text:
What causes the activation of "Late acting deleterious genes" in late age but not in young age, whose accumulation causes ageing according to Medawar?
Sir Peter Medawar proposed that aging is the byproduct of "late acting deleterious genes". Evolution is good at weeding out genetic mutations that are harmful at an young age, before the organism has a chance to reproduce, because the organism will not survive to pass on those genes (genes that are weeded out are genes that reduce fitness, confer disability and generally reduce chance of living long enough to reproduce). However, genes that exert their effect at a later age pass through the sieve of natural selection, because natural selection cannot act on them. According to Peter Medawar it's the accumulation of such late acting deleterious genes that causes aging.
I have two questions: What kind of "genes" are we talking about (whose accumulation in late age and its deleterious effects lead to ageing)? Genes with some essential function at young age: such as genes involved in reproduction, survival, functioning of organs etc - or "neutral" selfish genes (i.e genes that are "neutral"or have non-essential functions during the organism's youth, but individually  mildly deleterious  during late age) that kind of "hitched a ride" to the next generation? These kinds of "neutral genes" could arise over evolutionary time simply due to genetic drift?
Second question: What causes these late acting genes to become activated at late age (but not at young age)? Epigenetic landscape in late age, internal biochemistry? Is there any experimental evidence, and examples of such genes? I am guessing they are mildly deleterious on their own but collectively debilitating.

Austad, Steven N., and Jessica M. Hoffman. 2018. “Is Antagonistic Pleiotropy Ubiquitous in Aging Biology?” Evolution, Medicine, and Public Health 2018 (1): 287–94. https://doi.org/10.1093/emph/eoy033.

It's not that genes become 'activated' at late age, but that they aren't relevant until late age, so high performing versions aren't selected for and poor performing versions aren't selected against. As for which genes, we can see some in the answers to another question,
What is the longest-lasting protein in a human body?
The accepted answer is crystallin, in the lens in your eye. These proteins eventually cross-link and degrade, leading to cataracts and blindness, which decreases fitness. Newts can regenerate their lenses, and more stable versions that take longer to degrade could presumably exist, so it's biologically possible to avoid this loss of fitness. However, doing so wouldn't affect the fitness in the first ~50 years of life, so selection can't maintain those mechanisms against genetic drift.
Crystallin is one example of long-lasting proteins, and those are just one example of how genes can have fitness costs that don't reveal themselves until late in life. When 'accumulation' is used in the context of Medawar's hypothesis, it refers to the accumulation in the population over many generations of these late-acting mutations, because natural selection can't remove them the way it can early-acting mutations.

Maybe more precisely, it isn't that the genes aren't relevant until late age, it's that the deleterious effects aren't relevant until late age.

I went back + forth on how to phrase that, and decided to be more focused on the OP's misunderstanding. Also, if we think of, e.g. "a gene to regenerate crystallin", it doesn't exist because it wouldn't be relevant to fitness until late age

That's fair; I agree we do not need to get into all the detailed debates about what exactly a "gene" is for this Q&A.

I thought that it was mutations accumulated throughout life that affected genes. Which genes are responsible for ageing, and whether they are activated or their product is just changed, I have no idea, but I find an answer solely in terms of damage to long-lived proteins very constrained. Could you cite references that this is the modern interpretation of Medawar's hypothesis, and perhaps mention other ideas about ageing.


text:
Is it true that all spiders are venomous?
This is a factoid I heard as a kid at some point, probably on a playground somewhere, and just accepted without question in the way that children do:

All spiders are venomous, but most of them aren't venomous enough to harm humans.

(I'm pretty sure the wording used was actually "poisonous", because the distinction between venom and poison is a little too technical for a nine-year-old, but I understood it at the time to mean what I now know is called "venomous".)
Is this true? Are all spiders venomous? Or is this just one of those made-up "facts" that circulates playgrounds and campsites?

If threre are herbivorous spiders, then no, not all spiders have venom.

@anongoodnurse I have never heard of herbivorous spiders. Are there some? That also doesn't mean they don't have venom for self-defense or just vestigially, either.

There is an herbivorous spider, yes, Bagheera kiplingi. It may have been too subtle, but my point was, you should have researched this a bit before posting.
We get a lot of "I heard..." questions here, which is rarely a reliable source.

@anongoodnurse I did look it up, but the state of search engines right now means it's hard to find anything, especially anything debunking common misconceptions and playground rumors (you're more likely to get some LLM arguing that they're true).

Um... I don't believe you're correct. I'll leave it at that.

Try (not for herbivorous spiders): Uloboridae.

@anongoodnurse Bear in mind that I'm an electrical engineer, not a biologist or zoologist or anything, and I almost certainly don't know the right terms to make a search engine give me actual scientific articles and not "10 cool facts about spiders you won't believe" repeated a million times. Yes, I'm exaggerating, but it's hard to find information that's actually reliable these days.

https://s3.amazonaws.com/scschoolfiles/552/non_venomous_spiders.pdf

@NilayGhosh Beware of the information in  your link, it states they are non-venomous, but that is incorrect in absolutely every case listed there. They may have venom insignificant to most humans, but that's a different thing.

@anongoodnurse: B. kiplingi aren't 100% herbivorous, though, and will sometimes hunt e.g. ant larvae. I couldn't confirm with a quick Google search whether they have venom, but it seems that most jumping spiders (Salticidae) do and use it as a key part of their hunting method, so there's a decent chance that B. kiplingi have also retained the trait.

I would add that the venom of many (most?) spiders is technically dangerous indeed to humans, but because it is administered in such a small dose, it is not efficient. Also, while all spiders can bite, most of them won’t bite humans (except in rare cases of extreme self-defence), as they “know” their fangs are not long enough to pierce the skin. (In Québec, no spiders are harmful to humans, although we are starting to see some Latrodectus mactans—the (in)famous black widow spider.)

@IlmariKaronen - I've read that the way they 'eat' ant larvae has never been explained. However, that wasn't really my point. I guess subtlety is not my forte. I had (erroneously) assumed all spiders were venomous as they prey on animals.

@PierrePaquette Is it true that many spiders' fangs are too short to pierce human skin? That's another thing I heard on playground rumors (usually in the form of "(whatever spider species they just saw) is the most poisonous spider but it's harmless to humans because its fangs are too short"; I expect the "most poisonous spider" part is wrong, but I'd never realized the "fangs are too short" part was actually true. (The spider in question in that rumor was usually the daddy longlegs in my experience, which I know isn't even a spider.)

@Hearth: I would almost say that most spider’s fangs are too short, as there are multiple species of very small spiders—those I find in my apartment rarely exceed 2–3 mm in body length (when measuring a spider, only its body length is considered). Those definitely have fangs that are too short to pierce human skin! Even a black widow’s fangs are only about 1 mm in length: long enough to pierce skin, but it would rather run away than bite someone! (This does NOT mean you should try to manipulate them!) Only larger spiders have fangs that are long enough to pierce human skin.

@Hearth There are three different kinds of creatures that are called "daddy longlegs".  One of the three is a spider.

Note that "factoid" means something that looks like a fact but isn't, which in this case is indeed accurate.

@OrangeDog https://www.merriam-webster.com/dictionary/factoid both "an invented fact believed to be true because it appears in print" and "a briefly stated and usually trivial fact" are definitions.

I searched Google for "non-venomous spiders".
The first result that came up was Uloboridae (Wikipedia):

Uloboridae is a family of non-venomous spiders, known as cribellate orb weavers or hackled orb weavers. Their lack of venom glands is a secondarily evolved trait. Instead, they wrap their prey thoroughly in silk, cover it in regurgitated digestive enzymes, and then ingest the liquified body.

However, non-venomous spiders are atypical, and it is true that most spiders that humans don't consider harmful are still venomous to their prey; the playground statement is a reasonable approximation.

I don't know why this got a downvote; it definitely answers the question. Have an upvote. It didn't occur to me to use that specific search term; I just tried "all spiders poisonous", "is it true that all spiders are poisonous", and so on--which didn't turn up any useful results.

@Hearth Which makes sense, because being poisonous is not the same as being venomous. Venom is injected, poison is ingested or touched, so for example Pitohui dichrous is poisonous but not venomous, while Acharia stimulea is venomous but not poisonous, despite physical contact being the hazard for in both cases.

@AustinHemmelgarn I didn't really realize that "venomous" would be the correct term until I was typing up the question here, yeah. It's not a distinction that comes up often when working as an engineer!

You know, after this description I have decided that I actually prefer the venomous spiders ;-).

Considering that all spiders inject digestive acids into a prey, the method and speed of the venom is debatable. Here's an interesting spitting spider: https://www.youtube.com/watch?v=vUUm2OCMCzY they catch their prey by spitting a fluid that congeals on contact into a venomous and sticky mass. The fluid contains both venom and spider silk in liquid form, though it is produced in venom glands in the chelicerae. The venom-laced silk both immobilizes and envenoms prey such as silverfish.  https://en.wikipedia.org/wiki/Spitting_spider found in America.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
Can someone with a positive test line and a negative control line in a Covid lateral flow test be Covid-negative?
If someone does a Covid lateral flow test and the control line is not visible, the test is invalid regardless of the visibility of the test line. A missing control line could be due to insufficient buffer volume or damage to the membrane coating in the area where the control line should appear. In either case, the visible test line would be true-positive. Is there a scenario where the test line is visible, but the control line is not visible, and the sample is Covid-negative? If so, how does this work on the molecular level?

I’m voting to close this question because it is a question about the interpretation of a clinical test, and not about a problem in biology.  It may be appropriate for our sister site, SE Medical Sciences

@David I'm not asking for the clinical interpretation of the test. This is something I already know. I am asking about how such a result can occur on the molecular/technical level.

Indeed, but that is neither a problem in biology or a in a laboratory research technique. It  is about the operational details of proprietary clinical tests, which falls within the remit of the newer SE site I mentioned. Please move it there.

If someone does a Covid lateral flow test and the control line is not visible, the test is invalid regardless of the visibility of the test line.

Your first sentence is your entire answer. If there's no control line, one or more of many possible issues have occurred, making that test's results null and void. The test should be rerun using fresh reagents 100% of the time. That's it. Without control, you cannot trust the appearance (or lack thereof) of the test line.
The same is true in laboratory settings. If I'm running an assay and my control doesn't work, I toss the entire thing and start over.

As far as how this could happen, as I said there are many possibilities, some of which could have influenced others. Typically the tests are arranged so that the buffer reaches the test area first, then the control area. As you say, lack of a control line could indicate that there was not enough buffer present to successfully diffuse the detection reagents to the control area.
However, you claim that the sample is supposedly "COVID-negative". I would first question how that conclusion was arrived at. PCR testing is the gold standard, and viral load can change relatively quickly in the body, so unless both types of tests were performed at the same time, you can't draw any conclusions about presence or absence of detectable levels of SARS-CoV-2 in the lateral flow test.
Let's assume, for the sake of argument, that the sample truly is negative for SARS-CoV-2. The most likely cause of this test pattern is some sort of manufacturing deviation, most likely several that worked together. Multiple possibilities come to mind - incorrectly formulated reagents, reagents being applied to incorrect areas of the strip, damage to the strip itself, possibly leading to the removal of the detection reagents, and so on. Most if not all eventually lead to human error of some sort, whether it is imperfect quality control, lack of verification/validation of all manufacturing steps, machines not working properly due to lack of maintenance, etc. An awful lot of complexity goes into producing these tests, and there are many steps where errors can occur. Without having access to the test strip in question and the manufacturing facility itself, it is impossible to definitively identify the cause(s) of the erroneous result.

I'm aware of how it should be interpreted. I'm interested in how this (positive test line, negative control line) can happen on the molecular level of the test, and whether/how this can happen if the sample is Covid-negative.

@AnjaM my apologies. Please see the edited answer above.

Thanks, this answers my question! As a context: The sample was indeed Covid-positive, as confirmed by another test. I wondered about the theory behind this since the manufacturer claims that a T-line without a C-line is not a valid test, but I couldn't think of a situation how a sample with a T-line would not be positive (except for if additional errors happened, like you listed - but they wouldn't influence the C-line). So in the case of T-line positive, it seems to me that chances of the sample being positive are the same independently of the C-line being visible or not.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
How is the Gibbs Free energy of Redox reaction during Electron transport of the Mitochondria utilized to pump protons across mitochondial membrane?
I understand basics of the electron transport chain..that electrons "donated"  from NADH and FADH2 moves through redox centers within respiratory complexes I,  III, and IV (II is not involved in proton pumping)..Each step releases some energy..How is this energy harnessed by the respiratory complexes to pump protons across the mitochondrial membrane (against the gradient) to build up the Proton Motive force (which is ulitmately used by ATP synthaze nanomotor)?*.
Does  the Free energy  cause  conformational changes in the Respiratory protein complexes*, and the conformational changes ultimately pumps protons against the gradient? Does the details of  how the    Free energy is utilized depend on the Specific respiratory complex?
I am looking for a mechanistic explanation how the energy of redox reaction  is harnessed to pump protons against the gradients.

There are a number of questions in your post, which would require a fairly long answer. Please use the [edit] function to concentrate on the most important question, as the policy in SE is one question per question (more within reason if strongly related, some of which aren't in yours.) Thanks.

For the mechanistic part of your question, a good place to start might be Paul D. Boyers' Nobel lecture Energy, Life, and ATP

I suggest you read a biochemistry text book. I would recommend Berg et al, and an old edition will suffice. You can pick up the 5e second-hand for about £5 on eBay (a search for Stryer Biochemistry gives more results).


text:
Is the Mycetozoa phylum part of Amoebozoa or Protozoa kingdom?
I'm not sure if the two kingdoms are essentially the same thing. I was looking at mushroom data collected by citizen scientists, and a lot of the data is labeled as belonging to one of three kingdoms: fungi, protozoa, and amoebozoa. However I don't really understand the difference between protozoa and amoebozoa.


text:
How can I determine statistical significance in seed length and width measurements?
I am researching seed size variation in cereals. I used ImageJ to measure the seeds and generated arbitrary values. Later I converted the measurements to micrometers. I took length and width measurements of 151 unique accessions of single cereal species. I measured ten seeds per accession and generated a mean. I have summarized the mean values by length and width of the ten smallest, medium, and largest seeds. I have calculated SD and SE. In GraphPad, I have grouped these into three data tables and summarized them into one summary figure. I would like to determine if there is any significant difference between the different accessions.
I am unsure of how to best conduct this analysis. I am looking for any suggestions!
Thanks!

If this question is more about statistics (which I strongly suspect), it would probably be a good idea to migrate it over to statics.stackexchange: https://stats.stackexchange.com/.

I’m voting to close this question because it belongs on Cross Validated

I will repost in stats.stackexchange. Thanks.


text:
Nernst Equation and Membrane Potential
I am a bit confused on how to use the Nernst equation to determine polarization.
I saw in the textbook that if potassium channels were open in a neuron cell, there will be a net diffusion of $\ce{K+}$ out of the cell, making the membrane potential more negative.
However, if you use the Nernst equation
$$V = \rm 62\;mV\times log\left(\frac{[ion]_{outside}}{[ion]_{inside}}\right),$$
it seems that the potential become less negative if there is a net diffusion of $\ce{K+}$ out of the cell.
For example, if we had 6 $\ce{K+}$ ions inside and 2 $\ce{K+}$ outside, and the channel opened, increasing the extracellular $\ce{K+}$ count to 3 and the intracellular to 5. Doesn't this lead to a less negative value?
I am having difficulty where I am going wrong with this. I saw other posts regarding this question, but I do not understand the explanation.
Is there an easier way to understand why this change doesn't correlate with a more negative potential?

Possible duplicate: https://biology.stackexchange.com/questions/57064/why-is-it-possible-to-calculate-the-equilibrium-potential-of-an-ion-using-the-ne/57066#57066 (probably should have pointed to this one rather than answering; I can remove my answer if it's agreed this is a duplicate)

Are you just counting up the potassium ions and subtracting them? Don't do that! That's not how it works. Potassium ions don't just exist by themselves, they come paired with negative ions of some sort which dissociate in water. There are lots of other ions of various charges too, we're just ignoring them all because the only ones that matter are the ones that can move.
In your story, a potassium ion has left the cell. A potassium ion has positive charge. When positive charge leaves the cell, what is left behind is more negative, not more positive.
Potassium ions will keep leaving down the potassium concentration gradient because all things tend to move down their concentration gradients. But as positive charge leaves the cell, potassium ions that leave are moving both down their concentration gradient (to lower concentration) and up their electrical gradient (toward positive charge). So, how do you know when those two forces will balance out?
That's what Nernst tells you: the voltage where a given concentration difference will be balanced so no more net flow of that ion occurs. That's what equilibrium means.
If you're thinking that after some ions move, you need to re-calculate the Nernst equation, that's not correct. For one thing, the ion concentrations don't actually change that much: very few ions have to actually move to change the voltage a lot and halt the flow of ions. For another, you can't ignore the ions that have already moved: the voltage they've created is already there and needs to be accounted for.

I think the OP was thinking that the outside of the cell is charged negatively relative to the inside, that's why they are confused.

@DamocleDamoclev Could be. I think it's more likely that they keep recalculating the Nernst potential after ions move, rather than using Nernst to understand when ions stop moving. The linked duplicate explains that not many ions actually move so it's not necessary to recalculate.


text:
Sequencing a PCR product with no band
I did a PCR that successfully showed the appropriate bands one time, but when I tried to re-do the same PCR just at a larger quantity to send for Sanger sequencing, very faint or no bands were seen. This same primer set has been used successfully for larger quantities before, it may be possible that the issue is in the gel. I cannot afford to run any more gels with this product, so my question is; how important is a visible band for Sanger sequencing? Will sequencing fail with a faint band?

How much did you scale up your reaction? How much do you usually scale up (2x, 5x, 10x)? Do you have any other way to measure DNA concentration reliably?

So for the functioning PCR reaction, the total volume was 10µl; 0.25µl each for forward and reverse primers, 2 µl of 5x premade mastermix (including the dNTPs, Taq polymerase, MgCl2, dye, etc), 5.5µl PCR grade water and 2µl DNA. The upgraded one was 25 µl, 0.5 each for the primers, 5µl of the mastermix, 17µl water and 2µl DNA. Do you think the DNA volume is a problem? It never caused issues before

As for the DNA concentration, we do have a nanodrop machine but it isn't exactly reliable

It looks like you're using the same amount of template DNA in your scaled up reaction as your smaller one ( 2µl), which essentially means it's at a lower starting concentration. Assuming the same number of cycles, you would ended up with the same amount of amplified product, just in a larger volume, which could be why the bands are faint in the larger one (though, that level of dilution shouldn't be enough to make a band disappear completely).

Not really responding to the issue but: agarose responds very well to remelting many times, if all I'm doing is looking for bands and not gel purifying, I used to reuse the same agarose to pour new gels dozens of times until it got really gross. Granted, this may not work so well for precast gels. My opinion: if you haven't evaluated it on a gel I'm not sure that it's a good idea to sequence.

Thanks, and while the template amount staying the same has not affected it before, I will try to increase it next time. And by not affording to test any more, I had meant I needed to retain a certain amount of the PCR product to send for sequencing, so I had no more left to run gels with. However, the remelting of gels sounds useful, how do you erase the previously added PCR samples from it?

@Nalonda understood. btw tagging with a "@" is necessary to notify us. Why can't you simply repeat the PCR with more template and use that? Are you out of template? As for remelting, once you remelt the DNA diffuses/degrades over time. Any particular band will still be brighter than background for visualization purposes. However the DNA doesn't get erased so you shouldn't purify from it! and it could contaminate e.g. your gel rig if post-pcr contam is a concern. You might consider having one gel rig for this and then a separate dedicated "clean" one.

@MaximilianPress Thanks, I just joined Stack Exchange so I didn't know. And also thanks for the gel tips! As for the PCR, I'm trying to keep the number of times I repeat the PCR to a minimum as I want to make sure there is enough of the other components left for a bigger project I have coming up. Anyway I have my answer now, so appreciate it!

In your original post you asked if the failure to detect the expected amplified product could be due to the gel.  What issue with an agarose gel would reduce the yield of a PCR product?


text:
What could those shiny spots on the walnut kernels be?
I bought the shelled walnuts — many were mouldy — but those small round reflective spots don't look like mould (ascomycetes). It reminds more of E.coli colonies. I couldn't find anything on the net about that.
I would like to know how to isolate or stain that, since I have some access to the lab.


text:
Can you store 5% BSA, in TBST, in -20C?
I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means of storage, but I've found online that people recommend just 4C. Would -20 and freezing harm the potency of BSA? I haven't observed precipitate so I haven't assumed so, but perhaps there are other consequences..

The question is, if freezing is necessary. I usually made small batches and kept them in the fridge. I also made sure to not store them too long to avoid contamination.

Have you had anomalous or unexpected results from your Western blots?  If you do positive controls and negative controls and they are well-behaved, then I would infer that freezing the blocking agent has not been detrimental.  If the blocking agent is not doing it's intended job, then I would predict higher or unacceptable background on a Western.  You can use many different non-specific proteins, e.g., casein, gelatin, in addition to BSA.


text:
Trying to identify a plant by its root
My kids were digging through a pile of dirt I had made for them to play with (my son wants to do bike jumps off it) and they brought in the attached root. I never got to see what kind of vegetation was growing from it, and the kids can't remember what it looked like.
This is from our backyard in central Texas.
The closest I have found was potato dandelion but there are very little picture references to this.


text:
What is the optimal pO2 concentration for automated reactor batch mode EColi expression?
I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? As a rule of thumb?  I guess Iower 20 % is bad because it will limit growth. On the other hand I would assume too much oxygen will also be harmfull for E. Coli. Which level is too high? 40, 80, 100 %? Or is as high as possible always best? I would check this with an OD curve, right? What would happen to an culture when the oxygen is too low (1-2 % ?) for an longer amount of time? Would the bacteria just die or just decrease in activity? In my current culture I used TB media with Bl21 3DE at pH 7 and 37 degrees.. Oygen levels were controlled by gasmix, gas flow and stirrer speed.


text:
Cell culture disasosiation
I am doing to passaging cancer cell ( Dld-1 Cell line). Trypsination was conducted with 0.25 trypsin-edta 1 ml to t-flask 25 in 2 min. Then I add 6 ml complete media (have 10% FBS for inactivated trypsin. Cause queue in sentrifuge, my Cell is at solution for 40 min, this is clear for my Cell? How long cancer cell can survive in trypsin and complete media (1:6) solution in room temperature (not incubated).


text:
Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?
Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for "variable heavy domain of heavy chain". I assume the reason for this name is that the variable domain in the heavy-chain camelid antibody is heavier than other domains. However, I haven't been able to find the weight of each domain in the camelid antibody in order to verify my assumption.
Why are single-domain antibodies derived from camelids called "variable heavy domain of heavy chain"?

Do you know how "normal" antibodies are composed?

@Chris thank you for your reply. I am familiar with how normal antibodies are composed but I am not an expert in immunology. Normal antibodies have two heavy chains and two light chains, whereas camelids also possess antibodies with two heavy chains. The VH domain of the heavy chains of normal antibodies is somewhat equivalent to the VHH of the chains of a camelid antibody. I don't understand where the second "H" in VHH comes from, and I was wondering if it comes from the fact that the VHH domain is bigger/heavier than other domains in the chains of camelid antibodies. Thanks!

Apologies. Quite frequently computing scientists enter bioinformatics without realizing the need to acquire the background molecular biology. Clearly this is not your situation. I was misled by your suggestion of the VHH domain being "heavier", which doesn't make sense to me. However I agree the additional H in the nomenclature is strange. I'll see if I can track it down.

No problem @David, I could have made my question less ambiguous to reduce confusion. Thanks a lot!

First, the definition of VHH (and VH) from the article by S Muyldermans
— “Nanobodies: Natural Single-Domain Antibodies” in Annu. Rev. Biochem. 2013. 82:775–97.

VHH: antigen-binding variable domain of the H chain of heavy-chain
antibodies

VH: the variable domain of the heavy chain of
immunoglobulins

So the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.
Why use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess both ‘normal’ antibodies composed of heavy and light chains, as well as these special ones with only heavy chains. This is shown in the diagram below, adapted from the original Nature paper describing these antibodies. It actually uses VH in both cases:

So one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.

In conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) Heavy-chain antibody”.


text:
Is there a way to isolate bacteria from a bacteria/phage plaque in order to PCR bacteria only?
I am writing a paper for a class that involves a mock grant proposal. I am looking at an experiment which requires sequencing of host DNA from a virus/host model, and am having a hard time finding a protocol which keeps bacteria as opposed to phage. From what I'm seeing, my two options for separating the phage and bacteria are either centrifuging or filtration, neither of which keeps the bacteria. Am I missing something?

What specifically are you trying to learn about this hypothetical system by conducting the experiment? You presumably already have the bacteria available in pure culture. That's what the plaques are forming on. If the phage are lytic then the infected bacteria are mostly lysed by the time plaques form.

make the PCR primer only bind to DNA found in the bacteria?

I think you may be confusing some of the terms.  On can only see, or visualize a phage plaque, if you have added an aliquot of infective phage to a growing bacterial culture, and then mixed that together with molten agar in the pour plate method.  As the bacterial lawn grows, the plaques are where the phage particles are either killing (lytic growth, like phage T4), or retarding (non-lytic growth like phage M13) bacterial growth.  If you are growing lytic phage and there are bacteria in the plaque, then those are bacteria that are resistant to that phage.

Some phage, like phage lambda, are capable of lysogenic growth, so they are integrated into the host chromosome like a hitch hiker and are basically dormant, until they are induced.  Depending on growth conditions, after induction they can grow lytically.  If you add lysogenic phage to a bacterial lawn, then the resulting plaques are said to be turbid, because there are some immune bacteria, growing in the middle of the plaques (i.e., lysogens).

Electrophoresis will separate DNA by size.


text:
Can a deletion occur on only one strand of a human chromosome?

Hello. Is it possible that a deletion can occur in the middle of only one strand of a human autosomal chromosome?

When people say "strand" in DNA, they refer to one sugar-phosphate backbone with one series of nucleotides. DNA is typically double stranded and RNA is typically single stranded. But when you talk about a "chromosome pair", you're not talking about a pair of strands, you're talking about a pair of chromosomes. Each chromosome is double-stranded. So, what do you actually mean in your question?

I have altered the question title from "Can a deletion occur on only one strand of a human chromosome pair?" by deleting the word "pair".  This matches the version of the question in the body and makes the most sense as a question.  It is also the question that had been addressed by the two answers that had been posted at the time I made the change.

This is a somewhat semantic question. In terms of WHEN a deletion happens, I think it's commonly on only one strand as most mutations are caused by a collision from radiation or sometimes a chemical.  That will typically only affect one base.  BUT there are repair mechanisms that come in and can cause a deletion on both strands or repair the damage.  In the long term the repair mechanisms work pretty hard to make sure both strands are the same in the end.

As it appears that most deletions occur by mechanisms that do not involve large-scale strand separation (e.g. during crossing over or by translocation etc.) this is unlikely to happen (see e.g. Wikipedia article). These vary in length from perhpas a dozen base pairs to thousands or more, and differ from mutations caused by radiation and chemicals.  Any small deletions on one strand (e.g. at single-strand breaks) need to be filled in if replication is to occur.


text:
Why is the maximum propotion of MII 2/3 in the ordered tetrad analysis? How is it different from normal recombination?
My textbook says that the maximum propotion of MII gametes in the ordered tetrad analysis is 2/3, and if we put it into the formula RF(recombination frequency)=MII/2(MI+MII), we can find out that the maximum RF is 1/3, instead of 1/2. The textbook persumes that each of the 4 gametes(actually 8) are randomly dominant or recessive, and gives a perfect provement, but I wonder if the persumption really exists.
I've found out that four-strand double crossing over provides 4 recombined gametes, while it's MI in this model, which may make the calculated RF smaller than real RF, but I can't figure out why it is 1/3 from the aspect of exchange and recombination.
My textbook:Genetics:Analysis of Genes and Genomes
Maybe my English isn't very good:(


text:
Water-soluble vitamins involved in amino acid metabolism in the citric acid cycle
I have never seen anything comprehensively written about the vitamins necessary to metabolize amino acids through the citric acid cycle and gluconeogenesis pathway other than the following diagram written in Japanese. (I added the English translation) The source for this was created by a Japanese health food manufacturer(https://www.orthomolecular.jp/nutrition/vitamin_b/), so it's not completely reliable, but I'm looking for a well-organized diagram like this one.

The abbreviations for vitamins are as follows. However, the active forms of the vitamins are not distinguished, for example, TPP is vitamin B1, FAD is vitamin B2, NAD+ and NADPH are Niacin.

B1: Vitamin B1
B2: Vitamin B2
N: Niacin (vitamin B3)
P: Pantothenic acid (vitamin B5)
B6: Vitamin B6
Bio: Biotin (Vitamin B7)
F: Folic acid (Vitamin B9)
B12: Vitamin B12
C: Vitamin C

The above figure may be summarized as sentences as follows;

(1)Enter the citric acid cycle via pyruvate : Gly, Ala, Cys, Ser, Thr, Trp

Glycine becomes alanine, cysteine, serine, or threonine with the help of folic acid.
Alanine, cysteine, serine, and threonine are converted to pyruvate with the assistance of niacin and vitamin B6.
Vitamins required for the process of converting the Tryptophan into Pyruvate are not mentioned in the figure.
For(1), this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference.(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%83%A9%E3%83%8B%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AA%E3%82%B7%E3%83%B3%E3%80%81%E3%82%B7%E3%82%B9%E3%83%86%E3%82%A4%E3%83%B3%E3%80%81%E3%82%BB%E3%83%AA%E3%83%B3%E3%80%81%E3%83%88%E3%83%AC%E3%82%AA%E3%83%8B%E3%83%B3)

(2)Enter the citric acid cycle via α-ketoglutarate : Gln, Arg, His, Pro,Glu

Glutamine, arginine, histidine, and proline are converted to glutamic acid with the help of niacin, vitamin B2, vitamin B6, and folic acid.
Glutamate is converted to α-ketoglutarate with the help of vitamin B6 and niacin.
For(2),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference.(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%83%AB%E3%82%AE%E3%83%8B%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AB%E3%82%BF%E3%83%9F%E3%83%B3%E3%80%81%E3%82%B0%E3%83%AB%E3%82%BF%E3%83%9F%E3%83%B3%E9%85%B8%E3%80%81%E3%83%92%E3%82%B9%E3%83%81%E3%82%B8%E3%83%B3%E3%80%81%E3%83%97%E3%83%AD%E3%83%AA%E3%83%B3)

(3)Enter the citric acid cycle via succinyl-CoA: Met, Ile, Val

Methionine is converted to succinyl-CoA with the assistance of F, B12, P, and N.
Isoleucine and valine are converted to succinyl-CoA with the assistance of N and B1.
For(3),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference
For the methionine:
(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%83%A1%E3%83%81%E3%82%AA%E3%83%8B%E3%83%B3)

For the Isoleucine and Valine:(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A4%E3%82%BD%E3%83%AD%E3%82%A4%E3%82%B7%E3%83%B3%E3%81%A8%E3%83%90%E3%83%AA%E3%83%B3)

(4) Enters the citric acid cycle via fumaric acid :Phe, Tyr

Phenylalanine is converted to tyrosine with the assistance of N.
Tyrosine is converted to fumaric acid without the need for special vitamin support.
For (4),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference;
(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%83%95%E3%82%A7%E3%83%8B%E3%83%AB%E3%82%A2%E3%83%A9%E3%83%8B%E3%83%B3%E3%80%81%E3%83%81%E3%83%AD%E3%82%B7%E3%83%B3)

(5) Directly to oxaloacetate: Asp, Asn

Asparagine and aspartic acid transfer to each other without the aid of specific vitamins.
Aspartic acid is converted to oxaloacetate with the help of vitamin B6
For(5),this is also written only in the Japanese Wikipedia, but since chemical formulas are universal, I give it as a reference;(https://ja.wikipedia.org/wiki/%E3%82%A2%E3%83%9F%E3%83%8E%E9%85%B8%E3%81%AE%E4%BB%A3%E8%AC%9D%E5%88%86%E8%A7%A3#%E3%82%A2%E3%82%B9%E3%83%91%E3%83%A9%E3%82%AE%E3%83%B3%E3%80%81%E3%82%A2%E3%82%B9%E3%83%91%E3%83%A9%E3%82%AE%E3%83%B3%E9%85%B8)

(6) Enters the citric acid cycle as acetyl-CoA  (i.e., as a “ketogenic amino acid”)
Ketogenic only :leucine, lysine
Also glucogenic: isoleucine, tyrosine, phenylalanine, tryptophan, threonine

Tryptophan and lysine are converted to acetyl-CoA with the help of B2, P, N, and B6.
Of those exclusively ketogenic, it is not written about what vitamins are needed in the process of converting leucine to acetyl-CoA.
Of those that are also glucogenic, it is not written about what vitamins are required in the process of converting isoleucine, tyrosine, phenylalanine, and threonine to acetyl-CoA.

This is a long introduction, but what I want to accomplish in this thread are as follows;
My questions

What are the Vitamins required for the process of converting the Tryptophan into Pyruvate?
What vitamins are needed in the process of converting leucine to acetyl-CoA?
What vitamins are required in the process of converting isoleucine, tyrosine, phenylalanine, and threonine to acetyl-CoA?
If you notice, I would also like to know if there are any facts that are critically missing or apologized for in the above diagram or summary in terms of amino acid metabolism in the citric acid cycle.

FYI: I could not find any articles written in English that was compact enough for my purposes. Therefore, I would like to share the content of a Japanese university's website with minimal annotations;http://www.sc.fukuoka-u.ac.jp/~bc1/Biochem/amino_met.htm
(1) Groups that enter the citric acid cycle via pyruvate: Gly, Ala, Cys, Ser, Thr, Trp

There is no mention of vitamins in the process of Ala → pyruvic acid.
ASP-(using NADPH2,NAD)→Thr→Gly-(using tetrahydrofolate)→Ser→pyruvic acid
Although not much has been written about Asp, it seems that it also enters the citric acid cycle via pyruvate.

(1)'Amino acids in this group other than alanine (Gly, Cys, Ser, Thr, and Trp) can also become succinyl-CoA.

All amino acids pass through threonine (except alanine)
Serine-(using THF) → Gly → Thr
ASP-(NADPH2, use NAD) → Thr
Thr is converted to succinyl-CoA with the assistance of NAD.
In the process of converting glycine to threonine, acetyl-CoA is produced as a secondary product.

(2) Group that enter the citric acid cycle via α-ketoglutarate: Gln, Arg, His, Pro, Glu

All amino acids pass through Glu
Gln becomes Glu without any special vitamin support
His becomes Glu with the assistance of THF
Pro becomes Glu with the assistance of FAD and NAD
Arg becomes Glu with the assistance of NAD
Finally, Glu becomes alpha-ketoglutarate (α-KG) with the help of NAD.

(3) Groups that Enter the citric acid cycle via succinyl-CoA: Met, Ile, Val

Valine and leucine, with the aid of NAD and FAD, go through similar pathways to methylmalonyl CoA, which is then converted to succinyl CoA.

(+1) For "There is no mention of vitamins in the process of Ala → pyruvic acid." Vitamin B6 (pyridoxal phosphate), surely?


text:
Plant growth regulators for Grape berry elongation?
I want to make a formulation for grape berry elongation, planning to use

GA3,
NATCA (N Acetyl Thiolidine Carboxylic Acid),
IAA (Indole-3-acetic acid),
IBA (Indole-3-butyric acid)

What else can I use?
Ultimate goal is to increase auxin level in plants.
All auxins are compounds with aromatic ring and a carboxylic acid group so will it be helpful to use carboxylic acids as a solvent with the above plant growth regulators?

While near everything from cosmology to psychology is about chemistry this way or another, chemists are rarely the best choice to ask about it. // I assume such a specific targetting is more matter of genetics than of growth regulators.

What research have you done?

Actually I am new to this site,

For any elongation like purpose for example elongation of sugarcane, apple, grape etc we use gibberellins.
You can get this result by just a single Google search.
My source: Biology NCERT Class 11 chapter 15 (2021 edition) and this site

Actually I am new to this site, I have used GA3 + NATCA N Acetyl Thiolidine Carboxylic Acid + IAA Indole-3-acetic acid + IBA Indole-3-butyric acid all these are dissolved in aceton & water. ok results, is there more pGRs I can use?


text:
Fridge vs freezer for short-term DNA storage – how long until freezer is better?
I know keeping DNA products in the freezer (-20°C) is preferred for long-term storage, but the downside is that freeze-thawing can cause shearing/breaking of the DNA. For short-term storage the fridge (+4°C) may therefore be better. But how short is "short-term"? I'm working with many samples of DNA products in several steps over the course of a few weeks (extractions, checking concentrations, PCR, cleanups, gels), and I can only do a few samples at a time. Questions is what I should do with the others in the meantime. If I keep them in the fridge to avoid freeze-thawing, the end-result may be that the samples spend these few weeks totally in +4°C (except for when I'm processing them at room temperature). On the other hand, I could save quite a few freeze-thaw cycles by having them in the fridge, because I'm doing something with each sample every few days. On the third hand... I'm working with amplicons (400-600 bp), so having long, intact DNA fragments is not really that important to me. I should also add that my DNA extracts are in water, not TE buffer.
So, at what point would you put these samples in the freezer instead? If we would generalize, how long until the "break-even point", when the degradation in the fridge can be comparable to the degradation from one freeze-thawing cycle?

The concern for freeze-thaw cycles is a bit overblown, I think, but it's hard to generalize. TE probably helps stabilize DNA, but any nucleases present will strongly contribute to degradation. If you're really concerned, I would check for myself by putting a dummy sample at 4 C and checking stability on a gel or bioanalyzer.

https://openbiotechnologyjournal.com/contents/volumes/V7/TOBIOTJ-7-10/TOBIOTJ-7-10.pdf


text:
What wavelength of light should I use to measure the absorbance of an anabaena population?
I am trying to use a spectrophotometer/colorimeter to measure the relative amounts of anabaena (cyanobacteria) in different samples.
What wavelength should I use to get the maximum absorbance?

Welcome to the Biology Stack. Please take the [tour] and visit the [help] for more information on this site and how it works. Please also note the homework page - so what have you found in the literature about measurements of Anabaena cell density using spectrophotometry? I can find the result within the first few papers on PubMed.


text:
How do I find the derivation for the formula for total clearance?
In Rang & Dale (10 ed) on page 152, the formula for total clearance is given by:
$$Cl_{tot}=\frac{Q}{AUC_{0-\infty}}$$
$CL_{tot}=$total clearance, Q=initial does given, $AUC_{0-\infty}$ Area under the concentration/time curve from time 0 to infinity. No explanation for this formula is given, at least not as far as I can see, it's just stated as some kind of obvious fact. How do I arrive at this formula (i.e, where is the derivation?), is it given by some kind of elementary rule?
I did consider posting in math.stackexchange.com but they didn't have tags for pharmacology.

In the version of the textbook I have access to, it says "See Ch 8 and Birkett 2002" - have you looked there?

I found an explanation on my own (see below), but thanks for feedbak.

Previously on that same page it says that:
$$Cl_{tot}=\frac{X}{C_{SS}}$$
Where $Cl_{tot}$ is volume of plasma cleaned per unit of time, X is the amount of drug supplied per unit of time and $C_{SS}$ is the plasma contentration at the steady state. This formula is quite similar to the one in my question, although that concerns a single bolus dose, not a continuous supply of the drug.
The first thing I needed to do was to realize that this too describes a unit of time. More precisely, it describes the time between o and infinity. If $Cl_{tot}$ is interpreted as the volume of plasma cleared of that drug between 0 and infinity, the formulae are almost equivalent.
The only remaining stumbling block is whether or not $AUC_{0-\infty}$ can be said to be equal to $C_{SS}$. In a philosophical sense you can, since that "is" the total "sum of concentrations" which the body has gotten exposed to between 0 and infinity. We can make this even more similar to the formula for continuous drug administration by assuming that "sum of concentrations" could probably be spread out evenly over the entire timeline, giving us a mean steady state concentration (which would then hopefully yield the same result).
There might be some incorrect formalities somewhere but this is what made sense to me intuitively.


text:
Hello, i was wondering if this is an isopod or a springtail

I want to make a terrarium so i was in need for a springtail is this it or is this something else

Springtails are generally about 5 mm (1/4 inch). Photo is too blurry for me to tell what that might be. Possibly a woodlouse.

I say the same, regular woodlice, 4 of, so, isopods.

Those are isopods. Springtails are hexapods.
Some of them are superficially similar, such as Podura aquatica:


text:
Anatomy of mature juice vesicles in hesperidium fruit?
What is the cellular structure of mature juice vesicles?
In a mature juice vesicle what cell types are present, how are they arranged and does this differ between species?

Can you provide any references describing what you mean? Why do you want to know? Editing your answer to add more information may make it easier to answer.

Sorry can’t find any references

In a mature juice vesicle what cells are present ,how are they arranged and does this differ between species

I have edited your question to include more info

I'd suggest taking a look at this paper linked through the wikipedia page. It has a variety of information about the structure and distribution of juice vesicles across different types of fruit e.g.:

The distribution of vesicles among segments
within the same fruit was similar (fig. 3). The un-
attached terminal ends of all vesicles exhibit a dis-
tinct orientation within the carpel; these terminals
point slightly toward the stylar end of the fruit. The
seeds within the segment are oriented so that the
chalazal end extends toward the stem end and the
micropylar end extends toward the stylar end of the
fruit.

Most citrus fruit possess roughly 130-400 ves-
icles per segment (table 1). Pummelo fruits contain
the most vesicles per fruit, followed in order of
decreasing vesicles per fruit by grapefruit, citron,
sweet orange, meyer lemon, papeda, lemon, sour
orange, mandarin, Satsuma mandarin, Citrus
miaray, trifoliate orange, Gabon cherty-orange, and
kumquat

etc. You should be able to answer most of your questions by reading that fully, but if there are follow up questions that come up, you should feel free to post another question.

What is the nature of the fluid filled cavity?                                            Is it a coenocyte? A schizogenous cavity? Perhaps a lysogenous cavity?

@Harrychink did you read the paper?

Indeed I did read the paper

If you are interested in the histology, I advise you to look on the first page at the section beginning with the sentence "To
summarize these past studies, juice vesicles are initiated just before or during anthesis as multicellular primordial bulges on the locular side of the endocarp surface usually on the radial wall." See also the cited references.

I am still unable to find the nature of the cavity

@Harrychink This is written quite clearly in there, I'm not sure what the issue is: The mature vesicles are elliptical multicellular sacs enclosed by a membrane, usually containing a minute oil gland in their center and connected to the segment wall by a multicellular stalk. What about that doesn't answer your question when you read the paper? There's a lot more information there about its development, but at some point you have to sit down and read closely for the details you're interested in, I'm going to reproduce them all here for you.

What types of cell compose the vesicle?

What is the nature of the central cavity

I still do not know what cells compose the vesicle or what the nature of the central cavity is.

@Harrychink I have given you a variety of paths to follow to answer your question, and I've put as much effort as I care to into this answer given that you have put very little effort into your own research. I know that you're dissatisfied that I'm not going and copying everything here to satisfy you, and you're free to exercise your various options to express that dissatisfaction.

Please provide a source explaining the nature of the central cavity and/or the types of cell present in the mature vesicle

I am having trouble accessing the articles


text:
Who put Cephalopoda in Mollusca?
Cephalopods are considered mollusks due to homologies such as a shell, a muscular foot, and a mantle. But, they also have closed circulatory systems, two giant eyes, and eight prehensile legs. When did Cephalopoda get classified as part of Mollusca? Also, in a case like this, is there a way to quantify homologies pointing to one classification vs. another?
In researching this question I came across this blog that states Linnaeus taxonomized Octopus and Octopoda in 1758, though there is conflicting information on Wikispecies here and here

The title of your question, asks “who”, its text asks “when”, but then answers that, but you actually seem to want to know “why”. It would be good if you could edit your question to clarify.

This seems more suitable for our sister-site, [hsm.se] as it's not about the biology itself, but about an action taken in times past by a person, committee or other body of people. Flagging for migration.

why focus on the differences and not the similarities like radula or circular brains, of course it hard to see how groups are related if you only look at the apomorphys.

Modern classification (cladistics) is according to common descent as the backbone for our entire understanding of biology, superseding previous classification schemes based on observed traits/features.
Cephalopods are mollusks because they share a common ancestor with other mollusks; if we want Mollusca to be a clade, it must include the cephalopods. If we didn't treat cephalopods as mollusks, we'd be missing part of the "family tree" and it wouldn't be a clade. We already have a separate name for them if we want to distinguish them from other mollusks based on the properties you describe: cephalopod.
Sharing features like a shell, muscular foot, and mantle are hints that there may be common descent rather than a means for classification by themselves in modern taxonomy.

cephalopods are inferred to share a common ancestor with mollusks due to evidence like homologies, or as you say, hints. i'm asking for the basis of that classification, who placed cephalopoda within mollusca, and when

@imrobert If you literally mean who, Cuvier: https://hsm.stackexchange.com/q/13664/13861 that question has already been asked and answered on the history of science site.


text:
Why are there error bars for zero concentration in some cell viability graphs, if they are assumed to be 100%?
Take these for example:

As far as I know, the formula for cell viability is % Viability = (Treatment OD - Blank OD) / (Control OD - Blank OD) where each OD is the average of three wells (technical replicates). Say I want to check the cytotoxic effects of increasing concentrations of a drug. The treatment wells in this case contain the drug, the vehicle, and cell medium for the rest of the volume. The controls in my experiment contain the corresponding amount of vehicle and cell medium but no drug. So to check 5 different concentrations of a drug, I have five controls containing the corresponding volume of the vehicle for each drug concentration, each of which is used to normalize the treatment groups (or alternatively, if I serially dilute the drug stock beforehand, one control group to normalize all treatment groups since all treatment groups will contain the same amount of vehicle). However, when I plot such an experimental design, I naturally get no bars for a zero concentration because the group does not exist. I may assume 100% for such a group for each trial and add them to the graph, but it would have 0 SD (and SE) since every value is 100%.
I tried to make a table for a design to make everything clearer:

Three plates with cells from different passages, so n = 3, each group is applied to three wells (technical replicates but their average is counted as one biological replicate). As you can see, you still get 100% from every trial for controls and their SD when plotted is still 0.
How then, do the researchers of these experiments get error bars for zero drug groups while at the same time normalizing their treatment groups to obtain a % cell viability? What sort of design do they use?

They're probably (incorrectly) assuming equal variance among groups. If you want to know what method they used read the methods section: what do they say? If they say nothing then they're not doing science.

In the shown data analysis your are taken average and standard deviation after normalizing. So evidently you will have mean = 100%,  std = 0.
You can take average and standard deviation in the raw data (1.87, 1.808, 1.787, mean = 1.821, std = 0.0352). Then you will have a non zero std in the control group. Then you can normalized by the control average (mean = 100%, std = 1.93%).

I doubt they're doing this, they're almost certainly normalizing before doing any statistical analysis. I think they probably don't understand the analysis they performed and are just reporting the output of their statistical software blindly.


text:
Given an F, R pair of SSR primers of 20 bp, which is the active portion of each
I'm a math & physics person with a general understanding of PCR. For my question, consider this F, R pair of SSR primers:
TTGTCCGTTTCTTATACAAT
TCTTTTTAGGCAGATGTTAG
It is my understanding that if the 1st sequence is annealed with chromatin DNA from our specimen that a PCR product of about 260 will form with instances of the 2nd in the sample, using Beckman Coulter hardware. Likewise, annealing the 2nd will produce products with instances of the 1st in the sample.
I also have been instructed that only a portion of each primer is involved in composing the PCR products. If true, how do I determine what it is? In addition, a citable reference would be appreciated.
Thank you in advance.


text:
Can placing a culture plate upright introduce contaminants from the lid?
Discussion
I have developed a habit of keeping culture plates always inverted, especially those of non-selective media. This precaution is followed after the poured plate is placed inverted in the incubator for 24hr to dry and test for contaminants. The reason is that I'm afraid when the plate is opened for streaking or subculturing, some contaminants might fall on the lid which is not given as much care as the dish itself when used for inoculation or subculturing: as the lid is kept on the bench underneath the bunsen flame. I fear that such possible contaminants might fall from the lid when the plate is kept upright on a surface, as I need when taking pictures of the cultures.
My fear might be right in theory, but i hope I'm missing something that would make such a scenario practically impossible.
Question
Can placing a culture plate upright, as for taking pictures, introduce contaminants from the lid?

Are you careful not to have your arms/hands over the lid when you inoculate your plate ?
If yes, then I would not worry. But the best way to know if you worked clean enough is to have a control handled in the same conditions (and non inoculated of course).
You said "the lid is kept on the bench under the Bunsen flame" right ?
The habit of keeping media plates upside-down is mainly to prevent condensation from flooding your inoculum.

If condensation can fall, so do spores/cells. I meant to say the lid is placed on the bench with the side that normally faces the base being upward.

I would say that if your lid is not clean, whether the plate is upside-down or not will not matter.

-Upside-down: contaminants would have to go against gravity to reach the culture
-Upright: ......... with gravity

Why don't you just try ?

What if its a borderline theoretical concern: has 10% of practical occurrence?


text:
I found a mossy thing on my plant
I was just wondering if this is a moss and if so what type of moss

looks like a moss to me. A bryologist or local botany expert would be best suited. Where are you located? What plant? Having a picture of this directly on your plant would be best.

I agree it's moss. Like most plant ID, a close up (I know it's tiny; can you crop and enlarge?) and in its habitat (on your plant) is important. Thanks! (Pretty, too.)

Definitely moss. Which one depends strongly on where you are in the world. There are about 12,000 species in total. For proper ID we would need to be able to see the leaf, particularly the nerve (if present) and cells at the base of the leaf under magnification with a hand lens or microscope, as well as habitat (what type of environment you found it in) and habit - how it grows.


text:
Why does harper states that aldehyde dehydrogenase is a oxidase? Is it a misnomer then?
Oxidases are those which uses O2, but dehrydrogenases doesn’t? Then is my book wrong ? Is it a misnomer that aldehyde dehydrogenase is correctly a oxidase?

Can you quote from your book?

Nevermind, I dug it up for you. But please, in the future, if you're asking about something written in your book and you want to know if it's right or wrong, quote from your source. Otherwise, we don't know if the book is wrong or if you're misinterpreting what the book says.

In Harper's Illustrated Biochemistry 32nd edition Chapter 12 in the section "Other Oxidases Are Flavoproteins" there are several enzymes listed and described. Quoting from that paragraph:

and aldehyde dehydrogenase, an FAD-linked enzyme present in mammalian livers, which contains molybdenum and nonheme iron and acts on aldehydes and N-heterocyclic substrates

The "FAD-linked enzyme present in mammalian livers, which contains molybdenum and nonheme iron" is aldehyde oxidase. This is a different enzyme than aldehyde dehydrogenase. It appears to be a typo in the textbook.

Seems worth noting that oxidase and dehydrogenase are both used in common nomenclature, but not in systematic names. The IUBMB guidelines for enzyme classification and nomenclature suggest that 'dehydrogenase' could be used in the common name of any oxidoreductase, while oxidase may only be used for the special cases where oxygen is the final acceptor. (https://iubmb.qmul.ac.uk/enzyme/rules.html)
The author of that chapter still should have known that the commonly accepted name for this particular enzyme is aldehyde oxidase. So, yes, likely a mistake.

@MikeyC Systematic naming conventions and nomenclature tendencies aside, there are two separate enzymes commonly called "aldehyde oxidase" and "aldehyde dehydrogenase".  The description given is clearly consistent with one of them, and it isn't the one called dehydrogenase.

I agree with you, @Bryan. Just thought that a little more context about the relationship between oxidase and dehydrogenase classifications might be useful to the reader.


text:
Mapping Ion Channel mRNA Copy Number to Channel Conductance
At least in invertebrates, it appears that within identified cell types, there are robust correlations between ion channel mRNA copy number (as identified by single-cell qRT-PCR) and the maximal whole-cell conductance for that ion channel species. For an example, see the following paper:

Variable channel expression in identified single and electrically coupled neurons in different animals (Schulz et al., 2006)

These results suggest that in general, we can model the relationship between ion channel mRNA copy number $m$ and conductance $g$ as
$$ g = \alpha + \beta m + \epsilon $$
where $\epsilon$ is some noise term and $\alpha$ and $\beta$ depend on cell type and ion channel species. In general, one would need to fit these parameters from data. I have two questions:

Due to issues with capture efficiency, etc., is it reasonable to expect there to be similar linear relationships between UMI counts of ion channel transcripts from scRNA-seq and ion channel conductances? Or is only qRT-PCR sufficiently accurate for estimating copy number?

If one does not have conductance data available to fit a regression model, are there theoretical models (e.g. involving gene regulatory networks) from which one could derive expected mappings between ion channel copy number and conductance?

I don't have access to the paper so I can't fully evaluate the relationship you describe. I'm also neither an electrophysiologist nor a
However to answer your questions:

This to me is a solid "probably?". It is reasonable to expect a correlation, but that doesn't mean that one will exist for any given mRNA species, especially given the rather noisy nature of scRNA-seq data. (Maybe it's gotten better more recently, I haven't tracked the tech closely). Briefly, RT-PCR will almost certainly be more accurate, but scRNA-seq will probably approximate the same answer (one possibly helpful though slightly old reference).
I'd be pretty skeptical of such a model constructed without regard to empirical conductance measurements. I can readily find people claiming to have accomplished something like this. These models are directly based on conductance measurements so they are likely somewhat trustworthy, and their fit to data appears to be pretty good (see figure; I have only the vaguest idea of what's being plotted here, so read the paper!)

Thanks so much, this is really helpful. If possible, could you update the second link you posted? As of now, both links are identical, leading to the same "Briefings in Functional Genomics" paper. If not, no worries. Thanks again.

@nguzman sorry fixed


text:
Recovering DNA from an RNA-extraction/purification kit
We are extracting RNA from single insects with the later purpose of performing RNA-seq. We are using the RNeasy Plus Miniki from Qiagen, which involves the use of eliminator columns as you can see here page 7.
However, we would love to be able to recover some DNA to perform a PCR which would help us confirm the insect species we are dealing with. Ideally, we would like to do this without losing any RNA-containing material. We were therefore wondering whether it was possible to retrieve some DNA from a column, which would otherwise be discarded ? Does anyone have experience with this ?

Have you looked to see if there is DNA in your RNA extraction?

We have run it on a gel yes, there was none after the DNA removal step.

Test it with a PCR; gels are about the least sensitive method of looking for DNA. almost every RNA extraction contains some DNA. So long as you didn't add DNase that is.

The idea however is that we would use material which would be otherwise discarded, we are reluctant to take away some of our pool of RNA.

The procedures for DNA and RNA extraction are almost identical; the difference is a small change in pH. You could try collecting flow through from the sample binding step and then put it through a DNA column or DNA extraction procedure (precipitation). Surely the cDNA generated in the RNAseq will result in something you can use for ID of the species; even the RNAseq results should tell you that.

We would rather not use the cDNA generated in the RNAseq process because we are extracting from single small insects, and we might have just enough for RNAseq.
The DNA/RNA separation step happens on a column : the DNA will bind to the eliminator column while the RNA will flow through. Then the RNA is placed on an other column to be further purified and eluted. Which is why w would like to recover the DNA from the previous column.

Simple - don't use the eliminator columns... Note that most RNAseq preps use in the fmol range of sample loaded and have a PCR amplification step to help you get there.


text:
Is UMI necessary when analyzing samples from Formalin-Fixed Paraffin-Embedded tissues?
We have FFPE-tissues we would like to use for a sequencing run. we think we can get enough biological material, so the amount of RNA shouldn't be an issue, but we're not sure.
A unique molecular identifier (UMI) corrects for PCR bias resulting from multiple PCR cycles, but if I have enough material, I don't need to do too many cycles. On the other hand the library preparation protocol using UMI is more complicated and error-prone.
So, my general question is

Is it always recommended to use UMI in a sequencing run originating from FFPE-samples, regardless of the amount of the RNA that can be extracted?

Is there anything in the literature concerning this problem?

I think you need to think about what you aim to gain out of the run? Expected outcomes alter how you should process the sample input.


text:
How to generate PDB file for custom single strand DNA squence(46 bp)？
I need to generate a pdb for ssDNA to research the interaction of DNA and proteins.
I will really appreciate if you can please guide me.
Thank you all for your time.

A related question on SeqAnswers does not seem to have meaningful current answers.
However, a question on ResearchGate points helpfully to this RNA structural modeling server (RNAComposer) that might be useful, once you create secondary structure predictions. Secondary structure is not enough to predict information needed for a PDB.
An alternative somewhat older path to a PDB for RNAs would seem to be MC-fold and MC-sym.
Granted: most of this is for RNAs, which will have a somewhat different structure and mode of folding.
The toolkit seems a little less rich for DNA, but you can still use tools such as ViennaRNA for secondary structure prediction, and there do seem to be some recently published tools for DNA structure prediction (see also here).
There are some further DNA/RNA resources here that may be helpful.


text:
Gene Mapping - Please explain in Lay terms
Taking an AP bio course, and for some reason I cannot comprehend the mechanism of how one determines the location of alleles on a chromosome. The math is simple and I can memorize it, but its bugging me that I don't understand a seemingly simple concept. Please explain to me like I am utterly inexperienced in biology (because for the most part, I am).

Stack Exchange isn't great for "explain this concept for me"-type questions; it's better if you can provide a specific explanation of what you understand and where you're stuck and ask a specific, directed question about that particular point. If you want a concept explained to you, better to use a textbook or Wikipedia. If you read that Wikipedia article or your textbook, can you identify where specifically you are stuck? What's the specific concept that you need to be further explained?

thanks, I'm still new to this, so I appreciate the advice. I will be sure to be more specific on my next post.

It's the 21st century.  You want to know where a gene is located in a species that's been studied?  You look it up.

Recombination happens every meiosis at some random location on every chromosome pair. If two loci are close on the chromosome, is unlikely that recombination happens between them, meaning they are "linked". If you look in a lot of meioses you can use the math to detect this linkage.
Gene mapping consists in considering every position in the genome, and measuring the linkage between that position and a phenotype (how frequently does recombination in meiosis separate the phenotype and the position).
Real world analogy: you measure how close two birds sitting on a telephone line are by measuring the rate at which some other bird lands between them. If they are right next to each other, then no other bird can land between them.


text:
Coefficient of fraternity between grandparent and grandchild from full-sib parents
I have the following pedigree and I would like to calculate the coefficient of fraternity between individual 1 and 5. R/AGHmatrix::Amatrix gives a coefficient of 0 for this pair. Shouldn't it be non-zero since there is still chance for individual 1 and 5 to have the same genotype? E.g. if the genotype in individual 1 is AB, there is still 1/8 chance to pass the alleles down to get AB in individual 5. Thanks.

ID
Parent 1
Parent 2

1
0
0

2
0
0

3
1
2

4
1
2

5
3
4

I think you're probably using the software wrong/there's a bug in your code.


text:
How did the fusion of Chromosome 2 spawn a separate smarter species?
I’m familiar with the evidence that two primate chromosomes fused into human Chromosome 2, and I understand that primates with such a mutation could still breed with those without it.
My question is, was it just a coincidence that the primates with 23 pairs became a smarter species branch?  Or did the mutation somehow enable our ancestors to become more intelligent than their relatives in the same biome?
Early on, the 23s must have coexisted with and interbred with the 24s.  But at some point, they became too genetically distant to breed.  So they must have genetically separated when they were still capable of interbreeding.
Was that separation because the 23s were somehow better able to adapt to new habitats or lifestyles that the 24s weren’t able to follow them to?


text:
Why and how do species diverge in the same region?
I want to begin by saying thatt I'm not a student of biology, so I apologize if this is an obvious question. My question is about species in general, but I'll be focusing on hominins since I'm more familiar with them.
I've been reading about human evolution, and it seems that at some point 3 different genera coexisted (Austrolopithecus, Paranthropus, and Homo) somewhat close to each other. My question is twofold:

Why did this three species diverge? One partial answer is specializing to a niche; e.g. the Paranthropus can eat less nutrient rich food, but there doesn't seem to be a concrete niche the Homo are filling compared to the Austrolopithecus. For some birds, it seems even less clear if they are filling a niche; e.g. sometimes just a couple of colors, feathers, or songs change.
How did they maintained the divergence? At least based on Homo Sapiens behavior with other relatives, I'd believe that these hominins wouldn't mind procreating with each other. It seems to me that they all live in a relatively small area, at least when considering that they are not sedentary and have hundred of thousands of years to move to cycle around all Africa, so I'd think there were plenty of opportunities to mix. Why didn't they mix until they got completely homogenized? Thinking of birds again, at least for those that don't have a very specialized mating ritual, I'd have expected all of them to mix so that there is at most one subspecies of bird per niche, but this is not at all the case.

There might be different reasons I guess. In general, there is a machanism for speciation in the same region, namely sympatric speciation. However, I doupt this is relevant for hominins. But, even if these species lived roughly in the same regions, there can become geographically isolated, for example by newly formed river, etc.


text:
Why aren't all B cells memory B cells?
If we have a B cell for every possible type of antigen, why aren't all of them memory B cells? From my reading, I have deduced that memory B cells are effectively the better version of normal B cells, activating faster and being more effective, which is why pathogens that are exposed again are typically dealt with much quicker. But why go through the trouble of getting infected, only to have to gain "immunity" to easily defeat the threat the second time. If all B cells are memory cells, the thought of autoimmune diseases and allergies being extremely common may arise. However, our own B cells have mechanisms that prevent them to attack self and allergies. I know that this could just be a product of evolution, but I wonder if there is a clear reason of why this wouldn't work.
(please note that I have no other experience of the immune system besides reading books, watching videos, and google searches, so feel free to point out possible misconceptions I may have [also this is my first post so hopefully I am clear with my question!])

When the naïve B-cell is produced, the body does not automatically "gain immunity" to a certain infection. There is only a certain amount of B-cells with a certain antibody for a specific antigen, and it is not enough to create an immune response on its own. When the antigen binds to the antibody and activates the B-cell, more of that B-cell is made, creating a secondary clonal selection process. This process is what kicks of the immune response. Some of the B-cells become plasma cells (the cell that produces large quantities of antibodies) and others become memory B-cells. The memory B-cells exist in greater quantities than the naïve B-cells, which means that the response will be better due to the greater number of cells present. The memory B-cells are also created to be more responsive than naïve B-cells when exposed to the antigen, which speeds up the process and leads to a better immune response the second time around.
In short, the reason why all B-cells aren't memory cells is because there are different types of B-cells that do something different:
naïve B-cells are the "parent" to all of the other types of B-cells which have to be activated to create other cell types, plasma cells produce antibodies, and the memory B-cells are cells that have improved upon the naïve B-cell to create a faster response. This is why the body needs to be infected once for the secondary immune response to be fast, the body needs to have that secondary B-cell selection that picks the right B-cell for the right antigen.
Source for Information: Prescott's Microbiology 12th Edition by Willey, Sandman, and Wood

Thanks for the response! However, why do naïve B cells have a slower response anyways? What's the point of created memory B cells that are faster when the naïve ones can be faster anyways? I mean evolution doesn't have a "point", but it would be a lot more efficient for naïve B cells to respond fast the in the first place.

I mentioned this in an answer for a different question (link), but evolution goes for survival of the fittest, not for efficiency. If it is good enough to survive, it doesn't need to evolve further. I hope that helps!


text:
Change of DNA concentration due to restriction digest?
Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about incubate the reaction at the optimal temperature for the endonuclease (e.g., 37 C).
Before you incubate the reaction, you measure the reaction's DNA concentration via a spectrophotometer. Then, you incubate the reaction for one hour and, afterwards, measure the DNA concentration again via a spectrophotometer again.
Q: Has the DNA concentration of the reaction changed through the restriction digest?
Most people would argue that the overall DNA concentration does not change due to the restriction digest, whereas the fragment distribution does, with the average fragment length decreasing through the digest. However, every time I have run this experiment with my students, we have observed a slight increase in the DNA concentration after the restriction digest. What could be the reason for this observation?

Did you clean up the reaction before the measurement? Have you tried running samples on a gel to make an estimation via a comparison of the bands?

@Chris Yes, we did both: after the restriction digest, we purified the DNA (i.e., removed any enzymes or other confounding components) via magnetic beads, and we compared the DNA fragment sizes before and after the digest via an agarose gel electrophoresis. The gel electrophoresis clearly showed the results of the digest: bands with smaller lengths than before the digest.

Summary
The poster wishes to know why spectrophotometric readings (presumably absorbance at 260 nm) on a sample of genomic DNA from an unspecified organism appear “slightly” greater after incubation with a restriction endonuclease, EcoRI. Assuming trivial explanations can be excluded — the effect is not statistically significant or results from components of the added enzyme preparation — it is evident that, under these conditions, absorbance measurement is not a measure of the concentration of DNA. The change would reflect an effect of the change of structure of the DNA on the absorbance, either as an intrinsic difference between intact and linearized species, or in their ability of the two strands to separate (melt) at the temperature and ionic conditions employed. Suggestions are made for cheap and simple experiments to clarify the situation.
More Detailed Consideration
Let me consider some different possibilities in turn.

The readings do not actually show a statistically significant difference.
The poster cites neither the magnitude of the effect nor the results of statistical tests done to show that the increase is significant. Without the latter we cannot be sure that there is any question to answer, and without the former we cannot judge whether a particular explanation could account for the observed change.

An increase in absorbance results from something in the preparation of restriction enzyme added. The poster argues against this on the basis of purification following the reaction, but more direct experiments are both possible and preferable. Comparison could be made between the reaction mixture at the end of the incubation and at the start, or after incubation with inactivated enzyme, and other controls are possible. A time course of the values of absorbance throughout the experiment would be useful to see whether the increase in absorbance correlated with the cleavage, as judged by the electrophoretic behaviour of the products.

DNA is being created during the experiment.
As the law of conservation of matter has been shown to hold at the molecular level, I reject this possibility. The obvious conclusion is then that ultraviolet absorbance is not a valid measure the amount of DNA, especially when comparing DNA of different structural forms. This point is developed further in 4, below. The question can be resolved by using an alternative method to measure the concentration of DNA — preferably a chemical method that is not affected by the physical form of the DNA†.

“When you have eliminated the impossible, whatever remains, however improbable, must be the truth.”
[Sir Arthur Conan Doyle — Sherlock Holmes]

The change reflects a change in the ultraviolet absorbance properties of different structural forms of DNA.
It has long been known that on heating double-stranded DNA so that the strands separate (melt) the absorbance at 260nm increases: the hyperchromic effect. This is thought to reflect the greater energy required for the π→π* transitions in the aromatic bases of double-stranded DNA, where the base stacking involves π–π interactions. It seems to me most likely that the changes observed reflect a change in the spectral behaviour of the bases in the DNA after the structure has been changed by cleavage into small fragments. This could conceivably be an intrinsic difference between the linear cleavage products and the original form of the DNA (supercoils etc.), unfortunately not specified in the question. I am not aware of reports of such differences, but this does not mean that they do not exist. Alternatively ‘melting’ of DNA could be occurring at the temperature and ionic strength used in the reaction, and the supercoiled or higher-order structure of the undigested DNA might be hindering strand separation and suppressing the hyperchromic effect.
In relation to the latter possibility, experiments are required with linear DNA (in the absence of enzyme) to see if there is indeed a hyperchromic effect on heating to 37C at the ionic conditions used. I would suggest three other main lines of approach to clarifying the situation. The first would be to employ different types of “genomic” DNA — animal, bacterial, viral, plasmid — in the digestion. The second would be to do a clean structural comparison without restriction enzymes. Plasmid DNA can be separated by gel electrophoresis and the supercoiled and linear form extracted. The spectrophotometric and chemical ‘concentration of DNA’ could be compared in the two cases, as could be their maximum percentage increase on melting at increasing temperatures. The third would be to
prepare linear DNA of different sizes, using either different restriction endonucleases or non-enzymatic physical shearing of the DNA. Indeed, experiments with sheared DNA would exclude the possibility of effects from the endonuclease preparations and allow experiments at temperatures and ionic strengths not possible with the latter.

Of course this is not Sherlock Holmes’ “all that remains”, as I am mindful of Shakespeare’s:
“There are more things in heaven and earth, Horatio,
than are dreamt of in your philosophy.”
[Hamlet]
Concluding suggestion
I would respectfully suggest that questions of this sort are framed in an explicit manner that clearly distinguishes between what was done, what was observed, and what conclusions were drawn.
––––––––––––––––
† This is something of a problem as the only chemical method I am aware of is the diphenylamine method, with the advantage that the reaction is with the deoxyribose ring. However this is several orders of magnitude less sensitive than spectrophotometric methods. The fluorometric method suggested in another answer depends on the interaction of fluorophore with the bases, and its access could well be different for single-stranded and double-stranded DNA.

As you did a clean up, then you lost some DNA in this process. There are always losses from clean up steps.
Note also that spectrophotometry is notoriously unreliable for DNA quantitation; it's more of a "there's roughly this amount of DNA there" sort of reading, especially as they are particularly prone to organic compound contamination (e.g. guanidine, phenol from your extraction) throwing your reading off. Interestingly, the original use for 280 nm measurement for DNA was for determining DNA contamination in protein samples. Have a look in Sambrook's Molecular Cloning: a laboratory manual for further detail 1.
If you want a more reliable reading, then you should use something like a fluorophore that is known to bind at a certain ratio to the DNA, as these are less prone to contamination problems and are more sensitive2.
Refs:

Sambrook, Joseph & Russell, David W. (David William), 1957- & Cold Spring Harbor Laboratory. (2001). Molecular cloning : a laboratory manual / Joseph Sambrook, David W. Russell. Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory

Green MR, Sambrook J. Estimating the Concentration of DNA by Fluorometry Using Hoechst 33258. Cold Spring Harb Protoc. 2017 May 1;2017(5). doi: 10.1101/pdb.prot093567. PMID: 28461657.


text:
Bone fracture and remodeling due to psychological stress?
I am reading up on this article:
click
Psychological stress causes bone fracture or the change of habits due to psychological stress cause bone fracture and remodeling?

Can you please provide a link to that article? It sounds like you're asking for medical advice rather than clarification/verification. Thanks!

Oops sorry will do!

What is your question?

The article you linked to is a review of the literature. Although your questions are related, I'll restate them as if they were independent questions. Please let me know if I'm not reading you correctly.

Can psychological stress cause bone fracture[s]?

The answer is "No." Psychological stress, which causes the release of hormones which may (over a long time) cause bone to weaken, cannot cause bone fractures. Fractures are caused by external stresses on bones obeying the laws of Physics. For example, any bone, healthy or not, will break if pressure of some kind bends or compresses it beyond it's limit to bend/compress. A very common example of this in people of all ages and bone health is a fracture of the distal radius from falling on an outstretched arm, or FOOSH (“fall on an outstretched hand"). We all reflexively stretch out our arm as we fall forwards to help break our fall. Depending on many factors, such as what surface we're falling onto, we may or may not sustain a fracture, but we've all been there. Little kids have less brittle bones, and such a fall commonly results in a "greenstick fracture", which is only partially broken, and on xray resembles the bend you see when a green twig is bent and straightened out again (hence the name). Older people don't get greenstick fractures; they have full fractures if the fall occurs on a hard surface, or under enough pressure (the FOOSH).

Does chronic psychological stress causing a change in habits cause bone fractures?

No. See above.

Does chronic psychological stress causing a change in habits contribute to bone strength and remodeling?

The answer according to the paper (and common sense) is, "In some people, most likely yes."
The paper gives a number of conditions which may well contribute to osteoporosis, a condition causing decreased bone strength. Such a decrease in bone strength means lesser external stresses can and often do cause fractures in those with the condition. Osteoporosis is most common in the elderly. Significantly decreased levels of activity over long periods of time (e.g. that may be present in depression) can contribute to the development of osteoporosis (again, multifactorial.)
I say, "...most likely, yes" because the article is not a study but a review, that is, the authors did not carry out any studies showing a direct cause and effect, but reviewed studies done by others which show a correlation between long term psychological stress (as well as the effects it has on physical behaviors) and osteporosis, which in turn predisposes people to sustain fractures which those with normal bones may not sustain. ("In some people" because it's multifactorial, e.g. sex, activity levels, genetics, and other factors contribute.)
I say "common sense" because there is much evidence in the literature about osteoporosis and fractures, but much less evidence about the effects of psychological stress causing osteoporosis, which is the subject of the review article. But common sense is not evidence.
Evidence informs us that prolonged immobilization (say, someone is in a wheelchair for a year and never uses their legs) leads to osteoporosis in those leg bones.
Evidence informs us that the incidence of fractures increases with osteoporosis.
Evidence informs us that prolonged use of glucocorticoid steroids causes osteoporosis in a percentage of those people (but not which people exactly).
Evidence informs us that psychological stress causes increased levels of glucocorticoids in people.
What evidence does not inform us of is that prolonged psychological stress causes osteoporosis.
We can infer (that is, hypothesize/make an informed guess which requires studies to obtain evidence for causation) that chronic stress may well cause ostoeoporosis in a percentage of sufferers. But a hypothesis requires "proof", through controlled studies, that our guess is correct.
That's why the paper concludes that further study is warranted. Common sense, informed guesses and hypotheses are not evidence.
I answered this question because the OP was kind enough to provide a good link, which is wonderful and fully deserves my respect. I hope that with this answer, people will understand the respective values of "common sense" and "evidence" in science, because so many of us human beings mistakenly think they are one and the same. Stepping down from the soap box now, requesting your grace for this very long... answer. Thanks.

Great answer!Thank you!

You're very welcome!


text:
Sourcing sulfur-oxidizing bacteria
For a research project, I need a species of sulfur-oxidizing bacteria but I cannot find a biological company that sells anything like that. I know ATCC sells some species of sulfur-oxidizing bacteria but those are usually too filtered out than I need thus costing more than $400. Can you provide me with any biological company that sells bacterial species under sulfur-oxidizing bacteria? I know I'm not making it very specific but at this point, I'm good with anything you can find. I would prefer green or purple sulfur bacteria, but anything that can use hydrogen sulfide is good for me.

There are numerous collections around the world that supply bacterial species. You've already found the American Type Culture Collection (ATCC). If you are in academia or even sometimes in industry, you can contact authors of papers who have an organism you want, and they will supply a starter culture to you, usually free (for the organism itself), but you will always have to pay shipping (whether from a supplier or a researcher), which will often run into the hundreds of dollars, depending on shipping type. Many species will only be able to be shipped under certain conditions, such as frozen on dry-ice (about -89 C), or frozen as freeze-dried. These types of shipping cost $$$.
In addition to the shipping there will be some legal things to sort out. Typically this is a Material Transfer Agreement, which is a legally binding document between your organization and the supplier and/or the people the supplier got it from. These often limit what you can do with the organism in question - usually limiting you to research applications only. If you are intending to commercialize you will need to get a commercial agreement signed up! Not doing so opens you and your organization to legal liabilities that will cost a huge amount of money to litigate and usually result in substantial fines.
In Europe there is the Belgian Coordinated Collection of Microorganisms, which has a price list here. There is also the Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (known as the DSMZ) in Germany and the Culture Collection University of Gothenburg (CCUG) in Sweden. The UK has the NCTC (National Collection of Type Cultures) too.
Japan has the  Japan Collection of Microorganisms at the RIKEN organization. China has the Chinese General Microbiological Culture Collection Centre
India has the NCCCC (National College Culture Collection Centre) in Pune.
In addition there are lots of smaller ones around the world. There is also the Global Catalogue of Microorganisms, which lists 152 current affiliates from all around the world, including those listed above.


text:
In mRNA translation, why are there so many factors?
When the small ribosomal subunit binds to mRNA’s 5’-cap, it looks for the complex of three eLFs bound to the poly-A-binding protein (PABP), which circularises the mRNA.  It is then this circular mRNA that the small ribosomal subunit binds to.

In low-nutrient environments, 4E-BP1 binds to PABP, inhibiting it from binding to the 5’-cap complex. I high nutrient environments 4E-BP1 is phosphorylated.

Why (what benefit is conferred?) are the eLFs there?  Why not just have the PABP bind to the 5’-cap to initiate transcription?  And why 4E-BP1?   Why not just phosphorylate PABP directly?
I mean I know that as is, PABP isn’t set up to be usefully phosphorylated, but why is it this way?  It seems a whole bunch energy and resources wasted making these extra proteins, and more room for things to go wrong, more DNA that has to be made and carried around with no mutations and transcribed and translated correctly.

The eukaryotic initiation factor (eIF) proteins are necessary for the ribosome to translate the mRNA. The main benefit is that they, when present, make it easier for the ribosome to find the AUG sequence, which is the start of the protein (as shown in this diagram) by "helping" the Methionine t-RNA find said sequence.
The reason why the mRNA doesn't bind to the PABP directly is for translation regulation. If the mRNA needed to just bind to the PABP and the mRNA for a protein is made when there is more than enough protein, then amino acids are being wasted to make the already abundant protein. If there exist some factors that can control the translation of protein, then the cell can better control protein translation.
Why 4E-BP1 is phosphorylated instead of PABP is because it evolved that way. I know that isn't a satisfying answer, but cells don't really evolve for efficiency, but for "good enough". If it is enough to survive, then why bother changing it?
I hope this answers your question!
Citation for Paper with Diagram: https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00607-9


text:
CO$_2$ in photorespiration
"Photorespiration is wasteful to plants as it reduces the amount of CO$_2$ available for fixation" my textbook says.
But we also know that photorespiration takes place when the concentration of CO$_2$ falls within the leaves. But CO$_2$ is also released in photorespiration. Why can't the CO$_2$ released here be fixed by RuBisCO?

Could you please give a complete citation from your text book and identify it by name, title, and publication date. That way we can cross-check it. You will be aware that posters on this site need to demonstrate that they have tried to answer this question themselves, but haven't done so. Have you searched this site for other questions on "photorespiration"? If not do so, and in any case tell us why what you found does not answer your question.