text:
Will proper autoclave treatment really "inactivate all resistant bacterial spores"? If not, how widespread are autoclave-resistant bacterial spores?
Wikipedia's  says:

A widely used method for heat sterilization is the autoclave, sometimes called a converter or steam sterilizer. Autoclaves use steam heated to 121–134 °C (250–273 °F) under pressure. To achieve sterility, the article is placed in a chamber and heated by injected steam until the article reaches a temperature and time setpoint. Almost all the air is removed from the chamber, because air is undesired in the moist heat sterilization process (this is one trait that differs from a typical pressure cooker used for food cooking). The article is held at the temperature setpoint for a period of time which varies depending on what bioburden is present on the article being sterilized and its resistance (D-value) to steam sterilization. A general cycle would be anywhere between 3 and 15 minutes, (depending on the generated heat) at 121 °C (250 °F) at 100 kPa (15 psi), which is sufficient to provide a sterility assurance level of 10−4 for a product with a bioburden of 106 and a D-value of 2.0 minutes. Following sterilization, liquids in a pressurized autoclave must be cooled slowly to avoid boiling over when the pressure is released. This may be achieved by gradually depressurizing the sterilization chamber and allowing liquids to evaporate under a negative pressure, while cooling the contents.
Proper autoclave treatment will inactivate all resistant bacterial spores in addition to fungi, bacteria, and viruses, but is not expected to eliminate all prions, which vary in their resistance. For prion elimination, various recommendations state 121–132 °C (250–270 °F) for 60 minutes or 134 °C (273 °F) for at least 18 minutes. The 263K scrapie prion is inactivated relatively quickly by such sterilization procedures; however, other strains of scrapie, and strains of Creutzfeldt-Jakob disease (CKD) and bovine spongiform encephalopathy (BSE) are more resistant. Using mice as test animals, one experiment showed that heating BSE positive brain tissue at 134–138 °C (273–280 °F) for 18 minutes resulted in only a 2.5 log decrease in prion infectivity.

The statistical discussion of "sterility assurance level" and "bioburden" already seems to preclude any possibility of absolute certainty, such as "...all resistant bacterial spores..."
Question: The research cited in Is it known how some heat-resistance Bacillus spores repair their DNA after having been heated to 420 °C? (see below) shows an abrupt transition between 420 and 430 °C. Can we therefore assume that the sentence "Proper autoclave treatment will inactivate all resistant bacterial spores..." is just plain wrong If so, just how widespread are autoclave-resistant bacterial spores?
Related: Why do we use an autoclave at 121°C (250F)? (Origin)

The 2018 Extremophiles paper: Beladjal, L., Gheysens, T., Clegg, J.S. et al. Life from the ashes: survival of dry bacterial spores after very high temperature exposure. Extremophiles 22, 751–759 (2018). https://doi.org/10.1007/s00792-018-1035-6 (also downloadable from researchgate).

Turns out no, though repeated autoclaving does: here

@bob1 that's excellent, thanks!

I assume that this question stems from this recent Q&A on Space Exploration?

@MichaelSeifert if you check my previous Biology SE question I've linked to above "Is it known how some..." you can get the bigger picture; there are several.

Comment on "The research cited in Is it known how some heat-resistance Bacillus spores repair their DNA after having been heated to 420 °C? (see below) shows an abrupt transition between 420 and 430°C." An important distinction here is that this research was utilizing dry heat, while an autoclave utilizes heat from pressurized steam, which are quite different physical processes. Consider that boiling water and steam can scald human skin almost instantly at 100°C, but a brief exposure to dry heat over 250°C (i.e. reaching into a pizza oven) has almost no noticeable effect.

@MikeyC I knew there was something missing from my answer, but couldn't for the life of me work out what it was. If you don't mind I'll edit something in to my answer covering that aspect.

@MikeyC yes that's a really important distinction, thanks!

Bacterial spores in most contexts are properly called endospores, formed within the bacterial wall and are a survival mechanism, creating resistance to desiccation, heat and cold, with tolerances up to 150 Celsius (300 F).
The vast majority of bacterial spores studied are from Gram-positive species, that are medically relevant. These include organisms such as Bacillus anthracis (anthrax) and Clostridium species (colitis (C. difficile), food poisoning (C. perfringens), and tetanus (C. tetani)), which are significant pathogens of humans. The reason that they are studied is that sterility of equipment and items ued in medical settings, as well as in the food industry is a great way to prevent illnesses and not have patients getting sick in the hospital from nosocomial infections.
In the context of autoclaving, the temperatures, times and pressures have been worked out to inactivate the bacterial spores from these medically relevant bacteria, and are suitable for the vast majority of bacteria that people encounter in their every-day lives. These conditions work even for things like Mycobacterium tuberculosis, which are incredibly resistant to many of the ordinary disinfectants used in health-care settings and in the food industry.
However, there are whole classes of bacteria that survive under unusual conditions of high heat and/or high acidity or alkalinity. These organisms are known as extremophiles. It turns out that some of these are quite resistant to autoclaving, as one might expect. It seems that they are resistant to up to 3 standard autoclave cycles and some other pretty extreme conditions:

Cultures of Desulfotomaculum sp. C1A60, D. kuznetsoviiTand D. geothermicum B2T survived triple autoclaving while other related Desulfotomaculum spp. did not, although they did survive pasteurisation. Desulfotomaculum sp. C1A60 and D. kuznetsovii cultures also survived more extreme autoclaving (C1A60, 130 °C for 15 min; D. kuznetsovii, 135 °C for 15 min, maximum of 154 °C reached) and high-temperature conditions in an oil bath (C1A60, 130° for 30 min, D. kuznetsovii 140 °C for 15 min).

While this is interesting, and a real problem for those working with them, none of these sorts of species are medically relevant (as far as I know, I would love to be proved wrong!), so the fact that these are resistant to autoclaving is not a problem for the vast majority of us.
As a note, language is inherently difficult and to be scientifically certain that something is so, is almost impossible. This is particularly so with bacterial species, where it is estimated that there are about a trillion species and we can culture only about 3250 of them, so for the rest we know next to nothing about how they grow, their physiology or anything beyond a genome. This means that we have no way of determining if autoclave resistant bacteria are actually found almost everywhere or if they are as rare as the proverbial hen's teeth.
Basically what I am saying is that the Wikipedia article is incorrect and imprecise in its use of language. If it had said something along the lines of "inactivates all medically relevant spore forming bacteria", then it would have been correct and much more precise.

"I would love to be proved wrong." I would prefer it if you were right and all medically relevant pathogens could be destroyed by autoclaving.

@WaterMolecule - I was talking about these extremophiles being medicallt relevant here, but since you raise it; which medically relevant bacteria aren't sterilized by autoclaving? Note that I deliberately didn't use the term pathogen. I know in terms of pathogens prions aren't generally destroyed, but they aren't bacteria, so not in the scope of this question.

It would be very difficult for extremophiles to be medically relevant, as the extreme conditions that they need to grow/reproduce are not going to exist in the human body. Therefore, even though we have not exhaustively sampled all extremophiles and can't be scientifically certain, we can make a pretty good logical argument that there is no reason for concern.

@CodyGray - my point entirely. Though we do have environments in the body that are highly acidic (stomach) where bacteria such as Helicobacter pylori can thrive. I think you could easily classify H. pylori as an extremophile and pathogen. There's also the gall bladder (alkaline), anaerobic environments (e.g. appendix, prepuce), dry environments (skin) and environments which undergo rapid changes in salinity and humidity (skin) - all of these are colonized by a range of bacteria that may or may not be pathogenic.

@bob1 I never thought about myself as a host for extremophiles (beyond H. Pylori), yikes!


text:
How does the hydrophobic amino acid fuse the corona virus with the host cell membrane?
I am reading the article How the coronavirus infects cells — and why Delta is so dangerous.
It describes the fusion process of the virus into the host cell as follows right above an animation demonstrating the process.

First, TMPRSS2 cuts a site on the spike’s S2 subunit8. That cut
exposes a run of hydrophobic amino acids that rapidly buries itself in
the closest membrane — that of the host cell. Next, the extended spike
folds back onto itself, like a zipper, forcing the viral and cell
membranes to fuse.

Is the hydrophobic property of the hydrophobic amino acid crucial for the burying into the closest membrane and folding back onto itself? What is the physics of this mechanism?

The way you pose your question is problematic. First you appear to be asking two questions, one of which you demand to be answered with “detailed physics”. If that is so you would seem to be posting on the wrong site, although another interpretation is that you require an explanation of the “hydrophobic effect” — chemical thermodynamics of proteins, covered in the introductory chapters of biochemistry texts such as Berg or Lehninger. If this is the case (and the obviousness of the answer — yes the hydrophobic nature is crucial — suggests so), your question comes under the category “homework”.

Your second question, which, if valid for this site, needs to be posed separately. Again, it is not sure whether you are familiar with proteolytic enzymes in general (use of the word "cut" suggests perhaps not) and the frequent activation of proteins by hydrolysis of peptide bonds. Even if you are, the phenomenon is widespread in RNA viruses because of their tendency to synthesize polyproteins (for reasons discussed elsewhere on this site). There are numerous articles on the effect of proteolysis on Covid spike protein, suggesting you are not searching in an appropriate manner. Why not?

As you hace accepted an answer that only addresses one of the questions, and as the second should have been posted as a separate question I have edited your question and removed it. I have also cut unnecessary material about homework questions etc. as this has been addressed and is not part of the question.

Hey, @David--while I appreciate the edit to remove the close vote discussion from the question, I disagree with removing the part about the cleavage initiating the process. The answer does address this (see paragraph beginning: "The cleavage of spike is crucial..."). While the asker did write separate sentences ending in question marks, they both describe the same process, as fusion does not happen without cleavage. The original way the asker formatted the question (without the ordered list) makes the most sense to me.

Happy to discuss this further in chat if you disagree! Just ping me and I can jump in. Will not edit in case you want to chat.

@David: Actually I was planning to say things along the same line as Luigi several days ago but had been really busy. I will raise my objection in details later.

@Luigi — I am away and only checking SE to respond briefly to direct messages. As far as I recall the first part of the question requires an answer that relates to the precise molecular details of proteolytic cleavage on the structure of the spike protein, an answer in which the latter is represented by a triangle does not do. Nor do I see anything in your answer that would seem irrelevant to the question as abbreviated. If you go ahead regardless I feel that will only diminish your answer, but on your head be it.

Interesting question! Yes, the hydrophobic amino acids are very important; they facilitate interaction with the hydrophobic (inner) portion of the lipid bilayer. A useful review focusing on the bilayer side that I'll reference throughout this answer is here: Mechanics of membrane fusion, doi: 10.1038/nsmb.1455.
(a) shows a model of two lipid bilayers fusing (minus protein contributions). Essentially, the spike makes this process thermodynamically favorable.

The hydrophobic residues are key because they are what enables the other end of the spike protein to interact with and deform the cell membrane. Here's a model of protein-mediated fusion from that same review (they emphasize that the deformation is key):

The cleavage of spike is crucial to initiate this process because the hydrophobic residues are not accessible/cannot interact with the cell membrane unless the spike has been cleaved. This works to the advantage of the virus, since if the spike is close enough to be cleaved by TMPRSS2, it's close enough to stab the membrane of the correct cell. A virus with hydrophobic residues that are always ready-to-go, in comparison, would likely fuse with a lot of random/off-target membranes of cells or vesicles that would not be permissive to viral replication.
Mechanisms of membrane fusion disparate players and common principles is a review paper.
A detailed discussion of the physics of this process is beyond the scope of this site, but here are some potential starting points (disclaimer: I am not a physicist):

Mechanics of membrane fusion/pore formation
Membrane tension and membrane fusion
The hydrophobic force: measurements and methods
Reconciling the understanding of ‘hydrophobicity’ with physics-based models of proteins

+1 and accepted. This is exactly the kind of answer I am looking for! Much appreciated!

I added one more physics reference that is more recent. Hope you do not mind.

(+1) But to avoid confusion: if we consider the lipid membrane a bilayer, the interaction is with the hydrophobic portion of the outer layer of the bilayer? (And this is due to the 'oil in water' (or hydrophobic) effect)

Release of S1 trimer should be what allows conformational changes of S2 whose transition to lower energy state curves the membranes (assuming the fusion peptide anchored into the host membrane). https://www.pnas.org/content/114/42/11157 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112261/ There is more than one spike trimer involved, curving the membranes at different points together induces a hole and fusion of the two membranes. But it is very difficult to be sure because CryoEM doesn't fit well with membrane stuffs and conformational transitions. @Hans

@reuns: I appreciate your technical point. Let me read the paper you link to and respond later.

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Appropriate cell lines to study depression
Short introduction
I'm studying depression from a biochemical point of view. My interest lies in the study of protein biomarkers and I was wondering which cell lines may be appropriate for this purpose. It is not important that the biomarkers occur in easily accessible tissue or matrices, as this is not the exploration of a new diagnostic method. Rather, it is important to obtain the most accurate information possible about protein expression in the neuronal environment, where depression is supposed to occur.
In my literature research, I came across two quite commonly used cell lines, both of which have their advantages and disadvantages. Let's have a look at them:
LCL cells
LCL cells are produced by infecting lymphocytes with the Epstein-Barr virus.
Advantages:

They are relatively easy to have produced individually, so it is perfectly possible to get cell lines from patients with a diagnosed depression and from patients that are very unlikely to be depressed.
They were already used for studying depression-related topics [1, 2]

Disadvantages:

LCL cells are not neuronal cells, which means that they might (and probably will) express a different set of proteins than neuronal cells.

SH-SY5Y cells
SH-SY5Y cells were subcloned from a cell line that was isolated from a bone marrow biopsy taken from a four-year-old female with neuroblastoma. The subclones were chosen such that individual cells with neuron-like characteristics were selected.
Advantages:

One could argue that SH-SY5Y cells are pseudo-neuronal cells, which is why they are commonly used to study neuronal diseases such as Parkinson's disease and other neurodegenerative diseases. [3, 4]

Disadvantages:

The cell line is not personalized, i.e., it's impossible to get cells from depressed and non-depressed patients, thus it's tricky to find biomarkers for depression, if you cannot compare a "healthy" with an "unhealthy" protein expression.

Question
Do you know any readily available cell line that could be used to find differentially expressed proteins in depressed subjects that is close to neuronal cells? Neuronal cells from the cerebrospinal fluid (CSF-contacting neurons) would probably be the best one could get from living subjects, but the setup of an approveable study and the recruitment of subjects that voluntarily accept a lumbar puncture is a bit tricky to say the least.

tl;dr there is no 'depression' cell line. Cell lines would be suited for studying pharmacology, cellular or molecular mechanisms, none of which are depression. Depression also has no good correlates on the molecular level which can be used as a proxy by virtue of using in vitro cell lines. For instance, you can use cell lines to study amyloid protein biosynthesis or clearance to better understand the proteostasis that occurs in neurodegenerative disease, which are thought to arise through aberrant proteostasis. But depression itself is poorly defined and is less characteristic than that on a molecular level, and I certainly don't know of any cell lines that can be used to study "differential expression of genes in depressed folks". You'd be better prepared by taking brain biopsies and even that would be very incomplete of a picture to begin a study.

Hi Sam. Really interesting idea, you certainly pose the question diligently. Do not be discouraged from thinking about such things following a read through my response. But... I think many first impressions here would include critical thoughts about how you formulate and think about the experiment.
Thus, I would challenge your question. First, depression is a syndrome, and is not very clearly defined, certainly not well at the molecular level. If you want to reduce depression to a mechanism study-able in cell lines, you first need to justifiably operationalize it somehow. This I think is very problematic already.
Additionally, depression does not occur at all in cell lines, or even between neurons in synapses, but rather (loosely speaking...) in vast, interconnected circuits, as its readout - symptomatology - are observable only as the output of entire nervous systems, in organisms. Depression is not caused by faulty enzymes as results of single mutations; they are very highly multi-faceted. As such, cell lines cannot be used as proxies. What cell lines can be used for is to study specific molecular interactions, say with how pharamaceuticals are metabolized, or which compounds may impact proliferation. However, here I quote a few things from one of your sources that jump out even during a quick skim read:

On the basis of the neurotrophic hypothesis of antidepressant’s
action, effects of antidepressant drugs on proliferation may serve as
tentative individual markers for treatment efficacy
Peripheral proliferation is unsuitable as surrogate marker for
antidepressant response
Although the in vitro treatment of patient-derived LCLs with fluoxetine presents high inter-individual variability regarding the LCL proliferation behavior, this phenomenon has—according to our data—no association with the patient’s clinical outcome.

The paper merely screened for differential expression in genes in white blood cells following fluoxetine exposure, and found only two candidate genes, SULT4A1 and WNT2B, which they have some reason to believe may be involved in drug metabolism, which were correlated to a donor clinical response and remission, respectively. This is a paper which suggests potential candidates for further study, but does not at all implicate or demonstrate any connection at all between depression or the efficacy of the drug, or the genes involved. It is meager in lieu of your question! The key here is that they compare cells before and after fluoxetine exposure, not that they are comparing depressed or non-depressed neural tissue. They tried to use remission to correlate things, but it just didn't work well. Which I think is expected!

Thank you for this very detailed answer. Reading your take on this gives the impression that you don't think that it's even possible to study depression in cell lines. This may be true if you want to correlate your findings with a clinical outcome but it's certainly not true if you're interested on the cellular level only. It's clear that depression is a very complex syndrome and I think that it's also safe to say that many factors play an important role here, but nevertheless there are multiple studies showing that subjects with a diagnosed MDD do show differentially expressed proteins. (1)

A polymorphism within the promoter region of the serotonin transporter gene (SERTPR) was thought to be a risk factor for the development of depression (Mandelli et al 2007). Significant associations have been described between single nucleotide polymorphisms in the FKBP5 gene and antidepressant response and recurrence of depressive episodes (Binder et al 2004). A polymorphism in the GNB3 gene was also found significantly more often in depressed than in healthy controls (Zill et al 2000). This shows that it's safe to say that there are proteomic differences in depressed subjects. (2)

We want to take this further by determining potential biomarkers for depression by bottom-up LC-MS analysis from neuronal cells to subsequently identify possible long-term risk factors, for example, long-term use of specific drugs. For this purpose, cells are needed that can be incubated with the drugs. (3)

As a counter-example to your opening sentence, see Lithium-responsive genes and gene networks in bipolar disorder patient-derived lymphoblastoid cell lines, published in Nature in 2016 (Lithium has been used as a very effective drug in the management of manic depression since the 1960s)

@Sam You can look for biomarkers in a cell line but how do you know they have anything to do with depression? Your cells won't be depressed. You can certainly study a gene of interest in a cell line, but still that cell line won't be depressed. The cell type you use probably doesn't matter much - HEK cells, primary neurons, whatever you want, they won't be depressed either, they will just express your allele of interest.

@BryanKrause That's absolutely right. That's why the LCL cells are so interesting. With them it is possible to get cells from a depressed and a non-depressed subject and to compare the protein expression in both (actually you'd obviously need more subjects in each group). This would then allow to correlate the differential protein expression with the clinical manifestation of a depression. But as depression is something psychological, I guess that neuronal cells are way more interesting than lymphocytes. (1)

@BryanKrause We have to remember that each cell type expresses a different set of proteins. I think that it's clear that neuronal cells are way more likely to show differences in their protein expression, that are in fact related to the manifestation of a depression, than those of lymphocytes do. That's why I was interested in different cell lines that may combine the neuronal aspect of SH-SY5Y cells and the easiness of individual production of LCL cells. (2)

@Sam Your question asked about cell lines, not about which cells to isolate from patients (and controls).

@BryanKrause Yeah, I wasn't clear enough in my explanation, I'll edit the question, but in short my problem is that I have to do both, search for biomarkers by bottom-up LC-MS (untargeted) and check whether or not these proteins are differentially expressed in normal, i.e., "healthy" cells when the cells are incubated over a long period of time with pharmaceuticals of interest. At least for the latter project, I'd need a cell culture to be able to incubate the cells with these substances.

Hi Sam - I see your points, cell lines can be relevant for depression research in some way. Interesting ways too. However, I side with @BryanKrause, you can only study correlates of depression with cell lines, not depression itself, and I am under the impression that you suggest you are using 'depression cell lines' as opposed to just looking at gene expression in unrelated cells following pharmacological treatments. Certainly there are some reasons why LCLs, but they are only convenience and approximation; as long as you are fully aware of (and open about) that, the science is fair game!

@sam A big problem I see in this is that the cells will change with culture, so correlates outside of the body will be different to those found inside the body, even if you could isolate cells from a depressed person, there is no guarantee that those cells will maintain the phenotype or that they are actually the "depressed" part. If you want truly neuronal cells you might try iPSC neurons, my understanding is that these are as close to true neurons as you can get without getting actual brain tissue.

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text:
Does a rapid cooling step improve pasteurization of medical equipment?
I learned that pasteurization consists of two steps: first heating and then rapid cooling. The rapid cooling was explained as "it's a thermic shock for the germs, so the ones remaining after the heating step will be definitely killed with this". But on Wikipedia, the rapid cooling is explained as being part of a step that protect food product and it is not mentioned for the medical equipment.
I am actually asking the question to find out the best solution for this situation: let's say I am in some remote undeveloped place and I need to disinfecting a piece of equipment (something akin to a medical equipment, not food). I only have hot water (between about 60°C and 80° C) and cool water (both of them are clean water) in clean containers (I also have soap and have washed the equipment with it before). Will it improve the disinfecting process if I do the rapid cooling step after the heating step or is it unnecessary? If yes what procedure is the best?

Because if you continue with the heat, you'll have (partly) cooked food?

Because the remaining bacteria (pasteurisation is not sterilization) will grow fast when it is warm.

@PolypipeWrangler, if it's to reduce the growth of the remaining bacteria, why isn't this cold phase mentioned for the medical equipment on the wikipedia page? is it an omission or it is really never used for pasteurizing equipment and only for food?

@MagTun because pasteurization is very different then sterilization. medical equipment is sterilized, the goal is to kill ALL bacteria.

@John but the Wikipedia mentions it for some medical equipment. Also what I have to pasteurize is not medical equipment only akin to, it doesn't need to be sterilized, just pasteurized.

@MagTun there is no cooling phase for that equipment, in fact they are heated for a long time.  the intent is to sterilize, it is just  sterilized at a lower temperature than other equipment because high heat or chemical sterilization would damage the equipment.

@John, I get uit now, for medical equipment, the pasteurization is long enough so that it doesn't only remove the parasite but really sterilizes the equipment [killing or deactivating all forms of life].  But what if I can't keeping heating long enough. I am in a remote place with limited means and I can't only keep it at around 60-70°C for 5-10min.  Would a fast cooling steps help the pasteurization by creating a thermic shock for the germs or won't affect in anyway the germs?

They cool it fast to maintain the taste and quality and to avoid the food danger range which is 5 to 60'C, because typical pasteurization is only 99.999% effective. A fast transition through 30-40'C improves the quality a lot compared to keeping the product at 30-40'C ... If you had limited means, you could easily use extra pasteurization at the expense of the taste, and you would achieve 99.99999 percent bacteria reduction, and the slower cool would then let that figure rise by i.e. one order of magnitude.
See the conclusions here:
https://onlinelibrary.wiley.com/doi/full/10.1111/1541-4337.12357
To know which process best suits your equipment and product, check the tables to achieve the reduction and follow similar times:
charts
graphs

Thanks for your answer and sorry for not being more precise, but what I have to pasteurize is not food but a piece of equipment akin to a medical equipment (I have added italic part in parenthesis to make it clearer). Your answer seems nonetheless to apply as the "danger zone" from 5° to 60° would, I guess, still apply for equipment for which we want to remove pathogens. Could you confirm it please? Also I can easily have a fast cooling step. The problem is not here, it's just that I wondered if this step was useful for equipment as it is not mentioned on Wikipedia for the medical equipment.

I'd recommend that you select the pasteurization process and temperature that best suits your equipment. Study the temperature graph images, i'll add references. Some pasteurization processes take 40 minutes to cool. Industries deal with giant vats of 1-2 tonnes, so the cooling can be slow, their studies have established flash pasteurization national protocols and cooling times. see end graph and conclusion https://www.researchgate.net/publication/268799840_Investigation_on_a_Tunnel_Pasteurizer_for_Nocellara_del_Belice_Table_Olives_Obtained_with_the_Castelvetrano_Style_Process

the study is about table olive so it's food. Are you sure this is the  link you wanted to share?

Disinfecting medical equipment is not pasteurisation. Its 2 questions in one. Pasteurisation can use slow cooling. Medical equipments doesnt denature with heat so you sould keep long time close to 100C. At least 80C for 20 minutes is best.

@MagTun - the danger zone is a temp range where bacteria can rapidly multiply given an appropriate food source (e.g. in food). This should not apply to your "medical equipment", you should be able to get it almost entirely without substrate for the bacteria to grow in.

@bob1, thanks for this info, I thought the danger zone was related to the germs characteristics not the food sources, it makes more sense now. But still I wonder, what if I can't keeping heating long enough to remove entirely the bacteria. I am in a remote place with limited means and I can only keep the heat at around 60-70°C for 5-10min. Would a fast cooling steps help the pasteurization by creating a thermic shock for the germs or this fast cooling won't affect  the germs in anyways. Thanks for your help!

@MagTun it doesn't affect the bacteria/yeast/fungi as far as I know. What is your end point here? How clean/sterile does it need to be? Have you looked at chemical cleaning methods instead - formaldehyde (1-4%), phenol (conc??), alcohol (70% 1-5 min) all work well in general with fairly fast times.

@bob, I have limited means as I am in a remote place. So I am trying to find a solution but apparently this won't work this way. Thanks!

Are you in an igloo or a place with no energy?

@DeltaEnfieldWaid, sorry didn't see your comment, yes I am in a place without access to energy


text:
How old is the Pogona genus?
What it says on the title, how old is the genus Pogona, which includes all bearded dragons? I tried looking online, and all I got was the useless answer of “bearded dragons are descended from their parents, who are descended from their parents… etc.”

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not simply to be an answer site, but rather a site that promotes self-learning with some expert help along the way.

Another way to ask this question:

How old is the most recent common ancestor of Pogona lizards and their closest relatives?

Diporiphora is a sister clade of Pogona, as stated in Hugall et al. 2008.1 Figure 4 of the same paper suggests that Diporiphora and Pogona diverged around 12 million years ago (see star in red box -- annotations mine):

An ultrametric chronogram generated from the Bayesian combined data phylogeny (Fig. 2C), under penalized likelihood rate smoothing (PLRS; optimal smoothing factor 80). The Riversleigh Physignathus calibration discussed in the text is used (indicated on figure as equal to 21 Mya). Tree pruned to show Australasian group only. Markov chain Monte Carlo (MCMC) sampling 95% confidence interval shown for selected nodes.

So, a reasonable estimate for the age of the Pogona genus is 12 million years.

References

Hugall AF, Foster R, Hutchinson M, Lee MSY. Phylogeny of Australasian agamid lizards based on nuclear and mitochondrial genes: implications for morphological evolution and biogeography, Biological Journal of the Linnean Society, Volume 93, Issue 2, February 2008, Pages 343–358.


text:
Can a polymer coated with antibodies have enough attraction to wrap around a virus?

Archived source for image
Please ignore the signal release. Does anyone know if it’s possible for polymer to wrap around a virus?

Please cite the sources of content like images in your questions.

Yes, we can concentrate viruses and other objects of interest onto beads using antibody conjugated beads (such as these ones from New England Biolabs - I have no affiliation to any company linked in this post, but do occasionally use their products).  This is a process called immuno-precipitation and has been around for a very long time.
This is also the principle behind lateral flow assays, where an antigen (it can be a virus, they are available for e.g. influenza and SARS-CoV-2) is suspended and placed onto the strip, where it crosses an antibody panel and binds to it. This then travels with the liquid front to a second antibody that detects the first and causes a signal of some sort to be released.


text:
Why is ACE 2 located on the Alveolar side of Pulmonary Epithelium?
Location and Purpose of ACE 2.
Given that the primary purpose of the transmembrane enzyme ACE 2 is ostensibly to bind Angiotensin 1 and 2 in order to convert these to derivatives such as Angiotensin [1-7] in the case of AT2, and presuming that this function requires its expression in the endothelial cell membrane on the vascular side of pulmonary alveolar structures and indeed vascular endothelium generally (since Angiotensin 1 and 2 are circulating proteins), then what is its supposed purpose in the membranes of type 2 pneumocytes on the exterior side of alveolar epithelium where, if the presumption is correct, it does not bind AT2, and where it is peculiarly susceptible to destructive binding of the S1 spike protein of the SARS-CoV2 virus?
In the absence of a plausible explanation for that location of ACE 2, it might be possible, for example, to speculate rationally that part of that purpose, teleologically as it were, is in fact to bind that spike protein, in which case one is emboldened to inquire upon a broader evolutionary intention in such a relation between that virus and the human organism, and on the nature of that relation generally.
Part of this inquiry then requires further consideration of the extent to which ACE 2 receptors on the luminal side of vascular endothelium locally in the cardio-pulmonary vasculature and more generally are then implicated in the dissemination of the virus.  Part of this question involves the likelihood that some auto-immunity mediated by cytotoxic T-cells primed by mRNA vaccines to target the S1 spike protein might develop against AT2 itself by virtue of this common affinity for ACE 2; notwithstanding that such an effect has not been demonstrated in clinical trials of such vaccines to date.

I think you will find that just because a particular protein function is required at a particular surface of a cell, it doesn't mean that it is not also found on other cell surfaces...

@bob 1.. Yes, you may be correct; but truly, what is it doing there?  In this case, if the assumption is correct about the definitive function of ACE 2, then the very fact that it is also susceptible to destructive binding by the spike protein should militate against its persistence at such a site, just swinging in the breeze so to say; implying a real evolutionary disadvantage unless some higher consideration is afforded to the role of the coronavirus.  Of course, this requires a view of nature in general as precise and ruthlessly exacting with respect to intention, whatever that may be.

Almost all proteins are multifunctional, ACE-2 has functions in brain biochemistry, inflammation and immunology, cardiovascular... try this paper for basic information

@bob 1. Yes, I've read that paper. All those functions of ACE 2 you mention pertain to its effects on AT2 and AT1.  The issue though is not whether ACE 2 is multifunctional, which no doubt it is, but what its function is on the alveolar side of the pneumocyte membrane where, since it is unlikely to exercise the specific function of binding and modifying AT2, its role is in question. This is not an idle or inconsequential question since it is not outlandish to argue that at least part of its function there may be specifically to bind the SARS-CoV 2, and possibly other coronaviruses; therefore..

... therefore to imagine some useful function for these viruses -- indeed for viruses generally -- within the dynamic of human evolution.  Since this line of thought no doubt requires a challenging philosophical perspective upon reality which may or may not be valid, I would rather find some more concrete and immediate purpose for the ACE 2 at that alveolar site -- which is really why the question is asked.  Bear in mind too that until a few years ago, very little was known about ACE 2, and not much more now.

That paper covers it... it still involves the Ang pathway. There a section Direct Protective Actions of ACE2 on Lung Alveolar Epithelial Cells: ACE2 protects against lung injury by: (a) degrading Ang II, which is vasoconstrictive and proapoptotic for lung epithelial cells (Wang et al., 1999) and profibrotic (Li et al., 2008; Uhal et al., 2011), and (b) by producing the peptide Ang1-7, which inhibits the actions of Ang II through binding to the MAS receptor

@bob 1.  I've read the paper.  The point is that ACE2 can do none of the things you mention if it cannot bind Angiotensin because it is situated on the atmospheric side of the alveolar pneumocyte cell membrane.  Angiotensin 1 and 2 are circulating substances which are bound to ACE 2 on the luminal side of the vascular endothelium.  The question remains: if these assumptions about ACE 2 are correct -- and please correct them if not --, then what is the function of ACE 2 receptors on the atmospheric side of the alveolar cell membrane where it does not bind AT?  The best article I've found is..

.. M. Gheblawi: 'ACE 2: SARS-CoV 2 Receptor and Regulator of RAS', in which some of the physiological functions for ACE 2 to which you alluded are discussed; among which two may be relevant here: [1] the capacity to cleave proteins and [?] to facilitate amino acid transport across cell membranes (as an analogue of 'collectrin'); [2] the capacity to protect against dysbiosis of natural microflora, particularly in the gut but also possibly in the respiratory tract in cases in which such flora exists. Neither of these roles is very convincing however. What might SARS-CoV 2 be doing for us?

CoV-2; nothing, we have absolutely no seroprevalence before the advent of the virus in 2019. Other viruses possibly. Generally though ones which have co-evolved are no longer pathological or much reduced in pathology. ACE2 can do those things if there is some damage to the epithelium as would happen in an infection, releasing AT etc into the interstitial fluid. Check out any ISH staining for an epithelial ion channel and you will see some staining away from the surface on which they are active, despite having massive concs at the "correct" surface...

@bob 1.  Good.  There's probably part of an answer in there, with respect to the problem of interstitial AT which might conceivably be resolved by ACE 2.  I winder too whether ACE 2 is implicated in the reabsorption of the protein constituents of alveolar surfactant by the macrophages of type 2 pneumocytes since it is found in close association with those macrophages. Regarding any evolutionary benefit to humans of CoV-2 infection, it would consist in some facility of adaptation mediated by coronavirus infection generally, presuming that earlier coronaviruses have induced persistence of ACE2.

The problem is that ACE2 isn't the only receptor for CoV. There are a few other ones. MERS uses DPP4, HCOV-NL63 uses ACE2 also, but HCOV-229E uses APN, MHV uses CEACAM. Reasonable summary here

After some fruitful discussion in Comments with 'bob 1', and a review of several articles cited below, the likely answer to the question is that, in spite of the fact that ACE 2 expressed on the atmospheric side of type 2 epithelial pneumocytes cannot in the ordinary circumstance be exposed to circulating Angiotensin [1 or 2], its expression and activity appears to be strongly protective of lung tissue in conditions of inflammation or infection, as these two excerpts attest.  Whether this is due to the mitigating effect of ACE 2 during cell rupture or leakage of Angiotensin 2 into the interstitium or alveolar space is unclear, but would seem likely.
At the same time, as mentioned in the following, the fact that ACE2 has two distinct binding sites at this level suggests that its role is not restricted to that protective function generally; rather, more specifically its very presence as a portal with an allied tissue protective function presumably serves to mitigate the inflammatory effect of binding by SARS-CoViruses themselves, 1 and 2, notwithstanding the destructive effect on ACE2 of that process. This interplay between ACE2 expression and viral load/virulence may help to explain the widely varying clinical impact of COVID-19.
Article 3 further below suggests the manner in which such an interaction between host and virus would have evolved.
[a] Article 1 entitled' ACE 2: SARS-CoV 2 Receptor and Regulator of RAS' (Gheblawi etal.).

Lung epithelial cells express high levels of ACE2, which positively
correlates with airway epithelial differentiation. Involvement of ACE2
in Acute Respiratory Distress Syndrome [ARDS], which is triggered by
multiple diseases including SARS-CoV and SARS-CoV-2, has been
established in multiple animal models. ACE2 Knocked-Out mice exhibit
severe pathology of ARDS.
Additional ACE deficiency, or treatment with AR1R blockers of ACE2 KO
mice rescues them from ARDS implicating the benefit of ACE2 and the
critical balance of the protective versus pro-inflammatory and
fibrotic axes of the Renin-Angiotensin System [RAS]. These findings
are consistent with evidence of a beneficial effect of rhACE2 on
pulmonary blood flow and oxygenation in a pig model of
lipopolysaccharide-induced ARDS.  Age-related loss of ACE2 in the
lungs correlates with the increased mortality and worsened phenotype
in elderly patients with COVID-19.

[b] Direct Protective Actions of ACE2 on Lung Alveolar Epithelial Cells 2 [Article, 'ACE 2, Much More Than Just a Receptor for SARS-CoV2'].

In addition to its protective role in the cardiovascular system, ACE2
has a direct protective role in alveolar epithelial cells. In the
lungs ACE2 has numerous physiological functions, most of which are
protective against lung injury. Similar to the endothelial site, ACE2
degrades the octapeptide Ang II by removing a single amino acid from
the C-terminal end of the peptide to generate the heptapeptide Ang1-7.
Our laboratory and others have shown that ACE2 protects against lung
injury by:  (a) degrading Ang II, which is vasoconstrictive and
proapoptotic for lung epithelial cells (Wang et al., 1999) and
profibrotic (Li et al., 2008; Uhal et al., 2011), and (b) by producing
the peptide Ang1-7, which inhibits the actions of Ang II through
binding to the MAS receptor (Gopallawa and Uhal, 2014).
In support of this protective role for ACE2, pharmaceutical
preparations of recombinant ACE2, when administered to experimental
animals, protect against lung cell death, inhibit acute lung injury
and prevent lung fibrosis after chronic injury to the lungs (Li et
al., 2008; Rey-Parra et al., 2012).
As further evidence, the application of a specific competitive
inhibitor of ACE2, DX600, to primary cultures of isolated ACEs
increases the level of Ang II released into the serum-free culture
medium by autocrine mechanisms, reduces the amount of released Ang1-7
and, importantly, induces apoptosis inhibitable by the AT1 receptor
blocker (Menter et al., 2020). Thus, functional ACE2 normally
expressed by alveolar epithelial cells can be viewed as a critical
survival factor for these lung cells. In addition, the enzymatic
product of ACE2, the Ang1-7, itself protects against lung cells death
by antagonizing that actions of Ang II (le Tran and Forster, 1997).
If Ang1-7 is applied to cultures of lung epithelial cells, it can
prevent lung cell death in response to either Ang II or the ER stress
inducer MG132 (Nguyen and Uhal, 2016). The Ang1-7 receptor MAS and the
JNK-selective phosphatase MKP-2 appear to be critical in this
protective action of Ang1-7 response, because iRNAs or antisense
knockdowns of MAS or MKP-2 can eliminate the ability of Ang1-7 to
prevent lung cell death (Gopallawa and Uhal, 2016). Indeed, Ang1-7
itself and congeners of the peptide, such as cyclic Ang1-7 (Gopallawa
and Uhal, 2016), have already been shown to protect the lungs in
preclinical models of acute lung injury.

However, the not unrelated possibility also remains that since there are two distinct binding sites on the ACE2 found in these alveolar epithelial cells, one of which is the catalytic site implicated in its modifying effects on Angiotensin, and the other, the N-terminal protease domain which specifically binds the spike protein of coronaviruses, SARS-CoV2 in particular, at least part of the role of this binding domain has persisted for the purpose of facilitating entry of coronaviruses, more especially with as little immediate inflammatory damage to the portal as possible.
From the same article mentioned 1, the key observation is as follows;

ACE2 has an extracellular facing N-terminal domain and a C-terminal
transmembrane domain with a cytosolic tail. The N-terminal portion of
the protein contains the claw-like protease domain (PD), while the
C-terminal domain is referred to as the Collectrin-like domain. The
receptor-binding domain (RBD) of SARS-CoV-2 binds with the PD of ACE2,
forming the RBD-PD complex distinct from the ACE2 catalytic site.

This observation may suggest a type of evolutionary symbiosis between coronaviruses generally, SARS-CoV2 in particular, and the human organism which has adapted to permit the entry of those viruses via the N-terminal protease domain which is evidently distinct from the ACE2 catalytic site.  Naturally this sort of speculation presupposes that the role of this protease is not restricted to some ordinary physiological function, such as enhancing reabsorption of surfactant by alveolar macrophages for example.
Here it may be interesting to insert an excerpt from another article 3 from 2012 quoted below and dealing with the original SARS-CoV.
Article 3, 'Evidence for ACE2-Utilising Coronaviruses in SARS in Bats'.

In 2002, severe acute respiratory syndrome (SARS)-coronavirus (CoV)
appeared as a novel human virus with high similarity to bat
coronaviruses. However, while SARS-CoV uses the human
angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry, no
coronavirus isolated from bats appears to use ACE2. Here we show that
signatures of recurrent positive selection in the bat ACE2 gene map
almost perfectly to known SARS-CoV interaction surfaces. Our data
indicate that ACE2 utilization preceded the emergence of SARS-CoV-like
viruses from bats.
Cell-surface receptors often play a key role in defining viral host
range. New diseases can emerge when existing viruses evolve the
ability to bind the ortholog of their cell-surface receptor in a new
species.  Indeed, the principal genetic component defining host range
in coronaviruses is the spike protein on the surface of the virus and,
in particular, its receptor-binding domain (RBD).
It is believed that the severe acute respiratory syndrome (SARS)
epidemic resulted from the zoonotic transmission of a coronavirus from
bats to humans. The central role of the RBD in the SARS-coronavirus
(CoV) zoonosis was crystallized in an experiment in which a bat
coronavirus became infectious in primate cells when it was altered to
contain the RBD of human SARS-CoV.
Over long periods of time, co-evolutionary dynamics can develop
between viruses and their hosts. For example, host populations will
experience natural selection for receptor mutations that reduce virus
interaction affinity, and viruses will, in turn, be selected for
mutations that increase affinity with new receptor variants. This
back-and-forth selection will result in the rapid evolution of both
the host receptor and the virus surface protein.
The protein evolutionary rate can be analyzed by studying the rates of
accumulation of non-synonymous (dN; changing the encoded amino acid)
and synonymous (dS; silent) mutations in the underlying gene. Most
genes retain far fewer non-synonymous mutations than synonymous
mutations (dN/dS ≪ 1) because protein-altering mutations tend to be
deleterious.

These are some further pertinent extracts from the article 1 by M. Gheblawi etal. entitled 'ACE 2: SARS-CoV 2 Receptor and Regulator of RAS'.

Knowledge of the underlying biology and physiology of ACE2
(angiotensin-converting enzyme 2) has accumulated over the last 20
years since its discovery and has provided a major stimulus to further
our understanding of the renin-angiotensin system (RAS).  ACE2 has
distinct roles ranging from catalytic activities with various
substrates, as functional receptors for severe acute respiratory
syndrome coronaviruses (SARS-CoV), and as an amino acid transporter.
ACE2 functions as a master regulator of the RAS mainly by converting
Ang (angiotensin) I and Ang II into Ang 1–9 and Ang 1–7, respectively.
Whereas somatic ACE contains 2 active sites, ACE2 possesses only a
single catalytic domain. Both ACE and ACE2 act as zinc
metallopeptidases but of differing substrate specificities defining
their distinct and counterbalancing roles in the RAS.  Whereas ACE
cleaves C-terminal dipeptide residues from susceptible substrates (a
peptidyl dipeptidase), ACE2 acts as a simple carboxypeptidase able to
hydrolyze Ang I, forming Ang 1–9 and Ang II to Ang 1–7.
ACE2 does not cleave bradykinin, further distinguishing its
specificity from that of ACE while it is also insensitive to
conventional ACE inhibitors. The C-terminal domain of ACE2, which has
no similarity with ACE, is a homolog of a renal protein, collectrin,
which regulates the trafficking of amino acid transporters to the cell
surface, endowing ACE2 with multiple and distinctive physiological
functions. It is the multiplicity of physiological roles that ACE2
plays that has allowed it to be hijacked by SARS-CoV-2 as a receptor.
ACE2 is expressed in the vascular system (endothelial cells, migratory
angiogenic cells, and vascular smooth muscle cells), heart (cardiac
fibroblasts, cardiomyocytes, endothelial cells, pericytes, and
epicardial adipose cells) and kidneys (glomerular endothelial cells,
podocytes and proximal tubule epithelial cells). ACE2 is also
expressed and functions in the local RAS of the liver (cholangiocytes
and hepatocytes), retina (pigmented epithelial cells, rod and cone
photoreceptor cells and Müller glial cells), enterocytes of the
intestines, circumventricular organs of the central nervous system,
upper airway (goblet and ciliated epithelial cells), and alveolar
(Type II) epithelial cells of the lungs and pulmonary vasculature.
The entry of both SARS-CoV and SARS-CoV-2 into cells is facilitated by
the interaction between viral S-protein with extracellular domains of
the transmembrane ACE2 proteins, followed by subsequent
down-regulation of surface ACE2 expression.

From the same article, the following details of intestinal expression of ACE 2 may or may not suggest a similar role in pulmonary epithelium.

ACE2 As a Chaperone Protein for the Amino Acid Transporter, B0AT1
(SLC6A19).
B0AT1 is highly expressed in the intestines and kidneys with function
in the absorption of neutral amino acids. The ACE2-B(0)AT1 complex is
assembled as a dimer of heterodimers, with the collectrin-like domain
of ACE2 mediating homo-dimerization. ACE2 has a RAS-independent
function, regulating intestinal amino acid homeostasis, expression of
antimicrobial peptides, and the gut microbiome.  ACE2 is necessary for
the expression of the Hartnup transporter in the intestine, and the
differential functional association of mutant B(0)AT1 transporters
with ACE2 in the intestine regulates the phenotypic heterogeneity of
human Hartnup disorder.

Evidently ACE2 facing the gut lumen also serves to inhibit dysbiosis, and although it is considered unlikely by researchers to exert any corresponding function in the generally aseptic lower respiratory tract, it may play some such role in the upper tract.  Altogether, it is an extremely interesting enzyme, a zinc metallo-enzyme no less, whose importance is yet to be fully appreciated.

Nice synthesis of the current research. Looks like it could be an interesting PhD topic for someone. BTW, you might want to format the excerpts as blockquotes to make it more clear which bits are from papers and your comments.


text:
Fluctuations in disease burden of respiratory viruses (especially influenza/coronaviruses)
Compared to peaks in terms of disease burden (morbidity and mortality, or incidence of severely symptomatic cases and deaths caused by a viral strain within a population), is the relatively light burden of most endemic respiratory viruses due to
(a) a high level of population immunity
(b) the selection of variants that are less virulent
(c) something else?

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

Each cam play a role.
a:  Population immunization.  By this I mean evolved resistance.   Measles was not a big deal for Europeans.  But when they brought measles to Hawaii it killed 80% of the population.  Europeans had evolved resistance to measles; a degree of intrinsic immunity.  Populations that co-exist with a pathogen for a long time can evolve a degree of intrinsic immunity.   There are viruses to which humans have little intrinsic immunity, like Ebola.  We have not coexisted with Ebola for long.
b.  Variants that are less severe.  Nepalese peacekeepers brought cholera to Haiti.  Usually with cholera you pour out feces and die, but these soldiers were deemed fit for duty.  They had a less virulent strain and they were carriers.  That strain reverted to massive virulence in Haiti because they had a transmission advantage there.  But in circumstances where sick people are less likely to transmit disease because they are not getting out, less severe variants have an advantage as regards transmission.  As regards respirator viruses, this is probably relevant to the common cold - if it leaves you well enough to go to work, you will transmit it.
C:  Immunization.  Of vaccines US children get, 11 are to respiratory viruses or bacteria.   They can be bad diseases if you catch them but because of mass vaccination they are rare.  If we stopped vaccinating, they would eventually come back.  Except for smallpox, hopefully.

Neither have ebola coexisted long with humans. Population and pathogen usually mutually adapt or one or bothgo extinct.


text:
The reason behind red drop effect
I was reading about Emersion effect on Wikepedia, I was not able to correlate our current knowledge of photosynthesis with this effect,
First red drop effect

When Emerson exposed green plants to differing wavelengths of light,
he noticed that at wavelengths of greater than 680 nm the efficiency
of photosynthesis decreased abruptly despite the fact that this is a
region of the spectrum where chlorophyll still absorbs light

My Query is  this abrubt drop in rate of photosynthesis after 680 nm is because as PS1 absorbs wavelength greater than 680 nm till 700 nm , and PS1 does not evolve oxygen or fix Carbon dioxide? so rate of photosynthesis is very small at this point, as to reduce NADPH2 in Z scheme , photosystem 1 needed electron of Photosystem 2 , without electron of photosystem 2 it will not be able to reduce NADP, isn't it, I am very skeptic about this explanation, is it right?
Secondly it mentions

When the plants were exposed to short-wavelength light, (less than 660
nm), the efficiency also decreased.

Is this decrease in rate because of Photosystem 2 gets most activated at 680 nm and antenna molecules which broadens the spectrum as not very efficient result in decreased in rate of photosynthesis???

This graph is also adding to my confusion if PS1 active at FAR RED LIGHT only synthesizes ATP and not NADPH2 what does it have an equal bump( amplitude) like Red light(at which PS2 is active and carbon fixation in reality is happening here) So Amplitude of red light should have been greater than far red light
https://istudy.pk/emerson-enhancement-effect/ graph source

I recommend you to read taiz and zeigner's plant physiology. I read few years back it beautifully explains this concept. Right now, I'm preoccupied with some other question, if no one still answers this, I'll give a try


text:
What’s the largest animal in the evolutionary history of birds?
I know that birds evolved from dinosaurs (or a related clade).  However, some dinosaurs are large and others are small.  Did birds evolve only from a line of dinosaurs that stayed small throughout evolutionary history, or did the ancestors of bids get large at some point and then shrink?
Concretely, what’s the largest known animal among the ancestors of birds?

I think you need to clarify this a bit.  First, how do you measure "large" for birds, body mass or wingspan?  And are you asking only about ancestral species, or include lineages that have died out?

@jamesqf: Good point, I meant mass, since the goal was to include non-bird ancestors.  And by "ancestors of birds", I meant ancestral species.

It is basically impossible to identify direct ancestor, the best we get in paleontology is something closely related to the ancestral lineage.

consider Herrerasaurus the most primitive therapod, which is bigger than a human https://en.wikipedia.org/wiki/Herrerasaurus

The largest bird was Vorombe titan, 3m tall and weighing 650kg. It is likely that this was larger than any of its ancestors.
Working back through the lineage of birds in Theropoda, the animals that are on the avian linage are small. One finds some early therapods that may be close to the common ancestor that were "largish" but smaller than V. titan.    Going back to basal Archosauriformes one finds a side-genus like Proterosuchus, a crocodile-like animal that could be 3m long, but not as massive as V. titan. It is possible that there is a large semi-aquatic creature in the archosaur lineage, but it is more likely that the common ancestors of crocodiles and birds were smaller. The megafauna of the Permian were all synapsids and more closely related to modern mammals than to birds.
Prior to that, there are lizard shaped creatures, salamander-like creatures, back to lobe-finned fish and so on. No megafauna.
None of these potential ancestors is as large as V. titan.  I'd conclude that the largest animal on the "bird" lineage is this type of Elephant Bird.
Perhaps this is not so surprising.  Large creatures are vulnerable to extinction. The common ancestors of the extant clades tend to small adaptable generalists.

I was going to answer that, but V. titan isn't an ancestral bird, it is one of the extinct clades within Aves, just like any number of more recent species - passenger pigeon, dodo etc.  For it to be ancestral it must have direct ancestors now.

@bob1 I assume you meant it must have direct descendants, right?

@bob1, that is a very reasonable interpretation of the question, in which case it is likely that the African ostrich is the answer to the question: extant birds are descendants of generally smaller ancestors, though there may be some theropod ancestors that were larger. As your answer implies, we probably don't have actual fossils of theropods on the line to modern birds, we only have various side branches, but if we do, it is very hard to establish which, if any are ancestors and which are cousins. My interpretation is "clade Aves and ancestors", and V. titan is certainly in Aves.

I should say that “the largest ancestor is a large current or recent bird” is a good answer to the underlying motivation of whether the ancestral line went large and then shrunk or not, which is why I accepted the answer.  I should probably have phrased my question this way explicitly rather than trying to concretize it.

@GeoffreyIrving in that case the question should have been "what was the largest bird ever?", not a specific ancestral bird. BTW, Dinornis robustus was taller but probably not heavier than V. titan, having said that, there were Dinornis species that were about the size of a turkey too...

This is actually a very difficult question to answer - because how far back do you go. The clade Avialae which includes the true birds is fairly recent and contains a lot of new dinosaurs(! -debate over feathers), but the clade Avialae is included in the theropod (Theropoda) group of dinosaurs, which includes such things as Tyrannosaurus rex, Spinosaurus, and Giganotosaurus, all of which are fairly large. However, these are almost certainly sister clades to that of the birds rather than actual ancestors.
However, Avialae is a made up clade with no actual fossil representing it; it is purely hypothetical as an ancestral marker for birds.
It seems that there is quite a bit of debate among paleo ornithologists as to which groups of dinosaurs are most closely related to birds. It is thought that things like Archaeopteryx are part of the bird ancestral clade, but even this much is uncertain, as there are a number of other feathered dinosaurs within the larger clade, that definitely did not evolve into birds. You might consider Neotheropoda a suitable cut-off, as this contains the true birds, but is still quite diverse. You could also cut off at Averostra, which includes Aves, and Ceratosauria, a group of quite large feathered dinosaurs.
Having said all that, we are very unlikely to even know which species are directly ancestors of birds, it seems that there are a lot of species that are very similar and all closely related, but making the choice of which is down to experts and a paucity of specimens. See this bit on Birds for some of the difficulty in defining them. If I had to make a choice, I would probably go with Ichthyornis as a definite ancestor, but I am no expert (I'm a virologist...).

Interesting, thank you!  I suppose in the absence of known common ancestor species, answering this kind of question might require some entirely difference source of information to separate sister clades off, such as the presence or absence of genes related to large size.

@Geoffrey Irving: I doubt that genes for large size would work, considering that the elephants are closely related to the hyrax: https://en.wikipedia.org/wiki/Hyrax  Or that the dodo is descended from pigeons, or the considerable size variation among domestic dog breeds.

@jamesqf Not sure what your mean by that, since we know that, in humans, size is mostly genetic. So there are definitely genes for size.

@Konrad Rudolph: But those genes are obviously not... is stable the word I want, or maybe conserved?  Anyway, my point is that size can change drastically in relatively few generations, either through natural evolution (see e.g. "island dwarfism" and "island gigantism"), or by selective breeding.

@jamesqf I think it’s mostly that height is a complex, polygenic trait: hundreds of pleiotropic genes all have a tiny influence, and these genes are mostly not in linkage disequilibrium, so they are inherited independently and are subject to different selective pressures.

@Konrad Rudolph: Yes, and it doesn't seem as though there's a purely genetic constraint on size.  As with dogs (or indeed, with humans), the size can be increased until it causes other health problems.  Given a few million years to weed out those problems, and the proper evolutionary pressures, it seems like the only constraints are mechanical.  Consider whales and their much smaller ancestors.


text:
What’s so remarkable about position effect variegation?
I am reading Albert et. al’s Molecular Biology of the Cell and at one point the authors discuss the idea of “position effect variegation.” They mention that through events of DNA relocation, it’s possible for portions of echromatic DNA to become heterochromatic by being positioned next to heterochromatic DNA. They stress that “remarkably,” this heterochromatic state of DNA often gets inherited by the cell progeny. This phenomenon of inheritance is what they call, or I guess is called, position effect variegation. I don’t quite see what’s so “remarkable” about this, which is making me wonder if there’s something I’m underappreciating or misunderstanding. In particular, if the underlying DNA structure is changing, then wouldn’t we expect the progeny to inherit these epigenetic changes? Why is it so remarkable?
Here's the actual quote from the book:

In chromosome breakage-and-rejoining events of the sort just
described, the zone of silencing, where euchromatin is converted to a
heterochromatic state, spreads for different distances in
different cells in the fly embryo. Remarkably,
these differences then are perpetuated for the rest of the
animal’s life: in each cell, once the heterochromatic condition is
established on a piece of chromatin, it tends to be stably inherited
by all of that cell’s progeny (Figure 4–31). This remarkable
phenomenon, called position effect variegation, was first recognized
through a detailed genetic analysis of the mottled loss of red pigment
in the fly eye

and later on:

But in at least some cases, the covalent modifications on nucleosomes
can persist  long after the transcription regulator proteins that
first induced them have disappeared, thereby providing the cell with a
memory of its developmental history. Most remarkably, as in the
related phenomenon of position effect variegation discussed above,
this memory can be transmitted from one cell generation to the next.

Re:

In particular, if the underlying DNA structure is changing, then
wouldn’t we expect the progeny to inherit these epigenetic changes?
Why is it so remarkable?

Given the context of the quote, the "variegation" part of the phrase refers to gene expression sometimes being turned off by influence of newly-nearby heterochromatin. The extent to which this suppression of expression extends into the euchromatic region from the adjacent heterochromatin varies from cell to cell, but once established is stably inherited through further divisions of that cell. It is unknown what molecular mechanisms initiate and maintain the suppression of expression in the formerly euchromatic genes.
Since we do not fully understand the molecular nature of what is required to initiate and maintain heterochromatin, especially in a section of DNA that was formerly euchromatin and so presumably does not contain any global "make me heterochromatin" sequence signals, the "remarkable" likely means "we don't yet understand the details" -- it's like magic.

I added the quote

There's no evidence the actual DNA is changing. The molecular mechanism of this "creeping heterochromatinization" is unknown as far as I know. I think we would guess it might have to do with nucleosome positioning or state.


text:
Do quantum mechanical effects such as uncertainty, tunnelling and entanglement play role in the electron transport system of respiration?
The electron transport system of aerobic respiration involves an extensive pathway of electron and proton transfer from one centre to another. Now, since they are quantum mechanical particles, shouldn't they exhibit quantum behaviours such as uncertainty, quantum superposition, quantum coherence, or maybe in some cases even tunnelling or entanglement? Do these behaviours have any definitive role to play in the entire process? And how exactly does the biological system deal with these quantum mechanical behaviours? What about the wave-like property of the electrons? Is there any "more quantum-mechanical model" of respiration?

Why electron transport rather than any other chemical reaction? They all involve movement of electrons. You could ask this question on SE Chemistry, where it would be more appropriate, but if you are looking for anything "suprachemical" to explain biological chemistry because it is biological, then you will be joining a long line of disappointed physicists starting with Max Delbrück.

I would suggest you look into the field of quantum biology. This TED talk (https://www.youtube.com/watch?v=bLeEsYDlXJk) is a good place to start.

Check out work of Judith Klinman, in particular Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis (freely available Annual Review article)  and Hydrogen tunneling in biology and (an interesting wrt NAD(P)-linked enzymes) Tunneling and dynamics in enzymatic hydride transfer. I wouldn't even think of doing just to the work of JK in an answer here: you will need to ask a specific question

Very good evidence for quantum-mechanical tunneling comes from the magnitude of the isotope effect in hydride and deuteride transfer reactions (The magnitude of the effect is often much greater than that predicted from  'classical' isotope effect theory, especially for primary isotope effects. See here, for example). The mass dependence of QM tunneling makes it more likely to occur in electron transfer reactions but it can also occur, in, say, an NADP-linked enzymic hydride transfer. All in the free Klinman article cited above –


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Where in Africa did Homo sapiens evolve from?
I’m aware that the possible oldest homo sapiens fossil was found in Morocco. The vast majority of our fossils however is found in Eastern Africa. In recent years,a controversial study on mitochondrial DNA seems to suggest an origin from Southern Africa. Where is the majority scientific opinion on this issue at the moment?
You can read this article for my source on the study of mitochondrial DNA

Possibly the currently favoured view is that anatomically modern humans didn't evolve in one location, but evolved in a structure population that spanned Africa (and perhaps the Middle East):

We challenge the view that our species, Homo sapiens, evolved within a
single population and/or region of Africa. The chronology and physical
diversity of Pleistocene human fossils suggest that morphologically
varied populations pertaining to the H. sapiens clade lived throughout
Africa. Similarly, the African archaeological record demonstrates the
polycentric origin and persistence of regionally distinct Pleistocene
material culture in a variety of paleoecological settings. Genetic
studies also indicate that present-day population structure within
Africa extends to deep times, paralleling a paleoenvironmental record
of shifting and fractured habitable zones. We argue that these fields
support an emerging view of a highly structured African prehistory
that should be considered in human evolutionary inferences, prompting
new interpretations, questions, and interdisciplinary research
directions.

Scerri, Eleanor ML, et al. "Did our species evolve in subdivided populations across Africa, and why does it matter?." Trends in ecology & evolution 33.8 (2018): 582-594.
For a criticism of the mtDNA Southern Africa origins paper, see this paper.

This is rather interesting. I have 2 questions. Firstly, does this represent the majority of scientific opinion? Secondly, does this “African Multiregional” approach imply a sort of convergent evolution of multiple groups of archaic humans into modern Homo sapiens?

This view is scientifically so weakly supported that I wouldn't give it much credence at this point. The number of human fossils recovered is tiny, they are poorly dated and by no means a random sample. Similarly, the "material culture" (basically stones that are often hard to identify as intentional human artifacts versus naturally-occurring pieces) is notoriously difficult to link with any fossil or even date to an accuracy finer than a few hundred thousand years.  The identification of many more fossils and genomic sequencing will sort it out in the future.

@Armand So what do you think is the majority opinion then?

@DavidOkogbenin The correct opinion is "insufficient data, likely for at least a number of decades". Majority/minority doesn't matter in science -- data matters.


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On the Origin of Homo Sapiens
Paleoanthropologists are certain Homo sapiens originate from Africa. However where in Africa is still contested.
Could you give the reasons why it is thought that Homo sapiens evolved in Eastern Africa, Northern Africa and Southern Africa?

This seems like a question that could use some preliminary research. For example, why are paleoanthropologists "certain Homo sapiens originate from Africa"? Do those techniques extend to subregions of Africa?

How is this different from your previous question? And please take the trouble to read the [Tour] to find out how this site works and how to ask questions here. Armand’s remark reflects the requirement to demonstrate the effort you have made to answer a question yourself.

The reason is that the oldest and most primitive proto-human signs of life have been found in Africa. The seminal research was done by Louis Leakey, an anthropologist. It is possible that older forms of life may exist undiscovered in other places, but so far the evidence for that is scant.
Part of the challenge is that many geographic areas feature acidic soils which will eventually dissolve bones, which are composed of calcium carbonate, so it requires a neutral or slightly basic soil to preserve bones over millions of years.


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What are the additional considerations for primer design in ancient DNA?
I'm familiar with the principles of primer design and have previously designed primers for use in modern DNA. However, in my current project I am working with ancient DNA (nuclear gene) and need to design primers to work in this context - I am wondering if there are established additional considerations that need to be taken into account.
What I have discovered so far is mostly literature dealing with the damage patterns in ancient DNA (i.e., amplicons tend to have damage at the 5' and 3' ends of each fragment, so sequence data from the centre parts of fragments are more reliable). I have seen the suggestions that multiple, overlapping primer pairs might be used to detect low-copy number fragments, but this suggestion, while useful, doesn't tell me much about the design of the individual primers.
My own thoughts are that since ancient DNA is typically fragmented into ~150 bp (depending on age - my samples are around 250 years old), multiple primer pairs might help. My target is around 500 bp.

Why not contact some of the labs that do a lot of old DNA work (not sure 250 years counts as ancient :) ) and ask them for advice or pointers to discussions of primer design. Since it seems samples vary widely in their degree of preservation, perhaps they will have suggestions on how to evaluate the quality of your specific samples.

That's a great suggestion, thank you! I agree that calling 250-year old samples 'ancient' sounds and feels odd, but as of yet there's no distinction between "kind of old DNA" and "really old DNA".

@Armand 250 years is a lot of time for DNA, which is why it is commonly referred to as ancient. I agree that the term is misleading, but it is frequently used.

@natb could you link the literature you reference? I assume you've read this paper on ancient DNA damage and this paper on amplification of ancient DNA?

@acvill Yup, I've read both those papers. Unfortunately that's the closest I've gotten to finding the information I'm looking for. I can link other sources I've read but they are all less relevant.


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Why is BRCA-1 mutation a dominant mutation?
BRCA-1 gene is a tumor suppressor gene and undergoes a loss of function mutation to become cancer inducing. Why is it that only one allele needs to be mutated because loss of function mutations are usually recessive and requires the mutation of both alleles.

The answer depends on when and where you are identifying the phenotype. www.cancer.gov has much useful info, including a fact sheet:
https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-fact-sheet
From that:

Even if someone has inherited a harmful variant in BRCA1 or BRCA2 from
one parent, they would have inherited a normal copy of that gene from
the other parent ... But the normal copy can be lost or change in some
cells in the body during that person’s lifetime. Such a change is
called a somatic alteration. Cells that don’t have any functioning
BRCA1 or BRCA2 proteins can grow out of control and become cancer.

The pre-existing loss of one functional allele from conception makes any later somatic inactivation of the other allele a homozygous loss of function rather than just a heterozygous LOF.


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Can someone explain DNA methylation reprogramming in simple terms to me?
From what I understand, one of the challenges of cloning is that the DNA methylation that is supposed to occur during embryonic development does not occur normally and this prevents natural gene expression in the cloned zygote. However, the typical descriptions of these processes are highly technical and beyond my monkey-level intelligence. I was wondering if someone could explain in simple terms why DNA methylation does not occur normally in naive cloning processes.

Your description sounds a bit confused. Perhaps the best way to think about it is that a natural zygote's DNA has undergone epigenetic "programming" that places different genes in different expression states appropriate for that stage of development (for example, you wouldn't want to turn the cell into a cartilage cell at that point, so those genes should be off). DNA methylation is one method of such programming, there are others known, and likely additional unknown ones as well.
If you replace the nucleus of a zygote with a non-zygote nucleus, much of the programming won't be appropriate for the zygotic stage and development won't proceed properly.  Cloning technology involves developing processes and reagents to reprogram the nucleus into a state that is compatible with normal development once it is inserted into a zygote.


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Can one identify an organism based on its genome alone?
If one is given the complete genome of some unknown organism, would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a repository of genomes of known living organisms)?
In another words, do we currently have a model capable of translating any random genome of an organism to a graphical representation of the organism and information on its behaviour?
Are there such 'genome-structure' or 'genome-behaviour' relationships known to us that would enable us to accomplish such a task?

As you specifically state:

Would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a repository of genomes of known living organisms)?

No, no chance at all, we certainly wouldn't even be able to determine a single gene function, other than that it codes for a series of amino-acids. After all, even simple genes of say 100 bases in DNA will still have 33 amino-acids, and most people don't remember that sort of information without cause, and the only way we can acquire that easily information is through repositories of information. The only way we could do something approaching working this out would be to take portions of the genome that we could identify as genes (start/stop codons), then express them one-by-one and empirically work out the function through classic biochemical methods. This is very laborious and time consuming - it would take many many person-hours per gene and a LOT of resources. However, this is how functions of novel genes and their related proteins were and still are worked out.
With reference - perhaps, at least partially. From the sequence and with access to a repository such as Genbank we could deduce which type of organism it was by comparing to known genomes from other organisms in a process known as phylogenetic analysis. You could certainly tell which of the kingdoms it came from. In each organism there are conserved bits of the DNA (or RNA) that tell you which groups they are. For example all DNA based bacteria and archaea (that I know of) you can use the 16S ribosomal RNA sequence, which will identify bacteria and archaea down to genus and species level.
For instance, you might have a genome that gives you information that it is a bacterium of the Staphylcoccus group, meaning that you can deduce that it is very very likely that it will be a small bacterium which is a round ball shape, and will stain positive with a Gram stain. You could also likely identify some genes and their function based on homology.
You can apply this process to other genomes, for instance a mammalian one will tell you that it had fur, produced milk, was warm blooded, quadruped, spinal column etc.

No, current technology is nowhere near what is required to deduce the form of a species from its DNA alone without comparing it to the DNA of the same or similar species.
The reason for this is that genes in the DNA generate proteins and these proteins are simple building blocks that combine in highly complex ways that we do not understand. Currently scientists are simply trying to learn how to predict the SHAPE of the protein from its DNA sequence. That is the first step. We are getting close to being able to do that. Once we can predict shape, then we can start working on figuring how that shape translates into function.
I would also add that organisms have many expressed traits. That means that the trait expresses itself only after the organism grows and is not genetically determined. For example, fingerprints are an expressed trait. Also, colorings and pigmentation are expressed traits. For example, I have two cats that are genetic twins and have exactly the same same DNA, but one has a small patch of white fur on his chest and the other does not.

However, there are individual genetic variants with known function. For example, given a person's genome, we should be able to roughly predict what hair color and texture they have, eye color, etc.

@Armand, that doesn't fit the question, which specifies "without reference to anything else (ex: a repository of genomes of known living organisms)".

@Armand we know only that specific genes correlate with specific hair colors, but we don't know the full cause-and-effect chain. In the end, to determine "this gene encodes red hair" from first principles, you'd have to know the function of all the genes that are involved in creating hair cells, pigments in general, and how the gene is activated in hair cells but not in skin cells.

Yes, by OPs mentioning a "model" I was assuming that model would contain info like hair color genes and so forth. In re-reading the question it does seem the OP intends a de novo model based on structure prediction.

Echoing other answers, our ability to predict the function of individual genes is entirely dependent on either A) physical experiments (making the products of those genes in a test tube or performing genetic experiments) or B) inferring their function from their similarity to other genes that have been studied by physical experiments.  In other words, we can't currently predict individual gene functions with computers unless we have some similar outside reference to compare to.  Without the ability to do that for a single gene, there is no possibility of doing this for a whole genome.  Forget about predicting how all of these genes would express or interact to create a complex living organism.  If you could compare to other sequenced genomes, phylogenetic analysis would quickly tell you what species your unknown genome was most similar to.
I thought I might offer an alternate answer about what one might be able to do with some general knowledge of genomes but not the ability to actually compare your unknown genome to specific genomes / known DNA sequence.  With the right software, you could roughly predict where the genes were in your unknown genome.  This could tell you how many genes this organism has, how many of those genes are unique genes or repeats, and how much of the genome is made of non-genic sequence.  You could also look at the overall structure of your genome.  These factors could give you a rough guess about what kind of organism you have.  For example, if your genome is circular (which you could tell from the sequence), you have a prokaryote or archaeon.  If there are very few genes, you could infer that this organism lived a parasitic lifestyle, since the smallest known genomes are from parasitic species that no longer need to encode for all of the functions of a fully independent lifestyle.  A large genome, linear chromosomes, or multiple chromosomes would indicate a eukaryote.  If you see evidence of polyploidy, your organism could be a plant.  Through similar methods, you could probably tell a eukaryote's nuclear genome apart from mitochondrial and chloroplast genomes and guess whether it was a plant based on how many non-nuclear chromosomes it has (two distinct non-nuclear chromosomes would indicate a chloroplast genome is present).  Just a little thought experiment on what one could do with an unknown genome sequence without Genbank or reference sequence, but with current computational tools and some knowledge about genomes.

How would you know (without reference to genbank or similar) that a particular gene came from a mitochondria or a chloroplast? I can see the bit about eukaryote vs prokaryote, but I don't see that the next steps would work. I don't think people have solved how to determine ploidy with sequencing yet - please let me know if I am wrong, because I love to learn new methods.

Ploidy is a number-of-copies measurement.  If you had error-free sequence for all the DNA from a single cell, multiple alleles for the same gene could be tallied separately. You might reasonably infer triploidy if you found many genes with three alleles present, tetraploidy if you found many with four alleles present, etc.   Of course you wouldn't expect multiple alleles at every site,  but finding even a few such would be a strong hint.

@bob1, for mitochondria or chloroplast chromosomes, they're both circular (although wikipedia tells me that there's some debate about chloroplasts).   So, they should be identifiable apart from other eukaryotic chromosomes without having to worry about identifying the genes themselves.  Also, I'm guessing that both mitochondria and chloroplast chromosomes are much more gene-rich than most nuclear chromosomes, so they could probably be confirmed with that as well.

@bob1, as to polyploidy, I had allopolyploids in mind like wheat and other plants, which I think would be strikingly obvious if you were to look carefully at your sequence.  I'm not experienced in this area at all, but Ethans answer sounds pretty logical to me for cases like autopolyploidy.  That would depend on having a fair amount of heterozygous alleles though.

@Ethan - but modern sequencing technology (with perhaps the exception of PacBio and Oxford Nanopore) gives varying sequencing coverage and depth for a single sample, which in no way relates to ploidy as far as I can tell. There are tools out there to work this sort of thing out, but as far as I can tell they are  definitely imperfect to put it mildly.

@LTRretro Yes, mito and chloroplast are classically described as circular - my question here (and I should have been more clear) relates to how you would tell the mitochondrial/plastid genes from those of contaminating DNA from bacteria etc. These generally make up a significant portion of any sample taken from an animal, with the exception of deep tissue, even then you tend to get some.  But I guess this is getting away from the topic in hand, where one is given a complete sequence, not just the raw reads.

@Bob1 - The idea is not to rely on quantitative estimates of copy number.  The idea is to look for loci where N sequence variants are present.   In practice most of these will be artifacts, but as the hypothetical error rate goes to zero any remaining cases are due to multiple copies of the gene.  That would include paralogs and multi-copy repeats within a single genome, but also it would include the presence of multiple alleles due to polyploidy.