text:
In phloems, does the sap move through the sieve element cytoplasm?
We know that in xylems, the water move through the lumen of the vessel elements and move to the other vessel element through a pit. As the vessel elements are dead , there is no cytoplasm to block their way. The water can move through the cell walls(apoplastic pathway) or through the cytoplasm (symplastic pathway).
Phloems are living tissue and made up of sieve elements and companion cells. I have a doubt regarding the movement of sap in phloems.
In phloems, does the sap move through the sieve element and move to the other seive element through sieve plate pore? If yes, does the sap move through the sieve element's cytoplasm (like symplastic pathway) ? If no, then how does the sap move?
I guess there is no function of companion cells in the transportation. Their only function is to carry metabolic activities in sieve elements.

In phloem, the sieve tube elements are not lignified so no concept of 'pits' and since cell wall is permeable (cellulose) and also has plasmodesmata, substances can easily transfer through diffusion and/or osmosis. Sieve tube elements are living cells having reduced cytoplasm restricted to the sides and the sieve pores in the sieve plates are modified versions of plasmodesmata. This allows a nearly empty lumen for continuous bulk transport of organic food solution.
Companion cells keep the sieve tube elements alive and help them in their transport act.
For further details visit the following website:
https://academic.oup.com/jxb/article/64/16/4839/593231
You can also find many books explaining the whole process.
Hope it helps.


text:
How can a nucleotide falling *outside* a binding site affect a transcription factor's ability to bind to said site?
In this paper regarding a polymorphism within the AQP7 gene and its potential effects on one's metabolic profile, the authors use a luciferase assay to confirm that the alleles of this SNP have a definite impact on the expression of AQP7 in the presence of CEBPB, but the SNP itself falls outside the predicted CEBPB binding sequence:

The only thing I can imagine is a second transcription factor that cooperates with CEBPB has a binding sequence that overlaps this SNP, but I see no mention of such a thing in this paper. If this SNP truly affects the binding of CEBPB, then wouldn't the corresponding binding sequence have to extend through this SNP?
Edit:
To quote the paper, "A gel shift assay was then performed to investigate whether the A-953G SNP affects C/EBP binding. Compared with the radiolabeled oligonucleotide carrying the 953A, the one carrying the -953G variant showed a 30+/-7% reduced binding to C/EBP"
And here is the gel shift assay:

As far as I can tell, even if the scientists had reason to believe that this SNP affected CEBP binding in this region, it shouldn't be beyond science for someone to hypothesize how that is.

The authors of the paper presumably do not say — I assume you have read the discussion and this is the case — because they have no experimental evidence that bears on the question. They are professional scientists and are behaving as such. We can all think of possibilities, but it is hardly fruitful to discuss them without evidence.

Did they assess binding of CEBPB to the two different promoter sequences? Have you looked up what other factors are known to bind this promoter? There isn't enough information here to give a non-speculative answer without doing a lot of extra research, but the short answer to your question at the end is 'no' — there are many ways that SNP could affect expression, only some of which involve altered binding of CEBPB.

@David they state, "measurement of mRNA content in
adipose tissue and functional studies in transfected cells
clearly support a biological role of the -953G variant in
negatively modulating AQP7 expression by reducing
C/EBP-DNA binding" so apparently they had reason to believe that this SNP affected CEBP binding despite not falling within their predicted binding site, so that doesn't really follow what you're saying

@David You say that a scientist wouldn't extrapolate beyond the evidence and yet seemingly thats exactly what is happening here unless you can give we an alternative explanation

@tyersome see edit

No. They are just stating what their experiment shows. A results in B. Their experiments do not show WHY A result s in B, and so they leave it at that.  Some authors might present possibilities in the discussion. For whatever reason, these authors do not. It could be that they don’t want to appear foolish suggesting something that turns out to be wrong, or they didn’t want the referees of the paper to ask why they didn’t do experiments to test a suggestion, or they have an idea and don’t want to be scooped. But in professional science, if you stick out your neck…

@David Well even if these scientists didn't wish to include any postulations in their publication concerning this, I still wish to know what can be said outside of the paper. When I said "I see no mention of such a thing in this paper" it wasn't to imply that the authors left something out or that they had an obligation to speak on it, my question stands regardless of whatever is or isn't in the paper I cited.

If you have a question about the indirect influence of DNA regions on transcription factor binding, I think it would be better to pose in general terms, rather than relate it to a particular paper, which in any case few members of this list are likely to read. But you need to show evidence that you have thought about it yourself first.

@David from your very first comment you had no interest in actually answering my question, but rather you would much rather talk down to me as though I don't know what a scientific paper is. This is neither my first time reading a paper, nor my first time asking a question on stackexchange. "You need to show evidence that you have thought about it yourself first" yea thats exactly what I've done here. If I may ask, what to you merits "showing you've thought about it" if not citing exactly where the question arose? Additionally, the question has been answered, do not reply to me again.

I think the question is fine as-is. The question title asks about a general concept; the body of the question shows what motivated OP to ask the question and demonstrates that they've thought about it enough to rule out some obvious counter possibilities. I think it's fine that OP doesn't quite gather on their own the importance of structure in binding to DNA sequences, because a lot of general textbooks gloss over or fail to mention this when talking about recognized sequences, hence the question and resulting answer.

Thank you for the edit — that makes the question much clearer and helps it conform to the expectation that questions will be self-contained (not requiring users to visit other sites). However, please read the sites Code of Conduct — you may find David's approach frustrating and feel insulted, but he made no personal comments. Your last response is crossing that line and I encourage you to delete it. ——— David holds questioners to very high standards, but he has contributed many answers and they have been consistently excellent.

This is an answer to the general question posed in the title and not what is happening in the specific case of C/EBPβ.

How can a nucleotide falling outside a binding site affect a transcription factor's ability to bind to said site?

Transcription factors (TFs) associate with a specific shape of DNA. Two binding motifs that are identical at the sequence level may have different helical conformations due to torsional strain associated with flanking sequence context or proximal protein binding. See Figure 1 of Inukai et al. 2017 1 for an overview of the factors that affect TF-DNA interactions beyond primary DNA sequence:

TF-level features: (A) Several TFs can display binding specificity for multiple, distinct nucleotide sequence motifs. Motifs shown are examples of two motifs bound by the bispecific human forkhead TF FOXN2: FHL (red box) and FkhP (blue box) binding site motifs; motifs were obtained from UniPROBE (Accession Number UP00521). Interactions between (B) TFs and (C) TFs and non-DNA-binding cofactors can specify distinct binding site motifs from the monomeric TF motif.
DNA-level features: (D) DNA modifications, such as 5-methylcytosine (left), can modulate TF binding. (E) Numerous TFs use DNA shape readout, such as minor groove width (depicted by red arrows), and rotational parameters such as helix twist, propeller twist, and roll, as part of TF–DNA recognition. (F) Sequences and features outside of the binding site motif (depicted by blue box), such as GC content and / or DNA shape, can modulate TF– DNA binding. These features may immediately flank the core binding site, or may extend more distally from the motif. (G) Genetic variation in either the TF protein sequence (depicted by orange star, middle) or the DNA binding site (depicted by X, right) can alter TF–DNA binding.

References

Inukai S, Kock KH, Bulyk ML. Transcription factor-DNA binding: beyond binding site motifs. Curr Opin Genet Dev. 2017 Apr;43:110-119.

Thank you, situation B was essentially what I had imagined might be the case but this does broaden my horizons

source: Stack Exchange

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

sort: votes


text:
Can CRISPR knockout of a gene be referred gene inhibition?
Can gene knockout (e.g. by CRISPR) be referred to as gene inhibition? I am trying to use precise words for a manuscript. We first showed siRNA of a gene has effect X. We also found knockout of the gene has the same effect. For the MS, could I say:
Knockout of the gene showed effect X, confirming inhibition of the gene causes X.

This is really a question of English rather than science. Look up inhibition in a good dictionary, do a Google search for “inhibition of the gene” or search your electronic reprint collection to find that no reputable native speaker would ever use that phrase. That is how you check usage in a foreign language. You say you want to be precise. What precisely does knockout do? Remove the gene? inactivate it? Or what? Read a review to find what words are used.

Looking to a standard source of definitions, the Systems Biology Ontology definition of inhibition is "Negative modulation of the execution of a process."
As such, it doesn't really make sense to talk about inhibiting a gene per se. What people are actually doing when they say that is using a shorthand to describe inhibiting either the expression of the gene or the activity of its product.
siRNA fits this quite well, as there you are talking about inhibiting gene expression. Knockout, on the other hand, means the gene isn't there to have its expression inhibited.
I would thus recommend not referring to knockout as inhibition. A better phrasing of your sentence above might be: "Knockout of the gene showed effect X, consistent with the prior result in which siRNA inhibition of the gene also produced effect X."

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


text:
How many drinks were consumed by each test subject in this study?
I was reading this study and came across the following line:

...subjects consumed either 500 mL of whey protein (25 g; PRO), alcohol (1.5 g·kg body mass⁻¹), 12±2 standard drinks) co-ingested with protein (ALC-PRO)...

Does the 12±2 translate to 10-14 drinks? This seems like a lot, so I went to the equation, 1.5 g·kg body mass⁻¹, but I'm not sure how to go about calculating that. Is "body mass" just bodyweight in kg here?
This is probably very wrong, but, if I take a bodyweight of 87kg and plug it in:
87kg⁻¹ (191lbs) = 0.01149425287
0.01149425287 * 1.5 = 0.0172413793

What am I doing wrong here?

"1.5 g·kg body mass⁻¹" can be equivalently written "(1.5 g)/(1 kg body mass)" or read "1.5 grams per kilogram body mass".
So, a 87 kg person would be given 130.5 g of alcohol. The units work out as:
(1.5 g EtOH)/(kg body mass)  * 87 (kg body mass) = 130.5 g EtOH
That is, you have (kg body mass) in the numerator and denominator, these cancel and you end up with just the g EtOH. When working with units, it's always a good check to write out the units you have and see that the units you end up with make sense for the answer you're trying to get.
Written out another way, you have the dose per weight; you want to multiply that dose per weight by the actual weight to get the dose.

Does the 12±2 translate to 10-14 drinks?

A standard drink in the US is about 14 grams, but these authors aren't in the US. A UK standard drink is 8 grams. Australia is 10 grams. However, they write in the paper:

The alcohol ingestion protocol (1.5 g·kg−1 BM; 12±2 standard drinks) began 1 h post-exercise and was consumed in 6 equal volumes of 1 part vodka (∼60 mL) to four parts orange juice

So if they are taking a standard drink to be 30 mL vodka (approximately 1 fluid oz) and giving 12 of those. 30 ml vodka is going to be just under 10 g ethanol, so by the Australian measure that all works out.
And, yeah, that's a lot of alcohol to drink, especially over just 3 hours. The paper begins "The culture in many team sports involves consumption of large amounts of alcohol after training/competition" - they're targeting the binge level of drinking observed around team sports.

The term "standard drink" seems to be particularly used in Australia.  Here in the UK we'd use "unit" in the same contexts

@ChrisH My understanding is that "standard drink" is used everywhere except the UK, though you'll also find "standard drink" and "unit" used interchangeably for the UK measure. https://en.wikipedia.org/wiki/Unit_of_alcohol reads "Standard drinks were referred to in the first UK guidelines (1984) that published "safe limits" for drinking, but these were replaced by references to "alcohol units" in the 1987 guidelines and the latter term has been used in all subsequent UK guidance."

Maybe so - "standard drink" is certainly never used here in public-facing material.  Perhaps my reading is biased in such a way I've mostly seen the term in an Australian context, or perhaps it's discussed more there even if it's the  correct term in more countries


text:
Monoclonal antibody mass production
There is a long conversation taking place these days about monoclonal antibodies against COVID-19. From a few biology courses I had a long time ago, I remember that the process of creating mAbs was a very complex and delicate one, with relatively small yields, something that contributed to the reduced availability and the high price of such treatments.
I wanted to ask because after my research I got even more confused and I couldn't conclude: what is the current, "modern" procedure of mAb production? What are the yields and eventually how logical is to expect a mAb treatment to become widely accessible? Especially though, when "common" mAb therapies like adalimumab and infliximab cost a few thousand euros/year.

What recent reviews have you consulted? That is the way to find out the current status of technology, rather than expecting someone here to write a pale imitation.

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure. Please see our homework policy for more information.

I am going to edit my question and list the papers I have already read. So please wait before delete/downvote! :) On top of that please keep in mind that I'm not related in any way to Biology other than having an extra interest from childhood. My studies and expertise are lying in a completely unrelated field.


text:
Why is this bumblebee attracted to a methane leak?
In this video from Bloomburg Quicktake, the reporters discover at a methane well (Skip to 14:21) a GHG leak that has attracted bumblebees. Does natural gas smell sweet to bees? Why would the bees be attracted to the leak?

It's entirely possible they were there coincidentally (and got scared by the humans filming them, and decided to take shelter in the pipe), or they were just curious.

What did you find out when you googled this?

Please extract one or more frames from the linked video and add them to your post (this can also be done as GIF) — posts must not require leaving this site to be understood and links can change or break.

It is possible that the bees are attracted to the methane because it might replicate the emission of methane from appealing vegetation alive, dead or dying — specifically the kind of standing wood that might lead to a home for a carpenter bee (easily mistaken for a bumblebee).
"Methane emissions from trees: Tree trunks act as methane source in upland forests (from Science Daily)"

What we've found in this study is that some coarse woody debris acts kind of like the soil and consumes methane while other pieces of coarse woody debris emit small amounts of methane, which is also what we saw with living tree trunks," said Warner.

Welcome to Biology.SE! This is an interesting idea and could become a good answer with more reading and [edit]ing — in particular the linked Science Daily article doesn't say rotting wood is the source and I doubt that is what carpenter bees want. Answers are also more likely to receive a favorable response if they include supporting references to primary literature. This is a good example of how to format references.  ——— Please take the [tour] and consult the [help] pages for additional advice on [answer] and [ask] effectively on this site.


text:
What are the small white dots in an onion cell seen under an electron microscope?
We had to use an electron microscope in class for an assignment and used onion cells. On the 40x and 100x magnification there are tiny white dots and I was wondering if someone could tell me what they are? I have to draw them up and label what I can see but i'm just not sure and I don't want to do it wrong. I saw something that said it could be granules of inclusion but i'm thinking it is probably bacteria or air pockets? I was also wondering if someone could tell me what these bean shaped things are? Or any other organelle that you might see, it would be very appreciated!
I'm sorry the photo isn't great, I could only add one photo and I struggled to find one that showed everything that I was asking, so I hope you can see the tiny white dots I mentioned in my question.

We had to use an electron microscope in class — do you mean a light microscope?

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

Are you sure you were using an electron microscope?  They're quite complicated (and expensive (average $294,000, per Google), and generally used for much higher magnifications.  I also think you need specially treated specimens, not just a slice of onion.  To this non-expert, those white spots look like thin places in your sample, seen in a light microscope.


text:
What is this bird species in the Pacific NW?
I don’t think it’s a Black Phoebe, as they have black beaks not white. Is it a Grosbeak? This was taken in the Pacific NW.. . Sorry for the pic quality.
If this isn’t the right place to post this, please tell me where.

That is a Dark-eyed Junco, Junco hyemalis.  This one is a member of the "Oregon" subspecies, J. h. oreganus, which used to be considered a species, Junco oreganus, before a number of species were combined because they are capable of interbreeding.  The are small, ground-feeding birds, primarily consuming seeds and insects. There are two white outer tail feathers which are prominent when they are flying.
 (image: Andy Reago & Chrissy McClarren via Wikipedia Commons)

Thank you! That’s what it is. I have an app, Merlin Bird ID, that lists birds in the pac nw (or anywhere in the world actually), but the first pic didn’t look like it at all. Which is why I missed it. But as I went in and looked at all the pics the exact bird was there.


text:
Cannot seem to merge the two circles of a microscope (biological, binocular)
I have recently purchased a binocular microscope (Saxon Researcher Compact Biological Microscope 40x-1600x), and have had difficulty getting the two circles of light that I'm seeing through the eyepieces to merge. I've focused the microscope without much difficulty, but when I look through I still see the two circles. Researching this problem told me to bring the eyepieces closer together until the circles merge, however when I do this, I just stop seeing through one of the eyepieces (I close one eye, nothing changes, I close the other - and I just see black in the eyepiece. Also when I move my head slightly I can see through the other eyepiece, but as soon as it's adjusted so I can see through both there's the two circles ). Does anybody have any suggestions as to how I could fix this?
Additionally in my research I saw that you eyes should be 1.5-2cm from the eyepieces, but I cannot see anything but a small dot in the centre until my eyes are almost pressed up against the lenses, is this wrong?

One problem seems to be a small "exit pupal" typical of inexpensive equipment. It is the size of the circle you see in the eyepiece.

Your best bet is to measure your inter-pupillary distance and use this to set the lenses at the correct distance on the scale on the centre piece between the eyepieces. The black indicates that you have something mis-aligned, probably the eye-pieces are raised or lowered with respect to each other, rather than equally adjusted about a central point. It may also be that you have the dioptre incorrectly adjusted so one lens is a lot closer to you than the other.
To measure your inter-pupillary distance you need a ruler (marked in mm preferably, as this is the standard for most microscope inter-pupillary distance scales) and a mirror (or alternatively someone to do the measurement for you).
Stand about 15-20 cm (6-8") from the mirror. Close one eye. Align the 0 mark on the mirror with the centre of one pupil, look straight ahead, close the open eye and open the closed eye, and measure the distance to the centre of the now opened pupil.
Now, you should be able to set this on the microscope. Once you have done this, test to see if you can see with both eyes. If now, adjust BOTH eyepieces equally in small amounts.
As for the viewing distance. To be honest I had never measured how far away my eyes are when using a microscope, but having checked, mine are about the width of my index finger away from the lenses. This would be about 1.5 cm, but not much further than that. In your case I would put my eyes close to the lens and slowly move away to a point that feels comfortable and that the light almost fills your field-of-vision.


text:
How many different proteins are able to form prions?
The Wikipedia article on prions and other sources seem to only talk about variants of PrP protein.
I think I remember a previous version of Wikipedia saying something about another protein able to form a prion.
I know there are prion-like proteins, but for this question, I want proteins that are able to form true prions. It does not matter if the protein does not form prions in humans specifically, but does in other organisms.

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please take the [tour] and consult the [help] starting with [ask] for details.

@tyersome I tried searching, but it just ends up with a bunch of information of PrP, because there does not seem to be much interest in the others or how many there are.

No time to write a real answer but for the diversity see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131755/ The 2nd prion thing you might have heard of may have to do with Alzheimer's https://www.ucsf.edu/news/2019/05/414326/alzheimers-disease-double-prion-disorder-study-shows I think it's still controversial.

@Fizz I think it was Doppel protein which I remember, which is called Prion protein 2. It is similar and takes a bigger role in PrP null mice. No idea why researchers didn't try knocking it out too.  https://en.wikipedia.org/wiki/PRND


text:
Does the gas in blood remain constant when breathing? Is O2 and CO2 replaced by N?
Am a software dev and working on a non-scientific game that shall include "somewhat realistic" elements of the pulmonary system.
Effectively I want to roughly model the exchange of O2 and CO2 between blood and air when breathing.
From what I was able to gather here, roughly 20% of O2 are bound to blood when we are at full saturation: https://www.cvphysiology.com/Microcirculation/M002
Furthermore that O2 is replaced by CO2 due to our metabolic processes. As a result, the gas remains roughly constant (ignoring what's solved in the water and plasma).
However what happens if a human exhales all their air and then breathes an atmosphere of pure Nitrogen (besides suffocating, obviously)?
Will the exhaled gas contain any O2 or CO2? If yes, does that mean N is solved into blood in significant amounts? I haven't been able to confirm the later at all. Or does the overall gas concentration in blood decrease after all?
Hope someone has a rough answer.
Huge thanks in advance :)

If you want the model to be "somewhat realistic," no one should be able to exhale all their air.

I'm no expert, but my take is that there will initially be some CO2 diffusing from the dissolved CO2 in the blood into the pure N2 in the lungs and thus exhaled if there is breathing.  This will continue while the body's remaining metabolism continues to produce more CO2 and the heart moves blood, which primarily transports it as bicarbonate and carbonic acid.(1)  There would probably be trace amounts of O2 diffusing into the lungs.  There would probably be only slightly more N2 in the blood, as the partial pressure of N2 would not change much between air and pure N2.
I'm not sure what you meant by "the gas remains roughly constant" as the O2 and CO2 (and N2) in the blood are not in gaseous form.  They exist as dissolved molecules in the aqueous plasma, not as bubble of gas.
(1) "Transport of Carbon Dioxide in the Blood"


text:
Can someone identify this insect species
I found a dozen of these insects on my wooden floorboards in the city of Athens, Greece (Mediterranean climate) (altitude 200m, 10 km from nearest shore). Currently it's Autumn. Size is about 0.5cm (see photo below).
Can someone please identify the species?

(I've also noticed numerous shed wings)

Check if they are ants (queen or drone forms).


text:
How much percentage of substance does liver take in one pass?
The portal vein system is to feed the absorbed nutrition and toxin (defined as "substance" here) to liver first for it to take them up as fast as possible, before they reach other organs which may be harmful.
For this to be effective, liver should take as much substance as possible in one pass. For example, if the liver only take up 10% of the substance in one pass, then the portal vein system won't make much difference, since most of the substance will circulate to other organs anyway and get taken up by liver in the following circulation passes.
On the other hand, it seems to be very difficult for an organ to take up most substance in one pass since this is not a "effective design" (i.e. over designed).
How much percentage of substance does liver take in one pass? And if the percentage is low, why is the portal vein architecture important?

It depends entirely on the substance. Substances that are more hydrophobic or quickly metabolized by the liver are absorbed more completely. I think it's worth considering that it isn't as though all the drug must be absorbed quickly in one place, they are passing through a dense capillary bed with lots of distributed opportunity to take substances up throughout the liver.
https://tmedweb.tulane.edu/pharmwiki/doku.php/bioavailability_the_first_pass_effect has some examples... 75-85% propranolol is metabolized first-pass, 70% of oral morphine.

What about the main daily nutritions and toxins?


text:
Which approach is the common one in the literature for determining the bacterial growth rate?
I have the following data, which is OD600 (the second component) vs. time (the first component):
data = {{0, 0.046}, {40, 0.111}, {80, 0.291}, {120, 0.808}, {160, 1.742}, {200, 3.319}, {240, 5.017}, {280, 5.503}, {320, 5.897}}

I want to obtain the growth rate of bacteria from the above data.
If I fit a logistic function, that is, $$f(t) = \frac{L}{1 + e^{-k(t - t_0)}},$$ where $k$ is the growth rate, I obtain the following curve:

In this approach, the growth rate is: $k = 0.028$.
Now, if I fit the natural logarithm of the logistic function to the natural logarithm of OD600, I obtain:

In this case, the growth rate is: $k = 0.025$.
Which of these values (or, approaches) is the correct and common approach for determining the growth rate of bacteria?

Welcome to Biology.SE. I’m voting to close this question because this isn't really a biology question — it seems closer to statistics to me. Some questions for you: How much uncertainty is associated with each of the estimates? Based on that are they actually different answers? When measuring things you typically aren't finding the "correct value" you are estimating (with some amount of error). For details see the [tour] and [help] pages starting with [Ask] questions effectively on this site.

@user68022, this seems to be a continuation to the/your question on MSE. I also think that the question is not about biology or directly related to biology (even after your edit), but falls under data analysis/statistics. You have clearly defined your model, which is a nonlinear model. You have also clearly defined $k$. Therefore, there is no question anymore about what $k$ is because you have defined it in your model. What remains is how to properly estimate $k$.

If  given a chance, I would prefer the first approach. Reasons being: It looks similar to a normal Bacterial growth curve ( I can see different phases lag, log etc.), Easy to track the growth pattern, easy to understand.

@Domen tyersome I strongly disagree, and attitudes like yours generate a lot of terrible data-handling in biology papers that I read.

@jakebeal, I don't understand: Which part of my comment is it that you strongly disagree with? I don't see how your answer (below) contradicts with anything I said in the comment. In your answer, you advise to use more datapoints and obtain error estimations. But both of these are, once again, in the scope of how to properly estimate model parameter $k$. You see, everything you said in the answer will naturally follow from what I commented: When you start to think about how to properly estimate parameters, things like replicates, error estimations etc. will naturally emerge.

@Domen I disagree with your statement that "I also think that the question is not about biology or directly related to biology". Please note that critical portions of my answer have to do not just with data per se, but about thinking through the relationship between data and the underlying biological system (e.g., media effects, how OD measurements actually work).

The simple logistic function that you are using here is a fine first-order approximation for modeling microbial growth. Both logarithmic and linear scales are reasonable, with different tradeoffs as explained below. It is unsurprising that these two scales will give slightly different numbers, however, as the exponential approach gives more relative weight to fit errors on the lower values. I wouldn't be too concerned about the difference in numbers, though, since they are only 1.1-fold different, and that's within the likely limits of your assay precision.
Thinking about this from a biological perspective, however, there are a number of key limitations to fit accuracy that you need to take into account when you consider and present your data:

You show only a single replicate. I would not trust this data without at least three replicates, which will give some understanding of the degree of variability encountered with your protocol.
At the low end of the scale, precision will likely be limited by instrument precision and media density. What are your control blanks? Are the OD values that you present with or without media subtraction? Since you are showing a high final OD, I would guess that you are working with rich media, which typically has a significant OD even without any cells present.
At the high end of the scale, remember that OD itself is a logarithmic measure. Once the level of light penetrating is very low (below ~1%, i.e., above OD 2.0), most instruments will start having difficulty quantifying the penetrating light. Are you actually measuring an OD of 6, or is this a compensated measure from a much shorter path length? If it's a compensated measure, that will again imply decreased precision on the low end.

These questions can be addressed by using controls that determine the effective linear range of your instrument with respect to your media and path length, such as the method that we validated  in this interlaboratory study.
Once you know the range in which you can trust your data, then you can determine your answer on how to fit:

Since your primary interest is growth rate, you want to focus on the exponential portion of the behavior. For this, the log-scale fit is better, since it places more weight on the range where the exponential growth dominates the behavior. Based on what you've presented, this is likely the approach that will work for you.
If your low data is mostly outside of the effective linear range, however, you can fall back to the linear-scale fit, which will de-emphasize the low data.
If your primary interest were the saturated level, then you would want to prioritize the linear-scale fit instead, for the converse reason.

Bottom line: you need to figure out your data limitations, based on the interaction between biology and instrument, then see if that supports the log-scale fit or if you need to fall back to linear.

This answer suggests fitting the same equation to the same data on different scales to get better results. This is a very poor scientific practice. Note also that logistic is an ad-hoc choice - one could propose any number of curves with any number of parameters that rise exponentially in the beginning and flatten in the end, and have extremely good fits - mainly because one downweights the results in non-exponential region and "fits the noise" with extra parameters. This is no different from trancation, but uncontrolled and subject to arbitrary errors due to the curve choice.

@RogerVadim Every scientific data fit is done with respect to a model, and part of that model is the expected distribution of errors and outliers. Consider, for example, the difference between mean and median household income which are two different interpretations of the same dataset aimed at extracting different knowledge. For OP's data, different goals (e.g., focus on growth rate vs. focus on level) and knowledge about instrument range entail different choices.

Likewise, you are incorrect about the logistic function being an ad-hoc choice. The logistic function was derived specifically as the solution for constrained population growth ODEs, and remains the standard starting point for modeling for that reason.  Since you are not familiar with the derivation of growth models, here is a Khan Academy article that can serve as a starting point for you.

@jakebeal I know where the logistic function comes from - and this is precisely why I call it ad hoc - the basis for this ODE is that it is easy to solve, i.e., it is mathematical convenience rather than biology. Biology only tells us that the equation is $dN/dt=f(N)$, where $f(N)$ has two zeros and is positive between them: $f(N_{1,2})=0, f'(N_1)>0, f'(N_2)<0$. The early exponential growth than can be shown to be a general feature when expending near $N_1$, just like the saturation. The rest is completely arbitrary.

@RogerVadim Sounds like you've got a more general argument with population biology then, which supports the use of this model as a first approximation on the basis of far more than mathematical convenience. I will prefer to follow the scientific consensus until given reason to believe that it is incorrect.

The approach depends on what is known besides the data points. Non-linear regression for parameters $L, k, t_0$ is certainly a thing to try, as the OP author has already done in MSE - judging by the shape of the curve logistic is a good candidate and it is hard to think, how one could improve upon it without introducing additional parameters (and therefore weakening the results).
Fitting the log would make sense only if $L$ (the saturated value of the population) is known. In this case one could rearrange the equation as
$$
e^{-k(t-t_0)}=\frac{L-f(t)}{f(t)},$$
the logarithm of which is
$$
-k(t-t_0)=\log\left[\frac{L-f(t)}{f(t)}\right].
$$
That is, plotting the logarithm of the expression on the right against $t$ and performing linear regression one could determine $k$ as the slope of the line. Taking log of the logistic function itself does not make much sense to me...
Comments follow-up
Far from the inflection point ($t=t_0$) the curve approximately behaves as an exponential one, and for $t\ll t_0$ it indeed makes sense to make a linear fit to $\log f(t)$:
$$
\log f(t) =  \frac{L}{1+e^{-k(t-t_0)}}\approx
\log\left[Le^{k(t-t_0)}\right]= \log{L} + k(t-t_0), t\ll t_0
$$
That is, one do first rough fitting using non-linear regression to estimate the inflection point $t_0$ and $k$, and choose to do linear regression of $\log f(t)$ against $t$ only for those data points that satisfy $k(t_0-t)\gg 1$.

@user68022 Indeed, this makes sense, but you use only the part of the data points, where the grow can be viewed as exponential. I added a discussion to my answer.

As an alternative to simple logistic (with more parameters obviously): https://www.pnas.org/content/116/29/14698 They seem to be doing non-linear regression though.

Fitting log-logistic vs. log-OD is perfectly reasonable as a data-handling choice: it's just an effective rebalancing of error weighting and doesn't require restriction to "far from inflection point"

@jakebeal please give more math details or a reference - I am interested to know.

@RogerVadim Mathematically, it simply depends on your expectation of distributions. If you are expecting variation to be dominated by +/- errors in the measurement, then you want to stick with an arithmetic scale. If you are expecting variation to be dominated by fluctuations in the exponential process, however, then the fit error magnitude will scale with the value, and you want to switch to a geometric (log) scale in order to avoid overfitting on the highest few data points.

@jakebeal I'd rather see formulas. While I agree about the errors, the main idea is to be able to replace the non-linear regression by a linear one - so I want to see the transformation that one has to apply in order to use the linear regression.

I would not advise attempting changing to a linear regression at all. I am also disagreeing with your comment about the non-linear regression: "Taking log of the logistic function itself does not make much sense to me..."

@jakebeal I guess we have different idea of why people do log-transformation. As for your last criticism - this is simply not serious, please read my answer to the end, as well as the relevant comments.

I have indeed read it carefully, and I disagree with your recommendation, since it entails disregarding more data than necessary from a dataset without many points to begin with.

@jakebeal Just saying I disagree is not an argument - please support your disagreement by solid mathematical/statistical arguments or references. I see no point continuing discussion on the current level.

Let us continue this discussion in chat.


text:
Vertebrae looking bone found on beach in New Zealand
I found this bone on a beach in New Zealand. Does anybody have any idea which part of the body or which animal it’s from?

(click to enlarge)

Are you looking to identify it beyond just being a vertebra? It's a vertebra for sure, but beyond that, it's hard to identify beyond "probably a large mammal", which for New Zealand would likely be some kind of whale or dolphin, unless it's something non-native like a cow.

Welcome to Biology.SE. It would help if you could give some measurements for the vertebra — we can only get a very rough guess based on the hand size. My understanding is that the most probable answer for New Zealand is always going to be sheep, but I think these are too large ... I agree with kmm that these are likely to be from a marine mammal of some sort.

It would also help to know roughly where in NZ (e.g. Northland, BOP, West Coast, 'Naki, etc.), as the animals present vary quite widely from North to South and East to West.


text:
How can the Na+-dependent Cl/HC03-pump pump several molecules against their gradient?
The molecular biology of the cell (6 ed) claims that:

"Another [antiporter] [...] is a $Na^+$-driven$Cl^--HCO_3$-exchanger
hat couples an influx of $Na^+$ to an efflux of $Cl^-$ and $H^+$. (so
that $NaCO_3$ comes in and HCl gets out)"

In the next paragraph, (regarding a transporter with an opposite direction) we can read that:

"The movement of $HCO_3$ in this case is normally out of the cell,
down its elecrochemical gradient, which decreases the pH of the
cytosol".

Meaning that intracellular concentrations of $HCO_3$ typically must be higher thatn extracellular concentrations. In addition, Khan academy (among other sources) tell us that the extracellular concentration of $Cl^-$ is higher than intracellular concentration.
This means that for the price of one $Na^+$, the pump is moving two molecules ($HCO_3$ and $Cl^-$) against their gradients. How is this possible?
Is the $Na^+$-gradient really so strong that it can power this simultanous unfavourable transport? Or are multiple $Na^+$ ions used? Have I misinperpreted the intracellular/extracellular concentrations of  $Cl^-$ and $HCO_3$?


text:
How to take professional SEM images of bacteria?
I am new to using SEM microscope I would like to take clear pictures of Bacillus subtilis. My sample is dropped on a piece of paper and carbon-coated. The picture is showing crumbs of something (maybe dust or burned bacteria). One of my images:

What is the problem here am I too using too much energy from the gun? or is it distance and magnification?

I'm no expert at all, but I don't think paper is normally part of the SEM sample prep...

Where did you find the protocol used for sample preparation? It's hard to troubleshoot without more details. SEM protocols for bacteria often include a fixative step to preserve structures and a dehydration step prior to sputter coating (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352184/). The one cell I can see in this image looks alright. Is it possible that you didn't apply enough sample, or didn't properly target the sample when collecting images?

The sample had a high optical density of bacteria. what do you mean by properly targeting the sample?

Loooooong ago, when I did some SEM, prep of a sample included fixating the specimen, removing the water by flushing the sample with acetone or ethanol, then liquid CO2, then letting the CO2 evaporate off, then putting the specimen on a stand in a vacuum chamber and bombarding it with electrons. I don't remember gold, but that was 40? years ago. It's not a simple process, and I'm surprised someone let you use their SEM without training you in its use.

Did you wash the cells before following the fixation procedure. I faced the same issues. Washing 3 to 4 times with PBS before and after fixation solved my problem and gave me crisp images of bacillus subtilis.
Let me know if that helps

I was introduced to SEM microscopy last year at school so I'm not the most reputable source. But here's what I think could be the reasons:

May need to coat in a more conductive heavy metal (like Gold) if you can access it
Smaller Aperture + Larger Distance (to increase the field of view)
Mount the sample on an aluminium stub with conductive sticky pads rather than paper
Adjust contrast

I have Mount the paper which is holding sample on an aluminium stub with conductive sticky pads. How about the gun power?


text:
What kind of spider is this? (Central Texas)
This is in Austin, TX, USA. Photos taken at night on a phone with a flash, so colors may not be entirely accurate.

I found this spider hiding inside my motorcycle cover, which I'd thrown in a pile on my front porch for a few days.
It wasn't aggressive nor skittish, although it did scuttle away at a relatively slow pace as soon as I tried to move it using a large envelope. I would estimate its diameter (legs included) at about 1-1/2 to 2 inches (38mm - 51mm).
I was very cautious around it since I thought it might be a brown recluse, but I know there are a number of Central Texas spiders that bear a resemblance. I couldn't make out the "violin" on its back but I also didn't get close enough to make sure.

Maybe a Southern House Spider? It appears very similar to the brown recluse although without the violin you were unable to find on the thorax.
https://en.wikipedia.org/wiki/Southern_house_spider

Photo from Spider ID

Not sure why the downvotes - I think you're likely correct! (I'll leave this open for contributions but then accept your answer if there's not a better guess soon.) The picture in the Wikipedia article doesn't strongly resemble my photo; but, that species has strong sexual dimorphism. Of the other photos I googled, I found a few that look spot-on. Maybe the Wikipedia photo shows a male and this was a female, or vice-versa. This photo, for example, looks like the exact same spider (note eye position, abdomen size & texture, leg gradation, etc.): https://www.pinterest.com/pin/391109548883253068/

@Bungle & JEJS: I can't speak for the downvoter, but answers are more likely to get a positive response if they explain why an 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, which is inappropriate for this site. ——— You may also wish to consult the [help] pages for additional advice on [Answer] effectively on this site.

I agree with K. hibernalis. The answer should probably be modified from "Maybe a..." to "This is a..."


text:
Can plants grow healthily being watered in either deionized or distilled water?
I want to use deionized/distilled water to water plants from some. I have the choice whether to use tap water, deionized water or distilled water that come from a closed system that has a water cycle, with a preference of "the purer the water the better" for use in the system.
Can someone please provide me references to whether plants in general (most species) need the missing mineral and salt ions for healthy growth? And references to whether they need what's missing in distilled water for healthy growth (no mineral and salt ions and non-volatile organic compounds, to my understanding)? By references I mean scientific studies - papers or meta-analyses that were done on the topic
I can't provide more specifications on the plant species I'm asking about since I have no particular one I already selected to grow but I'm considering using Picea abies (Norway spruce) if I can get it to grow to a Bonsai form.

The question as-is shows no research - which we are expected to do here. (There's also the factor of pH, Picea Abies will prefer something more acidic than the  pH7 of distilled water being ericaceous). Can you edit in what you've looked at so far, and tell us where you got stuck.

I recommend you to start your googling journey by learning about plant macronutrients and micronutrients and compare plant needs with declared content in tap water from your area. Most likely you will find, that salts in drinking water are optimized for humans consumption and not really beneficial for plants. Consider including rain water + fertiliser in your list of options.


text:
Are coding DNA and invariant DNA independent as subsets of the human genome?
Within the human genome we can identify the coding DNA and the invariant DNA i.e. the DNA that is shared by all humans. For example here the authors claim to identify a sequence that is shared not only by all humans but some other species as well.
What is known about their intersection?
Can they be considered as probabilistically independent (i.e. the chance that a random base pair is in both coding DNA and invariant DNA is the product of the chance that it is in coding DNA and of the chance that it is in the invariant DNA)?
I found a relevant preprint but additional references would help.

Related: Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

The more common related concept here is "highly conserved", meaning a sequence that is difficult for an organism to change and still remain viable.
Every base pair of DNA is potentially subject to change via copying errors and other sources of genetic perturbation.  Many such changes, however, will break something important and not produce a viable organism. This is true both for big, complex organisms like people and also for small, simple organisms like bacteria.
The more fundamental a region of DNA is to the operation of a cell, the more difficult it will be to change without breaking, and thus the more highly conserved the sequence is likely to be. That generally means that the conserved regions are either protein coding sequence or functional RNA sequence. Likewise, the most highly conserved are the ones involved with core cellular activities such as transcription, translation, and replication (see citations below) --- which are exactly the type of sequences identified in the reference that you link.
Now, since 2007 we've dramatically increased the number and diversity of organisms whose genomes have been sequenced, and it's not clear to me whether their purely invariant sequences will have held up. Those areas are certainly quite highly conserved however, and that is only to be expected.
Bottom line: the probability that a DNA region is conserved is highly dependent on it being a coding sequence or functional RNA.
Some relevant citations on the nature of highly conserved sequences:

Isenbarger, Thomas A.; Carr, Christopher E.; Johnson, Sarah Stewart; Finney, Michael; Church, George M.; Gilbert, Walter; Zuber, Maria T.; Ruvkun, Gary (14 October 2008). "The Most Conserved Genome Segments for Life Detection on Earth and Other Planets". Origins of Life and Evolution of Biospheres. 38 (6): 517–533. doi:10.1007/s11084-008-9148-z
Harris, J. K.; Kelley, S. T.; Spiegelman, G. B.; Pace, N. R. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803.

Do you have any data that bear on the question? As far as I can see you are merely expressing an opinion, which does not constitute an answer on this site.

Then please include them in your answer.

@David I have added them.

The problem (at least for me) is that the references are not linked to any of your statements, so I don’t know which supports what.

I've added a pointer.


text:
At what cold temperature at thermoreceptors human feel pain (e.g. in fingers)?
I've tried web search but have not found that specific answer. As far as I know at least some people feel pain (e.g. in fingers) when exposed to cold for prolonged amounts of time. E.g. here sciencedirect - thermoreceptor

The temperatures that individuals report as painful vary, although
temperatures above 45 °C and below 15 °C are generally considered to
be painful.

As I understand 15 °C refers to ambient temperature, probably when full body is exposed to it for prolonged time resulting in gradually drop of internal temperature. But at what temperature at the thermoreceptors (nerve sensory endings) pain signals are produced and after what time threshold? Are they (temperature level and time duration thresholds) same for different parts of the body?
That answer here Why do people feel extreme cold at different temperatures compared to other people of same body structure? implies feeling depend on many things, like differences in clothing,  distributions of body fat which does not look like they would change an answer to my question and some others, like neurotransmitter sensitivity which look to me like they could. However, I think there could be definitive answer to my question in the form of a reasonable range.

You are looking for the temperature threshold for noxious cold. It is believed that TRPA1 is the channel involved in the sensation of noxious cold. As for the physiology, the threshold is usually said to be 15 °C (ref1, ref2). As far as I understand it, this threshold indeed refers to the local ambient temperature (not, as you say, for the whole body exposure).

@Domen, just to confirm: do you mean "ambient" to the thermoreceptor, not ambient to body part / skin where / near where it is located?


text:
Ants carrying metal scew
Today I saw a few ants carrying a metal screw with them.
Video
What might be the reason behind this?  (nesting material?)

Is there any reason why they shouldn't be doing that?

I think the question is reasonable - this seems like very unusual behaviour. Perhaps there was organic material (food stuff) in the threads of the screw and they assumed it was wholly made of food.

Damn. It's just fascinating watching them cooperate like that. From the way they are sometimes stumble from lack of perfect coordination, they could probably carry it with fewer ants than there are. If you see a bunch of humans moving a couch, if we stumble like that the entire couch falls so those ants are working below capacity I think.

+1 for the video. Maybe they're building something. If so, please post the video of them using the screwdriver, which ought to be even more fascinating.

ants use the materials avaliable to them it is why you can find glass plastics and other non natural building materials in many ant hills.

How can you be sure the screw was made of metal?


text:
Are 99% of animals bilaterally symmetric?
The Wikipedia article for "Symmetry in Biology" claims: "Animals with bilateral symmetry are classified into a large group called the Bilateria which contains 99% of all animals (comprising over 32 phyla and 1 million described species)."
This claim that almost all animals are Bilateria can be found in other sources too, e.g. in "A new paradigm for animal symmetry" by Gábor Holló. In both cases, however, no source is provided. I'm no biologist so I don't no exactly how self-evident this claim is.
Does someone know a source corroborating these claims?

See: https://en.wikipedia.org/wiki/List_of_animals_featuring_external_asymmetry?wprov=sfla1

Well, you could count yourself.
Kingdom Animalia encompasses about 1.3 million known species. There is one large phylum where most species lack symmetry - Porifera (5,500 species). Cnidaria (10,000 species) have radial symmetry.
All the other broad phyla, from flatworms to chordates, have bilateral symmetry during embryonic development. Echinoderms (7,000 species) are pentaradially symmetrical as adults but bilateral as larvae and considered part of Bilateria.
Source:
Campbell biology (specifically, chapters 32 and 33)/ Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Rebecca B. Orr, Neil A. Campbell. -- Twelfth edition. | New York, NY : Pearson, 2020.

Strictly speaking, the Bilateria classification refers to animals with bilateral symmetry during embryonic development. Despite the lack of obvious bilateral symmetry in more developed specimens, Echinoderms are part of the Bilateria group.


text:
How do mRNA vaccines work with respect to presentation of the antigen?
As I understand it, mRNA vaccines operate by taking a gene for some distinctive feature of the target virus and arranging for the cells of the vaccine recipient to manufacture the proteins that make up the distinctive feature and present them to the body of the host, which will then form an immune response to the feature.
My question is: how is this feature, assuming it has been manufactured, presented to the body? In other words, is the expectation that it would exist as a separate unit and that separate unit would exit the host cell somehow and be recognized?

Your cited example is the concept behind recombinant viral vaccines, like the ChAdOx1 by Astrazeneca. Nothing to do with mRNA one.

@Shred I edited the question to remove irrelevant comments about how the genomic material enters the cell.

I came here by accident looking for an answer on whether the cells contracting the mRNA get destroyed by the immune system. For instance, Dr. Mobeen Syed suggests that the material exits the cell only as: (1) exposed via MHC I, e.g. in case of a muscle cell, or (2) exposed via MHC II in case of antigen-presenting cell, or (3) debris when the cell self-destruction is triggered by a CD8 T cell. Such interpretation seems to be in conflict with the answers here suggesting that the spike material can exit an intact cell by itself. Video: https://youtu.be/9EfToFXwx98

@RomanRiabenko Well, you should read my comments below in the answers. Concerning cell destruction, when a cell undergoes apoptosis there is a protease cascade that destroys all the proteins in the cell before it disintegrates. Also, as I stated in my comments, a disembodied viral protein would not have the same folded shape by itself that it would have on an intact and complete virus, so it would be unlikely that a fragmentary viral protein would have a useful immunological pattern that could be acquired by a B cell.

@Shred: It's rather unclear, I admit, but I think the OP means SARS-CoV-2 by "vector virus". Still the Q could be edited for more clarity.

@Fizz No, Shred is right. I simply made the error of assuming that mRNA vaccines used a vector virus, which is not true. I removed that erroneous statement from my question already.

You still have a mention of "vector virus" in your Q: "2) is it expected that the vector virus would grow that feature on its own self and that new vector virions would emerge from the host cell with the distinctive feature sprouting from their outer shell?"

@Fizz I removed that part of the question.

@Fizz: I still haven't found out, maybe it goes without saying: a recombined vector virus - Adenovirus - does not only have the gene for the corona spike integrated into its genome (artificial recombination) but "comes as" modified virus, carrying the Corona Spike on its coat, next to its Adenovirus-Antigenes? Recombined Adeno-vector virus "is grown" in vitro? To recap my self-answer: manipulation of genome prevents translation for purpose of virus construction, however, "patentlike", this attenuation does not prevent translation for presentation of MHC by target cells.

@Imprisoned Rhesus "when a cell undergoes apoptosis there is a protease cascade that destroys all the proteins in the cell before it disintegrates." That does not imply that piecemeal fragments of "epitopes" exist as debris? This interests me as it doesn't seem very clear what B-cells are able to take up. B cells never take up whole virus - do they just "contact" antigen - no, as they coherently present on MHC 2 which means uptake of foreign antigen as such. Not whole virus?

MHC presentation of cleaved spike protein is only part of the picture; afterall, the immunity conferred by vaccines is largely owed to neutralizing antibodies produced by B-cells, which do not recognize MHC-bound peptides but rather intact antigen. While MHC presentation is important for T-cell (and ultimately B-cell) activation, the fact is that the spike protein encoded by these mRNA vaccines is presented on the surface of transfected cells for B-cell recognition.
Here is a great review that not only discusses the mRNA vaccines but, as far as I can tell, all of the other vaccine strategies as well. It should answer your question in more detail than I would presume to.
Heinz FX, Stiasny K. 2021. Distinguishing features of current COVID-19 vaccines: knowns and unknowns of antigen presentation and modes of action. NPJ Vaccines 6(1):104

In the course of cellular SARS-CoV-2 infection (Fig. 1a), the S protein is synthesized from one of the viral subgenomic mRNAs and co-translationally transported into the lumen of the endoplasmic reticulum (ER) by the use of a signal sequence at its N-terminus, comprising residues 1 to 13 of its total 1273 amino acids... After completion of translation, the protein remains attached to the ER membrane through a C-terminal membrane anchor... When S is synthesized as an isolated protein (Fig. 1b) (as in mRNA and adenovirus vector vaccines as well as for production of recombinant subunit vaccines), the pathway of biosynthesis is very similar.

Fig. 1: a Infected cells: Subgenomic mRNAs for viral structural proteins are translated in association with the ER (S, M, and E) or in the cytoplasm (N), and virus assembly takes place in the ERGIC. Virus particles are transported through the TGN and released from the cells probably via lysosomes. During transport, S is cleaved into S1 and S2 by the cellular protease furin in the TGN. Some spike molecules, not assembled into virions, are also transported to the plasma membrane despite the presence of an ER retention signal15. b Transfected cells: Biosynthesis of S occurs in the absence of interactions with other viral proteins. Proteolytic cleavage into S1 and S2 occurs in the TGN similar to that in infected cells, but some shedding of cleaved S1 and conversion of S2 into its post-fusion structure (S2*) may occur in the absence of stabilizing mutations. ER—endoplasmic reticulum; ERGIC—endoplasmic reticulum Golgi intermediate compartment; TGN—Trans Golgi Network; RNP—Ribonucleoprotein; Viral proteins: S—spike, M—membrane; E—envelope; N—nucleoprotein.

I think you may be misunderstanding the paper. The diagram you embed shows S1, a viral peptide pool, mounted on the exterior of plasma membrane. This can only be possible via presentation by MHC by my understanding. Also, the spike protein has something like 316 different peptides. I would expect these subunits to be presented, not the entire peptide pool all at once.  When a proteasome cleaves a protein I don't think it is predictable what subset of peptide sequences are created. If you are suggesting that the entire protein or one of the pools gets excreted directly by the TGN (continued)

I think that would be an unproven assertion, because I believe there are range of conditions a protein has to fulfill before it can be transported this way and viral proteins would not, I expect, fulfill these conditions. Furthermore, even a viral protein was execreted directly, it would not have immunological benefit because T-cells can only analyze peptides mounted on MHC, not free-floating molecules. B cells on the other hand bind to structures on complete and folded pathogens. (continued)

It would seem to be unlikely that a disembodied S protein would fold properly without the presence of the rest of the virion, and if the protein is not properly folded, that would seem to make it unlikely that a BCR would bind to it successfully.

S1 is not a "viral peptide pool", it is a domain of the spike protein. You can see the structure of the complete spike protein, including S1 and membrane-bound S2 domains in Fig 2 of the review. It is this complete, folded protein (or at least the S2 domain) that is displayed on the cell surface.

In concert with the cellular machinery, the spike protein has evolved to fold and enter the secretory pathway of infected cells naturally. It is not unreasonable to expect that it would follow the same pathway regardless of the absence of other viral proteins. Here is a paper which detects intact spike protein on the surface of HEK293T cells after transfection with either the wild-type spike protein mRNA or the mRNA of the Moderna vaccine.

That said, nobody is claiming that it's a perfect process and that the spike protein presented by transfected cells is identical to that on the virus. There are issues with spike protein produced from the vaccines adopting the unwanted postfusion conformation. This has been addressed by a double mutation in the vaccines to destabilize this conformation. It has also been observed that the vaccine and virus spike proteins show different glycosylation patterns which may affect immunogenicity.

@canadiener A "domain" of a viral gene is the same thing as a peptide pool. For example, see this paper where S1 and S2 are referred to as peptide pools: https://www.nature.com/articles/s41598-021-92521-4

@canadiener Molecules are not displayed by themselves on a "cell surface". That is an old pre-2000 idea and is a mistake. Material can only be displayed outside of the cell by specific molecules designed to do that, called "Major Histocompatibility Complexes". Both B memory cells and T cells only bind to peptides, not large folded proteins. MHCs display peptides, not large folded proteins.

SARS-CoV-2 enters the cell by its spike binding to Angiotensin-converting enzyme 2 (ACE2 receptor) on the surface of the cell, e.g. in lungs or blood vessels. Instead, to egress, it disrupts function and "hijacks" lysosomes of the host cell. The quote in the answer assumes that the folded spike protein may exit the same way. This makes this path specific to SARS-CoV-2 vaccine, may be not all mRNA vaccines.

@RomanRiabenko That’s a good point, thanks.  I might try and add it to the answer later.

Heinz...  "It is believed (...)that muscle cells, fibroblasts, endothelial cells, and/or immune cells such as dendritic cells contribute to the expression of S after intramuscular vaccination..." What does "contribute" mean? My guess: there is no need of non-dendritic cells presenting antigen on MHC for immunizaton to occur. What is contributed to by muscle cells?

Heinz et al. (linked to) " ... requires the interaction of B cells with the native protein, most likely by recognition of the spike anchored in the plasma membrane of S-expressing cells ..." Did this quote initiate the question answered? What exactly are "S-expressing cells?" If so wished I'll be able to refer to paper(s) that show that B cells are presented antigen on MHC by APC cells (dendritic cells) in lymph nodes - very exciting: there, it's not presenting only (as with Tc's) but it is a "handing over" of presented antigen for uptake  by B cells!
So, no need to "shed" (misfolding) prot.

Your assumption is wrong. A mRNA vaccine only contains a mRNA for the protein against which you want to vaccinate, encapsulated in a lipid membrane. These membrane vesicle  fuses with the membrane of the target cell and releases the mRNA into the cell. There free ribosomes can bind to the mRNA and translate it into a protein. Part of this protein is presented on the cell surface by the MHC complex and thus presented to the immune system. The mRNA is degraded after some time (although it has been modified to slow down this process), no further copies are made or integrated into the genome.
Speaking of virus based vaccines (like Sputnik V or Astra Zeneca) rely on a virus to deliver a piece of DNA into the cell which contains the information on the protein against which you want to vaccinate. This is transcribed into mRNA and eventually translated into protein. From the virus DNA usually the genes which are responsible for replication are removed so you get no new generation of viruses. Also the virus cannot do anything on its own, since it is not alive and needs a target cell and its machinery.
This resource gives a nice overview over the different vaccine types.

First of all, this does not answer the question. Secondly, your understanding is incorrect, if you actually read the link you put in your non-answer, you will see that in the section on mRNA vaccines, it explicitly shows a vector virus being used to insert the mRNA into the cell in steps 2 and 3.

@ImprisonedRhesus Chris's answer is correct. You are reading the wrong section of the link, the part about viral vector vaccines rather than the mRNA vaccine (the top row in the image is the mRNA vaccine; no viral vector there). The part of this answer that specifically addresses your title question is "Part of this protein is presented on the cell surface by the MHC complex and thus presented to the immune system" while the rest addresses other misconceptions in the question.

@BryanKrause Huh, ok, so I stand corrected, but it is more or less irrelevant to the question how mRNA gets into the cell. I am asking about the presentation afterwards, so focusing on a minor and irrelevant part of my question that happens to be wrong seems like a comment, not an answer.

@ImprisonedRhesus The vast majority of the text in your question is centered around misconceptions of how things work and imagined solutions based on those misconceptions. I think an answer that failed to address those would be incomplete.

@BryanKrause The question is about how the antigenic material is presented. How the antigenic material gets into the cell is irrelevant to the question. In any case I have eventually figured out the answer to the question (with no help from this community), so I will post an answer.

@ImThen you should clarify the question.

@Chris I edited the question to remove irrelevant comments about how the genomic material enters the cell. You know this community would be a lot more useful if it spent more time answering questions and less time obsessing about minor errors in the question. The people who ask questions are typically those who don't understand the subject very well to begin with. If I was a PhD in immunology I would never have asked the question in the first place.

@ImprisonedRhesus You are still mixing vaccine types. A mRNA virus does neither contain virions nor does is replicate. It is simply translated.

I'd like to kno, about  manufactured adenovirus carrying the corona-spike on its coat? Aas a vaccine producer, how do I replicate the vaccine virus after recombining its (in case of Adenovirus) DNA? I have heard of some kind of helper cells to replikate attenuated "dead" virus in vitra, manufacturing vector virus. Does this technique lead to recombined adenovirus carrying the spike or not?

@PeterBernhard Please make this into a new question.

How do mRNA vaccines work with respect to presentation of the antigen?

According to a DynaMed article, the egress mechanisms expected to play a role are 3:

(Note that this image may be somewhat misleading, in that [skeletal] muscle fibers [which are very long lived, multi-nucleated cells] don't normally express MHC-I according to a (peer-reviewed) article. I'm unsure if satellite stem cells in the muscle, which serve to repair the multi-nucleated fiber cells by supplying nuclei, have MHC-I.)
As you self-answered, in muscle cells, the MHC-I pathway exposes peptide fragments to "killer T-cells" (CD8)... but there's also release of proteins into extra-cellular space from where they are picked up by B cells, which produce antibodies.
Further MHC-II is engaged in APCs present in muscle and lymph nodes; we know at least from the reported side effects of mRNA vaccines that lymphadenopathy (swelling of lymph nodes) does happen often enough following mRNA vaccine administration.
I think however that the relative ratios of spike protein (following mRNA vaccine administration) reaching these 3 routes haven't been
exactly quantified. (I've search a fair bit, but I could not find any papers on exactly that issue.)
Ultimately, both memory B cells and memory T cells (hopefully) give long-term immune memory against that kind of infection, which at least give the host a head-start in a race against a new infection.
It's worth noting that mRNA vaccines don't produce the same ratios of neutralizing to binding antibodies (to the spike) as a real SARS-CoV-2 infection.

vaccinees generate more non-neutralizing antibodies than COVID-19 survivors resulting in a lower ratio of neutralizing to binding antibodies. These data were already apparent in the early phase clinical trials but remained unrecognized at the time (Walter, 2020).
[...] the burning question of whether the abundant non-neutralizing antibodies do have a protective effect in vivo will need to be elucidated by follow-up studies

mRNA vaccines also produce a lot more (spike) neutralizing antibodies than a real infection (same paper), at least initially--there's apparently a fair bit of decay over time though. Both of these suggest that spikes produced by mRNA vaccines get a lot of B cell attention, which might indicate a lot of them spikes produced by mRNA vaccines egress into extra-cellular space.

As I commented to a different answer, I don't really believe the "extra cellular protein" stuff, unless you give me much more specific info. First of all, B cells only recognize FOLDED and intact pathogens, like a complete virus. The idea that a B cell would successfully memoize a disembodied protein fragment seems unlikely to me. Also, the shape of this fragment would be different than what it would be on a complete virus, so even if it did so, there would be no immunological benefit. (continued)

Secondly, you have not shown how a disembodied viral protein can exit a human cell. Viruses use a complex envelopment mechanism to get out of cells which is only available to a complete virus, not viral fragments. Genuine cell self-product proteins only can leave the cell through the Golgi apparatus which requires specialized carriers that human-generated proteins are designed attach to. There is no evidence I know of that a viral fragment would be able to adopt these carriers and use the Golgi apparatus to escape the cell.

"The idea that a B cell would successfully memoize a disembodied protein fragment seems unlikely to me." Please ask that separately as it's a simpler issue to answer on that level, not related to mRNA vaccines. You could even ask it on Skeptics SE. The 2nd issue (protein egress) is more interesting/challenging to prove directly, I admit, but again it's better suited for a separate question. You've basically used this Q of yours to ask two different ones, related to your disbeliefs. (Your counter-theory that only MHC-I works still doesn't explain anti-bodies, I'll note, though.)

"B cells only recognize FOLDED and intact pathogens" That is completely untrue. B cells will recognize foreign sequences or structures however they're presented to them, whether it's a protein fragment or an intact virion.

S.Seneff, G.Nigh suggested that muscle cell also presents MHC II. "Muscle cells do express MHC class II proteins (Cifuentes-Diaz et al., 1992). As contrasted with class I, class II MHC proteins specialize in transporting intact proteins to the surface as opposed to small peptide sequences derived from the partial breakdown of the proteins (Jiang et al., 2013)." https://dpbh.nv.gov/uploadedFiles/dpbhnvgov/content/Boards/BOH/Meetings/2021/SENEFF~1.PDF

@Fizz First view first  "figure" up above: seems like there are muscle cells expressing at least some - i.e. not zero - MHCI. As I read from you, just yesterday, muscle cells "overexpressing" MHC are subjet to myositis. Muscle cells do express MHC, correct? Compare picture above.

@PeterBernhard: Apparently that page with the pretty image is somewhat less reliable than I thought. The article is signed off by two MDs, but they work for DynaMed. I'm not sure why I wrote it was the Canadian Medical Association. I probably had a different page opened as well and confused the two. Looking at their bios, one of the authors [Iacoviello] looks like a fairly reputable academic in infectious diseases, but maybe that immunology detailed slipped them. Or it might be controversial whether muscle cells have MHC-I, but I've not seen the claim of MHC-I outside that image, TBH.

@PeterBernhard: On the other hand, there's a peer-reviewed article that says the opposite, so that seems more plausible to me. I would not be surprised if other cells in the muscle like stem cells (which produce nuclei that serve as replacements for those in muscle fibers) have MHC-I, but I'd have to check that.

@Fizz (removed to chat all right by me). The "article" you cite, I read, that's the one. Again, how did you google it? This is awesome as it beats basic textbook wisdom. Even found articles like "MHC2 - two - they shouldn't do! - on myocytes. Just one simple logic: it's undebated that muscle fibers are able to express MHC1 (they go the genes), so in case of infection (re question I found your statement, different question..) the very infection may induce expression. Anyway, why are muscle cells not autoimmunically killed for "misssing self"?

@Fizz How about setting up question(s) on non-APC cells expressing MHC1- and -2. Could you cite any basic textbook for MHC2 on non-APCs and - inversely - for non-APCs, nucleated -"aha", cells Not expressing MHC1. Aha: you did mention "nuclear production", ... "Do muscle cells "denucleate"...? Thanks for answering at all, even having received your message I haven't managed to scroll down and read your text. I was stunned by the picture. I will soon delete this comment as chat, except for not on "nuclei". My note on simpleminded infection inducing expression might be left undeleted.

The way the antigenic material is presented is via a peptide MHC complex which appear on the surface of the cell. The various proteins present in a given cytoplasm are randomly selected and automatically chopped up by proteosomes and the resulting short peptide chains are then channeled through a special kind of cellular structure called a major histocompatibility complex and mounted on its surface exterior to the cell. If the target antigen protein is indeed being successfully manufactured inside the cell, then we can it expect that these products will be periodically cut up in the manner described and be exposed. The exposed peptide then serves as an example both for helper T-cells to stimulate immune response (such as antibody class switching), and also serves as the epitope to cytotoxic T-cells which can kill the infected cell. Below is a diagram illustrating the mechanism:

Downvotes with no comments.

This isn't incorrect, but it's incomplete in a major way to the point of being misleading; the vast majority of mRNA vaccine studies measure (neutralizing) antibodies, but how do you get [any] spike antibodies from this "cytotoxic T-cell"?

@Fizz Helper T-cells (CD4+) can attach to MHC just the same way that cytotoxic T-cells (CD8+) attach. However, CD4+ cells stimulate an immune response that includes antibody signalling. I added a statement to that effect in my answer.

You're still missing direct B cell activation, which is a major part of the immune reaction. B cell receptors bind directly to antigen and cause B cell activation, which is then enhanced by $T_H$ cells, but not initiated by them. The MHC-I pathway is only part of the system. You're also completely missing the MHC-II pathway (which CD4s recognize, CD8s only do MHC-I)  and the effect of professional APCs.

@MattDMo Let me know if this comment of mine got go be removed, as maybe it refers to some other question, which might exist at Stackexchange.
Re "B cell receptors bind directly to antigen and cause B cell activation" . That should work without any uptake of antigen? Do B cells uptake whole virus? Or do they uptake "debris", see above, nothing left after "clean apoptosis"? And, what's more, if presentation on MHC2 needs incorporation, may contact and let go suffice in a situation of activation of memory B cells?


text:
Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015
I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others.
However, as this book was published 6 years ago (2015) I wonder if there's a newer and better book on the topic of genome-scale algorithms?
Thanks in advance!

A suggestion if you get no satisfaction here is our sister site [bioinformatics.se].

Please read the description of the purpose of this site o the [Tour]. It is a question and answer site about problems in biology. Subjective opinions of a book are not that.

The book I ask about is on topic to this site. If you cannot offer to help or answer my question, please refrain from commenting/posting.


text:
What is silicalemma and what is plasmalemma in diatom algae and how do they differ?
I try to understant the morphology (cytology?) of diatom algae. Does someone can describe what is silicalemma and what is plasmalemma in diatoms and how do they differ? Or they are the same?


text:
How are some exotoxins heat-stable, despite being proteins?
While studying microbiology, I came across bacterial exotoxins and endotoxins. It's understandable that endotoxins are lipopolysaccharides and hence heat stable.
Exotoxins are proteins and hence heat labile. But there are few exotoxins which are heat stable.
For example, Bacillus cereus produces two types of toxins that are involved in food poisoning— emetic toxin (heat stable preformed toxin) and diarrheal toxin (heat labile).
I don't fully understand the reasoning but I have a thought that, the heat stable exotoxins are small proteins/peptides which after denaturation (by heat) can refold back properly.
If anyone would help, it would be great!

Why do you think that these proteins should be heat stable?

Like I mentioned in the question, I think heat would destabilize the protein folding, but small proteins might fold back...just saying

@ANandiΨ The construction "Why few..." in your title implies "Why are there not many?" But the body of your question suggests that you want to know "How are some exotoxins heat stable"? I'll make an edit, but feel free to roll back if not correct.

@ANandiΨ A priori, unless heat-stability is being selected for, one would expect that most proteins would not be head stable.

@acvill the edit is helpful... thanks


text:
What butterfly species is represented on this painting?
I am wondering if the butterflies represented on this painting correspond to a real species.
Do you know if this is the case and if yes, what species they belong to? Or at least, what species could have inspired the author?
I think the flowers that butterflies land on are probably poppies.
The painting is from the book "Ehon mushi erami" (Picture Book of Crawling Creatures) by Kitagawa Utamaro, a Japanese painter (the book was published in 1788).

If this were in the US, I'd say this was a cabbage butterfly (Pieris rapae), which is white save a black or gray spot or two on each wing. But it's not in the US; it's in Japan.
Being interested in most things natural, I Googled "all-white butterfly Japan".
I think you've come across a partial depiction of a story, not an attempt to paint an actual, realistic butterfly. Googling "all-white butterfly Japan", there were many hits with the same theme: the soul is like the white butterfly and love is the power that transforms.
From another site:

In Japanese folklore, the white butterfly symbolizes selfless love stronger than death, as told in an ancient tale of lovers named Takahama and Akiko. In modern-day Japan, the moral of the myth has been retained, and a white butterfly sighting continues to hold special significance.

I don't know how true this is, as I do not much trust everything I read on the Internet. But it appears, as here, often on searches varying the words.
If it were meant to be an actual white butterfly, cabbages are also common in Japan, as seen on this stamp:

If someone could read the writing on the painting, it might help a lot.


text:
Would this be classified as a cross-sectional study design?
Let's say I'm conducting a study in which persons recently diagnosed with an infectious disease were recruited to provide a variety of different specimens and answer standardized clinical survey questions (with minimal follow up and no additional timepoints collected). The purpose is to study potential modes of transmission by correlating relevant clinical factors with quantitative infectious pathogen load found in different specimen types.
What's the most appropriate description of this study/recruitment design in the context of epidemiology or public health research?
I'm not epidemiologist by training, but I think I can rule out prospective recruitment along with longitudinal, cohort, and experimental study designs. It's not really a case-control study since there is no control group (hard with pathogen load as the primary outcome of interest). Basically leaves a cross-sectional observational study (unless my thinking is way off here).

Seems like this question would fit better on Stats.SE, though I personally feel like most of the study design terminology has little real use even though people in the medical field love to put those words first in their abstract.

generally cohort means you do your measurements (in each subject) at multiple points in time. Merely asking them to provide their own disease history etc. is still just cross-sectional.

IF the sample is representative of a population in some way, authors tend to add that to the title... so you see something like "representative cross-sectional". When it's a convenience sample though, they don't emphasize that :D

@Fizz - Thanks for helping to confirm my initial conclusion Fizz. Glad I'm not totally mistaken. I mostly asked so that I can provide some appropriate feedback to a colleague who asked me for edits on a manuscript.


text:
Do ethnic groups differ in non-coding DNA?
There are services (23andme, AncestryDNA) that will associate an ethnic group to you from your spit. Could non-coding DNA in theory be useful for this goal i.e. are there statistically meaningful differences in non-coding DNA between different ethnic groups?

We only deal with one question per post. The first would be about the standards applied in a test by a commercial service - this would likely be off-topic here as it could be seen as promotion of that service. The second might be on-topic , but you would need to show what researches you'd done on the topic and where you'd gotten stuck. (Personally I'm interested in the answer should it be different from expected heritable differences by a significant amount). You should take our [tour] and refer to the [help] for guidance to our ways - then [edit] the question to show your workings.

This answer links to the site of 23andme https://biology.stackexchange.com/a/7295/68099

Well then, perhaps it would be on-topic - but beware, that's from 2013 and the site-rules have significantly tightened since then - I'll let those with greater familiarity with this site on the stack tell you the current policy. (A cursory search of our meta didn't enlighten me on the subject). You would still need to show your researches into the remaining topic.

Personally I see nothing wrong with discussing particular direct to consumer genetic testing companies.

Not only 'in theory', but it is used for ancestry testing.
Coding DNA (exonic regions) tend to be more highly conserved between individuals, as changes to the sequence are more likely to have a deleterious effect on an important phenotype (think a mutation which makes someone only have a single arm). Non-coding DNA is less constrained by selection and varies more between individuals / ethnic groups. This makes it more useful for identifying variants specific to different ethnicities, which makes the basis of ancestry testing. Typically in ancestry testing SNPs which show evidence of being under some kind of functional selection (i.e. are out of Hardy-Weinberg equilibrium) are excluded from the analysis. Neutrally evolving SNPs (which are more likely to be found in non-coding regions) are more likely to reflect the true population phylogeny.
I'll try and update this post with some references.

But when people try to determine someone's ethnicity by looking at them they are relying on information (eyes, cheekbones, skin color, fat level, lip size, height etc.) primarily shaped by coding DNA right?

@fielanb The differences that you note between people of different ancestry groups are largely red herrings. They give a superficial impression of difference (which in some cases does not have a clear genetic basis), relative to overwhelming similarity in functional regions of DNA (https://nyti.ms/3CxBxcj, https://www.nature.com/articles/ng1456). Noncoding regions on the other hand tend to yield a reasonable historical record of population differentiation, because they are not functionally constrained, and mutations in regions without functions are therefore more likely to be passed on.

user438383's answer is correct. Non-coding DNA is much more useful for ancestral research, especially of ancient ancestry, because it preserves mistakes or changes that would damage a person if they occurred in coding DNA. For this reason people have SNP's in their DNA that date back thousands of years. By comparing and contrasting SNPs it can be determined absolutely how different people are related to each other. We are all related to each other, the only question is how far back you have to go to find the relation.
Concerning physical characteristics like eye and hair color, those are indeed determined by coding DNA, but are what are called "expressed traits" which means that how they get expressed is complex and depends on random factors. For example, I have seen a clone of a cat where the original was completely black, but the clone had a white patch on its chest. However, a littermate of the original did have the same patch. So, you see the gene codes for black, but when the organism grows in the environment, random differences can occur. Part of this is due to a process called "methylation". When a zygote is developed, the egg's genetic material is methylated and this inactivates or activates genes randomly (see "Methylation dynamics during the maternal-to-zygotic genome transition in dioecious species" Willian T. A. F. Silva for more information), thereby causing differences in physical makeup of the organism. Note that a person has many different copies of the same gene which can differ from each other, so which particular gene gets activated will affect the final form of the organism.
Physical characteristics can be a clue to a genetic heritage, but it is important to realize that for every gene that gets expressed many more are latent and go unused, perhaps to surface in a later generation.

The classic reference for reaction norms (gene x environment interaction) would be Lewontin 1974 (here is a republished version that is easy to access: https://pubmed.ncbi.nlm.nih.gov/16645033/).


text:
What is this plant (see the photo)?
EDIT: Found in Asia, China, latitude ~25 degree. Size about several centimeters.
I wonder what this plant is? It looks quite unlike the plants we see everyday. I have tried photo search engines and apps, but cannot find anything.

Looks like a fungus. Please [edit] your post to include location info about the photo and approximate size

Possibly: Genus Cordyceps (Kingdom: Fungi).
Greater than 600 species of this fungus exist worldwide, their fruiting body's are club-shaped and range in colour from white to bright orange.
The spores being entomopathogenic, find an insect-host and proliferate within until the insect's behaviour is conditioned for the survival of the fungi. This has earned some varieties the name of the Zombie Fungus for the strange behaviour observed in inoculated individuals.
The Wikipedia article indicates that is a part of the ascomycota division which indicating it's reliance on a sack-like (or "wineskin") fruiting body to reproduce, just like common edible mushrooms.
Popular in Chinese traditional medicine and as a food supplement increasingly in other parts of the world, there is yet no conclusive benefit medicinally.
Another photograph, showing a cluster of fruiting bodies.

In https://www.reddit.com/r/whatsthisplant/comments/qj0jj6/what_is_this_plant_have_used_photo_search_engines/ , @TinySpookyGhost mentions:

I think it's a fungus. Maybe like this https://en.wikipedia.org/wiki/Xylaria_longipes ?
Here you can see similar ones https://mushroomobserver.org/196852?q=2pXG

I think it is that one.


text:
What is the nature of these sprouts?
With zero knowledge of botany, but curious enough to do some research of what I observe, I would like to know the reason for this young sprout in the lower part of a 2 m long Hoya carnosa. I did not find this phenomenon after looking for it on the Internet.

It exhibits a different kind (shape, color, thickness, consistency...) of leaves, thinner and clearer stem, suction cups ... I've read about foliar heterophilia, sports, ... but these phenomena don't seem to explain what I observe. I've also thought about parasitic plants. Could you provide some insight into this?
EDITED (after digging a bit):
The roots are quite tangled, so it is difficult to identify if the wooden stem the sprout comes from is connected to the Hoya stems. If not, the creeper has managed to keep idle for ~5 years with no visible green parts.

That's a creeper of some sort (looks like Vitaceae family.) It cannot sprout naturally from your Hoya. Viruses and chance mutations can change some aspects (e.g. gall or coloration of leaves).  Mutations are called sports, as you mentioned. But nothing can turn a Hoya into a creeper. If I could examine the source carefully, I could tell you more, but the sprout probably came from the soil the hoya is planted in, or found purchase in part of the hoya (this is unlikely, as it would reach a limit of nutrients and die.) "Like produces like" in seed and within the plant itself.

@anongoodnurse I'm not sure what you mean by "the source". The sprout is inserted in the wood, which should be Hoya wood. And there seems to be no direct connection to the soil at that point, besides two thin "threads" that just fall on it. I added a 4th photo.

As I said, this cannot occur "naturally", i.e. the hoya cannot have given rise to the creeper. And, again, as I said, I would need to examine it more closely to determine what's going on here, and maybe a dissection would be in order. Wat you may be proposing requires part of the hoya to completely change its genetics, which it cannot do.

I guess the most probable reason for this is... the wooden part was already a creeper, which has been idle for at least 5 years.

Yep, looks like a completely different plant rooted in approx the same location as your Hoya. I don't think Hoya stem will ever look like that brown one.

Well, about appearance, it doesn't seem to me so different when compared to the right end Hoya stem at pictures 3rd and 4th.