text:
External "lungs" that process your blood the same as your real lungs do - would that stop your need for breathing?
So say your blood goes with a tube out of your body. In an external device all the chemical/biological magic would happen and it would be fed back to your body.
Of course this doesn't exist (yet), but if this would be possible - would it mean you automatically stop your need for breathing?
Is "gasping for air" linked to the amount of oxygen in your blood? Or is there something else going on?
Just a random (theoretical) shower thought. The idea that you wouldn't feel the need to breath feels weird to me.

A device that fits your description does seem to exist, namely an ECMO machine that delivers extracorporeal membrane oxygenation (Fig.1 ). It is defined as:

[A] machine [that] pumps blood from the patient’s body to an artificial lung (oxygenator) that adds oxygen to it and removes
carbon dioxide. Thus, it replaces the function of the person’s own
lungs. The ECMO machine then sends the blood back to the patient
via a pump with the same force as the heart, replacing its function.

The response of patients to ECMO appears to be variable (Crotti et al., 2017):

As the physiologic cardiorespiratory variability is increased in this condition, the dynamic interaction between patient respiratory activity and extracorporeal system function affects the clinical management. The effect of extracorporeal CO2 removal on patient respiratory drive is variable and not always predictable, with some patients responding to CO2 removal with a decrease in respiratory rate and effort and other patients demonstrating a persistently high work of breathing independent on CO2 unload.

Breathing and undoubtedly the exaggerated gasping for air after heave exercise is related to the concentration of CO2 in the blood that's monitored by the brain. Those chemoreceptors basically measure the pH of the blood. However, pulmonary pH receptors exist and a multitude of other physiological mechanisms are at play to keep the level of O2 in check . I happily refer to Brinkman et al. (2020) for an overview on O2 and CO2 homeostasis.

Fig.1. ECMO. source: University of Iowa
References
- Brinkman et al., StatPearl
- Crotti et al., J Thorac Dis. 2018 Mar; 10(Suppl 5): S661–S669


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Skeletisation in space
A space pod containing an astronaut drifts out to space and cannot be rescued. The space pod contains no insects, and the only bacteria present are those originally brought in by the astronaut. There is plenty of oxygen (assume 20%) and the interior is heated in the long term to 20 degrees C by a radioisotope heater.
The astronaut eventually dies through lack of food or water. His body is found many years later. What will the rescuers find? A body or a skeleton?

What's the humidity of the air? In dry air you'd get a mummy, like in the desert or in some church crypts.

First I assume many years equals 10 years or more, although the presence of oxygen may drastically speed this up or it may interfere it is hard to say. Nobody was tried to figure out how something will rot in sealed but consciously oxygenated container since is basically does not exist without a custom built chamber.
Your main factor is humidity that is whether the pod has humidity control, if it keeps a human comfortable humidity you will have a skeletal mummy since skin and hair will survive but much of the body will desiccate. If you just treat it like a sealed container the body fluids breaking down will ramp up the humidity and you will just a have a pile of bones and rather disgusting soup. A sealed container is one way to rot down an animal carcass to get bones, it is called maceration and something that has been well studied. I have done it many times and a few years is more than enough to reduce a carcass down to a skeleton.  Note depending on how long you wait even the bone may be damaged or destroyed although the restricted biota may prevent the final stages of this leaving you with extremely fragile skeleton remains.
I must emphasis the smell will be disgusting, as in even seasoned investigators will be tossing their cookies if they smell it. Almost nothing can describe the disgust of the smell of a human body rotting in a sealed container. Our brains have evolved to find human rotting flesh as disgusting as possible.
for additional comparison  a a paper comparing decomposition of several pig carcasses sealed in concrete.
Source link addresses
https://pubmed.ncbi.nlm.nih.gov/2738563/
https://onlinelibrary.wiley.com/doi/10.1002/9781118953358.ch33
https://journals.lww.com/amjforensicmedicine/Abstract/2013/03000/Burial_of_Piglet_Carcasses_in_Cement__A_Study_of.13.aspx

What breaks the body down in a sealed container? Is this purely microbiological?

yes you are covered in microbes as is your gut and many are more than happy to breaks you down if given access to your juicy bits. You also have a lot of microbes trapped in your clothing (this can actually be worse for astronauts). cell for cell you have about as many microbes as normal human cells.  Mythbusters does a rather telling experiment using a pig carcass sealed in concrete and a sealed car which might interest you. .

Mythbusters [https://mythbusters.fandom.com/wiki/Stinky_Car_(Episode)] certainly demonstrated that fresh pig corpses placed in a car sealed with pressure-sensitive tape for two months decomposed - I could find nothing about bodies encased in concrete. However, Mythbusters found the carcases were covered in maggots, so it seems flies still managed to penetrate the car and lay eggs. They would find that harder to do in space. I really want to know whether bodies will decompose in the absence of insects through the action of microbes naturally contained on or within the astronaught's body.

listed as Buried in Concrete MiniMyth

Presumably this process must end some time when all the chemical energy has been used up and all organic compounds basically have been converted to carbondioxide. Any idea how long this might take? Years, decades, millennia?

@StephanMatthiesen hard to say with the continuous influx of oxygen, likely never there are a lot of materials that will not break down without mechanical breakup. That is how fossilization starts after all. I have held mammoth bones that came out of Wyoming topsoil that have not fossilized.

@john That's true, but I was rather thinking of the disgusting smelly soup which can't be there forever and will at some point not have any chemical energy left to sustain microbial life. In an open environment like your mammoth bones it will disperse in the soil and enter the general carbon cycle again, but in a sealed container the mass must remain there but become really dead at some point, no?

@StephanMatthiesen The smell is some of the byproducts of decomposition, the chemicals resulting from the decomposition of amino acids mostly. it does not last forever but that is very different then when all chemical energy has been expended. expect it to last for decades or more in highly concentrated quantities many hundreds of years for detectable levels. the issue is these byproducts do not break down quickly in a sealed container.

@John Thanks, so it slows down a lot before the final oxidation products are reached. Although I guess at that stage it depends very much on the actual space pod (how large it is, if the systems keep circulating and/or filtering air etc.) so it's hard to say.

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How do people wake up just before their alarm goes off?
I can wake up less than 2 minutes before my alarm goes off regularly.
I read the common wisdom on the subject which says "circadian rhythm; PER proteins; internal clock". I am skeptical of this for two reasons:

I go to sleep at night at different times ranging from 11:00 to 2:00 and rarely check the time, so if I don't even know the sleep start time, how can my body measure out the duration of sleep and get the end time right?
People's chemical levels vary from day to day depending on a ton of variables (food intake, physical activity, stress, etc). It appears that we are not deterministic machines that are constant from day to day to that level of precision

I have a few hypotheses that I haven't heard before:

Maybe the subconscious is queuing off the light level in the room? (this a unique property of the specific minute of wakeup, as there would be less light a minute sooner and more light a minute later)
Maybe while sleeping, the eyes periodically open, view the clock, process the numbers, and wake up accordingly (just like people  can sleepwalk and use their eyes to process where the walls and doors are)

Any thoughts?

Not sure why this is receiving negative voting. If you fail to actually read the post, I'll admit the language (i.e., usage of I ) superficially sounds opinion-focused, but this question is , IMO, asking about a general biological phenomenon that certainly ican be addressed with non-opinion answers. @Noob I think you should add an explicit explanation of what you've already done to ty to answer your own question to help encourage further positive feedback. However, down- and close-voters, I encourage you to provide your rationale for this one since I do not see an issue

When changing the time of your alarm, would you wake up at the same time, or again 2 minutes before the alarm?

For what it's worth, this question could come from me - I have exactly the same experience as OP; had it forever.

The biological answer is presumably cryptochromes.  The foregoing applies to humans who have CRY2 blue light receptors in the inner retina (the neural layer, not the photoreceptors).  I've seen claims these respond particularly well to the light before dawn, though I didn't track those down just now.
That said, a proper skeptic would dismiss this as confirmation bias, at least until proven otherwise.

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How deep underwater could you breathe using a tube which breaks the surface until the water pressure makes it impossible to inhale air?
I'm struggling with a question asking how deep you can breathe underwater using a hollow reed before the water pressure makes it impossible to inhale. The question asked to use this data of maximal respiratory pressures:

The question also gave a hint that for every metre below the surface, hydrostatic pressure increases by 100 cm H2O.
I'm seriously lost on this question, from my research, all I could find was that a difference of approximately 50 cm H2O is needed in order to inhale, but I'm unsure if that is information I should deduce from the table instead of looking up. Even knowing that information, how would I then find out how deep that means you could breathe? Any help would be greatly appreciated.
Thanks

It shouldn't affect the question, but note that to get sufficient air past a certain point (depending on the tube volume), two tubes would be needed, one for inhalation and one for exhalation, otherwise you'd be rebreathing too much of your own exhaled air.

Different graph here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501025/table/T3/?report=objectonly your lungs and the different levels of the tube equalize to the surrounding water pressure, so the maths is simple, a male can fill their lungs till about 50% full at 75cm  although it would take your maximum force and it would require a tube with almost zero flow friction. To breathe comfortably at that depth, the tube body could be about 7cm diameter. Applying maximum force to achieve only 50% breaths would require training because it would be claustrophobic and cause heart acceleration.

I won't write an answer because I don't know the tube resistance relative to diameter, however the faster the breath the higher the tube resistance so the maths chart requires a tube with nearly zero friction, which is probably 4 inches or forearm sized.

First, a sanity check.  Snorkeling isn't generally done at much depth, and this question reflects some subjective sense of that.
My guess (after much confusion) is the table they're providing is apparently the pressures that the subjects were able to apply, when striving to breathe in or out at various levels of "Lung Volume".  But what is "Lung Volume"?  Not Total Lung Capacity - is it Tidal Volume, Expiratory Reserve Capacity, something else?
If I read it that the person, at 22-54% "Lung Volume", can apply only 53 cm H2O of pressure differential while inhaling, that implies that at this depth of external pressure, they can't inhale.  (Oddly, if they lose the battle and go to 1%, the data says their ability to inhale is reduced!) In theory the fluid pressure of water or air on the body should be similarly positioned.
Even so, there are two things that make me doubt this.  First, the inability to inhale should be coupled with a greater ability to exhale.  So I still wonder if sort of shallow breathing might still be possible at the limit of the expiratory reserve, or even in the range of "residual volume", as the external pressure is opposed by connective tissue.  Second, the diaphragm and the external intercostal muscles are, well, muscles, so it should be possible that someone could train those muscles well and resist more pressure.

It should not show greater ability to exhale as exhaling is controlled by inhalation, if you can't inhale your lungs are already at equilibrium pressure so you can't exhale either.

I'm a moderately-experienced scuba diver who's also done quite a bit of snorkeling, mostly no deeper than 10m.
I think the simple thing is to consider inhalation vs exhalation separately looking for the limiting factors. At best, the inhalation table suggests you can generate -53 cmH20 pressure.
Therefore the max breathable depth would be 53/100 x 1m = 0.53m.
That also roughly matches the assertion in the article of 1.5 to 2ft.
The link Mike Serfas used to a snorkeling site makes the same argument about CO2 remaining in the tube when you exhale as outas's comment.
That's a common mistake - yes with a normal snorkel you inhale and exhale through the same tube but that is not mandatory! If you were breathing through a long tube, assuming bubbles were allowed, you could exhale through your nose to avoid pushing CO2 back into the tube.


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Mutation rate breakdown by original and mutated nucleotide for Coronaviridae
In a discussion of the mutations S:Q677H and S:Q677P in SARS-CoV-2 it was mentioned that the mutations leading to this result are "against the tendency" of preferred mutations on the nucleotide level. It was also stated as a well known fact, that the rate of mutations depends on the original and mutated base.
So I'd like to know the mutations rates for all possible base pairs in Human Coronaviruses, or a pointer to reference where I can look them up. A less specific but still applicable reference is also welcome, as well as relative mutation frequencies given in some arbitrary units.
EDIT in response to comment by @David: This is the relevant part of a preprint by Hodcroft et al. on the top of page 5

The amino acid Q changes to H due to a mutation at nucleotide position 23593. Notably, in four of these six lineages, the mutation changes from G to U, whereas in the other two, it changes from G to C (FIG 2B). In contrast, the S:Q677P variant occurs by virtue of an A to C change at position 23592. All mutations leading to Q677H or Q677P involve transversions. Hence, their spontaneous occurrence is generally disfavored relative to transitions. In SARS-CoV-2 samples from human infections, A to C and G to C transversions occur at only ~10% the frequency of C to U transitions, while G to U mutations are more common, occurring half as frequently as C to U. (Wright, Lakdawala and Cooper, 2020) (Ratcliff and Simmonds, 2021).

EDIT 2: Learning more about the terminology, I am looking for a Nucleotide Substitution Model or a Mutation Profile in the described environment, especially in a best fit of the empirical data.

Please provide a reference for your assertions, and explain what you mean by source and target base, as the terms are unfamiliar, at least to me. Also let us know the results of your own attempts to answer this question.

The sun is shining for a change, and am going out for a walk, but it looks like a reference to a general difference in frequency of transitions and transversions, which has a straightforward structural basis. There may already be an answer on this topic here, but if not and nobody else does, I’ll post later.

Here is an answer to a question about transitions and transversions. Do you understand how the different in overall frequency of these types of mutations is a general thing and has nothing to do with the gene, in the first instance? If this answers your question, I would delete it. If not, explain what more you wish to know. But in any case remove the terms "source" and "target" — they are non-standard and IMHO badly chosen. "Original" base and "mutated" base is clear and unambiguous.

The linked question is a good resource, thank you for finding that one, but it does not go down to a quantitative level. I am interested in mutation rates occurring in the wild, not under some mutagene agents.

The general knowledge about transitions and transversions IS based on observations in what you term "the wild", as is knowledge about, for example, the greater mutation rate of  RNA viruses. The details of the mechanisms that explain these observations is necessary  for a rational scientific understanding of them. I suspect that you were unaware of this, in which case I think you would be better advised to do some serious reading in this area rather than responding with vague statements about "being interested in mutation rates occurring in the wild". And "target mutation" still doesn't work.

Does this answer your question? Transition/Transversion ratio

I finally found a paper with numbers, it is Host-directed editing of the SARS-CoV-2 genome by Tobias Mourier, Mukhtar Sadykov, Michael J.Carr, Gabriel Gonzale, William W. Hall, and Arnab Pain.
The authors give relative numbers in percent, so all mutations make up 100%. C>U is by far the most frequent one, making up 36.9% of all mutations, followed by G>U 17.6%, U>C 12.6%, A>G 10.9%, and G>A 10.6%. The rest are much rarer: C>A 2.6%, A>U 2.4%, A>C 1.6%, G>C 1.6%, U>G 1.5%, U>A 1.4%, and finally the rarest one, C>G 0.3%.

are dna mutations random in the quantum mechanical 'unknowable' sense, or are transcription errors determined in the dark by what molecules happen to be close by, ph-levels, etc during dna replication?

This one is specific to RNA mutations, and the article cited suggests some mechanisms responsible for the differences in the rates. Also read the comments below the question about transitions and transversions, in general transitions are more probable than transversions.


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What are the effect of radioactivity on grey wolves in Chernobyl?
I am doing some research about the effects that radioactivity has and is having on grey wolves in Chernobyl and more particularly on their genetics, but maybe also looking at the populations in the area as a whole.
I was wondering if anyone has any knowledge or resources they could share. It would be great!

Is there evidence that the radiation has any effect at all?  Other than keeping most humans out of the area, of course.

Sorry I forgot to point out that I am not only researching the effects that radiation has on wolves now, but also on wolves that were present in the area not long after the disaster. Surely the radiation should have caused genetic mutations in those wolves.


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How to extract oxygen from grow chamber
I have been developing LED grow lights for a year or so and one of the things I am trying to do is to build a grow chamber where I can control temperature, humidity, light intensity and quality and levels of $\ce{CO2}$ and $\ce{O2}$.
I don't have any problems with most of the variables except the gases. I can inject $\ce{CO2}$ and monitor the gas, but as the chamber is hermetically sealed, how do I get rid of excess oxygen produced by the plants? Is there something similar to the $\ce{CO2}$ scrubbers used in aquariums? As a matter of fact, plants also need oxygen for their metabolic processes occurring during darkness, but they produce oxygen in excess of this requirement during the day. It is the excess of oxygen the one I want to extract, and not the whole amount of oxygen in the air of the chamber.
The whole idea is that through the chamber, I can adjust light conditions to each crop based on performance. Gas exchange is an important proxy for Chlorophyll fluorescence and has shown a good correlation with performance.
Any ideas?

A basic problem is that metabolic (life) processes require oxygen. You could flow CO2 through the chamber to eliminate oxygen, but the plant will die. On the other hand, you could seal the chamber with a known composition (e.g., normal air) and then analyze the gas contents some time later. So, it seems to me that you need to have some kind of gas analyzer (and this seems to be a non-trivial problem).

Hi Jim. Yes, plants also need oxygen, particularly during dark periods of time, but they produce oxygen in excess of their metabolic needs. I will edit the question to reflect this.

Absolutely, this is actually looking more as an engineering problem rather than a biology one.
In any case, I think I have found a satisfactory answer on a paper from the 1997 Proceedings of the Sixth European Symposium on Space Environmental Control Systems. The article is called: Oxygen Scrubbing and Sensing in Plant Growth Chambers using Solid Oxide Electrolyzers.
Basically, a disk of non-porous yttria stabilised zirconia (YSZ) is sandwiched between platinum electrodes and inserted in the chamber half-way, with the other half enclosed in whatever will store the extracted oxygen. The electrodes must be porous to allow gas diffusion. The only problem is, that sort of electrolysis cell needs to be maintained at an elevated temperature (800 to 1000 Celsius) in order to work.
By means of electrocatalysis and thermal dissociation the oxygen molecule dissociates to form two oxygen atoms, these in turn pick up two electrons from the cathode and become ions. The ion is then transported by the electrolyte (YSZ) by means of electron vacancies located in the crystal lattice (basically a similar process to that of a N-doped semiconductor whereby impurities create electron holes).
I think I am satisfied with the above explanation. Doable at home? No way, but it does answer the core question.

It's going to be tricky to strictly regulate CO2 and oxygen in a chamber.
We use a palladium catalyst to maintain an anaerobic environment for microbiology purposes, but this requires a source of hydrogen to work, and it doesn't work well for fine adjustments, but rather for maintaining extremely low oxygen conditions. We also have a hypoxic chamber that regulates O2 concentrations with good precision (0.1%), but it's expensive to maintain, and requires sensors for oxygen, CO2, and nitrogen, and an automatic gas injection system for each component.
A simpler design would probably be to have some gas exchange with the room your chamber is in, using a tyvek membrane to minimize water loss (and HEPA filters if you're worried about pathogen contamination). My friend who farms oyster mushrooms did something similar, and also rigged up a humidity sensor to a humidifier using a RaspberryPi to manage the moisture loss.
However, if you're dead set on having a strictly regulated atmosphere for you grow chamber, you might want to consider consulting with Coy Labs. When we needed a chamber with the ability to tightly regulate oxygen levels for microbiology research, they came to the lab and worked with us on our specific needs and together we develop their first working model nearly from scratch (we modified one of their existing anaerobic chambers). But it worked so well that they now sell hypoxic chambers as part of their standard line of products. As far as I know, they haven't done any work with plant grow chambers, but they're a small company with a lot of experience building contained atmospheric control systems. Pretty much every order is custom built, so they're used to answering a lot of questions and tailoring their products to the specific needs of a customer, and they're very helpful and responsive with maintenance and upkeep. Just know that they're products aren't cheap.
https://coylab.com/

Hi @MikeyC, good stuff on your above answer! There are plenty of clues on what direction to take, even more so after checking the company's site you've recommended. I'll leave it open though as it does not necessarily answers the question of how to extract the extra concentration of O2 from within the chamber.

Fair point. The system I'm describing is additive, not subtractive. Essentially, the gas injectors would add other gasses (either Nitrigen or CO2) to keep the O2 below a set concentration. To avoid over pressurizing the chamber, it would need a vacuum pump to purge some atmosphere after injection, or maybe even a simple water-filled airlock system like beer-brewers might use. It's starting to sound like your problem is one of engineering, rather than biology. Maybe try an engineering forum.


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What does genetically tractable strain mean?
I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this kind of data, I wanted to have a look at some work that was already done. I found this interesting article: Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.
I think that it could be a good starting point. However, it is not easy to understand the whole article for me and I suspect
that the source of this difficulty is mainly due to the fact that I do not know what "Genetically Tractable Pyrococcus Furiosus Strain" means.
Searching in Google I found this article: Systematic evasion of the restriction-modification
barrier in bacteria, that explains:

Bacteria that are recalcitrant to genetic manipulation using modern
in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems.

Then it tells also that:

A strain that is not amenable to alterations of its genome or to the introduction of new genetic information during genetic engineering is termed genetically intractable.

Therefore, from this short explanations, I have an idea of what genetically intractable means. But, I still wonder why in the first article that I mentioned, the scientists should have been interested in sequencing such a genome (genetically tractable) and in comparing it with the one that was firstly sequenced (the so called reference strain) ? Moreover, what does genetically tractable mean?
Indeed, in the case of the first article, the following description is reported:

The best characterized of the Pyrococcus species is P. furiosus, the first to be isolated (19) and the first to have its genome sequenced (49). This organism has been studied by numerous “-omics”-based approaches, including transcriptomics by tiling (59) and DNA microarrays (14, 35, 51, 54, 57), comparative genomics (8, 33, 60), proteomics (32, 42), metallomics (11), and structural genomics (25). In many ways, it has become one of the model hyperthermophiles, a status recently sustained by the development of a genetic system for the organism (37). This was based on isolation of a variant in a lab strain population, designated COM1, which was highly efficient in taking up and recombining exogenous DNA in both circular and linear forms. The COM1 strain was obtained by targeted gene disruption of the pyrF. locus (PF1114) using a plasmid designed for double-crossover recombination (37).

Then what they do is:

The genome sequence of COM1 has now been determined, and comparison with the published sequence of the P. furiosus reference strain (49) (NC_003413) revealed a surprisingly large number of changes.

Thus, I do not understand (both in the case of this article and also in general case) what genetically tractable means (the description given by the article is not sufficient for me to understand) and why are we interested in doing the alignment between the reference genome sequence and the genome of genetically tractable strain ?
Sorry if my question could be trivial but my biological backgrounds are really poor. I reported the extracts of the articles because they give me an idea of the answer but, to be honest, I do not have fully understood them. Therefore, if you can explain me also those extracts, it would be great. Thank you in advance.

You've already basically got the idea of "genetically tractable": if we can readily modify an organism's genome using known techniques, then it's genetically tractable.
That's a moving target, of course, because the set of available techniques is constantly expanding, so this is more of a pragmatic definition than a taxonomic definition. It's a notion that's quite important, however, because it's far harder to study an organism or to develop applications if you can't manipulate its genome.  If you can manipulate genetics, then you can make knock-out strains, introduce new functionality, and apply many, many other powerful and useful biological techniques.
So now to the last part of the question: assuming you've now got a tractable strain, why compare it with the reference strain? Well, if you're working on engineered applications, you probably really don't need to (other than from curiosity).  If you want to use the tractable strain to study things about the original, reference form of the organism, however, then you need to know their differences in detail, in order to have some idea of how much your results obtained by manipulation of the tractable strain are likely to inform your understanding of the reference form.

Thank you @jakebeal . I have a last question: so, for example, if they destroy a gene (PF1114) and then they compare the "modified" genome with the reference and they see (by DNA sequencing) that the tractable genome has two large chromosomal segments that have inverted order with respect to the reference order and that, despite this, there are no apparent consequence for proper metabolic function, is this a sort of assessment of the fact that they are resistant to distruptions (that maybe caused by gamma irradiation) ?

@Manuela I think this is really a separate question about how to interpret the relationships between genomes. Destroying a gene and rearranging chromosomal segments are quite different types of activities, and I'm not really sure how you're trying to put the pieces together here.

Ok thank you again .

I was thinking about this discussion again... What I still can't digest is why it is correct to compare the genetically tractable strain genome DNA sequence (that is a variant of the Pyrococcus Furiosus species) which has undergone targeted gene disruption with the reference ? I mean... I would compare the Pyrococcus Furiosus genetically tractable variant strain after targeted gene disruption with the genome DNA sequence of the  Pyrococcus Furiosus genetically tractable variant strain before the modification (so before the targeted gene disruption)...

Could the reason be that a variant can be considered the same as the "original" or "main" strain? I think it is not a separate question but if you do not know and you think I should do an other post about this, I will do it.

@Manuela I think it would be good to ask your more focused question, specifically about comparability, as a separate follow-up, linking to this question.


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Can we decode memories?

Premise: I don't have a strong background in neuroscience or human biology, so I would ask you to answer like you would at a 5 years old child. I have done a couple of research on the web, as well as here on StackExchange, but the answers that I have found are either pretty old or difficult to understand for me.
I have read that memories are not stored in a unique place in our brain.

If you knew the region where the particular memory you are looking for is, would you be able to decode it?

Example: Let's say that someone said to you something you perfectly remember even after a few years. Since you remember the exact words, I suppose that those words are stored in our brain somehow. Is it possible to retrieve what those words were?
To summarize my question, what do we know (and don't know) about how we encode memories?
Thank you all.

Given recent advances in AI related neuroscience, I can easily imagine a future where it is possible to decode thoughts and impressions. In fact, we are already nearly there.
It seems like the limitation is not the decoding of memories, but their detection or measurement: While you are seeing an image and the brain actively is working on it its perception, causing your neurons to fire in certain patterns that can physically be measured with fMRI, there is the possibility to decode some information out of these signals. Same if you remember a scene in your memory.
However, I don't see any theoretical potential to read memories out of inactive/dead brains. So I hardly can imagine that any machines can read anything that's not currently happening in the brain. Maybe your brain can be stimulated somehow and its response can be read, but in the end you need physical measurements.


text:
How many cells need to be damaged before a human can feel it as pain?
I'm guessing the answer to this question is rather large. Skin cells die all the time, it seems, and that never registers as painful. But suppose you rupture or otherwise destroy a group of cells, say in the dermis or something, which enough precision to be able to specify the exact count. How many would you have to destroy before it would be perceptible? What if you add a delay between the destruction of each cell in the group? If it was staggered in time, would that make it imperceptible again?

Although any number estimation would be inaccurate, I can think on two factors that can influence the count.

Cells location: Pain is trigger when specialize cells (Nociceptors) fires action potentials. The density of those nociceptors is greater in the tip of your finger than in your back. So the number of cell damage that trigger the pain would be different in those areas too.
Cell death rate: The delay that you mention is a key factor. Slow death like the normal on skin is done by a regulated mechanism (Apoptosis), in this process the cellular components are recycled. In fast cell death, the cellular components are released causing inflammation, which increases the nociceptors sensitivity.

Would it still be true that "any number estimation would be inaccurate" if we hold the cell location constant? Surely this could be studied empirically? Not that it would necessarily be a good idea to do that.

Have in mind that pain is felt when nociceptors are activated. If you have a method clean enough to kill cells without activate nociceptors directly, then the debris of the death cells can cause nociceptors activation because of the inflammatory process.

@bxw the location matters a mot, for instance you could destroy most of the brain without pain, since it has few pain receptors.

There is no specific number of dead cells to be honest that serves as the threshold for pain, it is the molecules that are responsible for decreasing or increasing the threshold of pain either peripherally (at the site of nociceptors) or centrally (endogenous opioids). Here is a diagram that kind of summarizes pain pathophysiology at nociceptor level.

For example, sunburn produces temporary sensitization of the affected area. As a result normally innocuous stimuli, such as light touch or warmth, are perceived as painful (a phenomenon referred to as allodynia), or normally painful stimuli elicit pain of greater intensity (referred to as hyperalgesia)
As correctly stated in the previous answer, Apoptosis would never initiate pain since it doesn't involve any inflammation.

Reference-  Basbaum AI, Bautista DM, Scherrer G, Julius D. Cellular and molecular mechanisms of pain. Cell. 2009;139(2):267-284.
doi:10.1016/j.cell.2009.09.028
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852643/


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If aging is caused by "DNA Damage" why is the process of aging generally similar between people?
When I hear the phrase "DNA Damage" I imagine completely random changes in the DNA of a person's cells. If this is the case, then it seems like every person would age differently depending on what happens to their DNA. But that is not what we see. In general people age in very similar, predicable ways almost as though it was programmed into the system.
Is it just that most random DNA changes result in cell death and that most of aging is just having fewer healthy cells in any given tissue?

Hi Mark. Welcome to Bio.SE. DNA damage is one aspect of ageing. Ageing was definitely not programmed into the system, and in fact is probably entirely plastic. See here for more about ageing: https://www.youtube.com/watch?v=-hCkVHioBVA Crucially, we have not lived longer than about 30 years old during evolutionary timescales. I'd also challenge the idea that we all age similarly.

It's worth pointing out that processes causing DNA damage are not necessarily random. Telomere shortening in somatic cells, for example, seems to be controlled mostly by deterministic factors. Likewise, somatic cell mutations, which probably occur stochastically (not necessarily at random), can affect fitness at the cellular level, and therefor persist or accumulate in predictable ways that affect cell proliferation and/or survival.

People do age differently.  Consider perhaps the most obvious signs, like grey hair or baldness.  Some peope go grey (and men start to lose hair) in their 40s or so.  Others can hit their 70s with a full head of hair that has only a few streaks of grey.

https://biology.stackexchange.com/questions/98428/biochemistry-of-ageing-new-discoveries I think as is said there ageing has to do with dna changing structure more than code. But also sunburn seems to leave same traces on people, for some reason. Great question though

Nit that clear to me tbh @jamesqf. There are epigenomic chanfes, mutations due to methylation ,UV, ROS, telomere shortening, some energy troubles with the mitochondria too..


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What fraction of bacterial proteins are membrane bound?
Almen et al. showed that around 27% of the human coding proteins are membrane bound.
How does this compare with bacteria such as E.coli or B.subtilis (or any other bacteria)? Is there a paper out there demonstrating this?
I assume that there would be massive variation among bacteria, so although one specific example would be enough as a ballpark, I expect that this may not represent all bacteria well.

As a proxy for asking which bacterial proteins are membrane-bound, we can ask which proteins harbor transmembrane domains. A popular tool for detecting transmembrane domains is TMHMM, which looks for transmembrane helices in protein sequences using a hidden Markov model.1
For E. coli strain K12, UniProt reports 4,391 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,072 proteins have at least 1 transmembrane helix (24.4%), and 775 proteins have 2 or more transmembrane helices (17.6%).  Expanding this analysis to the E. coli pan proteome, which contains 165,127 non-redundant protein sequences, TMHMM predicts 28,369 proteins have at least 1 transmembrane helix (17.2%), and 16,105 proteins have 2 or more transmembrane helices (9.8%).
For B. subtilis strain 168, UniProt reports 4,260 protein sequences corresponding to unique genes. Of these, TMHMM predicts 1,175 proteins have at least 1 transmembrane helix (27.6%), and 845 proteins have 2 or more transmembrane helices (19.8%). Looking at the pan proteome for this species, which contains 18,046 non-redundant protein sequences, TMHMM predicts 3,967 proteins have at least 1 transmembrane helix (22.0%), and 2,463 proteins have 2 or more transmembrane helices (13.6%).
The relative depletion of transmembrane domain-containing proteins in the pan genomes of both species relative to their reference genomes could point to a functional skew of accessory genomes towards proteins that are less likely to be membrane-associated, such as strain-specific virulence factors, antibiotic resistance genes, integrated phage proteins, and proteins involved in niche-specific metabolism.2,3 Additionally, the relative enrichment of transmembrane domain-containing proteins in B. subtilis compared to E. coli could reflect the different membrane compositions of Gram positive and Gram negative bacteria, though it's hard to say without sampling more species.
One important caveat to TMHMM -- predicted transmembrane segments in the N-terminal region are sometimes just signal peptides. Signal peptides are likely to appear as single transmembrane domains, which is why I've also reported the fraction of proteins with 2 or more transmembrane helices, above.  A more complete analysis may run the same protein sets through SignalP 4 and cross-reference the TMHMM hits to identify transmembrane domain-containing proteins that also contain signal peptides.
Note that the cited publication by Almen et al. uses TMHMM and directly references the results of the original TMHMM paper,1 which reports transmembrane protein abundance in the proteomes of several species.

One of the most referenced papers regarding the percentage of membrane proteins in proteomes is from 2001 where the membrane topology prediction method TMHMM was applied on a number of proteomes from different species to estimate the membrane protein content, for example, Caenorhabditis elegans (31%), Escherichia coli (21%) and Drosophila melanogaster (20%).

Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001 Jan 19;305(3):567-80.
Kung VL, Ozer EA, Hauser AR. The accessory genome of Pseudomonas aeruginosa. Microbiol Mol Biol Rev. 2010 Dec;74(4):621-41.
Álvarez VE, Quiroga MP, Galán AV, Vilacoba E, Quiroga C, Ramírez MS, Centrón D. Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1. Front Microbiol. 2020 Mar 18;11:342.
Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 1999 Jan;12(1):3-9.

A very thorough answer! Thanks!

It's interesting how much discrepancy there is between modern uniprot annotation and the original TMHMM paper.

I assume you are referring to the values for E. coli, 24% vs. 21%?  I haven't read the original TMHMM paper in detail, but the difference may be due to different inputs (was a complete E. coli proteome available in 2001? Or perhaps a different strain) or differences in TMHMM parameters.

Yes I realise my comment was misleading. I am actually shocked that they are so close even 20 years apart!


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Why are disaccharides less reducing than monosaccharides?
My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?


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Why are cells in blood smears undetectable after absorbing moisture?
I'm a student learning how to prepare blood films and today I was curious about something, so I performed an experiment.
After preparing a thin blood smear and drying it (no staining), I took a look under the microscope (at a total magnification of about 200X... I have a cheap microscope). Even though it was zoomed out, the red blood cells were easy to distinguish. The cells were clear but they had dark edges.
Then, I blew some hot air onto the same slide, causing the dry smear to absorb some moisture. Then I let it dry once again.
I observed the same slide under the microscope once more, but this time, I could barely make out the red blood cells. They were certainly still there, but their features/borders were extremely hard to make out and distinguish.
I'm wondering what causes this. Are the cells absorbing moisture and thus changing their morphology? I couldn't find any answers online, so I thought I'd ask here.

It might be helpful if you are able to post a picture of what you're seeing, however, it sounds like the blood cells are lysing.
The water you introduced to the cells through the moisture in your breath is likely creating a hypotonic environment, causing the cells to intake a lot of water and then lyse, causing their appearance to become atypical.


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Why don’t bone marrow donations harm the donor in the long term?
I have googled about this, and the most I can really find is that donating bone marrow/blood stem cells is not harmful in the long run, but I want to know why and how much is really known about this.
My question “stems” from my maybe cartoonish notion that you have all the stem cells you’ll ever have at the beginning of your life and that their depletion relates strongly to aging.
In my googling, I have read studies that lifespans of older mice can be extended with bone marrow stem cell transplants from younger mice. Based on my cartoon, I guessed that perhaps older mice have some depletion of and/or damage to their own hematopoietic stem cells that reduces overall formed element production, and this is the state that a transplant helps to fix. With this frame of mind, I have a hard time imagining that even a young donor of blood stem cells is not harmed in the long run. Hasn’t their pool of stem cells effectively been aged somewhat by the donation? Or is damage to the population of cells over time by environmental factors much more significant, more the “bottleneck” in cell health than the gradual deterioration caused by repeated division? Is it that donation effectively only forces something on the order of one extra division per cell? I also wonder whether that “bottleneck” could vary depending on the typical longevity of the animal under study.
Regarding my question about what is known—I suppose I’m asking what kinds of principles or studied effects are likely being referenced in laypersons’ articles declaring that donors do not experience long term harm.
I’m sure that I am probably saying some nonsense things because biology is not my field. Any corrections and disentangled conflations would be appreciated!

Hematopoietic stem cells (HSCs) can regenerate themselves, with no loss of "stem-ness". When bone marrow (which contains high numbers of these cells) is harvested for a transplant, the remaining HSCs divide and eventually repopulate the area that the marrow was harvested from, leaving it no different than before. There is absolutely no identifiable difference between the "old" and "new" HSCs - they both have the same lifetime, the same markers, the same functionality, etc. There is no long-term damage to the donor.


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Why hypothyroidism causes body ache?
In the condition of hypothyroidism the Thyroid Stimulating Hormone level is high in individuals. What signalling/metabolic pathway mediates this sensation of pain which is mostly experienced in feet and joints.

This isn't my field, and I'd love to see my answer surpassed by someone with expert knowledge.  But I should say a recent case report (Pantazis, 2016), though it dealt with an unusual situation, discusses some of the current thinking:

hypothyroidism is characterized by decreased synthesis and degeneration of collagen. Hypothyroidism also inhibits epimerase, which results in reduced chondroitin sulfate and elevated hyaluronic acid, hence weakening the matrix. Moreover, it causes accumulation of glycosaminoglycans (GAGs) in the extracellular matrix (ECM), being involved in the pathogenesis of carpal tunnel syndrome during hypothyroidism and predisposing patients to tendon calcification

THs have known effects at the cellular level on the proliferation and differentiation of bone and cartilage. The hypothyroid state appears to induce abnormalities in these tissues, which results in such clinical manifestations as epiphyseal dysgenesis, aseptic necrosis, possibly crystal-induced arthritis, and an arthropathy characterized by highly viscous non-inflammatory joint effusions primarily affecting the knees, wrists, and hands. Neuropathic and myopathic symptoms accompanying hypothyroidism may manifest as joint region abnormalities when in fact there is no underlying arthropathy.

These paragraphs cite three much older sources.  I don't see a tremendous amount of activity on this narrow issue in PubMed - the broader issue that this case illustrates is whether there are better ways of diagnosing and treating hypothyroidism to restore the balance more effectively; see Midgeley, 2019 for example.

Thank you so much :)


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Are there phage-eating bacteria?
If phages (bacterium-eating viruses) prowl on bacteria, are there bacteria (or other micro-organisms) that hunt phages for food? They are rich in proteins anyway... Are there studies on this subject? Thanks

Minor quibble, the phages despite their name aren't really "eating" bacteria... More major quibble: most bacteria don't "eat" proteins https://en.wikipedia.org/wiki/Bacteria#Metabolism

It's suspected that some protists (namely choanozoans and picozoans) are proper/direct "virus eaters" due to the size of their "eating apparatus" and scarcity of bacterial remains inside them (unlike viral remains), but the evidence is pretty recent; the (2020) study:

used modern single-cell genomics tools to sequence the total DNA from 1,698 individual protists in the water. Each of the resulting Single Amplified Genomes (SAGs) consists of the genome of a single protist, with or without associated DNA: for example, from symbionts, ingested prey, or viruses or bacteria sticking to its exterior. The technique is very sensitive, but doesn’t directly show the type of relationship between a protist and its associates.
The researchers found a range of protists including alveolates, stramenopiles, chlorophytes, cercozoans, picozoans, and choanozoans. Nineteen percent of SAGs from the Gulf of Maine and 48% of those from the Mediterranean were associated with bacterial DNA, suggesting that these protists had eaten bacteria. More common were viral sequences, found in 51% of SAGs from the Gulf of Maine and 35% of those from the Mediterranean, with a frequency of 1–52 virus types per protist. Most were from viruses known to infect bacteria – presumably representing parasites of the protists’ bacterial prey.
But choanozoans and picozoans, which only occurred in the Gulf of Maine sample, were different. These groups, neither of which have chloroplasts, are poorly known. Choanozoans (3–10 µm; also known as choanoflagellates), are of great evolutionary interest as the closest living relatives of animals and fungi. The tiny (up to 3 µ) picozoans were first discovered twenty years ago and originally known as picobiliphytes. Until now, their food sources were a puzzle, as their feeding apparatus is too small for bacteria – but ample for viruses, most of which are smaller than 150 nm.
Every single one of the choanozoan and picozoan SAGs were associated with viral sequences from bacteriophages and CRESS-DNA viruses, but mostly without any bacterial DNA, while the same sequences were found across a great diversity of species.
“It is very unlikely that these viruses are capable of infecting all the protists in which they were found,” says Dr Julia Brown, a researcher at the Bigelow Laboratory for Ocean Sciences and coauthor on the study.
The authors conclude that choanozoans and picozoans probably routinely eat viruses.

The news release also says that how these "virus eater" protists manage to protect themselves against viral infection isn't yet known/studied.
If this needs saying... protists (unlike bacteria) are eukaryotes. I haven't found any source suggesting that any prokaryotes (bacteria or archaea) manage to sustain themselves on viruses.

According to Sci. Am. coverage of the same research, the picozoans are themselves a relatively recent (2007) discovery


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Can spike protein induced cell fusion be triggered by the mRNA vaccine?
The mRNA-based vaccines cannot lead to COVID-19 or its symptoms since they only lead to the production of the spike protein in the cell.
However, the spike protein itself can lead to cell fusion:
Quantitative assays reveal cell fusion at minimal levels of SARS-CoV-2 spike protein and fusion from without
Is this a potential risk of the mRNA vaccine ?
I could imagine, that the spike protein needs to be bound to the virus to induce this effect ?
I could not find any literature where the effect of the unbound spike protein is tested.

Why the down vote ?

The virus membrane anchored spike provokes virion-cell fusion, the cell membrane anchored spike provokes cell-cell fusion, when encountering ACE2. In most vaccines the 2P mutation greatly reduces this behavior (not in the AstraZeneca vaccine).

The mRNA vaccines encode a mutant version of the spike protein in which the structural transition needed to to fuse membranes is blocked. This was done to make the immune response focus on the pre-fusion state, which is much better for neutralizing the virus.
From https://cen.acs.org/pharmaceuticals/vaccines/tiny-tweak-behind-COVID-19/98/i38:

Fortuitously, Graham and a former postdoc, Jason McLellan, devised a solution to this problem before the pandemic. Through a bit of structural biology and persistent protein engineering, McLellan discovered that adding two prolines—the most rigid of the 20 amino acids—to a key joint of a vaccine’s spike protein could stabilize the structure’s prefusion shape. This 2P mutation worked in preclinical studies of Graham and Moderna’s MERS vaccine, so they applied it to Moderna’s COVID-19 vaccine.

I don't know if cells expressing wild-type spike protein would fuse into syncytia, but it seems very unlikely to happen with the vaccine spike.

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


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Are there ribozymes that cut double strands
the header already says:
Are there any ribozymes known that cut double strands?
A kind of ribozyme equivalent to the Ribonuclease III.
With cut, I mean that the backbone of both strands, forming the double strand, is opened/broken.
Reaction:
one double strand -> two double strands

Please tell us what research you have done to try to answer this question yourself, and what you have found. Also use standard English if you can: “really cut like” doesn’t cut it, and I find it difficult to see how one can cut something that is already broken. It would be more useful if you specified whether you are referring to RNA or DNA. Context would do no harm either.

I tried to clarify the answer according to your suggestion. I do not mind if it is RNA or DNA that becomes cut, that is why I did not mention it.

I think you need to read about ribozymes a little before formulating questions. As they are thought to be relics of an RNA world they are not going to cleave DNA. As dsRNA is not central to modern organisms, even if it had been in early life, it would be unlikely to have survived.

Could you be more specific? And if the answer is obviously "no", then would you be so kind and answer the question and explain why it is not possible? I still do not understand your question regarding specifying if it is DNA or RNA that becomes cut, as e.g. hammerhead ribozymes cleave or ligate both DNA and RNA.

My question is not "did it survive" ;) I would also be happy to know about an artificially created ribozyme that cleaves double strands. But dsDNA is central in Biology. As a ribozyme constitutes the core or the Ribosome, I was conjecturing that there might be a ribozyme at the core of an enzyme able to cut double strands.

Sorry specifying hammerhead ribozymes in this context was wrong. I found this: "A highly conserved ribozyme in the human and in other species is the hammerhead ribozyme. Ribozymes are active in the cleavage or in ligation of RNA and DNA as well as participating in various RNA-processing reactions, such as RNA splicing, the biosynthesis of tRNA and in viral replication.", here

As far as I am aware from scanning recent reviews, most natural ribozymes act in cis, and none act on DNA. Do you have a reference to the contrary?

See the one above and here. Admitting that they report that the activity was less for DNA compared to RNA.

But like mentioned above, I do not mind if you can not find it in Biology. The question is, if it exists at all and if no, if there are reasons why it is not possible to create one.

The first reference you cited was a book chapter on protein synthesis in which there are 28 references to the ribozyme nature of peptidyl transferase. Please make sure you give correct references before wasting people’s time.

For completeness, here is one that states that a hammerhead ribozyme was used to ligate RNA with DNA. Kind of a mixed case.

"unphysiological" Are you kidding me? I did not ask if it exists in cells. It is a general question. There are people that develop self-replicating ligase ribozymes.

I just came across a paper where they found a DNAzyme that cleaves RNA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1283523/

Ribozyms are generally known to have a potential to introduce strand breaks. However, it's indeed a good question whether those may include double strands!
Unfortunately I don't know the answer as it's generally difficult to prove non-existance, but in this paper, they go as far as to imply that translation needed to evolve due to the lack of helicase activity of ribozymes.
In additional literature for helicase activities (which is generally associated with introduction of double-strand breaks), all ribozymes with helicase activity seem to be attached to proteins to be functional. So maybe it's indeed possible, that there are no ribozymes that cut double-strands.

It is well documented that they make single strand breaks, usually on themselves.

Yes, on themselves on homologius sequences. By the way, I felt the premise of the question was that it's impossible for rybozymes to introduce double-strand breaks.


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Covid-19 is a respiratory illness. So how could you catch it by touch?
The U.S. department of agriculture put out a statement in February 2021 in which they wished to underscore that at the time there is no epidemiologic or scientific information that COVID-19 spreads via food or food packaging.
The press release continues to state "that COVID-19 is a respiratory illness that is spread from person to person". Which stuck with me.
Why are touch surfaces even considered potentially contagious when Covid-19 is a respiratory disease contracted by breathing in virus particles?

I do think this sort of question is better posted on SE Medical Sciences than here, as it does not involve any basic biological principle. Anyone answering this sort of question here is unlikely to be a specialist and is more likely to be repeating what they have read recently in the scientific literature. There was an piece on this topic in a recent issue of Nature, which you could try searching for yourself.

https://skeptics.stackexchange.com/a/47225/29579

Transmission through inanimate objects is referred to as "fomite" transmission. It's really hard to know exactly how important fomites are for a particular illness. There is, however, strong evidence that respiratory viruses can spread via this method. Generally, the emphasis is on how contact with hands can lead to infection when someone touches their hand to their mouth, nose, or eyes.
The review by Boone & Gerba, 2007 touches on several issues of fomite transmission. In general, it is easiest to demonstrate evidence of the potential rather than the actual rate of fomite transmission, by looking at viability of viruses on surfaces and how well they transfer to other objects and the hands. However, they also write about epidemiological evidence:

Several epidemiological studies have supported laboratory studies by indicating environmental contamination as a potential vehicle for virus transmission. During an outbreak in a Honolulu nursing home, it was determined that staff hands or fomites (e.g., towels, medical cart items, etc.) spread influenza virus (51). An outbreak of coronavirus (SARS) in a Hong Kong apartment complex may have resulted from fecal-oral transmission combined with environmental contamination (62).

When natural rhinovirus colds were studied, rhinovirus was found on 39% of symptomatic individuals' hands (35). Additionally, volunteers touching contaminated objects and/or the fingers of symptomatic individuals had a higher attack rate of colds if they inoculated their own eyes or nose (35).

They also refer to studies of disinfection/hygiene intervention. The only practical way for these methods to interfere with transmission is by preventing fomite transmission, so if cleaning surfaces and washing hands reduces infections, you can infer that these are contributing routes of infection:

In addition, a review article by Barker et al. cited over 15 research studies that indicated a decrease in viral contamination and viral infection when hand washing was used regularly as an intervention (7). Subsequently, disinfection and hygiene intervention studies, which have cited a reduction in nonspecific illnesses, only support interruption of disease transmission.

I've also attached the reference from that Barker et al paper, which is a simple, informative read.
Barker, J., Stevens, D., & Bloomfield, S. F. (2001). Spread and prevention of some common viral infections in community facilities and domestic homes. Journal of Applied Microbiology, 91(1), 7-21.
Boone, S. A., & Gerba, C. P. (2007). Significance of fomites in the spread of respiratory and enteric viral disease. Applied and environmental microbiology, 73(6), 1687-1696.

In addition to the first answer that was posted, I would point out that, like many other coronaviruses, SARS-COV-2 is also an enteric pathogen, capable of primary infection in various GI tissues. To my knowledge, there's no conclusive evidence that an orally transmitted GI infection can cause severe respiratory symptoms (or even occur in the absence of respiratory infection). But it was something that was worth considering at the start of this pandemic, and is still being investigated as a potential risk for certain medical procedures (like fecal microbiota transplantation).


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Do factors other than concentration gradient and membrane permeability affect the diffusion potential?
If, hypothetically, the concentration gradients and the permeability of 2 different ions (Na+ and K+ for example) in 2 separate solutions are the same, will the diffusion potentials be different?
I'm trying to gain an intuition for the concept of diffusion potential and equilibrium potential.
It read this topic from 2 physiology textbooks but haven't really found an answer anywhere. I understand that the diffusion potential is the potential difference generated when an ion moves through a membrane down its concentration gradient. I also know that it is determined by both the concentration gradient and the permeability, but, does the type of ion itself matter if the charge on the ions is the same?

You can determine the diffusion potential mathematically with the Nernst equation. If it's not in the Nernst equation, it's not necessary.
The charge of the ion matters (including valance), the temperature matters. Some universal constants are in the equation but these don't vary.
Other factors that potentially matter are found in the other parameters, like the permability.


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Are all fish that can live in either salt water or fresh water bigger than some critical size that is larger than the smallest of fish?
I cannot understand this answer. I don't know much about biology or have a lot of trouble recalling stuff from a university biology book I bought for a course I never took because it was so long ago and it was confusing even then. I think I once learned that salmon can live in salt water or fresh water. According to https://fishcostarica.org/this-fish-lives-over-60-years/, tarpon can also live in fresh water or salt water. It seems to me that for tiny fish, they deed a different type of body with more solutes inside the cells in order to live in salt water and the tiny fish that can live in fresh water have a different type of body with fewer solutes inside the cells. And advantageous traits come with costly traits so a small fish that could do both would have more of a costly trait and therefore be outcompeted to extinction. There are plenty of fish in fresh water already eating the resources in the fresh water and plenty of fish eating the resources in salt water. And being able to move back and forth between them doesn't really enable a small fish to get more food. I think a big fish on the other hand would have a much slower rate of osmosis so it can easily pump water our as fast as it is getting absorbed into the cells or in as fast as it is getting absorbed out of the cells. Salmon also have some reason to go back and forth between fresh water and salt water.

Timothy, you should word the title better: bigger than the smallest of fish is about 8 millimeters:  what size is bigger than a critical size that is bgger than 8 millimeters, that doesn't seem very big?, i am confused already.

@aliential I guess I'm asking whether it's the case that there is some critical size bigger than the smallest of fish where it tends to be evolutionarily harder to live in both salt water and fresh water.

Theres small species known to be Euryhaline. The comment you just wrote is a lot easier to read wording than the original question text, you should edit the question with just those words.

"It seems to me that for tiny fish, they deed a different type of body with more solutes inside the cells in order to live in salt water and the tiny fish that can live in fresh water have a different type of body with fewer solutes inside the cells. And advantageous traits come with costly traits so a small fish that could do both would have more of a costly trait and therefore be outcompeted to extinction." Do you have any evidence for that claim? And what does body size have to do with anything? I'm struggling to understand what the purpose of this question is.

Also, please note that the answer you linked to was to a question about anadromous fish - those that migrate up streams to spawn. There's a big difference between that and euryhaline fish, which can survive in salt and fresh water. I would imagine that anadromous fish would tend to be bigger, given the strenuousness of their migrations, while euryhaline fish could be any size at all.

Mollies , there are a few kinds , many are 2 to 3 " , live in fresh or salt . They seem to prefer fresh but often live in sea coast areas where tides ,etc. may cause intermittent changes between fresh and salt ( and brackish of course) . I used black mollies to start a salt water tank, I had a couple in the salt for months because it was not easy to catch them in a large tank. I expect there are other small fish such as puffers.  The mollies adapt very quickly , just drop them in whichever water and they behave normally.

You just give a single example. That doesn't tell me whether they're a tendency that way.

There are also some really small fish. I guess I defined big to mean big enough to be able to live in salt water or fresh water. There are some really small fish. If an answer confirming that none of the fish that size can live in either salt water or fresh water will do.

I fixed my the titled of my question.

Wikipedia has a listing for brackish water aquarium fish ; most can be in fresh or salt water.

I didnt read beyond the paragraph about your study books situation, Euryhaline on wiki reveals tiny euryhaline fish... 4-5 cm Fundulus heteroclitus which presumably can withstand salt changes as juveniles, 2-3cm.
Probably there are species a lot smaller because individual cells perform the osmotic rebalance, and cells are much bigger thans water and salt, so a smaller fish can just develop more of apparatus for osmotic balancing.


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What are "inactive" cells during Ca2+ imaging of neurons?
I am reading this paper, and have found the following Figure (Extended Data Figure 5) where they show maps of active cells in the amygdala as imaged with a miniscope and GCaMP6m:

Legend:

Using the spatial filters provided for each neuron by the automated
cell sorting algorithm7,44, maps of all active cells detected in the
BLA on each day of the study were made. Standard methods of image
alignment43 were used to register these maps across the different
days. Approximately 50% of all neurons observed across the entire
experiment were detected as active on individual days. a, Example maps
of active BLA cells from three mice on the first (left), third
(middle), and last (right) day of the 6-day experimental protocol
(Fig. 1c). Circles indicate cells that were active in only one of the
three recordings (grey), on two of the three days (blue), or on all
three days (red). Scale bars, 30 μm. The maximum number of active
cells seen in one session was 192

As can be seen not all cells are active every day.
My questions:

What are "inactive" cells? I am asking as I assume that cells always do have some baseline spontaneous activity which could be recorded with Ca2 imaging. I guess my confusion is that if we define cells as inactive which only have baseline activity, I wonder how we quantify "spontaneous" activity where an animal is for instance just exploring the environment without an experimental stimulus being present (periods of time which would be used typically to determine baseline activity)?

Are "inactive" cells not visible at all during Ca2 imaging (is it not possible to even see the cell's morphology/shape when there is no GcaMP signal)?

They mention how they define active cells on the first page: "P≤0.01, evoked signals
versus baseline, rank-sum test". Then from the Methods (section "Identification of neuronal sub-classes"): "To compute the
baseline activity level of each cell, we averaged its fluorescence signal over the
complete imaging session excluding all stimulus presentations". Inactive cells are those that did not pass this test.

@vkehayas Thank you! I think that these would be the stimulus irresponsive cells (Ext Data Fig 2). I just read one of their older papers, and inactive is described as "inactive: no detection of a transient within the recording session". This to me seems stricter than the P<=0.01 threshold - in particular also because even when failing the P<=0.01 threshold the cell might be above baseline and hence still detectable (and not invisible as shown above). Also, how they could distinguish spontaneous activity from baseline (spontaneous activity being e.g. exploring the environment)?


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The Relationship between Copper and Alzheimer's Disease
I've been reading up about the research concerning the etiological factors behind Alzheimer's and I came across two papers - "Studies on Copper induced stability changes in DNA fragment (GCA ATC TAA TCC CTA): Relevance to Alzheimer’s disease" and "Copper interactions with DNA of chromatin and its role in neurodegenerative disorders." The issue I'm having is that the papers suggest that copper causes the DNA's double helix to unwind in some parts, and it causes it to coil more tightly in others (the fluorescence and circular dichroism research supports the latter).
My question is this: do high concentrations of copper cause DNA to unwind or coil more tightly?
If you could provide any help, I'd be very grateful, as I feel like I'm be missing something obvious.

I was able to find your second reference quickly and linked it above, but the first gives more trouble.  Can you post a bit more information - bibliographical info or a link?

Never mind - found the other link (Young Scientists Journal) online

I found your second reference online, which says

Hydrogen bonds are disrupted by the process of partial unwinding which induces structural changes such as loosening of base–base interaction, base tilting and destabilization of the DNA double helix leading to DNA denaturation [17]. The destabilization was due to most probable binding sites in DNA such as Cu2+ to N7 of guanine and N3 of cytosine in line with our present results and with the predictions of Eichhorn and Clark [18], [19].

With this in hand, we can Read The Friendly References.  #18 is on PMC and gets the first look - they say "perhaps the structure is"

The other references are less helpful for me right now - #17 is a paper from 1971 that's not online and never will be, and #19 talks about histone H1 blocking the copper interaction.
Now what I see here is only unwinding, and is dependent (as proposed) on the presence of G-C base pairs in the sequence.  So far from what I've seen, this is based at interactions at around 0.1 mM in in vitro studies, so I feel like it is possible a physiological situation could involve a completely different mechanism.
After writing the above, I found the other paper in Young Scientists Journal - it is quite a remarkable thing to consider.  The author is a 12th-grade student from Panama who was doing (among other things) a circular dichroism study and molecular docking with Discovery Studio 3.5.  Statistics is lacking and the experiments aren't very well integrated, and the model from the software, which doesn't agree with the image above (it doesn't bind a ring nitrogen in the cytosine), doesn't seem to be tested by the lab data.  Despite the sophistication of the software I'm afraid I'm about as skeptical as I was the first time.  Still, there is some Ph.D.-level thought there, using some methods that American undergraduates rarely access, conducted by a university in Panama with support from an Indian research institute.  Educationally, fascinating.
But I don't see much support for the interpretation in that paper that the DNA coils more tightly.  The fluorescence experiment suggests a competition between copper and ethidium bromide, but knowing what actually happens is another story.  The CD study ... well, some shifts are identified, one one way and one the other, but I don't see how they prove the DNA is coiling more.  But maybe I'm missing something!

Thank you, you have cleared this up for me!


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DNA mutations in humans are generally bad, but why to they make viruses stronger?
When I read about DNA mutations in humans, the mutations are generally bad.
When I read about mutations in viruses such as the recent emerging strains of COVID-19, however, it seems to be good for the virus and make it stronger.
Why do mutations seem to be good for viruses, and can we apply that technique to the human body too?

https://en.wikipedia.org/wiki/Survivorship_bias

So has my understanding been wrong? please enlighten me

Your title implies that most mutations in a viral genome are beneficial for the virus.  Is that the case? Can you better explain the logic that led to your conclusion that mutations "make [viral] bodies stronger"?

Viruses are said to always mutate so that they need antibodies that always change according to the type of virus. Corona viruses, for example, have several types because they mutate so that vaccines are always being developed. that according to my understanding, please correct

in fact you can and the human immune system is one good example of doing that; processes such junctional diversity on t-cell's that due to frame-shift mutations the v(d)j process can happen and create the tcr, are extremely important for our survival. furthermore, remember that the survival of the fittest law is always being applied in biology (or in life and everything..)

Thank you so much

Why do you claim that mutations in human DNA were generally bad? Mutations in general can be disadvantageous, beneficial or without immediate effect to the organism in question, afaik.

Yes thank you so much. now I know because of some hopeful  answer

The effects of mutations
As have been already pointed out, mutations are neither good nor bad - they are simply changes in the DNA sequence. The effects of mutations on humans and viruses are rather different, since humans are multicellular organisms - mutations in one cell do not affect the whole organism, but only this cell (except for the germline mutations in sperm and ovum, before these cells start to divide and become an organism with trillions of cells).
A mutation in a human cell may have different effects:

if it occurs in a coding region of a protein, this protein may start working better or its functioning may be disrupted (the latter is more statistically probable), leading to cell death.
if it occurs in a regulatory region, it may dirupt normal functioning of the cell, e.g., making it divide uncontrollably, and thus creating a cancer tumor.
it may also happen in a unimportant region, conferring no special changes.
Note also that severe disruptions, such as thsoe leading to cancer, are usually not a result of a single mutation, but an accumulation of many of them.

A mutation in virus may equally have different effects. Most mutations have either negative effect - producing a non-functional virus, or a neutral effect - resulting in no special changes (particularly the so-called synonymous mutations, which do not change the identity of the encoded amino-acid). Some mutations change the proteins in the virus capsid, resulting in viruses which either have different properties vis-à-vis antibodies or can better attach to cellular receptors - these are beneficial for virus survival.
The important difference with the hma, where mutations affect only one cell, is that a single infected cell produces multiple new viruses (from dozens to millions of them,d epending on the virus) - some of them will be disfunctional, some as good as their parents, and some more fit.
Classification of mutations
As could be already conjecture from the discussion above, depending on the effect of the mutation on the new viral particles, they can be classified in deleterious, neutral and beneficial.
Mutations and fitness
A single viral particle being more fit would not pose much problems. However this particle may infect another cell, producing new generation of fit particles, which will replicate again and so on. In other words, what makes a mutation good for a virus is the natural selection among the millions of viral particles.
On the other hand, when we speak about a mutatuion being bad for a huma, we speak about the effect of the mutation on a single individual. In otehr words, we are comparing here appels and oranges. If we were to make an equivalent comparison, we should consider a human population over the course of thousands or even millions of generations. We would see in this case mutations can have similarly different effects: the Neanderthal "human strain" turned out to be less fit and disappeared, whereas the homo sapiens "strain" has survived and populated the whole Earth.
References:

Population genetics
Viral ecology
Principles of virology

Thank you so much for the clear explanation really helps me.

Mutations of the genome are neither bad nor good. They alter. If the product of this alteration is advantagious to the virus or any organism, they may gain some advantage to reproduce better. If the alteration is deleterious, it may be bad for the virus and any organism.
With humans you see bad results with viruses not (they are too small).

Thank you so much for the answer


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What is this spider found in Brittany?

I found it in Brittany, in my kitchen. It was about 3cm in width and 5 in length.

Is it dangerous ?

How big is the spider? What sort of behavior did you observe? Where specifically did you find it - indoors or outside, in a bush (what kind?), under a rock, in the forest, on the beach...? Do you have multiple images from different directions? Did it bite or pinch, and if so, what was the reaction, if any? The more information you can provide, the better, especially if you have multiple clear images.

This is likely a hackledmesh weaver of the genus Amaurobius. There are several species in the area.

I agree with JimN - this appears to be one of the cribbelate ground spiders in the Amaurobius group.  The defensive position of the forelegs is pretty standard, and the rather diffuse abdominal pattern is also consistent.
Here's a picture of the common worldwide species Amaurobius ferox for comparison:

These spiders and their relatives can give a painful bite, but the venom is essentially harmless to humans.
It's not easy to make out from the photo, due to the light and shadow effects, but I suspect that yours is a male - which might explain why the spider ended up in one of your kitchen cabinets if there wasn't any fluffy silk nest/shelter/snare nearby.
Male spiders can be identified by the enlarged ball-like devices at the ends of their pedipalps (the "face arms" which hang like little legs in front of the face).  They're just looking for love and if left to their own devices will wander off after females for the relatively short time they have left to live.


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Calculating sequence divergence score for a protein from identity or similarity score?
I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue is that I wanted to have divergence scores instead. So in order to calculate divergence scores, I first looked for the conventional method to calculate divergence score from protein alignments. But turns out, most of the methods/tools calculate % identity and % similarity scores instead of divergence scores.
(1) So I wonder what is the conventional method to calculate divergence scores from protein alignments.
(2) Could I simply calculate % sequence divergence as 100 - % identity or 100- % similarity score? If that's ok, should I prefer 100 - % identity or 100- % similarity?
Any suggestions from experts are welcome.
Update: As suggested in a comment below, I should mention that the average % identity score is more than 70. I hope this information would be helpful.

It depends on how similar your proteins are, the quality of the alignements. Measuring distance between distant sequences is harder than for very similar sequences.

The sequences of the proteins very similar. Average % identity is >70. Thanks for suggesting, in the updated question, I mention this. Also, I started the bounty, in case you may know the answer!

Since you don't want to use similarity or identity calculating divergence as 1-(similarity | identity) won't do what you want. What exactly you want to find? Why you can't use similarity or identity

@Hachiloni, yes, indeed the answer of @Mike Serfas below, suggests that the 100 - (% identity) may not be the right way to calculate the % divergence. However, similarity score could be used, if some condition is met.
Well, that's what I was asking i.e. if I could calculate divergence score from similarity|identity scores.

This is a very tentative answer as I haven't done anything like this, but it's a learning experience for me and I hope it could be helpful to get a more knowledgeable response started.
I don't think you can do this.  Per Wang, 2009 and Yona, 2002, divergence scores could be Kullback-Leibler divergence or Jensen-Shannon divergence, but both papers opt for the latter.  Divergence scores are based on "empirical probability distributions between the 20 amino acids".  BLOSUM or PAM matrices may be used.  Simply counting the identical or similar residues wouldn't contain as much information.  Wang, 2004 compared JensenShannon to numerous other scoring methods in the context of PSI-BLAST.
The similarity score is related to the divergence score:  Score = 0.5(1-D)(1+S) where D is the divergence score and S is the significance score. It is equation #15 in Wang, 2009 paper.  If you could safely assume the significance score for some alignments was near 1 (no chance similarities) then maybe you could say D = 1 - similarity score.  Unfortunately, judging by the glossary because I haven't downloaded any of the datasets, for the Ensembl data similarity is merely "How well one sequence matches another determined by calculation by an alignment program of identical and conserved residues/nucleotides."  So from that I take it they may just be counting up the "conserved" amino acids in the old fashioned way, but don't know that.

thanks for the answer, it indeed clears things out. Especially the equation i.e. Score = 0.5(1-D)(1+S) seems to be very relevant to what I wanted to do. I wonder if the condition i.e. significance score for some alignments was near 1 (no chance similarities) is satisfied in the case of the alignments I have. Could you please point to a reference where I can get more details regarding this equation?

It's equation 15 from Wang, 2009 above, which goes through the derivation.  But I don't know if/when you could actually assume significance score near 1, though small deviations from that wouldn't affect the value of D very much.

Thanks! I just added source of the equation in your answer. I am indeed not sure if/when I could assume significance score near 1. I wonder what makes you believe that small deviations in that won't change D much.

I don't see your edit - I'd thought my hyperlink to Wang 2009 would be enough, given the context.  My comment about the significance score was trivial - since it's added to 1, a variation in that score only affects D half as much.

I think my edit which may not be that helpful indeed, will be checked by moderators I think before it shows up publicly.
Ok, indeed variation in D may not have much effect. Thanks for the clarification.


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Biochemistry - Plastic eating microbes at home
Is it possible for me to locate, without too much difficulty, and culture, at home, a bacteria (like yeast) on plastic?
I tried a similar process with yeast and I was able to culture it on extremely harsh medications at my home. However, I believe due to the lack of food they died.

Although you should be able to find bacteria that can grow on plastic, I think your criteria of 'not difficult to find' might be a challenging one to meet. Poly(ethylene terephthalate) (PET) is a commonly used plastic, and in 2016 Yoshida et al. discovered a species of bacteria, Ideonella sakaiensis, which can grow using PET as its carbon source. This study was significant enough to be published in the journal Science, and has since been cited over 700 times. Therefore, using impact as a proxy for 'difficulty', it could be said that this was a difficult bacteria to find!
In terms of how they did it, here is an extract from their paper:

We collected 250 PET debris–contaminated environmental samples including sediment, soil, wastewater, and activated sludge from a PET bottle recycling site. Using these samples, we screened for microorganisms that could use low-crystallinity (1.9%) PET film as the major carbon source for growth.

Similarly, only last year Espinosa et al. isolated a strain that was able to grow on Polyurethane, from their paper:

For the isolation of bacteria from soil, three samples from a site rich in brittle plastic waste (Paunsdorf, Leipzig, Germany) were used. ... 150 μL of the diluted soil solutions were added to agar plates containing mineral medium and different concentrations of 2,4-TDA (2, 5, and 10 mM) as sole carbon and energy source.

In both of these studies they isolated bacteria that could grow on plastic, rather than evolving bacteria to grow on it. These bacteria at some point did evolve to grow on plastic, so in theory you could probably evolve a strain that did as well, but it would be easier, although still difficult, to isolate bacteria that already grow on plastic.
EDIT: Adding information on Yeast to respond to question edit
Yeast are actually a member of the fungal kingdom, and are not a type of bacteria. What most people refer to as 'yeast' is a species of yeast, Saccharomyces cerevisiae, which is used in the brewing industry. As far as I am aware, no-one has engineered this yeast, or another yeast, to grow on plastic. However, in 2020 Chen et al displayed the enzyme, PETase, on the surface of the yeast Pichia pastoris. This is the enzyme that the bacteria I mentioned above use to degrade PET. This enabled the yeast to break down PET into other compounds, however the yeast cannot grow using these compounds. If you wanted to engineer a yeast to grow on plastic you would need more enzymes, such as a MHETase, to further break down these compounds into something the yeast can grow on.
As you are looking to use microorganisms to break down plastic for environmental purposes, Taniguchi et al., have written a review, Biodegradation of PET: Current Status and Application Aspects, which discusses the problem. This is from 2019, however, so doesn't include recent developments. You can read a news article from the Guardian, here, that discusses the impressive improvements made in 2020. A key thing to note about the most recent efforts is that they involve using the enzymes that degrade plastic, but not the microbes themselves.

Thank you so much for your response, I am also a new contributor so it was really helpful

Will it be possible to grow yeast to eat plastic? That's what I am trying to research as these researches do say that microbes are slow for now. Would it be possible to contact you?

By harsh chemicals, I meant, Calcarea hypophosphorosa, Budesonide, Alcohol solution, lactic acid capsules, etc. I also added some other substances for promoting growth - Vitamin E & B, Cod liver oil, milk, etc.

I would say that you should edit your original question to remove reference to harsh chemicals. This should probably be a separate question. You can also edit your original question to add your additional question about yeast, and I will edit my answer to reflect that. As for contacting me, this is not the StackExchange way as it hides information from the community (see here: https://meta.stackexchange.com/questions/431/any-way-to-send-a-personal-message-to-another-user).

Ohk I tried one option giving information in profile so you can contact me from there

@MikulRai To be clear, I agree with the link that moving questions to a private forum is not the best way to serve the community. If you have further questions you can post them and I can try to answer, or you can edit your original question. I've also suggested some edits to your question to make it clearer and I'll edit my answer once they're approved.

I understood your point, I wanted to ask for your recommendation to reduce the existing amount of plastic in the environment, according to my research there are major three ways: physical - burning without any harmful products, chemical - dissolving the plastics without any harmful by-products (requires advanced situation) and biological - microbes. Can you give your expert advise, please

I've edited my question to respond to the additional information you've provided. The key thing to note is that there is a difference between using enzymes from microbes to degrade plastic and actually growing the microbes on plastic. From my reading (I am not an expert in this area) it seems that most effort is being focused on using the enzymes, without actually using the microbes. Much like biological washing powder doesn't contain any live organisms, but rather the enzymes from them that can degrade the compounds that make clothes dirty.


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Can caffeine act as viagra
Recently I studied that cAMP which is a 2° messenger can cause various physiolocal changes under the action of proper hormones. Now cAMP is degraded by phosphodiesterase and this ceases the actions. Viagra drugs like sildenafil are phophodiesterase inhibitors and therefore prolong cAMP action. Also caffeine inhibits phosphodiesterase and therefore it should cause a similar phenomenon. But does it actually happen? Or some other mechanism stop it from happening. What are those mechanisms?

Is sildenafil a "phophodiesterase inhibitor"? Or is it a specific inhibitor of a particular phophodiesterase? If the latter, which one? How potent is it vs. caffeine?

To put it in everyday terms: caffeine raises blood pressure, and this is pretty much the same effect as that of viagra, just less specific and less long-lasting.

Didn't realize this Q only had DVs... given the amount of totally crap questions here that somehow get a lot of upvotes, this one was treated rather harshly... I mean we know the answer because it was actually investigated and published, so it wasn't a totally outlandish Q to consider.

Not much luck there. Although caffeine, sildenafil and cGMP share a basic ring structure, the specificity and potency of caffeine for PDE5 is rather underwhelming:

On the basis of comparative IC50 values, the potency of sildenafil is about 1 million times higher than that of caffeine (Corbin and Francis, 1999).

This is a lot of coffee.


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Infant tissues, organs, body parts or reflexes in an adult organism
What is the phenomenon, when a normal useful tissue, organ, body part or an inborn reflex or instinct existed in the infant organism and normally should disappear or at least completely lose its function in the adult organism but it won't? Atavism and vestigiality don't seem the right terms. Is there a specific word that refers to the phenomenon?

"Remnant" is the closest term I can think of; "residual" is also used. You can find both used to describe the foramen ovale for example, which typically closes at birth (and has served its purpose at that point), but remains patent in a substantial proportion of adults, sometimes causing symptoms.
However, these terms are of course not specific for the circumstance you describe; I don't know of any that is.


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Confusion about how to compute probabilities for linked genes
I am confused about how to compute probabilities for linked genes.
The problem that I am solving is this:

P generation: AAbbddEEff X aaBBDDeeFF. If A and B are 40 centimorgan apart, what is the probabilty to get aabbddeeff in F2?

Here is what I have:

F1 is: AaBbDdEeFf.
The next cross it goes through is this: AaBbDdEeFf X AaBbDdEeFf.
To compute this cross, I drew the 2 chromosomes for AaBb (in coupling), and then the probability for a is 0.5 (A or a) and the possibility for no recombination is 0.6. So 0.5 x 0.6 = 0.3. The same goes for b, so aabb is: 0.3 x 0.3 = 0.09.
For ddeeff: 0.25x0.25x0.25 = 0.015625.
Multiplying these gives 0.09 x 0.015625 = 0.00140625.
Extending that and for 2 gametes gives this: (0.00140625)^2 = 0.00197x10^-3.

But the correct answer is not what I have computed, but instead is 0.000625.
I'm really confused with this question. If we know that only 2 of the 5 genes are linked, is it still correct to multiply: 0.09 x 0.015625 = 0.00140625?  Maybe I should use a Punnett square somehow? Because in that case, the probability for a recessive homozygous is 0.0625 but I'm not sure it fits to this question.

0.000625 looks right to me.  On one chromosome, you have a 50% chance of a.  Then you have a 40% chance of b (if and only if a crossover occurs).  These multiply out to 20%.  You multiply that by 50% for three unlinked genes to get 2.5% abdef.
Your approach was correct overall, but you used a 60% chance of b, so your final answer was too high by (60%/40%)^2.  Don't let capital and small letters trick you - ab comes from a recombined chromosome.

Thank you. Just to clarify, when you say: "ab comes from a recombined chromosome", it's only in the case that the alleles are in 'repulsion'?
And for the unlinked genes I used 25% because I thought I need to use Punnett square (for example, if we want dd from Dd x Dd the chance is 25%). But the correct way is to say "50% chance of d/e/f", because I need to consider the chromosomes? @Mike Serfas

Repulsion is a sort of old-fashioned way to put it.  Just think that A and b are physically linked by a strand of DNA inherited from one parent, as are a and B.  The odds that these strands will be cut and spliced to make ab and AB is 40%.  For the unlinked genes your math was accurate - I multiplied by 50% chance of d, e, and f, then multiplied the 2.5% chance of abdef by itself, while you multiplied by 25% chance of dd, ee, and ff one at a time, but it works out the same.