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Expected number of mismatches between two alleles of a gene in a population?
I can't find any article about the expected number of mismatches in alignment of two alleles of an assumed gene. Any reference or information about allele mismatch ratio (in a species or higher taxa) is appreciated.
suppose we have 10 alleles for a gene in a population. if we pick two of this alleles and align them, which number (percent) of positions are expected to be mismatches (not gaps and matches). Of course, I know that in conserved genes and domains mismatch number are lower and in different genes and species this numbers are different. I want some information from scientific resources talking about this numbers.

Maybe it's just me - but I am a bit confused about what you are asking. Do you mean the expected number of pairwise differences which separate two genes samples from a population (population genetics)? Or is it specifically about the error in nucleotide alignment (bioinformatics)? Or maybe neither?

@user438383 suppose we have 10 alleles for a gene in a population. if we pick two of this alleles and align them, which number (percent) of positions are expected to be mismatches (not gaps and matches). Of course, I know that in conserved genes and domains mismatch number are lower and in different genes and species this numbers are different. I want some information from scientific resources talking about this numbers. I add this comment to question for more explanation.

I think the question needs to be more specific. There are plenty of resources dealing with sequence alignments, and, as the question correctly points out, it depends on the gene, the organism, etc. It is not obvious what one wants to know: how count the mismatches? How to estimate their frequency from the mutation rate and phylogeny? Something else?

Still not sure exactly what you mean, but this question might be what you need.

I think that the question is difficult to answer in the current phrasing. However, I will show how it might be easier to answer by filling in some blanks and defining some terms.
I am going to define as an "allele" any nucleotide difference between two sequences. This is the molecular genetic definition more or less. I am further going to interpret "mismatch" as also including sequence gaps, as in the case of indels your alignment will include gaps. I am assuming that you are talking about aligned sequence differences, because you mention alignments. I am going to ignore the focus on "genes" because at the molecular level visible in alignments, alleles are not necessarily tied to annotated genes (even though they are usually introduced in that context).
So in this case, if you assume that most alleles consist of single nucleotide variants (probably not true, but a helpful simplifying assumption), you can deduce that nearly all "alleles" thus defined will differ from each other at a single nucleotide position. A larger and more complex genotypic difference (for example a microsatellite variant or a transposable element (TE)) will involve a proportionally larger number of mismatches (i.e. gaps).
Indeed, if we look at the wikipedia page for "allele":

At the lowest possible size an allele can be a single nucleotide polymorphism (SNP).[7] At the higher end, it can be up to several thousand base-pairs long.[8][9]

You might however mean something different. It's possible that the question is rather something like this:
How much segregating genetic variation of an organism (say humans) consists of single nucleotide variants (SNVs) vs. larger/more complex variants?
That's a somewhat different but much more answerable question. It is unfortunately limited a bit by our ascertainment bias in favor of SNVs, which are just easier to find. But the best estimates that I'm aware of suggests that there are probably slightly more microsatellite variants than SNVs, and some work suggests possibly a similarly large number of large-scale repeat variants (such as TEs).
I can imagine yet another interpretation, which might be something like:
If we align two (or 10, or however many) homologous sequences of defined length drawn from a natural population of an organism (say humans), at how many positions can we expect the aligned portion of any pair of sequences to differ per base pair?
This is more straightforward: the alignable portion of the human genome is expected to show approximately 0.1% differences. However, this is pretty much only counting SNVs. This will vary from species to species. Off the top of my head, I remember that interfertile Arabidopsis thaliana strains can differ by anything from 0.1% to 1% per aligned base.


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ATP Synthase EC number
Why ATP synthase EC number is 7(Translocase)?
My textbook says it's a hydrolase but when i checked its EC number it was changed to 7.
And also ATPase(adensointriphosphatase) page that was previously classified as hydrolase is deleted in qmul.ac.uk

What textbook is this? An ATP synthase is not a hydrolase, since it does not use water to break a chemical bond (at least not in its primary function). However, it couples proton translocation with ATP synthesis. Therefore it is a translocase.
See the following passage from qmul.ac.uk what category 7 is and why e.g. ATPase is classified as translocase rather than as hydrolase. (It is a hydrolase as well, but it's not its primary function.)

Translocases (EC 7): A new EC Class
Six enzyme classes have been recognized since the first Enzyme
classification and nomenclature list was first approved by the
International Union of Biochemistry in 1961. These were based on the
type of reaction catalysed: Oxidoreductases (EC 1), Transferases (EC
2), Hydrolases (EC 3), Lyases (EC 4), Isomerases (EC 5) and Ligases
(EC 6). However, it has become apparent that none of these could
describe the important group of enzymes that catalyse the movement of
ions or molecules across membranes or their separation within
membranes. Several of these involve the hydrolysis of ATP and had been
previously classified as ATPases (EC 3.6.3.-), although the hydrolytic
reaction is not their primary function.

Thanks for your answer.I don't think it's a surprise that some "old" sources use this classification because as mentioned in qmul,ATP synthase was classified as 3.6.3 from 2000-2018.And if you don't mind i have another question:Do all enzymes that seem to belong in two classes regrading the direction that we are looking at,are classified regarding the "primary direction" that enzyme usually catalyzes?

Unfortunately, it's not that easy. There is a whole catalogue of rules for the naming and classifications of enzymes: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html.

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Is it incorrect to assume alveoli as spherical and distinct, especially when analysing lung inflation/deflation?
I have recently read the paper "Laplace’s Law and the Alveolus: A Misconception of Anatomy and a Misapplication of Physics". To summarise it, here is a section from its abstract:

The typical representation of the acinus as a “bunch of grapes”
bears no resemblance to its real anatomy; the alveoli are not independent little
balloons. Because of the prevalence of this misconception, Laplace’s law, as it
applies to spheres, has been invoked as a mechanical model for the forces of
alveolar inflation and as an explanation for the necessity of pulmonary surfactant
in the alveolus. . . . Alveoli do not readily
collapse into one another because they are suspended in a matrix of connective
tissue “cables” and share common, often perforated walls, so there can be no
pressure differential across them. Surfactant has important functions along planar
surfaces of the alveolar wall and in mitigating the forces that tend to close the
small airways. Laplace’s law as it applies to cylinders is an important feature of the
mechanics of airway collapse, but the law as it applies to spheres is not relevant
to the individual alveolus.

This paper made many claims that I want to investigate. I have tried reading other papers to make sense of them and it appears fully understanding the lung is still a difficult problem in physiology.
Please could you help me verify if any of the statements put forwards by the paper and listed below are true:

The lung's acini should not be thought of as "bunches of grapes". They are instead much more polyhedral. The interalveolar septa contain numerous interalveolar pores that, although some may contain fluid, can equalize the pressures in the lung and allow ventilation of alveoli with blocked airways. So it is more accurate to think of the lung alveoli as a foam or sponge.

The application of Laplace's law is then flawed in the traditional analysis of a smaller alveoli connected to a larger alveoli (see the image below for the traditional analysis). The alveoli are not spherical nor can they ever attain unequal pressures due to their interalveolar pores. It is instead the tensile properties of the lung parenchyma that keeps alveoli from collapsing, instead of the variable surface tension generated by surfactant.

These 2 points the author makes seem to be very fundamental, yet overlooked in the usual teaching of lung physiology, which is why I want to verify whether they are true or not. Additionally I have read a paper that states "In a healthy lung macro- and micromechanical properties
are dominated by surface tension at the alveolar air–liquid interface at low lung volumes while at larger lung volumes extracellular matrix components become stress bearing and define lung structure and mechanics (Bachofen et al. 1987; Wilson and Bachofen 1982; Bachofen and Schürch 2001)". This seems to state that surface tension of alveoli is in fact more important than lung parenchyma when considering lung collapse, contrary to the paper above.

Not quite getting your point. Applying  Laplace's law, the effect of surfactant should be relevant much more in smallest alveoli than in larger ones or "tubes"? Then, your question asks if alveoli are  interconnected - hence share same pressure, hence same effect of surfactant -  or,  are you assuming this to be a proven fact? If it'd be true ("to think of"...) - the role of surfactant seems over- or underestimated (that''s what your queston is "up to"  that kind of result would interest me.)?

The paper refutes the traditional idea of surfactant playing the major role in preventing alveoli collapse due to points 1 and 2 I mentioned in my post. I want to know whether points 1 and 2 are actually valid, as this conflicts with what I've been taught about lung physiology. Point 3 is just the author's explanation of what actually happens during lung collapse, and how it is only here the author thinks Laplace's law should be used. In hindsight, I should not have mentioned point 3 in my post as it only adds confusion - I will edit it out.

Is the following correct understanding? a. interconnecting alveoli lessens - does not heighten -  air pressure thus enforcing surface tension leading to "collapsing" i.e. tightening of alveoli? Hence, according to the paper, surface tension  is less relevant in spite of "bigger impact in smaller spheres.  What is confusing with point 3 and "hindsight", you say?`To me, biggest caveat, paradox is "drum role" of surfactant. If surface tension is heightend by "spooness", then surfactant becomes more, not less, important, correct?

It appears we are not doing a very good job of understanding each other - I apologise if I have been unclear. I am not putting forth any new ideas, I am just summarising what is in the paper. If you cannot understand my summary of the paper, please read the paper instead. If you do fully comprehend the paper and can comment on the paper's validity, then that is great - I would be very happy if you could post an answer explaining whether you think the paper is valid or not.

I read the paper, and "all this" I hereby  recommend to anyone into biology of the  lung.Your very question  reflects the gist of the paper: alveoli being interconnected contrary to common textbooks. Do I think if the paper is "valid"? No empirical knowledge - contrary to the author who apparently "on his own" has done autopsies and thought about it.If the answer is "no" to your question I'd find that valid! However, if you'd extend your question into the messing and mixing up in conclusions to be drawn from the empirical findings of the author that would make me want to answer.

I'm a newbie myself. Guess you should add some reference for the standard knowlege (alveoli are spheres) the author citicizes, and, second, add some searches you have done on any other authors confirming the .author's findings. P.S. You are right about you not having brought  up new ideas. Me neither, just conclusions right or wrong.

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Does LSD "stay" in your fat storage and then "returns" back?
This rumor was told me by a very anti-drug person. A stance I agree with only lightly.
The rumor was that when you take LSD, it stores itself in your fat storage, and then returns back in 3-6 months, returning back meaning there would be another series of effects of LSD (the trip).
Is this true? I highly doubt it. However, what I don't know, if the body is processing (burning?) fat and then processing substances (such as the rumoured LSD) found in fat stores.

Welcome to SE.biology. I downvoted because questions based on rumours from other people don't tend to encourage speculative and non-evidence based answers. Take a read of the help-centre to find advice on how to ask a good question. Thanks!

@user438383 This is actually a very widely-spread idea (with several variations) amongst the drug and hallucinogenic community. The version I've heard most is that it accumulates in CSF or just "the spine", however as I reference in my answer, it's not true.

@user438383 I haven't found much evidence on the web about this, so I had to ask here.

@TimotejLeginus showing a little research would probably keep your question from being closed. Alternatively you may want to drop this question the skeptic stack, urban legends like this area better fit there. I know a lot of scientists who believe this urban legend, until today myself included, so it deserves a little attention.

@John kind of interesting that sciencists believe these things too! I would have done some research, but before this, I would be unsure where to start, now I would be sure where to :p

@TimotejLeginus a scientist outside their specialty is not much better than a layman, and paleontology does not involve much pharmacology.

I've heard this rumor for years, both from pro- and anti-drug people, and it is not true. According to this review of LSD's pharmacology, its half-life in the body is about 5 hours, with it being completely cleared within about 15-28 hours. There is no evidence that it accumulates long-term in fat, cerebrospinal fluid (CSF), or anywhere else in any pharmacologically significant quantity.
Reference:
"The Pharmacology of Lysergic Acid Diethylamide: A Review" CNS Neurosci Ther. 2008 Winter; 14(4): 295–314. PMID: 19040555 DOI: 10.1111/j.1755-5949.2008.00059.x

My guess is that flashbacks are almost or entirely psychological, where the brain and the rest of the CNS somehow gets triggered in a similar way that acid does. Also, hallucinations can occur in a number of severe psychiatric diseases, independently of past drug use, so that likely has a role, too.


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Why V(D)J recombination only happens in B and T cell development?
Does V(D)J recombination only happen in B and T cell development? Can it happen in other types of cells?
If V(D)J recombination only happens in B and T cell development, why other types of cells cannot have V(D)J recombination?

Edit 1:
V(D)J recombination rearranges the DNA sequences of maturing B and T cells that encode proteins for recognizing antigens, so that different B and T cells may recognize different antigens for initiating further immune response.
Recombination  activating  gene  1  (RAG1)  and  RAG2  proteins are essential for rearranging the DNA sequences in V(D)J recombination. RAG recognize specific DNA sequences, called recombination signal sequences (RSSs), that are adjacent to the variable regions of the genes that encode proteins for antigen recognization.
V(D)J recombination occasionally happens in natural killer (NK) and dendritic cells [1, 2].
So the answer to my question is that V(D)J recombination is not restricted to B and T cell development.
I would like to thank @swbarnes2 for pointing out the importance of RAG1 in V(D)J recombination. Also thank @MattDMo for introducing me to the community guidelines.
This question is not my homework. I am just curious why V(D)J recombination seems to be only discussed in the context of B and T cell development.
References:
[1] Kuo TC, Schlissel MS. Mechanisms controlling expression of the RAG locus during lymphocyte development. Curr Opin Immunol. 2009;21: 173–178.
[2] Borghesi L, Hsu L-Y, Miller JP, Anderson M, Herzenberg L, Herzenberg L, et al. B lineage-specific regulation of V(D)J recombinase activity is established in common lymphoid progenitors. J Exp Med. 2004;199: 491–502.

Edit 2:
Added some highlights to my edit 1.

Why would other cells need to undergo somatic recombination like B and T cells do?

you are the one posing the question, therefore you need to support its validity. Hypothetical "what if...?" questions are off-topic here.

Your question already has 3 downvotes and 3 close votes because the Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please see our homework policy for more information. Your 2 questions can be easily answered with a Google search or by looking at a textbook.

"Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.

The genes that do recombination likely aren't expressed in any other tissues.  A quick look at expression of RAG1 shows expression in immune cells, and not really anywhere else.

It's not just "likely" they're not expressed in other cell types, they just aren't period. Otherwise DNA rearrangements could run amok and cause a lot of damage. They're very tightly controlled in developing T and B cells, along with mature B cells undergoing hypermutation.

I think genes like RAG1 are already tightly bound to work only on receptor genes and nowhere else; there's just no point in rearranging receptor genes in cells which will never express them.


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Reliable recipe to make DIY yeast slants
Does anyone have any good ideas on a reliable way to activate basic grocery store yeast?
I realize this is a total beginner's question.  I've built a small yeast ranch at home with my kid, and we're trying to learn how to innoculate agar'd petri dishes with home grown samples we're trying to make from basic grocery store yeast.  Eventually, want to do more advanced experiments, but for now...we're just looking for some growth.
So far, our best attempts at using grocery store yeast packets have yielded no results (i.e. no visible growth).  My best attempts to find a good recipe have lead nowhere.  I see lots of good advice on how to follow sterile procedure on making agar'd dishes and how to innoculate from an existing slant; but we thought it'd be easy to just start with grocery store yeast instead of buying a slant.
FYI -- there's obviously some kind of growth happening on the petri dishes.  When we break from sterile procedure and invite contamination; then it's clear something (not yeast) is happily growing on the plates.
My mistakes that could've lead to zero growth on the petri dishes include:
(A) Perhaps adding the dehydrated yeast to water that's way too hot?
(B) Perhaps I did not add enough wort or sugar for the yeast to feed on?
(C) Maybe i should've let the dissolved yeast ferment for a while before innoculation?
Would very much appreciate any help from someone more experienced on this.
best wishes...

You might actually get better advice at [cooking.se]. Make sure you search their site first.

Yeast grows very well in liquid. The initial innoculum from the store will visible grow (“prove”) in warm water with a little sugar.


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How long do Ziehl-Neelsen stained samples keep?
I have acquired TB slides from my city's health center that are supposedly acid-fast bacteria (AFB) positive. However, when I took a look at it, I see basically no carbol fuchsin stains.
They were individually neatly folded in paper. When I opened them, the stains were slightly wet with immersion oil, facing down. So far, so good (page 6). I've been later informed that these samples were prepared Q1 2019. Based on my research, the staining solutions themselves last up to 12 months (page 33). I can't find any data on how long a stained sample would keep though.
Do they decolorize over time? I expected the AFB to be bright, or at least slightly pink, but I see no such thing. I do see bacilli, though all of them are nearly transparent/methylene blue in color.

Here are some sample images. The first 2 are how I expected AFB to look like, while the next 2 are what I captured (and I think should contain AFB). The last pic is a 10um/div calibration slide for reference.

This TB study might help you: external page
Briefly, they used 6 to 19 months old samples of mostly bad quality (due to their age). The last sentence of the quote below sounds promising though.

The 12,543 sputum smears stored at the national TB reference
laboratory for 6 to 19 months were stored at room temperature in a
wooden slide box without a cover slip. Most of them had lost their
stain reflecting the counterstaining with methylene blue. Restaining
of 436 doubtful slides by ZN gave disappointing results throughout [...]
After a 6 to 19 months storage of ZN stained sputum smears in a
non-air conditioned atmosphere, the bright red color of eggs due to
carbolfuchsin had virtually disappeared. [...] In such case, the ZN restaining of sputum smears allows to rediscover AFB that were discolored.

When I did this the last time, we used fresh and few months old samples which looked similar to the first of your images. Just have a look at the paper, I guess.


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Is insect farming more efficient than shrimp farming?
Insect farming is sometimes advertised as the way to feed the growing global population with animal protein in a way that is more efficient (in terms of protein yielded/feed consumed) than growing cows, sheep, pigs or fish.
Would insect farming be more efficient than shrimp farming, even though these two broad groups of animals share some similarities in terms of "complexity"?

Maybe worth reading this and this

I don't have an answer one way or the other, but from what I've seen, shrimp farms require flooding large patches of land, often in coastal regions where, whereas insects can be grown in self-contained and relative dry environments that should be easier to scale up. It's a topic I've followed for years, but I still haven't seen an insect protein product that's priced competitively with other sources.

efficent at what? calories per acre, calories per kilowatt hour, calories per gram, water usage, cost vs profit, ect.

Insects have a very low feed conversion ratio, which essentially means most of what they're fed turns into edible protein for us. Cows, sheep, pigs, etc. typically have high feed conversion ratios. According to this site: https://in.virbac.com/aqua/health-care/aqua-advice/how-to-get-optimum-fcr-in-shrimp-culture, shrimp have a feed conversion ratio of 1.5 - 1.8., where Acheta domesticus, which is a cricket, is at about 0.9 - 1.1, pork is 5, and beef is around 10 (Huis. A., 2012).. So if we look at feed conversion ratios, they are approximately the same, especially when compared to cows and pigs. What's more efficient to produce depends on the area, and what resources are available. Hope this helps.


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How is SARS-CoV-2 'deactivated' for some Covid vaccines (for example Covaxin)?
Some Covid vaccines like Covaxin employ a 'Whole-Virion Inactivated Vero Cell'.
How is the virion 'deactivated' for the vaccine?

For Covaxin (BBV152), SARS-CoV-2 was inactivated by treatment with β-propiolactone [1]. β-propiolactone reacts with and modifies, among other things, nucleic acids, thus preventing their replication [2].
[1] Yadav P, Ella R, Kumar S, et al. 2020. Remarkable immunogenicity and protective efficacy of BBV152, an inactivated SARS-CoV-2 vaccine in rhesus macaques. Preprint.
[2] Perrin P, Morgeaux S. 1995. Inactivation of DNA by β-propiolactone. Biologicals 23(3):207-211.


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What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?
From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011)

The metabolic profile reported here is unique to GTPCH deficiency or a defect in the GTP activator protein. While there is no known demonstrated defect in this protein, it would cause similar functional deficiency. Other enzymatic defects in the pterin synthetic pathway present with very different metabolic profiles.

I googled but could not find a particular "activator protein" that interacts with GTP cyclohydrolase I. Is this one of the GTPase-activating proteins? They must be numerous, and I haven't found one that was shown to activate GTP cyclohydrolase I.
At the same time, the authors use the definite article, as if this protein is known. I'm intrigued.
I found this paper, in which GTP cyclohydrolase I is said to interact with Rho-GTPase-activating protein 7 (also known as DLC1), but the paper does not say that this protein is an "activator", they merely list it as part of the putative transcriptome of GTP cyclohydrolase I.
Further, in the quote the authors say that "there is no known defect in this protein", but the OMIM page for DLC1 says that a defect was known from at least 2000, although it is related to cancer, not to the BH4 pathway.

Perhaps this protein?

@canadianer - thank you! It might be it!


text:
Why are adenoviral vector vaccines safe in terms of insertion mutagenesis due to genome integration and E4 region's proteins effects?
Disclaimer: I'm neither a genetics professional nor an anti-vax fanatic, I just tried to compare COVID-19 vaccine types currently available on the market and got some questions that I'd like to answer rationally.
Some of the vaccines that are being actively used now are based on adenoviral vectors, such as ChAdOx1, Ad26, or Ad5. These vectors are replication-defective, usually due to removed E1/E3 regions.
I looked for existing information about adenoviral vectors and found some facts that may relate to safety, but I can't conclude if they are rational or not for vaccine applications, since most studies are made for gene therapy or animal models.
Proteins activity
Wild-type adenoviruses are considered to be able to lead to tumors in rodents (Wiki: DNA oncoviruses), mostly due to E1 region activity, but E4 also adds to its oncogenic effect
(Cell transformation by the adenovirus oncogenes E1 and E4), and may affect DSB repair (Expression of the adenovirus E4 34k oncoprotein inhibits repair of double-strand breaks). That may be related to the “hit-and-run” mutagenesis theory.
For Ad9, E4 alone can show that effect, E1 is dispensable (Adenovirus type 9 E4 open reading frame 1 encodes a transforming protein required for the production of mammary tumors in rats)
Genome integration
It's thought that adenoviruses do not integrate into the host genome, since they don't have a tool for that, but occasionally it happens with low probability (10^-3 .. 10^-7 per cell), particularly in cells where the virus can't replicate and lysis doesn't happen, which is always the case for replication-defective vectors (Chromosomal Integration of Adenoviral Vector DNA In Vivo, Frequency and Stability of Chromosomal Integration of Adenovirus Vectors, Insertion vectors for gene therapy, Illegitimate DNA integration in mammalian cells, Viral Vectors: The Road to Reducing Genotoxicity, Viral Epigenetics).
That raises questions about the possibility of insertional mutagenesis. As I see, such questions are often discussed in the context of DNA vaccines, but extremely rarely for adenoviral vectors which also deliver DNA into cells.
Finally, the question itself:
Should risks of insertional mutagenesis due to viral genome integration and E4 region's proteins activity be considered and discussed or they are not important / do not exists at all for adenoviral vector vaccines? Have I missed any studies about these topics?
Can these risks be estimated in numbers and compared with similar natural events?

This question envisages putative harmful changes arising in host tissue cells infected with the replication-defective virus of a 'vectored' vaccine.
The scenarios of the question leave out of account a significant factor that opposes such putative harms. That is, one of the main purposes and effects of such vectored virus vaccines, which is to produce an adaptive cytotoxic T-cell immune response, targeted on (cell-surface-displayable fragments of) the viral gene-products (i.e. proteins) foreign to the tissues of the vaccinated host.
The aim of stimulating cytotoxic T-cell responses from vaccination is especially important against pathogens such as viruses (or intracellular parasites such as malaria) that disappear into the interior of cells of the host, and thereby become 'invisible' to circulating antibodies of the host immune system. This makes the antibody part of the response less useful against such pathogens.
Once such cytotoxic T-cells have been developed, they circulate and can detect and kill host tissue cells displaying fragments of those 'foreign' proteins on which the T-cells are targeted.
All of the host tissue cells infected by the vaccine virus are in this targeted category, and the consequence is that those infected host tissue cells have only a short life. They also are generally somatic cells with little cell-division, e.g. where the vaccine is given intramuscularly. Also, the replication-defect of the vaccine virus means that the vaccine-virus-infected cells are number-limited by the number of infectious units in the vaccine dose, there is no production of fresh generations of virus particles.
These factors and the processes of the cytotoxic immune response altogether oppose any likelihood of the putative harms envisaged by the question.  The cited prototypes of those harms appear not to be reported in respect of situations that arise after vaccination with vectored virus vaccines.
(Supporting background can be found described and explained in the various editions of Janeway's 'Immunobiology'.  The original author died in 2003, but the later editions have been retitled "Janeway's Immunobiology", in memoriam, to mark his founding contributions, e.g. the 9th edition (2017) is from authors/editors K Murphy & C Weaver.)

Do you know of any - other -  empirical studies trying to find DNA integrated into cell genome?

@Peter Bernhard - not sure what you're seeking here. The cells infected with the vaccine DNA/RNA (depending on the type of the vaccine) express a foreign antigen, evoking a cell-mediated immune response  that among other effects targets them for cell killing. Not clear where you think a search for something could be directed.


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How do prodrugs exactly work? Are there multiple varieties of prodrugs?
I have been reading about a (new?) prodrug of LSD, 1CP-LSD, which is being synthesized in the body to LSD.
However, I don't know how exactly. I read somewhere, that another prodrug of LSD, 1P-LSD was put  into a vial of human blood, and it was synthesized to LSD. Which is kind of hard to belive, that just exposure in blood synthesizes 1P-LSD to LSD. What processes in the body are responsible for this, are there another processes for synthesizing another prodrugs to their respective drugs?
Are there multiple varieties of prodrugs? By that I mean that they synthesize themselves using another method instead of one another.

Prodrugs are extremely common; we often don't even think of some of them as prodrugs unless we're also familiar with the metabolite. Psilocybin, for example, is a prodrug; the active molecule is psilocin. Aspirin is a prodrug of salicylic acid (though there are also other active metabolites).
Prodrugs can be categorized according to where they are converted to active forms: intracellularly in target tissue or other organs like the liver, or extracellularly like in the gut or in the bloodstream. The Wikipedia link at the beginning of this answer includes a table with some examples.
Prodrugs may be converted to active forms by enzymes or by environmental conditions in the body, like pH. I'd argue they are diverse enough that it doesn't make all that much sense to study them as a category, rather that in any pharmacological class of drugs you should be aware that they may be administered in a modified form, often to improve bioavailability or storage stability.

So it is indeed true that prodrugs can be synthesized to drugs within blood too? That's cool!


text:
Why is DNA replication so much faster in prokaryotes than eukaryotes?
There are many statements to be found on the internet of the sort:

“DNA replication occurs at elongation rates of about 500 nucleotides
per second in bacteria and about 50 nucleotides per second in
vertebrates.”

However none that I have read attempt to explain this order-of-magnitude difference. Is it known why?

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

I am not sure why this question has been marked as needing detail or clarity. It seems quite clear to me. And as far as research effort, it would help if the poster had given a source and said he had searched the Internet, but if he had done so he would have found that this statement comes up repeatedly but providing reasons is avoided. The observation has been around for years — it's in the 1992 edition of the Biochemistry of the Nucleic Acids.

I have now rewritten to provide clarification and focus. I have deleted the remark "Intuitively, I assume it's just the base rate for growth." As I find this meaningless in molecular terms. I think it is a worthwhile question but I doubt if the answer is known. All I have found is vague statements about histones and greater complexity. However, if someone has anything concrete...

hah, I just saw your new comment. I hope my answer is not too vague.

Note that this is misleading in a way because the eukaryotes divide the replication process among numerous forks starting at multiple initiation sites "Drosophila, alias the
fruit fly, has ~ 5,000 such sites while mammalian cells have ~20,000. [...] Our typical animal cell has between 20,000 and 60,000
molecules of pol α whereas our regular bacterium, E. coli has 10 to 20 molecules of
DNA pol III."

The difference in DNA replication rate between prokaryotes and eukaryotes is still under current research, but the basics are understood. It is very much a matter of complexity, as eukaryotes are more complex in many different ways. I found a very useful reference for this and other kinds of related questions. Briefly, some possible reasons:

[...] in eukaryotes, the DNA template is compacted by the way it winds
around proteins called histones. [...]

The DNA-sequence is not as easily accessible in eukaryotes, the unwrapping and re-wrapping of the DNA takes some time.

[...] The coordination of the protein complexes required for the steps of
replication and the speed at which replication must occur in order for
cells to divide are impressive, especially considering that enzymes
are also proofreading, which leaves very few errors behind. [...]

This underlines another rather important factor. The speed of the polymerases replicating DNA is very much related to their accuracy.

[...] This proofreading capability comes with some trade-offs: using an
error-correcting/more accurate polymerase requires time (the trade-off
is speed of replication) [...]

And just for completeness, here is a compete overview of DNA replication in the three big systems.

Thanks for pointing out my mistake. Have corrected it. Yes, I’ve heard those arguments before, but I’d like to see some hard data.


text:
Using Nerve Conduction Studies to determine nerve regeneration
I was reading a paper investigating using MRI as a way to determine peripheral nerve regeneration: https://sci-hub.do/10.1016/j.expneurol.2009.10.012
They mention that

... nerve conduction studies are widely used but these studies are limited
only to the distal parts of peripheral nerves and not suitable to
measure regeneration early on and in response to proximal lesions
(Kimura, 1999). Furthermore,after complete axonal injury, particularly
as it relates to traumatic nerve injuries or proximal plexus lesions,
the distal portions of nerves are often inexcitable, which limits
electrodiagnostic testing's utility to assess the degree of
regeneration in proximal nerve trunks.

I understand this because normal nerve conduction studies wrap an electrode on your finger (where current goes in) and reads it down stream at your wrist.

I totally get why this wouldn't work if the injury occurred very high up at say the elbow, because the signal could not travel from your finger upwards since it's all degenerated.
However, what if we instead stimulated the nerve a bit above the elbow (maybe using a needle) and measured the signal downstream. We could move closer and closer until a signal was detected. This is where the nerve has regenerated to - thus this method CAN detect peripheral nerve regeneration. What is wrong with my reasoning?

I think that theoretically there's no fault in your reasoning. However, technically, to access the regenerating axon at the elbow level could be almost impossible. I also think that the labels in your draw should be: (in -> recording; out -> stimulation)

Remember that peripheral nerves come all the way from the spinal cord. When they write of

traumatic nerve injuries or proximal plexus lesions

they are talking about injuries to the trunk, nerves running more or less around the collarbone. They're not talking about elbow vs wrist. See for example https://en.wikipedia.org/wiki/Brachial_plexus and the image there from Gray's:

They're also not necessarily saying that it is physically impossible to do a nerve conduction study in these areas with traditional means, they are talking about practical matters and use in-practice, and their paper is touting their method using noninvasive imaging.

Great points but I don't see what's so impractical to stick a few pads on someone's collar bones? Is it that we would actually need to stick deep needles into the person?

@JohnHon Yeah the surface isn't anywhere near those nerves.


text:
Can I imbibe seeds before sterilization?
For an experiment I want to germinate lettuce seeds. For logistical reasons it would be convenient to imbibe the seeds by placing them in the cold for 2 days, afterwards I would sterilize the seeds using dilluted bleach. I mostly see people apply stratification or imbibition after sterilization, does the order matter? Would there be a difference for cold treatment (stratification) or wet treatment (imbibition)?

Personal anecdote: Once I planned to sterilize seeds of Silene latifolia for tissue culture but after the first step (washing the seeds in water for an hour) I had to do other things and the seeds did spend the night wet in room temperature. The next day some of the seeds were showing first signs of germination - a little crack in seed coat. I decided to sterilize them anyway, since there was nothing to lose. The result: Some seeds did germinate after sterilization and were fine. Some seeds died. Interestingly, in some seeds the bleach destroyed only the exposed root meristem resulting in rootless seedlings.
I have never worked with lettuce seeds but I would consider questions:

How fast the seeds germinate and what conditions they need for germinating? You cannot sterilize seed that have already germinated.
Could the inbibition change the properties of the seed coat and make it easier for the bleach to pass through and kill the embryo? I suspect not, but cannot be sure.
Wet environment is good for bacteria and fungi growth. "Dirtier" seeds are sometimes harder to sterilize - they need longer exposure to bleach or stronger bleach concentration to completely remove contamination. Stronger bleach or longer treatment can sometimes kill some (especially small) seeds. It is hard to say weather two days of wetness can make any difference. The cold should slow down the bacterial and fungal growth.

At the end of the day I reccomend you to try with few seeds and see the result. Maybe include negative control with usual order of steps. If the survival is the same for both groops you are good to go.


text:
With an mRNA-vaccine, would it hypothetically be possible to get that sequence transcribed into their genome for people who suffer from a retrovirus?
I recently read a bit about the mRNA-vaccines for COVID-2019. I fully understand that mRNA cannot enter the genome of a healthy person as they lack the required reverse transcriptase to transcribe RNA back into DNA. This made one question pop up in my head, though:
What about the people who do have reverse transcriptase in their body? As far as I understand it, a retrovirus like HIV does express the required proteins to form reverse transcriptase as it's part of the virus strategy to integrate itself into the human genome.
Wouldn't that mean that an HIV-positive person, upon being vaccinated using an mRNA-vaccine, could theoretically end up having the RNA-Sequence of the vaccine transcribed into their genome if reverse transcriptase is present in their cells at the right moment? Or am I missing something? Would that mean that the COVID-vaccine could essentially become the artificial equivalent of an endogenous retrovirus, even possibly immunizing future generations?

It’s relevant to note that all humans have reverse transcriptase from retrotransposons and mRNA can be reverse transcribed and integrated into the genome (this the mechanism by which processed pseudogenes arise).

https://medicalsciences.stackexchange.com/questions/25392/why-is-the-new-mrna-vaccine-unable-to-modify-human-dna

https://skeptics.stackexchange.com/a/53027/155

"if reverse transcriptase is present" - Case is use of rev. transcr. from HIV virus by CoV. There lies some analogy in  the fact that LINE1  which is a retrotransposon mentioned by canadianer above is being used by ALU elements to have themselves integrated.

Interestingly, there's recent news we may all have some reverse transcriptase activity and in some people it leads to serious disease.  The specificity of that reverse transcription is not yet known, but HIV reverse transcriptase is going to require a primer binding site - basically some lysine tRNA sequence - to get started.  Of course, with low odds, there may be some conceivable way to get around that by mutation, template switching, etc., but I don't know of evidence it happens.
Reverse transcription of random RNA transcripts (including the genomes of mRNA viruses that infect us) is surely a theoretical possibility, but we should bear in mind how rarely this must occur (otherwise, our genome would be even more overflowing with spam than it is).

The scientific PNAS article underlying the reverse transcriptase press release is available here.

Reverse transcriptase is not the whole story as I learnt. There must be "integrase" or the like to put it in (so to say). What is known about "free floating" DNA - retrotranscribed or not - "going into" host cells DNA strains? Any idea? Maybe that is rather unknown, do you know? I refer to the mechanism of integration in a narrow sense; how is viral DNA being put into (so to say) host DNA, if there is no integrase?

@Peter Bernhard - getting the DNA into the cell is "transient transfection", while integrating it is "stable transfection".  See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067914/ .  I don't deny that, in the absence of a viral vector or some other trick, stable transfection of random DNA in any given cell is very rare.

"...how rarely this must occur..." If there were a working principle that integration kills the infected cells (e.g. not by apoptosis, not like cytotoxic t cells) integration might be more common, and the less searched for (as that would be a way to get back up again).

@Mike Serfas Thank you for providing the link. You name it:  "The specificity of that reverse transcription". I think it would be interesting to read more on that issue in your answer. Provided link refers to my comment above which refers to Canadianer's. That link refers to ALU as one, special specifity of LINE1, I think. Are there any others or pertaining sources you know of?

"Even in non-retroviruses that lack integrase, such as the adenoviruses, integrase may be expressed through genetic engineering technique", this struck me first in the link you, Mike, provided above. What is the natural mechanism for integration of DNA, that comes in as such, not as RNA? Counterintuitively, integration of DNA suddenly seems more intricate than "integration of m-RNA" (because the enzymes are combined or not?). From your paper: DNA viruses, how do they integrate, in case they do?

From first link in your answer: "The buildup of a certain type of DNA in the cytoplasm, Alu, contributes to macular degeneration, the researchers found. This buildup appears to kill off an important layer of cells that nourishes the retina's visual cells." - This seems higly relevant in the context of the question, but not only, as it leads to some hypothesis that "integration kills" infected cells: no need to inherit embedded vaccine... Again: if integration kills, that's good if it's infection?

The first link you give is good. You point at some issue you should elaborate on, as it's about "specifity" you speak of: They say, "Different retroviruses use different host tRNAs as primers. HIV-1 uses Lys3." How can specificity lie in such thing as  tRNA. t for trivial? Sure there is some basic knowledge underlying. - If possible, more on "promoting" integration specifically, but, even more so, more on unspecific integration and if it exists. Thank you.

Is, in your opinion, specificity of insertion, of integration in a narrow sense, no issue? The question refers to transcription "into" the genome. So even if by unspecific HIV-retro-transkriptase were produced CoV-DNA that couldn't be inserted because of lack of integrase? ("transient DNA")
The paper linked in your answer surprisingly does not tell how insertion by HIV is produced. There is no integrase. Thus, HIV looks like illustrating some paradigm unknown: specific DNA may integrate into host DNA because it's specific, No enzyme needed. That cannot possibly be? Some other answer on that?

I think your answer is way not explicit enough about the rather exciting "result" the study linked to in you first sentence offers. All this may go unnoticed to people like me who think they knew already. Please be more elaborate about the HIV enzyme being blocked, thus having blocked not insertion of HIV RNA/DNA, but of ALU RNA/DNA. Again, retro-transcriptase of HIV was found to work on something totally different? Thus, "...to get around that by mutation, template switching, etc.," seems obsolete, not necessary.


text:
If you only ate fruits, vegetables or smoothies would you be able to skip drinking water?
If you only ate fruits, vegetables or smoothies would you be able to skip drinking water?
I do not see some animals (like squirrels) drinking water daily (doesn't mean they don't have a water source) so I am wondering if that's they case are they getting water from what they eat and can we as humans can go without water.
1st Researched Question:
https://www.livestrong.com/article/555187-can-you-drink-smoothies-in-place-of-fruits-vegetables/
Excerpt:

Fresh fruits and vegetables are considered low-calorie, energy-dense
foods. That means the food contains few calories in a high volume of
food. They tend to be high in water – dried fruits such as raisins are
an exception – high in fiber, high in volume and low in fat. The high
volume and fiber help you to feel full. A smoothie, in contrast, may
or may not be high in water, depending on how much fluid it contains.
Most importantly, a smoothie may have little fiber or the fiber it
does contain may have been chopped into tiny fragments by the
manufacturing process.

Summary:
Fruits and veggies contain water but smoothies do not. No answer if can be a replacement for drinking water.
2nd Researched Question:
Can you live just on smoothies and juicing?
https://www.quora.com/Can-you-live-just-on-smoothies-and-juicing
Summary:
Some say people can survive eating fruits and vegetables but do not specifically if humans can survive without water.
3rd Researched Question:
What would happen if I drank only a smoothie everyday for a month?
https://www.quora.com/What-would-happen-if-I-drank-only-a-smoothie-everyday-for-a-month
Quote:

Without diving all the way into Maslow’s Hierarchy of human needs, we
can pretty easily prioritize the elements of our diet according to
urgency and importance. The order will be something like:

Water
Energy
Proteins and lipids
Vitamins and minerals

Nobody will argue with the first one. A single smoothie would be harshly restrict fluid intake. Ideally a mid-sized person should have 2.5 liters of water each day. Estimates vary on the minimum required to maintain
life, but some sources estimate it to be just over 1 liter per day. If
it were a very large smoothie made with large amounts of either juice
or water, you might be ok here.

FYI This is not information for me but information in general. Some animals in nature seem to get by without drinking water but eating fruit. Would it be safe for a human do the same? We found out a human survived by drinking sea water (although it caused other issues). Also, I'm not advocating for it but I'm wondering if it causes issues.

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

@MattDMo I did not find any specific answers online regarding this question. I have added my notes for what I did find.

That looks a lot better. I'm voting to reopen.

Is there anyway to reopen this? It is not personal medical quesitons. It's general. It's an in general question.

Thanks everyone for voting this down! I didn't want to learn anything new anyway! Only 8 downvotes?

Note: this question is being discussed on Meta.

A good number of vegetables and fruits have >90% water contents; this includes cucumber, watermelon, etc. Even oranges, broccoli etc. have >80%. So it would not be hard to have enough water intake if the veggie/fruit/smoothie diet is not restricted to particular fruits or veggies.
Slightly less detailed, but more reliable source agrees:


text:
Get "DNA" of one parent based on its children
I'm no biology expert so bear with me, but I've been given a task to estimate alleles of an animal based on the animal's children and the children's other parents.
I've looked up Mendel's laws but I'm not sure I can possibly determine the correct result - better show an example:
Let us say that we want to get alleles of a mother. We know the following:
Child 1 has alleles: AG, the father of the child has alleles: AG
Child 2 has alleles: GG, the father of the child has alleles: GG
Child 3 has alleles: GG, the father of the child has alleles: GG
According to Mendel's laws and the example above it would seem that
For the first child x father pair - the mother would have alleles AG
For the second and third child x father pair - the mother would have alleles either GG or it could have AG, CG or TG.
How can I determine which anwser is correct?
If needed I can provide more examples.

EDIT: More examples / clarification

I have a database of animals (cows/bulls). Each animal has ~50 000 SNPs, each SNP has 2 alleles.
However, some of the animals data are missing, for instance I do not have SNPs for a certain bull, but I do have SNPs of the bull's children and their mothers.
Now I need to figure out an algorithm that based on the SNPs of said children and the SNPs of their mothers tries to compute the SNPs of the bull.
Additional example: (each row represents a child - mother pair)
SNP                                 | Child alleles | Mother alleles | Possible father alleles
ARS-BFGL-BAC-19454  | GG               | AG                   | AG, GG
ARS-BFGL-BAC-19454  | AA                | AG                   | AG, AA

From the table above it is clear that the bull can only have AG.
However I do not know how to handle the following case:
SNP                                 | Child alleles | Mother alleles | Possible father alleles
ARS-BFGL-BAC-14220  | AG               | AG                   | AA, AG, GG
ARS-BFGL-BAC-14220  | GG               | GG                   | GG, AG, CG, TG
From the table above it looks like the bull can have either AG or GG - how do I figure out whether the father's value is AG or GG?

It requires a bit of Bayesian statistics.

It would help to get the actual prompt or question that you are trying to answer. For example, do the alleles {A, G} cover the total set of alleles at this locus? In that case some genotypes could be ruled out. There are cases in which you can infer parental genotypes, but some more information is required. Is this a homework question?

You can't be certain. Is this a real data set you are working on or something used in, say, a course?

@MaximilianPress I've tried to make it more clear in the original post. I do not know if the alleles cover the total set of alleles at this locus, frankly I do not even know what a locus is (as I said, I'm not a biologist).

@BryanKrause It is a real data set.

If you have real data you can't always find the answer definitively. Vadim gives good advice for getting the probabilities.

@BryanKrause I'm not sure how would I get the probability for the SNP ARS-BFGL-BAC-14220. Three of the children - mother pairs are AG - AG, while nine of them are GG - GG. Howver all twelve pairs can get me either a AG or GG combination. To me it seems like it is always 50:50 between AG and GG, am I missing something?
(In this case the GG is the correct answer as I am testing the algorithm on data that I do have).

@toucheqt You aren't being very clear about the data you have, and I don't really want to go around and around trying to find out and solve your problem for you. I think you've got some information to run with - see where that gets you after you give it a couple days thought. You'll learn a lot more trying to figure it out.

Ok, I think I can answer somewhat usefully with the update.
It's helpful in this case to think in terms of sampling alleles. It's true that the cases that you give are not 100% unambiguous, but it is not true that we can't give a somewhat confident estimate. We can still make a statistical prediction of the most probable genotype.
The first thing to note is that you are working with pedigrees. That is, you have parents and multiple children. Pedigrees are great because they allow you to pool information across individuals.
The next thing to note is that your alleles are almost certainly not of uniform frequency in the population. In other words, If I sample a random cow from the herd, the probability of allele $A$ at some arbitrary locus is almost certainly not the same as the probability of allele $G$. You can use that information in inferring the most likely allele. Moreover, you can put a precise number on the probability of any given allele.
The simplest method I can think of is to use genotype likelihoods, to account for pedigree information, and to incorporate the background allele frequency as a prior probability (h/t Vadim for the Bayesian approach).
A likelihood is the probability of some dataset given a specific hypothesis. In other words, your data is your offspring genotypes and your hypothesis would be the different offspring.
In your first example, we can logically rule out alleles other than $AG$. (That's actually not true; you should account for the possibility of genotyping error, but we'll ignore that for now.)
In your second example, we can't logically rule out all but one genotype. But we can say some things nonetheless:

you have said that there are only 2 alleles per locus (i.e. $A$ and $G$ are the only possible alleles).
$A$ and $G$ have distinct frequencies in the population.
we now at least one paternal allele ($G$).

Let's take a simple case of the likelihood application, in which we say that frequency of $Pr(A) = 0.9$ and $Pr(G) = 0.1$ (I am making these numbers up). Now in the ambiguous case:
$$Pr(paternal=GG | offspring\_genotypes=GG,AG) = \\
Pr(offspring\_genotypes = GG,AG|paternal=GG) * Pr(paternal=GG) = \\
Pr(offspring=GG | paternal=GG, maternal=GG) \\
* Pr(offspring=AG | paternal=GG, maternal=AG) * Pr(paternal=GG)
$$
and
$$Pr(paternal=AG | offspring\_genotypes=GG,AG) = \\
Pr(offspring\_genotypes = GG,AG | paternal=AG) * Pr(paternal=AG) = \\
Pr(offspring=GG | paternal=AG, maternal=GG) \\
* Pr(offspring AG | paternal=AG, maternal=AG) * Pr(paternal=AG)
$$
Which evaluate to:
$Pr(paternal GG) = 1.0 * (0.5 * 0.5 + 0.5 * 0.5) * (0.1 * 0.1) = 0.005$
and
$Pr(paternal AG) = (1.0 * 0.5) * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.1) = 0.0125$
You can see that there are multiple ways for the offspring to get genotypes in the paternal $AG$ case, which is what leads to the terms with addition. Note also that the $Pr(paternal genotype)$ at the end handles the genotype frequency, as all the other terms are conditioned on the parental genotypes.
So in this highly artificial example, we prefer genotype of $AG$ somewhat (note that these likelihoods do not sum to 1.0). But, if we were to alter the genotype frequencies to 50% frequency of each allele, we would get:
$Pr(paternal GG) = 1.0 * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.5) = 0.125$
and
$Pr(paternal AG) = (1.0 * 0.5) * (0.5 * 0.5 + 0.5 * 0.5) * (0.5 * 0.5) = 0.0625$
and you would come to the opposite conclusion!
So it really matters what the background frequency is, if you choose to consider that term.
You could also think about genotyping error or whatever as part of these calculations.
I am certain that there is a more sophisticated way to do this, that takes better advantage of available information, etc. Maybe I've even made a mistake in the computation- but this is an approach that you might use to infer paternal genotypes.

Thank you for your detailed answer, it helped a lot.

Good! I should note that this is a Bayesian approach to compute a posterior probability, and therefore probably similar to what Vadim first suggested.

I think you deserve the full credit for working through the calculations.


text:
exercise of gene linkage in genetics
Could you help me solve this problem:
AAbbCC is crossed with aaBBcc and the offspring re-crossed with aabbcc. Considering that A and B are linked and their distance is 12 mapping units, while the gene C is not linked to them, find the percentage of the offspring that will have phenotype aabbcc.
I used this method to solve it (I know it's not correct but I don't know where I am mistaken):
P: AAbbCC x aaBBcc
F1: AaBbCc
AbBbCc x aabbcc
Since the distance between A and B is 12, their recombinant frequency is 12%
88% then is the recombinant frequency of the parental
Dividing by 2, 44% is the RF of parental AB/ab and 44% of parental aa/bb
In conclusion, since gene C is not linked, I calculated the probability to obtain cc from CC x cc, and that's 1/2
So my final result is: 0,44 x 0,5 = 0,22 = 22%

You did right for most of the exercise, but you got confused on one of the (apparently) easiest things.
Try to reason in terms of chromosomes, and not merely of genotypes:
F1 inherit their chromosomes from two homozygous parents, so you know that they are AbC and aBc.
You can visualize the cross with the recessive homozygote as follows:
Ab C     ab c

-- -  X  -- -

aB c     ab c

The second parent will always pass abc, so in order to have an offspring with genotype aabbcc you only need that parent 1 passes abc.
Given that the parentals are Ab and aB and that RF is 12% (0.12), regarding the first two loci, the frequencies of the gametes are
Ab = 0.44
aB = 0.44
AB = 0.06
ab = 0.06

Including locus C, the frequency of the gamete abc is then simply 0.06 * 0.5 (because c is unlinked), and that corresponds to 3%.


text:
Explanation of "differential transcript usage" (DTU)
This paper describes differential transcript usage as

Differential transcript usage (DTU) is a special case of alternative splicing in which a gene’s relative transcript abundance (RTA) profile, the proportion of total gene-level expression that arises from each of the gene’s transcript isoforms, differs between conditions (Soneson et al., 2016). [...] An example of DTU may be illustrated by the scenario where the total gene expression is the same between conditions A and B, but transcript isoform 1 is the predominantly expressed transcript in condition A while transcript isoform 2 is the predominantly expressed transcript in condition B.

My question is: is differential transcript usage essentially the same as the usage levels of particular codons? If not, what is the difference? I am unsure of what "transcript isoforms" are, so I'm not sure whether it's talking about codons here or something entirely different.

No, it is a completely different thing, which has to do with splicing and alternative splicing.
I refer you to some genetics text for details on splicing and alternative splicing, but I will give here a very brief and incomplete explanation fo what they are and how they fint into DTU.
Genes are composed of introns and exons. Exons are the only parts of genes that are usually composing the mature transcript (intron retention is possible, but we are not interested in that).
Splicing is the mechanism by which in a eukaryotic gene, introns are removed, and the mature transcript is assembled only using exons.
During splicing, not all exons are necessarily retained. Imagine a gene with exons 1, 2 and 3. It is possible that the main form (called isoform) is the one consisting of exons 1, 2 and 3. Let's call that Isoform 1. However, due to a phenomenon called alternative splicing, other isoforms, can be generated, for example one isoform composed by exons 1 and 3. Let's call that Isoform 2.
On average, we may imagin that the abundance of Isoform 1 compared to Isoform 2 is rather constant. However, some treatments or some changes in environmental stimuli, can give rise to a Differential Transcript Usage by which the relative abundance of the two isoforms changes.

Thanks, but doesn't codon usage bias directly affect splicing, which directly impacts differential transcript usage due to evolutionary selection/pressure for certain isoforms over others?  Would it be possible to update your answer relative to what's written in the "Patterns across a gene" section of https://www.nature.com/articles/nrg2899, specifically the first paragraph part that ends with "...in shaping codon usage near intron–exon boundaries".  There seems to be a lot more nuance here than first meets the eye.

I would say it's true codon usage could affect splicing, but that's mostly for comparing across species. In the same species, the codon is the same for a given gene, therefore it has nothing to do regulating alternative splicing. Differential transcript usage under different conditions should be regulated by other factors.


text:
Do animals with very small eyes see microscopic objects?
I understand that many small creatures have very elementary eyes: they are not scaled-down versions of the human eye but as I understand it often just light-sensitive organs for detecting movement.
However, a mouse I would guess has an eye that is like the human eye but probably less than 1% the size. So does that mean that a mouse sees details that humans can't?
There has been recent evidence that ants might recognize their own reflections. Now, I know the structure of insect eyes is very different from mammalian eyes but if indeed they can recognize themselves in a mirror, that implies that their eyes can perceive very small details.
I could also imagine that things like wavelength mean that details of very small objects simply can't be perceived by bouncing visible light off of them -- that is why their are electron microscopes and so I could believe that mice, etc. can see bacteria, etc. any better than we can.


text:
Is the number of nucleoli in a nucleus fixed?
A nucleus can have multiple nucleoli. But are there any constraints on the number of nucleoli in a nucleus?

Can cells of individuals of different species have a different number of nucleoli?
Can cells of different individuals of the same species have a different number of nucleoli?
Can cells of different types have a different number of nucleoli?
Can different cells of the same type have a different number of nucleoli?

I've found snippets of information implying the number of nucleoli is fixed per species, but none authoritative enough to stoke my doubts.

I'll directly go to your fourth question, as all of them can be answered with a yes. This rather old mouse paper already got to the point. Sadly, only the abstract is freely available. Briefly, the number can be variable in the smallest unit you are interested in, the cell type. From the abstract:

The distribution of the number of nucleoli in many diploid cells
exhibited a mode of two or three nucleoli per nucleus, and a range
from 1 to 6 nucleoli.

In the paper, there are histogram of different cell types of mouse and all of them seem to be variable in their number of nucleoli.

Exactly what I was looking for, thanks!


text:
What is the structure of heterochromatin?
A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is questionable". Obviously, heterochromatin exists, since you can see it on photomicrographs, but what about its structure?
Is it true that the structure is not confirmed? Are there any other candidate structures?

It has never been visualized in vivo because the sample preparation steps involved in imaging at that level of magnification will kill the cells. Electron microscopy is very harsh; it must take place in a vacuum, and SEM involves coating the sample with ultra-thin layers of metals such as uranium.

@MattDMo - your comment sounds as an excellent answer - could you turn it into one? It's best not to answer in the comments, because it may deter others who are willing to write up a full answer from doing so.

@AliceD sure, I'll see what I can put together.


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Why does the thickness of the Loop of Henle have to be less than the convoluted proximal tube and the distal convoluted tube?
We are currently being taught "Homeostasis through excretory system" in college. After seeing the structure of a nephron, it is not quite evident as to why should the Loop of Henle be the thinnest.
Only sense that I could make out of it is that- "Thin cross sectional area implies higher fluid velocity". Since, water and ions are majorly reabsorbed in the proximal convoluted tube, the loop of Henle is thin to increase the flow of fluid because there isn't much left to reabsorb and hence it won't require as much reabsorption time as the PCT. This decreases the filtration time and makes the process faster. I am not quite sure if this makes sense.
Can someone help?

there is a bit more to it actually,

The Henle -loop only occurs in birds and mammals, giving them the ability to make the urine hyperosmotic in comparison to their blood, other vertebrates can't do this.

how does the henle loop achieve this further concentration of urea(= more resorption of H2O)?:

-> by using the physical principle of countercurrent exchange
Beware: the explanation follows the opposite direction as the flow of the liquid!

A potential is build up in the bigger upgoing part Pars recta by active Na+& Cl- resoption , the water cant go out because the membrane is impermeable here.

this leads to build up of osmotic pressure (positive osm. potential of 1200 mOsmol/kg)

The Henle -loop  loops back up as a thin part(!) the Pars ascendens

the downgoing part right after the PCT (pars descendens) uses the potential of the corticomedullary osmosis gradient to let water (resorption) out using passive osmosis while taking urea in (no ATP needed).

CONCLUSION: So why is the left and bottom part of this henle loop thinner?!  to resrobe H2O using passive osmosis ! (also, if the lowest bottom part would be thick, it would not loop so nice, therefore hindering the coutercurrence effect)


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When the sister chromatids are joined in the centromere, why is it stated that the number of chromosomes is 46 and not 72?
Before the DNA is replicated in a human somatic cell, the cell has 46 chromosomes. Also, after the sister chromatids are separated during Anaphase, the chromosome number in the cell doubles to 72, so when the sister chromatids are joined, why isn't the chromosome number also 72? On the internet, some sources say that one chromosome in a cell that hasn't replicated its DNA is equal to one chromatid. Is this correct, or are chromosomes and chromatids structurally different?

When I was learning genetics for the first time I have also found naming the two chromatids joined at centromere as chromosome a little bit strange. The number of DNA molecules and their behaviour in cell cycle seemed to me more important for understanding of genetics.
What you need to understand.is the term chromosome predates knowledge of DNA structure. The name literally means colored (chromo) body (soma). It is an object visible under the microscope when using specific dye. In metaphase two chromatids joined at centromere look like a single object - a chromosome. Sometimes the two chromatids of one chromosome are so close together it is difficult to tell them apart. In anaphase the chromatids separate and one object (two-chromatid chromosome) visibly splits to two objects (single-chromatid chromosomes of daughter cells)


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Do animal muscles atrophy slower than humans?
Suppose I consider the silver back gorilla as an example.  I cannot imagine ever seeing one in the wild intentionally doing something akin to weightlifting like humans solely for the purpose of getting stronger (if I'm wrong about this, that would be fascinating to know as well).  However, last I checked a male silver back can easily lift several times its own body weight.  I used to workout heavily and used to hold my high school bench press record (330 lbs in the 160-171 lb weight class).  However, even then I would have struggled to do more than a few pull ups with a 170 lbs strapped to my waste.  Meanwhile, I've watched various types of monkeys and apes do handfuls of seemingly effortless pull ups at zoos as part of their play.
So do animals like gorillas have muscles that either start and stay stronger than humans or just atrophy much more slowly?  Or is it just a matter of constant use?  Or is it just a different proportion of fast vs slow twitch muscles as this study suggests?
I am skeptical of this last part because some estimates of gorilla strength suggest they can lift upwards of 10 times their body weight [e.g., https://storyteller.travel/how-strong-is-a-gorilla/].  I also recall reading a study in grad school of an orangutan pulling over 600 lbs with one arm clearly not straining according to the article (though I failed to find the reference while searching today, unfortunately).
If anyone has some useful references with quantitative data, that would be great as well.

No matter how much I excercise, my musculus maximus will be stronger than my abductor policis brevis by the virtue of being anatomically different musles. Why would you expect an animal with clearly different body proportions and anatomy to have the same strength as humans?

Well, it's more a matter of confusion.  Hafþór Júlíus Björnsson, for instance, is over 400 lbs and one of the strongest humans on the planet.  He weighs more than most apes.  Yet I would pick the apes in just about any strength contest over him and they never work out.  Plus, male humans have a larger fraction of our body mass as muscle than apes yet they are still stronger.

@honeste_vivere: You might consider that the normal activities of an ape are equivalent to a human "working out".  Likewise for that subset of humans whose normal activities include a lot of physical work.

@jamesqf - True, they are more physically active.  However, how often do mountain gorillas go out of their way to lift up more than 2000 lbs?  I am guessing almost never yet they can certainly do that without risking serious injury.  Hafþór Júlíus Björnsson has to constantly train and eat an absurd amount of food just to barely be able to lift that much weight.  His job is to get stronger and he wouldn't even be able to compete against a gorilla.

Few more points regarding anatomical differences: 1. A muscle can only exert so much force on tendon and bone until something breaks. Look at side by side comparison of gorilla and human skeleton. Look how much sturdier an wider are the bones and joins. Wide bone surface allows for wider and stronger tendon-bone binding area. 2. A short and wide muscle can have the same total mass as a long and thin muscle and be stronger since exerted force solely depends on cross-section area of the muscle. 3. Number of filaments in a muscle is already determined at birth. This limits what exercise can do.

@honeste_vivere: I dare say he wouldn't be able to compete against my horse, either.  I think we may be looking at two different things here.  I'm looking at the difference between a sedentary human (or other animal) and a trained one.  You seem to be more interested in species differences, no?  In that case, look at sled dogs.

@jamesqf - Yes, I am curious if there is something different beyond just a different fraction of fast and slow twitch muscles between humans and, say, great apes.  Suppose you could teach a gorilla to intentionally strength train.  I think the difference would be even more stark.  Is it really just skeletal and muscular differences that make up that much of a difference though?

Animal muscle does atrophy and gain depending on use.
First, animal muscle does atrophy if the animal is too sessile. However in nature it is hard to be sessile. Consider how physically fit hunter-gatherer humans are in terms of their cardiovascular systems. If you are constantly active you don't need to "exercise" to build muscle - you are getting loads of physical activity. Walking 10km a day or more is normal for most humans without advanced technology. We used to see atrophy in animals a lot more, but with animal welfare laws we usually don't keep animals in tiny cages that prevent them from moving anymore.
Some animals are less lazy than humans: many animals will also instinctively stay active even when provided with the conditions to be sessile, but when forced to not be active we do indeed see muscle atrophy. This is especially true of less intelligent species, because the conditions to be sessile are too rare to waste "instinct space" on, but humans who have a much more broader range of behaviors with far more learning behaviors, so we can become very sessile. The downside of intelligence is that you can use it in self-destructive ways.
Just like humans, animals can also build extra muscle by doing the same thing over and over again: a draft horse will build different muscles than a race horse just because it is using them differently.
Many animals also have physiology that makes atrophy harder. Hibernating bears are known to have special adaptations to prevent atrophy because hibernation is defined as long periods of inactivity. But we only only see this in animals that have something like hibernation or have drastically different muscular systems.
So why is a gorilla so much stronger?
Well to start, wild male gorillas mass between 130 to 260 kg. Note that gorillas in captivity often become overweight weighing even more. They have short legs so we don't realize how much bigger than us they are. For scale, Andre the giant (a human far outside the normal range) masses about as much as a large but normal range male gorilla. But there are several other factors.
Humans’ muscles are weaker than other primates’ in significant ways. We have traded strength for much better endurance and fine control of muscles - we do indeed have a significant difference in muscle composition and possibly muscle fiber recruitment, although it is hard to test the latter - you can't tell a gorilla to contract one muscle as hard as they can. As a gain however humans have amazing endurance for any animal and far finer motor control than any other primate. An active human can have better endurance than almost any other terrestrial organism, humans can walk a horse to death, that is a human walking side by side with a horse can keep going long past the point the horse has died from exhaustion.
Gorillas are only stronger in some aspects, a gorilla upper body is certainly stronger, gorilla have large arms and a deep chest drastically increasing the muscle mass of the arms compared to a humans. But the best human could probably beat the best gorilla at kicking power, gorilla legs are comparatively small. To use Andre the giant again, Andre has a lot more muscle mass in his legs than a gorilla and the gorilla has a lot more in the arms, humans have long well-muscled legs. Like all things, genetics can set you up with better musculature, and you will keep it as long as it gets some use.


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Would tinnitus be explained by perpetually-bent/opened hairs in the cochlea?
When I look around for what causes tinnitus and the like, the usual response is "Well, loud sounds and hearing damage" but I feel like that's a little plain and I am curious about the underlying mechanism / explanation on a physiological level.
My previous understanding of how the ear works can be found in my previous question (with a terrific answer by AliceD).
So my question is this: Let's say a really loud, fierce sound occurs - the sort of thing that is said to cause tinnitus. This is equivalent to a really strong pressure wave approaching the eardrum. I imagine it would hit the eardrum, causing it to move violently / harshly, causing a similarly strong movement in the stapes, which is already providing something like a 20x pressure amplification to the cochlea.
So the stapes hammers hard on the oval window of the cochlea, causing a harsh pressure wave through the perilymph / endolymph, also causing the basilar membrane to move very harshly and violently. To me this would imply a fierce smashing/dragging of the hair cells against the tectorial membrane above, possibly causing sufficiently harsh wear-and-tear along the tops of the hair cells, leaving them bent or maybe even chopped, allowing their channels to remain perpetually open.
If these channels are always open, they're always accepting potassium, always creating the action potentials, always triggering the nerves underneath, which would mean the person is always hearing that particular tone all day, every day, 24/7.
Is this more or less what happens, or am I way off in my little thought experiment daydream here? Is this why tinnitus is difficult to cure, because it would require somehow rebuilding / closing up hair cells that are always open?

Thanks for the credits!

What you're describing would likely cause hearing loss, which could later result in tinnitus, but not by the mechanism you describe.
Hair cells transduce sound via remarkably fragile connections between stereocilia. The channels are closed until tension pulls the channels open (see Fettiplace 2011 for a review that covers pretty much all of sound transduction including a detailed description of the tip links and channels involved). Disconnection would result in the channels being perpetually closed, not perpetually open.
Anything like the trauma you describe would irreversibly damage the tip links and sound transmission would fail. There are mechanisms in the ear to prevent this sort of damage, but for sufficiently loud sounds the damage is not avoidable.
@AliceD has another excellent answer on tinnitus specifically here for more realistic mechanisms proposed for tinnitus: What is the mechanism behind tinnitus?. These are all centrally derived in some way. In short, the absence of proper input to the auditory processing parts of the brain results in compensation that induces an illusory perception. Similar sensations are experienced in other parts of the body as well, such as phantom limb.

Fettiplace, R. (2011). Hair cell transduction, tuning, and synaptic transmission in the mammalian cochlea. Comprehensive Physiology, 7(4), 1197-1227.

Thanks for the credits!


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Why does high blood pressure not damage the body during exercise?
Exercise is commonly understood to lower blood pressure by making the heart stronger. Mayo Clinic says,

Regular physical activity makes your heart stronger. A stronger heart can pump more blood with less effort. If your heart can work less to pump, the force on your arteries decreases, lowering your blood pressure.

While exercising, though, systolic blood pressure will often go up significantly.
Why does this dramatic increase in blood pressure not damage the cardiovascular system? Stress, for example, can damage the blood vessels,

Increases in blood pressure related to stress can be dramatic. But when your stress goes away, your blood pressure returns to normal. However, even frequent, temporary spikes in blood pressure can damage your blood vessels, heart and kidneys in a way similar to long-term high blood pressure. (Mayo Clinic)

Does daily exercise, for example, not cause "frequent, temporary spikes in blood pressure"?
Why does a blood pressure increase from exercise not damage the cardiovascular system as a similar blood pressure increase from stress (or other sources)?

Actually it can. See https://clinicalhypertension.biomedcentral.com/articles/10.1186/s40885-016-0052-y for instance:

Deleterious effects of HRE [hypertensive response to exercise] on structure and function of left ventricle (LV) has been reported consistently. Theoretically, individuals with HRE would be exposed to abnormally high pressure loads to left ventricle (LV), which may result in global subendocardial ischemia due to mismatch between demand and supply from excessive rate-pressure stress. Indeed, a previous study demonstrated a greater likelihood of new or worsening abnormalities of wall motions from echocardiography in individuals with HRE, even in the absence of angiographically significant coronary artery stenosis.

The issue is that you're confusing somewhat high blood pressure with abnormally high blood pressure during/after exercise, i.e.

Thank you, that's useful. Even a healthy response to exercise, e.g. 160 mm Hg systolic, would damage the heart over long periods, though, so I guess it's just the fact that exercise lasts a relatively short period of time is the reason it's beneficial? I suppose, say, exercising 8 hours a day (or, for that matter, being stressed for 8 hours a day), would be damaging?


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What made this, is it an egg sac?
Found this "egg ball" on a gate near a greenbelt north of Seattle, WA. From other posts here, it looks similar to snail eggs, but they do not have the webbing. Two days later I went back out to measure it, but it was gone. Maybe hatched or eaten?

s://i.stack.imgur.com/tj6gT.jpg

similar: What is this agglomeration of pink cells I found attached to a stone?


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If silver nanoparticles kill bacteria by penetrating the cell membrane, why don't they also kill human cells on contact?
Apparently, the silver from the nanoparticles can penetrate the cell wall of bacteria and kill them from the inside. Why, then, doesn't the same happen to human cells, e.g. the skin on my foot when I wear nanosilver-coated antibacterial socks, or the stomach lining when people drink nanosilver-treated water? Is it because the cell wall is different in bacteria than in multicellular organisms?

The nanoparticles from your sock will most certainly not reach to your foots cell membrane (Walls are for plants/fungi)  because of the thick layer of dead skin, oils, than about 30 cell thick cornified layer (stratum corneum) build up from practically dead cells (with no nuclei or organelles) but lots of filamentous keratine. This is the most outer shell of your epidermis followed by layers and layers of 4 other tissue types , then comes the "actual" skin dermis and the hypodermis beneath.

If some of the silver-sock -nanoparticles would actually make it through there to basal tissue and reach the cells plasmamembrane, they enter via endocytosis, and start to release Ag+ they break all kinds of things, because Ag+ is cytotoxic it induces ROS, damages you Mitochondira, disturb some pathways... you get the point.

However this was proven to happen within human in vitro celllines.

a few in vivo studies showed that Ag-NPs cause adverse effects on reproduction, malformations, and morphological deformities indifferent non-mammalian animal model.

Says "Review: A systematic review on silver nanoparticles-induced cytotoxicity: Physicochemical properties and perspectives
https://doi.org/10.1016/j.jare.2017.10.008

conclusion, definitely enough evidence to be suspicious, but don't freak out, just change socks daily, wash feet and don't drink dubious solutions or liquids. (sunscreen could be a factor )

I'm not freaking out, just wondering. :)
So, in the case of skin contact, I'm protected by a layer of dead skin, OK.
But there are disinfectant sprays with nanosilver, meant to be applied to open wounds. And disinfected water that goes to your stomach.
Is it actually killing both bacteria and your cells, but you're fine because your cells get replaced? Or what's the idea?


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How to convert cell units (c.u.) to mole?
If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as
$1\;c.u.= \frac{1}{\text{cell volume}}$
and
$1\;c.u.=\frac{1}{\text{cell volume}}*(\text{volume of 1 mole of in 1 atm)} \; Mole$?
an example of c.u. units, belongs to this article
Thank you.

Where does this "cell units" thing come from (source)? I have never used such a unit.

I’m voting to close this question because it is the second posting of this question. It is also unclear.

@tyersome Yes it is the second posting. If you can read the last comment on the prior question which is "I will post two questions, as David suggested, and will not erase this one to be sure that you can read my comments. Please post a comment such that I can erase this question, thank you."  I am waiting for David to read my comments, I don't want to be rude to him. I will erase my prior question.

@Chris I edited my question, hope it is clear now.

You can delete a question you have posted if it hasn’t been answered. Then post again in a revised form.

Ok, i will, thank you.

Please read a definition of molarity. A molar solution contains 1 mole per litre. A mole is Avagadro's Number (approx 6x10^23) of molecules of a particular substance. So you can only talk about the molarity of a single substance and to calculate this you need to know its molecular mass. A cell is not a molecule, but is a structure made up of many different molecules and macromolecules. So cell units (which don't even come up in a Google search but seem to be some way of quantitating cells) can have no relation to moles.

The paper references c.u. to their "ODE model construction & simulation" which is referenced back to a 2016 paper that uses the term in reference to a simulation in MATLAB.
c.u. is abbreviation for CONCENTRATION UNIT not CELL UNIT.

Given the absence of experimental measurements of protein concentrations, we use concentration units (c.u.) as  unit to represent the relative concentrations of proteins in the model

quoting https://royalsocietypublishing.org/doi/10.1098/rsta.2006.1761

I'm having trouble finding that quote or any instance of "concentration units" / "c.u." in the referenced paper

@user338907 thanks!


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Antimicrobial susceptibility testing
To learn the Kirby-Bauer method, I've been looking at youtube videos where a bacteria's susceptibility is tested.
In this video, the researcher places the discs (containing antibiotics) right after she inoculates the lawn on the agar disk. Shouldn't you wait until the bacteria has grown before adding the disk containing antibiotics?

That's "a fungus" or plural "fungi"; I can't tell if the rest of your question also has the same type of error for "bacteria" or what you are actually trying to ask.

No; antimicrobial discs are almost always added at the time of plating. The antimicrobials will prevent growth. This covers both bacteriostatic and bacteriocidal antimicrobial agents. If you were trying to differentiate between bacteriostatic and bacteriocidal, I suppose you could treat with the antimicrobial only after growth. What are you actually trying to test? What is the purpose of your experiment? Can you give us more details?

Rarely do you have a single bacterium, @tripleee; multiple colonies, even of the same species, are typically referred to in plural.

@CodyGray I'm trying to test the susceptibility of the fungi M.furfur against different concentrations of neem extract. If I added the disks right after the inoculation, wouldn't the bacteria be killed even before it has grown? How would zone of inhibition occur if it has already been killed?

Yes, that's precisely the idea. The bacteria is not able to grow around the disc, because the antibacterial is inhibiting its growth. The zone of inhibition shows how effective the antibacterial is at inhibiting growth of the bacteria. Because a lawn was plated, the bacteria will be able to grow everywhere else that it is not being exposed to the antibacterial agent from the disc. Google for "disk diffusion test" or "Kirby-Bauer test" for more details; e.g., this Wikipedia article.

A more useful question to ask would be, Why do you place the disc on the plate before the bacteria have grown up? This test allows us to infer which antibiotics an organism is susceptible and resistant to by observing whether or not they grow in the presence of that given antibiotic.
But there's a good reason we don't wait until the bacteria are already grown and see which antibiotics kill it. The metabolic activity of bacteria growing on a plate will slow as their population grows and available nutrients are locally depleted. However, the most common modes of antibiotic action only function well when the target organism is metabolically active. So we apply the antibiotics at the same time the culture is inoculated to ensure some level of metabolic activity is going to be happening.
For example, Betalactams disrupt cell-wall synthesis but don't destroy existing cell walls. If the target population is largely dormant, there will be minimal cell-wall synthesis occurring, and any bactericidal effects would be difficult to detect, if not completely absent. The same goes for antibiotics that disrupt translation (aminoglycosides and tetracyclines), prevent nucleic acid synthesis (Quinolones), or interfere with synthesis of specific metabolites (Sulfonamides). Those are all disruptions of metabolic activity that are necessary during growth and reproduction, but largely shut down during dormancy. Some bacterial populations even take advantage of this loop-hole by maintaining a small proportion of their population as metabolically inactive "persister" cells.


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Why does DNA synthesis require nucleoside triphosphates?
Writing the DNA sequence is done with nuclosides that have three phosphates attached to them, and two of these phosphate are thrown away back into "phosphate pool" of cell. What are main reasons triphosphate structure is used? Conformational changes in the polymerase seems like it could be one of the primary ones.

Welcome. Do you know where the 'A' in the 4-letter DNA code stands for, and what function it has in the cell? That may give you a clue.

We expect questions to be accompanied by evidence of prior research. This requirement is especially important for homework questions. Is this a homework question?

unrelated to 4 bases, question is on why chain grows from nucleoside triphosphates

It seems I'm missing what your question is. Are you asking why phosphate links are used in DNA, or why a diphosphate is released (the latter seems to be the question)?

Please finish the [Tour].  Before posting read the Help on how to ask a good question. Then search for similar previous questions, which I know exist. But from your strange statement about conformation changes I wonder whether you might benefit from reading a chapter on basic chemical thermodynamics.

@AliceD it's very clear, "why does DNA synthesis require nucleside triphosphates". if your answer to why is so self-evident and obvious that the mere question is absurd, then I apologize. if not, then nothing wrong with the question.

@David whoever you are, nothing wrong with the question. there's nothing strange about nucleoside triphosphates alosterically regulating protein conformation, very basic. that the same principles is at work when it comes to nucleoside triphosphates in DNA synthesis, seems likely to me, you can Google "polymerase conformation change nucleoside triphosphates" and read around for yourself

You still have not clarified your question. Do you understand that it takes chemical energy to make a phosphodiester bond, that the free energy change  of hydrolysis of the phosphodiester bond in dNTP is coupled to making the phosophodiester bond in DNA? Or are you asking why pyrophosphate rather than orthophosphate is released? The answer to that is discussed in an answer of mine here which also touches on biochemical energetics. Or what?

As OP suggested, was correct. From Stryer Biochemistry, https://www.ncbi.nlm.nih.gov/books/NBK22374/

"the binding of a nucleoside triphosphate (NTP) to DNA polymerase induces a
conformational change, generating a tight pocket for the base pair
consisting of the NTP and its partner on the template strand. "

Further, as Mike Serfas answer states, "Enzymatic reactions are inherently reversible. If you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs also. " This was also a good anwer to the question, since the OP had not considered that. The OP associates is with how the substrate for translation from RNA to proteins in ribosome is not amino acids but tRNA + amino acids.
Then, as some angry comments from some random person mentioned, and the good answer from Mike Serfas also mentioned, and, the standard explanation (but, not what OP was fishing for, OP was looking more in-depth) always focuses around, entropy etc.
There was nothing wrong with the question, no formally legitimate reason to close it. It helped the learning process of the OP, and potentially others that acesss this collaboratively generated content on this public Q&A site.

So what question does this statement answer? A change in conformation of the enzyme may be involved in binding dNTP, but the question was "What are main reasons triphosphate structure is used?". Enzymes adapt to substrates, the structure of which are determined by chemical and evolutionary factors, not the other way round.

Questions of "why" in biology are not completely proper - evolution simply happened that way, and the reasons we suggest are rationalizations that may not encompass the "real" reason.  Still...
Enzymatic reactions are inherently reversible.  If you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs also.  Plus, there's "entropy" to consider, which is to say, if you pop off an XMP it goes flying off into the solution, it's a lot harder to round it back up again. Last but not least -- we're talking about DNA here.  Every time DNA is degraded, even if the other strand is still intact, there is some chance that some mutation will occur with harmful effect.
All this can be set right by wasting a lot of energy every time DNA is extended.  We snip off two phosphates - a pyrophosphate which is rapidly broken down by pyrophosphatase.  The way equilibrium works, that second step pulls the reaction forward because it makes sure there is no pyrophosphate left lying around.  Even if a freak surge of thermal energy at the level of molecular vibration would allow the enzyme to reattach it, the pyrophosphate no longer exists.

"f you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs" good point, had not thought of that. In ribosomes transfer RNA would also fill same role I guess.