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Should vaccination be based on a principle of broad and rather unspecific immunization?
In the context of Covid-19, in Denmark all ferrets/minks in farms were killed, as there is infection in humans by virus from ferret.
Thus, a  virus transferred from ferret to man proves to find the same type of target cells.  This corresponds to  Jenner's vaccination (vacca means cow) against Small pox by transferring  cowpox virus from cow to man in so  far as cow pox virus does replicate in man if to a lesser degree, not causing disease.  The diffence between infection of man by CoV from ferret/minks  seems to lie in  "attenuation". Different to cow pox (that is named different from small pox)  CoV from ferret is dangerous to man to no lesser degree.
Still,  "attenuation" may not be the working mechanism that Jenner's vaccination was based on, as target cells not being infected in man in the same way as they are in  cow  must carry different antigen. Antigens of small pox are not identical to those of cow pox.
Jenner's technique seems to be unique in its use of a different type of virus: cow pox is different from small pox. In contrast, for example, live measles vaccine is not different from live measles virus.
Whereas live measle vaccine, e.g., uses the identical antigen, Jenner's vaccination apparently did not: Cow pox isn't small pox.
Hence, a principle of identity of antigen together with attenuation (live vaccine and others) can be distinguished from vaccination (Jenner) that found some so called cross-reactivity.  Difference of target antigen equals difference of antibody and t-cell specifity.
So, instead of using attenuation as a working principle, should we look for good cross-reactivity like Jenner did when developing vaccines?
The results of the following study   seems to be  in line with presumed  principle of non-identity and   unspecific immunization ("Jenner's"):
Jacob Schön, Wei Ran et al., A modified live bat influenza A virus-based vaccine prototype provides full protection against HPAIV H5N1, May 15, 2020.
Considering that according to this finding there exists flu virus from bat that is not pathogenic in other animal species, yet valid vaccine in other species, the question may be rephrased as follows: If there is no harmful infection of a  different species/different kind of target cells found in a different species, how can such non-pathogenic virus antigen lead to immunization against disease? The finding above contradicts any principle of specifity of immunization; how to explain?
Some other reference says:
"... In contrast, viruses of the recently identified bat-borne IAV subtypes H17N10 and H18N11 encode HA and NA homologs unable to interact with sialic acid residues despite a high degree of structural homology with their conventional counterparts...",  see Ciminski/Martin Schwemmle, 2019, Bat-Borne Influenza A Viruses: An Awakening, 2019
If the mechanism of vaccination were identity of antigen and  attenuation any immunization induced by "homologs unable to interact" (with target cells) should not be of any help against infection by "conventional counterparts" (as there is no identity of antigen, thus antibodies/t cell receptor).

You're talking about completely different things, and it's not at all clear (especially after reading your self-answer) that you have any idea what you're talking about. Vaccinia and variola are two entirely separate species, while both the mink and human SARS-CoV-2 viruses are just different subtypes of the same virus. Just because Vaccinia (usually) causes a sub-lethal and eventually protective infection in humans doesn't mean anything of the sort is going on with the mink and human SARS-CoV-2 variants. Jenner was extremely lucky.

"self-answer" is pejorative for "jeopardy question and answer style share your wisdom - did I choose the wrong form, it's encouraged to answer your own question.

To MatDMO: what you're explaining contentwise suits me well That's my very question, if vaccinia virus and variola virus are or are not different in respect of immunity, and to what extent exactly. as they quite strikingly  induce  "cross-reactive" immunity!  If you only told me what exactly the difference is between variola and vaccinia is  that could be the start of a great affinity (of ours, smile).However, "Jenner was just lucky" does in fact answer my question, in the negative and according to common wisdom and perspective.

Hint: to reply to someone's comment, simply use the @username convention. I would be @MattDMo, for instance. As you type, an autocomplete box will pop up, so you don't have to type out the whole thing. The reason I'm not pinging you in this comment is because you are the original poster (OP), and so are notified of all comments in this area. In comments under answers. you would be pinged if someone @ mentions you.

@MattDMo, thank you, so this is addressing you correctly? I do not understand why my self-answer has been deleted by Chris. without comment, not by you.  I will constantly enhance my question. Currently, it's focus on "attenuation". You say Jenner was lucky, I agree (by the way, allegedly  Jenner's vaccine had been used by the Chinese much ealier) - my question refers to the possibility that modern"er" (kind of German, it's my mother tongue) vaccination relies on attenuation and just does not make use of cross-reactivity. So, no security without attenuation, Jenner did not have to  - take care

I consider this question of mine as very relevant in respect of coronavirus,.Differentiating immune cells from body cells!. It seems possible, as common cold virus is corona virus just as "corona" is, that both infectiousnous and immunity/ are just the same, i.e. common cold just like corona, vice versa vaccination against corona just like against common cold, that seems possible, thus,  and, counterintuitively, it's "only" the severeness of harm that corona does to target cells that sets it apart from the Common cold.

Changing a question completely by editing after it was answered it seen as bad practice, as this also does not respect the work of the answer. Please stop this. I will rollback the edits and lock the post.

If user is not allowed to extensively edit question after it was answered all he may do is delete the question and start anew? If he dares to? What about the consent of those have spent commenting and even answering? As I have done extensive research I feel much brighter on the subject now (I would like shift focus to "bat virus" which is a different species. Answers are correct: ferret virus is same, however bat virae are different species. "Just" let me know if this is too hot a topic for casual writing...no problem to postpone or refrain, to me).

@Chris I very much revised my question as I felt unable to delete it because - according to the rules -  it had already be answered. What are the option? I may ask the person who answered to withdraw his/her answer, then delete question? I am very keen on putting up any completely changed question, as my question  did not raise any further interest. By the way, difficult to find out if any vote count with this question would vanish too and  go away.

We cannot say if the virus in ferrets gets less or more dangerous than the one which actually circulates in humans. There are two problems with this infection:

The ferrets can build a reservoir for the virus making it possible for circulation to occur among these animals and re-introduce it into the human population. It may also be possible that the virus jumps into other animals, also enabling transmission.
It is possible that the virus mutates in the animals (it does this anyways) and changes, so acquired immunity against the original SARS-CoV-2 it will not be present or at least less effective, enabling further infections. This can also render a vaccine directed against a mutated part ineffective.

So far, these things are concerns only, but to avoid them, swift action with the killing of all Danish ferrets has been taken.
About your example with Jenner: He was simply lucky that the cow pox he used for this experiment where close enough to the small pox to generate immunity. For the SARS virus we still talk about the same virus, not a different one.

I read your answer after having edited my question, and I think it is still valid and good. Again, deleting the question would be all right by me if that's the option you opt for.


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Are neurons capable of buffering a signal to sync up with other data?
The brain is the most complex thing that mankind discovered thus far in the universe. Super computers aren't able yet to outperform the human brain (running only on ~25 watt or so) on the domain of general intelligence.
With a computer it is fairly straightforward to capture an image stream and split it into 2 streams. So in a videoclip depth data could be contained by alternating the images from 2 streams from two different angles.
What if an organism would loose sight in 1 eye. And the other eye would be fed with data that contains actually 2 image streams, with these alternating angled images, at an always exact framerate. Would the organism (the brain basically) be able to comprehend the data and experience depth? For that it would kind of need to buffer every other image and put them through simultaneously, mimicking the feed from two eyes basically.
Would this be possible? Is there any research done on a topic similar to the example above? Where data is buffered by a neural network to be send in combination with other data?

For this answer, I'll use a very broad definition of "buffer" as a mechanism to integrate information at different delays. I have no interest in getting into specific computer science definitions of what a buffer is and I don't think it makes any sense to use them in biology.

Parallel processing and predictive coding
The brain is a massively parallel system, so of course there are different "streams" of information flowing at all times. Certainly the brain as a whole does some level of buffering, though the mechanisms available to individual neurons are unlikely to do what you suggest. The "buffering" in individual neurons has a lot more to do with learning and memory, for example in spike-timing-dependent plasticity which incorporates a physical record of past inputs in a learning rule.
One model of cognitive function is predictive coding, in which the brain holds a model of the world at different hierarchical scales and updates this model with new information. This model is effectively a buffer against which new incoming information is compared to draw attention to discrepancies that require further attention (such as the sudden appearance of a predator).
Audiovisual integration
One simple example of buffering is in audiovisual integration: the brain's processing of visual information is much slower than auditory information, and yet the perception of, say, a human speaker's voice vs. lips or the sound and sight of a bouncing ball are perceived in synchrony (see for example Recanzone 2009; note this has absolutely nothing to do with speed of sound vs speed of light).
It's important to understand that the visual system doesn't process visual information anything like a computer. There are no frames in biological vision. That said, humans can deal with a lot of unnatural sensory input, and they also use a lot of other visual cues besides stereo vision, the so-called "monocular cues".
Motion parallax and wiggle stereoscopy
One of these monocular cues is motion parallax (binocular vision can also utilize parallax without motion). Wiggle stereoscopy simulates motion parallax, as if your head were oscillating back and forth, to create an illusion of 3D, and seems much like what you are proposing. It doesn't matter whether you view the image with one eye or two.

Recanzone, G. H. (2009). Interactions of auditory and visual stimuli in space and time. Hearing research, 258(1-2), 89-99.

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Understanding David Chalmers claims on direct mappings between our vision and visual awareness systems
I am reading the popular 1995 paper "Facing Up to the Problem of Consciousness" by David Chalmers [PDF] as part of my philosophy course. I am only asking about the relevant vision related claims Chalmers makes, so you need not read the full paper.
In the section 7.1 (emphasis my own):

The properties of this [complex three-dimensional] space can be recovered from information-processing considerations:
examination of the visual systems shows that waveforms of light are discriminated and
analyzed along three different axes, and it is this three-dimensional information that is
relevant to later processing. The three-dimensional structure of phenomenal color space
therefore corresponds directly to the three dimensional structure of visual awareness.
This is precisely what we would expect. After all, every color distinction corresponds to
some reportable information, and therefore to a distinction that is represented in the structure
of processing.
In a more straightforward way, the geometric structure of the visual field is directly
reflected in a structure that can be recovered from visual processing.

"Awareness" is defined (earlier in the same section) as:

...the contents of awareness are to be understood as those information contents that are accessible to central
systems, and brought to bear in a widespread way in the control of behavior. ... Awareness is a purely functional notion,..

So, I believe visual awareness refers to "how visual signals are processed in the brain".
Chalmers gives vision only for example, as he states that "It is also a central fact that to each of these structural features, there is a corresponding feature in the information-processing structure of awareness." - that is - he generalizes these to all perceptions. However, we can restrict our question to vision for now.
Note the phrases I have emphasized in bold. From what I understand, Chalmers is claiming:

direct correspondence, in that 3D structures in real world ("three-dimensional structure of phenomenal color space") form 3D structures in our brain ("three dimensional structure of visual awareness").
the "geometric structure of the visual field" is directly reflected inside our brain in some structure, so that the original geometry can be recovered from this structure.

I wish to ask for biological justification/backing of these claims.
From what I understand, our two eyes receive 2D data, and our brain combines these (slightly offset) 2D images to produce 3D (depth) sensing. Our perceptional ability is severely limited, and it is only because of a lot of "postprocessing" done by the brain that we form our perceptions. This is also the reason why we often perceive motion in changing static images (animation) or are confused by optical illusions (for example, perceing 3d from 2d images on paper, and many more).
My points are similar to the ones raised by Torbjörn Skytt in their paper "The "hard problem" of consciousness is a dead end" (link).
I am not arguing against the claims. But, I am unable to reconcile these claims ("direct reflection" and "direct correspondence") with the day-to-day observations outlined above. Moreover, Chalmers claims that these are "central fact"s, however, I do not find them to be so obvious. If I can get some clear perspective/stand on these claims, it would be helpful.

I'm pretty sure from the context of your quote that Chalmers is talking about color vision here, not depth perception, and it is the information that is three-dimensional, not the physical representation in the brain. In any event, I think you could start with an undergraduate neuroscience textbook, I usually suggest either Purves or Kandel, if you want to know more.

As Bryan alludes to, the 3 dimensions Chalmers is talking about are not height, width, and depth, but hue, saturation, and intensity.

Hey @BryanKrause and mgkrebbs, thanks for the response. Indeed, I completely misunderstood what was being said. I'd be happy to accept your answers if you post them. Thanks.

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Why is this oxoglutarate dehydrogenase and not oxoglutarate decarboxylase?
I was looking at the oxoglutarate dehydrogenase complex and saw the reaction mechanism for its E1-TPP mechanism, which results in the formation of a stabilized carbanion intermediate.
The mechanism begins with a protonation, but since the "goal" of the enzyme is to form the carbanion intermediate, it seems to me that the decarboxylation is the key part of the reaction. So why is this a dehydrogenase-catalyzed reaction and not a decarboxylase-catalyzed one?

I'm new to citric acid cycle and I'm judging this question based on my previous knowledge of biochemistry and organic chemistry.
I've looked into several protein databases and shockingly it seems oxoglutarate dehydrogenase is the correct name for it.( See :Uniprot , PDB 1 , PDB 2 )
Although the nomenclature of biological enzymes sometimes does not sound right to me , I believe this naming is appropriate for this molecule. First take a look at these definitions:
(Definitions from Oxford Languages / Google)

Dehydrogenase :  an enzyme
that catalyses the removal of hydrogen atoms from a particular
molecule, particularly in the electron transport chain reactions of
cell respiration in conjunction with the coenzymes NAD and FAD.

(Wikipedia)

Dehydrogenase (also called DH or DHase in the literature) is an enzyme
belonging to the group of oxidoreductases that oxidizes a substrate by
reducing an electron acceptor, usually NAD+/NADP+ or a flavin coenzyme
such as FAD or FMN.

(Wikipedia)

Decarboxylation is a chemical reaction that removes a carboxyl group
and releases carbon dioxide (CO2). Usually, decarboxylation refers to
a reaction of carboxylic acids, removing a carbon atom from a carbon
chain

Here is why the usage of "decarboxylase" in the name of the enzyme is incorrect :
Recall amylase (Amylase-Wiki) . That enzyme consumes amylose as substrate and produces maltose out of it. It sounds weird if one calls it "Demaltase" just because it gives out maltose. Instead, in this case , consumption of amylose plays a more important role in digestion.
According to above definitions , the "goal" here is simply the movement of H+ and the electron to FAD (to generate FADH2) and then to NAD+ (To generate NADH), Not the removal of CO2. That is just a by-product resulting from the mechanism. see :Reaction
Here's why the usage of "dehydrogenase" in the name of the enzyme  is correct :
Take a look at this  .
The whole process involves the movement of one proton from thiamindiphosphate and one from CoA-SH and also 2 electrons from two S-H bonds (I've traced the Hydrogens for you. Trace the electrons yourself ! :) )
Recall the concepts of carbonyl functional group from organic chemistry. One way to perform any reactions on carbonyls is to use an acidic catalysis which is most of the times H+ resulted from H2SO4 or HCl.Take a look at this. Also see Morrison-boyd organic chemistry or Vollhardt's This H+ Activates the carbonyl functional group , allowing it to participate in nucleophilic substitution more easily. The addition of H+ to Carbonyl oxygen is reversible and thus it is important to optimize this equilibrium. The indicated enzyme operates on this equilibruim to gain the maximum yeild. Plus it may induce TPP to lose a H+ . These two processes (the removal of H+ from TPP and the addition of H+ to oxogultarate ) can not be done with the help of the enzyme , hence the name Dehydrogenase for the enzyme.

Your first mention of dehydrogenase is  missing the de.

@Polypipe Wrangler , Thank you for that . Actually the title of question is missing the de too!


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How does gas equilibration occur in the alveolus, numerically?
I am attempting to model gas exchange across the alveolar membrane.  My main question is there a direct exchange of O2 molecules for CO2 molecules?  If so, then my model predicts (assuming alveolar PO2 107mmHg and CO2 40mmHg; and venous PO2 40, PCO2 46) an arterial PO2 107mmHg, but PCO2 of only 37mmHg (taking into account pH change and equilibration with bicarb and haemoglobin carbamates).  If I remove the plasma bicarb equilibration process (as this takes ~15 seconds, but alveolar transit time is ~0.75 seconds), then the arterial PCO2 is even lower, ~33mmHg.  The expected results should be somewhere in the range of an arterial PO2 of 107 and PCO2 of 40.
The only alternative I can think of is that there isn't a molecule for molecule exchange, with the O2 absorption and CO2 removal being separate processes.  If this is the case then overall there will either be a reduction in alveolar air pressure and/or volume during gas exchange.  However, I can find no references to inhaled tidal volume being different to exhaled tidal volume.  Nor does there seem to be any evidence for N2 or H2O molecules to participate in this process (at standard atmospheric pressure).
Any ideas??
Ultimately I want to then extrapolate model to deal with pathology (eg high alveolar CO2, high venous CO2 etc).
EDIT to include references...
Mechanistic physicochemical model of CO2 transport in the blood
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5341128/
Modeling of the oxygen transfer in the respiratory process
https://hal.archives-ouvertes.fr/hal-00714239/document
Modeling pulmonary gas exchange and single-exhalation profiles of CO
https://www.frontiersin.org/articles/10.3389/fphys.2018.00927/full
Respiratory Physiology
https://derangedphysiology.com/main/cicm-primary-exam/required-reading/respiratory-system
Other materials I have read include:

Pilbeams Mechanical Ventilation
Nunn's Applied Respiratory Physiology
Guyton and Hall Medical Physiology

Can you explain your model in a bit more detail? How does it predict a PCO2 of 37 mm Hg? Why should it cause a reduction in alveolar pressure/volume?

Hi Adhish, thanks for replying.

In my model I know both the venous PCO2, the pH and from there can also calculate the total CO2 content (ie plasma HCO2, CO2 and erythrocyte content (CO3, HCO3 and HbCO2)).  At the alveolus I first calculate the new oxygen content (based on the alveolar/venous oxygen gradient, diffusion coefficient, haemoglobin content etc).  Knowing the alveolar volume I can calculate how many mols of O2 has been extracted.

If I then assume the exact same number of CO2 molecules have entered the alveolus in exchange, then I can calculate the both the new alveolar CO2 and (after redistribution through the CO2 compartments) in the now arterial PCO2.  Doing this gives me an arterial PCO2 of 37mmHg (and an alveolar PCO2 increase from 40mmHg to 41mmHg).

My assumption of 1:1 molecule exchange was based on presumed preservation of pressure/volume within the alveolus (as temperature is constant), as per Henry's Law, PV=nRT.

I understand your question now. I will try to write an answer when I have time.

Hmmm... So I'm thinking may be truly independent of each other, and that the alveolar volume must decrease with each breath, inferring from this summary that discusses the rate of atelectalsis formation at different FiO2's
https://www.openanesthesia.org/atelectasis_during_anesthesia_etiol/

There is no known mechanism for exchange of $\ce{O2}$ and $\ce{CO2}$ in a one-for-one fashion. Their transport across the alveolar membrane takes place by diffusion alone: both of them attain their equilibria with blood independently.
Note that it is not necessary for inhaled and exhaled tidal volumes to be the same. In fact, under physiologic conditions, the exhaled tidal volume is slightly less than inhaled tidal volume. This is because humans normally produce slightly less $\ce{CO2}$ than they consume $\ce{O2}$. In other words, the respiratory quotient is less than $1$.
Thus, we see that the assumption of preservation of alveolar volume and pressure is not valid. Apart from inspiration and expiration, the diffusion of gases to and from blood also affects alveolar volume.

Reference and further reading:
Boron WF, Boulpaep EL, editors. Medical physiology. 3rd ed (international edition). Philadelphia: Elsevier; c2017. 1297 p. (I found this textbook an excellent resource for learning physiology in general and respiratory physiology in particular.)

Brilliant thanks! I'll look at adding that text to my collection, cheers :)

Adhish, don't know if you check these after you've answered, but just wanted to let you know my copy of Medical Physiolgy arrived today, and it's everything you promised it would be.  Thanks again.

@ArkoFlake15 Glad to be of help. :)

No direct exchange, but there is interaction.
I used these wikipedia articles:
https://en.wikipedia.org/wiki/Hemoglobin
https://en.wikipedia.org/wiki/Bohr_effect
For Oxygen transport nearly all is transported bound to hemoglobin. Only one part in 71 is transported as soluble unbound oxygen.
For carbon dioxide, only about 20-25% is transported by hemoglobin. But it sticks to the amine groups and so doesn't directly compete with oxygen which binds elsewhere.
The Bohr effect causes the oxygen to bind more strongly where there is little CO2 and vice-versa. The wikipedia article has a mathematics treatment of this.
The rest of the CO2 is transported as hydrogen carbonate through the action of a carbonic anhydrase. CO2 is not very soluble at body temperature.
The volume of CO2 in the breath is still small.

I'm sorry, this is not at all detailed enough for my purposes.


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The relation of a schizophrenia drug side effect and caffeine intake
I am listening to the book Surviving Schizophrenia and in the book, it is mentioned that drugs like Clozapine increases in blood level if the patient takes Caffeine, and can have side effects due to elevated levels. In case the patient takes Caffeine, can't just less amount of Clozapine work since it'll be significant enough to help the patient and cause less side effects too? I am not from a medical background, sorry if these things are pretty obvious in medical community

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] or delete your question accordingly. In particular note that personal medical questions are not appropriate for this site. No matter how good your (and our) intentions are, relying on health information from people who aren't medical professionals is unwise and could be extremely dangerous. Thanks!

In general, since everyone metabolizes caffeine and clozapine differently, it would be extremely hard to make sure that the patient got the right dose.  It's easier to say "stop using caffeine while on this".  Grapefruit juice does much the same thing; makes it harder to break down drugs, doctors do not say "drink grapefruit juice and we'll halve your dose".  They say "avoid grapefruit juice".

The place to ask about medical topics is SE Medical Sciences. Here the focus is on defined biological mechanisms, rather than complex diseases and the varying effects of drugs.

I used Google Scholar with the search terms of clozapine, caffeine.
I only found small scale studies, but they agree that it is likely that Clozapine levels are affected by caffeine intake.
To really understand the implications of this it would be necessary to research what the range of Clozapine levels actually are in patients and what the effective level is, as well as the levels that give side-effects.
Only then can the changes due to caffeine be seen to be significant or not
Example paper studying 12 volunteers below (full text available)
Hägg, S., Spigset, O., Mjörndal, T. and Dahlqvist, R. (2000), Effect of caffeine on clozapine pharmacokinetics in healthy volunteers. British Journal of Clinical Pharmacology, 49: 59-63.
https://doi.org/10.1046/j.1365-2125.2000.00111.x
Available at:
https://bpspubs.onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2125.2000.00111.x

Your DOI link is incomplete.


text:
Are bleach solutions still routinely used in biochemistry laboratories to rid surfaces of bacteria, viruses, certain enzymes, and nucleic acids?
Decades ago I would stop by biology and biochemistry laboratories to see what was up, and I noticed a ubiquitous presence of a squirt bottle of bleach solution. When I asked what it was for I would get different answers in different laboratories. They ranged from disinfection of surfaces by accidental bacteria or phage contamination to denaturing of certain specific proteins or nucleic acids thought to be threatening to certain types of experiments.
Experimental techniques have developed dramatically over the subsequent decades.
Question: Are bleach solutions still routinely used in biology and biochemistry laboratories to rid experimental surfaces of bacteria, viruses, certain enzymes, and nucleic acids? If so, how can one solution be so reliably useful across all of these cases?

Does nobody use the ubiquitous Virkon?

@DDuck Virkon has a wide spectrum of activity against viruses, some fungi, and bacteria... However, it is less effective against spores and fungi than some alternative disinfectants See Assessment of in-vitro efficacy of 1% Virkon® against bacteria, fungi, viruses and spores by means of AFNOR guidelines

Don't forget hydrochloric acid, still used a lot for cleaning purposes in food production industry (like milk & cheese).

@PeterMortensen — I agree with your suggested edits, but I wonder why you are trying to include links in your editing comments? Links don't work in that context and just make the summary of your edit hard to read!

I'm a research post-doc working in a US-based microbiology research lab. We still use a relatively low-concentration bleach solution to decontaminate most liquid cultures before disposing of them, but most of our surface and equipment decontamination is accomplished with alcohol (either ethanol or isopropyl alcohol (IPA)). We do work with some organisms that are not effectively killed by alcohol, such as C. difficile. C. difficile makes endospores which are very resistant to alcohol-based agents, but they are readily killed by bleach.
So after working with C. diff and other spore-forming bacteria we decontaminate with commercial wipes containing a stabilized sodium hypochlorite solution at a little less than 1%, which isn't even enough to give off a strong bleach odor. On metallic surfaces and some kinds of rubber, we follow up with an alcohol wipe to prevent corrosion from the bleach.
We do have other sporicidal agents that are used for specific applications where bleach isn't suitable, but most of them are much more harsh (requiring use of respirators), require a longer contact time, and have a substantially shorter shelf life at the effective concentration (sometimes just days or hours, vs. months with bleach).
Bleach is also good for destroying DNA and RNA in clean areas used for PCR setup, but there are some commercial products specifically designed to do this along inactivating nucleases that might degrade a sample, so I personally use those products. (Note that ethanol and IPA solutions can actually precipitate nucleic acids, leaving them behind after the solution evaporates.)

I can only speak from my experience in many labs in different countries: We never used bleach for cleaning or disinfecting surfaces like cell culture hoods or lab benches. For this purpose we routinely used 70% Ethanol or commercial alcohol based disinfectants. Bleach was only used to inactivate culture media (cell culture and also bacterial cultures) so we could later discard it in the sink without the need to autoclave it (we usually had enough trash that needed this kind of treatment, so we didn't want to increase the amount further).
I think alcoholic solutions are used because they are more friendly to the skin if spilled, residues evaporate relatively fast and also because bleach is pretty aggressive to the surface, which can alter them possibly. There is also no need to remove residual bleach afterwards. However, for treating liquid waste, it was favorable.
Bleach can be used ultmatively because of its mechanism of action. It disrupts the cells and oxidizes its contents, so contaminants have no chance of reproducing anymore.

Thanks! From what I gathered in answers to How exactly does alcohol solution kill or neutralize viruses? (my own humble there in particular) alcohols are particularly good against viruses whose envelope includes lipids from the host's membrane, but may not be so effective against viruses that don't. But maybe those are not stable in the environment in general anyway?

@uhoh They are at least not a general problem you encounter in the lab. If you suspect something like that, you would use a more suitable disinfection agent.

I work in a C. diff lab where we have to decon benches and hoods with bleach wipes, as alcohol does not kill C. diff spores. We usually follow any bleach application with an alcohol wipe-down to prevent corrosion of stainless steel surfaces, like in a biosafety cabinet.

@MikeyC As I wrote, this is my experience. Since I never worked with spores, this might be the reason. Maybe make this into another answer?

@uhoh the point isn't that the lipids come from the host, it's only that they are lipids. Their origin is irrelevant, all lipid membranes are susceptible to detergents or alcohol or other disinfectants.

@terdon there's no such thing as an objective "the point". I could correct your statement and say "the point is that the envelope has soluble components, that they are lipids is irrelevant." We all write our own sentences and choose what to share in them. I like SE because it's a place to share what we know. I don't know much about viruses but I find them fascinating, and won't apologize for my enthusiasm.

@uhoh apologize? What in the world for? You didn't do anything wrong! I just thought that you had understood that the reason alcohol is effective against membrane-bound viruses is because they incorporate the host's lipids and I didn't want you to come away with that misunderstanding since alcohol would be effective against any lipid membrane whether it came from the host or not.

@terdon okay got it, thanks!

Bleach also destroys DNA/RNA, and kills bacteria, making it useful in an area where PCRs are done. 70% ethanol is very friendly to DNA, but it kills bacteria well enough. My guess for the preference of 70% ethanol is that it is not as corrosive as bleach. Best would be bleach, and then a wipe of ethanol.
References
Use of bleach to eliminate contaminating DNA from the surface of bones and teeth
Improved ethanol precipitation of DNA

Best would be bleach, and then a wipe of ethanol. If you do this (the genetics lab I work in does), do a water rinse in between. Otherwise, ethanol and bleach can react to produce chloroform, which you don't want to breathe. Whether or not it would produce a dangerous amount, I don't know, but there's definitely no harm in reducing the risk

I was associated with a lab in 2015 that used a lot of Streptococcus pneumoniae. They had ethanol squirt bottles to clean certain surfaces and in case of a spill. This was intended to kill that bacteria. In other labs previously I had seen bottles of hypochlorite (bleach) - but it was comical to see fungal growth in some of them due to the hypochlorite having decayed over time.
With regard to enzymes, (RNase particularly) the laminar flow cabinet stainless steel was wiped down with ethanol - not to denature any enzyme, but just to remove it and prevent remaining enzyme from becoming airborne.
Sorry for lack of refs yet

Yeah, people don't realize that hypochlorite is light-sensitive. I've fought a losing battle in a couple labs to store bleach solutions at least wrapped in foil or paper tape, if not in an entirely opaque container. I've found 1:10 bleach solutions dated several years previous that didn't even smell like bleach...


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Looking for study/genome data for HIV in different organs
I am looking for a research study or data base that has HIV genome data available in fasta or similar format. Specifically I need genome data of HIV taken from different organs in the same subject. I am interested in studying the way HIV diversifies and changes to infect different organs and in comparing the process across different patients.
If you are familiar with such a study, or if you have general pointers as to where I may find similar data, I would appreciate it very much. I have done a few hours of searching on NCBI GeneBank, but have had no luck.
Thanks!

Could be better of migrating to Bioinformatics.SE.

This website comes to my mind
https://www.hiv.lanl.gov/content/index
It is a HIV databases containing HIV sequence data and related immunologic information


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Why does ionizing radiation cause only DNA double strand breaks?
It's known that ionizing radiation such as X-ray and $\gamma$-ray, cause DNA damage, specifically double strand break. Why is it so? I mean, why not single strand break, why not pyrimidine dimer?

Ionizing radiation does cause single-strand breaks and other kinds of DNA lesions that are not double-strand breaks.  However, double-strand breaks are the most difficult to repair and are thus the most likely DNA damage type to result in mutation and / or cell death.  See Fig 1. from DNA damage response signaling pathways and targets for radiotherapy sensitization in cancer:

DNA damage induced by ionizing radiation. The major types of DNA damage induced by IR include base and sugar damage, single-strand breaks, double-strand breaks, clustered DNA damage, and covalent intrastrand or interstrand crosslinking


text:
Why does touch the face make more likely to be infected?
Why is it risky to touch the face although there is no direct contact with into the nose, eyes and mouth?
Is there any possibility that pathogens infect us from our facial skin?
Suppose we have viruses or bacteria on our hands and we touch the side of our nose with our hands.
Can these bacteria reach our noses by their own?

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, each question should be posted separately — this improves the chances that you will get answers for each question and makes the answers more accessible for future users. ——— We also expect 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). Thanks!

Do you have evidence or a citation to prove your claim that it is risky to touch the face without direct contact with nose, eyes, or mouth?


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metaphors for explaining the role of DNA in the cell
Various metaphors are used to explain the central role of DNA in a cell to laypersons. These include blueprint, recipe, catalogue, instruction manual etc. I even heard someone describing DNA as a 'boss' that yells orders.
Here are some interesting ones:

An ancestral archive
An archeological site
A prison (retroviruses and transposons)
A computer
A deck of cards
A clock

What are some useful metaphors that help to explain DNA function?

You just answered your question 11 times, if I count correctly. What is it you wish to know? Other metaphors? If yes, I think such a discussion-type question should be posted in chat, not on the main site.

It is clearly off-topic, but this doesn't appear to be homework @John. & homework questions aren't off-topic. Only if they do not conform to the other rules.

I answered. What about you? Good metaphors are essential to conveying complex or domain information and a pillar of education. Have a try!

It is a program executed by transcriptase (processor) inside a cell core (computer).

Since this is an off-topic question (it is opinion rather than fact based), it is better left unanswered. For future posts please note that 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. ——— Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

Thats my intuition also -  that 'computation' is occurring in the transcriptome rather than the genome


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What is the thinnest spot on the ilium called?
Is there a specific name for the spot on the human iliac fossa where the bone is the thinnest? (Or, is there a name for the thickness measurement of that spot, e.g. the left/right _________ is 2.1mm?)
Green arrow:

(image source: my own pelvis)
This point, for example (color maps thickness):

(image source: me)

The region is called iliac fossa. And it's basically the deepest part of the fossa. May be!!! I have never heard of a particular name of that thinnest part in my osteology books.

@A.N.Ψ it would just be called the thinnest or deepest part of the fossa, there is no special name for parts of a fossa you just use basic descriptive terms.


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Winogradsky column and hydrogen sulfide
For a science experiment for school, I have set up 15 Winogradsky columns, and will be looking at the microbial growth inside the columns over a period of 25 days.
I have read that, due to gas produced by the microbes, it is good to leave the cap loosely closed to prevent an explosion from gas buildup. However, I have also read that sulfate-reducing bacteria that grow in the column can produce toxic hydrogen sulfide gas. Wouldn’t the hydrogen sulfide also escape in small amounts and pose a health risk? What would be the correct protocol to follow here?

Hydrogen sulfide can be toxic at high concentrations, however, the amount that your columns will make is likely very low, and will almost certainly degrade/oxidize into something safer before it hurts anyone (who isn't a small organism in the column!). It will noticeably smell bad at levels well below what is dangerous. So maybe just make sure that the columns are in a ventilated space.
Remember, what is happening in the column is basically just rotting organic matter, like leaving a bunch of food waste in a highly compacted, sealed environment. It is sort of intrinsically gross, but it isn't any more dangerous to your health than forgetting to take out the garbage for a month (actually, it's probably a lot less dangerous than that!).
For example, this guide says the following (after constructing columns with different inputs such as e.g. eggs):

You may have seen worms, snails, shrimp or other small organisms in the water, but probably not many (if any) in the bottle with the egg yolk, because hydrogen sulfide is toxic to most organisms!

So, depending on what you put in there, a very H2S-productive medium is likely to create enough H2S to kill tiny animals that are trapped inside the column. But apparently not enough to hurt large animals like you, as long as you don't huff the column.

You will smell H2S at well less than 1 ppm . Long term exposure problem threshold is about 10 ppm . I smell it when i stir up the bottom of my pond or aquariums. I have never heard of a toxicity problem with the levels of H2S produced in a natural environment .


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Are there any organisms that are made of more than one (~5-12) cell?
Prokaryotes and eukaryotes are unicellular, made of one cell. Great. Eukaryotes are unicellular or multicellular. But the typical examples of multicellular eukaryotes we have are made of, often, trillions of cells, like us humans. Ants must still be made of many millions of cells. Are there known eukaryotes with very few cells that make them up? Like, 5, or something? Or maybe a dozen cells making up the whole organism in its fully developed state?

Well, there are multicellular prokaryotes too but they are not obligately multicellular. You may find the case of Caulobacter cresentus interesting. You can describe it as a bicellular bacteria however it exists as a single cell in one of the stages of its life cycle.

Does this answer your question? Are there oligocellular organisms in nature and, if so, what are they like?

It seems like there's overlap, but they are not the same. That question is about what oligocellular organisms are "like", whereas this thread seems to simply involve listing them out, as many as we can, and focusing on just how small, really, they can get. I think it's valuable to have both of these up.

There's Trichoplax adhaerens, a Placozoa, made of a few thousand cells. Then there is Dicyema japonicum, a simple mesozoan, made up of 9 to 41 cells. Arguably, the simplest multicellular organism is the algae Tetrabaena socialis, whose body consists of 4 cells. Then, there's the parasitic Myxozoa which have 7 cells.

An interesting follow up question would be: at this scale, how do we draw the line between unicellular and multicellular? E.g. can you kill a Myxozoa by splitting up the cells? What would that tell us?

This nematode always has either 959 or 1031 cells.
https://en.wikipedia.org/wiki/Caenorhabditis_elegans

An interesting note is that the nematode is the smallest multicellular organism with a nervous system.

Species from Gonium genus are typically 4-16 celled. Gonium pectorale is 16 celled.
Arakaki, Yoko et al. “The simplest integrated multicellular organism unveiled.”, vol. 8,12,  e81641. 11 Dec. 2013, doi:10.1371/journal.pone.0081641
Also, there is four celled Basichlamys sacculifera. See this picture for reference

There is a whole class of organisms called "oligocellular" organisms, see also here on SE.


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Does the apical bud grow back after being removed?
My question pertains to the apical bud which asserts apical dominance in plants. After it is removed, apical dominance is lifted, what happens to that part of the shoot after that? Does it stop growing? Can the (previous) apical bud be restored or do other axillary buds take over as the dominant apical tip?


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What is a 21q21 deletion?
I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement:

We report three patients affected with neurodevelopmental disorders
and harbouring 21q21 deletions involving NCAM2 gene.

I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21.
However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.

Two likely scenarios.
Interstitial deletion. More likely.
Where just a small internal part of the chromosome is missing. This is like pressing "delete" for a while in the middle of a text document.
Deletions from the end of the chromosome to some point.
Chromosome 21 is the smallest, and people survive having the whole p side of the chromosome  missing, even all the way down into band 21 on the q side.
There are more recent articles than the one you saw, look on google scholar for ncam2 deletion and sort by date.
Wikipedia article.
https://en.wikipedia.org/wiki/Chromosome_21
This document below mentions specific cases of (severe) 21q21 deletions (page 15).
https://www.rarechromo.org/media/information/Chromosome%2021/21q%20deletions%20FTNW.pdf

I would suggest looking more into karyotype nomenclature; it is admittedly a bit odd. Here is one related question/answer that puts it in context.
I haven't looked at the paper in detail but generally what it means is that there is some cytologically relevant big chunk of chromosome that is missing that roughly overlaps with the chunk of chromosome that we find at band 21 of chromosome 21 (not position 21). Note that these cytobands/karyotype/G bands visible in a chromosome spread under a microscope, so these are quite large deletions.
Looking at the paper methods, it is clear that in 2/3 cases they confirmed the deletions by looking at karyotype data (FISH/chromosome spreads):

For Case 2, CNV confirmation and parental studies were performed by metaphasic and interphasic FISH on leucocytes using BAC RP11-43A6 (chr21:18,414,905e18,567,253, hg19 build). For Case 3, CNV confirmation was performed by G-banded karyotype. Parental studies were not available.

The terminology is quite outdated now as usually we are looking at sequence data these days, which has much higher resolution, but a lot of the stereotypical chromosomal abnormalities still carry these confusing names. And seeing it on a chromosome under a microscope is still the gold standard for these large chromosomal events.


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Plant disease identification
I’ve noticed recently strange formations on the leaves of my flower.
No idea what could it be.
Could anyone help with the identification?

The white things look like scale insects, you can scrape them (and their waxy fluffy coats) off the leaves.
If you can identify the plant, that would also help.
The gardening SE is also a good place for these questions.

For the limited amount you have it will be much more effective to scrape them off than try to poison them.


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Indian Spider Identification
Today I saw this curious colorful spider on its web near a sapota tree in my garden.
I have never seen any spider like this,its around 2cm or a little less.
The most curious part is this part of its exoskeleton which looks like when a moth rests.Like a cape.

here's the underside and the yellow patterned legs.

But the spider was bothered by my presence and was trying to crawl away,and I took this angled shot:

I live in South India.
So what is this spider ?
Is there any advantage of the wing like part?
Links to websites with details of the spider are also appreciated.

That’s maybe an oriental spiny orbweaver (Gasteracantha geminata), according to its appearance and location. You can find many more observations of such spiders on iNaturalist: https://www.inaturalist.org/taxa/207992-Gasteracantha-geminata?locale=en-GB
However, I don’t know what advantage there is to the “spines”. They are not the only species. There’s a whole genus of them with at least 70 known species, according to Wikipedia: https://en.m.wikipedia.org/wiki/Spiny_orb-weaver


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Location of genes encoding ribosomal proteins
I have cited two sources below: the first, a textbook, says ribosomal proteins are imported into the nucleolus (from the cytoplasm) where initial ribosome assembly occurs.
The second is a journal which asserts, in the first paragraph, that ribosomal protein mRNA is processed in the nucleoplasm, distinct from the nucleolus.
I am therefore very curious about the location of ribosomal protein genes whose transcript is the mRNA; specifically whether these are located in the nucleolar region or not.
Sources:

"Histology a text and an atlas" by Michael H. Ross and Wojciech Paulina. 6th Edition; pg. 79.

"Nuclear and Nucleolar Targeting of Human Ribosomal Protein S6" (Carola Schmidt, Edgar Lipsius, and Joachim Kruppa) ; Vol. 6,1875-1885, December 1995.

This is a previous answer to a question on this topic. It references a review of the topic with a poster that summarizes the situation. Of course all proteins in eukaryotes are translated in the cytoplasm, so any proteins that are required in the nucleus have to be reimported.

@David, I'm afraid that doesn't answer my question. I am interested in knowing whether the genes that encode the mRNA which then gets translated into ribosomal proteins are part of the nucleolar region or not.

Ok. Look at the distribution of ribosomal protein genes across different chromosomes. Massively diverse. Why would you expect the genes in the nucleolus if the mRNA has to go to the cytoplasm? It’s the rRNA transcripts that need to be in the nucleolus and the ribosomal proteins etc. to move there from the cytoplasm after synthesis.

Ok. This helps.


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What species is this golden fly?
Last summer I was visited by this unusual golden fly, whose kind I have never seen before. It was impossible to scare away so I could take relatively good pictures.
The pictures on this hobbyist page suggest, it is a  "Golden blowfly". Those pictures were taken in Australia. The only paper I could find on golden blowflies locates the species in Australia as well. However, I took my pictures in southern Germany.
What is this fly? Is it an invasive species or native to Germany as well as Australia?

is it tachina fera?


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What is this nighttime creature?
I almost stepped on this little critter. It blended into my garage floor. It is about about the size of my hand, with huge bulbous eyes that immediately caught my attention. There was a distinct white bump below\between the eyes.  It froze when I turned on the light and did not move at all until I turned the light off. Then it moved faster than my eyes could follow in the direction of my garden.
I am on an island in the San Francisco Bay, California. The current temperature is ranging from 50 (night) to 65 degrees and rainy season has just started (late this year). It blended so well with the garage floor that my camera had problems focusing on it.

Likely some type of gecko, they are active at night.

Welcome to Biology.SE! Any noise when startled (e.g. "barking")? Please also [edit] your post to include the location. Location can be an essential clue for identifications and should not be hidden in comments, which are ephemeral and often overlooked. ——— If possible clearer, closeup photos of the creature from multiple angles would also be helpful since this could be one of several salamanders native to your area. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Thanks!

Something like this perhaps? Found here while searching for "gecko" in California Lizards It may not be an exact match due to geography, but perhaps it's a start. It at least sometimes has a white spot between the eyes, though not as pronounced as this one.

I believe this is an Arboreal Salamander (Aneides lugubris).
http://www.californiaherps.com/identification/bayareaherps.html#Lizards
http://www.californiaherps.com/salamanders/images/alugubrisbr1108.jpg


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What's a cells membrane potential without any leak channels?
Consider the following ion concentrations on either side of a cell membrane (in = inside cell, out = outside cell):
$[\text{Na}^+]_{\text{in}} = 10mM$,
$[\text{Na}^+]_{\text{out}} = 142mM$,
$[\text{K}^+]_{\text{in}} = 148mM$,
$[\text{K}^+]_{\text{out}} = 5mM$,
$[\text{Cl}^-]_{\text{in}} = 4mM$,
$[\text{Cl}^-]_{\text{out}} = 103mM$.
Let us further say that there are no leak channels or voltage-gated channels
in the cell membrane, and also that ion pumps stop working once they achieve these concentration gradients (i.e. the state is at equilibrium with respect to the ion pump.
There is a greater net positive charge on the inside compared to the outside. This should give me a positive membrane potential when I think about the cell membrane as a capacitor.
I know, Nernst and Goldman equations say otherwise. (For my example it would be zero membrane potential due to zero permeability).
Can someone explain why there is or is not a positive membrane potential, with appropriate sources?
There are already multiple questions with a similar background but none of the answers are satisfactory.

can you say anything about why the other answers are not satisfactory, and link to those questions?

Goldman equation is not applicable in this case. If you have a non-permeable membrane, all the permeabilities of the ionic species ($P_x$) are zero, which leads to an indeterminate form of the argument of the logarithm in the Goldman equation. The logarithm does not equate to $0$. Consequently, Goldman equation cannot be used to find the membrane potential ($E_m$) in this case.
Nernst potential is the potential when the ionic species are in thermodynamic equilibrium (i.e. the diffusive force and the electrostatic force are balanced) and there would be no net flow of the ionic species across a membrane even when the membrane is permeable to the ion. This again is not the case for your impermeable membrane since there is an "unbalanced" force which will cause a net ionic flux given some permeability.
The usual equations of a capacitor, however, are perfectly usable given that you know the spatial arrangement of the charge inside and outside the membrane (i.e. if the ions are closely pressed to the membrane or distributed in the cell and outside).


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Is Pork more prone to carrying higher loads of parasites than Beef?
My friend told me that pork is dangerous due to containing worms.
I told her that beef contains worms too and that's why we cook it.
We went to steak restaurant and ordered "medium" beef.
And that makes me think a lot. Why I can order medium beef? It's still rare inside.
I have never heard people ordering medium pork.
Is pork more prone to worm investation than beef/cows?
What sort of worm we have anyway?

Depending where you are , Brucellosis  ( undulant fever ) is more likely a problem with beef ( and milk ).  Not deadly but debilitating ; my mother lived with it for 40 years,  If treated "soon" antibiotics will cure it , but if it becomes chronic ,there is no cure.

Cooking pork to rare or medium rare depends on where you live ; A friend , native of Scotland said he never saw pork roasted past medium rare until he came to the US. I usually cook pork roast to medium rare in the US.

@jamesqf Yes, there is an actual historical basis for some food restrictions, including not eating pork or shellfish - the lack of refrigeration or other safe methods of preservation.

Trichenellosis from pork occurs in about about 5 people per year since the 1980's in the US. it has a 0.2% mortality rate there. We can say that 1 American/ 1 European dies from pig meat every 20 years. That's a fair concession. Worldwide the death rate is in the 100ds per year from pork, compared to 3 million who die from the fat in beef and chicken and lamb and excess sugars, and 1.35 million attributed to cars.
The other pork parasites are less dangerous and have less than a 90 cases per year in the USA, mostly people coming from epidemic areas. https://www.oie.int/doc/ged/d9157.pdf
Beef can transmit tuberculosis, E-Coli, BSE/CJD and sarcosystosis. E-Coli from unsanitized beef kills many times more people than pork born diseases, i.e. 100 times more people in the US die from E coli from beef, it is one of the main vectors and a lot more difficult to control than via pork. E-Coli is uncommon from pork. Worldwide many thousands of people die of E-Coli from beef every year.
There were an estimated 147 000 new cases of zoonotic tuberculosis and some 12 500 people died of the disease in 2016. Beef are the main causal agent. All animals have tape worms and other worms.
Beef, Lamb, Pork, chicken, and milk all increase the risk of heart attacks and strokes because animal fat can increase cholesterol dramatically, and eating beef from one region can make you more susceptible to heart attacks than pork from another region, because the fat content can vary a lot. Far more people die of heart attacks than animal parasites these days, about 1 million times more rich people die from animal fat and sugar related disease than from pork parasites.

No pork parasites are counted on this list of parasite deaths, globally it's perhaps 50-350 per year.

About 99.999 percent of people that die from meat, die from the fat and other high sugar diets, and it doesn't matter if it's pork or beef. (source WHO)... 5 million people die every year from tobacco, and 2.5 million die every year from Alcohol, especially in very poor countries.
The income levels of people that die from parasites and alcohol are very low, something like 99.9% of parasite deaths are poor people and 90% of alcohol deaths.
So you can concede that alcohol kills many poor people, but that animal parasites from pigs kill 10,000 times less people than alcohol. Pork kills a million times less people in the west than cars or fatty foods.
Details:
There are three important parasites found in pigs which pose
a risk to humans who ingest raw or undercooked pork
products. These parasites are Trichinella spiralis, a nematode
or roundworm, Taenia solium, a tapeworm, and Toxoplasma
gondii,

You're basically saying that tapeworm is a problem for pork however they won't kill you anyway because you're rich. Okay. Is pork more susceptible to worms than beef

It's a very good answer. However, the main question, to response to that religious dogma, is if pork more likely to have worm than beef?

Oh, yes, you are right. I added paragraph 3 and 4. It appears that bovine tuberculosis and E Coli kill at least 20,000 people every year. and that pork doesn't harbour them... A trivia thing: The Chinese have banned imports of beef from Brazil that tested positive for covid 19, although that's probably more of cause of deforestation than a human risk.

is pork more likely to have worm than beef?

Case study I (Chungcheongnam-do, Korea)
From November 2009 to April 2010, a total of 241 fecal samples of pigs and beef cattle (136 and 105, respectively) were examined by direct smear and centrifugal sedimentation methods. The overall positive rates of intestinal parasites among pigs and beef cattle were 73.5% and 4.8%, respectively, and the double-infection rate was 10.3% in pigs. Of 136 specimens from pigs, Balantidium coli, Ascaris suum, and Entamoeba spp. infections were found in 88 (64.7%), 24 (17.6%), and 5 cases (3.7%), respectively. Of 105 beef cattle, Entamoeba spp. infections were detected in 5 cases (4.8%). From these results, it is shown that pigs raised on rural farms in Chungcheongnam-do had a high B. coli infection rate and a moderate A. suum infection rate than cows.
Case study II (Poland)
Sera of 3111 pigs and 2411 cattle from 16 regions of Poland were examined for the presence of anti-T. gondii IgG using the direct agglutination test (DAT). Pepsin-digested samples of diaphragm and heart of seropositive animals were examined for the presence of T. gondii DNA (B1 gene) by nested PCR and real-time PCR, while non-digested samples were only examined by nested PCR. The B1 gene DNA samples were genotyped at 11 genetic markers using multilocus nested PCR-RFLP (Mn-PCR-RFLP) and sequencing.
Seropositive DAT results were found in 11.9% of pigs and 13.0% of cattle. The highest seroprevalence was found in pigs from Podkarpackie (32.6%) and in cattle from Mazowieckie (44.6%). Data analysis showed that cattle > 5–10 years-old, as well as cattle and pigs from small farms, and pigs from farms with open production systems, had higher odds of testing seropositive (P < 0.05). Among the examined tissue samples, positive PCR results were found in samples from 12.2% and 10.2% of seropositive pigs and cattle, respectively. Among the samples successfully genotyped by Mn-PCR-RFLP and sequenced, four samples were identified as T. gondii type II and one sample as type I.
Case Study III (US)
The prevalence of viable Toxoplasma gondii was determined in 6,282 samples (2,094 each of beef, chicken, and pork) obtained from 698 retail meat stores from 28 major geographic areas of the United States. Each sample consisted of a minimum of 1 kg of meat purchased from the retail meat case. To detect viable T. gondii, meat samples were fed to T. gondii-free cats and feces of cats were examined for oocyst shedding. Initially, 100 g of meat from 6 individual samples of a given species were pooled (total, 600 g), fed to a cat over a period of 3 days, and feces were examined for oocysts for 14 days; the remaining meat samples were stored at 4 C for 14 days (until results of the initial cat fecal examination were known).
When a cat fed pooled samples had shed oocysts, 6 individual meat samples from each pool were bioassayed for T. gondii in cats and mice. Toxoplasma gondii isolates were then genetically characterized using the SAG2 locus and 5 hypervariable microsatellite loci. In all, 7 cats fed pooled pork samples shed oocysts. Toxoplasma gondii oocysts were detected microscopically in the feces of 2 of the cats; 1 isolate was Type II and the second was Type III. Analyzed individually, T. gondii was detected by bioassay in 3 of the 12 associated samples with genetic data indicating T. gondii isolates present in 2. The remaining 5 pooled pork samples had so few oocysts that they were not initially detected by microscopic examination, but rather by mouse bioassay of cat feces. Two were Type I, 1 was Type II, and 2 were Type III. None of the cats fed chicken or beef samples shed oocysts. Overall, the prevalence of viable T. gondii in retail meat was very low.
Conclusion
Beef and chicken have negligible amounts of the parasite, while pork has low levels that are effectively eliminated by proper cooking. Also, death from pork consumption is way less and uncommon than other means of dying.
References:

Ismail HA, Jeon HK, Yu YM, Do C, Lee YH. Intestinal parasite infections in pigs and beef cattle in rural areas of Chungcheongnam-do, Korea. Korean J Parasitol. 2010;48(4):347-349. doi:10.3347/kjp.2010.48.4.347
Sroka, J., Karamon, J., Wójcik-Fatla, A. et al. Toxoplasma gondii infection in slaughtered pigs and cattle in Poland: seroprevalence, molecular detection and characterization of parasites in meat. Parasites Vectors 13, 223 (2020). doi: 10.1186/s13071-020-04106-1
Dubey et. al. "PREVALENCE OF VIABLE TOXOPLASMA GONDII IN BEEF, CHICKEN, AND PORK FROM RETAIL MEAT STORES IN THE UNITED STATES: RISK ASSESSMENT TO CONSUMERS," Journal of Parasitology 91(5), 1082-1093, 2005, doi: 10.1645/GE-683.1


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Can trial participants get tests?
I saw a news story about someone who had participated in a COVID vaccine trial, and he said that he had taken an antibody test that came back positive, and he had concluded that he had not gotten the placebo, but the vaccine, and it had made him immune.
Isn't that problematic behavior? The trial is supposed to be double-blind. Are there ethical guidelines about trial participants getting tested?

Just because an Ab test came back positive doesn't mean the participant got the vaccine - they may very well have gotten the placebo and later acquired a non-symptomatic infection.

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. In particular, this question seems to be off-topic since it is about ethics rather than biology and "answers" will thus be opinions rather than facts. Thanks!


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Need for -70 degree temperature for Corona vaccine
Recent news of Pfizer vaccine for corona needing -70C temperature, made me thinking why such a low temperature is needed for mRNA based vaccine?
Are there other vaccine around which need such a low temperature?
NewsLink

This is the temperature at which RNA is stored for long term storage without the occurance of degradation. It is also standard lab routine to store RNA at this temperature. Conviniently, this temperature can be reached by dry ice (-78°C), which makes shipping a lot easier.
However, there are indications by Biontech themselves that the vaccine will be stable at refrigerator temperatures between 2-8°C for five days and probably even for prolonged times (see here). This is actually being tested, storing below -70°C is simply the safeguard to ensure nothing bad happens. For injection, it will have to be warmed anyways.


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What do they mean by “most single-gene traits are recessive.” How can a gene be recessive; isn’t it an allele which can be recessive or dominant?
Here’s the paragraph pg. 45 of “Principle of Neural Science”: “Although most single-gene traits are recessive, rearrangements that lead to duplication or deletion of multiple genes often have dominant effects. For example, individuals with three copies of chromosome 21 have Down syndrome due to the increased expression of multiple genes; no single gene when present in three copies is known to cause the cognitive and physical manifestations of Down syndrome.“
In addition to the question above, when they refer to the dominant effect of multiple genes, what do they exactly mean?

Yah, that is kind of sloppy.  I guess what they mean is that single gene traits usually follow the classic Mendelian pattern.  (Though I wouldn't be surprised if that wasn't true, if incomplete or co-dominance were more common)
I'd say that having extra copies doesn't really follow the Mendelian pattern at all, so it's weird to say its "dominant".
I'm guessing that this book only barely touches on genetics.  Honestly, it strikes me as kind of juvenile to take Medelian genetics as the touchstone of genetics, and try to squash everything into that paradigm.  Perhaps that made sense historically, when Mendelian genetics was the first attempt to really understand inheritance, but with what we know now, it makes more sense to think the the Mendelian paradigm as something that applies only sometimes; easier to realize that it just isn't particular relevant when taking about, say, gene dosage.


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Using coefficient of variation (CV) for GCaMP6 'synchronised episode' spikes, good idea or not?
Using GCaMP6 we have recorded fluorescence activity of kisspeptin neurons that exhibit synchronised pulsatile firing activity. I measured the intervals between each episode, which are quite variable. However, I am unsure whether or not using the coefficient of variation to analyse their variability is a good idea (since most papers I read have applied it to individual neuronal firing to analyse variability between spike intervals but not to population spike activity). Also, do I need a minimum number of 'spikes' to use CV (since in my recordings there are only around 4-10 spikes in around 3 hours)?

You can use the CV with a small sample but of course, it may not have converged yet. But 4-10 spikes/ 3 hours does not sound right to me. You may need to reconsider the event detection algorithm you used to get these numbers and/or the quality of the recordings. Additionally, the CV metric is useful when there is considerable bursting activity and you do not expect to see much bursting with calcium imaging given the temporal dynamics of GCaMPs.


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Why is urobilinogen reabsorbed from the gut just to be excreted via the kidneys?
The Wikipedia article on Urobilin states:

Bilirubin is... excreted as bile, which is further degraded by microbes present in the large intestine to urobilinogen... Some is reabsorbed into the bloodstream and then delivered to [the] kidney.

This process is puzzling to me since it doesn't mention any function or reason for urobilinogen to be absorbed into the body, aside from it being there so it can be removed by the kidneys.
The only reasons I can speculate are that:

Urobilinogen shares a transporter/receptor with a similar, useful compound.
It has a direct useful function when in the bloodstream, not mentioned on the wikipedia article or a few other sources I've skimmed.
High urobilinogen is harmful to the gut and it's necessary to remove it via the blood to the kidneys.
Urobilinogen is inherently able to diffuse across the intestinal barrier into blood as a result of its chemical structure

Is it one of the above, or some other reason I haven't taken into account?

I think that it is missing some details. Note that the vast majority of urobilinogen (~80%) is actually eliminated via fecal elimination. I would recommend looking at the article on enterohepatic circulation, which provides more context on this issue. Basically, bile salts can be useful (even or especially after metabolism by bacteria), so a fraction is reabsorbed by the large intestine and then dumped back into the digestive system:

However, just like bile, some of the urobilinogen reabsorbed is resecreted in the bile which is also part of enterohepatic circulation. The rest of the reabsorbed urobilinogen is excreted in the urine where it is converted to an oxidized form, urobilin, which gives urine its characteristic yellow color.

...

The net effect of enterohepatic recirculation is that each bile salt molecule is reused about 20 times, often multiple times during a single digestive phase.

Obviously urobilinogen isn't one of the salts recirculated that much if most of it gets excreted in feces, but apparently it still happens (possibly just because it is chemically similar to the other bile salts, as you suggest).
I think that the mechanism which is emphasized in the urobilinogen wiki page is a secondary mechanism for excretion when urobilinogen is at toxic levels in the bloodstream (e.g. jaundice). These high levels come for example from blood breakdown as pointed out in the article, which may be emphasized because it is a common medical issue (which is of course not a focus of SE Biology).
So, in other words, the wiki article is targeted towards the potential medical problems (toxic levels requiring elimination via kidney) rather than the normal physiology (mostly eliminated in feces, sometimes-useful salt that helps digest stuff), possibly leading to confusion. This flash card resource succinctly notes the functions of bile salts such as bilirubin and its derivatives and may be helpful for other basic info:

Functions:
(1) Digestion and absorption of lipids and fat-soluble vitamins
(2) Cholesterol excretion (body's only means of eliminating cholesterol)
(3) Antimicrobial activity (via membrane disruption)

More about (unfortunately medical focused) physiology of bilirubin etc. can be found here.


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What is a proximal deletion breakpoint?
I am reading a journal paper about the relationship between NCAM2 and autism. I have come across the following statement in the paper:

Based on analysis utilizing the UCSC Genome Browser (hg18, build 36),
there are a total of 19 genes deleted (Table I). The proximal deletion
breakpoint falls within the NCAM2 gene, deleting 17 out of 18 exons,
and the distal deletion involves 16 out of 17 exons of the GRIK1 gene.

I am not sure what is meant by a 'proximal deletion breakpoint'. I have tried searching for the definition online but I have not found anything useful. Any insights are appreciated.

Just break it down: look up "breakpoint" for chromosomes, look up "deletion" if you have to, and look up "proximal" and "distal".

This paper is not very helpful with understanding the role of NCAM2 in Austism, as the patient had chromosomal translocations in addition to the deletion.

Let's break down the phrase as one of the commenters mentioned:

"proximal": in the context of chromosomal position, this means closer to centromere, whereas "distal" means further from the centromere (the middle part of the chromosome).
"deletion": referring to the genes that were deleted as a result of the chunk of the 21st chromosome being missing.
"breakpoint": points at which the chromosomes was broken leading to the deletion.

Putting it all together, this says that the deletion breakpoint closer to the centromere falls within the NCAM2 gene, whereas the deletion breakpoint further from the centromere falls within the GRIK1 gene, with the other 17/19 genes falling between the two.
To verify this interpretation, we can use the USCS Genome Browser as mentioned. We can see that if we compare the position of the NCAM2 gene and the GRIK1 gene on the 21st chromosome, the former is closer to the centromere than the latter. We can also do a spot check to verify that ADAMTS1 one of the other 19 deleted genes, lies between the two of them.


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How many copies of RNA per cell are usually reached through overexpression in human cell-lines? (any technique)
After 8 hours of online-research I was unable to find any info at all..
I was able to get some concrete copy numbers of DNA (e.g. plasmid) per cell after transfection of diverse transfection techniques, but I was unable to get any concrete copy numbers of RNAs that correspond to the transgene (of any overexpression technique).
My main interest would be the hek293T overexpression RNA levels using the viral plasmid, but concrete RNA copy numbers from any possible overexpression technique would be of interest. (for human cells like Hela, Hek, HepG2..)
Ideally I would need a reputable source, but 'gut-feeling comments' are welcomed as well.
In the end I would like to compare overexpressed RNA concentrations to naturally extremely high concentrated endogenous RNAs. Are these levels comparable, or are the (viral) transgene promoters that much more effective?
EDIT: Please also mind that the nucleus is a strong barrier to foreign DNA. Might complicate this answer.


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What does 21q21.1-q21.2 mean?
I am reading a journal paper about the association between NCAM2 and autism, and I have come across the following:

We performed microarray analysis and identified a 1.6-Mb deletion of
21q21.1-q21.2, containing the NCAM2 gene but no other functional gene.

I am not sure what the '-q21.2' after '21q21.1' in '21q21.1-q21.2' means. Does it mean that the deletion goes between band 21.1 to 21.2 on the long arm of chromosome 21 (21q)? Any insights are appreciated.

Cytogenetic map notation uses the following form:
A[p/q]BC.D
Where A is the chromosome number, p is the petit / short arm, q is the queue / long arm, B is the band, C is the sub-band, and D is the sub-sub-band.
So, 21q21.1-q21.2 designates a region on the long arm of chromosome 21, band 2, sub-band 1, between sub-sub-bands 1 and 2.
Source:  NCBI Genetics Review (archived version)


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Identification of Ulva lactuca
I am trying to find an ID guide that I can use to identify macroalgae. I specifically want to differentiate between Ulva species.


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Flexor/extensor group in lower arm and limb bud rotation
Have the flexor and extensor groups in the lower arm have rotated laterally 90° towards the humerus epicondyles independently of the rest of the lower arm? The pre-axial and post-axial veins are still in aligned with their segments in the upper arm, so I assume that the muscle mass that forms the flexor group was initially located on the anterior side aligned with the flexors in the upper arm. The other option is the entire lower arm rotating relative to the upper arm but it seems less likely.


text:
Average masses of atoms / amino acids
I recognized that there is some controversy about the average mass of amino acid masses in different online sources.
Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ones. However, the monoisotopic masses are always the same.
Does anyone know where these differences come from or where to find a definite source for the masses?
In the end, the question boils down to the average masses of single atoms. The UWPR names UniMod as a source for their calculation. What different ways of calculation for average mass exist and who defined them?

This is chemistry not biology. If there is still any interest in the topic it should be reposted on SE Chemistry. Otherwise it is best closed.

A bit more link following reveals on the UniMod site: "All mass values in Unimod are calculated from the IUPAC atomic weights and isotopic abundances tabulated by WebElements:"
So, the answer is the isotope abundances are from the IUPAC; you can find links to references at webelements.com by drilling down in the periodic table there.

I guess confusion comes from either:

Inclusion vs exclusion of H2O (free AA vs in chain)

Averaging with
equal weight between all AA vs weight of their relative
occurrence

(EDIT) The Wikipedia link states:

Alanine  A   Ala     89.09404

ExPASy link:

Alanine (A)  71.03711

So ExPASy lists the weight without H2O, 18 Dalton lighter due to the condensation reaction in the form you would find the amino-acids in a peptide.

cannot be the cause, the differences are minimal, nothing like 18 Da. 2. No average is calculated over AA. The average weight is calculated out of the relative occurrence of different stable isotopes of the atoms. I guess that there are different reports of the relative occurrence of stable isotopes that lead to the difference in AA average mass.

I keep this answer because it might be relevant for people, who arrive here via search engines.


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Sprawling locomotion, are knee/elbow joints perpendicular to erect locomotion?
The first terrestrial animals used sprawling locomotion. Is the knee and elbow jointed perpendicular to the joints in erect locomotion? It is easy to assume so, based on how the limbs move in sprawling locomotion.

There was a question on exactly what is meant with jointed perpendicularly. It means the joint angle is perpendicular. Here is a rough ugly sketch, does not have to be a joint like that, question is if the movement in the joint is in any way in that direction.

Here, Baier seem to support that the knee and elbow joint in sprawling locomotion supports movement perpendicular to the simple hinge joint in erect locomotion, which is exactly what question is asking.

"The elbow was not a simple hinge; motion entailed substantial
abduction/adduction"

Baier, D. B., & Gatesy, S. M. (2013). Three-dimensional skeletal kinematics of the shoulder girdle and forelimb in walkingAlligator. Journal of Anatomy, n/a–n/a. doi:10.1111/joa.12102
Edit: the "diagram" caused some controversy in comment section. It was a copy+paste, simplest fastest possible I could make, in response to comment "What do you mean by "jointed perpendicular"?", because I considered that comment to be asking something that is clear. It is meant to show the perpendicular movement direction, not the joint design. It is not needed for the question, at all.

They don't appear to be in the images, why do you think that they would be?

It is easy to assume so, based on how the limbs move in sprawling locomotion. In that particular image, they are jointed perpendicular, but it is a rough schematic, could be wrong.

What do you mean by "jointed perpendicular"? They appear to be jointed in the same orientation in both pictures.

What do these diagrams have to do with the comparison in the original images?

They were a response to your comment. But nevermind. If you could falsify that abduction/adduction in the elbow joint of alligators is not the perpendicular movement I ask about (since besides flexion/extension, and pronation/supination, it is what is left..), then you prove my question to be wrong. I would guess it is correct though. If it is correct, why are you critiquing it so much?

A question is not correct or wrong, only an answer can be. I am critiquing because it is unclear. Probably it is just an issue of writing it in English, but that's still important because you won't get good answers if the question is unclear. In the diagram you drew, it seems like you are calling "perpendicular" motion to be the hinge-like motion you indicate in green, but when you write "perpendicular to the simple hinge" it sounds like you mean motion not in the direction indicated in green.

But it isn't unclear. Forget the diagram. You were asking questions, "What do you mean by "jointed perpendicular"?" it was a response to that, nevermind it. The question is clear. I suggest the answer by Baier, that there is significant adduction/abduction movement, means that there is some perpendicular movement. This means my assumption was right.

Probably the simplest source of lack of clarity is that you wrote "are knee/elbow joints perpendicular to erect locomotion?" when it seems you meant to ask "can knee/elbow joints move in a direction that is not the primary hinge direction?" These are not interchangeable questions.

This question could be better explained, perpendicular to a previous orientation? what the migration of the joint and bone orientation is through evolution? perperdicular is a very specific word which requires more specific references to it's surroundings than you give. Are you saying that the knee could fit image 4 rather than image 3?

This article by Baier seem to support that the knee and elbow joint in sprawling locomotion supports movement perpendicular to the simple hinge joint in erect locomotion, which is exactly what question is asking. The joints in sprawlers also supports flexion/extension axis though, and the question could have been a bit clearer on that. If I misinterpret Baier feel free to point that out (but since besides flexion/extension, and pronation/supination, it is what is left, I think I do not), and if not, question answered.

"The elbow was not a simple hinge; motion entailed substantial abduction/adduction"

References
Baier, D. B., & Gatesy, S. M. (2013). Three-dimensional skeletal kinematics of the shoulder girdle and forelimb in walkingAlligator. Journal of Anatomy, n/a–n/a. doi:10.1111/joa.12102


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What makes a protein structure discernible?
In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape that makes it difficult for scientists to understand the structure?

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

There are two main methods for discerning a protein's structure; x-ray crystallography, and more recently cryo-electron microscopy. Both methods work by firing a high-energy beam through the sample and observing how the path of the beam has been changed by passing through the sample. The data obtained by measuring the beam includes "signal" information on the structure of the sample, but also a lot of random data, or "noise". If the signal from large numbers of copies of identical proteins can be averaged together coherently, it can be separated from the noise and the positions of the atoms that make up the protein can be determined. In crystallography, this is achieved by getting the proteins to arrange into a crystal, and in cryo-EM by a computational process after data has been collected. Either way, if the many copies of the protein are not quite identical, the signal averaging will not work, and the positions of the atoms cannot be determined as accurately, or at all. In some cases, the protein has two or a few distinct structures that it switches between, and these can be separated and determined accurately. In other cases, the protein only takes a specific shape when it is bound to another molecule, and just flops around randomly when nothing is bound. Here is the abstract of a review on this second type of protein:

Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold. Disordered regions can be highly conserved between species in both composition and sequence and, contrary to the traditional view that protein function equates with a stable three-dimensional structure, disordered regions are often functional, in ways that we are only beginning to discover. Many disordered segments fold on binding to their biological targets (coupled folding and binding), whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.

Finally, some proteins will not crystallize unless a portion of their sequence is removed. These portions may have a consistent structure, but it can't be determined by crystallography.


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Is it possible to exclude article types in a PubMed search?
I have a question about searching PubMed. I want to search for original research papers while omitting reviews. Is this possible in PubMed?
Example
If I am interested in the relation between Acute Renal Failure and Salt, I could use the following search string:

("Acute Kidney Injury"[Mesh]) AND ("Sodium Chloride"[Mesh])

Using the column on the left of the article overview list, you can select which article types you are interested in.
Question
But I wondered if it was also possible to exclude a specific article type (e.g., reviews) from the search?

I believe this will work:
((Acute Kidney Injury[MeSH Terms]) AND (Sodium Chloride[MeSH Terms])) NOT (Review[Publication Type])
Using the advanced search settings on PubMed it was easy enough to set up, here is the link in case you don't have it already:
https://pubmed.ncbi.nlm.nih.gov/advanced/


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How to correlate CNV with transcriptomic data?
I have a list of differentially expressed genes. I want to correlate these genes with CNVs. I have downloaded the data from both TCGA and FireBrowse. But I am not able to understand how to do the correlation? How should I analyze the CNV data. Do you have to do some processing to get a list of CNVs with a score or something to do the correlation? Please help

Might be better off moving this post to https://bioinformatics.stackexchange.com/

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In particular, I'm voting to close this question because it better fits [Bioinformatics.SE], but please do not crosspost, instead request migration. ———— In addition, 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). Thanks!


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Do antigen presenting cells present only antigens they have receptors for?
As APCs  take up whole virus or bacteria  their receptors may be restricted to antigens "they have receptors vor", i.e. those antigens that are on the outside of virus or bacteria. Put simply: do they uptake "inner" antigens their receptor doesn't contact with AND, then, present them?
It should make sense for antigen presenting cells - APCs - to present only antigen that can be used for recognition. In other words: why should APC present antigens to T-cells if these cannot use such kind of antigen  to recognize and attack cells because those antigens are part of inner structural proteins that do not show on the external surface?
That may be different with B cells/MHC2.
Admittingly, this question is awkwardly put, as it should be known to any advanced learner that the APC's, the antigen-presenting-cells of the immune system have very broad receptor specifity. So there should be no antigen at all "they do not have receptors for" - same s for B cells as a wohl class or set.
I have not found any  or textbook passage on  B-cells taking up, via B-cell-receptor, "inner" antigens that come as cell debris. But then, the B-cell receptor in fact is a receptor in terms of my question. Which interestingly makes it seem a possibility that macrophages and dendritic cells have receptors that do not recognize any inner structural protein that comes as cell debris.
Having gone through and read Kuby, Janeway, Roitt on immunology, my understanding  is that not each and  every antigen of a  virus will find its way to the MHC complex on the cell membrane of antigen presenting cells. If that is correct,  how could eukaryotic cells possibly differentiate between antigen of viruses they present and those they would not? Do they present not "all sorts" of antigen but only those "they have receptors for" (awkwardly said)?
Regarding  "normal" cells of the body  that become infected and are not part of the immune system, do, for instance, CoV-19 infected body cells  present only the spike protein on MHC1?  The spike is the antigen they "have receptor for".
So any antigen that cannot be considered antigen to a receptor and becomes presented would answer my question to the negative. If so, is there any selection within that set of "inner" antigens ("non-uptake antigen").

"On MHC II, do cells present only antigen they have receptors for?"
Thank you for boiling your question down to its essence. The answer is no. Professional antigen-presenting cells (APCs) such as macrophages, dendritic cells, B cells, etc., which present peptides in the context of the major histocompatibility complex (MHC) Class II to CD4+ Thelper cells, initially obtain the source proteins through non-specific phagocytosis. Receptor binding doesn't necessarily have anything to do with it, unless you're looking specifically at B cells and antigen's binding to the B cell receptor (BCR) before being endocytosed.

From immunology.org
Where you might be confused about receptors is that only some of the peptides generated by cathepsin-mediated proteolysis in the phagocytic endosome have high-enough structural affinity to bind the MHC II receptor by displacing the CLIP fragment and being exported to the cell surface.

Very valuable advice on Clip "selection", thanks!Part of my "confusion" may be derived from viewing MHC as a kind of receptor. Anyway, question above may lead to better awareness of receptors that exist inside the cell - they do exist -, and MHC looks like one - which is, as it occurs to me writing this - as an unspecific one, like the others!

... considerung "CLIP" in the context of "crosspresentation". Still cryptic, it's just a new look at things. If MHC were "some" receptor - then answer would go like: yes, of course, why you ask. - -  "Clip" to me denotes position at handing over of antigen betw. 2 "receptors", new view. –
See, for instance,   to illustrate Ciminski, "...findings show that bat IAV HAs make use of the major histocompatibility complex class II proteins of different vertebrate species to gain entry into host cells, ...".

Sorry, one more and last: not so trivial to see MHC as a "receptor", as one got to know: 1. there are "inner cell" receptors, and 2nd consider your word "affinity" in "enough structural affinity". To paraphrase: there are, do exist, antigens which there is no affinity for. There are antigens there seems to be no receptor for. Jokingly: no demo to/for/of them... no chatting: no mad demo for those.


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Is there any non-human animal social group that punishes members with "imprisonment" or a similar method?
I was reading this blog on Scientific American, which discusses whether wild animals are happier than domesticated ones. I've also read about strong territorial instincts in some species. This reading led me to ask whether there is any non-human animal social group that punishes members with something similar to "imprisonment".
When I say "imprisonment" I mean restricting the mobility and survival freedom of members, for some social or cultural reason.
By "imprison", obviously I don't mean the use of cages or prisons or any of the manmade ways of imprisoning. I wish to know about whether, in any species, a member acting alone (or acting together with others of their own), build a virtual territorial wall/ring around another member(s) of their own species, acting almost like an imprisonment? This may not be physical exertion of muscle force, but may by making (say, for example) continuous noises as a group to restrict the territory of their own member.
Maybe, one can exclude adult members forcefully protecting their young ones, because that would be in their instinctive interest, even if the young ones' instinct is to violate a restriction. Also please avoid answers on behaviour of one species defending their territory. That's not the same as restricting by "constructing" a limiting threshold in an enclosure-like fashion.

does slavery count, as e.g. ants? https://en.wikipedia.org/wiki/Slave-making_ant

Interesting, thanks. I knew about bees for class-divide. I meant imprisoning for bad behaviour or for some kind of misfit in the community.

whoof... that is a really big topic that seems to be more about animal social/cultural structure than a particular sort of social tool (imprisonment). Editing the question to reflect this new information. i'm not the person to answer this, other than to suggest to read more. maybe there is something here that can help you: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936173/

Welcome to Biology.SE! Your recent edit has made your question quite a bit clearer, but I have no idea what you mean by "survival freedom". In addition, you seem to be excluding the large group of animals that modestly refer to themselves as Homo sapiens. I've edited your post to make that clear and also removed your last paragraph, which seems both disingenuous and irrelevant to your central question. I also made some small corrections of typos etc. Please make sure that I have not altered your intended meaning.

consider that very few human societies use imprisonment, only ones with a large food surpluses and large populations, most human societies use shunning instead which is quite common in social animals, but that does not work with groups much larger than dunbar's number, where most people are strangers. Imprisonment is an invention created due to limits in our evolved social controls not something instinctual. Also consider whether shunning would count as imprisonment by your definition.