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Is there an antidote for caffeine, e.g. as a supplicant for caffeine-intolerant persons?
First, let me state I'm not talking about a medical emergency. No one is in a serious condition.
My girlfriend is, we think, caffeine-intolerant. She loves the smell of coffee and the habit of coffee drinking, so naturally she risks drinking caffeinated beverages every now and then, even knowing she'll suffer. She experiences the regular effects of coffee, but they are uncomfortably strong and last much more time than usual. We've read that it's because her body metabolizes caffeine slowly, likely due to a gene mutation. We think it's not caffeine allergy.
We were wondering if there's kind of an antidote, a molecule which metabolizes or deactivates caffeine specifically. Then one example use could be

drink regular coffee;
wait some time (e.g. half an hour);
take a pill to take care of the excess caffeine in your bloodstream.

We're asking mostly out of curiosity - she's not that addicted to coffee as to actually take pills just to be able to drink it. The real (bio-chemical) question is - can an antidote, which targets a this very specific molecule, be actually manufactured? Or is it that it's not researched purely because of market size reasons?

Why not just drink de-caffinated coffee?

@CharlesE.Grant, she still gets some of the symptoms if she drinks decaf e.g. three days in a row. We think the prolonged exposure to even relatively small amounts of caffeine is what's bugging her.

Is it that it's not researched? Probably this. I've looked through literature and there seem not to be any references to any things studied which may sequester or adsorb caffeine, save for activated charcoal. People with hypersensitivity to caffeine usually have a gene variant which is involved in metabolizing caffeine in the liver. Aside from a hypothetical gene therapy, the best course of action would be to avoid it, especially if she is not in any way addicted. Can an antidote be manufactured? Yes, it is almost certainly possible, though I don't think it'd be profitable nor advisable.


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Exhalation in human breath, through mouth or nose: which is most usual?
Until now I believed that breath exhalation through the mouth is common for most human beings, and this fact is implicit in several technical contexts of which I can think (sports, music, medical checks...). But recently a friend was surprised when I claimed this, and conducted a small poll around himself, giving a 100% of people inhaling and exhaling both through their noses in normal breath (then I was surprised!).
This issue is not without practical interest in these COVID-19 days, because when using a surgical mask (which filters the air going out but not the air coming in), people exhaling from their mouths and not covering their noses with the mask are still giving more or less the same protection to others, so if most people actually exhale through the mouth, this common "faulty" usage would actually not be so dangerous.
Can someone point to any scientific paper having evidence or statistics about normal mouth exhalation against normal nose exhalation?

Ok, there seems to be a possible misconception here. Breathing from the mouth, though a helpful evolutionary trait, can also have its downfalls. I didn't find many peer reviewed research papers on the reason however the internet is flooded with articles. here's a example: https://www.healthline.com/health/mouth-breathing.

@ArkLomas Thank you for your comment, but it does not really address my question. I'm talking about exhalation (the air going out), not breath intake (the air going in). Also, I need research data, online "health" or sports sites are not good enough.

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Honeybee relatedness: workers and nephews
This is my first question on this site. If anyone could help me get to the bottom of it, I would be very grateful.
I am currently working on a lecture on kinship in animals. It goes without saying, it includes a part about the good old honeybee and its unusual relatedness coefficients. One of the interesting points I'd like to cover is worker policing, where workers remove eggs of other workers because they are more closely related to their brothers (the queen's sons) than their nephews. The resources I'm using state that this situation depends on whether the queen is monogamous or polygamous. When a queen mates with a single drone, workers are more closely related to their nephews (r=0.375) than their brothers (r=0.25). However, if a queen mates with more drones, the situation is flipped, workers are more closely related to their brothers and therefore eliminate unfertilized eggs laid by other workers.
The issue I'm having may seem silly and purely technical, but I can't for the life of me figure out how we arrive at a relatedness coefficient of 0.375 for worker and nephew when the queen is monogamous. I'd really like to understand this because I want to be able to answer as many potential questions students may have, and I can't do that if I'm not 100% sure about it. Any and all help is greatly appreciated. Thanks in advance!

Queens are generally not monogamous. Although they make just one mating flight, they store the sperm of multiple drones. Might your numbers work if you plugged in two, three, or four mates?

@KarlKjer Thank you for your reply. I'm aware that queens are generally not monogamous, and that the second situation is far more common than the first. My issue was in understanding how we calculate a relatedness od 0.375 for worker and nephew in the event when the queen mates with a single drone. I don't want to include this information in my lecture if I don't fully understand it myself.

Is this as simple as: Father of both workers is same, so are their paternal genes b/c he only had one set of chromosomes. The two workers are expected to share half of their maternal DNA. Both parents contributed equally, so the sisters are considered each related to each other at relatedness=0.75. The son of one is related to its mother by 0.5, as it only gets one set of her chromosomes. To determine the relatedness of the aunt to this son, multiply how related she is to her sister times how related he is to his mother: 0.75*0.5-0.375?

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Structure separating the left atrium from the ascending aorta?
With reference to the (adult) anatomy of the human heart:
The left atrium (LA) and the proximal part of the ascending aorta (Ao) abut one another, as shown nicely in this image [1].  Is there a name for the wall(s) separating the LA and Ao?  And is this a single structure (i.e. septum), or is there a sinus?
[1] http://www.radiologyassistant.nl/data/bin/w440/a5097978b829cd_3-chamber.jpg

There isn't any particular structure there: you have the wall of the aorta/adventitia, and if you have an explanted heart there is a space and then the auricle of the left atrium on one side and the right atrium on the other. These would all be contained within the pericardium.
Where the aorta is most "touching" the left atrium is where the pulmonary veins come in: I think this picture from Gray is most helpful.

Figure 494. Henry Gray (1825–1861).  Anatomy of the Human Body.  1918.
There really isn't much to distinguish these veins from the non-auricle part of the atrium, similar to the vena cava on the right side. If you were to cut along the veins eventually you would just open up into the atrium.
The Visible Heart Lab is another good reference http://www.vhlab.umn.edu/atlas/aorta for cardiac anatomy.


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Hemoglobin question- how many alleles?
So I know that Hemoglobin is made of 2 alpha and 2 beta subunits. The alpha consists of 2 genes on chromosome 16, and the beta of 1 gene on chromosome 11.
So why does Hemoglobin only have 4 alleles? Why is it not 6? In my way of thinking each alpha subunit consists of 2 genes, so 4 total. And each beta subunit consists of 1 gene, so 2 total. Together that makes 6. Confused! Thanks in advance

Can you cite where you are getting the idea that there are only 4 alleles across the three genes you are referencing? There are certainly disease-involved and normal alleles at all three genes so there are certainly more than 4 alleles across the three genes. I'm suspecting your source is talking about something more narrow. That said, Remi.b's answer is still good to consider.

Meaning of Allele
The word "allele" is often used with two slightly different meanings in biology.
The first, probably more appropriate usage is the one in Remi.b's answer: an allele is a variant of a gene in a population; there are many many possible alleles for a given gene, depending on the length of the gene, though typically only a few are common in a population and even fewer may be known.
The second use of the word "allele" is to mean "copy" of a gene; because those copies can be different, in this context an allele is a potential variant of a gene in an individual. For a diploid organism like a human, you might say that an individual has "two alleles" but what you really mean to say is that individual has "two copies of a gene, which could be the same or different alleles." The relationship between the two copies is called zygosity. I'd argue that this is a slightly sloppy use of the term, but nonetheless it is common and if you understand the meaning it is still clear.
Genes for hemoglobin
For hemoglobin, there are at least 3 important genes: two each encode alpha subunits, and the third encodes the beta subunit (there is also a delta and gamma subunit, but we can omit discussion of those for now).
For the beta subunit, each individual has two copies of the gene, which in human populations are typically thought of as one of two population alleles: either a normal allele or an allele associated with sickle cell anemia. Individuals with two of the sickle cell alleles will have sickle cell anemia.
For the alpha subunit, each individual has two copies of two different genes. There are alleles for each of those genes that produce non-functional products. Individuals with alleles that produce non-functional alpha subunits, for either gene, have Alpha-thalassemia. The severity of Alpha-thalassemia depends on how many alleles are present across the two genes that do not product functional alpha subunits.
Why 4 alleles for hemoglobin??
I suspect if you read somewhere that there are "4 alleles" for hemoglobin, that source was probably talking about Alpha-thalassemia in particular, in which case there are indeed 2 copies of 2 different genes so that an individual has four possible alleles. The severity of Alpha-thalassemia depends on the total number of defective alleles across the two genes, where having 4 defective copies is fatal, and having just 1 defective copy is not noticed clinically.
In the population, however, it is likely that there are actually many other alleles for each gene. For the purpose of describing disease, however, we can group these into "functional" and "non-functional" and say that there are two population alleles for each of these two genes.

An allele is a variant at a given locus. If at a given locus, there is no variance in the population, then the entire population is fixed for a single allele. If there are different variants in the population, then there are severeal alleles in this population.
A locus can be defined as a DNA sequence of any length. For a locus of size n the maximum number of alleles is $n^4$ and the minimum number of alleles is $1$. In practice, that being said, we sometimes group allele together and hence the maximal number of alleles is somewhat lower. But let's not go into these details.
The point is that it does not matter how many subunits you want to consider. The number of alleles is simply the number of variants that exist in the population. If for the hemoglobin, there are 6 alleles, then there are 6 alleles!


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Replicate DNA so its visable to the naked eye
So my question has a few sub sections after the main title question.
Firstly, is it possible to replicate a pure sample of an individuals DNA to an amount that is visible to the naked eye?
If possible, how long would this take?
What would be the estimated cost?
How could you preserve the sample once obtained? I.e. Under acrylic or some other medium.
Thank you for any help provided.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, each question should be posted separately — this improves the chances that you will get answers for each question and makes the answers more accessible for future users and your last two questions are not biological and so are off-topic for this site. In addition, for the first two questions to be answerable would require more information: how much DNA are you starting with? Visible under what conditions? ⋯

I think you would greatly benefit from exploring some of the introductory material available online such as Khan Academy. That will help you avoid asking questions that seem to fit this sites criteria for "homework".  ——— Finally, we encourage you to always do some research on your own first and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

Are you only interested in human DNA? There are children's science kits for extracting DNA from onions, strawberries, or other fruit, and vegetables, which produce readily visible amounts of DNA. See for example https://www.amazon.com/ScienceWiz-7811AZ-DNA-Experiment-Kit/dp/B001DTD0H2 (I have no connection to the vendor, it's just provided as an example).

I downvoted this because it appears to be an inquiry about services which might provide a visible lump of DNA (supposedly many copies of a particular human's genome) preserved in the form of a knick-knack conversation piece for a gift.  That seems inappropriate for this biology site.

The general steps involve lysing the cells (breaking the cell membrane) in order to get a mix of nucleic acids (some of which you want), sugars, proteins, lipids, and other detritus (which you don't want). Then you separate out this mix with a series of steps of washing, spinning down with a centrifuge, and extraction.
A DNA extraction kit is involved. Here's one from Qiagen, for example. A kit usually contains a mix of salts and buffers specific to the source of DNA, to get as much pure sample back as you can.
You might not start with much DNA, so picking the right kit can help you get back a high enough yield of genetic material to do other experiments.
Kits are often based on ethanol or isopropanol, which precipitates out the DNA from the rest of the gunk. You add some buffer and run it through the centrifuge, removing and discarding what is on top (the "supernatant"). After repeated wash and spin steps, what's left is mostly purified DNA, in visible pellet form.
As a specific example, here is a paper that describes one approach to isolate DNA from human sperm, with a detailed protocol: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486329/

No need to replicate the DNA in a test tube by PCR, there are protocols out there galore to extract enough DNA from buccal swabs or from isolated white blood cells.


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If a cell has two different GPCRs, how does the cell differentiate between the phosphorylation cascade caused by each?
In my biochem course, we learned that GPCR receptors trigger a phosphorylation cascade, with the end result being a large amplification of the signal in the form of cAMP. We never studied any particular GPCR individually, but we were told that GPCRs always end in the formation of a large amount of cAMP, which will go on to phosphorylate key targets that achieve the end result.
My question is as follows: If there are two GPCRs on the same cell membrane (let's say GPCR-A and GPCR-B triggered by substrates A and B respectively), how does the cell "know" which GPCR triggered the phosphorylation cascade if the end result is the same (large amount of cAMP). In theory, couldn't substrate B bind to GPCR-B and cause a phosphorylation cascade identical to that of GPCR-A, thus triggering GPCR-A's cellular response?
Is there some deeper specialization/uniqueness to each type of GPCR receptor that we didn't cover in my course? Does each GPCR produce a slightly different cascade that ends in something similar, but not exactly cAMP? Or is there some restriction, like each cell limited to only one GPCR (I would find this surprising, if this is the case)?

First, it would be an oversimplification to say that GPCRs act only through increases in cytosolic cAMP. This is true for receptors coupled to Gs proteins, but there are other G proteins like Gi, Go and Gq which act differently [1].
Now, a cell can have receptors coupled to many different G proteins. Vascular smooth muscle, for instance, has Gs, Gi and Gq-coupled receptors [2]. Further, a cell can have different receptors coupling to G proteins of the same type (e.g., hepatocytes have glucagon and beta adrenergic receptors [3], which both couple to Gs).
In such situations, the effects of different hormones add up. The final effect is a function of the total cytosolic concentration of second messenger (e.g., cAMP). Thus glycogen breakdown in a hepatocyte depends on the overall effects of glucagon and epinephrine [3]. The hepatocyte has no way of 'knowing' which cAMP molecule was formed by which hormone.
References

https://en.wikipedia.org/wiki/Heterotrimeric_G_protein
https://cvphysiology.com/Blood%20Pressure/BP026
https://www.nature.com/articles/emm2015122

So, if cells have several different GPCRs of the same G-type but triggered by different substrates, the effects must be additive and can't be unique (i.e. the different substrates can't trigger entirely different cellular responses)?

@SullyChen No, I think. They can't be unique. Do you have any particular counter-example in mind?

I don't have a particular counter-example, but I can faintly remember a professor remarking that a single cell could have dozens (or hundreds? not quite sure) of GPCR proteins on its membrane, so I was curious if they were all duplicates of the same receptor or if they could possible all be unique. I think you've answered my question, thanks!

Actually, there is the phenomenon of 'spatiotemporal signalling'. Basically, the cAMP or other signal is restricted in space, so that it can only activate certain proteins. It has recently been shown that GPCRs can create cAMP signalling domains of nanometer size. So very much the cell can tell which cAMP molecule was formed in response to each hormone. Its extremely complicated and researchers are only just beginning to understand the significance of such signalling, but just imagine, all these receptors being located to distinct regions of the cell (cholesterol rich lipid rafts in the plasma membrane, endosomes after internalisation, cilia), and that each downstream signalling molecule or protein can only get so far before being down-regulated. As such, you can get very distinct signalling paths between different GPCRs, even in the same cell. (It gets much more complicated but).

Excellent answer, but we do ask that answers for anything beyond basic textbook info contain sources/references to support what is written and allow avenues for follow up reading.


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What insect is this? Looks like a spider but with six legs and long antennae
I've been spotting some of these insects in my house lately, they look like spiders but it seems like they have six legs and antennae instead of eight legs.
Can someone tell me what insect is this? Is it dangerous? I don't mind having them in my house but if they're dangerous I might have to do something.
A photo of the insect:

Their body seems to be relatively flat when you look at it from a side, the location is Costa Rica, we are in the wet season (no winter,summer,etc. here) but I'm almost sure I've seen them during the dry season as well, also, the insect's body size (ignoring legs) is similar to a thumb. In case that helps to indentify it.

In general, it looks like it could be a cricket of some type.  They typically have long antennae.

Welcome to Biology.SE! Please [edit] your post to include an estimate of the size (e.g. around 5 cm long) — thumbs are highly variable and it isn't clear which part(s) of a thumb you might mean anyway! Also, could you try to get clearer pictures and, if possible, include one from the side and another from the front? Thanks!

https://biology.stackexchange.com/questions/112103/what-kind-of-insect-is-this-it-looks-like-a-huge-spider-with-one-long-antenna-a

I am think that I have narrowed it down to either Amblypygi (i.e., whips spiders, tailless whip scorpions), or Solifugae (i.e., camel spiders, wind scorpions, sun spiders). The thing is, in part due to the quality of the photo, I find both clues for and against each option. Long thin antenna-like appendages suggest Amblypygi, but the pedipalps aren't quite right. If it weren't for the think anterior legs, I would say it's a Solifugae. There's also the unidentified appendage that cast shadows don't explain.

My perspective, annotated photo
Rights belong to the initial poster/creator of this post.

This creature is an amblypygid (aka, whip spider, or tailless whip scorpion). Amblypygids are arachnids, but not spiders, and they are not venomous. Like other arachnids, they have eight legs, however the anterior legs have been modified into very long antennae-like limbs used to feel for prey. Anterior to the antennae-legs are the pedipalps, which have been modified to be long and spiny, used for capturing prey.


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What is the smallest visual unit perceptible to the human eye, like a pixel? (esp. in visual static)
If you close your eyes, you can often see visual static, where individual pixel-like things are much more visible than with the more smooth, crisp images one gets with open eyes. This led me to wonder a few things:

Is there a name for this unit, like "pixel"?

What is the biological correspondent? A single rod or cone or something?

Are the individual pixel-like things making up the static noise the same underlying mechanism (and size) as the smallest perceptible units of vision one gets when actually looking at something? I suppose this is related to visual acuity. I've read that the cause of static is suspected to be excitation of neurons, but that's not what I'm asking.

Thank you.

The analogy between the human visual system and electronic screens does not go very far. While an electronic display can be described as the sum of individual pixels, what the human eye sees cannot be described as the 'sum' of inputs from all the rods and cones. The inputs from one cell interact with those from other cells at various levels: retina, lateral geniculate nucleus, visual cortex. Plus, there is interaction with neurons from other brain areas. This processing creates a complex 'image' very different from that of an electronic screen.

The human eye has two types of sensors that become stimulated when wavelengths of visible light (photons) hit the pigments in these sensors. They are known as 'rods' and 'cones'. Rods detect the brightness of light, cones detect the color. There are three different cones in the human eye: red, green and blue. Each cone reacts to the corresponding waves of light. When they are stimulated due to their corresponding wavelengths, they send a signal that travels through the optic nerve to the visual cortex at the occipital lobe.
individual cones don't have different levels of stimulation and always send the same frequency, it's the lack of the stimulation of other cone types that causes certain colors to appear.
in short:

signal or photon of the appropriate wavelength I suppose.
rods for brightness, cones for color.
probably not since the cones are microscopic and tightly packed, too close and too small to see what each cone is literally receiving. The moving static you're seeing is called phosphenes and is comprised of the inherent electrical charges the retina produces both during resting state and with the eyes open. they're just easier to notice when your eyes are closed. Try covering your eyes and you may get static just like when you close your eyes.

The electrical charges get sent to the visual cortex. that's where your brain processes the image. Here's an diagram of how the rods and cones send their electrical signals to the optic nerve (the optic nerve is the [4] label).

Here's a diagram of how those signals travel to the visual cortex:

Thank you. So a phosphene is a single pixel-like light? What would be the path from this electrical charge to a person's awareness of the light? The charge activates a single rod (or very small clump) and then travels down a nerve to the visual cortex or something? And each rod would have its own nerve line?

"So phosphene is a single pixel-like light?" It's a phenomena that causes your rods and cones to still send signals even when the eyes are closed, the rods and cones (or arguably the gangion cells) are the real 'pixels'. I made edits to the answer so that you see the pathways. Multiple rods can cones can be joined to one bipolar cell and multiple bipolar cells can join to one ganglion cell meaning that multiple rods and cones can send a signal through one pathway. to the visual cortex.

ganglion cells could be argued as the pixels since they send the signals to the visual cortex. The rods and cones just depict what the pixel will display (e.g. brightness and/or color of each pixel)

Thank you. This clears things up for me. A very informative answer!


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Help identifying an insect by its remains
Yesterday i hiked in Bolsena lake, Italy. I felt this insect moving into my ear. So i smashed my ear and this is the result. Please tell me that there are no risks related to Lyme desease or similar.
Sorry for the bad quality of the photo.

It is probably a beetle.
The shape of legs and the two big eyes are an insect thing.
Lyme desease is transmitted by ticks, so i would not worry.

Thank you. One more question: so beetles could own wings?

@FedericoJuvara many (though not all) beetles have wings. They're usually protected and hidden under the elytra when not in use though. Check out https://simple.wikipedia.org/wiki/Beetle#Wings for a picture and more information.

I'll check it out, thank you very much!


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Why is it (allegedly) dangerous to feed ducks with breadcrumbs and pieces of bread?
I used to go down to the local lake all the time with leftover bread and throw little pieces of it to the hungry duckies, who very eagerly fetched it and ate it while happily quacking away.
I thought I was doing them a favour, but apparently, it's bad for them? Can even kill them?
Is this really true, or is this a false rumor spread by people who don't like ducks and want to deprive them of their favourite food?
Why exactly would bread, especially soaked in water, somehow damage wild ducks? Isn't it a very neutral food which feels filling and nice for the ducks? Nobody says that they have to only eat bread thrown from humans -- they can still eat little insects and algae in the lake or whatever they normally/naturally eat.
What exactly can happen? I never noticed any dead ducks or ducks in pain whenever I visited them. They seemed to love the bread and consider it a luxury dish from a fine restaurant from their perspective.

This web page from National Geographic can give you some idea: https://blog.education.nationalgeographic.org/2017/03/27/stop-feeding-ducks-bread/
Also, you can give a look to this page from the Wildlife center of Viginia:
https://www.wildlifecenter.org/problem-feeding-ducks

This question was asked and answered on Skeptics.

the simple answer to this is white bread is carbohydrate(sugar)and not a lot more so it causes malnutition.


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What is the role of pyrophosphatase in RNA polymerization?
In Molecular Cell Biology (8th edition) there's a fragment in chapter 5.2 that says:

The energetics of the polymerization reaction strongly favor the addition of ribonucleotides to the growing RNA chain because the high-energy bond between the α and β phosphates of rNTP monomers is replaced by the lower-energy phosphodiester bond between nucleotides. The equilibrium for the reaction is driven further toward chain elongation by pyrophosphatase, an enzyme that catalyzes cleavage of the released PPi into two molecules of inorganic phosphate.

How does the pyrophosphatase make the reaction more favorable? Does it make "harder" for triphosphates to form back again (now you have to attach phosphates one by one, not two at once)? If so, isn't one additional phosphate just as bad as two? To remove either you have to break one bond (between the first phosphate and the second), and you have a specialized enzyme to remove two of them (the RNA polymerase). Isn't forming a diphosphate (which needs to form in order to later make triphosphate) actually worse? Or maybe it somehow "reuses" energy stored in the bond between the two phosphates left?
Sorry if I didn't use the proper vocabulary, I'm new to biology.

No problem being new to biochemistry and molecular biology. You might find it helpful to understand Sethi's answer if you read this section from Berg et al. Biochemistry which explains the thermodynamic concept of Gibbs Free Energy which is often applied to biochemical reactions. There is a worked calculation on the pyrophosphatase topic in relation to a different reaction in the same book.

This question can be answered by considerations of chemical equilibrium. For any chemical reaction:
$$\ce{A + B <=> C + D}$$
It is a property of nature that removal of product ($C$ or $D$) from the reaction mixture drives the reaction in the forward direction. This is an example of le Chatelier's principle and can be explained as follows:
In a reaction mixture containing $A$, $B$, $C$ and $D$, the rate of forward reaction ($A + B \rightarrow C + D$) depends on the frequency of collision of $A$ and $B$ molecules. Similarly, the rate of backward reaction ($C + D \rightarrow A + B$) depends on the rate of collision of $C$ and $D$ molecules. The collision frequencies, in turn, increase with concentration of the relevant species. An abrupt reduction in the concentration of $C$ hinders the backward reaction while leaving the forward reaction unchanged. Thus the forward reaction begins to dominate.
The reaction catalysed by RNA polymerase is:
$$\ce{RNA + NTP <=> Longer \ RNA + PP_i}$$
By removing $\text{PP}_i$ from the reaction mixture, pyrophosphatase does exactly that and drives the reaction in favour of RNA polymerisation. Note that hydrolysis of pyrophosphate is favoured because of the negative free energy change associated with it (thanks to David for pointing that out).

And why can’t the pyrophosphatase reaction just be reversed? Seems to me that is the key point that needs to be explained.

@David The hydrolysis of pyrophosphate is favoured because of the negative free energy change associated with it. (Should I add this point to my answer?)

Yes. That is why I raised the point. The standard deltaG for the polymerization is ca –3 kcal per mol. That for the pyrophosphorylase reaction is an additional –4.6 kcal per mol. There is actually a worked example of the latter point for acetylCoA formation in Berg et al, available at NCBI Books online.

@David Done. Here is another interesting point: if the standard deltaG for pyrophosphate hydrolysis were zero, or even positive, having the pyrophosphatase enzyme would still help. This is because we are starting with PPi alone, and to reach equilibrium, at least some of it must be converted to Pi. Thus, in any case, some amount of PPi would be removed.

I think there are aspects other than the thermodynamics of the reaction. If I am not mistaken, polymerization is almost irreversible. Also, in vitro RNA/DNA synthesis can happen without pyrophosphatase. There are some old studies on PPi being a competitive inhibitor of polymerization. Perhaps you can check them out.

@WYSIWYG — I don't want to muddy the water, but I found a 1992 Annual Review in which the author argues against the orthodox view in order to make an argument for a role of the reverse reaction in RNA repair! He bases his case on measurements of PPi concentration in E. coli! I suspect this has died a death, but haven't got the facts to argue against it.

Thanks to all of you.


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Where can I get info about A. thaliana proteins' locations?
I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's inconvenient for me, because I need to locate 1.6k of proteins and process the results further. Is there a dataset or an API I could use instead?
PS. If this is not the right forum to ask this, please notify me.

cross-posted https://bioinformatics.stackexchange.com/questions/18111/where-can-i-get-info-about-a-thaliana-proteins-locations

You can also try using The Arabidopsis Information Resource (TAIR).
It is the database specifically created for model higher plant Arabidopsis thaliana.
You can download the files in .fasta, .gz, .txt, .csv formats from their DOWNLOAD WEBPAGE. The website also provides links to other A. thaliana information resources.
PS:  The database is weekly updated.
Edit 1: Try this or track to download_files/Proteins/Properties/AtSubP_results

That's where I looked first but I haven't found any file with protein locations. In an NCBI article about SUBA I've found a link to some .csv files used by the website, although they have to be cleaned to be usable.

can you point to where on TAIR specifically these localisome data reside?

@micoay, I have added a link to my answer. Please let me know if it works for you. I'm assuming you already have the protein-ID list.

Thanks, I missed this file. For people searching for the file on the website: Downloads/Proteins/Properties/AtSubP_results.

@micoay, If that has solved your problem, then please accept my answer by clicking a tick button on the left side of my answer on your forum. I would appreciate that.

If you click through to the actual SUBA4 publication, you can see in the data availability section that they have reposited source datasets from which their predictions are derived, at http://dx.doi.org/10.4225/23/581055ddcb1ce.
These appear to be standard e.g. CSV files of various data layers, such as here. It may take some effort (e.g. their algorithm) to integrate these data sources, I am not familiar with these datasets.
It is of course inconvenient that they don't choose to advertise this on the server itself.

Thanks, I found it too, after posting here. I was hoping there was a link on their website I missed.


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How is boiling oil tolerated by some people?
There are people who can withstand exposure to extreme heat with no apparent side effects. One such person is Kann Trichan, a Thai street vendor who dips his bare hands in hot oil. An old TV show featured another person who, as a child, was found touching a red-hot hotplate. On the show, he was filmed holding a piece of food in a deep fryer for tens of seconds, and his hand showed no visible change when it was removed, not even surface redness.

Is science any closer to explaining the phenomenon?
Although there are no visible ill effects, are there any that might be developing (eg. a risk of cancer due to DNA damage)?
Why is blistering not occurring? What specifically triggers blistering, and how might it be being suppressed in these people?

For some of these cases, look into the leidenfrost effect (https://en.wikipedia.org/wiki/Leidenfrost_effect). people can literally touch molten metal for a fraction of a second and it's find simply because of the moisture in our hands providing a protective barrier when super heated.

In a biology forum, you may be asking about a biology question by proxy, though what we'll really be getting at is that one must first correctly apply a healthy amount of scientific thinking to questions about any observations. This is more a discussion on  science and skepticism rather than a mechanism in biology, but I will humor you briefly.

Is science any closer to explaining the phenomenon?

Why yes, in almost all of such extraordinary feats of inhuman ability, you are seeing fraud and quackery.
There are a great many 'phenomenal' people and feats who appear in Guinness record books and on TV programs and on YouTube videos, performing amazing and unbelievable feats. Very often these involve the presence of an 'expert' making sure everything is kosher, a science professor standing by, making sure there is no trickery and that the experiment is controlled. We've seen this plenty of times, with homeopathy demonstrations, extrasensory perception, free energy devices, wireless power transfer at a distance, conducting, storing or generating copious amounts of electricity from within their bodies (e.g. Battery Man), the list goes on.
Unfortunately, there a few things that tend to go wrong upon presentation to the audience at the very end:

The shows edit out much of the scrutiny or discussion of possible confounding factors. The oil may have bubbled to indicate it's boiling, but did we measure its temperature with a thermometer? Was the hand covered in a heat-resistant gel or a layer of insulating water which doesn't mix with oil and provides temporary heat resistance? Was the hand a prosthetic?
Expertise is faked by an accomplice who poses as an authority. Alternatively, an authority fails to spot the trick. You can convince many persons by virtue of a proxy; this is very human tendency that is quite easy to exploit.
Relatedly, with clever tricks, illusionists are often better candidates for spotting cheats than most scientists. This is well-understood among illusionists; 'trained folks' tend to think in certain ways and the exploitation of their expectations or predictions can proceed more easily. Analogously, visual artists may be better trained to spot fakery in videos than your average scientist (e.g. Captain Disillusion?). This is the artful aspect of deception, and no one individual can be said to be immune from professional quacks at all times; there are myriad ways to overcome a single individual's scrutiny.

There are plenty more possible explanations, I only touch on the obvious ones. Certainly many more probable explanations than exposed human skin not reacting to boiling oil upon prolonged exposure.
Rather disappointingly, in almost every single case, performers who achieve extraordinary and inhuman feats are charlatans. A rather simple answer!


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Gametes produced after single and double cross overs
A female genotype, shown as abc / +++ produces 100 meiotic
tetrads. Among these, 68 showed no cross over (NCO) events; 20 showed
single crossover (SCO1) between a and b; 10 showed single crossover
between b and c (SCO2) and 2 showed a double crossover (DCO) between a
and b and between b and c. Of the 400 gametes produced, how many will be
of the following types? Fill your answers in the table. (Source)

According to me, the answers should be,
A. $68\times4=272$
B. $20\times4=80$
C. $10\times4=40$
D. $2\times4=8$
However, the answers are $336, 40, 20, 4$ respectively. What am I getting wrong?

You are not taking into account that crossovers happen at the four-chromatid stage and between cromatids. Take a look at the following picture1:

I suggest you draw down all the crossover events:

Now count the number of gametes that will be formed:
$$
\begin{align}
\text{(+++) and (abc)} &= 4\times 68+2\times20 + 2\times10 + 2\times 2=\mathbf{336} \\
\text{(+bc) and (a++)} &= 2\times20 = \mathbf{40} \\
\text{(ab+) and (++c)} &= 2\times10 = \mathbf{20} \\
\text{(a+c) and (+b+)} &= 2\times 2 = \mathbf{4} \\
\end{align}
$$

Introduction to Genetic Analysis 11th Edition, W. H. Freeman and Company, 2015.


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Is Pars intermedia functional in humans?
My textbook says, "Pars intermedia secretes only one hormone called melanocyte stimulating hormone (MSH)."
My teacher says that in humans MSH is secreted by the anterior lobe because the Pars intermedia is poorly developed and almost merged with the Pars distalis. I am confused as to what is correct. I find nothing wrong in both the arguments. So, is the Pars intermedia in humans functional or not?

Both- the textbook and your teacher are right.

The most obvious function of the pars intermedia in lower vertebrates is the secretion of melanocyte-stimulating hormone (MSH) for the purpose of pigmentary control.
In human fetal life as well, this area produces MSH which causes the release of melanin pigment in skin melanocytes.
In adults,

The human pituitary has no distinct pars intermedia (PI). Instead, the proopiomelanocortin (POMC) producing, adrenocorticotropin (ACTH)- and β-endorphin-immunoreactive PI cells are incorporated within the pars anterior, thereby participating in the formation of the pars distalis.

Edit:

POMC is cut (cleaved) to give rise to multiple peptide hormones. Each of these peptides is packaged in large dense-core vesicles that are released from the cells by exocytosis in response to appropriate stimulation:
α-MSH produced by neurons in the ventromedial nucleus has important roles in the regulation of appetite (POMC neuron stimulation results in satiety) and sexual behavior, while α-MSH secreted from the intermediate lobe of the pituitary regulates the movement of melanin produced from melanocytes in skin.

Sources:

https://link.springer.com/article/10.1007/BF02738816
https://pubmed.ncbi.nlm.nih.gov/6912095/#:~:text=Abstract,the%20purpose%20of%20pigmentary%20control.
https://en.wikipedia.org/wiki/Pars_intermedia

So according to you in human adults Pars intermedia is merged with the Anterior Lobe and therefore cannot be assumed functional?

@NeeravSingla PI is merged with pars anterior, but secretes its own MSH. Hope the edit makes it clearer.


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Why don't sodium Voltage Gated Channels open during Repolarization?
During Depolarization the Sodium VGC open when they receive the Threshold Stimulus. But when Repolarization occurs there comes a point when the cell interior has exactly the the same potential that it had during Depolarization i.e.,60mV but the Sodium VGC remain closed. Am I getting something wrong? If no, please explain.

Voltage-gated sodium channels have three basic states that represent different conformations of the protein: closed, open, and inactivated.
When a voltage-gated sodium channel is open at depolarized voltage, there is space for part of the channel to shift into a position that blocks the pore. When this happens, it gets stuck blocking the flow of sodium, and it requires a negative membrane potential to remove the block. We call this the "inactivated" state, and this model is called the ball and chain model of sodium channel inactivation.
The inactivation gating process is also referred to as the "h-gate", because h is the variable representing the gating in the classic Hodgkin-Huxley model.
Wikipedia currently has a useful table on the sodium channel page showing the different states that a sodium channel goes through during different phases of an action potential.


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How can poliovirus and other pathogens lead to permanent conditions if the bodies adaptive immune system is still functioning?
Wont the lymphatic system eventually create antibodies that completely eliminate the virus in the body?

Welcome to biology.SE! I think this question would likely attract a good answer if you include some discussion of what research you've already done. Please take the tour. It seems like there are two major assumptions coded in your question: (1) A functioning immune system should be able to clear poliovirus and (2) in the absence of virus, all damage done by a viral infection should be resolved.  I encourage you to read up on how viruses evade immunity and the etiology of poliomyelitis and the human nervous system.

When polio causes paralysis it's because it has destroyed nervous system cells. Once those cells are destroyed they typically cannot be replaced, so it doesn't really matter what happens to the virus after that in terms of the immune system. See the Wikipedia page on polio:

In around 1 percent of infections, poliovirus spreads along certain nerve fiber pathways, preferentially replicating in and destroying motor neurons within the spinal cord, brain stem, or motor cortex. This leads to the development of paralytic poliomyelitis, the various forms of which (spinal, bulbar, and bulbospinal) vary only with the amount of neuronal damage and inflammation that occurs, and the region of the CNS affected.

The post-polio syndrome may be the result of a persistent infection. Indeed most persistent viruses hide inside neurons and conversely viruses infecting neurons are often persistent (the neuron infection often happens in a minority of patients)


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What did Darwin mean by "degraded flowers"?
One of the chapters of The Origin of Species says that "Certain plants, belonging to the Malpighiaceæ, bear perfect and degraded flowers;" Full passage for context
Do you know which plant characteristic was he referring to? Is this morphological difference still recognized? Is there a new name for it?

Perfect flowers have both male and female parts.
"Degraded" isn't used anymore - just "imperfect".
"A bisexual (or “perfect”) flower has both stamens and carpels, and a unisexual (or “imperfect”) flower either lacks stamens (and is called carpellate) or lacks carpels (and is called staminate). Species with both staminate flowers and carpellate flowers on the same plant (e.g., corn) are monoecious..."
ref https://www.britannica.com/science/perfect-flower
Found by searching for "perfect flower"

I focused on "degraded", my mistake! Thank you very much!!


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What is blood pH for different animals?
So we all know that humans average blood pH is 7.4. But is it the same for the animals?
I need examples of animals with the same blood pH as humans and the ones with different blood pH.
I guess dogs and cats have almost the same pH am I right?

This question has been asked before -- Chart of blood pH across different animal species?.  However, since there is no answer to the original question, yours is not technically a duplicate.  I recommend looking at the comments on the older question, as they link to some resources for blood pH of reptiles, insects, and birds.

It would be helpful to know which species or groups you are interested in. Can you be more specific than "the animals"? Note that many animals don't even have blood! e.g. insects and hemolymph. For example, sharks have relatively acidic blood: https://www.researchgate.net/figure/A-Mean-SEM-blood-pH-levels-in-the-Atlantic-sharpnose-shark-during-a-60-min-stress_fig2_226732907, https://academic.oup.com/conphys/article/5/1/cox012/3055083. But I don't know if that is something that you are interested in.

I'm interested mainly in carnivores v/s herbivorous. The alkaline diet claim that as we humans have a slightly basic pH we shouldn't eat acidic food like meat. It would be a nice counter-example if carnivores have a similar pH as herbivores.

@heracho a little confused as you are different from user Jane who posted the question. But it would be helpful to have this directly in the question rather than in comments discussion.

I don't think I should edit the question to my particular interest. Although I believed that my question (Is there any correlation between species diet and blood pH?) is too close to this one as to be a new one.

The alkaline diet claim that as we humans have a slightly basic pH we shouldn't eat acidic food like meat. It would be a nice counter-example if carnivores have a similar pH as herbivores. -- I think a question concerning animal diet and blood pH is more interesting and easier to answer than the very general question posted above.  This seems to be an XY problem.

Good point @acvill, I'm going to post this specific question.


text:
How do you write genotypic and phenotypic ratios?
If two homozygous recessive parents are crossed, I know that all of the offspring will be homozygous recessive as well. Would you write the genotypic ratio as 0:0:4 then and the phenotypic as 0:4? (Does order matter? i.e. compared to 4:0)
Also, if the results are 2 homozygous dominant and 2 heterozygous, is it necessary to put the zero for recessive (2:2:0) or would 2:2 be fine?

I don't think there is formal notation for those ratios.
One would note that perfect dominance and recessivity, perfectly discrete phenotypes without pleiotropy and without environmental variance is extremely rare and these examples are pretty much only encountered in intro classes but never in the real life. There is hence, for the phenotypes at least, really no need for any formal notation here.
That being said, out of clarity, I would definitely prefer 0:0:4 (genotypes) and 0:4 (phenotypes) over 4 (for either genotype or phenotype) and I would definitely prefer 2:2:0 over 2:2


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How to produce and isolate an enzyme?
I have recently learned that one of the best ways to isolate a protein in industry is via Chromatography. What are other ways enzymes are isolated in industry? Are there other ways?

Chromatography is one of the best ways to isolate a protein, full stop. It is extremely widely used in both academia and industry.
Before we get into the details, though, a definition is in order. Chromatography is a means of separating components of a mixture using a mobile phase (liquid or gas) traveling though a stationary phase (a solid, gel, or very small beads, frequently with something attached to them). Chemical and/or physical interactions between the components of the dissolved mixture and the stationary phase cause those components to migrate at differential rates, separating them out from each other.
There is a huge variety of protein-stationary phase interactions that can be utilized in chromatography. Microscopic beads made of different substances can be used to create a matrix of pores where larger proteins will migrate more quickly than smaller ones. Epitope tags such as Myc or FLAG can be recombinantly added to a protein's sequence and purified using beads that have epitope-specific monoclonal antibodies covalently bound to them. The tagged protein is "grabbed" by the antibodies while the rest of the mixture washes through, then the binding is reversed by various chemical means that interrupt the protein-antibody interaction, such as high salt concentrations, varied pH levels, or chaotropic agents and the concentrated protein collected all at once.
Sometimes it is known that a certain class of proteins (such as antibodies, for example) will bind very specifically with another protein or protein fragment (in this case, the bacteria-derived Protein A). That protein is covalently bound to beads and used to purify and/or concentrate all antibodies in a solution, regardless of the antibody's specific target. Protein A binds to a section of an antibody known as the Fc region, so that sequence is sometimes fused to a non-antibody recombinantly-expressed protein so that it can be easily purified by this method. Antibodies that are specific for the protein of interest itself can be used for purification.
Many other chemical reactions can be harnessed to cause a protein of interest to bind to a stationary phase substrate and later eluted by reversing or inhibiting the chemical reaction. One example is purification based on electrical charge, called ion-exchange chromatography. If it is known that a protein has an overall positive charge, negatively-charged beads can be used to bind it (and all other positively-charged proteins in the mixture). Once washed, the protein(s) can then be eluted by changing the pH, hence neutralizing their overall charge and breaking the ionic bonds which bound it to the stationary phase. Positively-charged beads can also be used to purify negatively-charged proteins.
There are many other strategies besides the ones I've highlighted here – the term chromatography encompasses a huge range of possibilities for protein purification. I would say that in the majority of large-scale industrial purifications, combinations of different types of chromatography are the only methods used. There are of course other methods involved in the manufacturing of a protein therapeutic, such as cell lysis, filtration, concentration, dialysis, formulation, etc., where chromatography is not used, but for purification it's typically the only one. One reason for this is automation. Chromatography columns can be loaded, washed, eluted, cleaned, and regenerated without the need for any human interaction other than to provide the necessary buffers and materials. It can often also be scaled up quite a bit from benchtop to manufacturing suite, allowing for more material to be processed per batch. And, once everything is tweaked and optimized, you can get extremely pure material out of it.
There are some other protein purification methods, such as organic extraction, density centrifugation, and differential precipitation/solublization, but these are typically (but not always) used more in research and development than manufacturing, for various reasons. You don't want toxic organic chemicals like phenol, chloroform, ether, etc. involved in your manufacturing process if at all possible, because it takes a lot of work to prove to the FDA that all traces have been removed at the end. Centrifugation is not very scaleable, and is rather difficult to automate. One of the issues with precipitation is ensuring that re-solublization is both complete and consistent between batches. The amount of work that goes into validating manufacturing processes for injectable drugs and getting FDA approval is absolutely mind-boggling. Trust me :)
Hopefully I've answered your question! Please let me know if I missed anything or you want to know more about something.

Hi MattDMo, that answers my question very well. If I could ask another question in relation to 'manufacturing of a protein therapeutic, such as cell lysis, filtration, concentration, dialysis...' how do I find out what steps are appropriate if I only know the protein? Journal articles? Or online databases?

@Andrew Yes, those, experience, and trial and error. If you gave me a new protein to purify, I'd first check journals and look at several protein databases to get as much info as I could. What you're going to be using the protein for is another consideration - are you treating cells with it? Injecting it into mice? Doing biophysical experiments? Do you want just the natural protein, or can I epitope-tag it to ease purification? Another thing I'd check for is whether there are good antibodies available for the protein, as you can use them both for purification itself and for detection. [...]

[...] Just starting out, I'd probably epitope tag it just so I can easily purify it, detect it, and test my protein-specific antibodies on it, then go back to the natural sequence if you need it in that form. You have to be able to look at a sample or column fraction and figure out if your protein of interest is there, and check quantity and purity. Western blotting is usually the best tool for that, along with Coomassie or similar gel staining. Then, it's just a matter of trying different column types based on the protein's predicted biochemical characteristics and seeing what you can get.

You also need to remember that there's not necessarily only one "right" way to do it. I might do ion-exchange followed by nickel followed by size exclusion, whereas someone else might do three different types of ion-exchange.

Thank you for all your help. I appreciate it heaps.

”Microscopic agarose beads can be used to create a matrix of pores where smaller proteins will migrate more quickly than larger ones.” Perhaps I am mistaken, but this sounds like you are describing gel filtration. If that’s the case, however, it is larger proteins which elute more quickly than smaller ones.

@canadianer good catch. For some reason I was thinking of electrophoresis, where smaller goes faster.


text:
Tree Identification - California Bay Area
I've seen these trees in the Bay Area in Mountain View and Fremont, and have been searching for different pine tree varieties that have wider canopies. Does anyone here know what trees these are, they are very beautiful.

Here is the link to the exact location where I saw them recently:
https://goo.gl/maps/NSfAXZSgzypWXKqj9

Welcome to Biology.SE! Identifications questions should include clear closeup photos of the organism (photos from multiple angles if possible) — for trees please include pictures of the bark, leaves/needles, and any reproductive structures. Habitat information and an estimate of the size of the organism are also helpful. Please [edit] your post to include this essential information. ——— You may also benefit from taking the [tour] and then going through the help pages starting with [Ask] questions effectively on this site. Thanks!

For California trees, my go-to is A Californian's Guide to the Trees Among Us by Matt Ritter (Heyday, 2011).  California trees can be challenging due to the extremely varied habitat and many introductions over the years.
Your trees appear to be younger specimens of Pinus pinea or the Italian Stone Pine, based on the description on page 14 in Ritter. No other conifer in the book matches better.  Going to Wikipedia the description also seems to fit, in particular they mention "...in youth it is a bushy globe..."  There is also good information at Kew where I found this image, which looks to be very similar to what you observed.
Of course, if you can visit the location again you can check for needles in pairs, and orange-brown scaly bark.

Yay, this is perfect! Thank you for the book link - checking out!


text:
The blood pressure when blood comes out of body
Is there any certain amount of pressure difference between our blood pressure and barometric pressure when blood of our body begins to come out?

Blood pressure is the pressure above barometric pressure.  When you pump up a blood pressure cuff, or a tire for that matter, you don't have a gauge with a line at 760 torr / mmHg; you're measuring the pressure relative to the air in the room.
Note that blood pressure is only 16% of normal atmospheric pressure.  Imagine what your blood pressure would be if you were the victim of explosive decompression in outer space!


text:
Is there a metric for “evolutionary agility”?
By "evolutionary agility" I mean how fast an organism can adapt to changes in the environment. I’d imagine that a population with more offspring and a shorter time between generations would be more “evolutionary agile”.

Yes, there is a measurement laid out by Haldane (1949) called 'Darwins'. One Darwin is given an $e$ fold change in a trait over the period of 1 million years.
As to your second point, yes there are different variables which control the rate of adaptation within a population. The classic factor is genetic variation, as given by Fisher's (1958) fundamental theorem of natural selection, which states:

The rate of increase in fitness of any organism at any time is equal
to its genetic variance in fitness at that time

So broadly speaking, individuals with more additive genetic variation will adapt more rapidly.
Of course, there are many other factors such as generation time, effective population size and mutation rate will influence the response to selection. However, such as in the case of generation time, the relationship is not necessarily a simple one (Gandon and Mikalakis, 2002).
EDIT
After re-reading your question, I think I perhaps misunderstood it.
I suppose the term you are looking for is 'evolutionary potential', which is defined by Steeves et al (2017) as:

The capacity of a population to evolve in response to environmental
change.

There is a nice chapter in this book which gives a good overview of the topic. The chapter may perhaps be available for free on certain websites.
References

Haldane, John Burdon Sanderson. "Suggestions as to quantitative measurement of rates of evolution." Evolution (1949): 51-56.
Fisher, Ronald Aylmer. The genetical theory of natural selection. Рипол Классик, 1958.
Gandon, Sylvain, and Y. Michalakis. "Local adaptation, evolutionary potential and host–parasite coevolution: interactions between migration, mutation, population size and generation time." Journal of Evolutionary Biology 15.3 (2002): 451-462.
Steeves, Tammy E., Jeff A. Johnson, and Marie L. Hale. "Maximising evolutionary potential in functional proxies for extinct species: a conservation genetic perspective on de‐extinction." Functional Ecology 31.5 (2017): 1032-1040.

Even things like what form of reproduction it uses can be an influence, sexual selection can both speed up and slow down the spread of genes for instance.

Of course - this being biology there are an infinitude of variables which can influence the rate of adaptation - too many to include in a short post!


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'Big ideas' behind constrained selective breeding (optimization)
I'm looking for help in finding the 'big ideas' behind a project I'm beginning and want to make sure I'm not missing anything since I wasn't trained in Biology.
My idea is investigating constrained selective breeding, say, a farmer who wants to balance crop yield with artificially selecting a desired trait (can't select too strongly because this will reduce yield). I've found many models for selection and found Haldane's classic useful but I'm not sure how to incorporate a constraint.

I believe that you are talking about "multidimensional selection".
E.g. you are selecting on not one trait (yield) only but more than one (yield+some other trait). There's quite a bit of work done on this in crop science for example.
See e.g.

here
here
here

Figure 3 from the last talks about this in terms of evolution by reproductive isolation, which is pretty much the same thing except it's natural rather than artificial selection.

The most important thing practically is to try to measure the correlations of the traits in question. If they are positively correlated or uncorrelated, it shouldn't be too hard. If they are negatively correlated then you might have some difficulties due to constraints on the kinds of phenotypes that can exist.
For a recent technical treatment with good references, see here.


text:
Constitutive Dark Skin vs Facultative Tanned Skin
Most can easily spot the difference between a tanned and dark person. But from my research, the only difference is in the size and concentration of melanin (Jablonski). But this continues to increase with sun exposure, so I was wondering what specific differences are there between people who tan or are naturally dark. Surely they are not the same color, so what is different?

note there are several forms of melanin.


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Parasympathetic effects on digestive tract - motility versus absorption
The parasympathetic nervous system's purpose is often referred to as "rest and digest." As part of this purpose, parasympathetic innervation increases motility in the digestive tract to move food through. However at the same time, slowing gastric motility and peristalsis is important for absorbing nutrients, which is accomplished by enterogastrones like secretin.
So on one hand, the PSNS promotes more motility to move things through the digestive tract. On the other, certain hormones are released in response to the presence of food that slow down motility for better absorption.

If one of the main purposes of the PSNS is to promote digestion (and thus I would subsequently think absorption), why does it cause increased motility, which gives less time for digestion and absorption?
Is it important during digestion to sometimes increase or decrease motility? If so, how does it related to the PSNS and SNS in terms of when either happens?


text:
Consequences of abnormal blood pressure unrelated to cardiac output?
A question from Kaplan's MCAT Biology Review asks:

In bacterial sepsis (overwhelming bloodstream infection), a number of capillary beds throughout the body open simultaneously. What effect would this have on the blood pressure? Besides the risk of infection, why might sepsis be dangerous for the heart?

The answer is:

Opening up more capillary beds (which are in parallel) will decrease the overall resistance of the circuit. The cardiac output will therefore increase in an attempt to maintain constant blood pressure. This is a risk to the heart because the increased demand on the heart can eventually tire it, leading to a heart attack or a precipitous drop in blood pressure.

I had always viewed blood pressure as a means to achieve appropriate blood flow, and a system with lower resistance would simply operate with lower pressure (via Ohm's Law). However, the answer implies that maintaining normal blood pressure is a goal in itself, such that the body would naturally raise cardiac output to dangerous levels in order to maintain it.
Can someone help explain:

Does blood pressure play a role in blood circulation that makes it more important than just a means towards appropriate cardiac output?

What are health consequences of abnormal blood pressure unrelated to cardiac output from a biochemical perspective? If I search for "abnormal blood pressure" I'll get broad symptoms like "dizziness" that don't explain its effect on different tissues that cause the symptoms.

For the second part of your question, I suggest you use better search terms. E.g., 'pathophysiology of hypertension' gets much better results than 'abnormal blood pressure'.

Blood pressure, as you noted, is just a means to an end: the flow of blood through tissues. The trouble is, many of the body's regulatory systems use blood pressure (rather than flow) as an index of cardiovascular status. A key example is the baroreceptor system, which senses changes in blood pressure and tries to correct them by effects on the heart, blood vessels and kidneys.
In sepsis with decreased blood pressure, baroreceptor firing increases in an attempt to increase cardiac output $^1$. This increased demand on the heart can be counterproductive and cause the heart to fail. But this phenomenon is not unique to sepsis. There are many other conditions where a hyperdynamic circulation leads to heart failure: such as anaemia, thyrotoxicosis and thiamine deficiency $^2$.
All of these examples highlight a basic principle in pathophysiology: adaptations can sometimes turn maladaptive.
Note: The effects of sepsis on the cardiovascular system are complex and go beyond vasodilation. For more details, you could read a textbook of pathophysiology/medicine. Or go through any of the review articles on this topic, such as the one by Lelubre & Vincent $^3$.

References:

Gattinoni L, Carlesso E. Supporting hemodynamics: what should we target? What treatments should we use? Crit Care [Internet]. 2013 Mar 12 [cited 2020 Aug 24]:17(Suppl 1):Article S4 [8 p.]. Available from: https://ccforum.biomedcentral.com/articles/10.1186/cc11502
Mehta PA, Dubrey SW. High output heart failure. QJM. 2009 Apr;102(4):235–41. https://doi.org/10.1093/qjmed/hcn147
Lelubre C, Vincent J. Mechanisms and treatment of organ failure in sepsis. Nat Rev Nephrol. 2018;147(7):417–27. https://doi.org/10.1038/s41581-018-0005-7


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Is grip force a reflex?
When we reach for an object, for example, a cup, is the force used to hold it a reflex? Which sensorial information is used to select the force to hold it?
Why I am interested in this question

With the development of robots with dexterity, it is necessary to develop a minimal amount of sensors so they can choose the strength to hold an object. Objects that look heavy and slippery need more force, while objects that are delicate need a lower force. Do we unconsciously use visual information to decide the force to hold an object? Can this be called a reflex?

When we reach for an object and it feels painful to hold it (it is too hot or too sharp) we immediately release it, is that a reflex?

In my search I found mostly results about the grip reflex of newborns. Is it Completely lost in adults?

(a personal reason) recently, I noticed that my grip force calculation is kind of “uncalibrated”. I am dropping cups, tools, my cellphone, more frequently than before. However this is not a problem of grip Force or shaking, I can hold myself on a bar with one hand and I have zero hand shaking on my hands. So, when I consciously choose to hold it, I have force, but when I am not thinking of which force to apply, I drop things. Note: this question is not for self diagnosis, this is just the initial observation that sparked my interest in the question.

Seems more like a feedback loop than a reflex.  That is, the grip force is adjusted depending on the weight & texture of the object.  That is, when you hold an empty paper cup, a full on, a ceramic mug, or a mug used as a container for nuts & bolts, you automatically use feedback to control how much force to apply.  And you can do this with your eyes closed, so visual information isn't the primary source.

holding an object is usually a task that requires visual and mechanical processing (i.e. what the object looks like (i.e. what material does it seem to be made of, what is your former experience with that material, how heavy does it feel) and muscle memory.
according to the physiological definition of a reflex:

Reflex, in biology, an action consisting of comparatively simple segments of behaviour that usually occur as direct and immediate responses to particular stimuli uniquely correlated with them.

according to this same source, innate reflexes such as walking, blinking and swallowing require skeletal muscles but are still considered reflexes despite the fact that for some of these tasks (such as walking and standing) we do not know from birth (meaning reflexes can be taught and unlearned/lost).
There are other reflexes such as intestinal smooth muscle contractions etc... that we are usually completely unaware of and are controlled by the central nervous system (CNS) unconsciously.
The response to pain is also a reflex; the thermal/mechanical neural sensors in your arm (for example) send the information to your spine which directly sends a signal to your muscles to contract in order to avoid/release the object.
the palmar grasp reflex is one of many reflexes babies have that they do not need to be taught. Adults usually unteach these reflexes as some of them are not as frequently necessary in later stages of life. Newborn apes for one use the palmar grasp reflex to hold on to their mothers (it is possible that is where that reflex came from from an evolutionary standpoint).
consider that all reflexes are caused by cues that your nervous system senses and responds to. Some of these reflexes can be controlled and others not and may vary depending on your environment. A famous example of this is the pavlov's dog experiment which proved that you could also be conditioned to respond to a certain stimulus. In your case, seeing or feeling the cup is supposed to provide a stimulus to your brain reminding you that you are holding an object that requires a specific mechanical maneuver which you have learnt over time.


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The Proofreading Function of Coronavirus Polymerases
I have heard that the Coronavirus family have a proofreading and editing function in their polymerase enzymes which can recognize and excise mutations. This is obviously disastrous for the population of infected individuals. Is this true, and if so, would it be possible to knock out the proofreading and editing subunit selectively so that the mutational burden would progressively increase in the viral population ?  Could this then lead to something like Muller's Ratchet and dampen the virulence in the population or would there still be a mechanism to remove the mutated viruses from the population and retain the virulence over time?

Welcome to SE Biology. Please finish reading the [tour] and check the help on writing good questions. You will find that you are expected to research a topic for an answer before posting, ask one question at a time, and make sure that questions relate to problems in biology. If your question is whether coronavirus polymerases proofread and edit, then that is one question. If not, you need to cite references that it is so. That would leave a question that is not a question but a suggestion for an anti-viral strategy, which is off-topic here.

Not an answer but the keywords are exonuclease and nsp14. You could look up how lopinavir and remdesivir work and how ribavirin does not work.


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During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment?
I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. I understand that it is labeled so in order to locate the fragment on a gel, but I don't understand why it is only labeled on one end? If the DNase cleaves it in two, wouldn't the other end be un-labeled and untraceable? Therefore kind of defeating the purpose of labeling it at all?

I assume you know the starting length of the labeled DNA. What can you can infer from that information? What would happen if you labeled both ends? ——— To understand this you probably need to draw some pictures ...

Preamble
Although there is a Wikipedia page with a general account of DNA footprinting, this perhaps does not put sufficient emphasis on the general strategy, making reference to the Maxam & Gilbert DNA sequencing method, with which contemporary students are not likely to be familiar. Elsewhere on SE Biology I have summarized the strategy of different DNA sequencing methods, so I shall use that as a starting point for this answer.
The Strategy of DNA Footprinting
In DNA sequencing there are two conceptual pieces of information one is trying to discover: the identity of a base, and the position at which it lies. A third point of importance is the practical technique one uses to realize a strategy. The method of DNA sequencing developed by Maxam & Gilbert used specific chemicals to fragment pieces of DNA:

The particular chemical used identified the base as the last one on one of the fragments produced.
The length of the fragment indicated the position with respect to one of the ends, which was used as a reference point.
End-labelling of one end of the original DNA allowed fragments containing the reference point to be visualized, distinguishing them from others that were unlabelled and hence generated elsewhere.

In DNA-footprinting we are not concerned with identifying the bases: the DNA has probably already been sequenced or we can do that separately. We are in interested in positional information, and we shall see that this also involves fragments — generated by the non-specific DNase — and their visualization, as in the method of Maxam & Gilbert.
This is explained in the figure below, my own modification of Coutney2008.jpg, in the Wikipedia article mentioned.

The frame on the extreme left addresses the question of labelling and visualization by showing the fragmentation of uniformed-labelled DNA by DNase. In this example the DNase cleaves at three points (arrows), generating four fragments of different sizes, A, B, C and D. If these fragments are separated and visualized by their radioactivity (by autoradiography) there is no way of knowing their position in relation to the reference point. So whatever our strategy is in relation to protein-binding (explained below) the positional information is not revealed. We cannot tell that fragment A contains the reference point.
Now let us turn to Frame 1, which is in effect the Maxam & Gilbert strategy without the base-identification. The DNA is labelled at one end and treated with DNase at a concentration that will generate a range of fragment sizes. The ones we are interested in are those that include the reference point, which is the end we have labelled. These fragments have been coloured pink. Other fragments (light blue) that do not include the reference point will be generated — including some of the same size as those of interest — but these will not interfere with our analysis as they are not labelled and will not be visualized after the fragments have been separated according to size on denaturing gels and subjected to autoradiography (see gel lane 1). (The unlabelled ‘light blue’ portions may have been fragmented further, but this has not been shown for clarity.)
The footprinting strategy is shown in Frame 2. The experiment of Frame 1 is repeated with the DNA-binding protein (bright blue oval) added. Now the region of DNA to which the protein binds will be protected from DNase. Thus, fragments terminating within this region will be missing and be absent from lane 2 of the gel. Hence the position at which the protein binds is specified as the distance of the missing fragments from the labelled reference point. (There are likely to be fragments of the same size as the missing ones in the mixture, but, to repeat, because of the end-labelling they will not be visualized.)


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How does Ran GDP get from the cytoplasm back to the nucleus following nuclear import and export?
I understand that in Ran-dependent nuclear import Ran GTP binds importin in the nucleus, and after diffusing through the nuclear pore complex Ran GTP is hydrolyzed to Ran GDP and releases importin. How does the hydrolyzed Ran GDP get from the cytoplasm back through the nuclear pore complex to the nucleus? The same question applies to nuclear export after Ran GTP is hydrolyzed following export of the Ran GTP-exportin-cargo complex. Does Ran GTP freely diffuse through the nuclear pore complex? Is it actively transported?


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What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?
One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome can translate mRNAs before they've even finished being exported from the nucleus. So what stops localized mRNAs from being translated all over the cell before they reach their designated location?
I was thinking maybe they're bound by hnRNPs that inhibit their translation, which dissociate when they're bound by localized mRNA binding proteins, but I could be wrong.
Or is it that they are translated all over the cell, but the concentration at their locale is just way higher in their locale?

Could you give a specific example of the type of localization you are referring to, please. Are you talking about mitochondrial or nuclear localization or something else? At the moment your question is too broad and imprecise.

Sorry, I guess a good example could be Calmodulin Kinase mRNA being transported to the synapse of a neuron on the cytoskeletal microfilaments. So in the case of that mRNA, how is it not transcribed at all on route to the synapse? I see that Nicolai has answered that particular example below though.

That’s an example I’m not familiar with. I must check out the reference from @Nicolai.

The answer to your general question is 'it depends':

A lot of RNA localisation to the ER and mitochondria happens co-translationally (based on the protein targeting sequences), so these mRNA actually depend on translation to be localised. However, RNA localisation to mitochondria can also happen due to targeting sequences in the mRNA 3'UTR - in these cases translational repression would be possible, but it's unlikely and I don't think anyone ever checked it in this particular case. (see i.e. this review)
the translation of many mRNAs that are actively transported along the cytoskeleton is inhibited during transport, either by specific RNA binding proteins or larger RNP (ribo-nucleo-protein) complexes (see another review).

There are also bound to be some specific mRNA that have very specific regulation mechanisms and others that are exceptions.


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What types of cells HPV can infect?
I am wondering if there is any new information on which cells HPV is able to infect. Is it still limited  to squamous cells or are there other cells such as columnar cells it is able to infect?


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instances of virus transmission-enhancing research approvals
In February 2019 this article by epidemiologist Marc Lipsitch and professor Tom Inglesby raised concern about secret virus research.
Washington Post article link.

In 2014, U.S. officials imposed a moratorium on experiments to enhance
some of the world’s most lethal viruses by making them transmissible
by air, responding to widespread concerns that a lab accident could
spark a global pandemic. Most infectious-disease studies pose modest
safety risks, but given that these proposed experiments intended to
create a highly contagious flu virus that could spread among humans,
the government concluded the work should not go on until it could be
approved through a specially created, rigorous review process that
considered the dangers.
Apparently, the government has decided the research should now move
ahead. In the past year, the U.S. government quietly greenlighted
funding for two groups of researchers, one in the United States and
the other in the Netherlands, to conduct transmission-enhancing
experiments on the bird flu virus as they were originally proposed
before the moratorium. Amazingly, despite the potential public-health
consequences of such work, neither the approval nor the deliberations
or judgments that supported it were announced publicly. The government
confirmed them only when a reporter learned about them through
non-official channels.

Have there been other instances of transmission-enhancing research approvals since the apparent end of the moratorium?


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Microarray experiment validation meaning
I have a quick question: what does microarray experiment validation mean ?
I was reading a paper in which they say that the data of the experiment show that the 3 genes radB, dp1 and dp2 are co-regulated following gamma irradiation "validating our microarray experiment".
I tried to find something in Google but it is not yet clear.

I think here it means the results of their gamma irradiation experiment give the same results as the microarray experiment.  Here 'validating' means 'support'.

ok thank you @user438383


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Why does B12 deficiency enlarge red blood cells?
I'd like to know why B12 deficiency enlarge red blood cells

Welcome to Biology.SE, Adriana. @SPr has shared a reference with you that may answer your question. If not, it may help to know more about what you understand and what you don't. See the help center article on how to ask a good question

The technical term for enlarged blood cells is macrocytosis (macro means large, -cyto- means cell).

Macrocytosis due to vitamin B12 or folate deficiency is a direct
  result of ineffective or dysplastic erythropoiesis. These important
  vitamins and cofactors are required for normal maturation of all
  cells. Marrow erythroblasts are no exception. When either of these two
  factors is deficient, RBC proliferation and maturation result in large
  erythroblasts with nuclear/cytoplasmic asynchrony. These abnormalities
  are caused by a defect in DNA synthesis that interferes with cellular
  proliferation and maturation. RNA synthesis and cytoplasmic components
  remain relatively unaffected. The marrow is hypercellular with all
  forms of the myeloid cell line being increased and erythroid elements
  being dominant on the marrow aspirate smear preparations. The
  erythroblasts become large, oval shaped and contain a characteristic
  immature, lacy nucleus. These bone marrow features are called
  “megaloblastic” and are highly suspicious of a vitamin B12 or folate
  deficiency. Megaloblastoid (megaloblastic-like) abnormalities of the
  marrow are frequently seen in other hematologic disorders not
  associated with vitamin B12 or folate deficiency, (e.g.,
  myelodysplasia and leukemia) and a careful examination of the bone
  marrow is necessary to make this distinction.

Source: Megaloblastic Anemia and Other Causes of Macrocytosis
Erythropoiesis simply means the process of red blood cell production.
Erythroblasts are immature red blood cells that still have a nucleus. Mature red blood cells lose their nucleus before they enter the bloodstream to become active oxygen carriers.

I'm not the down voter, but I suspect this may have been because your answer is mostly a reference with a small glossary. Your answer is correct, and I think better than an explanation with no reference.

Indeed, why paraphrase when another has said it more accurately and concisely? I'll happily add that B12 is additionally known to affect epigenetic mechanisms as a coenzyme of methyltransferase that methylates, demethylates and remethylates various biological molecules including DNA. B12, and DNA methylation status, is important for structural stability of regions of chromosomes such as centromeres and subtelomeres. Medically it may explain why B12 deficiency affects pregnancy, and from a molecular point of view, why DNA synthesis is affected globally across the entire body!

that was perhaps an indirect way of saying I personally think your answer could be better (as a response to this basic question) with more than just a reference and a glossary. But I didn't think it was worthy of a downvote, specifically because it was correct and referenced.

Other things that compromise DNA synthesis also produce macrocytosis - nucleoside analog chemotherapy / antiviral therapy are good examples.

@SPr has given you a good reference in his answer. I thought I'd add some context to it.
The basic problem here is that red blood cells need B12 in order to synthesize DNA. Red blood cells live for about 4 months, and have to constantly be replaced, so when you have a problem with B12, this is one of the cell populations that will be affected. The problem here is actually the anemia. It's not that the cells are too big, but that there aren't enough of them (see the linked reference, as well as Robbins and Cotran Pathologic Basis of Disease, Ch 13, subsection "Anemias of Diminished Erythropoiesis"). The size itself helps identify why there aren't enough of them, distinguishing this anemia from other anemias that cause cells that are smaller than normal.
The mechanism in lay terms (which hasn't entirely been worked out, again, see both the article and Robbins), is that a problem with DNA synthesis causes the cells get larger before they divide. So you have fewer, larger cells. Because it's a universal problem with DNA synthesis, red blood cells aren't the only cells affected.

@user1136 that is a good question. Perhaps you could ask it? I'd be happy to answer.

@user1136 I'm not sure what the purpose of your comment is, but perhaps we can chat about it


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Statistical Analysis for Blood Sugar Measurements
I've conducted a lab aimed towards finding the impact of soluble fiber intake on the change in blood sugar levels. Following an 8 hour fast, I had test subjects consume a fixed amount of carbohydrates, with a varying amount of soluble fiber, and measured their blood sugar in 20 minute intervals. This was done for two hours each test, generally until blood sugar levels dropped to normal.
5 test subjects were used for the test, each with individual blood sugar responses - for instance, each had consistently different fasting blood sugar levels before food consumption, each had consistently different blood sugar peaks, and so on. Each test subject was tested 4 times, once with no soluble fiber, and 3 more with varying amounts of soluble fiber. The raw data I am now left with is simply a collection of scatter plot graphs displaying rises in blood sugar from normal condition, a peak, and a subsequent drop to normal condition.
I can visibly see from my graphs that more soluble fiber made blood sugar peaks smaller and longer to reach. Data did not always follow this trend, due to some source of error, but a relationship is nevertheless evident. I hope to make a conclusion from this data. What method of statistical analysis could I use to conclude a relationship from these scatter plots? I would like the method to take into account different individual responses, as well as the few data sets that did not confirm a relationship.
I appreciate your help!

You have a pretty complex experimental design. I think this question is better suited for stats.SE, where there are more likely to be those with expertise.

It would help to see your plots. The way I would imagine to present this data is not scatter plots but line plots:

(Each line would have a confidence interval/standard deviation from your different test subjects. This is just a schematic representation. Color represents different experimental conditions. Let me know if I misunderstood your experiment.)
Now, what is your actual question? Your hypothesis? You want to know if the time or height of the peak of blood sugar levels is different between the different fiber levels, right?
So, why not measure this? At what time do you find the peak for each subject and experimental condition and what's the blood sugar level at that time point? Your null hypothesis would be that there is no difference between the test conditions.

Here some mock data show the data spread from your 5 test subjects of the peak height measurements in the 4 different test conditions. Now you reduced your data to a question, where you could use a statistical test to see if you can reject the null hypothesis.
One thing you could do is to perform an ANOVA with e.g. Dunnett's post hoc test to compare your fiber conditions to the control condition
A problem with that is that your conditions are not really independent. And your actual question is not if any of these conditions is different. Your hypothesis would rather be if there is a relationship between fiber content and peak height/delay (null hypothesis would be: there is no relationship).
Here is the same mock data in a scatter plot (color represents test subjects, they overlap, but let's assume there are 5 data points for each condition) with a trendline showing, that with increasing fiber content there is a reduction in peak height:

You could therefore try a correlation analysis and test the statistical significance of your correlation coefficient.
As you see, the statistical analysis very much depends on your hypothesis and how you analyse your raw measurements. I hope, I have correctly identified the issue and this helps you with your analysis.

Yeah, that makes perfect sense! I very much appreciate your help.


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Do we know how dangerous six-eyed sand spiders are?
The Sicariidae family contains the well-known and dangerous Loxosceles spp. (fiddle-backs, violin spiders).
The family's other two genera, Sicarius and Hexophthalma (six-eyed sand spiders) have reputedly exceptionally cytotoxic venom, although they live in sandy deserts and rarely come into contact with humans.
Quite common in the exotic pet trade is Sicarius thomisoides (formerly terrosus).  I would be particularly interested in how dangerous this species is likely to be - many are now claiming that research has shown it to be minimally dangerous.  I'm not sure what work this is based on - perhaps this paper? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767091/


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What to do with this Araucaria sprout
I live in Santiago, Chile, and I see this Araucaria frequently:

For what I have read, it seems to be a female A. angustifolia individual (leaves are 2-3 cm long and a few mm wide, with a very sharp point; it gives round-ish cones with nuts, about 15 cm in diameter). Am I right?
Two days ago I found a nut in the ground, which I took without thinking about it too much. It was laying superficially and it took me no effort. Only when I had it in my hand I realized that it was a sprout, and become interested in knowing more.

Only then I learned Araucarias reproduced sexually, and understood the unlikeliness of my finding. It is possible that the sprout is A. angustifolia x A. araucana, since there are individuals of both species in the vicinity. (not very close, though!)
Considering the IUCN status of both species, I'm interested in raising it. I put it in a pot.
Q: How can I identify the child? Can I save it? How should I care for it? (especially, watering, temperature, lighting, and the like)


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What is targeted gene disruption?
I am a bit confused about what targeted gene disruption means. I was reading this article in which they compare the Pyrococcus Furiosus genome with a genetically tractable strain P. Furiosus variant genome, called COM1. When they described how COM1 strain was obtained they say:

The COM1 strain was obtained by targeted gene disruption of the pyrF locus (PF1114) using a plasmid designed for double-crossover recombination (37).

Since the definition from Springer about targeted gene disruption is simply:

Experimental replacement of an endogenous gene by a mutated (non‐functional) version within the otherwise unchanged genome is called targeted gene disruption.

I concluded that it is the replacement of the gene, that is called pyrF in this case, by the experimenter with a non-functional version within the genome of the genetically tractable P. Furiosus variant. So I thought it was a sort of "inactivation" of a gene.
Then, in this discussion about What is the relationship between a “main” strain genome and its variant genome in archaea?, someone kindly suggested me to read the original paper about how the COM1 strain was discovered. Here I find some contradictions with the idea that I built about "targeted gene disruption of the pyrF locus".
In this paper, they say that

In attempts to develop a method of introducing DNA into Pyrococcus furiosus, we discovered a variant within
the wild-type population that is naturally and efficiently competent for DNA uptake. A pyrF gene deletion
mutant was constructed in the genome, and the combined transformation and recombination frequencies of
this strain allowed marker replacement by direct selection using linear DNA.

Then also that:

there have
been no reports of genetic manipulation of the P. furiosus
chromosome. Here we used simvastatin and 5-FOA selections
to generate a ΔpyrF strain, designated COM1

And, finally, an other important extract:

Here we report the construction of a deletion of the pyrF
locus in the P. furiosus chromosome and the discovery that this
strain, designated COM1, is remarkably efficient and naturally
competent for uptake of both circular DNA and linear DNA.

I have to say that this article was too difficult for me and full of details that I am not interested in, so I did not read it in deep, but I selected these extracts that describe in simple words how COM1 was obtained. However, from these I get an idea of how COM1 is obtained that is different from the one I thought at the beginning by Springer.
Since the Wikipedia definition of gene deletion mutant is:

In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is left out during DNA replication. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome.

Considering this and the other two extracts that I reported, now my idea of how COM1 was obtained is that the pyrF was deleted (by the scientists) and that part was (naturally) substituted by a marker (that is "a DNA sequence with a known physical location on a chromosome") which is a linear DNA since this COM1 strain is remarkably efficient and naturally competent for uptake of both circular DNA and linear DNA.
Now my question is: is the Springer definition (linked above) "universal" or by targeted gene disruption one can intend not only "artificial" genetic manipulation but also deletion of a gene and natural replacement that could also lead to a new pyrF gene (in this case) that is functional (so not non-functional) ? What does it mean when I say "The COM1 strain was obtained by targeted gene disruption of the pyrF locus (PF1114)"?
I apologize for the long question and I thank you in advance.

You have it mostly right, however, you are misunderstanding what has gone on here a little.
The definition from Springer is correct - a targeted gene disruption is a direct replacement of the gene with a non-functional one. However, to do so you also need some method of detecting that your gene disruption worked and will persist. This is most commonly done by introducing marker(s) along with the disrupted gene in a form known as a cassette.
In the case that you present it seems that they have used simvastatin as a selection agent and 5-fluroorotic acid (5-FOA) as a reporter to show that while the gene has been disrupted (i.e. non-functional), expression from that location is still happening as it should.
The method they used for introducing this cassette is a recombination between a plasmid and the Pyrococcus genome. This is (or was) a common method of altering the genome of many organisms to effect some functional change. The plasmid will have sites flanking the cassette that match the host (in this case Pyrococcus genome) and these are used to get the genome to recombine in the manner described in the pictures here.

Thank you so much @bob1 !