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How can mutation of viruses lead to loss of fit to antibodies without loss of fit to antigen of cells they infect?
Viruses are known to mutate, thereby escaping immune cells and evading vaccination. Given that there is one and the same specificity of the key to both the receptor on the infected cell causing the disease after cell entry as well as to the antibodies or immune cell receptors of the immune cells how can it be that a virus that has mutated thus escaping defense is still able to connect to cells of the body?
It should be one and the same key to one and the same lock. As it is the same key it seems logical that both locks - antibodies' and antigens' are identical, as they fit to the same key.  If mutation leads to "unfitness" in respect of antibody, how can the key still fit to the body?
In the context of mutation and vaccination this question might intuitively be answered by "different epitopes".
Is there any opinion on that at all? Textbooks seem to be not explicit at all. Is it too trivial a question? Are there are two epitopes on viruses: one for the antibody, one for the body cell? Mutation somehow deliberately restricts itself to the former?
One line of thought added: if you think of some shared (intersectional) epitope it's one and the same mutation that influences both sides, adhesion to antibody and, plus, adhesion to target receptor. Logically, it is possible that there is one mutation that is successful in both ends, i.e. results in loss of antibody fit and improves adhesion to target cell at the same time. But then, illustrating my question, it is a question of probability - as on the antibody side it is the loss of fitness which should be - at the same time - be a gain on the side of adhesion to receptor. Intuitively, this is highly unlikely, with a shared epitope.
The above speaks for different, non shared epitopes, and a multistep strategy in the evolution of virus. Is it possible and is there any authority on my assuming that it is among those virus clones that do not lose their affinity to antibody and remain under attack (as losing antibody fit, see above, means losing target fit, in probability) that selection takes place: those who do not mutate away from antibody attack evolve receptor affinity, and become "a little bit better", in speed, attain advantage in targeting against being caught antibodies. This might explain and be coherent with CoV-2 making appearance not as a variant of CoV that antibodies would not reach anymore, but much more so as a variant that has improved its target cell affinity.
So, assuming relevant mutations being selected among those strains that remain within the reach of existiting antibodies and do not mutate away from the antibody side epitope would be consistent with findings that existing vaccines and the antibodies they induce remain valid against new and upcoming strains of CoV-19. If it were found that new strains are more pathogenic, that would be coherent with that assumpton, too.
For better understanding compare this passage of the answer giben: "... which do lose their fitness against the immune system, but undergo gene reshuffling with similar viruses and again become infectious." "Lose fitness against the immune system" in strict meaning of words would mean gaining fit the to the antibody - however, the author speaks of "becoming infectious", thus refering to target cells. This made me rethink the above to the following:
If you do not assume any shared, identical epitope of body cell (lose the fit to antibody means gaining fitness against the immune system, however at the same time losing fit against the target cells that define the disease) there is some successful "moving out" of the reach of antibody which means "sucess" and that same "moving out" of the realm of target cell epitope which means "failure", losing infectivity.  At both sides it's just "into the negative", to lose a fit (however, success and failure very set apart). One has to acknowledge that both sides make sense: just losing fit to antibody is success (epitope to body receptor remains unchanged). For success of the virus on the body cell side, however, no loss will do, there must be a gain of  fit to another receptor on body cell. Why then, to illustrate my question further, should a selective stress prefer to take the hard way: gain of function towards body cell, and not easily "fall apart" from the antibody fit, thus becoming fit against the immune system?
To sum up, two alternative answers seem possible:
a. there are two separate epitopes; virus escape the antibody fit, and this suffices
b. there indeed is a shared, common epitope: it is not enough to "opt out" and exit the antibody fit but one and the same mutation - as the primise is the existence of a shared, no separate epitope - must find a new fit on the body cell receptors side.
A third answer emerges, to me:
Epitopes are separate, not shared, and mutation is a multi-step process. Then first, interestingly,  the mutation to a new fit on the body target cell side should come first, as only this sequence - not the opposite - presevers selective pressure to escape the immune system in the following second mutation.

I'll address this q and ignore the rest of the (way too long) post/theories:

Given that there is one and the same specificity of the key to both the receptor on the infected cell causing the disease after cell entry as well as to the antibodies or immune cell receptors of the immune cells how can it be that a virus that has mutated thus escaping defense is still able to connect to cells of the body?
As it is the same key it seems logical that both locks - antibodies' and antigens' are identical, as they fit to the same key. If mutation leads to "unfitness" in respect of antibody, how can the key still fit to the body?

This premise is wrong in several ways.
First, affinity is not a binary (yes/no) proposition. More technically speaking, what matters for virus binding to a receptor is avidity, which is the combination effect of affinities at multiple points in a protein, but many papers in virology nonetheless use the former term when talking about viruses binding to receptors.
You can probably already see that multiple "solutions" or "keys" are (thus) actually possible for the same "lock". For example, the SARS-CoV and SARS-CoV-2 RBD (receptor binding domains) are only about 73% similar, even though both viruses bind to the ACE2 receptor in humans, "well enough" to infect (and ultimately replicate).
Furthermore, the "lock and key" metaphor is only a very crude approximation of the more complex mechanism of viral entry.
But to single out one aspect of that, the "key" basically can "shape-shift" (undergo conformational change) so that it "looks different" during viral entry than it might otherwise look to antibodies, e.g.

The RBD in coronaviruses can be in either a standing-up state, which enables receptor binding, or a lying-down state, which does not bind to the host receptors. Cryo-EM studies have shown that, in SARS-CoV spike, the RBD is mostly in the standing-up state; however, in SARS-CoV-2 spike, the RBD is mostly in the lying-down state. Therefore, compared to SARS-CoV, although SARS-CoV-2 RBD has higher hACE2 binding affinity, it is less accessible, resulting in comparable or lower hACE2 binding affinity for SARS-CoV-2 spike. To maintain its high infectivity while keeping its RBD less accessible, SARS-CoV-2 relies on a second strategy—host protease activation. [...]  Protease activation of coronavirus spikes potentially leads to the final structural change of coronavirus S2 needed for membrane fusion; this process is irreversible and needs to be tightly regulated.

As further discussed in that paper, RBD masking/shielding is actually rather common in several other virus types (HIV, Hepatis C, Ebola etc.)
As an interesting point here showing how affinity can decrease but avidity can increase (probably in tandem with antigenic drift), a 2017 paper on H3N2 finds that:

Recent reports have suggested that current human H3N2 viruses no longer have strict specificity toward human-type receptors [using typical hemagglutination tests]. Using an influenza receptor glycan microarray with extended airway glycans, we find that H3N2 viruses have in fact maintained human-type specificity, but they have evolved preference for a subset of receptors comprising branched glycans with extended poly-N-acetyl-lactosamine (poly-LacNAc) chains, a specificity shared with the 2009 pandemic H1N1 (Cal/04) hemagglutinin. [...] Remarkably, these human-type receptors with elongated branches have the potential to increase avidity by simultaneously binding to two subunits of a single hemagglutinin trimer.

As final "food for though" as to the [in]appropriateness of the key-lock analogy, poxviruses don't seem to use any particular receptor to bind to cells, being capable of attaching to glycosaminoglycans (GAGs), which are present in all eukaryotic membranes, although various cells differ in degree of sulfation of their GAGs, which in turn changes affinity with poxviruses.

The second reason for which your premise is wrong, antibodies are not mere copies of the receptors found the on the actual cells that the virus may enter. Antibodies need to "solve" a simpler problem than the virus-cell entry; namely an antibody (if we restrict discussion to those targeting a receptor binding domain) only needs to "screw up" the RBD somehow, so the latter doesn't "fit" with the cell receptor anymore. For example, these two antibody fragments against SARS both manage that disruption, even though one only binds to the side of the RBD:

Third, there is actually a rapid evolution process of antibodies themselves known as antibody affinity maturation:

The extensive sequence diversity of antibody molecules derives from several sources: (i) combinatorial diversification, whereby two sets of light (L) chain gene segments, VL and JL, and three sets of heavy (H) chain gene segments, VH, D, and JH, rearrange to produce functional variable (V) regions; (ii) imprecise joining of these gene segments; and (iii) somatic hypermutation, by which point mutations, as well as insertions and deletions (indels), are introduced throughout the sequences encoding L and H chains. B cells expressing antibodies with improved affinity are better equipped to compete for antigen and thus receive signals that result in preferential expansion and further antibody sequence diversification via additional rounds of somatic hypermutation. Through this rapid evolutionary process of mutation and selection, antibody affinity typically improves 10- to 5,000-fold during the course of an immune response, bolstering host defense.

If the host is lucky, it might even produce antibodies that work against multiple viruses. E.g. there's a known example
of an antibody from a Covid-19 patient which also neutralizes the orignal SARS, even though this patient had
no history of infection with the latter/older virus. This is basically known as cross-reactivity of anti-bodies. However note that this antibody is not equally effective against both viruses, it needs higher concentration
to achieve the same affect against SARS-CoV than avainst SARS-CoV-2.

The antibody COVA1-16 was recently isolated from an individual
recovering from COVID-19 and cross-neutralizes SARS-CoV-2
(half-maximal inhibitory concentration [IC50], 0.13 μg/mL) and
SARS-CoV (IC50, 2.5 μg/mL) pseudovirus.

One has to distinguish the cause and the consequence: the only viruses that survive the natural selection are those that can evade the immune defenses while effectively infecting cells. A virus strain not successful at either of these tasks is less fit and likely goes extinct.
One can pose a question of what modifications in virus proteins allow it to be so specific in what it (does not) binds to. However, the answer will necessarily depend on the specific virus/strain and specific conditions (which may mean the epidemiological conditions during the time of its spread, the existing vaccines, or even the specific patient).
It is also necessary to point out that statement Viruses are known to mutate, thereby escaping immune cells and evading vaccination. is generally not true, but presents only one possible evolutionary strategy for virus survival,  characterized by  establishing a chronic infection. The typical example here is HIV. To some extent one could also use this description for influenza-like viruses, which do lose their fitness against the immune system, but undergo gene reshuffling with similar viruses and again become infectious. However one could argue that this is not a mutation, but a new virus.
Other strategies that viruses use to survive include (viewed from the point of view of population genetics rather than virology):

Hit and run approach, characteristic of cold-like viruses, which succeed to replicate before triggering the response of adaptive immune system, and thus being able to reinfect the same hosts.
Coexistence, characteristic of herpes-like viruses, which avoid extinction by being relatively low-key, i.e., not triggering substantial immune response, while establishing a lasting infection (e.g., by integrating in the host DNA).
Permanent circulation - the most well-known case is smallpox, which continued to exist in the human population for thousands of years by simply moving around the globe. This entailed no adaptation, which is why it was possible to make this virus extinct by vaccination.
No strategy - Ebola epidemies in humans are an evolutionary dead end, as the virus killing nearly all of its hosts is bound to become extinct. The reason that Ebola outbreaks still happen is because this virus exhibits a relatively harmless, flu-like, behavior in some animals and only occasionally spills to humans. Thee difference with the smallpox is mostly a quantitative one: Ebola kills its victims too fast, to spread efficiently.

References
J. Flint et al., Principles of Virology


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In terms of Prions is there a possibility, that other proteins apart from PRPC could be misfolded
This is as from research PRPC seems to be the cause of all Prion related diseases. Thank you

Can you please provide citations for your claim? Use the [edit] function to modify your post.

Please write a question as a question. A title is a title not a question. Take care to make clear the context of your problem and the research you have done to answer it yourself. Currently that is lacking.

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There are many prions other than PrP; it is often helpful to e.g. read wikipedia for these cases.
For example, there are many yeast prions that are not homologous to PrP https://en.wikipedia.org/wiki/Fungal_prion.
But even in humans there are a number of other proteins that form amyloids and are described as "prion-like" even though they aren't the canonical protein: https://en.wikipedia.org/wiki/Prion#In_other_diseases

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What was the breakthrough behind the “sudden” feasibility of mRNA vaccines in 2020?
Several sources describe the initial failures in the realization of a successful mRNA vaccine. E.g., this 2017 article from Stat describes the following problem faced by Moderna while working on one of their mRNA vaccines:

The safe dose was too weak, and repeat injections of a dose strong enough to be effective had troubling effects on the liver in animal studies.

Another Stat article describes a similar challenge:

In animal studies, the ideal dose of their leading mRNA therapy was triggering dangerous immune reactions — the kind for which Karikó had improvised a major workaround under some conditions — but a lower dose had proved too weak to show any benefits.

The work by Karikó was conducted before Moderna and BioNTech were founded, so it does not seem to be the breakthrough that led to feasible mRNA vaccines. I am also aware that one of these companies, Moderna, is secretive about its technology.
However, I would like to learn, at least at a high level, the reason mRNA vaccines are a viable option against COVID-19, while earlier attempts to develop them against other diseases, such as Crigler–Najjar syndrome, were unfruitful.

I am aware of Why weren't mRNA vaccines clinically tried earlier?, which was closed for being opinion-based. However, my question is specific to the biological mechanism behind the breakthrough that enabled feasible mRNA vaccines, so is objective and within the scope of this site.

Your question is about vaccine development and medical application rather than the biology of the method. I would suggest it is more suited for SE Medical Sciences.

@David My question is about the biology of the method. According to the Help Center, “questions about techniques in a biological or biochemical laboratory” are on-topic here.

@David Also, this answer mentions that drug-related questions which “focus on biological concepts or drug mechanisms” are on-topic

Perhaps part of the reason is that Crigler–Najjar syndrome isn't a viral infection, it's an inherited genetic defect: https://en.wikipedia.org/wiki/Crigler%E2%80%93Najjar_syndrome  Then there's a lot more motivation (which means more resources) to find a vaccine for a pandemic, than a treatment for a condition that affects less than 1 in a million.

@jamesqf That's a good point, but I'm trying to understand what biological breakthrough came from the increased motivation and resources.

@user1136 thanks for the link. I will read it and, yes, post an answer if it completely answers my question.

Relevant: https://www.youtube.com/watch?v=XPeeCyJReZw

Answering my own question after reading the 2018 Nature review article “mRNA vaccines — a new era
in vaccinology”
The resources and motivation engendered by the COVID-19 pandemic are a major factor in the development of the first mRNA vaccines approved by national governments. However, before the COVID-19 pandemic, there were recent advances in mRNA vaccine pharmacology, which made everything possible.
Introduction
The Nature review points out that it was not a single breakthrough, but a lot of research that was conducted during the last couple of years.
Demonstrations of protective immune responses by mRNA vaccines against various infective pathogens were published in recent years. In the first one, published in 2012, direct injection of non-replicating mRNA vaccines was shown to be immunogenic against various influenza virus antigens in multiple animal models1. Since then, several studies on animals, and in some cases, healthy human volunteers, have managed to induce protective immunity against rabies2,3, HIV-14,5,6, Zika7,8,9, H10N8 and H7N9 influenza10, and other viruses.
The authors of the review, which was written before the COVID-19 pandemic, believed that “mRNA vaccines have the potential to solve many of the challenges in vaccine development”. Therefore, had the pandemic not happened, it is likely that we still would have seen effective mRNA vaccines being developed, albeit at a slower pace.
Recent technological advancement has largely overcome the main challenges in the development of mRNA vaccines.
The Challenges
1. Instability
Protein expression after the vaccine is administered might be insufficient if, for instance, the half-life of the vaccine is too low, or if in vivo mRNA translation is insufficient11,12.
2. Inefficient in vivo delivery
mRNA vaccine delivery is tricky. For instance, mRNA can aggregate with serum proteins and undergoes rapid extracellular degradation by RNases. Therefore, formulating mRNAs into carrier molecules is often necessary, and delivery formulations need to take into account factors such as the biodistribution of the vaccine after delivery, mRNA uptake, and protein translation rate13,14.
3. Safety
The complexity of modulating the immunogenicity of the mRNA used in vaccines can potentially lead to unwanted stimulatory effects on the immune response15,16,17.
The Recent Advances
1. Optimization of mRNA translation and stability
Sequence optimization techniques such as replacing rare codons with more frequently used synonymous codons18, as well as enrichment of G:C content16, have been examined for increasing in vivo protein expression.
2. Progress in mRNA vaccine delivery
There are numerous delivery methods for mRNA vaccines that have been examined in the literature. In recent years, the limitations of some of these, such as using physical methods (e.g., electroporation) to penetrate the cell membrane, were demonstrated19. On the other hand, progress was made toward the increased efficacy and reduced toxicity of other delivery methods such as cationic lipid and polymer-based delivery13,16,20,21.
3. Modulation of immunogenicity
Recent studies have demonstrated that the immunostimulatory profile of mRNA can be controlled more precisely using a variety of techniques. These include chromatographic purification to remove double-stranded RNA contaminants, the introduction of naturally-occurring modified nucleosides to prevent the activation of unwanted innate immune sensors, and complexing the mRNA with various carrier molecules (this includes novel approaches to adjuvants that take advantage of the intrinsic immunogenicity of mRNA)15,17,22,33.
Apart from the advances in techniques such as purification and the introduction of nucleosides, there was also an improvement in the understanding of when these techniques should be used, based on factors such as the mRNA platform used, RNA sequence optimization, and the extent of mRNA purification under consideration16,24.
References

Petsch, B. et al. Protective efficacy of in vitro synthesized, specific mRNA vaccines against influenza A virus infection. Nat. Biotechnol. 30, 1210–1216 (2012).
Schnee, M. et al. An mRNA vaccine encoding rabies virus glycoprotein induces protection against lethal infection in mice and correlates of protection in adult and newborn pigs. PLoS Negl. Trop. Dis. 10, e0004746 (2016).
Alberer, M. et al. Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first‑in‑human phase 1 clinical trial. Lancet 390, 1511–1520 (2017).
Pollard, C. et al. Type I IFN counteracts the induction of antigen-specific immune responses by lipid-based delivery of mRNA vaccines. Mol. Ther. 21, 251–259 (2013).
Zhao, M., Li, M., Zhang, Z., Gong, T. & Sun, X. Induction of HIV‑1 gag specific immune responses by cationic micelles mediated delivery of gag mRNA. Drug Deliv. 23, 2596–2607 (2016).
Li, M. et al. Enhanced intranasal delivery of mRNA vaccine by overcoming the nasal epithelial barrier via intra- and paracellular pathways. J. Control. Release 228, 9–19 (2016).
Pardi, N. et al. Zika virus protection by a single low-dose nucleoside-modified mRNA vaccination. Nature 543, 248–251 (2017).
Richner, J. M. et al. Modified mRNA Vaccines protect against Zika virus infection. Cell 168, 1114–1125.e10 (2017).
Richner, J. M. et al. Vaccine mediated protection against Zika virus-induced congenital disease. Cell 170, 273–283.e12 (2017).
Bahl, K. et al. Preclinical and clinical demonstration of immunogenicity by mRNA vaccines against H10N8 and H7N9 influenza viruses. Mol. Ther. 25, 1316–1327 (2017).
Weissman, D. mRNA transcript therapy. Expert Rev. Vaccines 14, 265–281 (2015).
Sahin, U., Kariko, K. & Tureci, O. mRNA-based therapeutics — developing a new class of drugs. Nat. Rev. Drug Discov. 13, 759–780 (2014).
Kauffman, K. J., Webber, M. J. & Anderson, D. G. Materials for non-viral intracellular delivery of messenger RNA therapeutics. J. Control. Release 240, 227–234 (2016).
Guan, S. & Rosenecker, J. Nanotechnologies in delivery of mRNA therapeutics using nonviral vector-based delivery systems. Gene Ther. 24, 133–143
(2017).
Kariko, K. et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol. Ther. 16, 1833–1840 (2008).
Thess, A. et al. Sequence-engineered mRNA without chemical nucleoside modifications enables an effective protein therapy in large animals. Mol. Ther. 23, 1456–1464 (2015).
Kariko, K., Muramatsu, H., Ludwig, J. & Weissman, D. Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA. Nucleic Acids
Res. 39, e142 (2011).
Gustafsson, C., Govindarajan, S. & Minshull, J. Codon bias and heterologous protein expression. Trends Biotechnol. 22, 346–353 (2004).
Johansson, D. X., Ljungberg, K., Kakoulidou, M. & Liljestrom, P. Intradermal electroporation of naked replicon RNA elicits strong immune responses. PLoS ONE 7, e29732 (2012).
Schlake, T., Thess, A., Fotin-Mleczek, M. & Kallen, K. J. Developing mRNA-vaccine technologies. RNA Biol. 9, 1319–1330 (2012).
Reichmuth, A. M., Oberli, M. A., Jeklenec, A., Langer, R. & Blankschtein, D. mRNA vaccine delivery using lipid nanoparticles. Ther. Deliv. 7, 319–334 (2016).
Fotin-Mleczek, M. et al. Messenger RNA-based vaccines with dual activity induce balanced TLR‑7 dependent adaptive immune responses and provide antitumor activity. J. Immunother. 34, 1–15 (2011).
Rettig, L. et al. Particle size and activation threshold: a new dimension of danger signaling. Blood 115, 4533–4541 (2010).
Kauffman, K. J. et al. Efficacy and immunogenicity of unmodified and pseudouridine-modified mRNA delivered systemically with lipid nanoparticles in vivo. Biomaterials 109, 78–87 (2016).

So in a nutshell, we're just really lucky that this pandemic came along just when mRNA technology had developed to the point where it could be used to make a vaccine.  Otherwise we'd probably facing years more to develop conventional vaccines that might be much less effective.

@jamesqf Isn't China's CoronaVac based on the usual (non-mRNA) technology?

@jamesqf Indeed, one of the advantages of mRNA vaccines mentioned in the review is the capacity of their rapid development and low-cost manufacture. However, I'm not sure how Sinovac was able to develop their CoronaVac, which is a conventional inactivated SARS-CoV-2 vaccine, so quickly.

@jamesqf Lucky? No. DARPA and other agencies have been strategically investing in rapid vaccine development for a decade (including specifically Moderna's mRNA technology, which has been receiving federal funding since at least 2013), because everybody paying attention has known it was only a matter of time before we needed a rapid response like this.

@jamesqf There are other SARS-CoV-2 vaccines using conventional mechanisms that are on the cusp of completion. Pedro already mentioned Sinovac’s CoronaVac. Others are the DNA-based Oxford/AstraZeneca collaboration vaccine AZD1222, as well as the Russian Gam-COVID-Vac (“Sputnik V”).

@jakebeal: Lucky, yes, because COVID-19 or something similar could easily have appeared a decade ago.

This is a good answer, though I'm assuming all of your assertions are backed up by the linked Nature review article.  This would be a much better answer if you directly cited the primary literature referenced in the review, such that the answer is self-contained and does not rely on readers to go to the review itself for citations.

@acvill Thanks, and you are right. I edited the answer to include the citations.

@jamesqf also lucky because it if the advances had been made earlier it could have been used on a non-emergency illness, and taken years to go through the system...

Refering to "increased efficacy and reduced toxicity of other delivery methods such as cationic lipid and polymer-based delivery13,16,20,21."  Have you already read all this and are able to tell if is considered "efficient" if the nano particles not only transfect the cell efficiently (not get lost on their way etc) but also target specific cells, which is also called "tropism". Is there report on progress in targeting specific cells? This definitely matters in respect of cancer cellls, but need not in the context of vaccines. So, is there progress in targeting too?

@PeterBernhard I tried to focus more on vaccines against infectious diseases in my answer here, but the review article I linked also covers mRNA cancer vaccines in the same detail. You can check out the "mRNA cancer vaccines" subsection which begins on page 9 of the article. It also refers to other more extensive reviews focusing on mRNA cancer vaccines.

@hb20007 Thank you! Are you familiar in any other way, by any chance with "nano lipid vaccines cell targeting"? As you are in respect of cancer, you might. Would you think that there maybe none, bedause vaccines may target any cells, it just doesn't matter (in contrast to cancer which needs to be hit?)

@PeterBernhard I assume you are talking about the "cationic lipid nanoparticle" delivery system. According to the review article, it was tested on HIV-1 as well as OVA (ovalbumin-expressing cancer models). Reference #152 in the article is the relevant one; you can probably find more details about this delivery system there.

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What is the use of having 3 antipodal cells and 2 synergids?
The embryo sac which is developed from functional megaspore contains 8 nuclei.2 polar nuclei and egg fuses with sperms.3 antipodal cells and 2 synergids degenerate after fertilization.Then what is the use of having 3 antipodal cells and 2 synergids?

This botany textbook mentions:

The synergids help guide the pollen tube for successful fertilization, after which they disintegrate.

In one of my older (1965) comprehensive books (not in English) on plant morphology:

The synergids usually start disintegrating before the fecundation. In special cases, they may develop into a haustorium (specialized absorbtion organ of the embryo) or even produce an additional embryo.

Later in the same book, we find that:

apogamy (one of the three types of apomixis, alongside parthenogenesis and apospory) is the phenomenon through which the plant embryo does not develop from the egg, but the synergids or antipodes, as can be seen in Plantago lanceolata or Allium odorum.

Also, notably:

in rare cases, the number of antipodes may vary; some plant ovules may have up to 150 antipodes, while others have two, one, on no antipodes at all.


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Decreasing signals in assay measurements
I'm working with a calcium assay to study the effects of different virulence factors. The assay works, but from day to day the signals of cell lysis go down. Unfortunately, I haven't found an explanation for why this is happening.
The particular assay I use measures cell lysis. The virulence factors I use cause pore formation and lead to a calcium influx (from the buffer). Esterase proteins activate the fluorophore and need calcium. Increase in cell lysis leads to an increase in signal.
As I already mentioned my signals are dropping (from day to day). But I don't know why.
Have you got an idea of what could lead to such effects?
Here are some factors that might be involved.

The virulence factors lose their activity? (I don't feel like that this causes the problem because new stocks also show a decrease in activity, and also the signal from the positive control decreases. I would say it decreases in a similar ratio. The positive control is triton.
The dye loses its activity? The bottle is normally stored in a freezer. I just take it out for the assay. Before I use it, I place the bottle on a shaker for about 30 minutes. I just open the bottle for a few seconds and then put it then back in the freezer.
The plate reader is broken or the reading protocol has changed? I already checked the protocol and every thing is the same as in the beginning. Coworkers get the same results with the same plate reader as before. So I guess, this should not be a problem.
The buffer gets destroyed from the procedure? I store it in the freezer and take it out and put in a waterbath. After I used it I place it back in the freezer. I carry out this procedure every time, can this lead to negative effects? The medium contains calcium, can something happen with it (Calcium plays an important role in this assay)? A colleague already told me that he stores his buffer in the fridge not in the freezer, and he didn't got such effects. But perhaps it's not the only thing he does different..
The cell number changes? The negative control does not change over the experiments, and the signal from it is still higher than the values from the blank. But i will check that.
Could my cells cause problems? They look still good under the microscope.

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I've edited your post to correct language problems, but I suggest you add much more detail about exactly what fluorophore you are using (and in what solvent) and the constituents of the various other buffers you are using. Please check to make sure I've not changed your meaning. ——— I'll post a preliminary possible answer as well, but you probably need to get someone in your lab to teach you how to trouble shoot. IMO learning how to trouble shoot experiments is the most important lab skill!

Freeze-thaw cycles are often suspected of causing degradation in organic molecules 1,2. My first guess would be that your fluorophore is breaking down due to those repeated cycles. Alternatively, you might be getting precipitation of a calcium compound from the buffer you are freezing that your colleague is not.
Standard laboratory practice is to make aliquots of frozen solutions. Before thawing the solution for the first time, set up pre-labeled smaller containers (e.g. Eppendorf tubes) and then aliquot the amount you expect to use for each experiment. That way potentially sensitive compounds are only thawed twice.
References:
1: Kozikowski, B. A., Burt, T. M., Tirey, D. A., Williams, L. E., Kuzmak, B. R., Stanton, D. T., ... & Nelson, S. L. (2003). The effect of freeze/thaw cycles on the stability of compounds in DMSO. Journal of biomolecular screening, 8(2), 210-215.
2: US Food and Drug Administration. (2008). Guidance for Industry. Drug Stability Guidelines.

Hey MattDMo, thanks for your answer! Today I made a special test, to eleminate some of the possible factors which could lead to such mysterious effects.  I seeded out some cells and instead of treating them with my virulance factors i treated them with triton X. By the way I also seeded out higher and lower cell numbers than normaly used in the assay. More Cells led to more fluorescence, but the effect was small. I found something! When I observed the cells afterwards with the microscope, I saw that they haven't been lysed. How can that happen? They incubated over an hour in triton X?

I guess that the triton was fine because also the virulance factors showed a signal loss. At the moment I feel like that the cells have changed, dispite the fact that they look like they should. Perhaps I should mention here, that this culture was startet about 3 weeks ago, the Inocolum was stored in liquid nitrogen. No abnormalities.

*The cellline was startet 3 weeks ago. I guess the cells have been splitted now for about the sixth time.


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Is it possible to conduct scientific research without actually getting close to the sample/specimen?
For example, I have never get closed to a whale. The only source I have is research from who has get close to it. If I read their research and find a new thing, would my "discovery" be scientific? If yes, can you give some example of such research?
There is a related question in Philosophy SE: “Dinosaurs did exist once”. Is it knowledge or is it only justified belief? However this question is more about the knowledge directly produced by field researchers, while in this question I focus more on researchers who can only access secondary research. Plus that dinosaurs extincted, so in a sense I and a paleontologist are equal: neither of us can have direct experience to a living dinosaur. But whales are still living, and that equality is gone. So maybe the threshold for scientific research between a living organism and an extinct one is different?
Follow up questions:
• Is it possible to have a scientific review of a method if the author doesn't have direct experience of it? on Philosophy SE
• Can one have good understanding on a method without having direct experience with it? on Data Science SE
Meta question: Why are questions about whether research without direct experience is scientific or not subjective?

While interesting, I feel this question is not well suited for Biology.SE.  Any answers you receive will be necessarily subjective; re: What constitutes a scientific discovery? Is research conducted from second-hand data truly research?

@acvill I've considered asking on Philosophy or Academia, but I would like to have insight specifically from biologists. I suppose there are good subjective questions?

@user1136 does that discovery produce any falsifiable theory?

Would you consider the following scenario "close to"? If so, I can turn it into an answer and cite examples.  Say a data scientist reads a paper and contacts the authors for a collaboration. They collaborate to extract further insights from the data and eventually publish.

@Punintended yes, that can work. But if you have examples of having no contact or exchange with the one who has direct experience with it (perhaps they are dead), then it would be more convincing

To build on @Punintended's comment: you have immense amounts of publicly available data (see for example GEO Datasets) that anyone can download and analyze without any necessary interaction with the original authors.

Hard to answer but you can look into meta-analysis and see if that's appropriate or even feasible for whatever you're trying to do.

How close do you think astronomers get to the subjects of their studies?

@swbarnes2 one can argue that telescope is no difference to microscope

It depends on one's field - whether what you study actually requires first-hand knowledge of the experimental subject and the methods of dealing with or not. Moreover, one could invert the question and ask, whether a field, based solely on the knowledge of the experimental subject, can be considered science?
Theoretical physics/chemistry/etc.
In some sciences, such as physics, there is traditional division into experimentalists and theoreticians - the former are people who actually work in a lab, but who limit themselves to very basic statistical analysis of the phenomena observed. The latter are providing deeper, model-based, analysis of the data and description of the phenomena. Very often their work is not tied to any particular experiment, bordering on very abstract math. Looking at the list of the Nobel prize winners in physics one can easily convince oneself that this work is no less valuable than the experimental work.
Similar division exists in other fields, e.g., one can freely talk about quantum/theoretical/computational chemistry.
Computational biology, bioinformatics, biostatistics, epidemiology, population genetics
Although biology is relatively young science, the times when it was frowned upon by physicists as mere stamp collecting have long been gone: evolutionary theory and epidemiology have been put on a firm mathematical footing, and the explosion of genomic data in the last couple of decades has ushered in the professions of bioinformatician and computational biologist - all complete with designated job descriptions and advanced university programs. Less noticeable, but no else widespread is the observation using modern technology - such as video and sound recording - every conference features a few talks like this, related to swarms of insects, flocks of birds, or behavior of whales (incidentally, whales have been extensively studied in connection to tracing enemy submarines. The analysis of the data is often done very far away from the sea.)

All science is either physics or stamp collecting. - a quote attributed to Ernest Rutherford, but likely of even earlier origin.

Is it possible to have a scientific review of a method if the author doesn't have direct experience of it?

@Ooker could you clarify your point?


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Are drugs made bitter artificially to prevent being mistaken for candy?
All drugs I remember tasting (with the notable exception of Aspirin) have bitter taste. Is the taste due to the active substance, or is a bittering agent added to them, perhaps to prevent overdose?
Take Paracetamol for instance: adult pills taste bitter, while the syrup for babies is sweet without any noticeable bitterness. Or is the dosage simply so low that I couldn't distinguish the drug taste behind all that sugar they put in?

Why do you think aspirin doesn't taste bitter?

Not sure why Dmitry said it, but I know that some Ibuprofen (who many call "aspirin") are covered in a sort of 'candy shell' which is bit sweet to my senses as well. I've never had Acetaminophen that were coated, but I use the Ibuprofen that is coated specifically because I don't have to rush the chaser to get the taste out so fast.

Or perhaps he's only used that expensive coated brand, instead of the generic stuff.  So he's never actually tasted the aspirin.

I've seen paracetamol confused with aspirin, not ibuprofen with aspirin. Ibuprofen itself shouldn't be tasted, since it's usually either shelled or in a liquid-cap for good reason @coblr

@jamesqf Because I tasted it. Aspirin is an acid and has a typical sour taste.

@coblr, Not sure which part of my question you a referring to. The sweet paracetamol I was talking about was for babies, so it was certainly not in "candy shell", as babies cannot swallow pills without the risk of choking.

I’m voting to close this question because it is not about a problem in biology, but is solely about commercial/social marketing practice. It may possibly be relevant on SE Medical Sciences.

@Dmitry Grigoryev: Apparently your taste buds are more sophisticated, or perhaps I should say capable of greater discrimination, than mine are, because I certainly can't tell the difference.

@coblr you may be confusing Aspirin with Advil, which is a brand name for ibuprofen. Aspirin is acetylsalicylic acid

Sorry, I wasn't so much confusing it as I was just pointing out that many that don't know/could care less about the specific compound (including my wife) will call Advil an "Aspirin" in a similar way to how people call facial tissues a "Kleenexes", sodas "cokes" and vacuums, "Hoovers". I didn't realize that baby Aspirin had something extra or that, that's what was being referred to. It was just a reason I could think of for why a certain type of "Aspirin" may have been sweeter than expected. I didn't assume an adult was taking baby aspirin when it wasn't mentioned as such.

Short answer
A bittering agent may be applied to therapeuticals to prevent pediatric poisonings, but many drugs inherently taste bitter by themselves.
Background
Bitter taste is thought to have evolved as a way to decrease the risk of ingesting toxic substances, which may explain why many drugs taste bitter. In other words, classes of compounds that may harm the body often taste bitter (Menella et al., 2014). These include the often dangerous compounds like alkaloids and glycosides (source: University of Delhi). These include the familiar psychotropic compounds found in hallucinogenic plants, and the potentially deadly heart glycosides found in Digitalis species, respectively, among other classes of substances.
Paracetamol can be regarded as an alkaloid (Fig. 1), but not aspirin, as it lacks a nitrogen atom (Fig. 2). An alkaloid is defined as

any of a class of naturally occurring organic nitrogen-containing bases. Alkaloids have diverse and important physiological effects on humans and other animals. Well-known alkaloids include morphine, strychnine, quinine, ephedrine, and nicotine...

All of which are quite toxic. As cleverly noted in the comments, aspirin is not an alkaloid in its strictest sense, as it is not naturally occurring. However, it is chemically obtained by acetylation of salicylic acid (Mund et al., 2016), as shown in Fig. 2. Both of the reactants in themselves are naturally occurring; salicylic acid can  be sourced from willow bark, and acetylation is a widely occurring biochemical reaction (Gibbs, 2017).
I myself have never had the chance to taste aspirin, unfortunately (although I performed the acetylation shown in Fig. 2 for my Organic Chemistry class :-). Originally, aspirin was developed from salicylic acid (Fig. 3) just because the taste of salicylic acid was so bitter. Acetylation diminished the bitterness, yet the anti-inflammatory action remained (Wu, 2000)). Besides reducing bitterness by chemical modification, masking the bitterness of drugs with, e.g.., sweeteners, can help to overcome the aversion to the bitter taste. This can aid in helping patients, especially pediatric ones, to take their medicine and adhere to their treatment regime (Chauhan, 2017).
Reversely, coming back to your question, adding bitter-tasting additives to drugs indeed seem to be an effective way to reduce pediatric poisonings (Menella et al., 2014)
References
- Chauhan, J stem cell Bio transplant (2014); 1(2): 12
- Gibbs, Trends Plant Sci (2015); 20(10): 599–601
- Menella et al., Clin Ther. 2013 Aug; 35(8): 1225–1246
- Mund et al., J Occup Med Toxicol (2016); 11: 32
- Wu, Circulation (2000); 102: 2022–3

Fig. 1. Paracetamol, or acetaminophen. source: Wikimedia Commons

Fig. 2. Synthesis of Aspirin, or acetylsalycilic acid, from salicylic acid. source: Imperial College, UK

I recall an advert in the 90s advertising a form of aspirin "without the aspirin taste" - it showed a bunch of people taking aspirin dissolved in water, screwing up their faces.  I also recall experiencing the same.  I can't find the advert anywhere however, and I haven't taken aspirin in years.

Interesting read: The importance of taste in pharmaceutical development but that yummy chewable baby aspirin now seems somehow evil...

@RossPresser Notably, nowadays aspirin is the last thing you want to give to a kid because it might cause brain damage.


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How do frogs fight?
I've seen a video in this link, where two frogs fight. One of commenters asks

How...exactly...does one establish dominance in their world? I mean, they’re fat, slippery, no claws, their teeth are practically vestigial, they are hard to drown—although it is possible—so...how does one frog or toad kick another’s ass?

And this is exactly my question

Some frogs do have claws. Also, frogs have a hard lip with sharp-ish tooth-like ridges on them. I've been bitten by frogs before, it can hurt...

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Also, as is made clear from MattDMo's comment and answer, this question is probably too broad and we'd almost certainly expect different species to behave differently.

I found this article ([free PDF on ResearchGate) from 1989 in Behavioral Ecology and Sociobiology entitled "Fighting, assessment, and frequency alteration in Blanchard's cricket frog". The author analyzed the sound wave frequency of the frogs' dominant call to see if it negatively correlated with fighting. In other words, were the frogs with deeper calls better fighters, and did other frogs use that to decide whether or not to fight?

 Larger frogs have deeper calls, and smaller frogs tended to retreat from broadcasts of a synthetic low frequency call, which indicated a large male. In contrast, frogs attacked a high-pitched call, which indicated their "opponent" was smaller. He also found that small frogs modulated their call to appear bigger to their opponent – they bluff.

Fighting (which was apparently only between males) was initiated when one frog was calling and another nearby kept calling after a series of calls from the first that were increasingly aggressive. The first frog would search for his opponent, and

When contact was made, a male moved onto the dorsum of his opponent and attempted to grasp the lower male with his forelimbs. Contact rarely lasted for more than a few seconds and was terminated by the lower male jumping away. Such wrestling bouts were followed by another period of aggressive calling, continued wrestling, [and terminated] by either retreat or satellite behavior by one of the males. Wrestling contests were generally short, lasting from 1–18 s (N=15, $\bar x$=7.2, SE=1.42), and they were composed of from 1 to 6 bouts (N=9, $\bar x$=2.7, SE=0.58).

So, it looks like these particular frogs fight by wrestling until one of them either leaves or adopts submissive "satellite behavior". I don't know if this is representative of all frog species, but it sounds reasonable.


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Has anyone tried using functional near-infrared spectropathy to quantitively measure sodium concentrations in the brain?
Functional near-infrared spectropathy "fNIRS", is a biophysics/medical technique that uses the near-infrared part of the electromagnetic spectrum (around 680nm to 810nm in wavelength) to image the blood oxygenation level dependent "BOLD" effect in the brain to image brain function for more on BOLD look here. Recently, in 2018 a study was done link to study showing that High-field MRI could be used to functionally image sodium quantitively in the brain.
I'm wondering if the same thing (functional sodium imaging) can be done with fNIRS or an Infrared spectropathy type deal.
Does anyone know if this has been attempted?

How would you get near infrared through the skull?

@Chris take a look at this link


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Why certain COGs appears more often in Humans Bacteria but not in plants Bacteria
I'm doing a Bioinformatic project from the university where I  got a DB of COGS from Human & Plants Bacteria genomes and I need to find distinguishing sets in this DB and explain the biological reason behind these results. Unfurtinly my Biologi knowledge is very basic and I do not know how to explain the results so maybe someone here could help me.
Here are some of the distinguishing COGs I found and the known info about them:
Results for FreqItem: ['0049', '4465']
IG of FreqItem:  0.6682341035127484
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG4465;K;INFORMATION STORAGE AND PROCESSING;Transcription;GTP-sensing pleiotropic transcriptional regulator CodY;
Number of occurrences in Human Bacteria genomes: 63
percentage of genomes that carry it in Human Bacteria genomes: 25.0%
Number of occurrences in Plant Bacteria genomes: 4
percentage of genomes that carry it in Plant Bacteria genomes: 5.56%

Results for FreqItem: ['0049', '3833']
IG of FreqItem:  0.6952252521930348
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG3833;G;METABOLISM;Carbohydrate transport and metabolism;ABC-type maltose transport system, permease component;
Number of occurrences in Human Bacteria genomes: 109
percentage of genomes that carry it in Human Bacteria genomes: 43.25%
Number of occurrences in Plant Bacteria genomes: 8
percentage of genomes that carry it in Plant Bacteria genomes: 11.11%

Results for FreqItem: ['0049', '1847']
IG of FreqItem:  0.7334916442185917
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1847;R;POORLY CHARACTERIZED;General function prediction only;Predicted RNA-binding protein Jag, conains KH and R3H domains;
Number of occurrences in Human Bacteria genomes: 122
percentage of genomes that carry it in Human Bacteria genomes: 48.41%
Number of occurrences in Plant Bacteria genomes: 9
percentage of genomes that carry it in Plant Bacteria genomes: 12.5%

Results for FreqItem: ['0049', '1115']
IG of FreqItem:  0.6323046964671385
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1115;E;METABOLISM;Amino acid transport and metabolism;Na+/alanine symporter;
Number of occurrences in Human Bacteria genomes: 161
percentage of genomes that carry it in Human Bacteria genomes: 63.89%
Number of occurrences in Plant Bacteria genomes: 15
percentage of genomes that carry it in Plant Bacteria genomes: 20.83%

Results for FreqItem: ['4585']
IG of FreqItem:  0.3643909812004458
COG_INFO semantic description per each COG in the itemSet if exist:
COG4585;T;CELLULAR PROCESSES AND SIGNALING;Signal transduction mechanisms;Signal transduction histidine kinase;
Number of occurrences in Human Bacteria genomes: 118
percentage of genomes that carry it in Human Bacteria genomes: 46.83%
Number of occurrences in Plant Bacteria genomes: 49
percentage of genomes that carry it in Plant Bacteria genomes: 68.06%

Results for FreqItem: ['0049', '1006']
IG of FreqItem:  0.8034282332952798
COG_INFO semantic description per each COG in the itemSet if exist:
COG0049;J;INFORMATION STORAGE AND PROCESSING;Translation, ribosomal structure and biogenesis;Ribosomal protein S7;
COG1006;P;METABOLISM;Inorganic ion transport and metabolism;Multisubunit Na+/H+ antiporter, MnhC subunit;
Number of occurrences in Human Bacteria genomes: 50
percentage of genomes that carry it in Human Bacteria genomes: 19.84%
Number of occurrences in Plant Bacteria genomes: 23
percentage of genomes that carry it in Plant Bacteria genomes: 31.94%

Thank you for your time!

Bacteria in human and plants are adapted to different life conditions: different food and different environment. E.g., human gut bacteria are more likely to be anaerobic and adapted to processing organic food. So I would search in this direction (disclosure - I am not a biologist either.)

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Why is thymidine incorporation (DPM) normalized to per mg protein content while testing for cell proliferation?
Sorry for this naive question. After performing the thymidine incorporation assay to test proliferation, many papers report normalization of disintegrations per minute (DPM) to per mg protein content? What does this normalization or ratio of DPM to cellular protein content exactly signify?
Thanks in advance.

I'm not sure that there is a strongly disciplined reason for the mg protein content as the normalization, but there is obviously a need for some normalization for different amounts of tissue- if you use 10X as much tissue, you should expect DPM to be 10X as high!
For example, in this somewhat old paper, They normalize not to protein content but to wet tissue mass or to intestinal crypt count (as they are looking at incorporation in intestinal crypts). So the normalization that you observe is not universal (or more likely, is a more recent innovation). They observe that the cruder measure of wet mass provides a poor normalization:

Instead there was a positive intercept of dpm/mg tissue which represented about
25-30% of the maximal tritium content of the intestine. (abstract)

That is a good reason to use a more precise normalization! They find that the more precise normalization of dpm/crypt works better, presumably because the crypt is the incorporating tissue.
I would suspect that the dpm/mg protein is simply a more precise method for normalization.
A yet more precise method would be the one used in this 1987 paper, in which thymidine incorporation is estimated as dpm / microgram DNA- here, you are actually directly comparing to the mass of the DNA, which is where thymidine is incorporated. That is a more obvious normalization than protein content.
However, for crude tissue extracts I suspect that it is more straightforward to estimate protein content than DNA content. So protein content is used as a "good enough" normalization.


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What are the advantages of mRNA vaccines?
When the mRNA vaccines for COVID-19 are administered, mRNA molecules are introduced into the cells of the subject. The translation of this mRNA determines the productions of antigens, which in turn stimulate the immune response.
Wouldn't it be simpler to have this translation happen in vitro, and then inject the antigen into the subject's body? What are the advantages of making the translation happen in vivo instead?

Quick answer - typical protein-based subunit vaccines tend to produce a strong antibody response (humoral immunity), but not a very strong cellular response. By using an mRNA vaccine that produces the viral protein of interest (in this case the SARS-CoV-2 spike protein) in cells, a strong cellular response can be elicited in addition to the humoral response. This allows for the body's full defenses to be used against an infection right away. I don't have time to give an expanded answer right now, but I'll try to later.

see paragraph here: https://en.wikipedia.org/wiki/RNA_vaccine#:~:text=The%20benefit%20of%20using%20mRNA,COVID%2D19%20in%202%20days.


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Which animals can see (or feel) the Moon’s infrared radiation?
The luminosity (bolometric) of the Moon in infrared is several times greater that its luminosity in visible light. Moreover, it may be rather possible for the Moon to be obscured by some fog or haze which lets only the infrared radiation through. It is known that some snakes have “pit organs”, but the decent Moon’s infrared flux can, probably, be detected by something more crude. Can any other animal (than snakes) take benefit from its sensitivity to medium-wave infrared to see (feel) the Moon?

It is notoriously hard to find reliable information on the Moon’s infrared flux in Internet, although its density at Earth’s surface should be several µW/cm² (or tens mW/m²). My estimate is about 30 to 40 milliwatts per square metre under favorable conditions, which is probably not high enough to be detected with every pit organ (crotaline snakes are claimed to have threshold at about 107 mW/m²). Research on Agkistrodon contortrix (see graphs) states that 60 mW/m² and as little as 15 mW/m² (albeit not in infrared) produce a nerve response in receptors. On the other hand, pit organs are optimized for such localized and agile sources as small animals; some other sensory system might be more appropriate for nearly stationary sources producing more incident energy (heat).

Welcome. You seem to assume snakes can sense the moon by IR, but can you provide evidence that that is so?

@AliceD: probably not with every pit organ, but Ī̲ deem 90 mW/m² high enough to be felt by anybody claiming an excellent sensitivity. Some research on Agkistrodon contortrix (see https://journals.physiology.org/doi/full/10.1152/ajpregu.00024.2002#_i2 , graphs) states that 60 mW/m² and less (albeit not in infrared) produce a nerve response in receptors. Those having threshold at 110 mW/m² (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080012/ ) are probably not among most sensitive.

Please include that information in the question proper - it makes the post a lot more substantial. Thanks! Interesting question.

@AliceD: tried my best. Sorry for delay.


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Does the fact cordyceps mostly affect insects have something to do with chitin being polysaccharide?
This is just a conjecture of mine based on those observations:

Fungus seems to be very good at attacking tough chains of sugars like cellulose and starch.
insects are covered by Chitin, a polysaccharide.
cordyceps only attacks arthropods and in rare instances other fungus. Both arthropods and fungus have chitin in their body.

My initial guess was no but there might actually be some evidence for this. For example, host-switching between fungus and insects apparently happens within relatively small taxa of cordyceps, suggesting that host specialization is not too dramatic.
Moreover, there does seem to be some evidence that chitin is a relatively important metabolic input for at least one cordyceps species.
I don't know that we could say that chitin is the thing that allows the host switching or that it is the most important nutrient for cordyceps or anything like that, but it looks like it at least helps.
It's worth noting that ecological characteristics may play at least as large of a role. The phylogenetic study noted that host switching likely occurred from cicada nymphs (which hibernate underground) to truffles (which have their main mass underground), so it's possibly just an opportunistic jump in the soil environment.
It would be interesting to see if there is a "chitin sensor" mechanism in cordyceps that yields a signal to cordyceps that there is a host to invade. But I don't think that I saw anything that suggests that (though it's far from unprecedented in biology).


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How does blood reach skin cells and other closely packed cells?
When I see diagrams of cellular structures such as the layers of the skin, these diagrams show the cells as being closely packed together. For example here is a typical such diagram:

So, it shows the capillaries of the vascular system going only to the bottom of the many layers of tightly packed cells. So, I assume that all the cells need oxygen, so they all need to be in contact with the blood cells that bear oxygen, so how does this happen? Obviously each individual cell can't have its own personal capillary. If blood were to be released just loosely around the cells that would not work either because the blood would have no way to get back. All the blood has to be in vessels of some kind so it can circulate. But these vessels are not shown as reaching the upper skin cells in any way, so how are those cells getting oxygen?

Would you be interested in "plasma" defined as blood minus erythrocytes, and plasma being pulsed around cells as "interstitial fluid", then reabsorbed into blood stream? This interests me, and I'd be willing to elaborate in some answer.

The skin is highly vascularized up to the epidermis, with dense vessels right at the top of the dermis (your picture omits these, but you will find them in better diagrams like this one). The epidermis itself gets substantial oxygenation from the outside air (see Stücker et al, for example), though the very outermost layers are not metabolically active ("dead") and do not require oxygen.
As a gas, oxygen moves quite well through tissue, and cells can get sufficient oxygen from sources up to a few hundred micrometers away. No need to be in direct contact with blood cells (and typically no tissues of the body are in direct contact, besides vascular endothelial cells that line all blood vessels). Many small animals have no need for a circulatory system because their entire body is close enough to the outside for gas diffusion.

Stücker, M., Struk, A., Altmeyer, P., Herde, M., Baumgärtl, H., & Lübbers, D. W. (2002). The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. The Journal of physiology, 538(3), 985-994.

What is the largest "small animal" which doesn't have a need for a circulatory system?  (Approximately, to an order of magnitude, I'm just trying to get a feel for how much depth you're talking about.)

@davidbak Flatworms and roundworms are probably a good place to start. Some of these can be quite large (some flatworms can be meters long) but in that case they are also quite thin. Jellyfish, too, can be quite large but their bodies are also quite thin despite the space they take up; they also don't have a lot of metabolic need.

It's also worth noting that the ~15-60 most superficial layers of keratinocytes (epidermal epithelial cells) are not metabolically active (i.e., "dead") and therefore do not need to receive nutrients/gasses or eliminate wastes. Therefore, exchange with blood is not needed beyond 10-15 layers of "living" epithelial cells in the deeper epidermal strata.

The deeper, active strata are approximately 20-100 μm thick 1, which is within the "few hundred" μm range for interstitial gas exchange that @BryanKrause mentions in his answer.

See here and here for more info.

 Modified From: wikimedia

Citations:
 1. Olatunji, O. and D.B. Das. 2011. "5.48 - Drug Delivery Using Microneedles." Pages 625-642  in Moo-Young, M., editor. Comprehensive Biotechnology (Second Edition), Academic Press, ISBN 9780080885049.

Ok, so you are saying that the oxygen just diffuses out of the hemocytes through multiple layers of cells? What about nutrients, can nutrients diffuse the same way? I guess my question applies to muscle as well as skin. Like when I eat say a chicken breast, I don't see any blood vessels in the chicken breast.

@ImprisonedRhesus My post is really more of an extension of BryanKrause's answer and is only meant to point out the anatomy of the skin (i.e., that superficial layers aren't alive). I wasn't gong to extend my post with further physiology (e.g., interstitial exchange and transport) due to current personal time constraints. I hope someone else can provide you an adequate response in a separate answer

@ImprisonedRhesus Also, I would keep your question focused on skin here. If you're interested in muscles or tissues more generally, it might be worth taking what you've learned here and asking another question that builds from this one.


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What is neutral theory of evolution?
The question is not about the very basics, but more about where the line separating the neutral theory from the rest of population genetics lies.
One often reads/hears claims that "the findings of the neutral theory are still disputed" or that "there's no experimental proof for its validity". It is hard to accept these claims wholesale, since:.

It is hardly in doubt that some mutations are neutral
It is hardly in doubt that neutral or even slightly deleterious mutations may fix in the population due to genetic drift, or that beneficial mutations may fail to fix for the same reason.

I therefore interpret such statements as attacks on specific points of the neutral theory, or its most sweeping claims (e.g., that most mutations are neutral), or perhaps as attacks on specific meaning of the term. Moreover, such wholesale rejection seems to ignore that the theory may have very different degrees of validity for different organisms (say, more likely to be true for RNA viruses than for mammals).
I will appreciate clarifications of these points.
Update
Here is an article that raises several issues regarding the applicability of the neutral theory framework to bacteria: Neutral theory, macrobial practice: challenges in bacterial population genetics

I don't often read or hear these claims, but maybe I don't read the correct references.  Are these claims being made by population geneticists? Can you provide a few links?

@BenBolker It recently surfaced quite forcefully in the comments to my answer to another question in this community: https://biology.stackexchange.com/a/97296/59521 There's a more cautious statement in the Gellespie's little book (that the neutral theory is not generally accepted), and I remember reading in more recent reviews that the debate between the proponents of the neutral theory and the neo-darwinists is not over.

@BenBolker this is a very good way to think about it! Thanks.

@BenBolker I think that does deserve to be an answer

A short answer (converted from a comment): I would call neutral theory a useful null model: in particular, it may be less important that it be a factually correct description of natural systems (i.e. "most alleles can  be treated as being neutral (or weakly deleterious") than that it provides a useful standard for distinguishing which alleles are clearly behaving otherwise.
Satta et al (2018) say:

A decade ago, Crow (2008) viewed the then present status of the neutral theory of Kimura (1968) as a standard null model in evolutionary genetics: “Vast regions of the genome are near enough to being neutral for neutrality to be assumed. In fact virtually every study of molecular variability, evolutionary rates, and coalescence is based on this assumption.” At the same time, since he knew Kimura’s devotion to the theory, he felt irony when seeing that reduced neutral variation around a focal site often provided the strongest evidence for selection acting on the site.

In contrast, Gillespie (1994) says (see here):

... we can conclude that both [silent and replacement mutations] are undergoing the same brand of neutral evolution. There cannot be one neutral theory to accept or reject.
The case for neutrality of replacement subsitutions seems particularly weak ... In my view, the neutral theory must be abandoned for replacement substitutions.
Silent substitutions, on the other hand, may well be neutral, although the evidence at the time of this writing is incomplete ... patterns of codon usage and GC% evolution imply that at least some of the silent variation is moderately selected ... we cannot rely on statistical procedures that assume that silent variation is weakly selected and at equilibrium ...

Gillespie, John H. The Causes of Molecular Evolution. Oxford University Press, 1994.
Satta, Yoko, Naoko T Fujito, and Naoyuki Takahata. “Nonequilibrium Neutral Theory for Hitchhikers.” Molecular Biology and Evolution 35, no. 6 (June 1, 2018): 1362–65. https://doi.org/10.1093/molbev/msy093.

Your question would deserve a long essay. R.C. Lewontin wrote a book ("The genetic basis of evolutionary change" - Columbia U.P) on this subject in 1974, right after the neutral theory had been explicitly formulated in the previous few years. The reasons for the controversy over this theory are still alive some 50 years later, despite the enormous advancements in DNA technology. For example the not so hidden polemical tone of this recent paper would not be understandable if some profound ideological issues were not involved; these issues involve something more than "attacks on specific points of neutral theory, (...) or perhaps as attacks on the specific meaning of the term".
In essence, Lewontin argues that the neutral theory has its philosophical roots in the Platonic notion of "ideal" or "type", for which real objects (the genes, in the present case) are only imperfect approximations. This view, applied to the genetic variation in animal species, implies that the role of natural selection is mainly “purifying”, that is, it acts by removing the slightly deleterious mutations that happens continuously and degrade all genomes (when mutations are perfectly neutral, selection does not act at all). As Kimura and Ohta have said, quoting Muller, “the gene through the long course of evolution has finally found itself in man” (quoted in Lewontin, above, p. 30).
The opposite view (can we refer to it as Democritean?) sees all natural populations, man included, as being continuously modeled by unstable and ever-changing environments, so that any attempt to define an “optimum” is intrinsically meaningless. Genomes are highly integrated pieces of firmware, but they are much more fluid, over the generations, than once thought. This means that all genetic variation may have or may acquire meaning, as their molecular or ecological context changes.
Consider an applied consequence of the two views. One of the claims of most anti-racist geneticists is that the variance component among populations of gene frequencies is much higher than the component within populations; this allegedly falsifies the racist argument according to which the differences observed among human population (races) are mostly genetically determined. But if you claim that most of that genetic variation is irrelevant (“neutral”), what remains are the genes responsible for the differences in phenotypic traits, and it becomes obvious that the variance component among populations in the frequency of these genes is lower with respect to the component within populations; and this may be interpreted as supporting a racist view.
It is not automatic that scientists who prefer one theory to the other also support the philosophical implications of that theory. However, the dispute about the neutral theory of evolution cannot be understood without reference to the above conceptual basis.

This is an extremely interesting prospective! This is not what I had in mind when asking the question, but it does give food for thought. Thanks!

Also, thank you for the references to Lewontin and the Jensen et al.


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What is the significance of the phospholipid bilayer being two-dimensional?
I'm wondering about the significance of the phospholipid bilayer being a two-dimensional fluid.
I found this powerpoint:
I also found that thetwo-dimensional fluids have limited degrees of freedom.
My question is the following: if you can please explain two-dimensional fluid, please explain the/a/any proximate cause for why the fluid is two-dimensional as opposed to 1 or 3 dimensional.
I'm guessing that based on the powerpoint I found that the limited freedom of movement is optimal for the purposes of the phospholipid bilayer in, let's say, a human brain cell, as having too much freedom in a 3-dimensional fluid would be bad in some way (break apart???), or a 1 dimensional fluid would be bad since fluidity is important for the addition or removal of membrane proteins.
Sincerely,
Carlton III
Edit:
I realized after reading The fluid-mosaic model (Singer and Nicholson, 1972) and Revisiting the fluid mosaic model of membrane structure, I realized that I did not have a basic understanding of the thermodynamic principles espoused in Singer’s article.
So, after combing the internet, I found an essay by Erwin Schrodinger titled “What is Life.” I’ve been reading, and this passage seemed relevant to my question about the significance of the phospholipid bilayer.
“PHYSICAL LAWS REST ON ATOMIC STATISTICS AND ARE THEREFORE ONLY APPROXIMATE
And why could all this not be fulfilled in the case of an organism composed of a moderate number of atoms only and sensitive already to the impact of one or a few atoms only? Because we know all atoms to perform all the time a completely disorderly heat motion, which, so to speak, opposes itself to their orderly behaviour and does not allow the events that happen between a small number of atoms to enrol themselves according to any recognizable laws. Only in the co- operation of an enormously large number of atoms do statistical laws begin to operate and control the behaviour of these assemblies with an accuracy increasing as the number of atoms involved increases.”
—Schrodinger
It was here that I realized that a higher number of atoms allowed not only for statistical laws to control the behavior of the assemblies, but that the higher amount of smaller parts created a recognizable pattern that conforms to the laws of statistics.
At first glance, It doesn’t matter how large or small the parts are, what matters is how they compose a larger whole due to their behavior, and the behavior is determined by their properties.
Maybe atoms are the “smallest” parts because less surface area allows for more powerful and simple properties. And in relation to biology, more complexity is added to the larger “wholes” that are made of smaller parts.
A single Atom is simpler than a single cell by virtue of cells being comprised of many atoms.
Another thing Schrodinger wrote is this:
“ An entire newcomer should not expect to obtain from the following few pages a full understanding and appreciation of the subject, which is associated with the illustrious names of Ludwig Boltzmann and Willard Gibbs and treated in textbooks under the name of 'statistical thermodynamics'. If you fill an oblong quartz tube with oxygen gas and put it into a magnetic field, you find that the gas is magnetized. The magnetization is due to the fact that the oxygen molecules are little magnets and tend to orientate themselves parallel to the field, like a compass needle. But you must not think that they actually all turn parallel. For if you double the field, you get double the magnetization in your oxygen body, and that proportionality goes on to extremely high field strengths, the magnetization increasing at the rate of the field you apply. This is a particularly clear example of a purely statistical law. The orientation the field tends to produce is continually counteracted by the heat motion, which works for random orientation. The effect of this striving is, actually, only a small preference for acute over obtuse angles between the dipole axes and the field. Though the single atoms change their orientation incessantly, they produce on the average (owing to their enormous number) a constant small preponderance of orientation in the direction of the field and proportional to it. This ingenious explanation is due to the French physicist P. Langevin. It can
be checked in the following way. If the observed weak magnetization is really the outcome of rival tendencies, namely, the magnetic field, which aims at combing all the molecules parallel, and the heat motion, which makes for random orientation, then it ought to be possible to increase the magnetization by weakening the heat motion, that is to say, by lowering the temperature, instead of reinforcing the field”
—Schrodinger
By lowering the temperature, you lower the environment’s resistance to the behavior of the assembly of oxygen. By doubling the environment, you double the behavior of the assembly of oxygen.
Likewise, maybe, through optimal conditions and or more and more atoms, you are able to increase the output of the behavior that is controlled by statistical laws.
Finally, maybe, the phospholipid bilayer is but one step towards a more complex system. From atoms to molecules, to a whole cell... and optimal conditions or more atoms increase the likelihood of life, from the simplest to the most complex.
Of course, I have no idea what kind of conditions would allow a transition from let’s say a fish to a reptile.
Edit2: So basically, the bilayer being a two dimensional fluid is a function of the distinct parts of the bilayer conforming to statistical laws to create a more complex system by necessity.

My reading of the slide is that the author is just repeating himself for emphasis. He explains how proteins are able to move about in a lipid bilayer. Then he uses a physico-chemico description of the lipid bilayer adding that this is "crucial". The reason the author regards it as crucial is because it allows proteins to move about. So there doesn't seem to be a question, unless you want to know why proteins have to be able to move about in membranes. If that is your question, do ask it. (Oh and please finish the [Tour]).

this may be what you are looking for https://www.youtube.com/watch?v=Ym3mTa5WEOY

The cell membrane is a two dimensional fluid because individual molecules can move freely in 2 dimensional plane but not in three dimensions. in this image phospholipids can move left and right and in and out of your screen but they are not free to move up or down.

This is true becasue each phospholipid has a polar and non polar end, the similar ends are attracted to each other but the dissimilar end repel each other, making the membrane sheet like layout one of the only chemically stable layout for significant numbers of them. if a phospholipid tries to move up or down (in or out of the cell) the other molecules around it repel it pushing it back into place, meaning it requires a great deal of energy to disrupt this layout.
It is a two dimensional fluid because, while in water it behaves in the following way.  To use the existing image, if a phospholipid moves in or out of the screen or to the left or right, the repelling parts of the molecules have not moved closer to their opposite part on other molecules so the can freely move in this way, that is 2 dimensions of movement. If however they try to move in the third dimension (up and down on the image) they cannot becasue the hydrophobic (nonpolar) ends of one phospholipid would have to approach the hydrophobic (polar) end of other phospholipids and move away from the hydrophobic (nonpolar) ends of other molecules both of which are energetically unfavorable (that require a lot of energy to do). likewise the hydrophilic ends are attracted to water (which is also polar) while the hydrophobic ends are repelled by water. So unless a tremendous amount of energy is put into the system they will stay in this arrangement, you can disrupt it with enough heat, which is one of many reasons enough heat will kill organisms.
All these behaviors are import for the many functions plasm membrane fulfill, most importantly as a barrier that can stop some molecules from passing through it and allow others, while still being flexible and self repairing.
This is actually difficult to explain with static images, if you are still a little fuzzy on the details try this video, it shows the full range of movements I am talking about. It is actually difficult to find material that goes into this part of the fluid mosaic model so I don't blame you for having problems.

Compartments
A two-dimensional fluid like structure, like a phospholipid bilayer, can generate closed surfaces that can envelop an entire region of space. This is what allows life to compartmentalize, to create separate pocket environments that are set apart from their surroundings. A single compartment generated by a single bilayer folding in on itself is what is called a liposome. A non-2D variant of a liposome would be a micelle.
A micelle is formed by surfactants (things that are like phospholipids, with a polar group and a non-polar tail) with a single fatty-acid chain such that they can't form bilayers. Instead, a sheet of micellar surfactants, when surrounded by water, close in on itself with the fatty acid towards the interior of the micelle, away from the water.

The two things might look the same, by they are not. Micelles have an inner chemical environment very different from their outer environment. Whereas micelles are surrounded by water, like liposomes, their inside is strongly hydrophobic. Only the polar heads of the surfactants in a micelle act as a surface, but the entire structure is solid and filled. When micelles assemble, they pack like a solid sphere.
Contrast that with the 2D character of the bilayer in the liposome. The bilayer acts as a boundary between an inner aqueous compartment and the outside, also aqueous. The two compartments can be kept separate even if their chemical nature is pretty similar.
The most important application of this property is that a cell can become insulated from its environment. But this is useful in all sorts of compartments inside the cell such as the maintenance of electrochemical gradients across the inner and transmembrane spaces in mitochondria, or the upkeep of specific control systems inside the nucleus.
Besides this property of working as a boundary without disturbing the interior, the fact that the membrane acts as a two-dimensional environment in an of itself means that stuff can diffuse laterally through the membrane without having to go through the interior of its inner compartment. This allows the cell to have specific arrays of proteins and glycoside-bound phospholipids freely diffuse through the membrane, controlling access and proving sensory perception of the outside without disturbing the ongoing chemical work inside the cell or any of its compartments.
I am not sure if this is the relevant information that the slide's author was referring to, but it striked me as a pretty big deal. So there you have it.
Also, welcome to Biology SE!

So, why wouldn’t it work if the proteins were fixed in position in the bilayer? The question was not about how the bilayer works as separating membrane, but about dimensional fluidity. (Also, answers are to questions, not people, so that personal remarks are not appropriate. Once a question has been posted, ownership is to the list, who can improve it or reject it. That is why We restrict personal remarks such as welcome to comments.)


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

Initial spike protein priming by transmembrane protease, serine 2 (TMPRSS2) is essential for entry of SARS-CoV-2.After a SARS-CoV-2 virion attaches to a target cell, the cell's protease TMPRSS2 cuts open the spike protein of the virus, exposing a fusion peptide in the S2 subunit, and the host receptor ACE2. After fusion, an endosome forms around the virion, separating it from the rest of the host cell. The virion escapes when the pH of the endosome drops or when cathepsin, a host cysteine protease, cleaves it. The virion then releases RNA into the cell and forces the cell to produce and disseminate copies of the virus, which infect more cells

What happens next? Can this cell stop to produce the virus and start to divide ?
For example this article (SARS-CoV-2 RNA reverse - transcribed and integrated into the human genome) suggests that virus also inserts its portion into DNA so the person can have PCR-positive tests even if "no replication - competent virus was isolated or spread from these PCR-positive patients".

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

Comments are not for extended discussion; this conversation has been moved to chat.


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Why is neuronal firing rate proportional to axonal diameter?
I know that a larger axonal diameter results in faster speed of action potentials due to reduced resistance. However this doesn't explain why the firing rate of neurons is proportional to neuronal diameter. Is it because higher spike rates require larger capacitance (since each spike charges the neuron) meaning a larger surface area and diameter of neuron is needed?

Can you quote a source for firing rate being proportional to diameter?

Principles of Neural Design (Simon and Laughlin), chapter 3 page 54. Also https://pubmed.ncbi.nlm.nih.gov/19525561/ (Balasubramanian, Sterling 2009)

Also a short quote from each and edit into your question please (comments are meant to be temporary).


text:
How do we regulate the production of proteins when designing plasmids?
I think it should be no surprise that I, as many others, am interested in the new COVID-19 vaccines being developed. In my region of the world there are two mayor candidates. One is mRNA based and one is, as far as I understand, plasmid based.
I have a passable understanding of the mRNA based vaccine.
I also know what a plasmid is, and how it is transferred between cells, but my understanding is otherwise limited.
As far as I understand we want the plasmid to be "unlooped" and grafted onto our target cells DNA. This, as far as I reckon, should enable the cell to produce whatever protein the plasmid coded for. In vaccines this lets us device anti-measures (vague because of my lack of knowledge) against the virus... But, how do we regulate the production of these anti-measures? Can we include a "regulator" for the production in the plasmid, so that the modified cells only produce the proteins when the virus is present? Or do we just let the cells continuously produce the anti-measure proteins, regardless of their necessity?
My main interest here lies in where the permanency of the vaccines induced changes lie. With the mRNA vaccine I understand that the permanency lies in the regulated immune system, with other cells being otherwise unchanged after the mRNA decomposes. Regarding the DNA/plasmid vaccine I'm still unwise.
Thank you for your time, and happy holidays.

The DNA vaccine does not "graft onto the target cell's DNA" or change its genome in any way whatsoever. That's a common misconception and line of attack for anti-vaxxers, and is completely false. Nothing personal against you, I just wanted to emphasize that fact.

Thank you. Can you elaborate on what it does do instead? My question stems from the fact that it is hard for me to find information on this subject on the internet, and while I appreciate your negation of my false understanding, it is in not the negation alone I seek but a correction which includes the correct understanding.

I was waiting for someone who had the time to flesh out a real answer, and I'm still hoping someone does, but the quick and dirty answer is that all expression plasmids have an upstream regulatory sequence (before the protein-coding region starts) that includes one or more promoter elements. These elements attract and bind cellular transcription factors which help initiate transcription of the coding region, which is then translated into protein. Typically this process happens continuously until the plasmid is eventually degraded - it doesn't depend on the presence of virus.


text:
What happens if a circulating naive B cell is met with a polysaccharide/lipid antigen?
These antigens should provoke a T-independent response, so will they differentiate then and there to form short-lived plasma cells?
Or do they have to go to lymphoid tissue, enter a B follicle, and then differentiate?
and can they differentiate into short-lived memory cells and short-lived plasma cells? Or only the latter?

Depending on the class of the antigen, B cells can be activated via different mechanisms. T-independent (TI) immune response can be induced by two types of antigens, namely TI-1 and TI-2 antigen (1).
TI-1 antigens are mostly lipopolysaccharides (1). They activate naive B cells by directly binding to the Toll like receptors expressed on the surface of B cells. Binding induce proliferation and differentiation into effector B cells, which secrete antibodies against particular antigen (2). Eventually, most of these effector B cells will mature to become large plasma cells. Most plasma cells will die within a few days, but some can survive in the bone marrow for months or years and continue to secrete antibodies into the blood (2).
TI-2 antigens include polysaccharides, glycolipids, and nucleic acids (1). They have no intrinsic B-cell-stimulating activity and activate B cells via repetitive cross-linking of membrane immunoglobulin receptors. Such activation has only been found in mature B cells, meaning that they won't activate a naive B cell (3).
Resource
(1) Cruse J, Lewis R, Wang H. Immunology Guidebook. 1st edition. Academic Press; 2004. ANTIGENS, IMMUNOGENS, VACCINES, AND IMMUNIZATION. Available from: https://www.sciencedirect.com/sdfe/pdf/download/eid/3-s2.0-B9780121983826500261/first-page-pdf
(2) Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. B Cells and Antibodies. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26884/
(3) Janeway CA Jr, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. B-cell activation by armed helper T cells. Available from: https://www.ncbi.nlm.nih.gov/books/NBK27142/