text:
How difficult is it to adapt an existing vaccine to a virus variant?
There is (at least in France) an ongoing discussion about the Astra-Zeneca vaccine which is perceived as "outdated" because of the prevalence of new variants (the vaccine was designed based on the initial virus)(*).
How difficult is it to create a new vaccine that targets a new variant of the virus? (specifically adenovirus vector vaccines like the AstraZeneca one, but any general information is welcome as well)
My understanding is that the clinical trials are not needed anymore (in the same way as a flu vaccine is recreated each year without clinical trials because the difference is in the virus variants only) so is there a strictly biological, incompressible delay? (ability to target the new variant)?

My main question, related to biology, is above, the following alternative questions are OT for the site, but I am asking them in case they would be relevant:

Or is there a financial aspect? (too expensive to create a new vaccine)
Or is this because Astra-Zeneca believes that the current vaccine is OK, despite the backslash?

(*)

An example of the reluctance (in French): https://www.dna.fr/sante/2021/02/19/haguenau-la-moitie-des-50-64-ans-refuse-le-vaccin-astrazeneca.
In SA the AZ vaccine was stopped due to concerns about efficacity on the new variant, which influenced the French opinion as we also have SA variants in the wild (again, in French): https://www.midilibre.fr/2021/02/08/coronavirus-lafrique-du-sud-suspend-lutilisation-du-vaccin-dastrazeneca-juge-inefficace-sur-le-variant-9360903.php.

Please note I am not saying this is the case - I am just curious how hard it is to create a new vaccine for a variant.

Can you share some info regarding the fact that AstraZeneca vaccine is "outdated"?

@FabioMarroni: there is an ongoing discussion in the French news about the AZ vaccine (vs the others). This is the default vaccine for <65 yo patients and there is a reluctance of the population to use it because of reports about the fact they are not effective for the new strains. It may or may not be true (and is another interesting question), this triggered my main question (and the extra ones in the exact context of AZ).

@FabioMarroni (cont'd) An example of the reluctance (in French): https://www.dna.fr/sante/2021/02/19/haguenau-la-moitie-des-50-64-ans-refuse-le-vaccin-astrazeneca. In SA it was stopped as well, which influenced the French opinion as we also have SA variants in the wild (again, in French): https://www.midilibre.fr/2021/02/08/coronavirus-lafrique-du-sud-suspend-lutilisation-du-vaccin-dastrazeneca-juge-inefficace-sur-le-variant-9360903.php. Please note I am not saying this si the case - I am just curious how hard it is to create a new vaccine for a variant.

@FabioMarroni: I updated the question with the last part of my comment to indeed give some context (in French, unfortunately)

Are you asking about vaccines in general or specifically about adenovirus vector vaccines like the AstraZeneca vaccine? I can imagine that the steps to adapt to new mutations differ between different types of vaccines.

@Arsak: I am particularly interested in adenovirus vector vaccines like the AstraZeneca vaccine, but any general information is welcome - if relevant (= if there is a common trend between different kind of viruses)

This question seems to me to be off topic as it relates to industrial pharmacy, rather than a biological problem. And I don't think we need to know about the attitude of the French public. Pasteur must be turning in his grave.

@David: France was for context. If you feel that my question about a "strictly biological, incompressible delay" is indeed off-topic please vote to close. I was not completely sure myself that this would be in-topic but I do not think there is a better place (and I tried to keep it limited to biology)

I did vote to close. You might try SE Medical Sciences, but this sort of question is in the realm of Pharmaceutical Engineering, where even the most experienced people on this list are dependent on general articles in Nature and the like.


text:
What makes a bacterium move away from a neutrophil cell?
In this video we see a bacterium seemingly moving away from the neutrophil that is chasing it. What mechanism makes it "want" to avoid the neutrophil? It doesn't seem to mind being around other cells of the same organism. Why does it react differently to a neutrophil?

In the video doesn't it look like it's just moving passively in the solution? As the neutrophil moves around it displaces solution that has to go somewhere, and the third dimension is impeded on the microscope slide. Like when you try to scoop something from your soup and it gets pushed away by your spoon.

yes, it seems it does. This makes the question obsolete

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text:
Medium preparation, using calcium hydroxide instead of potassium hydroxide
As the question states, I am interested in growing alkaliphile bacteria. I have seen many media use KOH, mainly to neutralize, and was wondering if it is possible to change this to Ca(OH)2?
Is there a reason KOH is used instead of any other alkali solution to neutralize media?

Calcium is a bad choice as it will form precipitates with either phosphate ions as well as with carbonate or CO2.

As @Chris said, $\ce{K+}$ salts are soluble in water whereas plenty of $\ce{Ca^{+2}}$ salts such as $\ce{CaSO4}$ and $\ce{Ca3(PO4)2}$ are insoluble in the aqueous medium. Therefore it leads to the precipitation of phosphate-containing proteins and sulfate-containing metabolites. In addition, $\ce{Ca^{+2}}$ forms coordination complexes with calcium-binding proteins which participate in discrete signaling pathways. Interfering with this system could lead to subtle and irreproducible results. $\ce{K+}$ ion mostly participates in creating a voltage gradient across the membrane, nothing more.
Moreover, ionic strengths should be considered. $\ce{Ca^{+2}}$ is a divalent cation. A solution of $\ce{KOH}$ and a solution of $\ce{Ca(OH)2}$ with the same pH would definitely have different ionic strengths. Therefore despite achieving the same pH of the medium, ionic strengths vary depending on the salt used. Abnormal ionic strengths affect the structure of proteins in many ways. In general, it has been proven that changes in $\ce{K+}$ concentration lead to less severe outcomes compared to $\ce{Ca^{+2}}$.
EDIT: $\ce{Ca(OH)2}$ forms precipitates in an aqueous solution because it is barely soluble in water ($K_{sp}$ $\pu{=5.5 \times 10^{-6}}$). The pH of a saturated solution of $\ce{Ca(OH)2}$ is 12.347. To achieve other pHs one must add strong acid or base (a standard $\ce{KOH}$ solution perhaps) or use dilution; so as you can see, introducing $\ce{Ca(OH)2}$ just leads to unnecessary complexity, best to be avoided. Also, $\ce{Ca(OH)2}$ leads to the formation of $\ce{CaCO3}$ in the presence of atmospheric $\ce{CO2}$, making it even a less appropriate material for the preparation of the medium. Calculations using $K_{sp}$ shows a saturated $\ce{Ca(OH)2}$ solution has pH = 12.347 and [$\ce{Ca^{+2}}$] =  0.01111

For my research I am interested in using bacteria to precipitate CaCO3 and at the same time prevent the formations of soluble salts like potassium and sodium sulphates/chlorides. As such, my approach was to try replace them with Ca-containing buffers and salts. Would there be any other Ca-containing salt/buffers that would be better suited? I am new to media preparations so still trying to understand how everything plays a role in bacterial growth. Ideally, I will find alkaliphiles that are low-sodium/potassium demanding.

@Franco Grosso
If you need to create an environment with a determined Ca+2 ion concentration and little Na+ and K+, you’ve got to consider some items. First Many famous culture mediums contain NaCl and using it is most likely inevitable even in your research. See [1] [2] [3] [4]. As you know a 15mM NaCl, 150mM KCl solution renders the cytosolic environment perfectly while a 150mM NaCl, 15mM KCl represents extracellular medium nicely [5].
Therefore K+, Na+, Cl- ions should exist in your system at least in trace amounts for successful cell culture.

@Franco Grosso, Still, you can use R-NH2/ (R-NH3+ Cl-) buffers if you insist on lowering Na+ and/or K+ ions demand. Examples of such organic compounds are CAPS, PIPES, TRIS, TAPS, glycylglycine [6]. Subsequently, adjust pH by adding HCl. Here arises another problem.  Chemicals mentioned above as well as Phosphoric acid, carbonic acid buffers have the potential to chelate your Ca+2. Therefore, it is best to avoid them. Look in some papers for the exact protocols and the best buffer systems. CAPS can be appropriate. Its pKa is 10.4 and can be used to grow alkali bacteria.

@Franco Grosso, But still search for better results. Avoid making mixtures of buffers.
Inject Calcium ion by simply adding CaCl2(aq) to the system. Remove the excess amounts by EDTA (forming stable EDTA-Ca complexes). In this way, you can adjust your calcium ion properly. A somewhat related paper about similar calculations on Mg+2 ion.[7]
The precise ingredients of your culture depend on your research topic but you get the general idea. [8]
I hope that I’ve understood your question correctly :)  good luck!
[1] : https://microbenotes.com/chocolate-agar/

[2] : https://microbenotes.com/new-york-city-agar/
[3] : https://microbenotes.com/sorbitol-macconkey-agar/
[4] : https://microbenotes.com/category/culture-media/
[5] : Molecular Cell Biology of Lodish 8th edition page 496 Figure 11-18
[6] : Wilson and Walker’s Principles and Techniques of Biochemistry and Molecular Biology 8th edition Chapter 0
[7] https://pubmed.ncbi.nlm.nih.gov/11772/
[8] : https://www.sciencedirect.com/science/article/pii/S0091679X08611152

thank you very much for the detailed explanation! I think you have understood the question better than I did haha. Now I understand better what parameters and considerations I need to include on my medium. Also, great references.

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text:
Skin (epithelial) stem cells: unipotent or multipotent?
In a video on the Khan platform on stem cells, epithelial stem cells are described as unipotent stem cells, i.e. only producing one kind of specialised cell: epithelialor skin cells.
However, on a website describing the hierarchy of [stem] cell potency, skin cells are shown to be the product of multipotent stem cells:

Which category is correct for skin stem cells - unipotent or multipotent?
UPDATE

In order for the epidermal stem cells to become multipotent or pluripotent, they have to be induced. This involves some precisely timed chemical exposures that don't occur in nature. I think when some people refer to unipotent stem cells, they are referring to them by their natural function.

In this article on sciencedirect.com epithelial skin cells are described as the products of epithelial multipotent stem cells and/or unipotent "progenitor" cells (which I presume is a way of describing a stem cell that only produces one type of cell - in this case an epithelialor skin cell). The epithelial multipotent stem cells can produce a variety of cells.

Most epithelial tissues self-renew throughout adult life due to the
presence of multipotent stem cells and/or unipotent progenitor cells [emphases mine].
Epithelial Stem Cells and Their Lineages Epithelial stem cells can generate tissues that display a fascinating array of cellular
architectures, each of which are specifically tailored for distinct
functions. In this review, we will focus on four well-characterized
epithelial stem cells whose tissues possess diverse architectural
designs and physiology: intestine, epidermis, mammary gland, and
cornea.

So it seems the answer to my question is: both.

I think the main cause of the discrepancy is a lack of formal definition for "unipotent". We don't really talk about "unipotent" cells, there are "multipotent" ones like in the figure above, and then "progenitor cells". We don't really think of progenitor cells as multipotent even if they technically produce more than one final cell type; they're just the last level of stem cell before you have the final differentiated lines. There's a lot of "lumper vs splitter" issues when you get down to that level. It's not really even that clear how many "cell types" a human has.

@BryanKrause OK, thanks I get it.


text:
Why can't certain nucleoside analogs be used to label bacterial RNA?
A 2020 publication in Nucleic Acids Research 1 includes the following passage:

A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among them, 4-thiouridine (4SU) and 5-ethynyluridine (EU) are two most widely used noncanonical nucleosides that can be conjugated via thiol coupling chemistry and click chemistry, respectively (9,10). Although the metabolic RNA labeling technique has been instrumental for studying RNA dynamics in eukaryotes, it is not applicable to bacteria.

The authors give no citations or further explanations for the bolded claim.  Indeed, I have found at least one publication that contradicts this statement,2 showing 4SU labeling in E. coli:

We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine.

One explanation is that 4SU is a natural RNA modification in bacteria, as Rogers et al. 3 states that most bacterial tRNAs contain 4SU. So, while bacterial RNA can be labeled with exogenous 4SU, naturally occurring 4SU confounds analysis. Concerning EU, Blenkiron et al. 4 used this analog to label nascent RNAs from uropathogenic E. coli in order to track the fate of bacterial RNAs in membrane vesicles:

We then looked at whether we could track uptake of MV RNA cargo into treated host cells by labelling UPEC nascent RNA in the bacteria before it was packaged with MVs. This was achieved by adding an excess of a modified uracil, 5EU (5-ethynyl uridine), which was incorporated into the newly synthesised and MV associated RNA.

Additionally, the text of this research grant award abstract 5 suggests that EU is suitable for labeling both E. coli and B. subtilis:

We have been investigating whether bacteria can incorporate the “clickable” RNA analog 5-ethynyl uridine (EU) for subsequent attachment of fluorescent label (Alexa Fluor) for microscopic detection or a chemical tag (desthiobiotin) for streptavidin-mediated RNA capture. The results for both aspects so far are a qualified “yes”. Both Escherichia coli and Bacillus subtilis grown with EU can subsequently be detected by fluorescence microscopy, but E. coli becomes considerably more brightly labeled.

I can find no research stating EU / 5EU naturally occurs in bacterial RNA.
My question, in short: What aspects of bacterial metabolism or RNA composition justify the claim that 4SU and EU are "not applicable" for bacterial RNA labeling?

Edit, 1 March 2021 -- I'm adding a bounty to garner more attention. From further reading, I suspect the answer to be one of 3 possibilities.

Per David's comment, the bacterial cell wall may be impermeable to certain formulations of nucleoside analogs or the reagents subsequently used in thiol coupling / click chemistry.
Certain nucleoside analogs are toxic in bacteria to an extent not seen in eukaryotic cells, perhaps by a mechanism that causes the elongating RNA polymerase to stall.
4SU and EU labeling are applicable to bacteria, and the claims of the authors are unsubstantiated.

References

Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576.
Favre A, Bezerra R, Hajnsdorf E, Lemaigre Dubreuil Y, Expert-Bezançon A. Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis. Eur J Biochem. 1986 Nov 3;160(3):441-9.
Rogers KC, Crescenzo AT, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie. 1995;77(1-2):66-74.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, Hong J, Print CG, Swift S, Phillips AR. Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLoS One. 2016 Aug 8;11(8):e0160440.
Click-chemistry labeling of RNA: A new tool for microbial ecology?

I don't know the answer, but could it be something to do with poor uptake through the bacterial cell wall, which isn't a problem in eukaryotes where there is only a cell membrane? That might affect either or both of the nucleosides and the other reagents needed in the method. It might also explain the counter examples if people were working at  the edge.

Perhaps, and thanks for the feedback. It makes sense to me that bacterial cells would be impermeable to NTPs because of the negative charge, but the bacterial studies I've linked all treat with either the free nucleobase or nucleoside (base + sugar). I'm leaning toward a conclusion that 4SU and EU are more toxic to bacterial cells than they are to euk. cells, based on the use of nucleoside analogs as antibacterial agents.

Meng et al. actually give their explanation in the first paragraph of their results section. The main reasons for their claim are that they did not detect any labeling with 4SU or EU and that both analogs suppress bacterial growth. Also they raise the issue with the naturally occurring 4SU in tRNAs.

Aiming to develop nucleoside analogs compatible with bacterial RNA labeling, we first set out to evaluate the two nucleoside analogs widely used in eukaryotic cells. E. coli cells were incubated with 4SU or EU at varied concentrations for 2 h, which resulted in no detectable labeling even at high concentrations (Supplementary Figure S1A, B). Moreover, severe suppression of bacterial growth was observed with both 4SU and EU (Supplementary Figure S1C, D), which was in agreement with previous observations that 4SU impaired cellular metabolism in E. coli (31). Cell viability was significantly impaired with 4SU at concentrations higher than 100 μM, while EU did not induce significant decrease in cell viability (Supplementary Figure S1E, F). In addition, tRNAs of bacteria contain endogenous 4SU generated via thiolation of uracil (32), which may interfere with metabolic labeling if exogenous 4SU would be used. Of note, although EU does not incorporate into DNA in mammalian cells (10), significant labeling of DNA was observed in EU-treated E. coli, presumably due to metabolic conversion of EU to EdUTP (Supplementary Figure S1G). Together, these results demonstrate that 4SU and EU are not applicable for bacteria.

This explanation is not necessarily incompatible with the results in the other references mostly because the strains and the test approaches are different.
In Favre et al. they use a different strain of E. coli,"an Escherichia coli
pyrD strain" that is optimized for 4SU incorporation :
In Material and Methods :

pyrD used to control the level of 4-thiouridine incorporation

and in Results :

a) growth of E. coli AB1157 sfiA pyrD in the presence of 4-thiouridine
Preliminary studies showed that the level of s4U incorporation into the rRNA of strains MRE 600 or K12 AB1157 grown in a standard glucose medium in the presence of 4-thiouridine remained at the detection limit. We therefore use AB1157 pyrD mutant deficient in the pyrimidine biosynthesis pathway. To our growth medium we systematically add 40 μg/ml uridine because it is  the minimal concentration required to supplement growth fully. The growth of the pyrD mutant was first examined at different temperatures and different exogeneous s4U concentrations from 40 μg/ml upwards in the conditions defined in Material and Methods, In Fig. 1 we report  the growth curves obtained for two s4U/U ratios,1 and 2.5, and four temperatures: 25°C, 28°C, 30°C, 35°C. When the ratio is 1 there is practically no growth inhibition. With  a ratio of 2.5 the  growth  inhibition becomes strongly dependent on temperature. The culture does not grow at all at 20°C, the  growth is linear between 25°C and 30°C and for temperatures above 30°C it escapes inhibition, becoming exponential. As will be described below significant s4U incorporation occurs in  conditions where growth is linear.

In Favre et al. as seen at the end of the paragraph above as well as in another publication (Bezerra and Favre, 1990) from the same lab shows that incorporation of 4SU depends on several factors.
Concerning the work of Blenkiron et al., it is harder to explain but they also use a different strain so that may impact the incorporation and they do not use the same approaches compared to Meng et al. to detect it. Confocal microscopy for Blenkiron et al. vs Dot blot and In-gel fluorescence for Meng et al..
Finally as far as the grant abstract is concerned, it's hard to conclude because the information is scarce but as Meng et al. they also observed an effect (although milder) of 5EU on bacterial growth and again, they used a different approach to observe the labeling based on fluorescence microscopy as Blenkiron et al..

References :

Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576.
Favre A, Bezerra R, Hajnsdorf E, Lemaigre Dubreuil Y, Expert-Bezançon A. Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis. Eur J Biochem. 1986 Nov 3;160(3):441-9.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, Hong J, Print CG, Swift S, Phillips AR. Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA. PLoS One. 2016 Aug 8;11(8):e0160440.
Bezerra R, Favre A. In vivo incorporation of the intrinsic photolabel 4-thiouridine into Escherichia coli RNAs. Biochemical and biophysical research communications. 1990 Jan 15;166(1):29-37.

Welcome to Biology.SE! This looks like a good answer, but please do not post text as images. Instead copy and paste the text into your post. Images are not searchable, and can not be interpreted by screen readers for those with visual impairments. Use the [edit] link to modify your question. See this for more information. Thanks!

In addition, please include the complete reference information since links can break. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. Note also that quotes must always be referenced. Thanks again!

Thanks for the feedbacks @tyersome. I've edited the answer accordingly.

Great that is much better! (+1) I'm gathering that the first quote is from the Meng et. al. (2020) paper — I'm going to edit your answer to make that clearer. Thanks!


text:
Will Covid-19 wipe out the Humanity that we know of?
As there are multiple variants of Coronavirus and every couple of weeks later there are new, deadly and highly contagious variants of COVID-19 virus emerging from the backdrop, I am just wondering is this the end of Humanity that we know of?
Dr. Anthony Fauci yesterday warned during press conference that it will take a long time, I mean more than seven years, to return to normal state that was like pre-pandemic state.
White House officials have predicted up to 240,000 people in the U.S. will die from COVID-19 with a bulk of those deaths peaking over the next several weeks.
White House briefing
No country can be in a lockdown state for that long. I mean it can never happen. It's just impossible or implausible.
So if six billion population in this planet called earth is wiped out by then by the Coronavirus then is this it? Is this the Doom's day scenario instead of the sunny day scenario? Is this the post Jurassic Era for Homo Sapiens after which they will be extinct just like dinosaurs--T-rex, Pterodactyl, herbivorous and carnivorous dinosaurs? Our ancestors have been here around for six million years and modern day humans are here for 200,000 years. Does it say that it's time to leave the stage forever?
How long humans have been living here?
Here is the number of tests and cases per million in the world in curved graph. Seems slow rising exponential graph.
Some Graphs

No.  In the US, roughly 500,000 people have died from the COVID-19 virus in the last year.  In the same period, there were about 3.7 million births.
Many people do not get the disease, either through natural immunity or lack of contact with contagious carriers.  Of the people who do get it, most recover.  The fatality rate differs by country, but it doesn't appear to be more than 10% in any country: https://coronavirus.jhu.edu/data/mortality  Most of those who do recover have immunity that lasts for months, at least: https://www.nih.gov/news-events/nih-research-matters/lasting-immunity-found-after-recovery-covid-19
Given this, and even in the absence of effective vaccines, it seems highly unlikely that the virus will even have a noticable effect on the rate of population increase, let alone render humans extinct.  (Even the Black Death, or the post-Columbian virgin field epidemics in the Americas didn't do that.)
As for a country being in a "lockdown" state for very long, whyever not?  It may require some people to make lifestyle changes - no more cruises, clubbing, or other activities that put a lot of people in close proximity - but it is perfectly possible to live a productive and enjoyable life without those things.  Anecdotally, while I'm no doubt an outlier, the only real change in my life is that I wear a mask when I go to the store.


text:
What's the survival benefit of blue plants?
I'm working on a science-fiction worldbuilding setting and have been trying to find out what the survival benefits are of blue in plants, like this or this.
I have researched this but most of the answers that a Google search brings up are more to do with blue flowers, blue structural colouration in animals, and garden centre blogs and online stores selling conifers. The best I've been able to find has been a page about encouraging spruce plants to become as blue as possible by making sure they're fed planty of iron-rich fertilizer (but not fertilizing in the first year, so early impoverishment of nutrients seems to be a factor, but I don't see how that makes blue needles beneficial).
All I really want to know is what environmental conditions would cause a plant, any plant, to evolve blue leaves or needles.
Thank you in advance.

That's great, but I'm more interested in the time period long before Russia even existed. It's these plants' evolutionary bias towards being blue, and the pressures in their native environment that I'm interested in.

I’m voting to close this question because this question belongs on the worldbuilding stack.

According to at least one gardening tutorial I found, the blue color of the Colorado Blue Spruce is not actually related to the color of the pigments in the leaves.

"...the intensity of the blue of a Colorado blue spruce (selections of Picea pungens ‘Glauca’) depends on the concentration of its “bloom,” a powdery white wax that coats its needles."

I can't say if this is the case for all "blue" conifers, but given that this tree is especially tolerant of cold and drought, it seems likely that the waxy "bloom" is related to retention of water vapor and possibly exclusion of external water from the needles. Since there are lots of other plants with waxy coatings that don't have such a powdery blue appearance, I'd speculate that it may also contribute some protection from UV radiation for these high-altitude trees.


text:
Introns and miRNA
From this paper, it is stated that some introns may contain genes coding for miRNA, miRNA is essential in regulating gene expression by pairing with RNA, hence disrupting regular translation.
From this answer, it is stated that introns are broken down and the nucleotides will be recycled by ribonucleases.
Question:

How do ribonucleases sense the presence of miRNA genes in introns, hence not breaking them down, what is the mechanism for that?
How to 'extract' the miRNA present in the introns? (My thought is by a mechanism which is similar to splicing, but we are extracting the DNA sequences in between i.e. switched the positions of introns and exons than regular splicing)

Thank you.

The answer to Question 1 is:

The ribonucleases responsible for digesting removed intron RNA do not recognize the miRNA as such. They are unable to digest it because (or to the extent that) it assumes a double-stranded structure, as they are specific for single-stranded RNA.

The answer to Question 2 is briefly:

By the same mechanism as the many microRNAs transcribed from the DNA using their own promoters rather than from the promoters of the genes containing the introns in which some occur. (And some intronic microRNAs have separate promoters.) This involves a different enzyme that does recognize the microRNA region.

The mechanism of generation of microRNAs from their precursors
This is shown in the diagram below adapted from a review by Lucas et al. of the situation in Drosophila. It is initiated by the recognition by Drosha of the double-stranded RNA formed by the self-complementary miRNA sequences in whatever single-stranded RNA.

The pre-miRNA moves to the cytoplasm where it is further processed to the single-stranded active form.

But in general…
…it’s not quite so simple. MicroRNAs are not the only small RNAs found within introns. It is quite common to find small nucleolar RNAs (snoRNAs), which function to recognize methylation and pseudo-uridylation sites on rRNA; and although these snoRNAs have double-stranded regions, these are less extensive than in microRNAs (see e.g. this review). Our knowledge of the details of digestion of excised introns by RNase is sketchy, but it may be better to consider the situation in terms of competition between two types of RNA-binding proteins for the small RNAs (and even mRNA). On the one hand there are the RNases that will digest the RNA completely — on the other hand there are proteins (like Drosha in this case) that recognize some feature of the RNA and bind to it. Once the latter bind, the 5′-end of the RNA would be protected from digestion by exo-ribonucleases. So it would not be a question of all or nothing, but a balance, which has the advantage that it can be regulated — tipped one way or another — depending on the relative proportions and activities of competing proteins.

That same review also mentions mirtrons.

@canadianer — I have amplified my answer. I don't think it helpful at this level to go into details of which intronic microRNAs have their own promoters or not, unless someone requests it.

I have now added a rider to my answer, discussing the situation with other intronic small RNAs.


text:
Are there epigenetic effects in the regulation of human height?
Development of human average height
Human average height has fluctuated significantly throughout history. For instance, in the last 100 years or so, it has increased sharply by about 10cm. OWID (Our World in Data) has data and figures on, among other measures, the average height over the last 18K years, average male height by country over the last 200 years, annual change in average male height, and annual change in average female height.
Regulation of human height
Already the genetics of human height seem to be complicated and to involve a large number of different genes (and hundreds of loci) according to, e.g., this article by Lettre (2011). However, since the time spans are too short for significant purely genetic effects, there must be either developmental or epigenetic effects at play or both. Developmental effects have been linked to socio-economic status, perhaps via steady and good nutrition before birth and during childhood. This paper by Komlos (2007) (without paywall here) shows data for English youths in the 1700s and 1800s by socio-economic status and finds a height gap of up to 22.6cm, his sample sizes are a couple of thousands for the lower-class group and less than that for the upper-class group.
Epigenetics human height
Carey reports in her book "The Epigenetics Revolution" (2012) that people born after the Dutch Hunger Winter would not only remain small for their entire lives but that there was still a significant difference in their children, born decades later. She does not seem to refer to height differences though (I guess?), but to differences in the risk to develop certain diseases as reported in this paper by Heijmans et al. (2008) (not sure if there's a paywall; same paper is also here). They trace this to differences in the expression of a certain gene (IGF2) because of hypomethylation of that region.
Since other phenomena are thus shown to be subject to epigenetic effects, it is possible that the regulation of human height is too. To be clear, I am not aware of any study that suggests this (or investigates this). It would certainly be very difficult to identify, so I suspect this has not been thoroughly investigated. Note that the epigenetic effects shown in Heijmans et al. (2008) could only be shown because of the very specific conditions of the Dutch Hunger Winter, a short but horribly severe famine with intact medical records. But I am hoping there is some information out there.
So my question is
Are there indications that epigenetic effects may be present in the regulation of human height and its rather interesting development in recorded history? (Or is this unlikely, e.g. because the variation is sufficiently explained by other factors or because studies have tried and failed to find epigenetic effects? Or has this not been investigated so far?)

Would you care to explain your downvote? Evidently you think that whatever is wrong with my question is so blatantly obvious that I should not have dared asking this in the first place. Is it off-topic (not biology?)? Is it trivial? Is it more than one question? Is it a duplicate? Is the question unclear? Does it not show any evidence of research? Is it that you feel I'm promoting some commercial interest/ideology/conspiracy theory/bad paper? It is more likely that I can fix it if you tell me what's wrong.

https://www.nature.com/articles/ncomms13490

@user438383 Thanks, this is very helpful. I was not aware of that paper. I should probably have searched more thoroughly. I guess, this also means that the question is indeed trivial and should be deleted. I will do that shortly.

The Hunger Winter thing worries me. First it should be realized that this is all based on statistics of gross observations. There is no mechanistic evidence of a mechanistic basis for the observations. Second, if the nutritional environment has epigenetic effects during a famine, one would expect a reversal during the glut that prevailed when the Dutch were rutting in the 60s. But it appears to have persisted. I don’t buy it.

@0range no problem. I dont think it renders the original question trivial and in need of deleting. Hopefully someone with knowledge of epigenetics can give a comprehensive answer.

@David I am not sure what problem you see with statistics of gross observations. Heijmans et al (2008) say "Clinical examination, including blood sampling, was completed for 311 exposed individuals, 311 same-sex siblings, and 349 unrelated controls." Without having done a calculation of the statistical power of their analysis (I am not sure I understand the statistical properties of their assumptions well enough for that), I would assume that the statistical basis of their methodology is probably sound.

@David Regarding your second issue, Heijmans et al (2008) seem to suggest the explanation of methylation (of this IGF2 gene) being subject to changes in the early embryonic development which could account for the lack of a reversal in the same individuals in the 1960s. Note that other studies (Veenendaal et al (2013)) do not find this epigenetic effect, but they emphasize explicitly that they nevertheless find it plausible.

My point about statistics is that it says whether an correlation is likely to be true, but nothing about its basis — i.e. whether its basis is epigenetic. And as for blood sampling — not much DNA there — what does that actually mean? Such a lynchpin of human epigenetics needs more than plausibility.


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Why when measuring turbidity do we use the minimum wavelength?

As a preface, I read a few other related posts and was able to gather some knowledge, though without any background in physics I am having some trouble here piecing together a coherent view. I looked up videos of Beer-Lambert law on Khan academy and it gave a relationship between transmittance and absorbance as
$$Transmittance (T)=\frac{I_1}{I_0}$$ $$Absorbance(A)=-log_{10}(T)$$
Further, this post points out that turbidity is absorbance, and describes to be in relation to diffuse-reflected and scattered light?
Taking a step back, we see okay, turbidity is really just a measure of 'murkiness' and the amount of light that is scattered as a consequence. What about this diffuse-reflected light? And then this post says scattering is really just the sum of refraction and reflection. I don't think that is correct though, as this video shows refraction and reflection and scattering are different concepts, in so much as refraction is the bending of light as it passes through one medium to another, reflection occurs when light hits a smooth or shiny surface and bounces off, and scattering happens when the surface is rough sending the light in different directions. Then this post here. appears to detail out what would be a satisfying explanation but I haven't taken physics. Are there any good videos that might help better explain these topics?
Then, thinking about absorption my chemistry textbook talks about radiation and I had this concept in my head about light being absorbed then admitted at different wavelengths and I feel like that is true and perhaps that is where we are getting the relationship between transmittance and absorbance?
Bringing it back to the question that brought all this up, through other questions we were able to determine the answers to be To measure levels of pigment production it would be best to use the light of 450 nm, and to measure it turbidity would be best to use the light of 560 nm. In other words, for pigment production, we use the maximum value of absorbance and for turbidity the minimum value. The question we have is why this is the case? The most we were able to come up with is that the color of the Chlorella bacteria is green and that things are green because that wavelength of light is reflected, and that the wavelength of green light is 560 nm. I guess we can't use green light to measure the amount of green pigment because the light that would be returned would be a combination of reflected light (how much green pigment) + scattered light(not green pigment but returns green light) + (some combination of absorbed and reradiated light??). So we wouldn't be isolating the information we are after? If we want to know how much "green" is present this would be best measured by measuring the wavelength of light that is the least reflected, or the most absorbed, so the green pigment absorbs most of this light and the light that is not absorbed will tell of how much green stuff was there to absorb it. When it comes to the why for turbidity I am a tad stuck and I think it is because we appear to have a mixture of definitions above. Perhaps some more concise definitions will shed light. It appears the answer to "why can't we use green light" may help to give a possible answer, as the scattered light is the measure of turbidity and that would be with some margin of error, what we have isolated?

Usually when measuring materials in a spectrophotometer we want to use the absorption maxima to minimize the signal-to-noise ratio, that's why for pigment measurement you'll use the maximum point. But when you measure two materials you want to take two measurements with as little correlation as possible, that is to avoid one material influencing  your measurements of the other.
Imagine you are trying to breed C. marina for more pigment. Obviously more algae = more pigment so you want to measure how much algae you have and normalize by it. If you'd measure alga density in a wavelength correlated with chlorophyll content you'll get inaccurate results.
I think the question is ill-worded. You should measure at the pigment's absorption minima and not at the alga absorption minima. As the alga can have other peaks unrelated to chlorophyll. When doing this you should remember that chlorophyll and many other pigments are insoluble in water but your measurements of live cells are, usually, in water media.
The best in my opinion and that is the method I'm currently using is to build your own curve by counting cells in some manner (like hemacytometer) and measuring the full spectrum (Your graph stops at 750nm, I got up to 1000nm).


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DNA complementarity against reverse complementarity
I am sorry to bother with this question (i study genetics for about few hours, because I need to understand my data) and I am really confused about these two terms, because I dont know if the books uses word "reverse" interchengeably or what is going on here.
The main problem I am totally confused about are words reverse complementarity and complementarity of two DNA strands. Since I know that strands runs in antiparallel directions and two DNA strands are complementary to each other:
i.e. sequence ACTCTG is complementary to TGAGAC and vice versa.
But my question is: are two DNA strands reverse complementary to each other? Because at least in two books I have read that two strands of DNA are. But if I would apply it to my previous example and use reversion, then no way I can get to my other strand. Is the word reverse in this context use as antiparalel (5' - 3' and 3' - 5') or am I missing something and it's true that if I take the whole DNA strand, I can use complement and reverse it and it will be my other strand?
Again I am sorry to ask this really basic question, but I am so confused about this terms.
Nice day to all and thanks if someone will have time to answer my question.

There is already a comprehensive answer to a previous question of which this is essentially a duplicate.

I agree that the definitions can be somewhat confusing when first encountered.
Each nucleotide has a complement A-T, C-G. But the DNA strand are reverse-complementary because when aligned from 5'->3' they are not (necessarily) complementary.
For example:
DNA strand 5'-ATCCGG-3'
complement 3'-TAGGCC-5'
reverse    5'-CCGGAT-3'
Since we want to write all sequences in the same direction we must call the strand reverse-complementary

OK, thank you a lot. I did not realise that there is a convention to align two strands of DNA in the same direction and then speaking of reverse complementarity. But it seems like a pretty natural way for comparing. Thank a lot again, and have a nice day!


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Why exactly does UMN lesion cause hypertonia?
The corticospinal tracts are excitatory in nature (Glutaminergic). So damage of the CST would mean less excitatory input to the LMN. By this logic, there should not be hypertonia. What is the mechanism behind this spastic (hypertonic) state of the muscle in UMN type of lesion?

The main idea is that most Corticospinal tracts end up in inhibitory (GABA releasing) inter-neutrons, which then synapse directly into the Lower Motor neurons. This means that positive stimulation of inhibitory neurons occurs, which leads to overall negative regulation of Lower motor neurons.(1)
And the book goes on to say,

The corticospinal tracts are not the sole pathway for serving voluntary movement. Rather, they form the pathway that confers speed and agility to volun- tary movements and is thus used in performing rapid skilled movements. Many of the simple, basic voluntary movements are mediated by other descending tracts.

Note that the other descending tracts would be the extra-pyramidal tracts, which, are responsible for the most evident signs of UMN lesions, which include spasticity, hyper-reflexia, hyper-tonicity and severe paralysis.
Here is the list of symptoms of lesions localised to the pyramidal/coricospinal tracts:

Positive Babinski sign.
Absence of Cremasteric reflexes.
Absence of Superficial abdominal reflexes.

1- South Asian Edition Of Snell's Clinical Neuroanatomy


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renal portal system
I am a high school student.
In my textbook it is written that Mammals don't have renal portal system because they have four chambered heart. I understand that the four chambered heart keeps the oxygenated and deoxygenated blood separate but what does it have anything to do with renal portal system?

Excellent question!  The book is right, but ... well, biology has a hard time with the word because.  We read causes and effects into evolutionary designs to make them easier to remember, much as the ancients linked everything to the four humours.  There is an answer to because, somewhere in a very long period of geological history, but take all assertions (even mine!) with a grain of salt.  I will, of course, use this word quite often below, with great and misplaced confidence.
I would disagree with the statement that we don't need a renal portal system.  There are unfortunately many cases of acute kidney injury that result from something as straightforward as blood loss.  The kidney needs to shut down the blood flowing in (constrict the afferent arterioles) because filtrate production would further reduce the volume of the blood.  However, the kidney itself depends on the blood coming out (efferent arteriole; peritubular capillaries; vasa recta) to sustain its own needs.  It often dies in the attempt, and without kidney dialysis or a lucky transplant, so would the person.  The renal portal system would have prevented that by allowing blood to reach the peritubular capillaries (and presumably the vasa recta once it evolved) by non-leaky vessels.  The portal system means that blood is at less-than-arterial pressure, comparable to blood after it has been put through the glomeruli.  The system is cunningly wrought so that valves in the veins can force blood into the portal system only when the normal arterial input is reduced: (Akester, 1967)

How did we lose the system?  I have no idea.  Sometimes we lose things like the enzyme to make vitamin C apparently by pure chance - at some point in time, our ancestors didn't need it for a while, and key genetic information was corrupted because natural selection didn't fix it.  Other times, there is a small overhead in metabolic cost or the potential for other disease.  Maybe the excellent adaptations of mammals for water recovery with a long loop of Henle were incompatible with the structure.
What is clear is that we can do without it, normally, unlike many other species that frequently shut down some or all of their glomeruli by constricting afferent arterioles.  This is related to the heart, since the blood goes directly from aorta to renal artery instead of passing through the capillaries of the lung first, and therefore has a consistent high pressure (Keogh, 2021).  But it is also related to the issue of why we aren't shutting down urine production.  Mammals have a consistently high metabolism, requiring constant internal heating.  This goes beyond mere sugar consumption - our active bodies are continually generating urea, uric acid, creatinine, and other wastes that contain nitrogen that need to be flushed out of the blood.  So we pretty much do want to keep the glomeruli going all the time, and we have a powerful four-chambered heart that does that effectively while powering the rest of our lifestyle.  By contrast, reptiles are known for sudden bursts of action and long periods of inactivity.  Their cold-blooded physiology has much less need for food, and I think they don't need to excrete waste so consistently.
I should apologize for not keeping the answer simple, but understand this is a question that would stump good college anatomy and physiology students!  I've started linking some terms above - feel free to ask for clarifications on anything.

Sorry,but I am a high school student ,and only understood only half of what u have written, can u please give me a possible satisfactory explanation of how Four chambered heart helps us in this? It is due to four chambered heart that's for sure because in every biology textbook this is the reason given but I don't know why? My guess is that hear keeps deoxygenated are oxygenated blood separate and oxygenated blood also has less impurities than the deoxygenated, thereby in mammals comparatively less impure blood is supplied to tissues, whereas in fishes and amphibians mixed blood is supplied

In a 2-chambered heart, blood starts off going through the gills.  After that, the blood moves through the rest of the body.  So the pressure of the blood is LOWER when it enters the kidneys to be filtered than it would be if the heart were 4-chambered with the same pressure inside.  So when the organism is trying to increase its blood pressure, it will want to constrict the blood flow being filtered in the kidney, but that would drop the blood pressure moving the blood through the kidney tissue even more than it does in mammals.  Unless there is a backup plan.

Wastes in the mixed blood are not likely to be the explanation.  Though it is not the best thing for them, people on dialysis can go days between sessions.  So the body doesn't need to remove this waste right as it is formed before it mixes with other blood.

but even in the organisms having three chambered heart like amphibians renal portal system is present and well developed? why? they too can provide direct blood to kidneys as 4 chambered heart is not necessary for this


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How long would you expect a designed plasmid to remain in a population of E. coli after transformation?
When transforming E. coli with a genetically-modified plasmid, how quickly/often is this plasmid "lost" because of mutation, or horizontal-transfer, or "dilution" over reproduction over several generations?
How often are inserted plasmids lost/mutated/diluted in E. coli? How long would you expect to observe the plasmids' output after transformation?

It depends on a number of variables, like the plasmid you're using, the strain of E. coli, and the culture conditions. Most expression vectors require some sort of antibiotic selection for maintenance. I've been able to cure high-copy-number plasmid vectors in a single overnight culture without selection.

There isn't a simple answer.
There are a lot of factors which can influence how stable a plasmid will be. I'll describe what the main factors are, but to work out exactly how stable your plasmid is, unfortunately you'll just have to test it. I've given links to some studies which do this at the end.
Copy number
Copy number refers to how many copies of your plasmid are present in each cell. This can range from 1-10 for low copy number plasmids, to 300-500 for high copy number plasmids. Generally, low copy number plasmids can be lost easier than high copy number plasmids as there is a higher chance that the plasmid won't be present in one of cells after division. (https://www.nature.com/articles/s41598-017-05219-x)
Plasmid Size
Very large plasmids (in the mega base range) tend to be less stable than smaller plasmids as organisms, especially E. coli, can struggle to replicate them. This means that over time, less of the plasmid will be present in your system. (https://pubs.acs.org/doi/10.1021/acssynbio.0c00008)
Selection marker
Typically, synthetic plasmids will have a selection marker encoded which is used to provide selective pressure for keeping the plasmid. The exact marker used can affect the stability of the plasmid, as some are more effective than others. This paper has a good comparison of two different markers and measures the stability of plasmids for each: https://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-8-61.
Burden
Plasmids normally contain an insert which encodes your system. Some inserts will have relatively low burden on the cell (for example low expression of a small protein). Others may involve high expression of many proteins, or proteins which are toxic to the cell. Mutations are much more likely in high burden plasmids compared to low burden plasmids. This is because cells containing plasmids with mutations which reduce/stop expression will have a much higher fitness advantage over those cells with unmutated plasmids. Other time, these mutated plasmids will become dominant and eventually you will lose your original plasmid. There's some good reading about cell burden here (https://2019.igem.org/Team:Austin_UTexas/Measurement) and here (https://pubmed.ncbi.nlm.nih.gov/25849635/).
This is anecdotal, but I've managed to run 24 hour experiments with plasmids about 5kb in size containing a low burden insert and without using any selection marker without seeing plasmid loss. I've also had trouble even cloning plasmids of about the same size but with antibiotic selection and a high burden insert without any mutations occurring. So it really does depend on what your plasmid is and what it's expressing.
Measuring plasmid stability
Here are some examples for how you can measure plasmid stability:

https://link.springer.com/protocol/10.1007/978-1-4939-9877-7_16
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966108/ - This paper describes plasmid stability mathematically
https://academic.oup.com/femsle/article/232/1/45/490969


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Why are many skin depigmenting agents toxic to the body?
Coming from a developing country, I know many people who regularly use these creams to lighten their skin and some of them have developed liver and kidney problems as a result.
I know that many contain hydroquinone which is said to cause cancer and mercury which can cause neurological issues. Are these the two main problematic skin lightening ingredients or are there any else?

Not sure why your question got downvoted. I am upvoting.

I am not downvoting, but it seems to me that the question is really not about biology - perhaps more suitable for the medical sciences. It could be biology, if it were, e.g., about the mechanisms of damange caused by these cremes, etc.

In the late 19th and early 20th centuries, cosmopolitan women in the US and Europe would eat 'arsenic complexion wafers' because the arsenic made skin look pale and caused an attractive "rounding up" (generalized edema) of the skin. These "arsenic eaters" were partly why it was one of the first agents identified as a carcinogen. Accidental overdoses were also common, which made it difficult to prove murder by arsenic poisoning. But, to my knowledge, this kind of arsenic eating went out of vogue some time in the early 20th century.


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How do enzymes not change the overall energy change of the reaction they're catalysing if they lower the activation energy?
Based on the Induced-Fit model of enzyme action, enzymes catalyse a reaction by lowering the activation energy of a single forward reaction over and over. But I read that enzymes don't change the overall energy change of the reaction $(\Delta H_{solution})$ they just speed up the reaction.
How can enzymes reduce the activation energy of every forward reaction but still not affect the $\Delta H$? $\Delta H$ is sometimes called change in heat because it is measured in Joules and it's either endothermic or exothermic (this bit is chemistry).
I'm a highschool student and I'm just trying to find out how the required activation energy doesn't affect the energy change for the whole reaction.

Welcome to SE Biology. Please finish the [Tour] and learn how to ask questions here. One of the first things to do is to search for previous postings of the same or related questions of which there are many on the topic. You are incorrect in your recall of what you read. It is the Gibbs Free Energy of a reaction, ΔG, that enzymes do not affect. This is definitely not the same as ΔH:  ΔG = ΔH − TΔS. So your question is invalid as it stands. I would advise you to read (this section of Berg et al.) [https://www.ncbi.nlm.nih.gov/books/NBK22584/] which addresses this topic.

I’m voting to close this question because it is based on incorrect premises.

You're on a valley on one side of a mountain (representing some fairly stable state of your reactants), and you'd like to go to a town on the other side at a lower elevation (representing another stable state for your products, at lower energy than your current state: this is an energetically favorable reaction).
You can go over the mountain: high activation energy to climb up to the top, then you go down the slope to eventually get down to the town.
You can go through a pass between mountains instead: much lower activation energy to get over the pass, then you eventually get down to the town.
Whichever path you choose, you're at the same elevation (energy, $\Delta H$ compared to where you started), with the same products (your location in space), but if you took the pass you've gotten there via a different chemical route that was easier to achieve energetically at the peak.
Enzymes let you take the path through the pass rather than over the top of the mountain. They don't change where you started from or where you're going, so they don't change the overall energy of the reaction.


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What is this Patagonian biome?
This image was taken in Patagonia, near the Torres Del Paine National Park.
What type of biome this is? There are trees and other vegetation, but they seem mostly dried. I think this is either a semi-arid region or some type of transition zone to a forest, but I'm looking for a more concrete answer.

Certainly some kind of heathland. Looks too moist and shrubby to be Patagonian steppe. I'd guess a Magellanic subpolar forest type of ecoregion. Coloration appears to be due to it being autumn. I know that there has been a long history of grazing in this region with recent efforts of conservation returning steppe to shrubbier habitats. Hard to see details on my phone. I'll try to draft up an answer when I get a chance

Welcome to Biology.SE! It would probably be helpful if you provided more precise location information (altitude might also be informative) — Patagonia isn't a small area and I suspect it contains multiple biomes. If you could provide identifications for any of the plants in the picture that would also be helpful. Thanks!

@tyersome Unfortunately I have no information about the plants, but I did found out some more information about the photo, I'll add it.

A visual search (Bing) turned up several similarly stunning photographs at Culture Trip.  I think that the mountains are recognizable in at least one - with suspicion this photo may have been reversed.

If as @MikeSerfas has suggested this is not an image you produced it is important that you include a source and copyright information (you should not be reposting other people's work without acknowledgement and permission). Thanks!

I didn't mean to suggest any such thing - I only wanted to help understand the beautiful location.  The main thing that seems out of place about the photo above is that the animal in the foreground is not a unicorn. :)  But looking at the Wikipedia article I noticed great similarity of the mountain (not the photo!) to their lake image of Cuernos Del Paine from the Lago del Toro (but reversed), which should help to identify the biome.  Also see https://www.google.com/maps/@-51.144369,-72.6814447,14993m/data=!3m1!1e3 though it isn't as helpful as I'd hoped.

@MikeSerfas Yes, the photo was most likely reversed, already put the original, thanks!

Based on my experience, the answer to this question my further be complicated by grazing in the area. We have a horse in the image, and the ground vegetation looks like it has been grazed quite heavily (if this is a grassy type ecosystem). If this is a heathland then we seem to be missing many of the heath shrub species we would expect (Genus Ericaceae) unless they are quite small.


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What are the relative roles of coding DNA versus regulatory DNA thought to be in evolution?
Intuitively, once you have the idea that some DNA is responsible for turning on and off the DNA that codes for proteins, it's possible to imagine that the regulatory DNA is actually the most important part. In the ingredients list of a recipe, you might think the coding DNA gives you the list of ingredients, but the regulatory DNA gives you the amounts of each one, plus the order in which you add them to the bowl. If that's true, then different variants of regulatory DNA should be selected for and against, and evolutionary molecular biologists ought to be tracking those variants like they track alleles of genes. But evolution always is discussed as if it's just about different gene frequencies.
Is "regulatory evolution" a thing? If so, is there an understanding of how big a thing it is? Or, if not, why not?

Evolution is rarely about gene frequencies — much research does, however, focus on allele frequencies. In any case, in a modern context a gene includes its regulatory sequences. While allelic differences resulting from changes in regulatory sequences are harder to identify they most certainly are being considered, so I'm afraid your question is based on a false assumptions about both genes and evolution!

I think the focus on gene/allele frequencies is more due to the historical reasons - notion of gene is rather old, preceding even the knowledge about the DNA, whereas the existence of regulatory DNA is recent knowledge. However, most of the discussions about genes/alleles are easily transposed to the regulatory DNA. I agree with @tyersome that gene and allele are not the same thing... but these words are used interchangeably in many contexts.

Yes, a simple google search reveals millions of academic citations talking about "regulatory evolution".
But it's a little over-simplistic to divide coding vs. regulatory DNA. Indeed, some coding DNA is in fact also regulatory at the level of determining gene expression in cis (a well-known example of this would be codon usage).
It is moreover incorrect to think that coding DNA products don't do gene regulation. This was recognized very early on in the ideas of "structural gene" vs. "regulatory gene". These days we would call the latter transcription factors, we don't really use the structural/regulatory terminology anymore. Transcription factors do most of the actual active work of gene regulation in trans, in collaboration of course with regulatory DNA.
So in conclusion, yes it's important and there are tons of studies that you can google if you want to investigate these problems. I would suggest reading more about cis-regulatory and trans-regulatory elements. Of course, there isn't an exact mapping of coding<-->trans and noncoding<-->cis, it's just a helpful simplification.


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How do gene locations change during crossing over events?
Suppose you have two variants from the same species, which have slightly different chromosomes I's to each other. Genes may be in slightly different positions on the chromosome, and the lengths of the chromosomes might be somewhat different. Suppose these are crossed to produce offspring. If a crossing over event occurs in the offspring during meiosis, what happens to the positions of the genes?
A concrete example of what I'm asking is the following. Suppose that in the above scenario, the first chromatid is 1Mb long and the second is 1.05Mb long. "Gene A" occurs between 6kb-8kb on the first chromatid and 10kb-12kb on the second. If the crossing over occurs and replaces the first 9kb on the first chromatid, what happens to gene A there? Does it cease to exist? Or does the crossing-over process somehow know to grab DNA from above 12kb from the second chromatid?

Are we talking purely about the natural process here, or also about the artificial? In the latter, making cuts and realignments is possible.

Jabath, can you please add some reference?
(Interesting subject, I thought horse and donkey wouldn't have any off spring "any way".)

It depends on the regions of sequence homology between the two chromosomes. Crossing over occurs through pairing of homologous regions. If there's a substantial stretch of chromosome without a matching homologous region on its pair, that non-homologous region should loop out and not be involved in crossing over. Crossovers will occur only in paired homologous regions.
For example, if you have a chromosome I and I' as follows:
I   ABCDEFG
I'  ACDEHFGM
They should pair as:

A-(A)
B
C-(C)
D-(D)
E-(E)
(H)
F-(F)
G-(G)
(M)

Crossovers should not happen in the B, H, or M regions lacking homology with the other chromsome. Crossovers in a homologous region will just result in a new chromosome containing the left end of one crossover partner and the right end of the other.
Using I and I' above, a crossover in region E would produce either:
ABCDEHFGM or ACDEFG
Now, if you have repeated regions of homology in one or both chromosomes, or regions inverted on one chromosome vs. the other, pairing possibilities expand rapidly and all kinds of weird things can happen (and do in real life).

Please add some basic reference.
For instance, Wikipedia, Crossing-over, would not do.
"I'd go ahead" as form of addressing made me delete my comment above

"Molecular Biology of the Cell" by Alberts etc is a classic. I'm not sure of the best free/online into, maybe Khan Academy? That's why I suggest that you post a new question asking for the type of introduction you are looking for (with the usual evidence that you have done some searching on your own first).

Just to let you know, what I found was "As in mitosis, the sister chromatids in each pair are tightly connected along their entire lengths, as well as at their centromeres, by proteins called cohesins." Any pairing seems to lead to one single exchange, no more.

If a crossing over event occurs in the offspring during meiosis, what
happens to the positions of the genes?

Most of the time, things do not line up right, so the gametes do not contain the full information needed to make a complete organism, which is why when species are able to cross breed, usually the hybrids are sterile.

I've made a small edit to my post, but I actually meant to write that the variants are from the same species. In that case, is there a mechanism to make things line up?

Can you elaborate on "line up". Is there some adherence without exchange of DNS. Do homologous positions serve as point of adherence in any way (cp. answer by Armand: there is looping out). See also:    "Does crossing over happen in mitosis? It was a surprise for geneticists to discover that crossing-over can also occur at mitosis. Presumably it must take place when homologous chromosomal segments are accidentally paired in asexual cells such as body cells." (source: shortinformer, Emma Jonson). Maybe this is some other form of the foregoing comment.


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Recommendations for a haemocytometer (phase-contrast)
I'm looking for recommendations for a haemocytometer that can be used with a phase-contrast microscope. I want to use it to quantify the vegetative and spore fraction in my samples. Can I use any haemocytometer, or should the counting chamber be reduced in overall thickness?


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Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)
I came across the term ISHH in my document and discovered that it stands for In Situ Hybridization Histochemistry. I's translating to Russian a document that uses this abbreviation.
Example from the PubMed:

We then validated these findings by using a combination of tools, including the analysis of an additional brain region in an independent subject cohort, cross-validation with an alternate custom microarray platform, and follow-up with in situ hybridization histochemistry (ISHH).

Is there any difference between ISH and ISHH, or are these just synonyms for the same method, in situ hybridization?

Helpful histochemistry def'n: "the branch of science concerned with the identification and distribution of the chemical constituents of tissues by means of stains, indicators, and microscopy."

The term appears to be in use as a synonym.  PLOS ONE is a good journal, and in it Okubo, 2016 write "The protocol for ISHH was described in detail previously [22]."  Where [22] is Yamanaka, 2007, describing a classic ISH protocol.
Note that both papers use good old fashioned nuclear tract emulsion for S-35 labelled probes.  The ISHH protocol is in its own section separate from IHC.  It seems a bit odd because no literal "chemistry" is involved in recognizing the target - the RNA probe binds non-covalently and emits radiation.  However, as noted in the question discussion, IHC is formally defined (OED) as "the branch of science concerned with the identification and distribution of the chemical constituents of tissues by means of stains, indicators, and microscopy".  For example, though I have seen immunofluorescence and immunohistochemistry used to describe mutually exclusive visualization options, noncovalent binding of fluorophore-labelled antibodies is described as "fluorescent IHC".


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Are there any barriers to telomere sequencing other than length?
In the comments to an answer on this question, it was noted that long read sequencing methods (e.g., from PacBio or Oxford Nanopore) have largely eliminated repeat-based assembly problems for bacteria. This paper on centromeres suggests that this is nearly the case for those sequences as well.
Telomeres, however, can be much longer, up to 50kb for humans. Read length is thus obviously still a barrier for telomere sequencing, even with the best current technologies.
My question, however, is this: are there any other barriers besides read length? Telomeres also have other modifications, such as their loop structure, and are famously subject to degradation. Do these or other issues also pose barriers to sequencing, or are they readily dealt with in normal protocols?


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Do the nasal cilia move the particles trapped in the mucus out of the nose or down the throat?
Do the nasal cilia move the particles trapped in the mucus out of the nose or down the throat?
What is the direction of the pulse of the cilia? Is this changeable?

Mucus generally moves down the esophagus. If you notice , you will make many small swallow actions during the day, generally not enough volume to notice . It includes some saliva. As a result of cancer ,I cannot swallow so I am very aware of the mucus flow.

The movement is towards the pharynx (to be then swallowed).
It's useful, in the case of respiratory cilia, not to think of it as 'up' and 'down,' but rather as 'toward the pharynx.' In the lungs and the trachea, the movement is 'up' to move the mucus to the throat, and in the nasal cavity, the movement is 'down,' but again toward the throat. The aim is the movement of the mucus out of the respiratory tract and into the esophagus.

I knew that the returning is needed. The direction of the movement of particles that is caused by cilia is my question.

Where did this information come from? I'm wondering because there's not much detail and I don't know enough about the subject to know if it's reliable or not.

The nasal cilia beat toward the rear of the nasal cavity, driving nasal mucus into the throat (pharynx). From there, it is mostly swallowed. Cilia never drive mucus out the front of the nose (nostrils).

Where did this information come from? I'm wondering because there's not much detail and I don't know enough about the subject to know if it's reliable or not.


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Examples for oscillatory behaviour in the human body
I'm looking for examples in the human body which show periodicity, more precisely, I'm looking for examples of oscillating reactions that occur in the human body which can be modelled using the Hamiltonian of the harmonic oscillator.
for example, as someone mentioned to me before, the circadian rhythm is controlled by the oscillation of protein concentration. I wanted to know if there are some examples from biologists perspective?
I want to read more about it, and I will be grateful to hear more examples so I can look for information about it online or if anyone could refer me to some reading material regarding this subject.
Thank you very much for your time and attention.

it would be helpful to know more about the hamiltonian of the harmonic oscillator, what it is traditionally used to model, why you would want to find such a mechanism, and any other relevant data. you don't normally start with a model and then go around looking for systems; you usually start with systems and try to figure out models that might match them.

@MaximilianPress thank you for your comment. I'm sorry for expressing myself so poorly, I edited my post, I hope it's more clear now.

This is a very broad question since a) periodic changes are not necessarily oscillations in Hamiltonian sense (like circadian rhythms, which is hard to describe as oscillations - just like roration of Earth around the sun), b) non-linear oscillations are not necessarily Hamiltonian and/or harmonic (like those describing the dynamics of a heart). It might be too technical to discuss in the biology community, but this is something you should keep in mind. Perhaps, you could post a parallel question on phsyics exchange, since it borders on biophysics.

Mathematical physiology by Keener could be one place to look at - the chapter on wave propagation certainly has oscillators in it, but there shoudl be more material spread over the book: https://books.google.fr/books/about/Mathematical_Physiology.html?id=xWBb7b5eEFoC&source=kp_book_description&redir_esc=y

@Vadim Thank you very much for your advice. I will look into it and I will try posting also on physics exchange.

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


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How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?
I am performing experiments with the yeast Pichia pastoris where it will be beneficial to calculate product yield per cell. I plan to use a plate reader to measure OD600 of my cultures and then somehow relate this to cell number.
The Pichia pastoris expression manual from ThermoFisher says that 1 OD600 is equivalent to 5x10^7 cells/ml, and Weis et al (2004) have a similar number of 1.5x10^8 cells per 1 OD.
However, there are now calibration protocols (Beal et al 2020) and packages (Fedorec et al 2020) for using absorbent beads to convert OD measurements to cell density in E.coli. These rely on the beads scattering the light in a way that is equivalent to cells, so that one can compare measurements of OD with a standard curve of known amounts of beads to estimate cell number. Pichia is about 5µm in size size, compared to E. coli which is about 1-2µm, therefore I do not believe that using the same protocol will work for me.
Is it necessary for me to develop a new protocol, or can I just convert by multiplying OD by the numbers given above? If it is necessary, how can I develop such a protocol? Can I just use the E. coli protocol that I linked with different size beads?
Refs:

Weis, Roland, Ruud Luiten, Wolfgang Skranc, Helmut Schwab, Marcel Wubbolts, and Anton Glieder. ‘Reliable High-Throughput Screening with Pichia Pastoris by Limiting Yeast Cell Death Phenomena’. FEMS Yeast Research 5, no. 2 (1 November 2004): 179–89. https://doi.org/10.1016/j.femsyr.2004.06.016.
Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten 2020. Calibration Protocol - Plate Reader Abs600 (OD) Calibration with Microsphere Particles. protocols.io
https://dx.doi.org/10.17504/protocols.io.bgy6jxze
Fedorec, Alex J. H., Clare M. Robinson, Ke Yan Wen, and Chris P. Barnes. ‘FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data’. ACS Synthetic Biology, 27 August 2020. https://doi.org/10.1021/acssynbio.0c00296.

Is there a reason you can't plate serial dilutions of your culture, and then create a CFU/mL vs. OD curve for your given growth conditions?

@acvill CFU/mL is very noisy, per citation #2

From a technical perspective, for the FlopR package you mention (and I believe also for Jacob Beal's protocol) you can simply change the bead size and perform a new calibration. The only information that you need is the bead count at each point of your calibrant curve.
However, using calibration beads of a given size assumes that your cells will remain approximately the size of the beads for the duration of your experiment. We know that cell size and shape vary based on growth phase, antibiotics etc. [1] This can cause substantial misreporting of cell counts but is currently brushed under the carpet. I would suggest that if your Pichia change significantly in size or shape during their growth, it would be worth using a range of beads sizes and attempting to calibrate different growth phases of your samples against beads that correspond to cell size at during that phase.
[1] K. Stevenson, A. F. McVey, I. B. N. Clark, P. S. Swain, and T. Pilizota, “General calibration of microbial growth in microplate readers,” Sci. Rep., vol. 6, no. 1, p. 38828, Dec. 2016.

It's worth noting that the calibration of different bead sizes hasn't been formally verified yet, but there's not reason to expect it won't scale.


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Does anyone know what insect species this is?
The insect has an approximate length of 2.5 cm and It was found in Panama, Central America.
It was living hidden between the leaves of a papaya tree (Carica papaya).

it looks like some kind of grasshopper nymph, but I couldn't find anything particularly close to it.

A better view of the animal's topside would help in the identification; at present, we CAN say order Orthoptera, suborder Ensifera (long-horned grasshoppers AKA katydids and crickets); with four segments in each foot it isn't a member of Grylloidea (most of the "crickets").


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Why are almost all inborn errors of metabolism autosomal recessive?
Technically, the only inborn error of metabolism I know that is autosomal dominant is acute intermittent porphyria. Also, the only inborn of metabolism I know that is X-linked recessive is Lesch-Nyhan syndrome.

Have you considered what the effect would be if the error of metabolism was autosomal dominant?  How likely would it be that the affected individual would live long enough to reproduce and pass it on (etc., etc.)

i would suggest doing more research into mechanisms of the various inborn errors and seeing what you find.

Most deleterious mutations are partial or complete loss-of-function (LOF) mutations; most of those can be functionally compensated for by the presence of a wild-type (normal) copy on the other chromosome and so are recessive. Genes on the non-pseudoautosomal parts of X or Y are effectively hemizygous in males and thus LOF mutations there will likely be dominant.  Such LOF mutations in females may also be dominant, depending on whether mosaic expression (due to X-inactivation) results in the phenotype.

From How do I write a good answer? in the [help], Answer well-asked questions. Not all questions can or should be answered here.


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Difference in rose seedlings with red or green seed leaves
I tried to sowing roses from rose hips the first time. (In autumn I collected some rose hips random from different bushes in the neighborhood. I mixed the seeds while sowing.) Now the seedlings grow one after another. Thereby I noticed, that some have their first leaves in a more red color, and others in a clear green.
Could I conclude some characteristics of the grown up plant out of this?
(I tried to search for "roses red or green leaves" but only get an amount of results with red petals...)

The first leaves of dicotyledon plants are called the cotyledons. Similarly, the scientific word for colour is pigmentation. Even searching with those terms though, I haven't been able to find an answer - I guess you'll have to find out for yourself!

@smartse If there is no answer here in around 6 month - AND I am remembering my question - I will write an answer myself ;)


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What is intracellular retention?
On the wiki page for proto-cadherins, they write, "The cytoplasmic domain also mediates intracellular retention, a property which distinguishes the clustered protocadherins from the related classical cadherins." citing the following source.
Unfortunately, I was unable to find much anything to go off. Anyone know off-hand what this terminology is referencing?

Based on this line from the paper you linked, it seems like they are using intracellular retention to refer to proto-cadherins being taken up in to the cell via endocytosis.

It is possible that the effects of deleting the intracellular domain might be a result of loss of an organelle retention signal located in the cytoplasmic domain of the protein and/or a decrease in endocytosis of the protein accumulated in the membrane.

This paper also refers to intracellular retention of cadherins in the context of endocytosis of proto-cadherins: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216661/
Based on this information, the quote from the Wikipedia page ("The cytoplasmic domain also mediates intracellular retention, a property which distinguishes the clustered protocadherins from the related classical cadherins.") seems to be saying that the cytoplasmic domain regulates proto-cadherins on the cell membrane being taken back up into the cell via endocytosis, hence retaining them intracellularly.

Thanks, man. My understanding of your answer is that for proto-cadherins downregulation is via the endocytosis process. As to what happens after endocytosis? Lysosomal degradation? So how would this compare to the up-and-down regulation of non-proto-cadherins? What benefits arise from one mechanism relative to the other?

I'm not too sure, I'd have to do some reading. It might be worth asking another question about that to get a good answer.


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What terms or concepts are used to describe the morning metabolic phenomenon involving glucocorticoids, glucose, and blood pressure?
A recent conference report described using a vaccine-based strategy to blunt a surge of high blood pressure that occurs between 5 and 8 a.m.  Apparently most heart attacks and strokes occur during this period, which makes this of special importance.  Presumably this ties in with preceding work showing that ordinary blood pressure medication is more effective when taken in the evening.
When I read about the "dawn phenomenon" (reduced glucose tolerance in type II diabetics) it is often treated in isolation.  Because glucocorticoids are a factor in the dawn phenomenon, it makes sense they could be involved in raising blood pressure during the same period.
This makes me wonder how much more I have missed.  There seems to be something special about the morning period in metabolism, something deserving of some name as fundamental as "sleep".  Yet I don't have one to use, and I don't know why it evolved, how its timing is determined, what its advantage is, whether it correlates with worker productivity, whether early risers and late risers and night shift workers have this period at the same time and so on.  Medical labs typically open at 7:30 a.m. - do they reference the time in relation to any of these phenomena?
Thus the question: what terms or concepts would you suggest to help someone research and pull together existing knowledge about the metabolic changes that occur in the morning?

Hypoglicemia is a rather common condition - often pronounced in the morning, but also not uncommon in the late afternoon (hence snacking), and particularly common in small children: https://en.wikipedia.org/wiki/Hypoglycemia

Morning surge, Prewaking surge, Sleep-trough surge, Rising surge.
Example of article using the terms:
"Morning Surge in Blood Pressure and Cardiovascular Risk"
https://www.ahajournals.org/doi/full/10.1161/HYPERTENSIONAHA.110.157149
This one is interesting in that it lists other articles and the term they used for the period you are looking for.


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Is this flying bug swarm termites? Found in New York city, approx 7mm
Just saw a giant swarm of these fly out in between pavers and a door sill from a small crack in the ground here in New York City.  There seemed to be hundreds of them swarming out very quickly.  They are about ant-sized.  Are they termites?
Here are photos:

Yes it looks to be Reticulitermes flavipes aka the Eastern Subterranean Termite.

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Does Invertase catalyse the hydrolysis of other sugars other than sucrose?
I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a colorimeter. Our results indicated that lactose and maltose were more effectively hydrolysed than the sugar alcohols sorbitol, inositol and mannitol. I'm guessing this could be because lactose and maltose are similar in structure to sucrose, which it normally hydrolyses, however, I was hoping there was a more concrete answer.

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

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Are there adaptations in tropical fish to compensate for less oxygen in water?
Warmer water means that the amount of gases- especially oxygen- dissolved in it reduces, since solubility of gases in a solution in most cases decrease with an increase in temperature.
I'm interested in knowing if tropical fish have any adaptations to account for this reduced oxygen compared to fish in colder waters. Any modification of the gills maybe?
Referencing the below articles, I have come to the conclusion that tropical fish end up migrating to shallower waters or cooler habitats due to the oxygen depletion, showing that this decrease in oxygen is serious enough to affect them. However, this may be due to excessive heating of oceans due to global warming. I'm curious about whether fish in tropical regions have any adaptations for living in ocean water that is heated purely by natural means, not anthropogenic ones.

References:
https://www.usgs.gov/media/images/temperature-affects-dissolved-oxygen-concentrations
https://www.pca.state.mn.us/sites/default/files/wq-iw3-24.pdf
https://www.sciencedaily.com/releases/2015/06/150604162455.htm
https://www.nationalgeographic.com/science/article/150313-oceans-marine-life-climate-change-acidification-oxygen-fish

How having access to less oxygen would be accounted for by swimming faster?

I'm not sure, that was just me speculating that a higher rate of respiration would mean more oxygen could be inspired in less time.

Welcome to Biology.SE! While dissolved gasses do tend to decrease with increasing water temperature there are many other factors that contribute to the actual concentrations (e.g.s: rate of use, rate of mixing with the atmosphere). Please [edit] your post to include evidence that dissolved O₂ is actually lower in tropical waters, by how much, and whether this difference is biologically significant. Without that background research (which is expected) your question is based on speculation and is thus off-topic for this site. Thanks!

Thank you; I've edited my question for the same. I wasn't able to find how much in magnitude this oxygen depletion was, and most articles I checked were about how global warming is decreasing the (especially tropical water) oxygen levels. I understood that a faster metabolism ('swimming faster' @Exocytosis) does not allow for adaptations to less oxygen.

Fish that live in cold water for most of the year actually have particularly strong hypoxia-tolerance adaptations, i.e. from summer heatwaves and algal blooms, compared to fish that are better oxygenated by waves and flowing rivers.
Goldfish and other fish are able to rapidly change the surface area of their gills in less than a day.
Carp, killifish, goldfish and oscars have 2/3 times as much glycogen in their bodies than river fish i.e. rainbow trout.
There's a lot of research into the biochemistry of fish's oxygen response, i.e. gene expression changes, things like decreased expression of genes involved in the citric acid cycle.
Probably you will find most of the information on the wiki page, there are also summaries of current advances in the field.
On coral reefs, oxygen is a limiting currency for all the fish and zooplankton. The reading suggests to me that hypoxia adaptations depend mostly on heatwave events and low current waters vs rivers and coastal waves than by tropical vs pelagic and temperate regions.

Thanks for the answer, this is what I was looking for. These adaptations are only viable to a certain extent and not seen in all fish, correct? –

Many can breath air directly ; examples - bettas, gouramis, paradise , some catfish . No doubt others that do not come to mind .

Thanks.This is an adaptation seen only in tropical fish (Labyrinth fish are endemic to fresh waters of Asia and Africa), while @aliential 's excellent answer was more to do with fish that live in cold water.


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What is the effect of surfactant deficiency on dead space (of lung volumes)?
Surfactant deficiency in adults with acute respiratory distress syndrome has long been recognized. This deficiency causes decrease in lung volumes (tidal volume or redisual volume for example).
Dead space is the portion of each tidal volume that does not take part in gas exchange.
So this deficiency cannot cause decrease in the volume of dead space, right?
I am asking this question because our teacher told us that this deficiency causes decrease in all lung volumes, without exception.


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Measuring luminescence in a fluorescence plate reader
We're considering organizing some interlaboratory work on calibrating luminescence reporters (e.g., luciferase), and one of the key questions I don't know the answer to is whether most plate readers can measure luminescence or not.
From a first principles perspective, any fluorescence plate reader ought to be able to measure luminescence as well - just don't turn on the excitation light source. Thus, I would expect that a typical fluorescence reader should also be able to measure luminescence.
On the other hand, searching online, I am swamped by manufacturers eager to sell me specialized luminescence readers that emphasize their sensitivity, which leads me to think that maybe typical fluorescence plate readers can't measure luminescence.
My question, then, is this: should I expect that a typical current fluorescence plate reader will also be able to measure luminescence, or is this a much more specialized capability?

As the other answers here say, technically plate readers which are capable of fluorescent measurements can also make luminescent readings, but the sensitivity may be low (https://www.biotek.com/resources/technical-notes/use-of-the-fluorescence-optics-to-measure-luminescent-reactions-in-high-well-density-microplates-measuring-luminescence-in-1536-well-microplates/).
What I haven't seen mentioned is that there is potentially another hardware limitation depending on what type of luminescence you're using. Broadly there are two types: glow and flash luminescence.
Glow luminescence is probably most similar to fluorescence in that it builds gradually and can remain stable over an extended period (think of a lightbulb being turned on and warming up). Flash luminescence, however, is much more transient as the name might suggest. Reactions which cause flash luminescence produce a short burst of light (which could last seconds to minutes) which is typically brighter than that produced by glow luminescence. (https://www.bmglabtech.com/what-is-the-difference-between-flash-and-glow-luminescence-assays/)
As some flash luminescence assays will only produce a signal for a few seconds after the reagent is added, it is important to have immediate measurement, which can be provided by using auto-injectors within the plate reader. (https://www.biotek.com/products/detection-flash-luminescence-technology.html) These may or may not be included in a plate reader dedicated to fluorescent readings.
So to summarise, while luminescence can be measured by plate readers which can measure fluorescence, the sensitivity may be too low. In addition, extra hardware requirements, such as auto-injectors, may be required for certain luminescence assays.

Do you know if luciferase is flash or glow? I'm guessing it's glow, since otherwise it wouldn't be so popular, but I hadn't heard of flash before your answer.

It depends on the type of luciferase and the reagents/conditions used. I know from experience that bacterial luciferase (the lux operon) can produce a stable signal in vivo. There are luciferase assays using firefly luciferase for both flash and glow (https://www.thermofisher.com/order/catalog/product/16174 and https://www.thermofisher.com/order/catalog/product/16176)

Fascinating --- I didn't realize there was so much variety in luciferase.

I am René Inckemann and  I am PhD student at the Max Planck Institute in Marburg, Germany. In my PhD I am using luminescence on a regular basis and I was also responsible to organize some of our Platereaders.
So therefore I can tell you that you need a Platereader which is able to measure luminescence and you can not simply take a fluorescence platereader. The hardware for measuring luminescence and fluorescence is different.
However many Platereader models in these days already come with both options for the hardware, which means that you can measure luminescence and fluorescence in the same device. You just have to check your platereader model if it is capable of measuring luminescence.So you don't need a seperate platereader just for luminescence, but you need one, which has the luminescence addon installed.
Regarding your idea for normalizing luminescence, I also have strong interest in that and we have already started working on that. Maybe we can exchange ideas at some point?

Do you know if the hardware difference is primarily about sensitivity, or something else?

Anecdotally, all of the fluorescence capable plate readers that I have used have also been luminescence capable (BMG and Tecan models).
If access to luminescence capable plate readers is restrictive, we have also been able to measure luminescence using a GelDoc designed for imaging electrophoresis gels. This may be something to explore since I imagine gel imagers are more widespread that plate readers.

A priori what you say about the fluorescence and luminescence readers is correct,  even wikipedia states this directly:
Luminescence detection is simpler optically than fluorescence detection because luminescence
does not require a light source for excitation or optics for selecting discrete excitation
wavelengths.

However, it is worth comparing the fluorescence and the luminescence devices sensitivity and saturation threshold. It might well be that a luminescence device, designed to detect very weak levels of luminescence is blinded (i.e., saturated) by stronger light. What is more relevant to your case, the detectors in a fluorescence device might be insufficiently sensitive for practical purposes of luminescence study.
Still, it is better to consult a real expert before spending money on a new piece of equipment.