text:
Why is there a λ⁴ in the spectral overlap integral in FRET calculations
The Förster resonance energy transfer (FRET) spectral overlap integral looks like:
$$
J=\int_{0}^{\infty}\bar{F}_{D}(λ)ε_{A}(λ)λ^4 dλ
$$
Where $λ$ is the wavelength, $\bar{F}_{D}(λ)$ is the normalized fluorescence emission spectrum of the donor(normalized to unity area), and $ε_{A}(λ)$ is the extinction coefficient ($M^{-1} \ cm^{-1}$).
I am not very familiar with resonance energy transfer but was just curious why would a $λ^4$ term be contained in this spectral overlap calculation. The intuitive implication would be that the longer the wavelength, the larger the spectral overlap?

See for example Eq. 12.1 on page 471 in FRET and FLIM Techniques
(Theodorus W. J. Gadella, ed. 2008) or the corresponding  $\omega^{-4}$ in the integrals of Eq. 14.30 of Sect. 14.5.1  in David L. Andrews' Chapter 14: Resonance Energy Transfer: Theoretical Foundations and Developing Applications

I don't know  why the ^4, but think about excitation energy with longer wavelengths...

If you write the integral in terms of dipole strengths the $\omega^{-4}$ disappears[1]. Perhaps, look at the relationship between emission spectra and dipole strength to see if that explains the $\omega^{-2}$ per factor.

Why this is such a good question

After finishing teaching at 8pm EDT, it took me about 1 hour to find the answer and 1.5 hours writing this answer and confirming things. The Wikipedia article just gives that formula out of nowhere and cites [17] which is nothing but a table of contents (apparently not containing the string "rster" from Förster anywhere) for a book that I couldn't find online, [18] which is a Google Books preview of a book for which something related to the $\lambda^4$ does appear in Eq. 1.2 of pg 13 but explains nothing about where it came from apart from citations to {61}, which is missing from the Google Books preview, and 81-84 which are all books (unlikely to have a free PDF lying around), and [19] which gives the relevant formula in Eq. 14.1 but with no explanation and not even any citations to say where it came from.
Despite having worked in this field for a while, done my PhD in the general area, and even helped supervise a student whose Masters thesis gives a 5-page derivation of Foerster theory starting from page 30, I couldn't find where the $\lambda^4$ came from (the thesis presents the Foerster rate in a different way, which doesn't involve the $\lambda^4$, and I also looked at the reference in there to this paper on my friend Suggy Jang's generalization of Foerster-Dexter theory but it was done in the same spirit as my student's derivation, which unfortunately doesn't help us today with finding the source of the $\lambda^4$).  I thought I was in luck, because my thorough studying of the field meant that I knew one of the best reviews on the topic (this PDF of a paper by Greg Scholes currently with 1238 citations on Google Scholar), but it turns out he literally just gives the integral on Pg. 62 with no explanation. The textbook by May and Kühn might have the desired explanation, but I couldn't find a copy online. Every single paper and/or article I found online with a title like "Introduction to Foerster Theory" or simply "Foerster Resonance Energy Transfer" gave me nothing (some examples of the better resources I found were this, this, some detailed discussions here, this very interesting article by someone who hung out with Foerster in real life entitled "Förster's resonance excitation transfer theory: not just a formula" but then disappointingly it did indeed give "just a formula" at Eq. 4.
The original 1948 paper by Foerster in German (currently with 9994 citations on Google Scholar) doesn't seem to have anything resembling anything close to "the" desired equation. The only research paper by Foerster mentioned in his Wikipedia article doesn't have the equation either, and the famous 1953 paper (currently with 9977 citations on Google Scholar) by Dexter that earned him a spot in the name "Foerster-Dexter theory" doesn't have $\lambda^4$ or $1/\nu^4$ or $1/\omega^4$ anywhere, although now that I have the answer and double-checked all these articles to make sure I wasn't discrediting anyone, I do see that there's a $1/E^4$ in Eq. 16 but it's not as  close to your equation as what I'm about to show you.
The answer

This 1965 "report" by Foerster actually tells us how he got the $1/\nu^4 = (\lambda /c)^4$ right here:

Basically after 53 pages which largely set the reader up for it, he gets this expression for the transfer rate:

In that equation, you can plug in the following:

which will mean you'll get a factor of $c/\nu = \lambda$ in the numerator coming from the molar decadic excitation coefficient $\varepsilon(\nu)$ and a factor of $(c/\nu)^3 = \lambda^3$ coming from the normalized fluorescence quantum spectrum $f(\nu)$: the two combine together to form $\lambda^4$. Since Foerster tells us that these are "Einstein's well-known expressions" for $\varepsilon(\nu)$ and $f(\nu)$, I assume you don't need help knowing why those are proportional to $\nu$ and $\nu^3$ respectively...

... just kidding, explanations and more references about the Einstein coefficients can be found here and here and you'll see expressions proportional to $\nu$ and others proportional to $\nu^3$ in both of those resources.

I even got out my QM text and skimmed through a few chapters... I didn't find it because physicists don't use those functions (the Einstein coefficients physicists are taught are these [https://en.wikipedia.org/wiki/Einstein_coefficients]) Great detective work!

This is cool! Thank you so much for such clear answer!


text:
Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator
Hudson (1983) introduced a coalescent simulator with infinite-sites mutations and finite-sites recombination. This seems paradoxical because the documentation of the simulator (section on crossing over) states that "one should think of nsites as the number of base pairs in the locus."
To reconcile this tension, I've been thinking of the haplotype as comprising an infinite number of base pairs (to support infinite-site mutations) but that there are a finite number of initiation sites at which the sequence can cross over during meiosis (to support finite-site recombination). I.e. the sequence is "unbreakable" except at the initiation sites, and each segment between initiation sites still contains an infinite number of base pairs.
Is that a sensible interpretation or am I way off base?

I hope you get an answer to your question, although I suspect it will not be understood by many on this list (myself included). If you are unsuccessful, you might try SE Bioinformatics.

Thank you for the pointer! Will repost on SE Bioinformatics if this post doesn't prove fruitful.

The first sentence of the abstract of the Hudson paper states: "An infinite-site neutral allele model with crossing-over possible at any of an infinite number of sites is studied." (I don't have access to the full paper.) The documentation that you point to does say finite for recombination, FWIW. See also: https://en.wikipedia.org/wiki/Infinite_sites_model

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

@MaximilianPress, sorry, frustrating paywalls. They start with a finite-site crossing-over model but then take the limit to infinite sites. As you point out, the linked simulator sticks to the finite regime.

Caveat: never personally used ms, I might be missing a subtlety of how this model is intended to be used.
I think it's useful to see how Hudson himself writes about the utility of the infinite-sites model in the context of finite recombination. Recall, infinite sites is a simplifying assumption to make math easier. Tajima (1996) boils this down as follows:

...the infinite-site model proposed by Kimura (1969) assumes that the total number of sites in each gene is so large and the mutation rate per site is so small that whenever a mutant appears it occurs at a previously homoallelic site.

Thus, infinite sites just says (among other things) that any given mutation is at a new site where no new mutation has occurred previously. This is an assumption that is handy for doing population genetics, which Hudson employs. In one paper he (and a colleague) write:

HUDSON (1983b) has also developed an efficient method for simulating samples from the neutral infinite-site model with finite recombination. His method generates the "history" of a sample. The history of a sample is a collection of correlated family trees, one for each site (for DNA sequence data, each nucleotide is considered a site). The family tree for a site traces the genealogy of a site back to its most recent common ancestor indicating which sampled gametes are most closely related and when the most recent common ancestors occurred.

If the rate of recombination is zero, then each site has the same family tree and therefore the history of the sample consists of just one tree. The method for generating this tree depends on results of WATTERSON (1975) (for details see HUDSON 1983; TAJIMA 1983). On the other hand, if the recombination rate is infinite, then all of the family trees are independent of each other, and each family tree is generated in the same way as when the recombination rate is zero. If the recombination rate is finite, then the topologies and lengths of the branches of the Family trees are correlated because of linkage, and generating them is more complex but still possible (HUDSON 1983b).

In other words, infinite sites is an assumption that helps us study the behavior of recombination (which is, of course, finite). We could alternately consider models in which we make zero or infinite assumptions about recombination, to study the behavior of finite mutating sites.
Elsewhere in the documentation for ms, Hudson writes:

In this model, the number of sites between which recombination can
occur is finite and specified by the user (with the parameter nsites). Despite the finite number of sites between which recombination can occur, the mutation process is still assumed to occur according to the ”infinite-sites” model, in that no recurrent mutation occurs, and the positions of the mutations are specified on a continuous scale from zero to one, as in the no-recombination case.

So it seems that he is using the property of no recurrent mutations laid out by Tajima, but also the feature of assuming that coordinates of the region of interest are continuous rather than discrete. One can imagine that this is convenient to make computation simple.
I think that the mental model that you've laid out is not bad in terms of an intuition about behavior, but to emphasize the main properties that I think are useful, one might say that 1) every mutation/allele is in a different (continuous) coordinate (no recurrent mutation), and 2) the number of possible recombination sites is discrete (nsites). So there are nsites recombining regions, each without recurrent mutation (and possibly infinite continuous sites, though I don't see how this is actually implemented so it may simply be that each of a finite set of sites doesn't recurrently mutate).

source: Stack Exchange

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text:
How can I find/simulate mixed-ancestry DNA data?
Some collaborators and I are building an ancestral inference tool, and we're having trouble obtaining reliable ground-truth data for samples of mixed ancestry. All the ground-truth DNA datasets we're aware of (Thousand Genomes, Simons Foundation) are from persons reported as unequivocally belonging to some population (East Asian, African/African-American, South Asian, or even something specific like Somali, Icelandic or Cambodian.)
But we can't find any samples that are attestedly mixed-ancestry. We've thought about just generating simulated data using VCFs from two persons of different known ancestries, but we're not sure how to account for the non-random aspects of recombination, which are described here:
https://www.bio-itworld.com/news/2019/03/06/latest-genetic-map-finds-recombination-is-not-so-random
And we don't know of any tools that could perform this task for us.
Does anyone have suggestions for obtaining/simulating DNA data for persons of mixed ancestry? This is a natural enough problem that we suspect others must have encountered it also.

Price et al 2009 describe how to simulate admixed genomes in this paper.

We constructed 40 haploid admixed genomes (n = 1 to 40) from the 40
haploid Yoruba and 40 haploid French genomes by using haploid Yoruba
genome n and haploid French genome n to construct admixed genome n, so
that ancestral genomes were never reused. To construct an admixed
genome, we began at the first marker on each chromosome and sampled
French ancestry with probability α and Yoruba ancestry with
probability 1-α. Ancestry was resampled based on an exponential
distribution with weight λ (the number of generations since admixture)
so that a new ancestry was sampled with probability 1−e−λg when
traversing a genetic distance of g Morgans. Each time ancestry was
resampled, we sampled French ancestry with probability α and Yoruba
ancestry with probability 1-α. For each individual, we used a value of
α to apply to the entire genome by sampling from a beta distribution
with mean 0.20 and standard deviation 0.10 (typical for African
Americans [4])

You could apply this method to e.g. .bam/.vcf files from SGDP and use the sampled ancestry as regions in the .bam/.vcf file from different ethnicities.

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text:
Identification of black-and-white striped jumping insect?
I noticed this small insect with long striped antennae and legs hanging out on my parsley. I'd be curious to find out what it is.
When I got close to take a picture of it, it suddenly leapt, like a grasshopper, landing a good 12 inches away on another plant. Its body is about 1cm long. I live in Southern California if it makes a difference.

Excellent first post, great pictures. That being said, can you give us a rough idea of size (parsley comes in many varieties). Please enjoy our [tour] and refer to the [help] for guidance as to our ways.

@ARogueAnt. he said the body was about 1 cm long.

Ah yes, I was so taken by the images I must have missed that @mgkrebbs

Lovely, certainly looks like a hopper of some sort. I would guess an instar of something

Based on body shape and size, this appears to be a nymph of an assassin bug (family: Reduviidae).
I originally was thinking some species of Zelus (see bottom of post), but the orange body and bold leg-striping makes me think this is instead an early instar nymph of some species of Pselliopus.

 Credit: B. Newton (2004); Source: Univ of Kentucky
Pselliopus barberi (the orange assassin bug) is one option.
I'm on my way out the door, so I'll come back to this next week to see if a more specific species stands out...

Note: I was originally thinking the genus Zelus was a good place to start -- though native to South/Central America, about a half dozen species are found in the US. Zelus renardii (the leaf hopper assassin bug) is one such species that has an orange-bodied, black/white-striped legged instar. It's native to semi-arid and Mediterranean climates (both found in CA), and it's not too atypical to find them on crop plants even in suburban areas. [Source]. However, the leg striping just isn't predominant  enough

I doubt that this is a reduviid larvae especially due to the missing rostrum which is prominent in reduviid bugs (compare my answer below and this answer). Best, bathyscapher

Due to the

chewing mouthparts,
the greatly developed femurs specifically adapted for jumping (what fits well with the OP's observation of jumping behaviour),
prominent compound eyes and
long, filamentous antennae

we can conclude that this specimen is an orthopteran insect larvae.
Well known members of this insect order are grasshoppers, locusts and crickets.
Orthopterans undergo incomplete metamorphosis, progressing through egg, nymph and adult stages. Nymphs often resemble adults, but lack fully developped wings and reproductive structures. As this specimen lacks wings, we can conclude it must be a larvae.
Moreover, I assume this specimen belongs to the suborder Ensifera as its antenna are longer than its body (as opposed to their sister taxon Caelifera which have antenna shorter than their body).
It's often tricky to identify species from photos, so no guarantuee on that, but a genus with similar larvae would be Scudderia, the Bush Katydids, which is present all over the US with following similarities:

the "hat" with a dark lateral line
1st antenna segment brighter than the others
1st and 2nd antenna segments roundish
remaining antenna segments long, slender and dark with white ends
black eyes
white "cheeks"
typical slender, long legs with dark and bright coloration
the fine spines and hair all over the body

Image source: Katja Schulz CC-BY-2.0

Good answer, but do you this part around the wrong way? I assume this specimen belongs to the suborder Caelifera as its antenna are shorter than the body (as opposed to their sister taxon Ensifera which have more-than-body-long antenna). The pictures from OP clearly show antennae longer than body - as do the ones in your answer.

You are totally right, bob1! Thank you for reading carefully and pointing this out, I will change it accordingly :)


text:
Adh2 promoter in saccharomyces cerevisiae
I'm looking at expressing a protein in saccharomyces cerevisiae using the Adh2 promoter. My understanding is that the gene will be repressed by the presence of glucose, but when glucose runs out it should be activated. If my strain has deletions in ethanol biosynthesis, will Adh2 promoter still work?

Why wouldn't it? As long as you haven't deleted the transcription factor(s) that bind to the Adh2 promoter, it should work just fine.

I'm coming across publications talking about ethanol encouraging dimerization of the transcription factor into it's active state, and I just wanted confirmation if ethanol is necessary.

Ah. In that case, feel free to ignore what I said and do more research. I don't know much about Adh2 specifically (although I'm fairly well informed about transcription factors in general), so you'll have to see if the promoter is absolutely dependent on EtOH, or if that's just one way it's activated.


text:
How is brain calorie intake affected after hemispherectomy?
So, I hear brain consumes 20% of the body's energy, and also according to studies people with only one hemisphere can function mentally fine with little to no problems.
My question is, how does that affect calorie intake of the whole body or the brain? Is the calorie intake halved for the brain, cause it only has one hemisphere?
Source how it's done:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729844/

Welcome Hormoz. Do you have any reference to support that the entire central nervous system is halved? This is not simply a Q&A site, here we are expected to show the results of our own investigations into a subject here, you can [edit] to tell us what your searches found and where the sticking points are. You should also take our [tour] and refer to the [help] for guidance as to the ways of any site you post on, see our section on how to ask.

I mean that's what it is for, either partially or fully. That's like asking "do you have any source that addition is actually done in math?". A simple google search would suggest that such a thing exists. There are MRI scan pictures to suggest this too.
Of course I don't have all the details so I might not be right on everything, but that doesn't change the nature of the question which is about calorie intake after it.
I can include some source though regardless. Edited.

What I'm saying is, there needs to be a differentiation between "brain" and "cerebral hemisphere", there's a category mismatch in the question. Please re-read my previous comment.

So, as far as I know, there several ways to go about this, some which might not remove as much brain matter, some which can remove nearly half of it. Some parts might remain though.
As you say, the wording might not be completely accurate, but due to variety in how this is done, I am not quite sure how else I should word it? I can replace the word brain with hemisphere so edited.
I am asking for cases where nearly or completely half of a brain is removed.

How much energy is used by a missing hemisphere? None. Brain energy use is determined roughly by number of neurons. One would need to know the % of total neurons removed by that resection to give an estimate. If you provide that information, we'll approximate the reduction of energy by the reduced brain mass. Thanks

So the reason I am asking is not because I want to know how much energy on hemisphere consumes normally. It's mainly because when you remove one hemisphere, the other hemisphere takes over most of the work done by other. In other words, one hemisphere is doing the work of both. I wanted to know if that would mean the energy consumption of that hemisphere would rise due to that.

Ah, interesting. I don't think the remaining neurons do twice the work most of the work is "silent"), but they may increase dendrite formation. I don't think the answer is known, but it doesn't remain the same.


text:
Species identification: flaky worm
enter image description here
Recently our house got ABSOLUTELY INFESTED with the following creature.
Kindly identify.
Hapitat: damp shadowy regions of our house
Description: The outer flake is probably a shell, the shell is not very soft, not very hard. The smaller ones have really soft shells. I could not photograph it, but the shell houses a really small worm kind of thing that pokes out its head and then graples the wall or something and then pulls it shell to move. Movement speed is pretty small say about 5mm per second at max. The worm was black coloured with pretty undistinct and unclear yellowish rings. The worm thing can produce some spider web kind of thing which makes it stick to walls. I mean it sometimes appears to almost float against the wall/ceiling as it is hanging by its web. The spider web allows it to hang by a couple of millimetres above surface. Multiplies superbly fast like there are 20 new individuals within a day in some of the walls.
My best guess: a pupa of some moth. I spotted some moths flying around it once. Only once, in five to seven years.
enter image description here
[enter image description here
India. A place close to bangladesh. Plains temperature aroung 32 deg celsius in average

Also please do tell how to get rid of these.
Insect inside has no legs. Plus the shell, it appears to have the same colour as the paint of the room. Possibly the flaky shell is made out of the particle of the wall that the insect took up.

It looks reminiscent of Luffia ferchaultella a moth larva - a  lichen eater - but not quite, too flat. I can't find references of that species in India since the 1960s either so I'm not answering but leaving it to the experts to name.

Hmmm.... the species you mentioned does resemble my insect, but my insect is thinner in depth...

I would emphasize that the insect living inside does not have legs... plus there is no lichen in my house

Does this answer your question? What insect is this? (India) See also: this and this. ——— Please note that one part of the research expected of you is that you look for similar questions on this site before posting. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site for details.

@ tyersome yes i could not find these similar answers before thanks for pointing them out


text:
Does the kidney regulate sodium balance or total body sodium
Imagine the following situation. You have a person who initially eats 10 mEq/day of salt. He then, at t=0 begins to eat 150 mEq/day of Na, and will continue to do so, because you're forcing them to, forever. My question is about how the kidney responds to such a situation. There's two options.

Option #1: The Kidney ensures sodium balance (sodium intake = sodium excretion). In this situation, the kidney regulatory mechanisms ramp up Na excretion until it equals 150 mEq/day. But since this takes a couple of days, there is a bit of time in which intake > excretion and so total body Na rises. Because of osmoregulation, more water is drunk to balance the increased total body Na, and so the person's weight rises.
Option #2: The Kidney brings total body sodium back to normal. In this situation, the kidney regulatory mechanisms ramp up Na excretion, but it briefly ramps up excretion to more than 150 mEq/day (excretion > intake) to excrete out the increase in total body sodium that built-up. In this case, the weight gain is temporary.

See a graph describing the two different responses.

The situation is inspired by Chapter 40 of Boron & Boulapep's Physiology textbook. The reason for the question is that Boron states that Option #1 is correct, whereas my teacher in class said differently  ¯_(ツ)_/¯ .

What specifically does your book and instructor say happens? I suspect they differ a bit from the scenarios you've crafted in ways that make them quite the same, instead of in conflict...

I phrased the question to my teacher exactly as I have done so here. I asked, assume you have a person and you have them increase their salt intake consistently - a hamburger every day is the example I used - what would happen to their weight: would it go up then down, or up and stay constant at the new high value.

And what does the book say?


text:
Which varieties of Aurelia aurita do not have a polyp phase?
According to this "In some Aurelia aurita, the polyp stage does not exist.", but they don't cite anything. Is there a resource detailing life cycles of various jellyfish or do I have to find their list and search articles one by one?

I've edited your post to correct some formatting and improve the tags (please avoid creating new tags unless they fit many questions). I also replaced species with varieties in your title, since it doesn't make sense to talk about species within a species. ———  Also note that questions are better received here if they demonstrate that you have a done a significant amount of prior research — for example you could [edit] your question to tell us where you've looked for answers (other than the original website), what you do know about the topic, and where exactly you still have questions.


text:
Anticoagulation of black beans extract
How many ml of lithium heparin do I need to use on 2 ml blood to prevent coagulation for over 15 minutes?
I am comparing it to the 4 different dosages of black turtle bean extract that has polyphenols which I think have an anticoagulant effect.

At the very least, you will need to supply the concentration of lithium heparin, or work in milligrams rather than ml.

Thank you for responding. I only have  the lithium heparin from Vacutainer, which has 75 units and 4ml. Do you think I can use that as a control?

Is that Howell units, USP, etc.?


text:
Do plants digest substances they ingest?
I was thinking about plants having no digestion system (is that true at all?) and my conclusion was that they only ingest substances that they can use like that or that they can transform into usable ones (which then would maybe something similar to digestion).
So my question is:
Do plants "digest" substances that they ingested and then egest the "garbage"?
Also: can someone give me some hints where I can read about plant metabolism?

Welcome Chris. This is not simply a Q&A site, here we are expected to show the results of our own investigations into a subject here, you can [edit] to tell us what your searches found and where the sticking points are. You should also take our [tour] and refer to the [help] for guidance as to the ways of any site you post on, see our section on how to ask and see our homework-question policy.

As a starting-point, try plant-fungal-symbiosis and take a look at carnivorous plants for the other end of the spectrum.

for a starter, you might define (and possibly refine) what you mean by "digest" in the question.

Perhaps Plants can use protein as a nitrogen source without assistance from other organisms would also be of interest. This paper shows that roots have proteases that can digest (that is, breakdown by hydrolysis of the peptide bond) proteins

It's unclear to me if the question is asking generally about all plants, or only refers to digestion of food items by carnivorous plants.
If asking about plants generally, they don't to my knowledge perform any internal digestion. Non-carnivorous land plants take in materials in two ways, through their roots and through their leaves.
The roots take in water, along with molecules dissolved in the water. These include molecules containing nitrogen, phosphorous, and potassium, as well as other trace elements. Plants employ various strategies to enhance their uptake of water or nutrients, including pairing up with fungi or bacteria. Some also release low levels of acid to dissolve minerals for uptake. This could be considered a form of external digestion.
Leaves take in carbon dioxide. The CO2 is the primary source of carbon for the plant, and in turn is the main source of a growing plant's mass.
The waste that plants release is primarily O2, which exits the leaves through the same pores the CO2 enters. While roots release many types of molecules, these mainly have a functional purpose and aren't generally considered waste. Plants in salty environments also have mechanisms to expel salts.
So, no, plants in general do not perform internal digestion.
Now, carnivorous plants do capture and digest prey. This digestion is performed either by enzymes produced by the plant itself, or by microorganisms living in the environment of the trap. This would still probably be considered external digestion since it occurs either in open, liquid-filled pitchers, or on leaf surfaces that have folded over. The two sides of Venus fly trap traps do press together to form something of a seal while the prey is digested, but they open again when the meal is digested. The bladderworts, Utricularia spp., maybe have the best claim to "internal" digestion, with prey being dissolved inside small bladders covered by a trap-door mechanism. But these, too, originate from modified leaves or foliar structures.
Since the undigested parts of carnivorous plant meals are never really injested, they are not expelled.


text:
Is being able to interbreed and produce fertile offspring a transitive relation in biology?
Being able to interbreed and produce fertile offspring is one criterion to decide whether two populations are of different species.
Are there 3 populations A, B, C such that A and B are able to interbreed and produce fertile offspring, B and C are able to interbreed and produce fertile offspring however A and C are not able to interbreed and do not produce fertile offspring?

@worldsmithhelper: Would you be interested in the general answer on populations or in an answer about species?

If there exists such populations A, B, C examples with references would be awesome. If there are multiple "reason or mechanisms" for such tripplets of populations emerging examples of each mechanism with some elaboration on the mechanism would be appreciated. If there exists species tripplets A, B, C (and since every species is a population) they are welcome to. It doesn't have to be exactly triplets either quintuples or a continous spatially distributed population which has this property also works. If there is a strong reason or argument why this can't work that would also be accepted.

A useful example may be modern dogs, you have the chihuahua-great Dane problem, they can't interbreed without human intervention. and that is just breeds of the same species.

The ring species conundrum
As commented above, in essence this is the classic case study of ring species, and reading up on it will completely answer your question. A case of ring species is visualizable geographically (area A, area B, area C, and 'variant species' graduating across).
'Transitive', jargon and the idea of transition
Sure, something's transitive if A is B, and B is C, and it follows that A is C. But species are not transitive sets (of numbers). It's a bit along the lines of 'mixing'. Say, by analogy, if water dissolves soap, and soap dissolves fat, it does not mean that water dissolves fat. I wouldn't use mathematical terminology in biology (i.e. I would also not call species intransitive or nontransitive, it would not be helpful) but I would rather focus on the concept and word "transition". Lineages evolve and diverge gradually, some remain extant and co-exist with- and sometimes without interbreeding. I think lineages you can talk about in a very robust manner in the long term. The 'species' category is more about 'binning', deciding which section or degree of branching of the lineage you want to consider a unit.
Imagine the concept phylogenetically
Extant (currently living) canines are a nice example. Those similar can interbreed naturally, those dissimilar cannot realistically or even physically or genetically interbreed. Chihuahuas and wolfhounds or Great Danes could be construed as different species with our classical definition of species, because they truly do not interbreed. Yet they are widely and scientifically today considered the same species! You can surmise that there is difficulty with this classical concept of using 'species', when used stringently and in a strictly categorical fashion... let's consider it from another point of view...
Imagine the concept though time
If one's ancestors 5 generations back could interbreed with ancestors 10 generations ago, we could 'define' them as a species. Perhaps even those 5 and 1,000 generations back. What about 10,000? What about 100,000? 100,000,000,000? You see, every generation can interbreed with the next, yet at some point we choose to categorize them as different species. You have to understand that we define biological species not because there is such a real thing as a species boundary, but only because it helps us think about things by chunking them arbitrarily together. The concept of species is useful, but not objectively a feature in reality.
I would also refer you to my previous answer on what the definition of a species is and why it's always been problematic. I think that will help with a more complete understanding.

If you want to give a short summary what one is supposed to get from ring species i can accept the answer. As is the answer doesn't really answer the question but points to resources which do.

@worldsmithhelper An example may be to look up the classic example the Larus gulls. what we learned is these classical species definitions fall apart in light of modern genetics. they are useful tools of simplification not accurate representations of reality.

@worldsmithhelper I believe I've answered your question. Can elaborate when I find some time to spare... but as mentioned, ring species case studies are just an iteration (manifestation) of your abstract question. You asked for an example. There are many to find in ring species, and entire books have been written on this motif. Consider my mentioning ring species as simply grounding the question prior to expanding your understanding of the species concept. I rather think it more suitable to address your (mis)conception that there is such an immutable, exclusive identity such as 'species'!


text:
Why can't SARS-CoV2 antigen lateral flow tests be used for testing animals?
Real use case:
Two male neutered Felis catus individuals live in a household where up to three humans live of which all were infected with SARS-CoV2 at the same time, proven by antigen and PCR tests. All three humans were clearly symptomatic.
Funny sidenote: All three humans most likely contracted the infection at the same event, however two were diagnosed with omicron and one with delta by sequentiation.
After a week and with the symptoms of the humans already declined one of the cats developed symptoms with similarities to the humans in the following temporal order:

sneezing
coughing
repeated choking while feeding
sneezing with sputtering blood from the nostrils

After onset of symptoms and three days later an antigen lateral flow test designed for detection of SARS-CoV2 in humans was applied to the symptomatic cat. Sample was taken from the throat. Test kit was from brand Longsee. Both tests yielded a clear positive result. The cat was treated symptomatically and has recovered.
The results were reported to different veterinaries including the district veterinary office. All stated that the test result is void and most likely false positive, because tests designed for use on humans can't be used on other animals.
I want to discuss, which possible causes might lead to a false positive in this case.
I think it is very unlikely that we have a false positive here, my thoughts are

To my knowledge lateral flow tests for SARS-CoV2 detect either a spike protein or a capsid protein, so they react only on presence of parts of the virus.
The lateral flow tests are designed to be very specific to that virus. There are lots of corona viruses able to infect humans and provoke symptoms of a typical cold. So the tests should not react to other corona viruses.
There are corona viruses specific to other mammals (e.g. FCoV), however many of them have strong similarities to human corona viruses, so it is very likely that the tests are specific enough to rule out false positive

What aspects did I miss? Which effects you can think of preventing fairly good specificity of such tests when used in cats?
Maybe this question includes another question: What is the nature of false positives in lateral flow antigen tests for SARS-CoV2?

I had a look around the literature, and it seems that the tests are slightly less sensitive for some of the variants of concern on non-human saliva samples than they are for human1, but in general can be used to test for SARS-CoV-2 infection in animals. The linked study investigated bats, cats, ferrets, sheep, goats, cattle and pigs. RAT (Rapid Antigen Test, AKA LFA for Lateral Flow Assay) style tests have also been used successfully to test for SARS-CoV-2 in lions in Spain2
The tests largely detect nucleoprotein, as this is the most abundant protein in the virion.
to quote conclusion of the first linked article:

In summary, saliva of the species tested has no impact on the functionality and performance of SARS-CoV-2 RATs. Therefore, the use of RATs can be recommended as a point-of-care surveillance tool for SARS-CoV-2 infections in these species. However, the tests should be checked beforehand for their suitability to equally detect VOCs B.1.1.7 and B.1.351.

The only thing I would be concerned about is a false positive from the person sampling the animal contaminating the test.
However, I've also had a look around and the CDC and USDA do not currently recommend testing animals (admittedly, this is for farm-animals, not pets) unless all other causes of illness have been ruled out, and in consultation with state authorities, and it looks like the only authorized tests in the USDA regulated diagnostic labs are the PCR tests. Based on this, it is likely that your vet is being cautious and is following the guidelines published by your state/federal authorities on testing for SARS-CoV-2 in animals - which would mean a PCR test is needed for confirmation of symptomatic cases.

Hagag, I. T., Weber, S., Sadeghi, B., Groschup, M. H., & Keller, M. (2021). Impact of animal saliva on the performance of rapid antigen tests for detection of SARS-CoV-2 (wildtype and variants B.1.1.7 and B.1.351). Veterinary microbiology, 262, 109243. https://doi.org/10.1016/j.vetmic.2021.109243

Fernández-Bellon, H., Rodon, J., Fernández-Bastit, L., Almagro, V., Padilla-Solé, P., Lorca-Oró, C., Valle, R., Roca, N., Grazioli, S., Trogu, T., Bensaid, A., Carrillo, J., Izquierdo-Useros, N., Blanco, J., Parera, M., Noguera-Julián, M., Clotet, B., Moreno, A., Segalés, J., & Vergara-Alert, J. (2021). Monitoring Natural SARS-CoV-2 Infection in Lions (Panthera leo) at the Barcelona Zoo: Viral Dynamics and Host Responses. Viruses, 13(9), 1683. https://doi.org/10.3390/v13091683

Can you please define RAT?

@MattDMo - will do: Rapid Antigen Test. AKA LFA (Lateral Flow Assay).


text:
Habitat requirements of black ant Lasius niger
Does anyone know of any published information on the maximum slope angle and/or minimum soil depth on which the black ant Lasius niger will build its nests? I have read that they won't nest on "a slope that is too steep", but what does this constitute in numerical terms?


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Use of different biotinylated GTP compounds in molecular biology
In the Cappable-seq technique 3′-Desthiobiotin-GTP can be used to label the 5′ end of mRNA.

However in a commercial technical article on biotinylated-RNA affinity probes I encountered the following biotinylated cap, in which the biotin affinity tag is attached to the 2′-position of the ribose at the 5′ end of the dinucleotide.

This indicates that a 2′-biotinylated GTP had been used, and will be incorporated into mRNA.
What could be the reason for this difference in tag position?

Welcome to SE Biology. Could you please provide some context to your question, which seems rather specialized. You show the structures of two different derivatives of biotin and GTP, which presumably are commercial products (one appears to be from a catalogue). Are you asking what they are used for? And what do you mean by a “typical standalone biotin-GTP?”  And where have you encountered this RNA derivative?  Help us to help you.

Thank you Mr. David for the advices. GTP is a very common structure in biology. If biotin is incubated, then the biotin is bound by the 3' carbon, as shows the second image. If N7 methylated guanosine is incubated with biotin, then the biotin will bound by the 2' carbon, as shows the first image. In this image, the m^7-biotin-GTP has been flipped horizontally and has been added to the phosphate groups, by GTase (RNA Guanylyltransferase). Why this difference in the bounded carbon? I hope to help you. Thanks

You haven't answered my questions. I know all about GTP and about biotin, and — as far as I am aware — that they never occur in Nature covalently bound to one another. The structures you show are clearly of commercial reagents. Where did you encounter these structures? Why do you want to know about them? Is this some sort of homework? Or are you new to some research laboratory? And I see this same question on Biostars. Please only post your questions in one place — cross-posting, as it is called, is not allowed on SE sites as it wastes people's time when a question is asked somewhere else.

Biotinylation requires a catalyst or active group of some sort. If you just mix free biotin and pure GTP, you'll end up with free biotin and GTP, not biotin-GTP.

I apologize for the misunderstanding. I have found these compounds in the Cappable-seq methodology (Ettwiller et al 2016). In essence, RNA guanylyltransferase takes biotinylated GTPs and catalyzes the binding reaction with the diphosphate RNA. Cappable-seq is the subject of my thesis. So yes, these are commercial reagents, the structure of which I do not yet understand, as I told you. Lastly, in biostars I did not receive any reply so I deleted the thread and sent to this forum. Thank you

Ok. I’ll look at it tomorrow unless someone else answers first. It’s never explained, but on SE you have to address comments to people by @theirname unless they are the author of the question or answer you are commenting on.  Look at some other questions to see how it works. That way I get alerted if there is a comment for me.

You are absolutely right Mr @David. It was my omission. Every answer of you is valuable

@MattDMo thank you for this important note

@David regarding cross-posting - I don't see an issue with posting both here and at biostars, because they aren't affiliated with Stack Exchange, and are their own separate entity. Cross-posting to different SE sites is discouraged, but not if they post outside the network. Granted, both sites may share part of their user base, so some people will see the post twice, but that shouldn't be an issue.

@MattDMo — Not a big deal with me, but I thought that was the policy. Is what you say laid down anywhere?

You still do not provide the source of the diagrams. I can see that the second is from NEB and is the capping reagent described in the paper by Ettwiller et al. The second  comes from some page I cannot locate on the Biosynthesis company website. It does not show a biotinylated RNA but a biotinylated dinucleotide cap. Presumably it is generated with some reagent that Biosynthesis sells, and for all I know this reagent is different from that NEB cells for patent reasons. It would probably be able to form 5'-3' bonds in RNA, but you need to find data on the reagent.

@David Yes, the second image is from NEB and the first is from https://www.biosyn.com/tew/RNA-network-analysis-using-biotinylated-RNA-affinity-probes..aspx . So the answer is that these compounds are commercial and are produced in a specific way. Thank you for the answer

@DanK After reading your question and all the comments, I'm still not quite sure what you are asking. Is your question What are the different methodological applications of 3′-Desthiobiotin-GTP and 2′-biotinylated GTP? or Why is 3′-Desthiobiotin-GTP used in Cappable-Seq, and not a different biotin-GTP variant?

I've sorted the thing now, and rewritten the question. If you had followed the link in the legend to Fig 7 in the Biosyn article you could have found the explanation there.

Thank you very much Mr @David for the answer. You have helped me to understand all that I had a question about Desthiobiotin-GTP. The original question was What are the different methodological applications of 3′-Desthiobiotin-GTP and 2′-biotinylated GTP and the functional differences between them?. But in a more general manner, you showed me the whole biochemical background, which I did not know about. Thank you for your time and your informative response.

In the Cappable-seq technique, the aim is to biotinylate primary transcripts at the 5′-cap so that they can be separated by affinity columns, or with affinity beads, of the biotin-binding protein, streptavidin. It would not appear to matter if the biotin linker is attached at the 2′ or 3′ position of the ribose ring, and there may be non-scientific reasons (e.g. cost, availability) for the choice of the  3′ position.
The cap structure in the technical article is adapted from a paper by Bednarek et al. on the synthesis of a variety of such caps, for which one specific use was to pull down complexes of mRNA with eukaryotic initiation factor eIF4e. It turned out that having the biotin affinity tag in the 3′ position of the ribose ring impeded this interaction, to a greater extent than at the 2′ position. Hence the difference.
This is clear from the start of the results section of that paper, in which an additional advantage is also explained:

The affinity tag was attached at the 2′ position of m7G via an amide
bond, which was possible due to the presence of the primary aliphatic
amino group in the starting material—2′-amino-2′-deoxyguanosine—and in
situ biotin activation with
O-(N-succinimidyl)-1,1,3,3-tetramethyluronium tetrafluoroborate
(TSTU). The site for biotin moiety attachment was chosen in a way that
ensures the least possible interference with eIF4E interaction,
because the hydroxyl groups of 7-methylguanosine in the cap-eIF4E
complex are free and solvent exposed [16] (electronic supplementary
material, figure S1). The ability of the cap analogues conjugated with
biotin to serve as substrates for RNA polymerase in an in vitro
transcription reaction was of equally high importance. In this
context, the additional advantage of introducing the tag at the 2′
position is that, similar to 2′-O-methylated dinucleotides, the
resulting compound can only be incorporated into RNA in the correct
orientation (and, as such, belongs to a class of the so-called
Anti-Reverse Cap Analogs or ARCAs).


text:
Influence of pH on rennet coagulation of milk
I was looking for the reason why rennin works most efficiently at pH 6.7 (closer to a neutral environment than acidic).

Welcome to SE Biology. Please take the time to finish reading the [Tour], and the Help on asking questions. It would help us to help you if you provided some context to your question. Are you interested in the pH in relation to the mechanism of action of the enzyme or to its biological environment? Tell us why you might expect it to have an acidic pH optimum. This might be obvious to you, but not necessarily to us. And what attempts have you made to answer this question yourself from freely available resources like Wikipedia?

Can you quote a source for rennin working more efficiently at pH 6.7?  As I understood things, chymosin (rennin) has a pH optimum of about 3.8 (see for example Protein engineering of chymosin; modification of the optimum pH of enzyme catalysis), as you would expect for a stomach enzyme.


text:
Are introns conserved among cells?
To elaborate on the title: Among somatic, post-mitotic cells, would the same intron on a given chromosome have the same sequence among all cells descended from a progenitor cell?

Welcome to SE Biology! See here for some advice on ways to ask questions that are likely to get a helpful answer. Have you looked at any examples of introns on the same chromosome? Can you cite any sources suggesting what you ask is the case?

Hi I'm just asking out of curiosity. Not sure how, if I got a sequence, I would know whether that would be the same for each cell in a sample, given that genomes are assembled from several reads and sometimes individual bases are averaged, right? Just off the top of my head, I figured that since introns are not coding for proteins but do regulate gene expression, there would be less of a force for their sequence conservation between divisions from a stem-like progenitor, but that's why I'm asking.

Could you perhaps edit your query to include those details with any appropriate references as comments are ephemeral in nature and we want to questions to be self-contained and last over time. Please also take our [tour] and refer to the [help] for guidance as to our ways.

I think that ignoring genome assembly for now may clarify the issue. I still don't understand the question. Are you referring to the same intron across different cells, or different introns on the same chromosome? Your comment makes it sound like the first, but your question makes it sound like the second.

Sorry for being unclear. I meant the same intron, on the same chromosome, in different cells. Also changed the question to reflect this.

I believe that the kind of mutation that you are interested in is somatic mutation, as opposed to germ-line mutation.
Any given genomic locus (intron, exon, intergenic region) probably doesn't mutate most of the time. In the case of somatic mutation, it is yet more likely that no mutation happens.
Nonetheless, such mutations do happen, in all of those different regions. For example, here is a study that catalogs somatic mutations in introns that lead to a particular phenomenon called intronic polyadenylation; here is another that catalogs intronic mutations that mess up splicing.
The same is true for protein-coding somatic mutations, one can find similar catalogs of mutations for those.
Such mutations in different regions (intronic, exonic, and otherwise) are all of interest as events that can lead to cancer.
None of this should distract us from that fact that usually mutations don't happen at any given site. But it's a question of probabilities, not of absolutes.

OK humor me this. What if you were trying to engineer, using some DNA editing technology, several cells in a sample at once, and wanted to precisely introduce a double-stranded break at some intronic site. Would the risk of somatic mutation ever be a concern? Thanks

@UD22022 Somatic mutation is always a possibility. But, frankly, the efficiency of gene editing technologies is (at a guess) a 2-3 orders of magnitude higher than the rate of somatic mutation. You could not exclude the possibility without recovering and analyzing the edited cells. But you generally have to isolate, select, and culture edited cells anyways. I would say that it is a theoretical concern worth keeping in mind examining data, but likely not a regular practical concern for gene editing compared to e.g. the rate of off-target effects of editing.


text:
Do the quantum mechanical properties of the particles that make up DNA affect mutations in the genome?
Do quantum mechanical properties of particles, such as uncertainty, probability, tunneling, and so on, affect mutations in the genome?

Not that anyone has ever noticed, but it's not the sort of thing biologists look for as 1. They generally don't have the physics, and 2. There are plenty of macroscopic factors that affect mutations. It is interesting in a more general respect that the celebrated Max Delbrück, a physicist who made early contributions to molecular biology, did so without, as he had hoped, applying any of the new ideas of physics to biology. The supposition that explaining life would involve applying these was incorrect (or at least never realized).

@David Are you saying that quantum mechanics has no effect on life? But what about quantum biology?

I am only saying that the mechanisms in genetics are explicable in terms of general chemistry. Quantum biology, as far as I am aware, is mainly concerned with the energetics in systems like photosynthesis, which, although involving biological molecules, are essentially problems in their chemistry. Delbrück did not do quantum biology. However others may be aware of things I am not.

@David My question was about the processes and mechanisms in genetics that can be explained by quantum mechanics.

Did you google that question [processes and mechanisms in genetics that can be explained by quantum mechanics]? Because the answer is yes, they affect mutations, on the very first hit (of my search.) Third: Why does DNA spontaneously mutate? Quantum physics might explain.. [emphasis mine] So you probably knew the answer already, asking such a very specific yet detail-less question. Oh, and yeah, tunneling and waves and stuff.

@anongoodnurse I think David's point is that the quantum part is only necessary for understanding the physics of the chemical reactions, not things we ordinarily care about at the level of cells and organisms. Much like how relativity affects every physical interaction, yet if you want to know how long it takes for a ball you drop to hit the floor, Newton is entirely sufficient up to a very small rounding error.

@anongoodnurse I think these things raise some hackles because there's a tendency for people working in the quantum world to over-extend the value of their work into criticizing those who work with a simpler model or claiming their model is important because it's more accurate or is a "real" explanation or something, and it sounds cool because "quantum" is such a buzz word, yet offers no added real predictive value to models at a higher level that explain the world just fine. It's like if every time a physics TA writes F = ma on the board, a student in the back screams THAT EQUATION IS WRONG

@BryanKrause - "Not that anyone ever noticed" is a really broad (and possibly discouraging) statement. I'm not usually into physics (including quantum mechanics) much beyond the level you gave an example of. But I am curious by nature, and when someone asks something that takes me by surprise, I usually want to know something about it. Maybe because I don't know very much, especially about boundary pushing by quantum physicists, my hackles didn't get raised. And I find the question suspect. But thanks for the alternative way to look at this.

@BryanKrause But the question was quite specific: are there mechanisms and processes associated with mutations that can be explained only by quantum mechanics?

@АрманГаспарян I think what David is trying to get you to think about is what does it mean to be explained "only by quantum mechanics"? Given some chemicals that react in some way, you can measure all sorts of useful things like forward and backward reaction rates, equilibrium concentrations, you can model the effects of temperature and pH, all without knowing a single thing about quantum mechanics. Those numbers, though, do come from some physics. Does that physics matter?

If you want to understand the physics behind the chemistry, sure, maybe it does. But it doesn't matter to the typical biologist who just needs to know that the chemistry happens and in what conditions/how fast/to what extent, etc.

@BryanKrause I understand what you mean. However, not all processes in nature can be explained by ordinary chemistry (if it is not quantum chemistry).

@АрманГаспарян Well, electron transport is one area in biology where quantum chemistry is often invoked (as far as I know; this is really outside my area, except that people make bold, unsupported statements about quantum this and quantum that in my area as well :) ), and indeed, it seems like it may be important to understanding how exactly electron transport happens, but it certainly isn't necessary to understand the biology of electron transport, since you can write the end result in a simple chemical equation and go from there.

This issue in the philosophy of science is called "reductionism".

@BryanKrause I'll try to give an example. Quantum tunneling is a purely quantum effect that is not present in classical physics and conventional chemistry. If there was a mutation mechanism that would be caused by quantum tunneling, that would be the answer to my question.

@АрманГаспарян In biology we very rarely care about the mechanism of a chemical reaction, so there is no distinction. You can easily represent a chemical reaction that occurs due to quantum tunneling without invoking anything quantum at all.

Yes. (I mean, that's the answer to your question. You didn't ask for specifics.)
From Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs:

Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but biologically relevant point mutations that can further lead to gene mutation and, potentially, cancer.

So that's proton tunneling at work in DNA.
This isn't really a new idea. I found one paper theorizing this from the 80's.

authors: Арман Гаспарян


text:
Use of plasmid pXen5 for transposon screening
I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen.
It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409).
Is it a problem to use such a transposon, which contains the transposase within the IR regions?
I am concerned that because the transposase will always be expressed (since its coding sequence is carried around inside the transposon), the transposon will keep on "jumping".
How real is this problem from a practical point of view?
Thanks,
J

There are many natural transposons that are self propogating, hence your plasmid might be derived from one of those.
I can't be sure if it is a problem without knowing more details of the transposon or your experimental goals. However, it might be a good idea to make the transposon inducible, by replacing it's promoter with an inducible one such as pTet or pLacIq, along with including the cognate repressor.
A similar strategy is used in this paper, albeit not with transposons but other integrative and conjugative elements (ICEBs1) from Bacillus subtilis

Brophy, Jennifer AN, et al. "Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria." Nature microbiology 3.9 (2018): 1043-1053.


text:
Human gene number distribution on different strands of the chromosomes
I cannot find an article that describes the gene distribution based on their appearances on different strands and if I find one, like this from 2007, there are some aspects which are confusing, for instance:

A total of 12,692 loci were present on the positive strand, with
12,442 on the negative strand.

How are positive and negative strands determined in general if we are not talking about a particular gene at a particular locus?
Aren't both strands similar in a way that we can not name one as a sense, antisense, template, or coding? Are not both strands in a chromosome used for transcription in a symmetric way?
Any article related to my main question (in the headline) or explanation about this confusion in this article would help.

For humans and other eukaryotes, the convention is that the "start" of each chromosome is the end closest to the centromere:

In all human reference chromosomes, as for other eukaryotes [3], the plus (+) strand is defined as the strand with its 5′ end at the tip of the short arm [4,5] (Genome Reference Consortium, personal communication, March 27, 2012).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099125/


text:
Why do blood vessels in the eye not obstruct vision?
As light enters the eye, it reaches the photoreceptors at the "base" of the retina, which then pass that signal to the bipolar and ganglionic neurons -- the latter of which send the signal outside of the eye via their axons (collectively forming the optic nerve).

The exit point of the optic nerve is sometimes referred to as the "blind spot" because there are no photoreceptors present there and therefore no sensory information is gathered.

Now, I know photoreceptors exist everywhere else along the retina, so it's not surprising that we perceive vision from the otherwise broadly distributed photoreceptors.
However, my question: why do the blood vessels associated with the superficial vascular plexus (which exist between incoming light and the rest of the retina) not obstruct our vision?

More broadly, I guess of interest is: why none of the vascular plexuses (or cell structures of the bipolar and ganglionic neurons for that matter) obstruct our vision despite existing between the photoreceptors and incoming light?

 Sources: LEFT: Figure 1 from Zhongjie et al (2020) ; RIGHT: Figure 5 from Selvam et al (2018)

 Fu, Z., Sun, Y., Cakir, B., Tomita, Y., Huang, S., Wang, Z., Liu, C.H., S Cho, S., Britton, W., S Kern, T. and Antonetti, D.A., 2020. Targeting neurovascular interaction in retinal disorders. International journal of molecular sciences, 21(4), p1503
 Selvam, S., Kumar, T. and Fruttiger, M., 2018. Retinal vasculature development in health and disease. Progress in retinal and eye research, 63, pp.1-19.

To follow-up for clarity: I understand the brain is essentially integrating the overlapping visual fields from both eyes to allow us not to regularly perceive the blind spot. However, it seems these cellular structures (i.e., vessels and nerve cells) must be so prevalent that I'm wondering by what mechanism (perhaps similar) that this more [structurally-]complex process is accomplished.

Fun fact that many probably already know: Cephalopod eyes don't have a blind spot, having the retina in front of the blood vessels and optic nerve.  When Bryan's answer mentions an "inverted" eye, it's as opposed to the "better engineered" cephalopod eye.

I think there are experiments like this to make the blood vessels visible to you: https://www.aao.org/museum-education-healthy-vision/experiment-see-blood-vessels-in-your-eye

https://youtu.be/oAaG34WfsC0?t=9254 has an interesting anecdote about this. This is from an interview of a neuroscientist/Stanford prof/skateboarder, who explains, among others, why we don't see those spiderweb shadows.

Avoid the fovea
Figure 2 from the same paper shows the distribution relative to the fovea:
As you can see, it's pretty much devoid of this superficial vasculature, so anything you are directly focusing on, say, text you read on a computer screen (or even a book!) is not impacted.

Receptive fields might be bigger than you think
Receptive field sizes for retinal ganglion cells in the primate retina are about 50-300 um, depending on eccentricity (distance from the fovea). Capillaries are going to be around the size of a red blood cell in diameter, so about 10 um; it seems like by the time you get to the far periphery, these vessels are mostly going to be quite small relative to receptive field size, and they are even a bit small in the vicinity of the fovea.
Tissue isn't that opaque
I'm mostly focusing on the RBC size themselves, because RBCs have a bit of pigment in them, but otherwise, tissue is overall quite transparent. If you've ever looked at an unstained tissue section less than 100 microns thick, you know that it doesn't look like much at all. If you've lost track of one in any volume of water, good luck finding it. For the same reason that RGCs being on the "wrong side" of the inverted vertebrate eye, this thickness of tissue just doesn't seem to be that big of a problem, and it doesn't seem that any affordances for this issue have evolved outside of the fovea in primates (whereas you can see in the figure above that there is a clear exclusion of these vessels from the fovea).
We perceive with our brain, not our eyes
The general idea of predictive coding models of the brain is that you have some generative model of the world that is constantly making predictions, and sensory organs merely provide evidence to update those models which is propagated as an error signal with respect to the original model; if everything is static and as predicted, nothing needs to be propagated in the brain to alter the perception. Much of what you think you are "seeing" at a given moment you aren't seeing at that moment at all, but merely "remembering" what you saw previously, and having not seen any evidence to the contrary, continue to "see" it there. When a person looks at an object, they do not typically look at one spot, but quickly saccade around to scan different parts of it and form a complete model of the object. It will escape attention until it moves or changes in some way.
These blood vessels are going to be quite static, and not provide much of a changing visual image, so there's nothing there for the brain to be interested in.

+1 for everything, but especially the "it's all in your mind" paragraph!

"Tissue isn't that opaque" — but we do easily see the vessels in fundus photos, so they aren't that transparent either. And they are very noticeable in the Purkinje tree effect.

@Ruslan Those are much larger vessels than the bulk of them that are capillary-sized.

Thanks @Bryan! +1.  3 comments: (1) could you cite/link something about the primate fovea evolution you allude to [very interesting, by the way!]. (2) I've experienced thin cultures before and so can appreciate your comments about their near translucence. However, capillaries  would still have continuous RBCs -- which are more red than completely transparent -- so I'd guess these would stand out slightly more than thin epithelia. (3) final paragraph about predictive coding is informative and interesting -- some of it was familiar, but it's been a long time since studying this stuff. Thanks :)

@theforestecologist 1) I'm really just commenting on the structure visible in figure 2: it's clear that something particular has evolved around the fovea in primates to keep that area clear of vessels, and not elsewhere. I could perhaps comment on the evolutionary history of the fovea but it's a bit of a long story of convergent evolution. 2) Agreed, RBCs may stand out, I mostly meant this to defend my use of a RBC width as a reference point for the size relative to receptive fields, rather than using the vessel diameter. 3) Although I put this point last, it's probably most important.

 You CAN see your blood vessels!
Following-up from Bryan Krause's answer:
Bryan mentioned that the blood vessels are typically not visible partially because they are unchanging (i.e., static). In support of that, one could imagine that if you somehow make these structures appear more dynamic, then one might be able to visualize them.
The American Academy of Ophthalmology actually recommends trying an experiment to do just that: to "see" your retinal blood vessels!
https://www.aao.org/museum-education-healthy-vision/experiment-see-blood-vessels-in-your-eye
Paraphrasing their experiment:

Darken a room.

Hold black sheet of paper in front of face so that the paper fills your field of view.

Hold a small flashlight 1.5 cm in front of one eye so it's aiming just below the center of the pupil.

Move the lit flashlight slowly from side to side a short distance (~0.4cm) without letting your eye follow the motion of the light. Continue moving for ~20 seconds.

A tree-like pattern of blood vessels will become visible.
Why this works:

You can use a dim point of light to cast a shadow of the blood supply of your retina. This will allow you to see the blood supply of your retina, and even your blind spot...
Your light is causing a shadow from the blood supply layer to the other layers underneath. As you move the point of light, the shadow moves, making it visible to you. Normally, there would be no shadow and your brain would ignore seeing the blood supply.

One of my friends experimented with this using a computer program: stare at one point, and the program flashes dim dots elsewhere. Press button when you see the dot. Very slow but the mapping he got corresponds very well with a retinal photo from opthomologist.

Try looking at the blue sky or a white computer screen and focusing very carefully on what you see.  I usually can make out faint pulsing streaks of white/black (like phase contrast - different from floaters) if I really pay close attention.  These aren't continuous like vessels and they aren't even as frequent nor as regular as a heartbeat, so I'm not sure what they really represent (perhaps some type of smooth muscle contraction or leukocyte passing through?), but their repeated motion in one particular direction at any given location suggests some type of blood vessel should be involved.


text:
Which animal has the smallest percentage of their body mass made up of water?
It's a "well known" and interesting "fact" that the human body is made up of "mostly water".  With percentages from 65% to 90% often being repeated as if they were exact and proven amounts.
Obviously the exact numbers will vary from one individual to the next, and from one measurement method to the next, and from one to the other definition of which water is included in the measurement, etc.  And it will even vary within the same individual over time depending on water intake and excretion (in all its forms).
Moving on from humans, water is also going to be a significant component of the body mass of animals as well.  And the variations in percentages here is likely to vary even more, when you add different species in to the mix of factors to compare.  One obvious example is jellyfish, with an extremely high (compared to humans, at least) percentage of their body mass composed of water.
But which animal is at the lower end of the spectrum, with the smallest percentage of their body mass being made up of water?
In my attempt to research this topic, I was unable to find any documented information that was not behind a pay-wall, such as this article.
For clarity and simplicity, please limit answers to multi-cellular animals, assume a normal healthy adult specimen, averages and estimations are acceptable for measurement comparisons, as avoid answers that include grey areas in defined classifications (e.g. are viruses alive), and answers need not be reduced to a specific individual species if a genus or even family is enough to identify the animal to a layman, etc.

I'd guess Australian marsupials probably have pretty low water content, but can only find papers on water conservation in the marsupials.

@bob1 That line of thought was my first intuition as well, but the more I think about it, the more I find that I can't directly correlate "the ability to prevent moisture losses" to "total moisture content".  Just because they're exceptionally good at maintaining their hydration level doesn't necessarily translate to a lower overall water content.  They might still be the winners, for other reasons, but the retention ability alone isn't convincing enough for me.

I had that thought too. I suspect all mammalian animals will have similar water content, but its actually a hard question to find answers to because not many people take a dead animal and do the science by properly weighing and reducing it to ash under controlled conditions.

A Tardigrade, when exposed to extreme conditions, can suspend their metabolism and reduce water content to 1% of the normal; from 85% to 3%.

Good answer, and good information.  But I'm not sure that suspended metabolism in an attempt to maybe survive (no guarantees, despite their much higher likelihood of success compared to most other animals) those extreme conditions qualifies as 'normal' or 'healthy' ...


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Does alternative splicing contribute to the diversity of enzymes?
I understand the role of alternative splicing in generating protein diversity, but for enzymes specifically, is alternative splicing responsible for the diversity of it? My professor told me something similar to the 1941 “one gene one enzyme” theory, and he said that “Enzyme diversity is coded for in the DNA, each enzyme is coded for by a separate gene, and splicing doesn’t  generate the diversity.” I am a little confused because I thought one exception to the one-gene-one-enzyme theory was the mechanisms of alternative splicing… (obviously DNA itself also creates diversity but I don’t get why alternative splicing is not responsible for it)

It would help to get the exact words of your professor. AS definitely affects protein function (many papers out there, here is one random example). It may not dramatically affect qualitative enzymatic behavior but it certainly can change function.

Please define precisely your usage of the word “diversity” as it applies to enzymes, and explain why you think enzyme diversity (as you intend it) differs from protein diversity in general. At the moment this is quite unclear to me.

The "One-Gene-One-Enzyme" theory is rather outdated now and many of these "One-Gene-X" terms to define how genes work can be inaccurate. For example, after many modifications to that term, biochemist and geneticist George Beadle and geneticist Edward Tatum came up with the term "One-Gene-One-Polypeptide", and even then there are caveats. One is that Alternative Splicing means that one gene may code for more than "One" polypeptide. And two, that genes do not always code for polypeptides, that is, they may code for RNA strands that work to regulate gene expression (regulatory RNA), in fact, genes that encode for proteins constitute only around 1.5% of the human genome! (Source for this passage: Campbell's Biology 12th edition)
Back to the main issue, I wouldn't say that alternative splicing creates a "diversity" in genetic products, I think it is better worded that alternative splicing allows a greater range of products to be formed.
I do not have a specific, well-detailed example of how different enzymes are formed from the same gene that comes to mind, but it is definitely possible that if you can form different proteins from the same gene by shuffling the exon sequences, it can be possible that the shifting of the domains or usage of different subunits of an enzymatic protein by splicing exons in different fashions can affect how it functions.
I did, however, find a publication on PubMed whose abstract states that there are isoforms (protein variants) of Base excision repair enzymes (though at the time of the publication, their function does not seem to be explored).
There is also an example given on Wikipedia on protein variants that uses AMPK as an example of an enzyme formed by alternative splicing of subunits, where some combinations of subunits are more ideal in their function according to where they are located, such as the liver having a different preferred/abundant form of AMPK than human skeletal muscle.
I hope this answer gives you a nice clarification, if anyone finds something inaccurate please feel free to criticize!

There are a lot of different mechanisms by which the "one-gene-one-enzyme" theory doesn't work. Alternative splicing is definitely one of them, but there are other biological processes like post-translational changes that can affect enzyme function. Also, it is very important to take into account that there are many enzymes that work as functional complexes with multiple subunits in which every subunit might (or might not) be coded by a gene with a certain pattern of splicing.
In summary, alternative splicing does contribute to the diversity in enzymes.

Welcome to Biology.SE. Answers should focus on the question and are much more likely to receive a favorable response if they include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion and thus inappropriate for this site. This is a good example of how to format references. In addition, it is best to leave unclear questions unanswered. ——— Please take the [tour] and consult the [help] pages for additional advice on [answer] and [ask] effectively on this site.


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What insect in shell is this?
Location: INDIA(Tropical Monsoon)
I found an insect (approx 7mm) (marked with red in image) in my bedroom hanging from the roof.

It can spin some kind of thread, since it was hanging at the first place
It has a shell like structure (marked with blue in image), and it stays inside the shell.

I forced it out of its shell. Its image is given below. I also recorded a video of its behaviours.

Please consider converting your video (or parts of it) to GIFs and adding them directly to this post. Sites like ezgif.com have simple tools for converting videos to gifs, trimming length, and optimizing file size. Including this info here would be beneficial. Thanks!

Does this answer your question? What insect is this? (India)

I'm almost certain it's a bagworm, or a moth larva in the Psychidae family. I'm no lepidopterist, I can't confidently narrow it down to genus or species level from there.

You are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. Please also provide a citation/source for images. ——— You may also wish to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site.


text:
Difference between "biotroph" and "parasitic"
In the studying process for my exam I learned about ways of life of pathogenes in plants. There, it was mentioned, they can live nekrotrophic, hemibiotrophic or biotrophic.
As far as I understand, a biotrophic way of living includes being completly dependent on your host. Therefore, those pathogenes do not kill their host.
That sounds like a parasitic way of life. However, I neither found a source that proved me that this is the same nor did I found a source that specifically explained the difference.
I would be very grateful, if some one can explain this to me!
Thank you in advance!

I think the Wiktionary definition of biotrophic is enlightening (emphasis mine):

Describing a parasite or symbiont that needs its host in order to stay alive.

So, all non-necrotrophic obligate parasites are biotrophic, but not all biotrophic organisms are parasites.
Fungi of the lineage Glomeromycota (also called arbuscular mycorrhizal fungi) may be considered biotrophic plant symbionts. Association of these fungi with roots improves plant acquisition of nutrients from soil and, in exchange, allows the fungi to obtain photosynthesis-derived carbon sources from the plant.1 Textbook sources corroborate that such fungi are biotrophic.2

These fungi have a low, or negligible, saprophytic ability and can apparently produce viable propagules only upon the biotrophic colonization of a susceptible host root.

References

Corradi N, Bonfante P. The arbuscular mycorrhizal symbiosis: origin and evolution of a beneficial plant infection. PLoS Pathog. 2012;8(4):e1002600.
Azcón-Aguilar C, Bago B, Barea JM. Saprophytic Growth of Arbuscular Mycorrhizal Fungi. In: Varma A, Hock B. (eds) Mycorrhiza. Springer, Berlin, Heidelberg. 1999.


text:
Really having problem comprehending this Hardy-Weinberg example from biology textbook

Genetic equilibrium is a hypothetical state, but it is often used as a benchmark. Consider how the Hardy–Weinberg equations were used in early studies of an allele that causes hereditary hemochromatosis. Individuals affected by this disorder absorb too much iron from their food, and the excess accumulates in tissues and organs. Untreated, the iron overload results in fatigue and pain; in serious cases, cirrhosis of the liver, heart disease, diabetes, and other problems can occur.

The allele is inherited in an autosomal recessive pattern, so carriers (people heterozygous for the allele) have no symptoms. People of northern European descent have a very high risk of hereditary hemochromatosis compared with other populations; about 1 in 83 people of Irish descent have the disorder. Researchers discovered that about 28% of normal (unaffected) Irish individuals were carriers, which means the frequency of the allele among members of the Irish population (q) is 0.14. Thus, the frequency of Irish people who are homozygous for the allele (q2) is 0.0196, or 1 in 51 individuals. This calculated frequency is higher than the observed prevalence of the disorder,
so the researchers concluded (correctly) that other factors probably contribute to the progression of symptoms.

I'm really having problem on understanding what the last paragraph is trying to say. It says if (1/83) have the disorder, that means q^2 = (1/83), and q = 0.11
That means p = 0.89, since p+q = 1. That also means that the heterozygous population is 2pq = 2(0.89)(0.11) = 0.20, or 20%.
I'm having trouble comprehending how they figured out q=0.14. I don't even get what "28% of normal individuals were carriers" mean. Does it mean 28% of homozygous dominant and heterozygous individuals combined? If so, how do you get q = 0.14 from that?
I just do not get what this is trying to say.
Please help.

You get off track when you state:

(1/83) have the disorder, that means q^2 = (1/83), and q = 0.11

For that to be correct, each and every person who is homozygous for the problem allele must show symptoms of the disorder and no others can do so.  When they stated "have the disorder" they meant have clinical symptoms of the disorder, and nothing about knowledge of the frequency of the problem allele in the population.  Hence, you shouldn't have jumped to that conclusion and knew from that what q was.
The text says:

Researchers discovered that about 28% of normal (unaffected) Irish individuals were carriers, which means the frequency of the allele among members of the Irish population (q) is 0.14.

Here they are talking about results from genetic testing of normal individuals.  The tests revealed that 28% were heterozygous, having both a normal allele and a problem allele.  This is talking about the frequency of the alleles, and so this 0.28 should be the sum of the probabilities for the two heterozygous areas of the Punnett square, that is 2pq.  When I solve that I get q ≈ 0.168 whereas the text shows 0.14.  Whichever it is, the final sentence in the text excerpt would still apply.

Here the discussion is highlighting the subtlety between disease 'prevalence' and the 'penetrance' of the mutation causing the disease.  The prevalence is an estimated value for the fraction of the population afflicted by the disease (which really should have statistical errors associated with it based on the sample size of their data).  Even if the disease only occurs due to a genetic mutation, not all individuals with the mutation necessarily have symptoms. This is due to incomplete penetrance of the mutation.  Think of penetrance like some probability that the genetic component wins over the environmental component, epistatic interactions based on the rest of the genome, and any other complicating factors you can think of that disrupt genetic determinism for Mendelian disorders.  If the probability that having the mutation causes the disease is 1, and as mgkrebbs said no other mutations or environmental factors cause the disease, then the mutation is completely penetrant.  In that case, and in that case only, you can (post-hoc) infer the allele frequency from the disease prevalence, which is what you tried to do.  That said, measuring the penetrance virtually always requires knowing the allele frequency of the mutation, so this isn't how we figure out allele frequencies in human disease genetics.  (As an aside, penetrance is still really hard to measure, and estimates in the current literature disagree depending on if they condition on having affected family members or if they use an unbiased sample.)
As for the allele frequency itself, the authors of your textbook made a small mistake in the calculation, as mgkrebbs pointed out.  $2p(1-p)=0.28$ (again missing error bars), which can be solved to find $p\approx0.17$. There is another issue here, which is that there is very little information given about the allele itself with respect to the mode of inheritance (and other normal things to check).  The author's claim it is autosomal recessive (which is not necessarily $h=0$, since the medical definition only requires unaffected homozygote individuals, and that assertion is based on the sample size of heterozygote carriers assessed; they may have other medical conditions that are not the same as the homozygote-induced medical conditions).  I just looked up a few of the mutations responsible for hemochromatosis in OMIM (Online Mendelian Inheritance in Man, which is a database of genetic disease status, including mode of inheritance) and here are the results:
https://www.omim.org/search?index=entry&start=1&limit=10&sort=score+desc%2C+prefix_sort+desc&search=%22hemochromatosis%22.
If you click on any of the entries, they mention that compound heterozygous mutations (one mutation from the mother, one from the father, in different locations but both in the same gene) can also cause the disease.  This means that assuming it is a single mutant allele with a single frequency $p$ is incorrect (unless they included that in their estimates of the carrier frequencies via sequencing). If other mutations in the same gene can cause this disease, then one needs to compute both the carrier frequency over all possible mutations and then check the prevalence to see if the additional target size for compound hets is sufficient to explain the epidemiology. The allele frequency for compound hets if there are two alleles is $p_{c.h.} =  p_1^2 + 2p_1p_2 + p_2^2$.  If there are more than two alleles, this becomes a binomial expansion $(\sum p_i)^2$, which can grow quite quickly due to the cross terms $2p_i p_j$.  This could be part of the issue between the discrepancy in disease prevalence and homozygote status, but it goes in the wrong direction!  This likely means that there is a larger environmental component at work (back to this in a bit).
Looking more into this specific disease, here is an article about hemochromatosis in Ireland: https://www.liebertpub.com/doi/10.1089/109065701753145583, which cites the following statistic in the abstract:
"Over 93% of Irish HH patients are homozygous for the $HFE$ gene $C282Y$ mutation, providing a reliable diagnostic marker of the disease in this population. However, the prevalence of the $C282Y$ mutation and that of the second $HFE$ gene mutation, $H63D$, have yet to be determined within the Irish population. ".  Granted, this paper is from 2004, but I couldn't quickly find a more recent statistic on the allele composition of affected individuals. This means that there are not only multiple alleles involved, albeit with one responsible for the vast majority of Irish cases, but also that there are multiple genes involved (again increasing the target size).
So what's going on?  The key is environment and one other factor: sex.  "[A]pproximately 50% of women and
20% of men do not have an increase in serum ferritin
level", cited here: https://www.sciencedirect.com/science/article/pii/S1542356505004131.  Serum ferritin is responsible for the adverse component of the disease, so this paper tells us that women are a coin flip away from not having the disease even if they are homozygotes for the most common mutation causing the the disease in the Irish population.  Additionally, they measure the 'heritability' (https://medlineplus.gov/genetics/understanding/inheritance/heritability/), which is the fraction of the variance in the population explained by genetics.  They find that the heritability is $0.35\pm0.1$ (error bars, finally!!) out of a maximum 1.  This means that 35% of the distribution of disease in the population can be explained by genetics alone (indicating something about how likely you are to get the disease if your parents are both carriers), and the remaining fraction is unexplained!  Usually, we blame this on a number of environmental factors, but in this case, male/female status plays a major role (though not enough to explain 65% of the variance).  Compound hets are likely involved in the remaining "missing" heritability (I honestly can't guess to what extent), and the rest could be from a number of things that are too far removed from the topic.
So there is your answer: compute the homozygote frequency from the carrier frequency (properly) and the difference between that and the disease prevalence is wrapped up in all of the human genetic considerations I outlined.  So sorry this turned into a novel, but I wanted to address some of the details that go into the genetics of human disease!


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How frequent are transposons in action?

A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size.

Almost 50% of the human genome contains transposable elements. I have several questions:

how rarely are they changing positions along the genome?
Are these events most likely to occur during Meiosis, Mitosis? Or they could come in an action in other parts of the cell life cycle?
Do humans nowadays contains almost the same genetic information (99,9%) including these elements? or does similarity occur only in the protein-coding region?

Generally, we ask that answer-seekers only include one question per post, or, at most, a few highly related questions. It could be argued that your first two questions (1. how often do transposition events occur? 2. during what point in the cell cycle does transposition occur?) are related, but your third question (3. do measurements of inter-person genetic distance account for TEs?) is distinct. Please edit your post to focus on one question, and, after doing some preliminary research, consider writing your other questions as separate posts.

To answer your first question and address the title of your post, see this review on active TEs in the human genome. Some excerpts:

Although a large proportion (44%) of the human genome is occupied by transposons and transposon-like repetitive elements, only a small proportion (<0.05%) of these elements remain active today.

Active human transposons have been estimated to generate about one new insertion per 10–100 live births.


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Is the pyruvate dehydrogenase reaction considered part of the Krebs Tricarboxylic Acid Cycle?
I’ve encountered questions where I’m asked to find out the CO2 released, the number of oxidative carboxylations etc. in the Krebs tricarboxylic acid cycle. I always include the pyruvate dehydrogenase reaction (sometimes termed the ‘link reaction’) that converts pyruvate (from glucose) to acetyl-CoA which then feeds into the Krebs cycle. However my answers are only considered correct for certain questions, while for the others they are not.
How do I decide if a reference to the Krebs cycle includes the pyruvate dehydrogenase reaction?

It would help to get examples of such specific questions, where you got it right or wrong, to understand the point of confusion.

I have rewritten your question in a format that is more precise scientifically and focusses more on the scientific question, rather than your person difficulties interpreting your teachers' questions. If after reading and understanding my answer you still are puzzled by your marks you should ask your teachers why you were marked incorrect in particular cases. I see from an internet search that the term "link reaction" is used at an elementary level. This is imprecise and not used by biochemists, which is why I have substituted pyruvate dehydrogenase reaction.

It is outside both the remit and competence of this site to divine the intentions of university teachers in questions that they set to students. What we can do is explain the scientific points that may be at issue, in this case why:

the Krebs tricarboxylic acid cycle does not include the pyruvate
dehydrogenase reaction.

First is the obvious fact that the pyruvate dehydrogenase (PDH)
reaction is not part of this cycle of linked reactions, any more than
the conversion of glutamate to α-ketoglutarate (2-oxoglutarate) is.
But even if you consider acetyl-CoA as somehow “starting” the cycle,
the PDH reaction is not required to generate it. Acetyl-CoA can also
be produced from the breakdown of fatty acids or certain amino acids.
Further, acetyl-CoA produced from pyruvate need not feed into the TCA
cycle: in some circumstances it is converted to malonyl-CoA and to fatty acids.

The diagram below (a fossil of my biochemistry lecturing career) illustrates some of the various possible inputs into the TCA cycle in a general sense:


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Why does pancreatin affect the pH of milk?
I just finished a lab for college and I was really intrigued by this. Since we're in a rush to finish the semester on time my professor didn't go into details much she just said something about fatty acids? But I'd like something more in depth because honestly this is the only lab I've liked this semester and it's just fascinating to me. I googled it but it was a whole bunch of other stuff coming up and I want a direct answer on why this happens.
Lab: For the lab, we started out with two test tubes one filled with water and milk and the other with a pancreatin solution and milk. We then added bromothymol blue to each test tube and put it in a warm water bath for 40 minutes then we just recorded our results. We just had to explain what reaction was being used and what would happen with different types of dairy products. For each test tube with the pancreatin solution and milk it changed color usually to orange or yellow, showing that the pH had dropped.
This is NOT for a homework answer I'm genuinely just curious about the mechanics of it all.
Thank you!! :)

Describe the lab a little bit - what did you do, and what did you find?

@MattDMo For the lab we started out with test tubes that we filled with two test tubes one filled with water and milk and the other with a pancreatin solution. We then added bromothymol blue to each test tubes and put it in a warm water bath then we just recorded our results. We just had to explain what reaction was being used and what would happen with different types of dairy products.

@MaximilianPress not really? Sorry but I'd like for something more in detail and most of the responses are people getting mad about it being a homework question.

@wheeinsoup it's true that there are no detailed answers on that question. However, in this community we tend to consider one copy of each question as enough, and the one short answer there probably gives enough information for you to be able to do some research. If you still find something confusing you are very welcome to bring your research and to explain what about it is confusing and we will try to help if we can.

@MaximilianPress okay! thank you for the help :)