text:
What is the motivation behind the CCA -> CCU modification between SARS-CoV-2 and the mRNA vaccine when encoding the signal peptide?
The S glycoprotein signal peptide in SARS-CoV-2 and the mRNA vaccine is encoded by:
           3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3
Virus:   AUG UUU GUU UUU CUU GUU UUA UUG CCA CUA GUC UCU AGU CAG UGU GUU
Vaccine: AUG UUC GUG UUC CUG GUG CUG CUG CCU CUG GUG UCC AGC CAG UGU GUU
               !   !   !   !   ! ! ! !     !   !   !   !   !

What is the motivation behind the CCA -> CCU modification between the virus and the vaccine?

I would argue that the "answer" you quoted is exactly the sort unresearched speculation this site is intended to avoid. ——— Codons "code" for amino acids not peptides. Peptides are composed of multiple amino acids — these terms are not synonyms! In addition, codon usage tables for humans are readily available and don't support the idea that use of CCU is strongly favored over CCA (1.75% vs 1.69%).

@tyersome thank you for the feedback, great to know! (This is why such an answer should be posted as a separate answer and not within the question, so that people could vote on it.)

Please re-read the tour and the Help. A question is a question. An answer is an answer. If the poster of a question thinks a particular answer is correct he can accept it. He may be right or wrong but he has made his judgment clear. Posting an answer as an appendix to a question completely negates the SE Model, which is why I have deleted it.

@David Thanks for removing it from the question. Franck originally posted it as an answer, but as it was comprised entirely of a quote from one source, with no original content, it was outside the referencing guidelines here: https://biology.stackexchange.com/help/referencing therefore I deleted it. Better to write your own answer, Franck, using your own words, referring to other content by reference rather than duplicating.

@David -> No answer on my SE question, posted it somewhere else, got an answer there: what should I do?.

@tyersome: true, but that's not actually U being used there in the vaccines (the quote is incomplete/misleading) but m1Ψ.

The article mentioned says:

Why would you do that? As noted above, our immune system takes a very dim view of ‘exogenous’ RNA, RNA code coming from outside the cell. To evade detection, the ‘U’ in the RNA was already replaced by a Ψ.

However, it turns out that RNA with a higher amount of Gs and Cs is also converted more efficiently into proteins,
And this has been achieved in the vaccine RNA by replacing many characters with Gs and Cs wherever this was possible."
So codon optimisation - as Canadianer suggests.
RNA structural reasons
I expect the sequence was also put through a folding analyser (for the mRNA that is) and that may be why not all the codons were optimised to C and G, and why there is an A → U change as well.
If someone wants to use an online tool to show the folding differences, please feel free to add the graphics output to this answer.
It is also possible the designers didn't want the final sequence to exactly match the output of popular optimisation software, to reduce legal arguments about whether the software was used.
Differentiating between vaccine and viral sequences.
Even though the vaccine uses a different base instead of uridine, when researchers check the sequences of mRNA in the future the base differences will make it easy to tell the source.
Why?

In case the mRNA keeps being found in someone's cells long term.
Testing for contamination in the production facility or research lab.
Testing efficacy in cell cultures exposed to virus.
Adding messages such as patent info.

Some of your speculations sounds quite plausible — would you please edit in some supporting references? Does psuedouridine really help the exogenous RNA evade detection? Also note that the question is about CCA->CCU so increased GC isn't relevant, but if you want to include it please put in supporting references.

"reduce legal arguments about whether the software was used" why is that an issue?

A software company making optimisation software might make trouble, even if their software wasn't used. A bit like making sure your returned homework is very different from what you expect your classmates homework to be.

The other answer is a bit convoluted IMHO.
First note that as the article cited notes, that's not actually CCA -> CCU but CCA ->  CCΨ; they only used ASCII for convenience. Furthermore, these three all code for proline as the article also notes.
Second, Ψ stands for pseudouridine and it's the golden discovery of Kariko and colleagues (which made mRNA vaccines [more] practical) that you need to use as many pseudo-Us as possible to ensure that the exogenous mRNA doesn't get destroyed prematurely and/or triggers downregulation of transcription.
Third, that's not even pseudo-U that's actually used in the Pfizer vaccine but N1-methyl-pseudouridine (variously abbreviated as N1mΨ or m1Ψ), which is even more "potent" in these terms than even pseduo-U. (According to a book on RNA therapeutics, m1Ψ was actually discovered and is patented by Moderna circa 2012-2013, before any academic publications.) Actually a 2017 publication found that independently of reduced immunogenicity, m1Ψ seems to be more active "by increasing ribosome pausing and density on the mRNA":

We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.

And more research on the latter aspect (2019)

Global incorporation of different modified nucleotides often (but not always) markedly changed mRNA expression. This effect was seen across numerous synonymous coding variants of multiple proteins, in several different cell lines, and in vivo. m1Ψ generally gave higher expression than U or mo5U for the same sequence. Biophysical studies revealed that m1Ψ and mo5U have dramatically different and opposite effects compared to U (stabilizing and destabilizing, respectively) on overall mRNA folding, nearest-neighbor base-pairing thermodynamics, and secondary structure pattern as mapped by SHAPE.

There could be additional reasons, but these are probably marginal.
Now, canadianer asks an astute question below (which was not asked by the OP), whether it's (still) preferable to do UUU -> UUC (which normally it is) if m1Ψ is going to be globally substituted for U anyway. I don't actually know the answer to that; Pfizer or Moderna might have researched it, but I haven't found any publication on the trade-off.
The actual reason for the latter (especially since UUC is about 3 times as inefficient as UUU) might be that real goal is to slow down the protein folding there. The WHO doc does say that the protein is folded in a particular way "to ensure the S glycoprotein remains in an antigenically optimal pre-fusion conformation". In general, there's a trade-off between the speed of translation and accuracy of folding. (ΨUU is actually twice as efficient as UUU already, even with naturally occurring pseudouridine. In fact UUU is one of the most common places where one finds a naturally occurring pseudouridine.)

Then why change UUU->UUC,  GUU->GUG, etc?

@canadianer: Frankly that one is even more mysterious because "The proofreading ratio of the UUC programmed ribosomes is one-third that of their UUU programmed relatives. From these results ribosomes programmed with UUC are apparently more prone to errors than those programmed with UUU" https://www.pnas.org/content/pnas/86/18/6888.full.pdf

I raised the question because all of the substitutions made in the coding sequence for the signal peptide are towards the most frequently used codons and tend to result in less methyl-pseudouridine in the final product, which seems to contradict your answer with respect to this specific sequence. I don’t know how they selected codons for the entire mRNA, but I wonder if for this sequence their selection was simply based on codon usage rather than trying to incorporate methyl-pseudouridine. Regardless, I found your answer quite informative.

The modification "to ensure the S glycoprotein remains in an antigenically optimal pre-fusion conformation" is the 2P modification of 2 amino acids, not due to codon synonym optimization (that I'm aware of)


text:
What is the motivation behind the AAAAGCAUAU GACUAAAAAA of the mRNA SARS-CoV-2 vaccine when encoding its polyadenylated ending?
The very end of mRNA is polyadenylated as usual, but the BNT162b2 vaccine ends the following sequence, as denoted in this article:
                                     ****** ****
UAGCAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAGCAUAU GACUAAAAAA AAAAAAAAAA
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAA

This is 30 A’s, then a “10 nucleotide linker” (GCAUAUGACU), followed by another 70 A’s.
What is the reason for this design choice?

To enhance stability and translation efficiency according to {1}:

The 5′UTR (TEV) [8,21] and 3′ UTR (F-I) of this construct have been shown to enhance stability and translation efficiency, as has the 100-nucleotide poly(A) tail interrupted by a short linker (A30LA70, where L = GCAUAUGACU) [22]

References:

{1}
Stadler, C., Bähr-Mahmud, H., Celik, L. et al. Elimination of large tumors in mice by mRNA-encoded bispecific antibodies. Nat Med 23, 815–817 (2017). https://doi.org/10.1038/nm.4356 https://www.nature.com/articles/nm.4356
{21} Gallie, D.R., Tanguay, R.L. & Leathers, V. Gene 165, 233–238 (1995).
{22} Vallazza B, Petri S, Poleganov MA, Eberle F, Kuhn AN, Sahin U. Recombinant messenger RNA technology and its application in cancer immunotherapy, transcript replacement therapies, pluripotent stem cell induction, and beyond. Wiley Interdiscip Rev RNA. 2015 Sep-Oct;6(5):471-99. doi: 10.1002/wrna.1288. Epub 2015 Jun 9. PMID: 26061157. https://pubmed.ncbi.nlm.nih.gov/26061157/

It’s curious that, as far as I can see, reference 22 doesn’t mention linkers in the poly(A) tail at all.

@canadianer yes I got stuck there too… next steps is likely to email Stadler, C., Bähr-Mahmud, H., Celik, L. et al. They might have mixed up some references.

Patent referring to that linker: https://patents.google.com/patent/JP2018525410A/en

source: Stack Exchange

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sort: votes


text:
Why use two stop UGA codons instead of one in the spike protein mRNA for the BioNTech/Pfizer SARS-CoV-2 vaccine?
Unlike the SARS-CoV-2 virus, the BioNTech/Pfizer SARS-CoV-2 vaccine has two stop UGA codons  at the end of the Spike protein:
          V   L   K   G   V   K   L   H   Y   T   s
Virus:   GUG CUC AAA GGA GUC AAA UUA CAU UAC ACA UAA
Vaccine: GUG CUG AAG GGC GUG AAA CUG CAC UAC ACA UGA UGA
          V   L   K   G   V   K   L   H   Y   T   s   s
               !   !   !   !     ! !   !          !

What is the motivation behind using two stop UGA codons instead of one in the BioNTech/Pfizer SARS-CoV-2 vaccine?

The two stop codons are obviously to prevent read-through of the termination codon.  Why this should be necessary is not clear to me, but the following may be relevant:

The synthetic mRNA differs from the natural mRNA in a particular respect that is easier to explain with reference to the transcript map of the virus, below.

The two ORFs 1a and 1b are translated directly from the virus RNA as polyproteins, which are subsequently cleaved, but the proteins at the 3′ side of the viral RNA are transcribed into a series of nested mRNAs, each starting from a different 5′ position immediately preceeding the gene that will be translated. These mRNAs also retain RNA corresponding to the remaining genes (coloured grey, and not translated because of the monocistronic translation of eukaryotic mRNA) and the common 3′ polyA tail. The synthetic mRNA for the spike protein (S) lacks the RNA for the non-translated genes, and has the polyA tail near to the stop codon. Hence the secondary structure near the stop codon in the synthetic mRNA may well differ from that in the natural mRNA and possibly influence the likelihood of readthrough.

The stop codons used in this artificial mRNA are not UGA but m1ΨGA, as U is replaced by m1Ψ (N1-Methylpseudouridine)* in the synthetic mRNA to prevent degradation. As the anticodon is recognized by a termination factor — not a tRNA anticodon — the interaction with m1ΨGA may possibly be poorer than for UGA.

Footnote
*The structural relationship between uridine, pseudouridine and N1-methylpseudouridine is shown below. The NH and CO involved in base-pairing are similar in each case.
In displaying the base in RNA sequences — where single characters are normally used to represent nucleotides — N1-methypseudouridine is generally represented as Ψ, rather than m1Ψ. However this is not necessary in other circumstances, and, because of the ambiguity it introduces, is highly discouraged.

As was observed (by others) under related q's here on material from that site, it seems Pfzier/BioNTech has done a global optimization to increase CG contents in the sequence, generally thought to be beneficial to mRNA expression (in addition to all the other things they've done, like U -> m1Ψ global substitution, specific to mRNA therapeutics).
That (global CG target) may also explain why they replaced UAA with UGA, even though the latter is actually a "worse" stop codon, in terms of allowing more read-through. As one paper (preprint) notes:

despite having the lowest efficiency of translation termination among the three, UGA is the most common stop codon in many multicellular eukaryotes. The relative frequencies of the three stop codons are dependent on multiple factors and strongly associated with regional variation in GC content. The frequency of UAA is strongly negatively correlated with GC content, while the use of UAG and particularly of UGA increases with increasing GC content.

Using two UGAs may be a way to compensate for this choice (of using the lowest efficiency stop codon).
Actually, one more complex theory is that the stop thing is actually a tetranucleotide:

In both bacteria and eukaryotes, the base immediately following the STOP codon (position +4, with the first nucleotide of the termination codon marked as +1) exerts the strongest influence on RT (readthrough) efficiency. This has led to the hypothesis that an actual translation termination signal consists of a tetranucleotide sequence, not only the STOP codon itself. Which tetranucleotide is the most efficient in eliciting the RT in eukaryotes remains controversial. [...]  For example, the level of basal UGA-C readthrough in mammalian cells (3–4%) was shown to be 3–6 times higher than for the remaining UGA-N tetranucleotides.

If we go by this, then UGAU is the stop tetranucleotide here, which is perhaps better than just UGA, especially if see that a C follows the 2nd UGA in the actual WHO doc, so that might have tripled (or more) the read-through chance if the UGA were not doubled before it:

ΨGA ΨGA CΨC ...

Aside: The CΨC begins... a "double UTR" (dUTR) as they call it (even though this one is composed of two different UTRs) for which there is a published paper that it is more efficient (in terms of stability etc.) than a single UTR. So, generally speaking, the doubled stop seems part of a strategy to "double everything" in that terminal region if it helps with translation efficiency.

Detailed Dissection and Critical Evaluation of the
Pfizer/BioNTech and Moderna mRNA Vaccines hypothesizes that it is a fail-safe against misreading (but maybe not a very good one (and the premise that m1Ψ leads to misreading may itself be incorrect)):

When nucleotide U in stop codons was replaced by Ψ, the rate of misreading of a stop codon by a near-cognate tRNAs increased [17]. Such readthrough events would not only decrease the number of immunogenic proteins, but also produce a longer protein of unknown fate with potentially deleterious effects.
…
Pfizer/BioNTech’s BNT162b2 mRNA features two consecutive UGA stop codons. Moderna’s mRNA-1273 uses all three different stop codons UGAUAAUAG.
…
One might think that the consecutive stop codons in the two vaccine mRNAs would offer a fail-safe mechanism
…
However, in many cases, misreading UGA stop codons in prokaryotes is associated with a +1 frameshift [81–84].
…
With such a +1 frameshifting, a downstream in-frame stop codon cannot serve as a fail-safe mechanism. UGA is a poor choice of a stop codon, and UGAU in Pfizer/BioNTech and Moderna mRNA vaccines could be even worse.

Thanks for sharing this interesting quote!

From my knowledge of frameshifting, the wider sequence context of the position of the shift seems to be the primary determinant. Hence I am highly dubious regarding this postulate of Xia. One imagines the developers of these vaccines analysed the products of translation of the artificial mRNAs very carefully. To suggest that they achieve the opposite of their presumed purpose seems rather naïve.

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text:
How many Watt-hours can an electric eel produce in a day?
Electric eels are cited as being about to produce about 860 watts of energy. But I haven't been able to find information on how long they can sustain their charge.
https://www.youtube.com/watch?v=y9wktSQdyaE
In another question, it was shown that they can continually power a Christmas tree, albeit the lights flicker, just when it's hanging about and doesn't appear to be defensive. This suggests that it has some ability to sustain a low level of current... so I'd be surprised if there is no study that has measured the potential Wh. Sadly, I cannot find it.
Does anyone know any estimates for the energy an electric eel can produce over the course of a day?

I don't understand why this question has been downvoted. There is a common curiosity about the power of electric eels, and potential utility for that power.

Someone thinks that eels are not funny :)

@aliential I quote like electric eels, and find them quite funny, because they're some sort of catfish. And I'm pretty sure it was a kind of catfish that climbed onto the side of a boat, and accepted beer from the occupants. Quite an intelligent fish, they show fish possess higher brain activity than they're given credit for, just in my opinion.

I found some information on how much energy an electric eel can theoretically produce for an hour, but not per day. Thanks to this excellent answer from dtrades and my own research.
Apparently, electric eels can produce up to 860 watts, at up to 1 amp, with 1ms pulses and up to 500hz, with older/longer eels being able to produce a more stable output. That would theoretically make for a 50% duty cycle, with square waves, but will be something more like a 25% duty cycle when we average the pulses (if I'm not mistaken).
River Monsters S03E06 Electric Executioner claims they can produce a shock for "over an hour," I'd like to find more definitive data on their potential length of shocks. I did see a video of an electric eel being bitten by a reasonably sized gator, and shocking into into unconsciousness or death after 40~45 seconds, so I would believe they could keep it up for an hour, especially since they can still shock even eight hours after death.
Conclusion
So, all that together, suggests that an electric eel could theoretically produce 215 Wh, after one hour. It might be too exhausted to keep that up.
Of course, that is the most ideal result for one hour. What the average eel will manage, averaged over a day, is much harder to say. Still, I'm skeptical they are only capable of less than 1 Wh, and I'd figure a result in excess of 215 Whs would be more likely, under ideal conditions.
Containment
They also, as an aside, have to be careful to not electrocute themselves and stop their own hearts, and they have to take care not to electrocute each other. The father will keep his fry in his mouth, and signal them as to where they should go to be safe, when he performs a shock.
For those reasons, if you did use electric eels for power, you'd have to be careful how you contained them, so they had enough space to not electrocute themselves or each other.

This research states that an eel whose size is 90 cm can provide 6.05 mW, which is 145 mWh every day. They say you'd need 165 eels to be able to read for 24 hours using a 1W lightbulb like the one on a phone.
An electric eel should be able to flash a 0.6W L.E.D. light for 10 milliseconds at full power every second, which would be very visible in daylight, and would light up the room.

Thanks, I'll check out the paper! It's interesting that they got such a small wattage out of the eel. They can apparently go up to 860 watts of charge. There's a video somewhere out there, where an eel electrocutes an aligator to death over 45 seconds (you can find it if you search). The gator was spasming from the shock, so I figure it can't be a few miliwatts. But then, the fish was fighting for its life. Notably, another report states that they can emit a shock even hours after their death, and Wikipedia claims they can maintain a charge for an hour (no source, sadly).

That video is evidence for 50w to 500w pulses for 40 seconds, if it's 1ms pulses of 500w to the caiman's gums, every pulse is 500w/60000 ms = 0.008 Wh. In total the eel exhausted perhaps 0.4Wh to stun the caiman. No evidence the eel and caiman actually died. Caimans do eat the eels sometimes. A small watch battery is also enough to cause death at 600v.


text:
What favors the active transport in a membrane?
I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this conformational change can transport molecules from low concentrations to high concentrations areas i.e. opposite in their concentration gradient. My problem is that for this to happen we must couple the hydrolysis of ATP with the "reaction" of transport along the membrane.
But I can't find it in textbooks and also I can't imagine if such coupling makes sense. In many textbooks it is stated that the energy that released due to the hydrolysis fo ATP is used to drive the pumping. I don't know if it is possible to couple two reactions with no common intermediates. Also in the pictures that show the active transport like the one in the left side the molecules can't go through the lipids.

So the molecules just move from low to high but the moving from high to low (diffusion) is blocked because the molecules can't move through the lipids. In other words it isn't like molecules make something that it would be otherwise violated because at first the motion from one side to the other is blocked. I mean even if we have no ATP the molecules won't flow from high to low concentration. Then what is the point of "active" transport? For a moment I thought to describe the above scheme for active transport as the following reaction: $$\ce{ATP + H2O + M_{in}} \rightleftharpoons \ce{ADP + P_i + M_{out}} $$
Which can be thought as the sum of:
$$\ce{ATP + H2O } \rightleftharpoons \ce{ADP + P_i}$$
and
$$\ce{M_{in}} \rightleftharpoons \ce{M_{out}}$$
But as I stated I haven't find a coupling reaction with no common intermediates and also it doesn't make sense to write the second equilibrium as the molecules can't go through the lipids. Also from the second reaction we should expect the concentrations on both sides to be equal (because the equilibrium constant must be equal to unity) no matter the concentration of ATP.
So can the first equilibrium alone describe the "active" transport? I mean if this reaction is exergonic then indeed by varying the amount of ATP we can alter the concentration of M outside of the membrane due to the Le Chatelier principle.
Edit ATP hydrolysis causes conformational changes to the protein channel which in turns "passes" molecules from one side to the other. Fine. But what if the lipids were permeable to the molecules? Then shouldn't the two concenctrations on the two sides (in and out) be equal or because the ATP hydrolysis is exergonic we will expect to have an imbalance in the concentrations?

Welcome to SE Biology and to Biochemistry. Biochemistry requires a different attitude than chemistry, but you still need to find a textbook that is written from a chemical standpoint and not a biological one. In this respect the best one available to consult online is Berg et al. on NCBI Bookshelf. The section you need is in chapter 13. You also need to stop thinking you know better ("I can't imagine if such coupling makes sense" indeed!) and read the sections of this book about this coupling, which is the energetic underpinning of life.

"But what if the lipids were permeable to the molecules?" - It will save you a lot of time to first discover whether this is true for the molecules being actively transported.

@BryanKrause Thanks for the comment. I think this is where I get it wrong because in thermodynamics we can treat diffusion as a "reaction". But here we have also the exergonic reaction of "pumping". So with no pumping allowed we will have passive diffusion. Whereas with pumping we will have a difference in the in and out concentrations because this reaction of "pumping" is favored.

But I can't find it in textbooks and also I can't imagine if such coupling makes sense. In many textbooks it is stated that the energy that released due to the hydrolysis fo ATP is used to drive the pumping

I've been reading Molecular Cell Biology of Lodish and it has used "coupling" of hydrolysis of ATP with other reactions a lot, ergo it is probably correct to phrase it that way.

I don't know if it is possible to couple two reactions with no common intermediates

It may be a little different for each transport but I consider active transport as a result of multiple equilibria each of which as important as the others. You may notice that by multiplying the Ks of different equilibria, the intermediate particles would be omitted.
For example
$\ce{H2SO4 + H2O } \rightleftharpoons \ce{HSO4- + H3O+}$   : $K_1$
$\ce{HSO4- + H2O } \rightleftharpoons \ce{SO4^{2-} + H3O+}$  : $K_2$
by multiplying these two we'll get:
$\ce{H2SO4 + 2H2O } \rightleftharpoons \ce{SO4^{2-} + 2H3O+}$ : $K_{overall}=K_1 \times K_2$
By doing so, a few problems arise, firstly you'll totally ignore the existence of $HSO_4^-$ as an intermediate by summarizing. Secondly, you may falsely consider the order of reaction as 3 instead of two related reactions with the order of 2. Thirdly, molar concentrations calculated with $K_{overall}$ tend to have deviations from reality, and so on...
Therefore

$\ce{ATP + H2O + M_{in}} \rightleftharpoons \ce{ADP + P_i + M_{out}}$

is too minimalized to be considered as a good representation of the reaction. As an example for better clarification, here is a paper about the active transport of $Ca^{2+}$ in the muscle cells and one of its pictures
The process involves 6 different species of the enzyme (E). Also, remember that the whole process should be displayed by these 6 equilibria. (Well, forming a complex between a molecule and a multi-charged ion requires several other equilibria which we may also be considered(stepwise production of $Ag(NH_3)_2^{+}$ for example).

because the equilibrium constant must be equal to unity

I didn't catch that pretty well, Anyway

What favors the active transport in a membrane?

The hydrolysis of ATP provides the energy for the next reaction(s). In our calcium transport example, an aspartate becomes phosphorylated which unstables the protein current conformation eventually leading to the consumption of the extra energy. The extra energy is consumed via the movement of the $Ca^{+2}$ against its entropy. The cycle can happen again and again.
For more readings on the conformation and stability of a single molecule read Force field (chemistry) and alkane conformation.

If you've just read about coupling in a Cell Biology text and from this deduce that "it is probably correct", you are perhaps not best placed to answer this question. I don't think the understanding of ATP and energy coupling lies in consideration of reactions of sulphuric acid, force fields or  alkane conformation.

@Sam So if the ATP hydrolysis doesn't take place at the protein, pumping won't happen? Because as you have written the reaction the protein is regenerated (like a catalyst).

@Anton Correct...


text:
Purpose of EF1 alpha promoter
Context: I have seen promoters used to have gene therapy viruses target specific cells, so I am referring to that apparent function of theirs.
As an example I have seen GFAP promoters used for targeting astrocytes (I have seen this in many more papers but this is the first one I found on google).
I am curious what the purpose of the EF1-alpha promoter in a lentil/retro/Adeno-Associated virus for gene expression is?
It would seem that it is often used for targeting embryonic stem cells, but then I had also seen else where that "The Lenti-X Expression System (EF1α Version) enables you to produce exceptionally high titers of recombinant lentivirus for expression of any cDNA in any cell type susceptible to lentiviral transduction." This made me think that perhaps since this promoter 'targets' stem cells which later turn into any type of cell, that this quote meant that the EF1-alpha promoter can be used to indiscriminately target cells? Is this true?
Please forgive any incorrect assumptions on my part, I am a novice in this field.

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, please clarify your question. You appear to be unclear on the function of promoters (driving transcription) — they don't have any direct connection to viral targeting. Thanks!

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

I've heard though that GFAP promoters are used for astrocyte targeting? Is this a special case?
P.S. I have seen this done in many more papers this is just the first one I found on google.

thanks for the recommendations!

EF1-alpha is considered a ubiquitous/constitutive promoter; it is effective in all animal cells and tends to provide strong expression. Embryonic (and other) stem cells are more difficult to target than other cells because they don't express genes under the cell-type specific promoters that are often used for other populations of cells, which is why you're seeing it used specifically for that application, but that's not the only use.
You'll find a lot of the promoter information on individual commercial sites and rather than promoting specific ones I'd suggest searches like https://www.google.com/search?q=ef1+alpha+constituitive or https://www.google.com/search?q=ef1+alpha+ubiquitous - use of EF1-alpha isn't "owned" by anyone so when they say these things it's not just because they're trying to sell you on some special method of theirs, they are just using a field standard approach.

Thanks, ya I wasn't trying to 'promote' a site. I just wanted to understand their claim in the wider context of the field of genetic engineering itself.

So to clarify your saying that yes it can be used to target any cell type?

@profPlum Yes. With the caveat that any time you say "any" or "every" or "always" or "never" in biology someone will find you a counterexample (the previous sentence with "any time" in it also follows this rule). Also every species has a different EF-1 alpha promoter, and they may or may not be compatible.

Haha I think you may have stumbled upon a rule that is not limited to biology but more or less universal. In CIS it is called the law of leaky abstractions. But great that is what I wanted to know!

P.S. here is the link to what I mentioned: https://en.wikipedia.org/wiki/Leaky_abstraction


text:
What is this worm like animal found on a well water filter?
This was found in the water filter on a private water well that feeds a house in southeast Colorado, USA. The well has hard water, and is shallow (25’). There are several of these creatures all over the filter. They range from 3mm-5mm long.
The picture is of the water filter. In a video we have of them on the filter they move their arm like appendages.

Welcome to Biology.SE — this looks very interesting! I can think of a couple of marine invertebrates this vaguely resembles, but I have no useful idea about what it might be from well water. Can you [edit] in clearer pictures and/or possibly give a more detailed description of your creatures? Posting a link to your video might also be helpful. ——— Finally, it might be worthwhile to preserve specimens (e.g. stored in a clear high proof alcohol) — that way if no one comes up with a good answer you might be able to find a specialist at a college or university nearby who could identify them.


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How does the eukaryotic cell synthesize all of the proteins of a protein complex (like ETC complex I) at stoichiometric ratios/numbers?
(eg synthesize all proteasome proteins at the appropriate ratios to which they are used)
How often are proteins of the same complex (eg all the proteins of the 20S/19S parts of the proteasome or complex I of ETC) controlled by the same enhancers/promoters? Is it often the case that you just have non-stoichiometric synthesis and then the cell degrades the excess protein if it can't put them both together?

You seem to have reputation here, so you should know that you are expected to demonstrate that you have done some research before asking questions here. This is a complex question, the answer to which differs between eukaryotes and prokaryotes (e.g. for ribosomal proteins) and probably between organisms and protein complexes. Tell us what you find when you search for something like “coordinate regulation of ribosomal protein synthesis” or whatever.


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How could I make my fish gold?
I'm doing research on how the pigmentation of fish. I want to know how could you change it with the help of genetic modification. I have some Silver Dollar fish (Metynnis argenteus) and I want to make them have a shimmering gold appearance like a gold piranha. I was told by someone on reddit that it would be much easier to breed them to create the desired phenotype, but I don't think that's possible since they don't produce many observable differences in pigmentation. So, I want to know if anyone has any experience with this and could help me out. I'm still trying to understand all of this so it would help to not be too technical.

Did you figure out how the gold appearance in a gold piranha happens? Is it a certain chemical or rather a physical effect?

I think you need to clarify what kind of research you are doing. Breeding and genetic modification might both produce the desired result, but in research it is likely not the main point (but instead getting to this result in a certain way and obtaining the insights from doing this).
There are many studies on coloring of zebrafish and guppies, producing all kinds of differently colored mutants... but I doubt that one can predict the result in advance, since the link between the genotype and the phenotype is not well understood yet. In fact, understanding this link is precisely the point of these studies. You can start with exploring the work done in this domain by Nüsseln-Volhardt's group, see, e.g., here.

Im trying to find information on what genes cause the coloration in charcins. I also want to know if all fish have the same genes for pigmention. I know that the relation between genotypes and phenotypes are not fully understood yet. I'll try to find out if guppies and danios (zebrafish) share the same genes. If they do there is a possibility that piranhas and silver dollars do as well.

@PrinceZay You'll get the best answers here if you ask the questions that get exactly to the answer you want. If you want to know "if all fish have the same genes for pigmentation" then do some research on pigmentation and ask about it. Asking "how can I make my fish gold" won't answer the other question. We call this the XY problem at StackExchange.


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Plasmolysis and turgor pressures
I am a high school student and I am a little confused in plasmolysis,
when we study plasmolysis, we say that at limiting plasmolysis, the turgor pressure OR pressure potential reduces to 0 what do we mean this by saying that turgor pressure becomes 0, like in gases if pressure becomes 0atm it simply means that there is no gas molecule left which can collide with the walls of container, but here water is still left in cell, but still we say that turgor pressure has become 0? why?
And if plasmolysis still continues we say that it has not become negative and starts contracting the plasma membrane and separates it from corners of cell wall {incipient plasmolysis} ? How can the water starts attracting the membrane and not colliding with it? what do we mean by saying negative turgor pressure or negative pressure potential? please explain in simple language and by giving as many examples as possible because its my first time I am studying this and it will become easier for me to then understand.

A pressure potential of 0 doesn't mean there isn't any water left in the cell, it just means that the existing water available in a cell is not able to exert any force on the cell wall. This is because in extremely hypertonic solutions (solutions with a higher solute concentration than the cytoplasm), enough water leaves the plant cell that there is not enough water to "fill" the entire volume created by the rigid cell wall. This leads to a pressure potential of 0, i.e. no force (since pressure is force/area) applied on the cell wall.
Now if there isn't enough water to fill the entire volume of the cell wall, which is rigid, the plasma membrane detaches and pulls away from the cell wall (plasmolysis) in order to be able to surround the remaining cytoplasm. It would be physically impossible for this not to happen (I would guess that a vacuum would end up forming because of the empty space that was once occupied by the water, creating enough negative pressure to physically pull apart the plasma membrane).
This brings us to the idea of a negative pressure potential. This can often be observed in vascular tissue, such as the cells of the xylem, where water is physically being pulled from the cell, creating a situation where, in simple terms, a "vacuum" of sorts is created due to the lack of water, which ends up "pulling" the water from xylem cells (called vessel elements) via the cohesion of water molecules. This "negative pressure" can also be called tension, where the inside of the cell actually exerts a "pulling" rather than a "pushing" force (here the "pulling" is what causes water to travel up the xylem against gravity).
Source: Campbell Biology 11th ed., Chapter 36: Resource Aquisition and Transport in Vascular Plants

Might be worth saying explicitly at the beginning that people often use "pressure" as a shorthand for "pressure difference" or "relative pressure" since we don't have a separate specific word for it (like we have "voltage" for "electrical potential difference"), and/or that "pressure potential" is different from "absolute pressure". OP doesn't seem to know the differences.

I have 1 more confusion,,,,  we know that, xylem vessels have a diameter in the range of 15um -200um{ you can search for this} and in one of the videos of "Veritasium" he makes a statemen hat if have a capillary of diameter of about 10um then it could hardly raise water upto a height of 1m ,,if that's true then the "cohesion tension theory" should be wrong because it is entirely bases on cohesion of water molecules with themselves and with xylem walls, but water actually rises due o the pressure difference , i,e by transpiration plans actually generates a negative absolute pressure.

Negative pressure means that the liquid is under tension i,e if it has no air bubble in it so that cavitation can't occur, it actually can act like a solid o some extent, like when we stretch spring it generates tension in it which wants to regain its shape back jus like this I think that if we have a huge water loss then liquid molecules are no longer pushing the wall and themselves , they are now attracting themselves and their surrounding? I know it sound weird but his is the only way people can explain it


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How can the pressure during contraction vary between the left and right ventricles?
After reading this passage from my physiology textbook (Vanders Physiology p. 384), I'm confused about how exactly the right and left ventricle can create markedly different pressures as they pump blood even if they have the same stroke volume, i.e. they push out the same amount of blood.

Typical pulmonary arterial
systolic and diastolic pressures are 25 and 10 mmHg,
respectively, compared to systemic arterial pressures of 120
and 80 mmHg. Therefore, the pulmonary circulation is a
low-pressure system, for reasons to be described later. This
difference is clearly reflected in the ventricular anatomy—
the right ventricular wall is much thinner than the left.
Despite the difference in pressure during contraction, however,
the stroke volumes of the two ventricles are the same.

How can two ventricles push the same amount of blood but at different pressures? I always assumed that pressure was created by a change in volume of the ventricles, and so I expected that if both ventricles have the same "change in volume" as they contract, they should also push out blood at the same pressures. Why is this not the case?

Pressure doesn't just depend on the characteristics of the pump — it also depends on the system that is being pumped into! Think about what pressure you would expect if you took the heart out of an animal and allowed it to pump in a bucket of fluid — now what is the pressure?

The key is vascular resistance.
Pumps like the heart don't move fluid, they exert force ("push") on it, increasing the pressure. The movement happens subsequently because there is somewhere for the fluid to go, so it moves down the pressure gradient from a place of high pressure to a place of lower pressure. If you clamped their outputs (increased resistance to infinity), neither ventricle would push any blood out.
We can say that the flow rate is proportional to the pressure difference and resistance:
Flow ~ ${\Delta}$P/R
If we assume that the two ventricles push out over the same time frame, you could easily get equal "Flow" with different "${\Delta}$P" if RLungs is different from RBody, and this is exactly the case: pulmonary vascular resistance is much lower than systemic vascular resistance. It's easier to pump the same volume through the lungs than through the rest of the body, so less pressure is needed.


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Can high energy photoelectrons damage cell membranes?
I've read that in addition to ionizing radiation causing damage to DNA through direct absorption, but DNA can also be damaged through photoelectrons with enough energy.  The thing I was wondering is what kind of energy (in electron volts) would or might photoelectrons need to damage or penetrate the cellular membrane (like if x-rays excite photoelectrons outside of cells)?


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How do adenoviruses interact with muscle tissue that it makes them acceptable as vector viruses?
From what I understand certain attenuated adenoviruses are popular as a vector virus, meaning a virus that is used as the active agent in a vaccine to infect cells and trigger a helpful immune response.
Of course, this use assumes that the vector virus can indeed infect cells and cause them to replicate the target protein in the first place. From what I can tell, how adenoviruses attach to cells and their receptors is imperfectly understood and furthermore live adenoviruses seem to often prefer infecting cells in organ tissue, not muscle tissue, so what makes researchers confident that adenoviruses are effective as vector viruses when injected into a muscle?

There's research going back three decades that adenoviruses can infect muscle fibers, e.g. Quantin et al. 1992. This one in particular was conducted for the purpose of evaluating potential to treat muscle disorders, although the gene incorporated in the virus was just a reporter gene, i.e. "does nothing" besides allowing easy identification of the protein expressed.

We constructed a recombinant adenovirus containing the beta-galactosidase reporter gene under the control of muscle-specific regulatory sequences. This recombinant virus was able to direct expression of the beta-galactosidase in myotubes in vitro. We report its in vivo expression in mouse muscles up to 75 days after infection. [...]
To test whether the adenovirus construct is able to direct
beta-galactosidase expression in muscle, we injected 108 plaqueforming
units into the thigh of either newborn, 1-week-old, or
4-week-old mice. Very strong histochemical staining (>30
positive fibers) was detected in the muscle around the injection
site up to 2 weeks after infection, even in mice that were
infected at 4 weeks [...]. In the latter case, staining was
present over a distance of at least 8-9 mm, and most of the
positive fibers appeared stained over a length of 1.5-2 mm.
[...] These data were obtained by staining the
muscles as a whole. The internal fibers may not have been
accessible to the reagents because of the tight structure of the
muscle, thus leading to an underestimation of the number of
stained fibers. This was confirmed by incising some infected
muscles before staining: in addition to external fibers, some
internal fibers appeared positive.

FIG. 3. Expression of beta-galactosidase in muscle of infected mice. (A and B) Muscle of 4-week-old mice analyzed 14 days after injection. (C and D) Muscle of newborn mice analyzed 75 days after injection. (Bars = 2 mm.)

The vector used was just "run of the mill" Ad5 with E1 and E3 deleted, i.e. non-replicating.
Of the newer "stars" of vaccinology, ChAdOx1 has definitely been tested in this regard, in fact also compared with the Ad5 "gold standard":

To further investigate the difference in luciferase expression between vectors, BALB/c mice were vaccinated with HAdV-5 or ChAdOx1 vectors expressing luciferase and muscle tissue samples from the site of injection and draining popliteal lymph nodes were harvested 24 h post vaccination. Luciferase expression was detected ex vivo in both muscle and lymph node tissue of vaccinated animals (Fig. 2A,B). Since the extraction procedure differed between muscle and lymph node samples, absolute luminescence units cannot be compared between tissues. However, in lymph node samples, mean luminescence activity after HAdV-5 vaccination was approximately 20-fold higher than after ChAdOx1 vaccination (Fig. 2A). By contrast, mean luminescence activity within muscle samples was less than 3-fold greater after HAdV-5 vaccination (Fig. 2B). These data suggest that the greatest differences in transduction efficiency between HAdV-5 and ChAdOx1 in vivo occur within the draining lymph nodes after intramuscular vaccination.

Given this, I strongly suspect Ad26 was tested in this regard as well, but I can't be bothered to search for that paper.


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Poly-G tails in NovaSeq Paired-end sequencing from museum samples
I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years.
The DNA I'm analysing has been sequenced by Illumina NovaSeq 6000 with paired-end sequencing.
As far as I'm aware NovaSeq uses two-colour chemistry, where Green is T, red is C, yellow (green + red) is A, and no green, no red is G. Over time and increase in sequencing cycles the green and red signal will become weaker, resulting in mistaken categorization of the nucleotides as G in the tails of reads.
This poly-G pattern is however only observed in the 3' end of the 2nd read in the pairs, which I find a bit weird.
Is this an expected pattern (only in the 2nd read in a pair) from NovaSeq or could this possibly also have something to do with my samples being stored in formaldehyde for the last 100 years, thus degrading or affecting the DNA?

Have you tried sequencing some fresh sample to see if the same pattern appears?

unfortunately im not the one performing the sequencing, im doing the bioinformatic analysis. But yes some newer samples has been sequenced, however this has been done with Illumina Hiseq4000 and these samples does not show the same pattern with Poly-G. But the Hiseq uses a four colour scheme.

of course ideally the newer samples would also have been done with NovaSeq, to determine if it is the sequencing or the sample ages.

Is this from a single sequencing run or multiple sequencing runs? I would suspect that something got jacked on the sequencer if I saw that in my data. Did you monitor the sequencing run? What do the quality scores look like? Have you run FASTQC or FASTP? I would recommend investigating all of those things.


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Why protons flow back to the matrix through ATP synthase?
I am reading oxidative phosphorylation and I can't understand why the protons that are pumped out must go again into the matrix and finally produce ATP.
Suppose initially that the inside (Matrix-M) and outside of the membrane (Intermembrane space-IMS) are neutral (for sake of simplicity). The exergonicity of the redox reactions powers the proton pumping. As the pumping goes on an electrochemical gradient arises because of the concentration gradient the pumping produces and due to the electrical gradient which is produced due to the unequal distribution of protons.
After the equilibrium of the redox reaction an electrochemical gradient has established. I can't understand why the protons have to flow back into the matrix. The redox reaction equilibrium means that the ratio $\ce{H_{M}}/\ce{H_{IMS}}$ has a specific value. Do they flow back because of the electrochemical gradient? I was thinking that the flow back is coupled to the pumping, is that correct? I  mean we have the equilibrium: $$\ce{H_{M}} \rightleftharpoons \ce{H_{IMS}}$$
and by pumping we increase $\ce{H_{IMS}}$ so protons must flow back according to Le Chatelier principle. If that is the case then what is the purpose of ATP synthase? Why the protons must flow back through ATP synthase and not from any other region? Are respiratory chain and ATP synthase seperated and the only way for protons to flow back is throught ATP synthase?
I have read Biochemistry textbooks and still can't understand the importance of the so called proton motive force.

I will check it out.


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What species of duck is this?
What species of duck is this? See below photo. Head colour is green like a mallard, but that's pretty much the only similarity. Spotted in Leicestershire, UK.

I don't know what species it is, but it's a male duck and very, very common in the Netherlands.

Probably a domestic hybrid of a mallard.
From Cornell:

If your duck has large patches of white where you didn’t expect it, think domestic duck.

Mallards (Anas platyrhynchos), which have the identifiable green head in the wild, are only 1 of 2 species of ducks that have been domesticated. So it would be no surprise if a strange looking mallard was in fact, well,  a mallard.
Again, according to Cornell:

Another common form [of the domestic/hybrid mallard] is the bibbed version. It has a sort of normal body and head plumage, and a white chest.

Also:

The passion for weird plumage in domestic ducks does not stop with white, but can go the other way too.  Some breeds are darker than normal Mallard plumage

These descriptions both match your specimen quite well.
Although your picture is low quality, it appears to me that the posterior feathers of your specimen also are not straight. Again, quoting Cornell:

Watch for the little curled feathers on the back of the male, above the tail.  Only the Mallard and its domestic descendants have those.

Finally, most hybrid ducks that come from some domesticated origin tend to be larger than  non-domesticated specimens since early domestication efforts emphasized large size for food (vs simply plumage for appearances). Your image has no relative scale, so I cannot comment on whether this applies to your specimen or not.
In terms of a specific "name" for such a hybrid?
I did find evidence that some people refer to domestic-hybrid mallards like your dark-plumage, white-bibbed mallards as "manky mallards", though I'm not sure how ubiquitous this is. For example, see here and here.

Though 10000birds.com claims non-domesticated birds can also occasionally develop bibs similar to those seen on domesticated descendants.

Wikimedia Commons has a Category: Anas platyrhynchos (wild living, but not wild colored. And yes, the domestic duck, which is often white, is considered a subspecies, Anas platyrhynchos domesticus.

There's no "probably" about it.

@Alnitak due to the HUGE amount of misinformation online and the propensity for people not knowledgeable in a subject to believe the first thing they read as fact, I am very cautious to use my possibly-perceived "expert" position as an answer writer to establish any concept of definitive authority. This is especially true in instances in which I'm not well-versed in a topic or the question itself could be more clear. I appreciate your vote of confidence and the other upvotes that can stand as support for my answer, but I'll continue using cautious wording to avoid these issues. Thanks.

I think it's likely a mallard hybrid. These sites have examples of crosses between mallards and domestic ducks (and others as well):
https://www.birds.cornell.edu/crows/domducks.htm
https://www.birdsoutsidemywindow.org/2020/08/06/mixed-up-ducks/
https://www.gettyimages.com/detail/photo/manky-mallard-royalty-free-image/986875962
There isn't any specific pattern but the light coloring below the head seems to be a common occurrence in hybrids, with some variation in the rest of the coloring. It's hard to find more reputable resources because of the variation, but I don't know of any other duck that would fit the ID.


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What are examples of successful novel ecosystem integration?
The cultivation of novel ecosystems, while formerly disparaged due to being conceptually misappropriated by special interest groups, may be necessary in adapting to climate change or simply in innovating more sustainable farming practices.
What are successful contemporary examples of novel ecosystem development?

Could you share some sort of definition of a novel ecosystem? I assume you are not talking about pathological invasions or sub-pathological species introduction, as those are quite common, or e.g. Galapagos-style patchwork ecosystems made from periodic introductions. Can you link to some sort of resource explaining what exactly you mean? What time-scale, how many species, is it on top of an existing ecosystem?

It's quite possible I am referring to exactly what you suggest, though not limited to that example. I am referring to a certain circumstances wherein a new ecosystem emerges on its own as a result of climate change and possibly nonnative species which happen to either intentionally or unintentionally introduced while present in the process. I can't really be specific because the thing you are asking me for is what I am asking others for. It's just a theoretical concept but at this point in climate change it must be happening somewhere.

It might help if you could provide a few links (e.g. an example of "disparage[ment] due to being conceptually misappropriated by special interest groups"); I'm not skeptical of your claim, but I'm a little unclear what you mean.

I am still not 100% sure of what the intent is here, but I think that you should look into community assembly rules. The basic (not universally or even generally accepted) idea is that there is some set of "rules" that makes a "successful" or stable ecological community. You can use those rules to design communities accordingly, goes the logic. Here is a short blog post that has some handy refs and simple language.
You could also look into microcosm + mesocosm research, where people have designed small self-sufficient communities, sometimes sealed off from e.g. gas exchange with the outside environments. Sometimes these collapse, and sometimes they work. Occasionally it has to do with randomness, and at other points it seems to follow a deterministic path.
All of these are under the heading of "community ecology", which I would strongly recommend looking into if you are interested.
I would also strongly recommend looking into invasion research, which is the most prominent example of getting a "new" community by just adding a few species to an existing community and seeing what happens. As I suggested in the comments, looking at communities on islands that have been invaded or have recruited species from elsewhere could be handy- e.g. Galapagos, Oceania, are examples to look into, how they have dealt with biological invasions and what has worked and what hasn't. This subfield is called "island biogeography", I do not know how many people still take it seriously but there are at least a lot of empirical observations about what happens when you add species.

Thank you for this more general information, I'll look into it.


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Does the radula sac in any mollusc serve a purpose other than sheathing the radula?
According to Barne Gat Shellfish:

When not feeding the radula is retracted into this chamber which protects the mouth from the sharp teeth of the radula.

Does the radula sac serve any other purpose?

Do you have any reason to believe it does?

@theforestecologist no particular reason. I just thought if the sac can be protected from the teeth, why only that and not the rest of the mouth?


text:
How fast do lipids on the inside and outside of a lipid bilayer exchange?
Biological membranes normally have different composition of lipids on the inside and outside (ref 1, ref 2).  This is maintained both by how new lipids are added to membranes, and by specialized enzymes (flippases).  Certain lipids being on the "wrong side" is an important signal (eg for apoptosis).
My question is: how fast do lipids from the inside and outside exchange spontaneously?  In a patch of membrane with no enzymes, how long until half the "inside" lipids have flipped to the outside and vice versa through simple diffusion?
I did a search but couldn't find any specific paper that measures the spontaneous exchange rate.  I'd be very interested in a definitive answer - could be just order of magnitude, but based on real measurements.
UPDATE This is important for figuring out the inside/outside composition of membranes in real scenarios when they're no longer being maintained in an asymmetric state: for example enveloped viruses, but also microparticles, dead cells, etc.

A cursory search seems to show at least a few papers using sum-frequency vibrational spectroscopy to measure rates of flip-flopping/transverse diffusion in lipid bilayers.
This paper in particular ("1,2-Diacyl-Phosphatidylcholine Flip-Flop Measured Directly by Sum-Frequency Vibrational Spectroscopy") cites an activation barrier of 79 kJ/mol which corresponds to a rate on the order of 10^-4/s.
There is also this review which seems to have more information on the topic: http://dx.doi.org/10.1021/acs.accounts.6b00435.

Very well. Also, this paper may be helpful, as it has some data about the activity of Mdr2, a phosphatidylcholine flippase by the measurement of time and relative fluorescence . One may also find the rate of movement implicitly .   https://www.sciencedirect.com/science/article/abs/pii/0092867494904464                                       @Spencer Guo by the way, the first link of yours is not working.

@SpencerGuo - Good stuff, thanks.  From the first paper, looks like at human body temperature the half lifes are < 1 min for DMPC, 9 min for DPPC, > 300 min for DSPC.  Very dependent on lipid tail length...  The review is also excellent.

@AlexI Yes I should have noted that the barriers are quite strongly lipid identity-dependent.


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How do humans detect temperature differentials on the skin?
I just read this question on Physics SE about how the body detects cold or warm surfaces. As someone who already understands how heat flux devices like thin film gauges and thermocouples work (by exploiting the known relationship between temperature gradients and electrical/thermal properties of the relevant materials), I was actually more interested in how the nerve endings in my body actually implement this.
When I touch something warm or cold, what is the nervous mechanism that causes the correct signal to be sent to my brain, causing me to perceive a hot or cold surface?
How is the "thermocouple", which tells me whether a surface is hotter or colder than my finger, implemented?

Related: https://biology.stackexchange.com/questions/28520/do-humans-perceive-temperature-or-heat-flux-or-both

Sensory neurons in the skin express TRP channels such as TRPV1 channels, TRPM8, and others (see Voets et al 2004 for more information on how these channels work). Different sensory neurons express different combinations of TRP channels .
Changes in temperature shift the probability of whether these channels are open or closed. Opening or closing of ion channels changes the membrane potential of the sensory neuron, which changes the rate of action potentials which informs the rest of the nervous system about the temperature.
The TRP channels can have other ligands, as well, such as capsaicin or menthol. The activity of these ligands at temperature-sensitive receptors is why we perceive chilis or mustard to taste "hot" and menthol to feel "cold".
More generally, the nervous system typically responds to changes better than constant stimuli through adaptation. Therefore, if your hand is fairly cold and you touch something warm or hot, you will perceive a hotter stimulus than if your hand started out already warm.
There isn't really a thermocouple or temperature difference detector in the skin, just these two mechanisms: channels whose open probability is a function of temperature, and sensory adaptation which heightens perceptual sensitivity to changes in temperature.

Voets, T., Droogmans, G., Wissenbach, U., Janssens, A., Flockerzi, V., & Nilius, B. (2004). The principle of temperature-dependent gating in cold-and heat-sensitive TRP channels. Nature, 430(7001), 748-754.

Is it then correct to say that the proteins responsible for detecting temperature (the TRP channels) respond to absolute temperatures, but the nervous system itself causes us only to perceive differentials?

@quant That would be a reasonable birds-eye summary, though it's not precisely true that only differentials are perceived (they are just emphasized), there are ways that the sensitivity of the channels themselves can be altered by endogenous agonists and antagonists such that absolute temperature isn't the only thing they respond to, and the channel gating itself is complex, non-linear, and voltage-dependent (the Voets reference would be a good place to start). Even seemingly simple things in biology are much more complex the more regulation you start to consider.

I also found it interesting that TRP channels play a role in spices being perceived as hot or cold. I had always thought this perception was cultural/linguistic.


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What are the advantages of long read sequencing for cancer oncogenomic research?
Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of nanopore sequencing in this field, e.g. fusion gene discovery, detection of large structural variants and copy number alterations (SV/CNA), as compared to Illumina and 10x?
I am struggling with generating my doctoral thesis proposal, so any advice will be appreciated!

https://www.nature.com/articles/s10038-019-0658-5

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, please summarize what you already know (with references to reliable sources) — this will make it clearer what information you need and also demonstrate that you have done the expected prior research. In addition, please write out abbreviations that are unlikely to be generally familiar. Thanks!


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How do snakes determine the direction of prey from their thermal infrared sensing pit organs?
This answer to How does the “heat vision” of some snakes work? explains the basic idea and there are several linked sources within that go into greater detail on the sensing mechanisms on a physical and a molecular level.
But searching these sources for terms like "spatial" or "angular" in an attempt to understand how they get direction information (specifically for striking a  pray) turned up nothing.
Some snakes have multiple pit organs that point in somewhat different directions, and I suppose it's possible that the heat-sensitive nerves across the pit membrane could have spatial resolution and the whole thing act like a pinhole camera, but so far I've found no actual explanation of how they obtain direction information from their pit organs.
Question: How do snakes determine the direction of prey from their thermal infrared sensing pit organs?

From Wikipedia:

The facial pit actually visualizes thermal radiation using the same optical principles as a pinhole camera, wherein the location of a source of thermal radiation is determined by the location of the radiation on the membrane of the heat pit. However, studies that have visualized the thermal images seen by the facial pit using computer analysis have suggested that the resolution is extremely poor

Individual pit organs act like pinhole cameras because they are arranged, well, like a pinhole camera: there is an invagination of tissue surrounded by heat-sensitive cells with a smaller hole to the outside world. From Sichert et al 2006 it looks like this:

The dashed lines here indicate heat originating from some distant point source. That point source covers some fraction of the heat-sensitive membrane. Points at different distances and directions will be picked up on different parts of the heat-sensitive membrane. For example, because this source is coming from below, only the top of the pit is illuminated; for a source coming from above, only the bottom of the pit would be illuminated, etc.
If you have access to the Sichert paper, they go into more detail about the mathematics that the pit organ geometry creates. In summary, for any cell you can map a receptive field of places in the world that can project to that spot, and through a summation of these receptive fields across the whole pit organ you can reconstruct a map of where heat is originating. At that point, the principles are no different from visual organs like the retina. The authors show that even with each individual detector having imprecise resolution, the combined activity can be decoded to form a clear image from a simple linear combination of the receptive fields.
Other studies like Chen et al 2012 show that vipers integrate retinal vision with their pit organ senses, because occluding a pit on one side and an eye on the other is worse for prey targeting success than occluding both on the same side. Neuronal evidence of this integration has been observed for quite some time, see for example Newman & Hartline, 1981.
Bothe et al 2019 is a more recent paper investigating some of the neural circuitry behind the processing of pit organ information and integration with vision.

Bothe, M. S., Luksch, H., Straka, H., & Kohl, T. (2019). Neuronal substrates for infrared contrast enhancement and motion detection in rattlesnakes. Current Biology, 29(11), 1827-1832.
Chen, Q., Deng, H., Brauth, S. E., Ding, L., & Tang, Y. (2012). Reduced performance of prey targeting in pit vipers with contralaterally occluded infrared and visual senses. PLoS One, 7(5), e34989.
Newman, E. A., & Hartline, P. H. (1981). Integration of visual and infrared information in bimodal neurons in the rattlesnake optic tectum. Science, 213(4509), 789-791.
Sichert, A. B., Friedel, P., & van Hemmen, J. L. (2006). Snake’s perspective on heat: reconstruction of input using an imperfect detection system. Physical review letters, 97(6), 068105.

Don't pit vipers have two sensors which would provide binocular sensing for a couple of feet?

@MaxW Yes, they do, though Chen et al showed that occluding one of each eye and pit (for example, left pit and right eye) impacted performance more than occluding both pits, both eyes, or both pit and eye on the same side. So, at least in their conditions, the conclusion would be that the ipsilateral integration is more critical than bilateral integration. That said, there isn't much benefit of bilateral sensing of light unless you can form an image with both individually. For sound you can use delay cues but only because sound is so slow.

@MaxW I added a citation to another paper that gets into the neurophysiology in the brain a bit more. It also has a bit of the anatomy, where there is an ipsilateral trigeminal hindbrain processing step prior to a crossing-over to the contralateral optic tectum. I don't see that they talk about any interaction with the contralateral hindbrain nuclei, though they also don't say anything to rule it out, it's just not addressed. Anyways, if that's the primary circuitry, it seems the two pits operate mostly independently within their respective 'visual' fields.

The pits may be located and angled too far laterally to have much "straight ahead" coverage.

This is fascinating! I'll download these references this afternoon and enjoy them in detail on a long train ride this weekend. There's a Phys. Rev. Letter even! :-) I got started on this yesterday talking with a theoretical physicist first about why clouds look white in thermal infrared weather satellite images and we were frustrated by the somewhat misleading graphic accompanying this Nature News item. Thank you!

@uhoh Based on your frustration with that graphic, I think you'll especially like Figure 3 of Sichert et al :)

Thanks again for your answer; this is really quite interesting! I enjoyed the ride and the read both. I think next I'll try to think about how lensed-eyes evolved and if this type of mechanism (large hole plus neurons configured to make the most of it) has any relationship to it.


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Finding All of the Genes in a given Genome
I'm interested in finding the start position of each nucleotide in a given genome.  I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout for other specimen.  So wondering if there is a database with more consistent formatting and such things.  I've been looking around BLAST (?), but got confused with the resources, and rather than spinning my wheels, thought I'd ask for some pointers where to start.

Are you working with annotated genomes? Is there a reason you can’t just pull a .gff file from NCBI?

"I'm interested in finding the start position of each nucleotide in a given genome." Do you mean the start position of each gene? And by "gene", I'm assuming you're restricting it to protein-coding genes? What algorithm will you be using to call genes, as just searching for start codons won't work.

@acvill I'm not opposed to any format, just fairly new to this work, and looking for good pointers to start off with; I'll read through the documentation you linked and some examples.  Any other resources you might suggest?

@MattDMo "each gene" is just a good place to start, to start working with stuff, as I'm fairly new to this kind of work.  For example, on the EcoCyc I link to, it has the position of the start of each gene in the given E coli genome.  Are there libraries of the genes in a given genome?

I think @acvill's point is that this work has already been partially or totally completed for quite a number of organisms...

Yes, there are numerous gene databases in NCBI and elsewhere. This is turning into an XY problem, though. What exactly is your goal in doing this work?

My goal here is to take a set of organisms (of any domain in life) and take down the locations of each gene start position; then doing so, making a bead-and-chain model, where a ball with a gene is of some type (maybe sub-types, etc), and a ball without a gene is of another type (and a ball corresponds to some few kilobases of DNA (or less)).  Ultimately the models should be more sophisticated, but this is the initial toying around step

Why would you want to break it up in such a way. Each part - even if it is not coding for any gene still has an immense role to play in coding for the genes and other things?

I would suggest using the FTP at NCBI to download GFF files for whatever organisms you are interested in, as suggested by commenters. GFF files will have annotations for the genome for genes and also for many other features (figure 1).

Not entirely clear about the goals of this, but if you want annotated coordinates of things in genomes GFFs are a good place to start.
Note that many/most genomes will not have assemblies at the chromosome level, but only at the scaffold/contig level. Depending on your application that may be an issue.
If you want to go to a specific genome/organism, you can search it here. You can access the FTP through the interface for each genome there.


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Osmotic pressure and turgor pressure details
I am a high school student and I am very confused in how we define osmotic pressure?
Osmotic pressure is defined as the pressure required to stop the diffusion of solvent into a solution by applying external pressure over solution, which means that when the pure solvent is diffusing into the solution then it will apply pressure on the semi permeable membrane and when we have applied the same external pressure over the solution then there is no net movement of solvent occurs across the membrane and mathematically it is equal to P=cRT, where c is the concentration of solution , T is temperature in kelvin and R is the universal gas constant, if we go by this equation and calculate the osmotic pressure of 1 molar concentrated solution at room temperature it comes out to be almost 2495Pa which means 2495Newton/m^2 which is very high pressure and it doesn't seem to be true as osmosis is very slow process it surely cannot generate that much of pressure( just to imagine how large is that pressure assume an area of 1m^2 and place Mass of 249.5kg on it), so I think that it should not be that higher, so ,I am unable to understand what is actually osmotic pressure ,on which does it actually act and how do we actually calculate it?
we say that when a cell is placed in hypotonic solution then osmotic pressure is greater than Turgor pressure and water will flow inside the cell, but I have a confusion that like turgor pressure acts on the wall of cell ,osmotic pressure should also act on the wall and in opposite direction of turgor pressure, so by this logic wall should compress more as osmotic pressure on it will cause it to compress and turgor pressure will cause it to expand but Osmotic pressure is greater than turgor pressure it should compress, but it doesn't happen? we only talk of turgor pressure to explain the expansion but not osmotic pressure why? I know I am going wrong somewhere if Osmotic pressure would really leads the cell to compress then an animal cell would have never burst in hypotonic solution. and if osmotic pressure is also acting on the wall or membrane then net pressure on the wall is O.P-T.P (in inward direction) , and not only T.P (outward) so the wall pressure here also should not be same as turgor pressure?
If anyone will explain me this by giving as many examples as possible than it would be very helpful for me to understand because its my first time I came to know about these things.

when we talk about external force applied in this case we talk about a setup that is made by us. like a U tube experiment that is filled with water and separates both the hands of the tube via semipermiable membrane and we add solute one side and due to this water starts to rise in that hand of the tube to avoid this rise in water level an external pressure is applied tht prevents this water rise and this pressure is termed as osmotic pressure. THIS IS THE CASE OF A ENVIROMENT WHERE EXTERNALFORCES CAN BE APPLIED BY US AND IT IS VERY MUCH DIFFERENT FROM THAT OF THE CELL WORLD.
in case of cells osmotic pressure is directly proportional to the concentration of the solution i.e more the solute more the OP and visa versa. in cells osmotic pressure are internal force that is caused due to  difference in concentration of the solutions.
and as we know water move from low osmotic pressure to high osmotic pressure
{ from less concentrated to more concentrated solution} thus cell swells up because of entering of water when cell is placed in pure water or hypotonic solution.
CONCLUSION : CELL DO NOT SHRINK BECAUSE NO EXTERNAL FORCE IS APPLIED BY US THE DEFINATION U GAVE IS CORRECT BUT IT IS NOT APPLIED IN CELL WORLD. IN CELL WORLD OP IS A PRESSURE DEVELOPED DUE TO DIFFERENCE IN CONCENTRATION OF SOLUTIONS AND THIS PRESSURE IS CREATED INORDER TO EQUAL THE CONCENTRATION OF SOLVENT (WATER) IN BOTH THE SOLUTIONS.

Welcome to the Biology Stack Exchange. You might want to consider your answer formatting and provide a bit more clarity to assist the question poster's question. Good luck!


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What is the duration between: the moment we stop breathing and to body's and involuntary mucle movement?
I studied that if someone stops breathing by pressing their nostrils with fingers and start to starve without oxygen, the body will automatically cause the hands to leave the nostrils in a certain time so that we can breathe. (a kind of reflex, I guess)
What is this certain time?

Could you include a source for where you studied that? Thanks.

I found it in many sources, one is https://www.healthline.com/health/holding-your-breath#what-happens

Have u seen the above comment @user438383

The link you gave doesn't say anything at all about the body "automatically" causing the hands to leave the nostrils. That will happen when you black out, as your muscles become flaccid and gravity causes your hand to move away from your face, but there's no "automatic" movement...

Your respiratory system has quite a number of neural and non-neural (e.g., physical, emotional, and chemical factors) controls in addition to the ability to be voluntary controlled.

A strong influence on much of our respiratory physiology is a response to changes in carbon dioxide in the blood (well, more specifically, it's blood pH that is regulated).  Oxygen homeostasis is also controlled.

As a result, the duration you're asking about almost certainly is dependent on total lung capacity, actual volume of air inhaled, diffusion capacities, activity levels, etc. as each of these would determine levels of oxygen and CO2 in the blood and available to tissues (such as the brain).

In other words, since gas homeostasis plays such a prominent role in respiratory control, the duration of any "reflex" response would vary between person to person (based on their anatomy) and even for an individual person based on circumstances.

Also, I'm not personally familiar with any such reflex that you mention.*

In fact, some children intentionally hold their breath until they pass out! This passing out is actually a useful adaptation because it allows the body to return to using involuntary breathing controls to prevent the child from depriving themselves of oxygen long enough to induce death. Seattle Children's Hospital suggests normal breathing returns in under 2 minutes.

Also see the fainting game that got popular among teens earlier this century that involved intentionally causing self syncope. [WARNING: DON'T BE THIS STUPID]

* If you can update your question with a source or any additional information about the "reflex" you mention, I or someone else might be able to address the reflex or your source of info more specifically.


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Why do some vaccines lose their efficacy with time?
Why do some vaccines lose with time their efficacy?
The two obvious examples that I have in mind are influenza and tetanus. The former case is clear, as influenza virus undergoes frequent gene reshuffling with similar viruses, which renders the vaccine inefficient against what can be essentially considered a new virus. So the question is about tetanus: does it have to do with the fact that it is bacterial rather than a viral effection? Why the immunity is lost? Are there other similar cases?

@user1136 Here's a study indicating "antibody responses to tetanus declined with an estimated half-life of 14 years (95% confidence interval, 11-17 years)."

@user1136 indeed, I presumed the need for "booster" is because of the declining vaccine efficacy (even if it remains quite high). If you have some experise on this subject, please share with us in an answer.


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COVID-19 infection data when partitioning to communities
Suppose we think of the disease in a certain country as follows.
We have a set of "communities" $C_1,\dots,C_k$ in the country where $k$ is some small constant, say $10$. Each individual is a member of exactly one of the communities.
The communities can be simply a partition of the entire population into groups of ages, races, cities, economical situations etc.
In each point in time there are $R_{i,j}$ for each $i,j\in[k]$ (which seems to be closely related to the infamous $R_0$). $R_{i,j}$ is the excepted amount of individuals in community $j$ that a sick individual from community $i$ is going to infect. Note that, not necessarily, $R_{i,j}=R_{j,i}$.
So, $R_{i,i}$ measures the infection inside the community, while $R_{i,j}$ for $i\neq j$ measures infections between different communities.
I don't know if this is relevant for here, but do you know of some data or estimates of such parameters $R_{i,j}$ from somewhere in the world using any partition?

While this is highly relevant, there are 2 problems: (1) Identifying transmission events is extremely hard (especially where the pandemic is out of control and track & trace is overwhelmed). (2) Demographic characteristics differ widely between countries and communities, so your estimates would only be valid locally. The closest thing to this I have seen is estimates for intra-household transmission (secondary attack rate) by demographic (e.g. Bernal et al.).


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Can anyone ID this microorganism?
I found this microorganism in a wet moss sample taken from my backyard in Richmond, Virginia (USA). I took some pictures of it at 40x, 100x, and 250x. I'm not entirely sure what it is, but I think it's some kind of rotifer based on it's behavior. It anchors onto a piece of moss while hunting. It stretches out to catch food, and once it's caught something, it snaps back into itself.

Any ideas as to what this is?

Appears to be a ciliate protist called Vorticella.

 Image source: Wikimedia (Author: Frank fox, 2010)
Vorticella always stood out to me because of their long, narrow stalk they use for anchoring with ciliate-lined bell-shaped oral end.

 Image source: MicrobeWiki (originally from Haw River Program)
Fun fact from Wikipedia:

The stalk is made up of the spasmoneme [also called "myoneme" above], a contractile organelle, with rigid rod filaments, batonnets, surrounding it. The coiled spasmoneme and batonnets serve as a molecular spring, so that Vorticella can contract. The cell body can move hundreds of micrometers in milliseconds. The spasmoneme is said to have higher specific power than the engine of the average car.

You likely mistook this for the more-commonly known rotifer due to the beating cilia at the oral end and tendency to anchor down, which are also both characteristics seen in rotifers. See this SE post about rotifers I wrote a while back which includes some nice animations.
Also, you can quickly differentiate Vorticella (which are typically free-living) from closely-related and morphologically-similar Carchesium, which are colonial.
See this video ("Vorticella - Under the Microscope) by Nick Moore for various videos and some more info; Journey to the Microcosmos (YouTube) also has some good videos of Vorticella.


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Meaning of "stripped" in "stripped antibody-depleted sera"
From a research paper:

FOLR1 autoantibody detection
The assay for identification of the presence and relative quantification of FOLR1 autoantibodies in serum samples was performed as previously published.41–43 Horseradish peroxidase (HRP) labelled anti IgG antibody (Cat#I8640 Sigma Aldrich) and IgM antibody (Cat#I8260, Sigma Aldrich) were used to detect IgG and IgM. Antibody-depleted sera (Sigma Aldrich) was used as negative control. Serum effect on blocking FA binding to folate binding protein was detected using HRP labelled FA (FA-HRP, Ortho-Clinical Diagnostics, Raritan, New Jersey, USA). FA in serum samples was removed as previously described. Unlabelled FA was spiked (0.01–2000 ng/mL) into stripped antibody depleted sera to generate the standard curve. The SuperSignal ELISA Femto Substrate (Cat#37074, ThermoFisher Scientific) was used as substrate for detection of HRP activity. Images were collected using a 96-well imager (Q-View Imager, Quansys Biosciences). Intensities were extracted from the images using Q-View Software. IgG, IgM and relative FA-blocking amount were calculated based on the standard curves.

What is the meaning of "stripped" in stripped antibody depleted sera? I think that "antibody-depleted sera" stands for "serum samples that contain a reduced concentration of antibodies". But why stripped? Does it mean that the authors applied some additional techniques to ensure an even lower level of antibodies in the serum samples?
I found it odd because the word "stripped" is used only in this particular place, and nowhere else. They mention 'antibody-depleted sera" earlier, without "stripped".

I think the word "stripped" refers to the depletion of FA (folic acid?). The previous sentence is "FA in serum samples was removed as previously described." They were probably clarifying that the standard was made using antibody-depleted, FA-depleted (stripped) serum.

@MattDMo - thank you! Indeed, in a paper referenced in "as previously described", a charcoal stripping method for removal of folic acid is described. You might post your comment as an answer, it was the correct guess!

All set - I posted an answer below.

While @mgkrebbs is correct in their answer that the meaning of "stripped" cannot be 100% determined without corresponding with the author, there are clues that point to  a most likely answer.
The previous sentence, "FA in serum samples was removed as previously described", cites this reference, which describes testing of different materials for their efficacy in removing radiolabeled folic acid from serum. I don't have access to the full text of that article, but according to the original poster of this question, this method was called "charcoal stripping."
The term "stripped" is also commonly understood in the lab as referring to some reagent which has had some component(s) of its makeup removed intentionally. The two uses I'm familiar with are this scenario, where some component of serum is removed (usually with charcoal), and western blotting, where stripping refers to the process of removing the bound antibodies from the membrane so that it can be reprobed with different ones.
So, with no other depletion method being mentioned aside from the antibody depleted serum purchased from Sigma, the arrangement of sentences, and the reference to charcoal stripping, I think it's safe to assume that "stripped antibody depleted sera" refers to the Sigma reagent which has undergone the folic acid removal process.

I believe this is a failure of editing, and the meaning in this paper of "stripped" cannot be determined without correspondence with an author.  "Stripped" is an informal term for either removal of some substance or treatment with a material such as charcoal which affects many substances. Normally in papers "stripped" is qualified (at least initially) to indicate the type of treatment.  Here it could plausibly refer to antibodies, folic acid, or any number of other things.  It may be an artifact of draft editing that was meant to replace "stripped" with "antibody depleted" as a more precise term.  I suggest writing the corresponding author.


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Is a pampa an example of ecological succession?
I'm not very sure if a pampa is an example of an ecological succession.
The reason of my doubt is due I've remember hearing that a Pampa is formed when a Valley which has had a river on it, no longer has it due the river changed its course and left the place without water.
But is it okay for this reason to imply that the Pampa (biome) is the result of an ecological succession?. The wikipedia entry doesn't give much details.
But it constrains the term for only the lands located in Brazil and Uruguay. It does not give any indication why some other places such as in Bolivia and Peru also use the term. Given these, could it be confused with a Mediterranean forest or with a Chaparral?.
Are those of the same origin?. Can someone help me here?. I'm confused about these.

This is a difficult question to answer. I would say that is uncommon (though not improper) to think of questions of ecological succession at the biome scale. In this case, the pampa is probably a good example of a climax community (if we exclude human-caused changes). After the rivers changed course there would have been a lot of bare substrate. Over time different plant species would establish and then  be replaced by other plant species. After thousands of years you would get to the somewhat stable state of the pampa biome. It is important to note that this biome is maintained by fire and grazing (Vignolio et al 2003). Fire/grazing prevent trees and shrubs from establishing in high densities and maintains the open grasslands of the pampa. In general, every place in the world that has natural life would be the result of ecological succession. Succession is a process that happens as life establishes and ecological communities change.
As for why other places are also called pampas, the word "pampa" apparently comes from a Quechua word for plains, that was then adopted into Spanish. Since Peru and Bolivia both have Quechua speaking populations, it seems reasonable that this work was applied to plains areas in those countries.
Edit in response to comments
Comment about biome scale
The reason behind the scale comment is that typically we observe succession for a given habitat. Part of this stems from the origin of the succession ideas, where Frederic Clements posited that climate was the major driving factor of successional trajectories (Clements 1916). This would actually fit well with the biome view of succession, however in order for this model to explain all the variation we see in the world (eg. why a tree grows in location X but not location Y 4 metres away), you devolve into splitting the world into infinitesimally small micro-climates. Henry Gleason proposed a more individualistic model, which suggested that climate was just one influence, and that each plant species responds to a myriad of different environmental cues (Gleason 1927). The sum of these responses results in the community at a given location. This seems to fit better with our current understanding of succession but is not without problems. In a Gleasonian model, any variation can be expected to result in a different community. Since it would be strange for the pampas region to be homogeneous over 1.2 million km2, there are likely distinct communities within the biome, each developing as a result of factors like soil moisture, soil chemistry, climate, wind exposure, and herbivore use. One can still talk about succession at a biome scale, but at that scale we would be thinking about what factors lead the pampas region to become a grassland, rather than what factors lead grass X, tree Y and forb Z to coexist next to each other.
Factors maintaining grassland type ecosystems are fairly uniform globally. You need some sort of event that will kill woody vegetation but not kill grasses and forbs. Fire and grazing are natural examples (Briggs et al. 2002), but mowing would also maintain grassland (Fidelis et al. 2012). Earthquakes are unlikely to maintain grassland as trees and shrubs are likely to survive earthquakes.
Comment about global pampas
Yes, and no. There are other wet grasslands in the world that would have similar moisture regimes and productivity levels seen in the pampas of South America. However, these are likely not called pampas. Temperate grasslands in Canada and the US are typically called prairies or plains, while the same kind of system is called a steppe in Eurasia. Ecologically they are very similar in function, though they may have very different species present. Perelman, Burkart, and Leon (2003) use prairie and steppe to refer to different sub-communities of the Pampa. Perhaps the closest analogue would be the Great Plains of North America. There is no other area called the Great Plains, but since the great plains are made up of prairie, steppe, and savannah (Oesterheld et al. 1999), there are many other areas globally that exhibit similar ecological function. This can get confusing, as there are cultural usages of these terms to refer to places, and there are ecological uses of these terms to refer to grassland sub-types.
I am not sure I understand how you are relating chaparral/Mediterranean forest to this. Both of those ecosystems will have much higher presence of trees and shrubs than pampas/prairie/steppes (Hanes 1971, Palahi 2008). Chaparrals tend to be dominated by evergreen drought tolerant shrubs, while Mediterranean forests will have more trees present. All of these systems are influenced naturally by fire and drought, so they are similar that way.
Sources
Briggs, John M., Alan K. Knapp, and Brent L. Brock. "Expansion of woody plants in tallgrass prairie: a fifteen-year study of fire and fire-grazing interactions." The American Midland Naturalist 147.2 (2002): 287-294.
Clements, Frederic Edward. Plant succession: an analysis of the development of vegetation. No. 242. Carnegie Institution of Washington, 1916.
Fidelis, Alessandra, et al. "Short‐term changes caused by fire and mowing in Brazilian Campos grasslands with different long‐term fire histories." Journal of Vegetation Science 23.3 (2012): 552-562.
Gleason, Henry Allan. "Further views on the succession‐concept." Ecology 8.3 (1927): 299-326.
Hanes, Ted L. "Succession after fire in the chaparral of southern California." Ecological monographs 41.1 (1971): 27-52.
Oesterheld, M., et al. "Grazing, fire, and climate effects on primary productivity of grasslands and savannas." Ecosystems of the world (1999): 287-306.
Palahi, M., et al. "Mediterranean forests under focus." International forestry review 10.4 (2008): 676-688.
Vignolio, Osvaldo R., et al. "Effects of fire frequency on survival, growth and fecundity of Paspalum quadrifarium (Lam.) in a grassland of the Flooding Pampa (Argentina)." Austral Ecology 28.3 (2003): 263-270.

Gee I had to wait for almost three months to get a reply from somebody. But it is nice that it finally happened!. Regarding your answer you mention that it is uncommon to think questions at the biome scale. Why is this?. Does this means that ecological succession is more used at higher scales?. Such as communities?. I'm okay with the second part of your answer. But I wonder, if other events but fire also maintain the pampa biome?, would earthquakes account?.

Regarding the last part of your answer, it isn't very clear to me if there are other places in the world which do have pampas? This stems from the confusion of the term with mediterranean forest and chaparral, are all of these the same? and do they exist in Asia for example?.

I'm already accepting your answer, but it would be very nice if you could add an additional details from my comments into your answer. Sorry for the late reply by the way.

Responded to your questions. See above.