people to self-quarantine, before spreading it around.


text:
COVID-19: size, real image
I'm an electronics engineer. I was thinking about how to detect the presence of COVID-19:

Obtain the sample.
Increment image/sample, (I need the real size to determine increment/magnification)
Digital image processing — detect presence using artificial intelligence or Recognition.

What is the approximate size of COVID-19? Is there a real image of COVID-19?

Reading good please, I'm asking for size and images proper of Biology field.

@tyersome The question asks simply the size of Coronavirus. It does not ask about image recognition.

SE Biology is concerned with the mechanisms of biological processes. General information about the coronavirus is available from a variety of reputable sources, some of which are listed here. As your concern is for detection of the virus you would be well advised to consult such sources for information about how this is currently performed and the problems actually faced. Others have hammers too, and don’t necessary think that everything is a nail.

2019-nCoV also has enveloped virions that measure approximately 50–200 nm in diameter
  with a single positive-sense RNA genome.

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study, The Lancet (2020)


text:
Could a virus produce prions, leading to prion disease?
Viruses can make cells produce proteins that are not a part of the new viruses themselves, but are used to help with replication. However in the case of rotavirus, one of these proteins (NSP4) is actually a toxin that causes diarrhoea. Prion diseases like Creutzfeldt–Jakob disease are caused by misfolded proteins that make normal versions of the protein also misfold, causing a chain reaction.
While this might not actually have been observed in real life, is there a biological basis for a virus containing genetic code for producing a prion, that after infecting an organism will cause the production of prions inside of infected cells (or perhaps proteins that cause the production of prions in the body), leading to a prion disease - in a similar way to how rotavirus causes the production the the NSP4 toxin? Since these prion diseases often have 100% fatality, would this mean a virus like the common cold could arise, that spreads quickly and non-fatally, but then triggers a fatal neurodegenerative disease in its victims by causing the production of prions in the host?

Perhaps not prions themselves, but viruses may possibly contain "pieces" or domains of proteins with prion-like chemical activity, which can catalyse refolding of prions from normal to disease state.
Mutation rates put limits on the size of RNA viruses. There is a higher cost for the average RNA virus to allot precious genomic space on encoding a normal protein that would take decades to be pathogenic, and which does not seem to help make copies of the virus.
Because DNA is a more stable molecule, and DNA polymerase has a higher fidelity rate than RNA polymerase, DNA viruses can have a larger genome. They could more easily carry code for encoding prion-like domains inside proteins.
There's a recent paper from George and Victor Tetz that looks for these so-called "prionogenic domains" (regions which encode portions of another protein that could potentially have prion-like behavior) in a catalog of viral genomes, and they find approximately three times more such domains in DNA viruses than in RNA viruses:

We determined that more PrDs can be found in the DNA-viruses compared with their numbers in the RNA-viruses, and in the enveloped viruses, compared with that in the non-enveloped ones. This may be partially explained by the larger genome size and protein numbers in DNA-viruses.

While the domains themselves are usually part of proteins that are not themselves prions, infection could lead to expression of those proteins, which in turn provides the domain templates that invoke misfolding in the host of normal prions into pathogenic (disease-causing) prions:

Some viruses may be implicated in the prion misfolding in humans since it was observed that the de novo appearance of prions can be facilitated by another PrD-containing protein

Also! There are retroviruses that have integrated themselves in our genome over millions of years. These are called "endogenous retroviruses" or ERVs, and have been called "junk DNA" by some biologists. However, some get expressed along with our normal genes:

Although a large percentage of ERVs are replication-defective or are suppressed by host defense mechanisms, some ERVs can be expressed and replicated. The activation of an ERV gene can bring positive co-opted functions to the host, which may be evolutionarily maintained [13,20]. For instance, some ERV proteins may provide important functions during normal development; for example, human protein syncytine-1, which is an ERV Env protein, is involved in the formation of the syncytial layer in the placenta [30,31]. Moreover, the expression of Env proteins encoded by ERVs has been suggested to mediate host resistance to exogenous pathogens [32,33]. However, because of their analogy to exogenous retroviruses, the activation of certain ERVs has been frequently implicated in disease.

The authors observed that some people who develop Creutzfeldt–Jakob disease (CJD) have ERVs that get overexpressed:

To evaluate the possible relationship between HERVs and human prion disease, we examined the retroviral sequences in cerebrospinal fluid (CSF) obtained from individuals with sporadic CJD. The frequencies of several HERV families, including HERV-W, HERV-L, FRD and ERV-9, were significantly increased in the CSF of individuals with sporadic CJD compared to the frequencies observed in normal control CSF. In addition, when compared to individuals with other neurodegenerative diseases that exhibit similar symptoms to CJD, such as dementia, the incidence rate of HERV-W and HERV-L were significantly higher in the CSF of sporadic CJD patients. Moreover, the frequency of increased HERV-W and HERV-L in the same samples was much higher in sporadic CJD than in either normal or other neurodegenerative diseases CSF samples, and there was no correlation between individual parameters, such as sex and age [61].

The cause may not be expression of proteins with PrD, but with the triggering of signaling pathways that lead to inflammation of tissues, which sets up conditions for normal prions to malform into disease-causing prions:

According to these studies, ERV proteins may be closely implicated in the pathogenesis of inflammatory diseases, such as multiple sclerosis and rheumatoid arthritis (RA) [51,54,68]. In prion diseases, a correlation between the inflammatory process and neurodegeneration has been suggested because of the activation of large numbers of glial cells and the up-regulated expression of proinflammatory cytokines, which are pathological features of prion diseases [69,70].

Life is complicated.

So is it possible that a DNA virus of some sort could spread without killing people, but then trigger prion misfolding that does? Has this ever been observed?

"Some viruses may be implicated in the prion misfolding in humans since it was observed that the de novo appearance of prions can be facilitated by another PrD-containing protein"


text:
Why are Aardvarks capable of burrowing given their size?
I was wondering if large animals could possibly dig extensive burrows for themselves to live in. The polar bear burrows, but snow is not dirt. The aardvark goes about 4' long, ~150 lbs: similar to a sheep. I think the aardvark might be the biggest dirt-burrowing animal, the only sheep-sized burrower.
I wonder why.
Is there anything special about the aardvark that at its size it burrows, while other burrowers are smaller?

Welcome to SE Biology! This question is quite broad and open-ended, making it difficult to answer. It's helpful to ask somewhat more targeted questions to get good answers. I'd recommend looking a little at the wikipedia page for aardvarks (if you haven't already) and see what it has to say on this topic: https://en.wikipedia.org/wiki/Aardvark. Perhaps you can find a way to sharpen the question to be more specific and easier to answer.

Thanks to ukemi for finding a good answer and thank you for the asking tips! I did read Wiki and a few other pages about the aardvark and burrowing before I asked. 'Fossorial' was a very useful search term to learn.

The following paper examines the link between burrowing ability and the stress and strain resistance provided by increased endosteal tissue formation (specifically compacted coarse cancellous bone (CCCB)) in aardvarks:

Physiological constraints associated with digging, however, are known to be strongly influenced by body size, and larger burrowers are likely to exhibit a histological profile more conspicuously influenced by fossorial activity. Here, we describe for the first time the limb bone histology of the aardvark (Orycteropus afer), the largest extant burrowing mammal...
We hypothesize that the unusual histological profile of the aardvark is likely the outcome of physiological constraints due to both extensive digging behavior and strong metabolic restrictions. Adaptations to fossoriality are thus the result of a physiological compromise between limited food availability, an environment with high temperature variability, and the need for biomechanical resistance during digging. These results highlight the difficulties of deciphering all factors potentially involved in bone formation in fossorial mammals. Even though the formation and maintaining of CCCB through ontogeny in the aardvark cannot be unambiguously linked with its fossorial habits, a high amount of CCCB has been observed in the limb bones of other large burrowing mammals.

Digging the compromise: investigating the link between limb bone histology and fossoriality in the aardvark (Orycteropus afer), PeerJ Life & Environment (2018)

Further reading:

Ecosystem engineering through aardvark (Orycteropus afer) burrowing: Mechanisms and effects

These articles discussed factors affecting burrowers, and linked to many more useful ones. They need strong limbs (probably short), a way to support their weight if they dig fast with all fours digging (e.g., tail), and not to overheat while digging hard. The first article seemed to take the body size for granted and discussed that eating ants limits further bone grown and higher metabolic rate. Other links in that paper make lower basal rate important for larger size. So I guess bigger burrowers would need that much more help working cool, and that much better diet, plus reason to burrow.

So that answers about bigger burrowers, though I still wonder why the aardvark itself is comparatively large :) Myself, I didn't figure that out from the article and the links I looked through there.


text:
Can virus and bacteria move on the surface?
Do viruses/bacteria have some motive mechanism? I mean if the virus/bacteria reach some surface by touching, can it move on that surface?
Life example: suppose the cooler is not so clean and has some viruses on his surface. My cup came into contact with the cooler in some little area, so virus migrated to that little area of my cup. Can the virus eventually move to another area of my cup's surface? Or can I be sure that it remained at the point of contact? If yes, is this also true for bacteria?
P.S. obviously parasites can move, but I can't figure out are the viruses and bacteria can..

What's a silent downvote? Please explain.

Viruses and bacteria are very very different from one another; asking about them both in one question is asking too many questions. I've marked a duplicate for the virus half of your question.

I didn't downvote but I can guess the reason. You did not do a simple search for this question yourself. It is elementary microbiology (also physics). And as @BryanKrause pointed out bacteria and viruses are very different.

@WYSIWYG Also easily found here. I located the duplicate by searching this site for the two words "virus move". The ask-a-question dialogue pretty clearly suggests askers search the site before asking.

@BryanKrause Indeed. There is a similar question. Sorry, it is because of my bad English..


text:
Do multiple axons innervate a single skeletal muscle fiber?
The typical text-book illustration of innervation of muscle fibers shows branches at a single position along the fiber. Does any given muscle fiber have more axons that innervate it though, given that muscle cells can be quite long, up to half a meter in Sartorius?

Until a better educated person contributes a more detailed answer, Hunt's article here from 1954 will likely be the best source,

studies have shown that muscle fibres in the frog's sartorius are innervated in two major zones and most of the fibres receive motor
  endings at at least two regions along their length (Katz & Kuffler,
  1941). In this case a multiply-innervated muscle fibre may derive its
  several end-plates from the same motor nerve fibre. The possibility
  also exists that a muscle fibre may receive end-plates from more than
  one nerve fibre, i.e. polyneuronal innervation.

HUNT CC, KUFFLER SW. Motor innervation of skeletal muscle: multiple innervation of individual muscle fibres and motor unit function. J Physiol. 1954;126(2):293–303. doi:10.1113/jphysiol.1954.sp005210
He in turn references an article by Kats and Kuffler from 1941,
KATZ, B. & KUFFLER, S. W. (1941). Multiple motor innervation of the frog's sartorius muscle. J. Neurophysiol. 4, 209-223.
As those are both 70 years old, it is likely that more documentation has been produced, and that it could contribute to a competent answer to the question.


text:
Nernst equation and equilibrium potential
Solutions A and B are separated by a membrane that is permeable to Ca2+ and impermeable to Cl−.
Solution A contains 10 mM CaCl2 , and solution B
contains 1 mM CaCl2.
Assuming that 2.3 RT/F = 60 mV, Ca2+ will be at electrochemical equilibrium when:
(A) solution A is +60 mV
(B) solution A is +30 mV
(C) solution A is −60 mV
(D) solution A is −30 mV
(E) solution A is +120 mV
(F) solution A is −120 mV
(G) the Ca2+ concentrations of the two solutions are equal
I eliminated A,B and E because of the +ve sign immediately, and G because it doesn't take into account the electrical potential factor.
I also understand the general idea (that Ca2+ ions will cross the membrane but Cl- won't so it will stop when solution A is negative enough for the electrical gradient to be > concentration gradient) but I don't know what to do next.
$ EMF (millivolts) = \pm 61 * log \frac{C_{1}}{C_{2}}$
Using Nernst equation (reproduced from the version in my book), I got that the equilibrium potential is about -60 mV (I did -61log(10/1))
But the book's answer is D which makes me think I might have a huge misunderstanding in the principle itself.

Can you try to format your question to be more readable? As-is it is a complete mess. Show your thinking step-by-step: which numbers actually matter to the answer, what is the equation you are using, etc. And remove the bits about your professor and your university being shut down - yes, that sort of thing is affecting all of us, but it doesn't change the on/offtopicness of questions here.

Thanks for the edits, this is much better looking! One last thing: can you write out the entire Nernst equation, and show where you have substituted numbers for variables? You're very close.

The Nernst equation should be:
$\frac{RT}{zF}\ln\left(\frac{\mathrm{Out}}{\mathrm{In}}\right) = 2.3 \frac{RT}{zF}\log_{10}\left(\frac{\mathrm{Out}}{\mathrm{In}}\right)$
You substituted for 2.3 RT/F (approximately 60 or 61 mV: use 60 because your instructor asked you to), but forgot about z. Calcium is divalent (and positive) so for calcium z=2. Substitute this and you can see how you get your answer.
(Also note the "out/in" which is how you get negative numbers when z is positive and out < in )


text:
Schematic of neural lineage tree and position of Choroid Plexus cells
I am trying to understand which are the different type of progenitors in the human brain and I am currently following this schematic.
My question is, are Choroid Plexus cells progenitors to Radial Glia (is this paper basically stating that they might work as progenitors)? Otherwise, do they reside out of the provided neural lineage tree? I am aware of their functions related to CSF.
Otherwise, do you have reference papers on neural lineage tree that you can share?


text:
What is the definition of a polybasic cleavage site?
I keep coming across the term "polybasic cleavage site" which is implicated in increasing the virulence of many viruses, but I'm struggling to find a definition. Is it just a sequence of amino acids where more than one has a basic side chain? I'd also love to know why it is so important to the function of a virus.

I would define a “polybasic cleavage site” as:

A region on a protein consisting of several basic amino acids (generally arginine (R) and lysine (K), rather than histidine) that determines the substrate specificity of certain classes of proteases for that protein.

It can also be regarded as a recognition site for the enzyme.
The relevance of this to the virulence of some viruses is as follows. Many RNA viruses are translated into one or more polyproteins that are subsequently cleaved proteolytically at specific sites to generate further proteins. In certain instances these sites are ‘polybasic’, and the products generated by the cleavage of such sites play a role in the virulence of viruses.
This is nicely illustrated by a paper by Nao et al. in mBio on the mutation of haemagglutinin (HA) cleavage site of Avian Influenza Virus, where increasing the number of basic amino acids increased the virulence. I included an illustrative figure from that publication.

HA cleavage site sequences of the ShimH5 virus strain and its variants passaged in chickens
The current (2021) interest in polybasic cleavage sites no doubt relates to the presence of such a site (PRRAR) at the S1/S2 junction in the spike protein of SARS-CoV-2 — see, for example, this paper by Peacock et al. in Nature Microbiology.

A polybasic cleavage site is a cleavage site consisting of polybasic amino acids. An acid is polybasic when it is able to donate more than one proton in aqueous solution. In a titration curve, polybasic acids show as many equivalence points as they are poly.
https://www.w3spoint.com/ionization-of-a-polybasic-acid

Unfortunately, your logical analysis of the word  —  a site with a single acidic amino acid residue with multiple ionizations — is incorrect because no such amino acids exist in proteins, and, as I indicated in my comment on the question, the usage is for a site with many basic amino acid residues.

You are right thank you for pointing this out


text:
Does a virus have a well defined shape?
I assumed a virus to be something with a very specific geometry,
similar to a crystal, but more complex.
In an answer to
What is the size (diameter) of the SARS-CoV-2 virus? some SARS-CoV-2 virus particles are shown.
It looks like they do not have the same geometry.
They may be soft and influenced by external forces, but they could also be of different, but similar shape. Also, they could simply be defective in some way.
I assume a structure of the size of a virus is not rigid. Assuming no external forces, would multiple exemplars  of the same kind of virus have the same shape?
Can a virus have a different molecular arrangement, but be equivalent for biological purposes?

You should check literature on VLP (virus like particles) for vaccine purposes. They spend a lot of time charactering their modified virus shells a lot as capsid protein don't tolerate fusions well.

The caption to the figure in the source linked in that answer says Figure 3. Visualization of 2019-nCoV with Transmission Electron Microscopy.
Negative-stained 2019-nCoV particles are shown in Panel A, and 2019-nCoV particles in the human airway epithelial cell ultrathin sections are shown in Panel B... They've been through quite a lot and I'm not completely sure those techniques can faithfully preserve the shapes of the virus particles.

Some parts of viruses are consistently shaped, in particular anything that is made of multiple copies of a protein sticking together. There are methods to determine the structures of these regular components to high precision, like single particle analysis (eg. zika) and X-ray crystallography (bacteriophage HK97). Other parts of the virus are less consistent, either because they are flexible or because they are produced slightly differently each time. The nucleic acid core is often arranged semi-randomly, and the lipid envelope of many viruses can vary greatly, dependent on the process by which parts of the host cell's membrane is pinched off to create new viral particles. Here's an example of pretty extreme variability of influenza particles, based on what cell type they have infected. Virus particles with different shapes can be just as infectious, but if they are too large the number of new viruses produced by an infected cell may be too low.


text:
Roughly speaking how stable are short sections of single-stranded RNA in exposed environments compared to double-stranded DNA?
A search following a recent news item led me to a CDC Morbidity and Mortality Weekly Report for 23 March 2020 which says in part:

SARS-CoV-2 RNA was identified on a variety of
  surfaces in cabins of both symptomatic and asymptomatic
  infected passengers up to 17 days after cabins were vacated
  on the Diamond Princess but before disinfection procedures
  had been conducted (Takuya Yamagishi, National Institute of
  Infectious Diseases, personal communication, 2020). Although
  these data cannot be used to determine whether transmission
  occurred from contaminated surfaces, further study of fomite
  transmission of SARS-CoV-2 aboard cruise ships is warranted.

Identifying bits of RNA does not imply a surface is infectious and that's not what I am asking about here.
This reminded me of answer(s) to Was 14,000+ year old DNA “laying around in cave dirt” protected from degradation, or is it just naturally this robust? which explain that small fragments of DNA can be quite stable in some environments; in some places on Earth the DNA in the soil can be ten thousand years old.
Question: Roughly speaking how stable are short sections of single-stranded RNA in exposed environments compared to double-stranded DNA?
The answer is likely to contain "It depends on..." as did the answer to the DNA stability question, I'm primarily interested in the differential stability between the two.

Because the cited source is a personal communication, we do not know if the extraction protocol used is sufficient to disrupt viral capsids, so it's hard to say whether the RNA recovered was naked RNA or virus-bound RNA.

@PolypipeWrangler that sounds like it could be quite a reasonable and acceptable answer.

Like stretching a rubber band until it breaks, comparing the elastic limits of dsDNA and ssRNA might be useful to do a direct comparison of energetic stability. I haven't found much online about RNA rupture experiments, but looking up ssDNA might serve as an upper bound on ssRNA stability, as ribose is less stable than deoxyribose.

The main difference in stability is due to the very high amounts of RNase in pretty much all fresh biological materials. Naked RNA is easily degraded by just touching it with skin. The first step in most RNA extractions is often to add an RNase inhibitor.
For example, from Wikipedia's Ribonuclease; RNase contamination during RNA  extraction:

The extraction of RNA in molecular biology experiments is greatly complicated by the presence of ubiquitous and hardy ribonucleases that degrade RNA samples. Certain RNases can be extremely hardy and inactivating them is difficult compared to neutralizing DNases. In addition to the cellular RNases that are released, there are several RNases that are present in the environment. RNases have evolved to have many extracellular functions in various organisms.

This covers it nicely, thanks!


text:
Identify this giant green moth(?) with great taste?
One evening in late February I sat down to eat dinner after a day of hiking in hills around New Taipei City and discovered that someone else shared my taste in clothes. A very large green moth-like insect had landed on my pants with a green floral pattern. The inset in the first photo shows that the body was about 5.5 centimeters long. Included are additional cropped top, side and front photos, the top one without flash for a better appreciation of the colors.
It frightened me at first because it was just sitting there and I have no idea how long I'd been walking around with it. After it's photo shoot I brought it outside and located some bushes and was able to convince it to move. It seemed quite sluggish though it wasn't very cool yet (I estimate perhaps 22 C)
Can anyone identify this obviously style-conscious insect, and speculate why it was lethargic and not interested in flying away?

related?

I came here for "with great taste" and left relieved, but a little disappointed. Perhaps a slight nudge to the title? Though I suspect the title may be why this is so high up on HNQ. Or maybe that's the point? ;)

Dissapointed this was not about eating moths.

@wwarriner https://youtu.be/1UM3JpcBHzY and https://youtu.be/eX97kQ8nWzo

@DKNguyen ditto, and see https://en.wikipedia.org/wiki/Charlie_the_Tuna

@wwarriner as for titles, I don't target HNQ but I think it's okay to add a little bit of intrigue to a title now and again, as long as the question itself is still there; Bird brain-eating Mantis - how does it crack the skull?

Am I the only one who finds the camouflage stunningly effective? Did it evolve on pants with floral patterns??

That appears to be an Oleander Hawk-moth a member of the Sphinx moth family.
I think the only other possibility for Taiwan is the quite similar Jade Hawk-moth, but that supposedly has a dark purplish colored head.
Image for comparison:

Source: Shantanu Kuveskar / CC BY-SA.

Interesting! Thank you for the speedy identification; it certainly looks the same. I wonder why this specimen has no antennae, while mine has a pretty big pair. Also, any thoughts on the lethargy?

If you visit the linked site you'll find pictures of male from both sides that shows the same beautiful antennae as your picture shows .. only the "lead" picture doesn't show antennae for unknown reasons

@uhoh: You're welcome. The antennae are sexually dimorphic in this species with the females having "slightly clubbed" antennae, but I don't know why they aren't visible in this picture. Not sure why he was so sluggish, but supposedly these moths are most active around dawn and dusk, so maybe you were disturbing his beauty sleep?

@uhoh: I’ve often seem moths in warm climates behaving like you describe; I’ve always interpreted it not so much as lethargy as just plain cussedness.


text:
Extract mutations from fasta sequences
I have a large amount of protein sequences in the .fasta format and I would like to extract only the amino acid mutations from these sequences, so that, in the end, I want to have a list that looks something like this:
I456L, W675T, etc
Is there a program or way to do this?
Thankful

Are all of your sequences of the same protein, are they all the same length, do you know which one is the WT / baseline?

Yes, the proteins are of the same, in the same length and I have a reference genome to compare

I'd blastp, and parse the alignment you get back.

I would suggest posting this question on https://bioinformatics.stackexchange.com/questions.


text:
Cellular respiration, why double membrane in mitochondria and not bacteria?
Bacteria perform cellular respiration across a single membrane, their plasma membrane. What are the benefits of having double membranes in eukaryotes (in the mitochondria), and, how do bacteria achieve the proton gradient?

This is incorrect. Mitochondria are derived from bacteria and their two membranes correspond to the inner and outer membranes of bacteria as pictured and described in this Wikipedia article on oxidative phosphorylation.

OK. Should have thought of that (that bacteria tend to have double membranes. ) The endosymbiont theory is beautiful, one bacteria sacrificing the other symbiont to oxidative stress. Taking one for the team :)

@David What about bacteria with a single membrane?

@canadianer — I know nothing about them. I suggest that if you are interested you do some research and then ask a specific question on that subject or edit this one, which certainly was not formulated with that in mind.

@David My question was rhetorical. The original question though clearly was formulated with that in mind given that it explicitly mentions bacteria having a single membrane.

@canadianer — Formulated with that in mind? Did you read the poster’s response?

As @canadianer implies, there are bacteria — gram-positive bacteria — that do not have an outer membrane. I have now found a previous specific question about oxidative phosphorylation in gram-positive bacteria, so I suggest this one should be closed. The answer given there is that it is not necessary to generate a pH gradient as it is the proton motive force that drives the ATP synthase, and that can consist solely of a membrane potential produced by the movement of protons.

I was unaware that bacteria have double membranes (or, I've heard it, but, did not make the connection), so Davids answer cleared it out for me. It is still relevant though how bacteria with a different structure do cellular respiration. Then another factor, new discoveries from the past decades, here published in 2009, show that a proton-gradient is part of the equilibrium phases of water in cells or in nature overall, water polarizes at contact-zones. This drives osmosis. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.618.291&rep=rep1&type=pdf.


text:
Toxicity of stannous fluoride in toothpaste?
I recently purchased a new brand of toothpaste, and when I looked at the medicinal ingredients, it listed stannous fluoride 0.454% w/w, instead of the regular sodium fluoride. I was a bit concerned because I thought that tin was toxic to humans, and that it might be absorbed in the mouth.
A couple of studies like this one say that stannous fluoride is great, and I can't seem to find any studies on how toxic tin ions are to humans, but on Wikipedia it says that stannous fluoride readily forms tin metal and ions in water. Should I be worried?

Readily soluble in water, SnF2 is hydrolysed. At low concentration, it forms species such as SnOH+, Sn(OH)2 and Sn(OH)3−. At higher concentrations, predominantly polynuclear species are formed, including Sn2(OH)22+ and Sn3(OH)42+. Aqueous solutions readily oxidise to form insoluble precipitates of SnIV, which are ineffective as a dental prophylactic.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular note that personal medical questions are not appropriate for this site. ——— Please consult with a dentist or other medical professional instead — any advice on medical subjects obtained over the internet should be regarded with extreme suspicion. Thanks!

https://fluoridealert.org/studies/acute01/


text:
Help me identify Grasshopper
I found this Grasshopper in Goa/India. It was about 2cm long. I suspect it is from Cataloipus genus or Gomphocerinae subfamily. Am i correct or it also seems to be juvenile from some other species?

This does appear to be a juvenile; zooming in shows me wing buds.  Under those circumstances further identification is unlikely.


text:
How does a protein molecule enter a cell through the cell membrane?
I can't find a good explanation as to how a whole protein molecule enters a cell membrane. Is it through endocytotic vesicles, with the help of ATP? How does this occur?
Thanks for the help!

Are you asking about translocation, or about folded proteins passing through membranes?

Learning about both would be great!

Wikipedia has some information on translocation, and follow that up with their article on the translocon (the machinery that threads nascent peptides through the membrane). The Nuclear pore complex is a good example of a machinery that allows larger folded proteins through the membrane.

For now, I am going to suggest that your question should be closed because I think it needs a bit more focus to fit the shorter answer Q&A style of this site, but if you have any specific questions along the way, please post a new question or edit this question. I hope that helps :)


text:
Why does plasma protein saturation of a drug increase its volume of distribution and clearance rate?
I need help understanding this statement from Goodman and Gilman's "The Pharmacological Basis of Therapeutics:"

For a drug that is metabolized
  by the liver with a low intrinsic clearance-extraction ratio, saturation
  of plasma-protein binding will cause both V (distribution volume) and CL (clearance rate) to increase as drug concentrations increase.

This is how the textbook defines distribution volume and clearance.
$$\text {distribution}\ \text{volume} = \frac{\text{amount of drug in the body}}{\text{concentration in plasma or blood}}$$
$$\text{clearance rate} = \text{bioavailability} \ \cdot \frac{\text{dosing rate}}{\text{concentration at steady state}}$$
I think I get the grasp of it somewhat, but I would like to verify if my reasoning is correct.
The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug. As a result, the amount of drug in the body increases while the concentration in plasma or blood stays the same.  Hence, the increase in distribution volume.
As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.
However, I am not sure why the fact that plasma proteins are saturated matters.
For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered. For clearance rate to increase, however, unbound drug in plasma needs to be able to increase when more drug is administered. What am I understanding wrong?

First a couple of clarifications:

You wrote:

For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered.
Actually, it is the total drug concentration in plasma (bound plus unbound) which matters while calculating distribution volume.

Clearance is better defined as $ \frac{\text{Rate of elimination}}{\text{Plasma concentration}}$. The equation you mentioned above is a derived formula for calculation of dosing rates.

Now for the answer. The basic principle is: when plasma proteins get saturated, increasing drug concentration increases both tissue concentration and unbound drug concentration in plasma, because the drug has "nowhere else to go".
Thus your reasoning is correct when you say this:
The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug.
Of course, our understanding here is that the increase in total plasma concentration is marginal as compared to the increase in tissue concentration.
However, the following does not seem to be correct:
As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.
(Perhaps you are confusing plasma proteins with drug metabolising enzymes?)
The answer to the clearance part can be obtained when you recall that we are talking of a drug with low hepatic extraction ratio. Thus, clearance is proportional to unbound drug concentration. As already mentioned above, unbound drug concentration increases on increasing drug concentration.
Hope that answers your queries.
Reference:
Buxton ILO. Pharmacokinetics: the dynamics of drug absorption, distribution, metabolism, and elimination. In: Brunton LL, Hilal-Dandan R, Knollmann BC (editors). Goodman & Gilman's the pharmacological basis of therapeutics. 13th ed. New York: McGraw-Hill Professional; 2017. pp 13–29.

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— Thank you for taking the [tour], but you may also want to consult the help pages for additional advice on [Answer] effectively on this site. Thank you!


text:
What is happening at the electrode interface when the electrical field is modified due to the change of ion concentration after an AP?
I have been working for quite a while now on electrophysiology and electrode fabrication.
I studied what is happening at the neuron level during an action potential (polarization/depolarization, change in ion concentration inside/outside the cell membrane) as well as the interface electrode/electrolyte (double layer, electrical model of an electrode, etc...), but I am still struggling to tie all of those principle together.
My question is, what is actually happening when an electrode is recording an AP (extracellular recording). To my knowledge, this is what is happening:

AP triggered, change of ion concentration outside the cell membrane.
As the ion concentration is modified, electrical field is modified around the cell

My question is now, how does the electrode record this change of electrical field? In almost all of the literature, a simple, but unexplained, shortcut is usually done: the authors usually speak about the change in ion concentration and then directly link it to a "change of potential at the electrode", but how can we explain this change of potential? What is happening at the electrode interface when the electrical field is modified due to the change of ion concentration after the AP? Is there any current flowing inside the electrode?
Thank you in advance

I’m voting to close this question because it seems to be about the details of what happens within an electrode (probably Physics or possibly Chemistry) rather than anything biological.

This is the field of biophysics and is on-topic here.

@AliceD — I could be wrong, but after rereading the question it still appears to be asking about what is going on inside the electrode. If that is on-topic for biology, then what isn't? For example why wouldn't a question about the details of NMR be on-topic (since MRI is used to study biology)? It seems to me that encouraging tangential questions is a disservice to the asker (since they are less likely to get a good answer and that answer is very unlikely to be properly scrutinized due to lack of expertise by this sites users).

@tyersome - the fact there may be a better stack to ask is not a reason to close the question. A comment to OP with your suggestion about a more promising stack is awesome. Also tell OP that cross-posting is discouraged and that if they decide to ask the question elsewhere, they should delete their first post. But again, many questions fit at multiple stacks. Many, if not all Neurosci questions here at Bio also fit at Psych&Neurosci.SE and vice versa. Some I see appearing here would receive better answers there, and vice versa. That is not a reason for migration.

There is an art to expressing the nature of any kind of uncertainty in writing, and especially in experimental literature, to stating no more than has been empirically shown.  An electrode interface only measures a one dimensional trace of what actually happens during an action potential cycle or spike, and it could be that in most of the literature, the precise mechanism by which the spike is measurable takes lower priority than the existence (or non-existence) of a particular signal.
According to Hodgkin-Huxley theory, the action potential is controlled through changes to the ionic permeability of certain membranes.  The precise mechanisms by which this happens depend on the molecular structure of channels through which sodium and potassium ions flow.  However, it is not hard to explain how a change in the permeability of a membrane can cause changes to an electric potential gradient (over 'large' length scales); the "deep concept" at work here is the second law of thermodynamics.
Let's suppose that you have two ions, one positive and one negative, confined to one side of a box as shown:

You might notice that there are more negative ions than there are positive ions, so there would be a nonzero electric potential gradient between the left and right hand sides of the container.
Now let's suppose that the confining membrane is replaced with one that allows only negative ions to pass (through the purple or tapered channels.)  You might expect a fraction of the negative charge to flow over to the other side of container where the potential is slightly higher (as shown):

The result is that the original potential gradient (from left to right) is dampened slightly.
The OP is probably aware of this, but it turns out that replacing the membrane with one that allows positive charge to pass through results in a fraction of the total positive ions moving to the left side of the chamber (even though it would be attracted to the right hand side by the net negative charge)*.  The reason for this is that the entropy gained by the first positive charge to move into the (log-macroscopically large) empty chamber vastly outweighs the (microscopic) entropy cost of leaving the occupied chamber with fewer positive ions to offset the negative ones.

This results in a slightly larger potential gradient than in the first (impermeable) case, as there are now positive charges in the region of higher electric potential.
The electrode can pick up on changes to the potential gradient by "grounding" the circuit at several points.  In particular, this requires a circuit that is soft or sensitive enough that it does not disturb the ambient potential significantly (a tape measure or height rod adapts to your height, not vice versa.)  That is, whatever current flows between the electrodes should be weak enough that it does not completely drain or equilibrate whatever local potential difference might exist, and other circuit elements should be weak enough that they do not cause flooding or, in a sense, drought of the natural electrodynamic state.  Beyond this, the complex and densely packed environment of neurons would make it a challenge to place electrodes to isolate a single action potential, or even a potentially useful signal across several action potentials.  Also, there is inevitably a certain amount of excessive unnatural current flow below a certain length scale (the scale at which the electrode starts to look like a bulk conductor.) Because of this, neuroscientists probably care more about the presence or absence of noise at this point than about the precise physiological origin of the signal, except insofar as the disturbance from the electrode is correctable and within tolerance.
*If the experiment is performed at nonzero temperature, which seems to be unavoidable.

Welcome to Biology.SE! While this looks like it may be a good (or even excellent — I lack the background to judge) answer, it is to a question that isn't about biology and thus is off-topic for this site. It would be better to leave such questions unanswered or have them migrated to an appropriate site. Second, for future posts please provide complete reference information since links can (and do) break. ——— You may also wish to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

@tyersome not about Biology? I don't agree -- It's about action potential generation, i.e., the field of biophysics, neurophysiology, neuroscience etc.


text:
Is Klebsiella pneumoniae found in the throat of healthy people?
Is Klebsiella pneumoniae found in the throat of healthy people?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For example, reading and linking to the relevant Wikipedia article and (if this is true) indicating that you were specifically interested in the throat and why knowing it is in the normal oral microbiome isn't sufficient. Thanks!

Klebsiella species, including pneumoniae, are normal members of the healthy human oral microbiome.
Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota
Saliva microbiomes from 6 healthy adults were analyzed by 16S sequencing over a starvation timecourse, where oral microbes were cultured in minimal medium (PBS or 1:1 PBS:cell-free saliva).  Figure 1 shows that the genus Klebsiella is initially low abundance in the healthy oral microbiome, but the proportion of Klebsiella increases over the starvation timecourse in the two media tested.  An excerpt from the results:

At day 1, several species of Streptococcus were recovered, as were Gamella sanguinis, Klebsiella pneumoniae, and Klebsiella oxytoca. At day 20, K. pneumoniae, K. oxytoca, Enterobacter homaechei, and Providencia alcalifaciens were the only recoverable species. Finally, at day 84 and day 100, only K. pneumoniae and P. alcalifaciens were recoverable under the conditions tested

Given the proximity of the mouth to the throat, I think it's fair to say that K. pneumoniae is likely a member of the healthy human throat.
If that's not convincing, you can check the supplemental data from this paper, which looked at 16S data associated with throat tissue samples from 29 patients with laryngeal carcinoma and 31 control patients with vocal cord polyps.  Looking at the relative abundance of different phyla, they found that Proteobacteria (the phylum containing the genus Klebsiella) accounts for 11% of the recovered 16S reads on average for all patients (range 0–67.1%).  The authors claim to have recovered 218 genera and >3000 unique OTUs at 97% similarity, though they only report the ~30 most abundant genera in their differential abundance analyses, and it doesn't look like they included the full dataset in this publication.


text:
Why do quaking aspens quake?
I've just finished reading The Hidden Lives of Trees by Peter Wohlleben, which I thoroughly enjoyed.
According to the author, the advantage of shaking the leaves is that both sides of the leaf are exposed to the sun, and therefore both sides can photosynthesize. This would be in contrast to other species, where the underside is reserved for breathing and transpiring. However, to me (a complete amateur), the underside of a quaking aspen seems paler in colour and doesn't "look" like it's any more suited to photosynthesis than the underside of any other leaf.
In addition, I can't find any other sources that back this claim. Most other sources (for example https://www.nature.com/scitable/knowledge/library/case-study-the-glorious-golden-and-gigantic-13261308/) seem to claim the shaking of the leaves reduces the risks that come with too much sunlight, which damages the leaves and actually lowers the rate of photosynthesis.
My question is therefore, what is the most convincing advantage the quaking aspen gains from this characteristic ?

I would have to ask whether there is in fact any particular advantage, and indeed, whether aspens "quake" much more than other broad-leafed trees.  My casual observation is that they really don't, it's just that they're often the only deciduous tree in areas with conifer forests, so the leaf movement stands out.

Quaking aspens do indeed "quake" in the merest of breezes, but aspen leaves are very light compared to maple or oak leaves and ave a flat petiole, another surface to catch the breeze. Maybe there is no benefit, it just is what it is. It's not like they attract other trees this way.

@jamesqf - If they didn't move more in a gentle breeze, they probably would not have been called quaking aspens.

@anongoodnurse: Many other deciduous trees - cottonwoods, willows, maples, ash - have leaves that move in similiarly gentle breezes.  But (at least in the western US) aspens are typically found in isolated groves (near springs, streams, & other places where there's plenty of water, surrounded by conifers, so the movement is noticable.

Hmm "why" do they quake? Impossible to know. The best the scientific process can do is determine if quaking provides any physiological or ecological advantages to the trees. I do not know of any specific research examining this (not too unusual) "phenomenon"  in quaking aspen, but I'll dig around to see if I can find any interesting papers for you...

Conjecturally: P. tremuloides is an early successional (i.e.,"foundational") species, and as a result is typically going to be exposed to more sunlight (due to less other plants shading them out). Their foundational role also means they use more of their energy to develop fast-growing foliage to out-compete other plants for sun (and therefore have less energy for developing UV defenses). I would guess that the added heat of the direct sun and less robust UV protection would decrease fitness, and so the plant would benefit from having less horizontal and still leaves. Natural selection etc..

Robberecht & Caldwell (1978) demonstrate that P. tremuloides experiences substantial UV protection from epidermal compounds. However, this could be interpreted in 2 ways relative to my previous comment. 1) reaffirming the need for and past evolution of traits to protect against high UV (which we know is common in its habitat). Or 2) no need for additional UV protection due to having adequate epidermal protection -- therefore reducing the odds of UV damage being the selective driver for quaking. Heat is still an issue though...

Dillaway & Kruger (2010) might also provide some insight relevant to my hypothesis above, but it's too late -- 2 am -- for me to read, so I'll just place this citation here for reference for the AM.


text:
Why and how do red bone marrow concentrations in humans change during traditional aging?
I have found several pictures that suggest this is the case.  As for peer reviewed papers I've found plenty of papers hypothesizing and testing as to the why of changes in populations of HSCs, a few on quantitative changes in MSCs, but none explaining why red bone marrow would become less active hematopoietically in long bones before flat bones.


text:
Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase
I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?

It's looking an interesting question. Can you kindly add bit more details?

Welcome to SE Biology. Please complete the Tour to find out how this site works. Also read about how to ask questions. It is unclear whether you want are appealing for someone to do your work for you (definitely not the purpose of this site) or information on how to go about it. Assuming the latter, it is impossible to help you without knowing what your gene is. If your Blast search is bringing up PPIs, then I would imagine your gene is a PPI. Show us the sequence comparison, not the tree.

I have edited your question to correspond to what I think your problem is and have provided an answer. If you disagree, you can revert the question but you would need to clarify it. I hope I have not inadvertently answered an assignment rather than a real research problem. If this was a real research problem, you would be advised to believe the evidence of your own analysis in future, and do some research on what they bring up.

Without seeing the sequence of the RNA-binding protein it is impossible to be sure, but the obvious conclusion is:

The RNA-binding protein is a peptidyl-prolyl cis-trans isomerase.

It has been known since 1989 that peptidyl-prolyl cis-trans isomerase is a multiple-function protein, also exhibiting properties of the cyclophilins, proteins which bind cyclosporin A. The post raised the possibility that it may have other activities and a literature search reveals several more recent papers that indicate cylcophilin A can bind certain RNAs. I list some of the titles:
A nuclear RNA-binding cyclophilin in human T cells (1996) FEBS Letters 398 201–205
Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain (2001) Cytogenet Cell Genet 95 43–47
Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly (2013) J. Virol. 87 13330–13342
Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants (2013) Scientific Reports 3 : 3001, DOI: 10.1038/srep03001


text:
How many SARS-CoV-2 viruses in circulation at the moment? Mass?
How many SARS-CoV-2 viruses are in circulation at the moment? And what is their total mass?
To clarify: if there are 10 000 viruses on average in an infected human and 100 000 humans are infected the answer would be (if all viruses are in humans, which probably isn't true) 10^4 x 10^5 = 10^9 viruses.
Of course I am only looking for a rough estimate, a number that, when multiplied with 10 or 0,1 (so two magnitudes) or so, is correct.

Welcome to SE Biology. You will have read in the Tour that this site is for "questions about an actual problem you have faced" in the areas of "biological concepts, biological mechanisms behind medical conditions, and techniques in a biological or biochemical laboratory". And that the idea of the site is to amass answers to questions that are of more lasting and general interest. It is hard to see how a count of viruses "at the moment" (has it passed yet) satisfies any of these criteria. How do you propose to use the answer? Say "Wow, that's a lot!". That is really not what the site is about.

Based on all species of viruses, Everyday you breathe in 100 million viruses. There can be 1mn+ viruses per ml of blood of patients. Covid-19 diameter = 125 nm.
Perhaps it's wrong, the maths would go something like this:
1mn * 1000ml * 5liters * 400k patients = 2^12 - 2^13 sars2 viruses.
total volume of viruses =  2^13 viruses / 1^15 viruses per cm3 = 0.02 cm3
(10^7 nanometers per centimeter, 125nm diameter, gives, about 10^(5*3) viruses per cm3.)
Weight of all the Covid Sars 2 in the human population = a raindrop or a teaspoon of hydrocarbons/mayonnaise, probably less than a teacup.
Perhaps i am wrong, it's reasonable to think that the people with major symptoms contain about 1 ml of virus. 20k x 1ml = 20cm3


text:
Unable to identify bug/insect in house
I am not able to identify this bug/insect.
I stay in Dubai and have been noticing this bug/insect in my apartment since a week now. It is so tiny that it's difficult to notice. The image below has been taken using a DSLR by placing it on a book page and cropped to more than 100% zoom.
I don't know the source, can feel it crawling on my skin and that's the only way to see it. One good thing is it cannot fly.
I went through all the questions about insect identification, but couldn't find any closest match for this. I also compared it to a book lice, but it's nowhere near to it.
I suspect it bites and leaves the skin itching with red spots similar to a mosquito bite.
Does anyone know about this bug if it is harmful, and how to get rid of it?

Hmm not a great picture. How small would you say it is? Do you have any pets or animals in the home? More importantly, do you have birds living in/on your home or any rodent probems?

Possibly related: Bug Identification: Tiny Bugs

@theforestecologist - Bingo! Thanks for the link. It is indeed nearest match to a Bird Mite. We don't have birds, animals or any pets at home. However, pigeons often visit our balcony just to be shooed away by us. Now will need to see how to prevent them from coming. Please post this as an answer, so I can mark it.


text:
How does species diversity vs Earth total biomass relate?
Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth?
While there is a lot of esoteric sort of talk "humanity dis-balances the live on the Earth", I thought, there are formally seen the following hard facts (correct me if I am wrong):

biomass of human species and species we need (plants/cattle etc) is increasing;
diversity of species is decreasing

So it looks like some sort of global system change (correct me if I am wrong), but how does biology science discuss them (in case my inquiry can be anyhow scientifically formulated)?

Biomass includes algae, plants, and insects. Humans are almost certainly negligible.

There are quite a few papers out regarding this topic e.g. this is a more recent one I've found that showed diversity and biomass being positively related.

Here's an older one focussing on theoretical foundations. I think the main idea is that a system rich in species is generally more efficient in resource use and also more stable resulting in a long term higher level of biomass.

I don't work in ecology, but my first thought is that I would not expect any relationship whatsoever between diversity and biomass. Biomass simply means the combined mass of all life on the planet. If that mass consists of one extremely fat goat the size of the moon, or several trillion different organisms doesn't make a difference, mass is mass.
Now, it is undoubtedly true that loss of diversity is a huge issue. However, the way this works is usually that we replace the local ecosystem with its several, varied species with a monoculture. For example, grasses like wheat and barley are taking over the world. Destroying a forest to plant wheat might easily result in no net change in biomass or even a net positive, but it will certainly be a significant loss in the diversity of the local ecosystem.
Finally, humans are a teeny tiny part of the world's biomass, most of which consists of unicellular life, plants and insects:

Note that the axes in the image above are logarithmic. You can get a clearer image, perhaps, from this:

(both images taken from Bar-On YM, Phillips R, Milo R., The biomass distribution on Earth, PNAS, 2018 Jun 19;115(25):6506-6511. https://www.pnas.org/content/115/25/6506)
See how all animals, let alone humans, are just a tiny part of the image on the right? That gives you a pretty clear indication of just how irrelevant we are in terms of global biomass. So yes, diversity is indeed decreasing, but there is no reason to think that the accumulated mass of living organisms will decrease, only the diversity of said mass will decrease.

thank you! wow did not think there is so much fish as one could think we have "fished out" seas!?

@J.Doe the idea of "fishing out seas" really is a major ecological/economic issue, but not to the point of eliminating life (biomass) from the seas. The concern is that extending beyond a maximum sustainable yield, we can cause an individual species to be extirpated or to go extinct. This presents 2 problems. 1) we rely on that fish species for a reason -- perhaps ease/cost of capture, nutrition, etc.. 2) I invite you to investigate further concepts of food webs, keystone species, and trophic cascades. A short summary: what you do to 1 species can and will impact the rest of the ecosystem...


text:
CRISPR-Cas9 knockout
With CRISPR-Cas9 I have conducted a targeted knockout of a DNA region encoding a certain protein (working with leukocytes). My question is, how long does it take until this protein is not detectable any more (e.g. via surface staining + flow cytometry) after the DNA has been manipulated? Or in other terms: how often are transcription, translation etc. taking place?

What cell line are you working with? Different celltypes can have fast differences in turnover rates of (DNA/)RNA/proteins.

Thank you! Actually I am working with fresh human PBMCs (and thereof with CD4+ cells)

To answer your question multiple parameters which one should be taken into account.
There are two main sets of parameters: gene specific and cell line specific.
Parameters related to your specific gene of interest :

Do you know the half-life of the RNA of your gene of interest? Most of the time it is not known but there are several tools and resources which can predict it based on a lot of different features such lengths and stability of 3'UTR, 5'UTR, number of exons introns, etc.
Another indication is if there are already people who have either perform a genetic perturbation (siRNA, CRISPR, etc) or a degradation assay. In this case you might be able to guess what is the relative half-life of the RNA or the protein.
Which leads us to the half-life of the protein of interest. Proteins which are soluble tends generally to have a smaller half-life than membrane proteins (not necessary true there are exceptions). For example doing a complete functional knockout of a transcription factor might be easier than a GPCR receptor. If it is a membrane protein, to which organelle does it localize? Is the organelle recycling the membrane a lot or is the cell dividing? In this case you might have chances that the viable proteins present before the genetic perturbation get diluted. In these examples, you might get ride of a soluble protein in less than 24-48 hours, whereas a very stable membrane protein might take 7-10 days.
The number of RNA copies is important as well as the number bound to ribosomes (less important) and their localization in the cell (less important)
The abundance of the protein in general.

Parameters related to your cell line of interest:

The lineage of the cell line you selected: different cell lines have different global transcription and translation rates.
The rate of division of the cell line (extremely important parameter): the faster the cell line will divide the faster  the mRNA copies which were not perturbed (wild-type) and the proteins present before the genetic perturbation will be diluted between daughter cells.
Number of copies in the cell line: if there are multiple copies of your gene of interest, you would need to make sure that each copy of the gene has been perturbed to lead to a functional KO.
Genomic stability of the cell line: some cells lines like HeLa are quite known for genomic instability where a lot of the genome can be rearranged can perturbed copies can be fix using viable copies

Last but not least, it depends technically how you do the CRISPR-Cas9 genetic perturbation: transfection of the gRNA, electroporation of the Cas9 with the gRNA, lentiviral mediated delivery etc. The time I have provided are after all the components have been delivered and are present in large amount in the nucleus.
I hope that helps!


text:
Values of the blood tests pancreatic amylase and lipase
Anyone know what is considered slightly elevated, moderately elevated and strongly elevated values of pancreatic amylase and lipase?
Many different laboratories in my country divide between these categories for interpretation, but they don't specify which values qualify for each category.
Hope this is the right place for this kind of question.
Thanks in advance.

It is not necessary a fixed value. I think it depends on the doctor that interprets it. For e.g if amylase's normal value is 70, and laboratoy value is 80, i would say it is slightly elevated. A value of 300 is strongly elevated.

The poster asks for a range that has some official or formal basis. What you consider normal etc. is of no relevance if it is not backed up by evidence that it is based on a scale that is in operation. Please read the Help on answering questions for this site.


text:
SARS-CoV virus stability at low temperatures
For SARS-CoV-2 and SARS-CoV1 this study published in NEJM by a NIAID team was done at a temperature of 21-23°C (see the Methods section in their supplemental material).
What's known about virus stability in general and for these two viruses specifically at much lower temperatures? (e.g. 4 °C, fridge temperature).

SE Biology is concerned with the mechanisms of biological processes. General information about the coronavirus is available from a variety of reputable sources, some of which are listed here. You are advised to consult them.


text:
how can we identify the novel protein amino acid sequence and function?
if there is a novel protein, how would you know the amino acid sequence and  how would you determine the number of subunits and the function of that protein?
Specifically what molecular techniques we can use to identify the novel protein?
Basically, this is a question asked during a biochemistry interview? It will be helpful, if someone just clarify it

What do you know about the protein?

This is very broad and sounds like a homework question. In any case you should show what attempts you have made to find an answer yourself.


text:
How lungs can inhale and exhale?
I know that lungs are extended and compacted by muscles to create partial vacuum to breath in, or to create elevated pressure to breath out. But one thing seems not right to me...
As far as I know, air comes through bronchi airways (like pipes) then branch like twigs and end up in tiny berry-like alveoli where gas actually exchanged... That's all clear, but I can't connect this 2 things together.
It seems to me, that bronchi + alveoli is a closed system. So how by creating partial vacuum inside lungs themselves (like in bags) makes air come into alveoli if it's a closed system and the air pressure outside alveoli does not has access to outside air at all (as it seems to me).

I hope this image will make it a little bit clearer...
So does bronchi have some kind of openings in them to let pressure inside "bags" connect to outside world or does alveoli walls are so thin, that it actually allows gas to flow freely? What am I missing here?

this may help your understanding. https://www.youtube.com/watch?v=H62wTF9vKPQ one video is worth a thousand words.I recommend turning the sound off.

Why do you say the "bronchi + alveoli is a closed system"?  The bronchi are open to the atmosphere through the mouth and nose.

I would require to your approx age. Are you high school student?

No, I'm 27 y.o.

(Note: Since the question language isnt clear; it just seems to me the
1. The purple-blue "Wall" (technically the plurae; containing plural space not shown) is being refered as the bag.
2. The ruptures are drawing artefacts. There arenot such ruptures.
3. I assume you know that the lumen of the broncheoles is continuous with the lumen of the alveoli ("grapes" in your analogy).
I would request you to clarify the language of the question.)

"So how by creating partial vacuum inside lungs themselves (like in bags) makes air come into alveoli"

Up to best of my understanding; atmospheric air has its own pressure, and own ability to expand. So when chest muscles expand and let the lungs to expand (probably you refer it with analogy of "bag")  gives space to the alveoli to expand, the atmospheric air shall come through the broncheole and fill the alveoli to expand them until and unless a certain equilibrium appear.
Update:
The "bag" you mentioned (Purple-blue mark?) isnt like an empty bag; it can transfer the pressure to alveolar wall. Because the "bag" is filled with compact alveolar wall (imagine your "bag" (blue) as a ruber balloon and remaining lung tissue as a mass of sponge tightly filled in that baloon) and there are some tissue fluids too.  so an improvised analogy would be like this:

Note the springs i have drawn are not real spring. I hypothetically drawn to mean the wall is able to rtansfer the push and pull to alveoli.
The realistic histological section will help to clear some confusion I hope.

(source: http://medcell.med.yale.edu/histology/respiratory_system_lab/respiratory_bronchioles.php)
Update:

So does bronchi have some kind of openings in them to let pressure
  inside "bags" connect to outside

If there were rupture in bronchi or alveoli; then opposite is expected.  it should leak the air to freely move to the "bag" you said, and would destroy the way to develop pressure difference and will cover up the alveoli and will crumble them (imagine the video that user @John has shared; if the red balloon is ruptured,  you will be no more be able to inflate the baloon the way they are inflating.

I see... So the actual partial vacuum/increased pressure are actually created in the alveoli themselves, and lungs walls are just there to compress/decompress alveoli themselves?

intuitively Seems so. But i am not sure whether alveoli has a significant elasticity to maintain their fluffy (enlarged) state by their own, but that too may be an effect.

Hm, that was a really good video. Didn't though about pressure differences in closed system that has and elastic open system inside of it... So, seems like this closed "bags" have constant pressure of about 1 atmosphere, right? So deep under water it would be crushed, but in outer space, where there is no pressure, it would potentially burst (or it's walls can actually withstand outward 1 atm)? And that's why on high mountains its so hard or even impossible to breathe? Cos alveoli are crushed by reliantly high internal "bag" pressure, and increasing it's size does not produce enough vacuum...

... to let low outside pressure to extend alveoli? So, it's just purely this internal gas pressure of sealed "bag" that affects alveoli, not a mechanical push on them from the "bags" walls? Cos in this case (if it where only mechanical) it would be easy to breathe on high mountains. Can you confirm my understanding of this matter?
P.S. Oh, and I see on that image that terminal bronchi and alveoli themselves transform into squamous type cells (like in top of skin) to be elastic, right?

Sorry for idiotic typos, today is no my day, in terms of writing stuff...


text:
is it possible to visualize coronavirus infection and what type of assays are routinely used?
There has been some electron micrograph of SARS-COV-2 published; but are there any fluorescent/ confocal-fluorescent image of them? or is it possible to do them?  I know that viruses are usually much smaller than capacity of light microscope but I think by using any immunofluorescent probe or FISH technique it is possible to visualise the locations occurance of the virus in cell or tissue. At least one website says it is possible to visualise viral infections using fluorescence techniques.
Now is there any such image for SARS-COV-2, and is it possible to take?

I'm voting to close this question as off-topic because asking for an image is not posing a biological problem.

should i delete the question?

It could be reformulated as a biological question: is it possible to visualize viral infections and what type of assays are routinely used?

Thank you I will do such change in language; still the question remains the same.

If you have an antibody against the viral proteins you can do an immuno staining followed by fluorescence imaging. For this type of technique you would need a very specific antibody. I am not aware that this exist at the moment and I don't think anyone had the time to do it for immunostaining purposes.
For FISH it would depend on the genomic nature of the virus (ssRNA, ssDNA, dsRNA, dsDNA), again you would need specific probes to capture it. Again specific is key.
EDIT 01.04.2020: This group says they have found specific antibodies https://www.centivax.com/covid19

Okay then its not available yet. No, I have not facilities to work with virus.

As far as I know it has not been done but who knows things are going extremely fast these days it is hard to keep track of all preprints and publications.


text:
What are the difficulties/challenges against developing a coronavirus vaccine?
Multiple groups of scientists are trying to develop a coronavirus vaccine but they are not yet being fruitful. What challenges or difficulties are there in the process that slowing down and/or causing failure in development of vaccine?

It a thing that takes time. The outbreak started only last year in november and was recognized some time later, what do you expect?

There is already a candidate vaccine in testing, less than three months after the virus's genomic sequence became available.

@Chris I didn't expect because i dont have the idea what to expect. Vaccine development takes time but is SARS Cov2 taking an unusually long time or its within usual range??

There are multiple challenges presented, and many of those are not limited to coronavirus vaccine.
As mentioned above, it just takes time. Before a vaccine can be used in patients, clinical trials must be performed to validate the safety and efficiency of the vaccine candidate. A Clinical trial includes three phases, which again, just takes time.
But to really answer your question, what are some challenges of developing a vaccine?
To begin with, from the perspective of lab research, we first need to develop a vaccine candidate. What protein on the virus should we take as an antigen? There are many many proteins on the virus, and for CoV, we know it is a protein called Spike protein. It is the neutralizing target on the virus. Which means, when an antibody bound to this site, it could prevent the virus from infecting the cells. Okay, then we have to know, do we need to do something to this protein to make a vaccine? For example, when we try to manufacture this protein into a vaccine, what if the protein is degraded? Or it somehow becomes a 'bad' protein that simply cannot stimulate immune responses in human? These are just some examples of roadblocks of developing vaccine.
Let's suppose we finally work those out. Then what's next? Each candidate vaccine needs to be tested in animals before going into human clinical trial. This step is time-consuming.
Now we are finally ready to start clinical trials. According to FDA, the vaccine for human trials (also for each drug) needs to be produced under Good Manufacturing Practices (GMP). It's basically a standard operating procedure to make sure that the vaccine candidate can be manufactured in a large-scale, quality-controlled manner. There are many many challenges, like how to purify the protein? How to scale-up production. This is partly of the reason why the first vaccine in trial in USA is an mRNA, and in China is a DNA, both of which does not require complicated protein purification.
As you can see, the list of challenges can go on and on. But there are scientists and doctors working diligently on it. Hopefully we'll get there.

Vaccine development is not as easy as just inject some inactivated virus as:

Vaccine can have side effects such as inflammatory reactions. So for a good vaccine the side effects must be negligible or within a tolerable limit.
Vaccine may not induce immune response. It may be ignored by the immune system as just some random debris. So a good vaccine must be recognised as a foreign object by the immune system.
The vaccine may be not so specific. I.e, the immune response may have high cross-reactivity that may undesirably interfere with some undesired biomolecule or unrelated  process.
The desired activity of the vaccine may be too specific, i. e. on slightest genestic variation of the virus, the vaccine may fail.
An attenuated strain as a vaccine, may have a possibility to revive and form revertant strains. A good vaccine must be safe from pathogenicity
The immune response may not last long. For a good vaccine the immunity have to last long.
The shelfed vaccine must have some stability with time, temperature, transport etc. If the vaccine quickly loses its activity then it wont stay usable.
Some individuals may not respond to the vaccine, such as depending upon genetic preconditions. So a good vaccine must elicit immune response to a wider range of population.
There may be challenges regarding isolation, preservation and maintaining a desired 3-D structure of the protein from virus.

Alongwith

Any research-process tend to be slow, and unpredicted problems may appear at any steps.

These are likely to make any vaccine development as conceptually slow, tedious, testing dependent, and safety concerned.
References:
Polio vaccination: Past, present and future
The ideal vaccine
Eliminating vaccine cross-reactivity
Vaccine efficacy article on Wikipedia

Immunology is very complex, with so many interactions that prediction is difficult.
For example, some vaccine candidates will probably be designed to provoke an immune response against the proteins on the spikes of the virus. If that protein is similar to proteins already existing naturally in the body, then the vaccine wont work, because immune cells that attack the self are destroyed during their maturation.

A vaccine needs to be able to neutralize the virus (bind to it and masking from entering the cell) with high affinity. Now the virus is a large complex structure, so it is not immediately clear how to design a vaccine that can achieve that.
Screening antibodies from recovered patients might be a good idea, but it takes effort and time. What is more, the antibodies isolated from those patients may not be optimal for a vaccine, and some rational design based on those antibodies might be needed.
Another challenge is how to get a sustained level of vaccine proteins in the human body. The cutting-edge in the field right now is to use mRNA instead of proteins. You can read something about Moderna, which spearheaded this effort in the pandemic. But we still do not know what those RNAs are doing and where they are going in the body, so it takes many experiments and creativity to send those mRNAs into the human body so it can function properly.
To make a vaccine, you also need very strict production standard known GMP to make sure that the product is clean, pure and safe. This is not very easy and not every lab in the world can do.

"A vaccine needs to be able to neutralize the virus (bind to it and masking from entering the cell) with high affinity" - that is not how vaccines work.

@OP what you are describing as "neutralising the virus" is the work of an antibody. Vaccine is an antigen not an antibody.


text:
Do all Viruses have the same RNA
Let's take the Influenzavirus as an example, and I have 5 of it. Would all 5 viruses have the same RNA with the same base order? Or would the RNA base order differ from eachother?

Different viruses have different viral genomes.  This is the case for different strains of flu, too.

A person infected with a strain of a pathogenic virus will have copies of that virus in their body.
Virus particle genomes could contain a number of substitution, insertion, and deletion mutations. The surface proteins on enveloped and non-enveloped virus copies could contain mutations. Most mutations are deleterious and those particles will not be infectious.
But the genome sequence of that virus will be largely identical, these mutations aside, and copies will be packaged so as to attempt to reinfect and reproduce.
Actual mutation rates depend on the virus type (RNA, DNA, single- or double-stranded, sense; see Figure 12.1 about the Baltimore classification of viruses), and how it uses reverse transcriptase, RNA, or DNA polymerase to make copies of its genome for use in expression (to make viral proteins) and reproduction (to make viral genomes).
For instance, RNA-dependent RNA polymerase has a lower fidelity rate — makes more copying mistakes — than DNA polymerase. Reverse transcriptase can also introduce mutations when turning the viral RNA genome into DNA, and vice versa. These processes can also introduce errors in expression of membranous or capsid proteins in enveloped and non-enveloped viruses.
The RNA virus family Orthomyxoviridae contains the strains of influenza that infect humans. These are enveloped, negative-sense, single-stranded RNA viruses. They use RNA polymerase to turn their genome into forward-stranded RNA molecules that can act as both mRNA (messenger RNA that is translated into viral proteins) and as a template (again, using RNA polymerase) for making copies of the influenza genome, itself.
Errors introduced at these two steps will result in copies that are different from the parent.

That's another way of querying the virus mutation rate. HIV has a 100,000 faster mutation rate than Herpes(HSV).

Then, the mutation rate is measured as the number of substitutions per nucleotide per generation, defined as a cell infection in viruses (μs/n/c)...
I think that means that every virus varies by about one base pair, which means that they are all different. most viruses that explode out of a cell are indentical except for 1/10,000th of their genome.

RNA viruses mutate 100 times more than DNA viruses.
Viruses with high mutation rates could be combated by the administration of mutagens. HIV develops drug resistance very fast (one day), that's why they have to use multiple drugs. Mutation rate evades the immune system and helps jump the species barrier.
ref: https://jvi.asm.org/content/84/19/9733
For lots of graphical illustrations of virus mutation, search images for "virus mutation rate".

AIDS is not a virus, but the disease caused by the HIV virus.

Ok, speaking a bit simply. corrected.

Do all Viruses have the same RNA

No, different viruses have different RNA. Some viruses have DNA which are also different depending on strain to strain.

and I have 5 of it. Would all 5 viruses have the same RNA with the same base order?

Have 5 of it in where? in a host due to an infection? Theoretically if the infection is caused by 1 propagule and thus the obtained viruses are clonal to the founder propagule; they would be highly similar in their genetic sequence; but some variations may happen.

My thoughts are that all Covid-19 have the same RNA sequence that transcript and translates to the spike proteins. So my goal is to know the following: if all Covid-19 viruses have the same RNA sequence that translates to the protein spikes, would it not be easier to develop a protein which has a very high affinity to this sequence in the RNA of Covid-19 and deactivate it to forbid any further transcription and translation of protein spikes, so the virus would be built in the cells but without receptors to bind to other cells, so it becomes useless?


text:
Can humans eat a greater variety of things than other omnivores?
One thing that I've always noted is that humans seem able to eat just about anything that isn't toxic (and many things that are). Even when compared to other omnivores, I have the impression that humans are capable of eating far more things without harm. Is this true?

I don't know about that.  My dog seems to eat anything I would (of course I don't give him things like chocolate, but he would eat it if I did), plus many things I would not, such as horse manure, hoof trimmings, long-dead critter bones...

Maybe so, but you COULD eat those things (disgusting, but that's all). On the other hand, your dog would actually get sick, and possibly die, from eating things such as; onion, garlic, chives, chocolate, macademia nuts, avocado, xylitol (sweetener), cherries, grapes/raisins... You get my point?

No, because even if I (as a typical human) could force myself to swallow many of the things that a dog happily eats, I would actually get sick, and possibly die, from eating them.  Sure, humans can safely eat some things that dogs can't, just as dogs can safely eat some things humans can't, but that is not saying that humans can safely eat more things.

@jamesqf Really? I know there are many things a dog eats that I would not like to eat, but I've not thought about them being "inedible" for me. Do you have a few examples?