text:
Is it possible for a plant extract to have different effects, depending on the type of cell line it was tested on?
My plant extract (ethyl acetate fraction) seems to have two different effects depending on the cell/cell line it's being tested on. On liver cancer cells (HepG2), it is moderately cytotoxic. But on lymphocytes and macrophages, it helps increase their proliferation. Is this really possible? What do you think is the possible explanation for this?
I've been trying to find studies that might have similar results as mine, but none so far. I found one study wherein their extract both exhibited anti-proliferative effects on both cancer cells and fibroblasts. However, the effect is much stronger on cancer cells.

"I found one study wherein their extract both exhibited anti-proliferative effects on both cancer cells and fibroblasts" - Could you please cite that article?

I couldn't find the study anymore (forgot to save it, I guess). But I found another one - similar results, wherein the extract had a lower level of toxicity against fibroblasts, compared to cancer cell lines: https://www.frontiersin.org/articles/10.3389/fphar.2017.00371/full

Of course different types of cells, or even the same type of cell in different conditions, may react differently to the same stimulus.  Regarding your "plant extract", it likely has many different molecular components. A typical biochemistry way to investigate further would be to separate the extract into fractions containing different components, and see whether an effect can be prodced by one or more of the components and not others.

Oh, actually, I used the ethyl acetate fraction. The hexane fraction is highly toxic based on my preliminary assays. I will edit my question to add this info, sorry for the missing info.

Cell lines can do wacky things
Have a look at Zhou, 2019, which discusses the genome of HepG2 cells.  These typically have 49 to 52 chromosomes... and many other interesting aberrations.  Awortwe, 2014 commented on the irreproducibility of drug-herb interaction studies in cell lines; they note Caco-2 cells could vary 100-fold in their ability to transport mannitol.  Cell lines are frequently subject to genetic instability associated with their immortalization from a tumor, followed by in vitro evolution that changes their behavior.  (Fusenig, 2017)  The old traditional cell lines are useful in some contexts - if you would like to find a protein that binds something you are interested in, for example - but they can't be counted on to react in a human way.

Thanks for the references. I would think the cell lines are useful for preliminary studies, like screening of plant extracts. I do primary cultures, I get murine macrophages and lymphocytes, since I want to screen for potential immunostimulants. My colleagues test their extracts on cancer cell lines.

Finding a consistent interaction is useful.  I imagine you could fractionate the extract and identify the compound that affects the HepG2 cells.  Injected into a mouse, maybe it causes elevated liver enzymes ... maybe it cures liver cancer. :)  Either way, it might be something that a person taking an herbal supplement would like to know about.

True! I'm still screening but this plant extract can be one of the candidates for further elucidation. Thanks!


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Why would this viral strain-specific antiserum fail to immunoprecipitate the same (98% identical protein) from another strain?
I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC392475/  and I can't work out why a certain immune serum didn't work on the same viral protein but from different strains.
The serum was extracted from tumour-carrying animals infected with the 'SR' strain of Rous sarcoma virus and was later used to immunoprecipitate out the viral protein p60-src from virusinfected cells. The cells in question had been infected either with SR or other closely-related strains, all strains express the same protein. But the antiserum only extracted the SR strain's p60-src and not the same protein from other strains. I thought it could be because the serum had by chance targeted an epitope specific to the SR strain, so you get a lot of proliferation of B cells complimentary to this epitope, therefore overshadowing the detection of other epitopes. But 1. I think the serum was taken from multiple rabbits and surely they wouldn't all have happened to do this. and 2. a later paper I read said that p60-src is 98% the same across SR, Pr, Br strain etc so it seems unlikely to have latched onto an SR-specific bit. And yet, the authors state that due to similarities between SRC genes, "... similar gene products are probably present in cells transformed by other strains of ASV, but they are not detected because of a lack of crossreaction with the currently available antisera."
So my question is, what is causing this lack of crossreaction? Apologies if the answer is very obvious, I am new to the subject and have very little knowledge of experimental methods currently. Thank you in advance for any insights, or corrections on the conclusions I've drawn so far as they might be inaccurate too.
Note: thanks mods for letting me edit the question to improve privacy.

Please don't delete upvoted questions with an accepted answer. If there is a fundamental problem with the post, please flag the question for mod attention, or post a question on it in meta. Thanks.

If you have concerns about plagiarism software please use the edit function in a meaningful way to change the question.

As you note, the viral strains are not identical; it's unclear from your question the actual amount and position of amino-acid differences among them, but it's not surprising that even a portion of the protein would have an immunodominant epitope and thus drive reproducible strain-specificity of any immune serum produced.
Remember that the rabbits or other animals used to produce antibodies are typically at least somewhat inbred strains raised for lab use and so are likely to have less genetic diversity among individuals than you might otherwise expect.
Another paper from this time period reports that different immune sera generated from related virus strains and produced in different animals ranged from immunoprecipitating the src viral protein in zero of the viral strains tested up to immunoprecipitating the protein in all viral strains tested: "Detection of the Viral Sarcoma Gene Product in Cells Infected with Various Strains of Avian Sarcoma Virus ..." Brugge et al (1979) Journal of Virology Vol 29 No 3 p 1196-1203

They may be; they also might not be. I would think that in general you would expect to see less variability in the immune response (not necessarily in the range of targets) among lab animals.  However naturally-generated immune sera are quite complex and need to be individually characterized once they are generated. Also remember that the paper you are reading is from 40+ years ago, before PCR, before easy DNA sequencing, before most bio-informatics, before most understanding of oncogenes, etc.

source: Stack Exchange

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

sort: votes


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How does free living nitrogen fixing bacteria fix N2 in aerobic condition?
If a Azotobacter is free living nitrogen fixer it will also require ATP through cellular respiration. I am confused here: if Nitrogenase is highly sensitive to oxygen molecule how will Azotobacter be able to fix N2 and carry out cellular respiration at the same time?

https://en.wikipedia.org/wiki/Azotobacter#Nitrogen_fixation

Nitrogen fixation is highly sensitive to the presence of oxygen, so
Azotobacter developed a special defensive mechanism against oxygen,
namely a significant intensification of metabolism that reduces the
concentration of oxygen in the cells.[40]

From that cite "Respiratory Protection nitrogenase complex in Azotobacter vinelandii"(google translated)

The second strategy, dubbed "breath protection ", is based on a
significant increase in the rate of the rate of respiration, resulting
in the concentration of oxygen in the cytoplasm decreases to a level at
which nitrogenase no longer experiences damaging action О2 .

https://en.wikipedia.org/wiki/Azotobacter#Nitrogen_fixation

Also, a special nitrogenase-protective protein protects nitrogenase
and is involved in protecting the cells from oxygen. Mutants not
producing this protein are killed by oxygen during nitrogen fixation
in the absence of a nitrogen source in the medium.[41]

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


text:
Are there any eusocial swarms which act prosocially?
My layman’s observations of eusocial colonies (like ants) is that while individual ants are extremely cooperative, different swarms in aggregate tend to act aggressively towards other swarms. Are there organisms where entire swarms will collaborate or otherwise act prosocially with other swarms?

Closely related ant colonies do this. E.g fire ant colonies in Australia don’t attack each other.

Are you using swarm interchangeably with colony? There are ant megacolonies.

Argentine ants.
https://en.wikipedia.org/wiki/Argentine_ant

Global "mega-colony":   The absence of aggression within Argentine ant
colonies was first reported in 1913 by Newell & Barber, who noted
“…there is no apparent antagonism between separate colonies of its own
kind”. [8] Later studies showed that these “supercolonies” extend
across hundreds or thousands of kilometers in different parts of the
introduced range, first reported in California in 2000,[9] then in
Europe in 2002,[10] Japan in 2009,[11] and Australia in 2010.[12]
Several subsequent studies used genetic, behavioral, and chemical
analyses to show that introduced supercolonies on separate continents
actually represent a single global supercolony.[11][13]
The researchers stated that the "enormous extent of this population is
paralleled only by human society", and had probably been spread and
maintained by human travel.

This is true only in the introduced range.  I read that in Argentina, this ant species is like any other and different colonies compete.  A mutation led to the strain of ant that has colonized the world because of its cooperativity.
I was interested to read in the comment by @Polypipe Wrangler that fire ants from different colonies in Australia do not fight each other.  Different fire ant colonies definitely fight each other in Florida.


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Does Ethylene Triple response provide any advantage to the Arabidopsis thaliana Etiloated seedling,?
As ethylene has a triple response effect on  Arabidopsis thaliana Etiloated seedling-
1 Shortening and thickening of Hypocotyl
2 Exaggerated apical hook
3 Short root
According to this site

Ethylene mediates the triple response, which makes the shoots of
seedlings that are buried under debris grow short and wide as well as
bend horizontally. This makes it possible for the shoot to push
through the debris.

I am not able to comprehend how this response of apical hook ,shortening can possibly help plant escape that condition? Does this response has some real benefit to plant or just a side effect of no importance to the plant, Although it was very helpful to the scientist


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Is there any relation between phyllotaxis and the Fibonacci sequence?
I had to modify the question to get into a clearer answer. I originally asked this:
Original question
Watching some TV series, I saw the claim that all flowers have a number of petals that is related to the Fibonacci sequence (1,2,3,5,8,13,....). I was wondering if this is always true and if so, why? I guess some flowers have defects, this has to be some kind of probabilistic law.
I found some websites with examples, [1]. The usual explanation claims that is an optimal packing and is somehow related to petals forming a spiral.
Looking a bit deeper, I found that to avoid petals growing in the same positions, the petals can arrange in such a way that the angle between each petals is the circumference $2\pi$ divided by an irrational number $r$ in order to cover the circle densely. The golden mean $\phi=(1+\sqrt{5})/2$ is irrational and is related to Fibonacci sequence. However, even if $\phi$  is irrational, that does not explain why would $r$ be proportional to $\phi$ in order to create the spiral, wouldn't any irrational number work?
Could anybody provide additional understanding on why the golden mean is so important here and if possible what is the biological origin of these sequences?
More insight
Some comments below were arguing that there are some clear exceptions to this rule. One answer even showed a list of flowers categorized by different number of petals (1,2,3,4,5,6,7...) which shows some violations to the rule. Others provided additional sources that claim slightly different observations but I cannot see which are right and which aren't.
Most websites agree that daisies and sunflowers inner small petals (or disc flowers) produce Fibonacci spirals. Do the external petals (or ray flowers) also count? Other links add more on phyllotaxis (the number of arrangements of petals/leafs in a plant) and consider spirals in pinecones and pineapples. Maybe it is only related to spiral patterns in plants?
I am still concerned to understanding if there is any common mechanism and why the golden ratio is important here.
In this page of UC Santa Barbara, it says that the angle is about 137.5 degrees which is equivalent to the complement of $2\pi/\phi$ or equivalently to $2\pi/\phi^2$ due to the properties of $\phi$. In this paper introduction Phyllotaxis: is the golden angle optimal for light capture? it is claimed that two other angles work too (including the Luca angle). Note that that makes the question harder to falsify, as for example the Luca sequence also includes additional numbers like 4 and 7, but I guess the important thing is some kind of ratio and not the total number of petals/flowers in a given flower/plant.
So a better question is, when and how is phyllotaxis related to the Fibonacci sequence?

Comments are not for extended discussion; this conversation has been moved to chat.

The claim that "all flowers have a number of petals that is related to the Fibonacci sequence" is simply false. Many flowers have other numbers of petals.
Consider, for example, dogwoods, which have a very clear four-petal form.  Lots of other flowers have four or six. A nice catalog of some common examples can be found on this "Ontario wildflowers" site, which lists by petal count.

The claim is still somewhat true for a certain subset of flowers as discussed in the comments above.

@Mauricio I think it's on you to show that it's actually interesting, though, or drill down to a better description of "when it's true". Birthdays follow the Fibonacci, too, as long as you exclude everyone that doesn't fit the pattern.

@Mauricio - Are you saying there are no falsehoods on the internet? Dead. Horse.

Thank you for that wildflowers site. Many years ago, I traveled the country photographing wildflowers. It brought back many happy memories.

What claim are you claiming to be "simply false"? That there is a relationship between phyllotaxis and the Fibonacci sequence? Surely not? This paper for example, states "besides the daisy head, other common examples of Fibonacci phyllotaxis—plant growth on Fibonacci spirals—include the arrangement of the sunflower's seeds, the pine cone, the petal sequence in a rose or a lotus, the sequence of leaves on a thistle, the fruit partitions of a pineapple, and the succession of twigs branching from the stem of a pear tree. T

The claim that is false is: "all flowers have a number of petals that is related to the Fibonacci sequence."  Given how much the question has changed, I have edited the answer to make it clear what I am addressing.

IMO that is trivially obvious. But this site (to pick yet another example) lists quite a few that apparently do (and that fact seems to have fascinated a  lot of people)

I will always admit when I am wrong, and I never argue this much when I am unsure of the facts. I grow flowers, have studied flowers, have photographed flowers, I know flowers. My objection is to the petals claim. It cannot be substantiated. Again, have you looked at the images of daisies I linked to? How do you explain it? By assuming I'm wrong? Yes, there is another possibility, but it's not that I am wrong.

I think this argument is not really going to go anywhere. The general claim is obviously false. jakebeal's answer is simple and clear. It may be worth looking at the extent to which specific flowers or parts of flowers follow Fibonacci sequences, but if we're going to do that we need to start with a specific question with a narrow claim about what is supposedly following this pattern, not "flowers", or this turns into a numerology game rather than science.


text:
Can Covid's RNA be nullified by an opposite RNA strand?
Firstly, I have scant knowledge of biology, epidemiology, virology, and related fields. If my question seems nonsensical or bewildering, I beg your pardon. I'm not sure how to phrase this, but I'll try my best.
As far as I know, when the Covid virus enters your cells, it releases its RNA so that it can copy itself and replicate and thus spread in body.
Can that Covid RNA strand be "nullified" when it comes in contact with an opposite RNA sequence? In other words, just like if you pour water on a fire, the fire will extinguish and thus the two elements can be considered "opposites" as per my logic. In the same way, can an "opposite" RNA thing exist, which can possibly "extinguish" the Covid RNA? If you know what I mean. The analogy is that the "opposite" RNA thing is water while Covid RNA is the fire. The former can take out the latter.
Is there something that works like this? If not, is it possible to develop something that works like this?
Because that way, the Covid replication process is halted at that first step, and ergo the virus can't infect the body.
Thanks.

Yes is the short answer.
These are known as silencing RNAs or interfering RNAs
The longer answer is
You would need much more RNA than you could easily administer to the epithelial cells of the mucosa and other tissues that viruses like SARS-CoV-2 infect, so as to cover each individual cell. In addition you would need to be able to deliver it to those tissues in a timely manner (inhalation is possible, several drugs are administered in that manner), have it enter the cells (essentially what the Pfizer/Moderna vaccine does)  and not have it be degraded.
These are not insurmountable problems, the Moderna team managed to do it for their much longer vaccine, but I don't know if the same base modifications that work for their vaccine will still work for interference/silencing.

I suspect that delivering to all the cells infected by the virus in large enough amounts to slow viral replication is indeed an insurmountable problem (otherwise the virus would have unprotected cells within which to replicate); the Moderna vaccine just has to get into some cells in modest amounts, not all affected cells in overwhelming amounts.

@Armand - I totally agree, but it could be possible to do, just extremely impractical and probably with horrific side-effects, if the transfections that I do regularly, can be taken as a basis.

Hmm silencing siRNAs notwithstanding I’m not happy that you’re answering OP’s question with “yes” since, frankly, the concept of “nullifying” or negating RNA doesn’t really make sense and does certainly not exist: the RNA is neither “extinguished” as in OP’s analogy, nor otherwise negated or nullified. No such effect exists: opposites don’t cancel out (RNAs are not physical forces), and what would this even mean for RNA?  The fact that RNAi superficially looks like it does exactly that is all the more astonishing but unlike OP’s proposal there’s actually a logical mechanism underlying it.

@KonradRudolph - if you can make a ssRNA into dsRNA the viral RdRP will no longer work on it properly, especially if you can make some of the bases non-conventional.


text:
Explanation for lack of wing-leg-fin transformations in arthropod evolution?
I don't know much about evolutionary biology so I may be missing something obvious.
It seems that vertebrate evolution somewhat frequently re-invents the fin out of the leg or wing and the wing out of the leg or fin.
If this pattern was extended, one would expect to see gliding spiders with leg-wings (dear God); insects whose ancestors had wings that now use their wings as a 4th pair of limbs for grabbing, sensing, or fighting; crustaceans or sea-spiders that swim with fin-like legs, etc. But as far as I know, for all their incredible number of species, we never see leg-fins, leg-wings, wing-legs, or wing-fins in arthropods. The occasional swimming bug (shrimp, etc) just uses its body segments and tail, and if it uses its legs at all it's just for stabilization or steering. Insects may or may not have wings, but they never have back-mounted limbs for grabbing, sensing, or fighting.
Is there a straightforward reason for this?

Life emerged in the water. Ancestors of insects, spiders, myriapods and crustaceans were probably terrestrial but then, crustaceans evolved to living in the water again. Finally, woodlice went back onto land!

Ancestral structure of wings in insects is somewhat unknown but it started out with 3 pairs of wings (could come from gills, could come from the exoskeleton). One pair was then lost in all living insects today. Drosophila lost a second pair afterward. Some lost both remaining pairs. In Membracidae, the first pair of wings became a whole bunch of crazy structure.

paddle crabs? e.g. Charybdis japonica


text:
Why is the author citation of Polypodium porosum (C. Presl) Mett.?
I would like to understand what constitutes a valid taxonomic description of a species in botany and by chance I encountered this example (which I otherwise know nothing about).
Either
Pyrrosia porosa (C.Presl) Hovenkamp
or
Polypodium porosum (C. Presl) Mett.
Ignoring the issue which one of the above genus attribution is better, my question is why the publication of C. Presl is the base when he only refers to the species by pointing to Polypodium porosum Wall.. However, that publication is considered invalid and was published again by Mettenheimer (Tropicos seems to point to Band 1 in error). However, why is the citation Polypodium porosum (C. Presl) Mett. and not Polypodium porosum Wall. ex Mett. or Pyrrosia porosa (Wall ex Mett.) Hovenkamp? And why the synonym is Niphobolus porosus C.Presl and not ... I do not know what it would be when he just points to a name used in an invalid publication.

As you state, the designation from Wallich is not a valid name, and I don't think it was even effectively published (the work appears to be just a hand-written manuscript, not even an "indelible autograph" [International Code of Nomenclature for algae, fungi, and plants. Article 30.6-30.6]). It does, however, indicate a specimen, #266.
Carl Presl both effectively and validly published Niphobolus porosus when he both pointed to a specimen (the one from Wallich) and provided a description on page 200.

Fasiculi vasorum in stipite duro tres, teretes, minuti, juxta se aut in triangulum positi, medio seu posteriore minore, in N. poruso quator teretes aequales.

[For Niphobolus generally:] Three bundles of hard, rounded stem, small, placed near each other or in a triangle, in the middle or smaller posterior, in N. porusus four round smooth ones.

Normally, this would lead to a citation of "Niphobolus porosus Wall. ex C. Presl", except in this case Wallich used the designation Polypodium porosus and Presl is using Niphobolus porosum. Since they're not the same combination, Wallich doesn't get credit (Article 46.4). Article 46, Example 27 states:

When publishing Andropogon drummondii, Steudel (Syn. Pl. Glumac. 1: 393. 1854) attributed the name to “Nees. (mpt. sub: Sorghum.)”. This reference to the unpublished binary designation “Sorghum drummondii Nees” is not ascription of A. drummondii to Nees, and the name is cited as A. drummondii Steud., not A. drummondii “Nees ex Steud.”

The combinations from Mettenius and Hovenkamp, therefore, use Niphobolus porosum C. Presl as the basionym.


text:
Large caterpillar with prominent eye-spots and a Morse-code pattern
I would appreciate any help in identifying this caterpillar.

Location: Goa, India. Tropical climate
Currently rainy season. Seen in the morning
Length: about 5cm, Diameter: about 1cm

Can you describe what’s happening in that video? Is the caterpillar being flipped around by a push of air, or is it moving on its own accord (in reaction to a visual stimulus?)?

@KonradRudolph The caterpillar was flipping on its own, most certainly reacting to the movement of the dog's paws (seen in the corner). The dog spotted it first and was  freaking out and barking at it, though keeping a safe distance.

This is really cool! Thanks for posting. :)

This appears to be an oleander hawk-moth caterpillar (Daphnis nerii) shortly before pupating. Otherwise the caterpillar would be bright green in colour:

Newly hatched oleander hawk-moth larvae are three to four millimeters in length, bright yellow, and have a black, elongated "horn" on the rear of the body. … As they get older, the larvae become green to brown with a large blue-and-white eyespot near the head and a yellow "horn" on the rear. […] Just before it pupates, the oleander hawk-moth larva becomes browner in colour.


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Does the cytoplasm include the organelles?
I am a student in middle school. My textbook says that

Cytoplasm is the gelatinous liquid part of the cell excluding organelles.

However my teacher said this is wrong. According to her, the correct definition is "The gelatinous liquid part of a cell excluding the nucleus is known as the cytoplasm".
I am confused now as to which is the correct definition. If my teacher's definition is correct, then the organelles (other than nucleus) are part of the cytoplasm.
Is that correct? What is the correct definition?

Does this answer your question? What is the difference between cytosol and cytoplasm?

@tyersome — I don’t think it does. It is a different question — the distinction between two terms — and if taken in the context of this question it would imply that one particular definition of cytoplasm is “correct”, which, I argue, is incorrect.

Edward2007- what an incredible question by such a young mind. I'm impressed that you decided to find out more about the topic and found your way to an open forum like this. While I do not have the exact answer to your question, I do believe that Bryan Krause's response offers a very nice approach about thinking contextually. "The cytoplasm is like the ocean." It depends on how you look at things. Some times it's not very important to get the definition 100% right, but to visualize the bigger concept, for instance the makeup of a cell, in this case. Any way, I'm sure you'll do great with whatev

Francis Crick (together with AFW Hughes) famously described the cytoplasm as follows: "If we  were compelled to  suggest a  model we  would propose Mother’s Work Basket - a  jumble of beads and buttons of all shapes and sizes, with pins
and threads for good measure, all jostling about and held together by “colloidal forces”.

The cytoplasm is like the ocean.
When you talk about the ocean, do you include the fish? What about islands? Sometimes yes, sometimes no.
You could use a cytosol/cytoplasm distinction, where cytosol is "just the liquid part outside the organelles" and cytoplasm includes all the fish, but context matters and I don't think it's actually necessary to have a distinction.
If someone is talking about the "pH of the cytoplasm", you can assume they mean the liquid part, not that they're taking some weighted average of pH over all the different organelles plus the space outside of them. Same thing for ion concentrations. If someone is talking about the "cytoplasmic face" of a membrane, it's clear they mean the side that faces the liquid stuff in cells, even if you're talking about vesicles and organelles where all the membrane faces are "inside the cytoplasm" since the whole organelle is. However, if one were to "remove all the cytoplasm from a cell" you'd expect the organelles (minus the nucleus) to come along; after all, they are in the cytoplasm so they go where it goes.
If you need to memorize a definition for a class, use what the teacher gives you. Otherwise, think critically about the context in which the word is used. I like your teacher's definition better, not because the two options are "liquid only" and "liquid plus organelles", but because organelles are in the cytoplasm, so sometimes when people say cytoplasm they mean the whole ocean including the contents. Your teacher's definition allows for both uses of the term; yours explicitly does not.

"The cytoplasm is like the ocean.": great analogy!

@Bryan given the upvotes taking your post to the top answer, I think it'd be good to provide a cited example (or two) of usages

Why doesn't the nucleus go where the cytoplasm goes? It is also in the cytoplasm.

@user253751 The analogy only goes so far, but if I want to take it there then the answer would be that the nucleus in this case is the "continents". Cytoplasm was named by looking at a cell in a microscope and seeing this spherical ball in the center, calling that the nucleus, and needing a name for all the other "stuff". It was only later that it was known what other "stuff" was in the ocean.

@theforestecologist Yeah, for sure, that would be good. I've tried to find examples that make some of these distinctions I am talking about clear, but that's been a bit difficult. I will certainly try to find the time, though. For now, I'd recommend a reader try searching Google Scholar for these terms: look for papers that talk about the pH of cytoplasm, or look for "cytoplasmic face" in discussions of cellular transport or transmembrane proteins. Or, conversely, look for measurements of "cytoplasm volume" relative to the nucleus. Vacuoles add a bit of complexity if you're into plants, though

The young scientist asks:

“What is the correct definition?”.

The old scientist answers:

“As is often the case in biology, there is no correct definition — different people adopt different usages.”

This answer attempts to explain why this is the case and how to find out other than asking people who despite greater age and knowledge, may be mistaken in their dogmatism.
General Answer
Often in biology a term is coined for a new observation or concept that has arisen from scientific research. Subsequently further research reveals new aspects or details. These expand rather than negate the original discovery, but can make original definitions inadequate. Individual scientists modify the terminology, and naturally do so in relation to their own concerns, which may differ from those of other scientists. Hence different usages arise.
One might have expected that there would be committees of scientists to lay down rules, but this tends to be confined mainly to the physical and chemical sciences where precise common terminology is important. Because modern biology is fast moving, people are inclined to either wait until the dust has settled (e.g. in enzyme nomenclature) or let “terminological Darwinism” take its course.
Specific Answer
I am not really a biologist in the traditional sense, so I lacked any dogmatic attitude to the question, and, instead made Wikipedia my first port of call. This is not a definitive authority on anything, as anyone can edit it. However in this case it is, I think, useful. Under History we read:

The term was introduced by Rudolf Bon Kölliker in 1863, originally as a synonym for protoplasm, but it later has come to mean the cell substance and organelles outside the nucleus.

There has been a certain disagreement on the definition of cytoplasm as some authors prefer to exclude from it some organelles, especially the vacuoles and sometimes the plastids.

Further in the article there is a reference to the term cytosol which is used in an experimental (rather than an observational) sense to refer to the portion of the cytosol from which membranous organelles have been removed.
The date 1863 is worth noting as it is before the discovery of organelles such as the mitochondrion (1880), and knowledge of others at the time was at a primitive stage.
Addendum: Advice to the young scientist

You have eaten from the tree of knowledge and have lost your innocence. Cry a tear then wipe it dry, as you did when you realized there was no Santa Claus. If you wish to become a scientist or even just to understand science you must understand how science works.

Do not reproach your teachers. They are fallible because they are human. Be charitable towards them as you would have them be to you.

It's going to depend on what definition is useful in what context.  If was was talking about an mRNA being translated in the cytoplasm, I am saying it is absolutely not translated in the ER or the golgi apparatus.  (Most proteins translated in those places are on their way to being transported somewhere else; they will not end up free-floating in the cytosol the way proteins translated in the cytosol usually are)

If you want to know about biology, go to PubMed.  If you want to know about semantics, go to Wikipedia.
Their articles may not be tremendously detailed or accurate overall, but if there is any one thing that inspires generations of bitter snipes and threats, it is a Wikipedia discussion about how to title an article or define the title term.  In this case it is perhaps not so severe; nonetheless, their talk page suggests that they've been around this merry-go-round at least two or three times.  They seem to stick with the standard idea that cytoplasm = everything but nucleus, cytosol = everything but nucleus and organelles.


text:
Identify bug found eating wood table
This bug came out of a hole in a wood table.
I'm in south-west France but since we bought that table one year ago, it was most probably in the table when we bought it so it could be from anywhere.
I'd like to know what it is.

More context and pictures in https://diy.stackexchange.com/questions/232607/holes-in-wood-furniture-identifying-the-cause.

I'm not an entomologist at all, or even in Europe, so take my answer with a grain of salt.
I think this is a beetle of the long-horn beetles, which are all beetles that have a larval stage that borrow in wood. In particular I think this is in the genus Clytus and may be Clytus arietis, which is quite common in Europe and North America. There are other species in the genus that look pretty similar too (e.g. C. rhamni, so I can't be sure).
C. arietis is pretty small - about 10-18 mm, which looks about right for your hole size, and it has very similar patterns on its elytra. It is also hairy, as yours is. Apparently it is called the "wasp beetle" as it is a Batesian mimic, and may even make a buzzing noise when disturbed.

Thanks. The Clytus aeietis is much more yellow but the patterns totally match, so I believe it is definitely from the same family.


text:
Are there any natural forms of aquatic vegetation which do not stand up in water?
We are carrying out some experiments where we study influence of underwater vegetation on waves. Unfortunately, the stalks of artificial 'vegetation' which we have seem to be too dense (or too stiff). The stalks sort of stand up a bit when you put them in water but they do not stand upright and all stay partly bent over.
This might be OK depending on whether there are any natural forms of aquatic vegetation which are sort of 'bent over' due to their weight under the water and which do not 'stand upright'? Is there any natural vegetation which does this?

Can you post a picture of how they are bent over? - many aquatic plants such as lagarosiphon will bend over near the surface. Are you thinking fresh or salt water?

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

Welcome to Biology.SE. Please clarify and focus your question. In particular, your title and body seem to be requesting the different information. Do you want examples of aquatic plants that are highly flexible or are you asking for plants that behave similarly to your artificial model. In either case specifying the type of environment (eg.s: marine vs. fresh, tropical vs. temperate vs. polar) ——— To me it seems like you should start with a survey of what plant(s) are most relevant to your research and then characterize their behavior rather than trying to find plants that fit your model.

If by aquatic vegetation you mean things that grow in deep water (as oppose to shore or marsh plants), I think pretty much all of them do, unless they grow as a carpet on rocks &c.  Consider kelp as a stereotypical example: why should it develop stiff stalks (which might break in strong waves) when flexible stalks and air bladders work better?  If you want something artifical to mimic typical seaweeds, try water ski rope.  (The kind that floats - polypropylene?)

double posted here https://pets.stackexchange.com/questions/32859/are-there-any-natural-forms-of-aquatic-vegetation-which-do-not-stand-up-in-water

@jamesqf do you know of any papers where the water ski rope is used to mimic floating seaweeds?  Are there particular types of seaweed which are well-modelled by this rope?

@Tom: No, pretty much all I know of seaweed and water ski rope comes from scuba diving and water skiing :-)

Yes there are many aquatic plant species which do not stand up in water.
You need to look at the lifeform of the plants, such as introduced by Raunkiaer ( https://en.wikipedia.org/wiki/Raunki%C3%A6r_plant_life-form ) and later work by Ellenberg & Mueller-Dombois (1967).
In fact, you're mixing up two different lifeforms :

true aquatic plants are unable to "stand up" : they are waterborne so they "bend over" depending of the water currents. You'll find rooted aquatic plants as well as rootless ones which float free above or within the water column.

European examples of rooted true aquatic (freshwater) plants are in the families NYMPHAEACEAE, CERATOPHYLLACEAE, HALORAGACEAE, RUPPIACEAE, ZOSTERACEAE, POTAMOGETONACEAE, ZANNICHELLIACEAE, CALLITRICHACEAE, NAJADACEAE and  RANUNCULACEAE (Ranunculus subgen. Batrachium)

helophytes is the name of plants which stand in water (usually have their roots and the basis of their stalk within water) but are erected and have aerial part standing up outside the water

European examples of helophytes are : Sparganium, Typha, ALISMATACEAE, many JUNCACEAE and CYPERACEAE, some POAECEAE (Phragmites, Glyceria, and a long etc.), and many other plants in many families.
For european France, Philippe Julve gives a comprehensive list of all plant species with mention of their life form, so you can look up species which correspond lifeform of your interest. Look here for the "CATMINAT" folder and then baseflor.xlsx and look in the first tab the column R "Type_biologique" (which means life form).
You will want to look the meanings of the abbreviations in the "Légende" tab of the sheet, column G. Julve consider true water plants as a sub-category of other main life form, so you'll want to search for "something-aqua".
Since you're interested in aquatic vegetation, you may want to look at some phytosociological catalogue like E-VEG (on the left side you can browse the tree to section "1 Marine waters" and "3 Freshwater aquatic vegetation".
Clic on one sub-category (latin names of vegetation units) will open the corresponding record in the main frame where you'll find indication to some litterature. But it may be of more interest for you to browse some academic catalogue for the latin name of the higher vegetation units + name of your area of interest. For instance you may want to look for Stuckenietea pectinati + Europe.
Be aware that E-VEG choose to follow botanical nomenclature (so when the main species after which the vegetation unit is named change its name, then the vegetation unit's name change as well, so when Potamogeton pectinatus became Stuckenia pectinata then the Potamogetonetea pectinati became the Stuckenietea pectinati). But many other phytosociological catalogues choosed to conserve the vegetation unit's names stable regardless of plant name's changes. So you may prefer to look for Potamogetonetea pectinati + South-East Asia (if that's your area of interest).
If E-VEG don't suit your needs, you may want to take a look at other catalogues referenced here.


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Is human skull size related to brain size?
Me and my dad have a disagreement about this. He thinks that if a person had a larger skull they would naturally have a larger brain. I think that he is assuming the evolutionary trend holds on an individual scale and that it is odd to assume that they would be correlated.
We are having a hard time finding information on the topic as everything is about skull or brain size when related to intelligence. Sorry if this is not the right place to ask this, please direct me to the right place if I have misjudged.
Who is right?

It is worth adding that larger brain does not necessarily makes one smarter.

It seems that there is a correlation between the two: https://pubmed.ncbi.nlm.nih.gov/20229240/

Are you asking about human skulls?

yes I am. Is there a separate human related biology stack exchange to ask?

This paper doesn't directly answer your question, but does say that skull size is related to brain volume

Have a look: https://en.wikipedia.org/wiki/Brain_size

Probably yes. There are reasons why this is not always the case. For example, a mutation can lead a person to have a thicker skull; a genetic disease causing a large skull unnecessarily, etc.

As a disclaimer, first please remember that brain size is only partially related to intelligence, and that whenever this comes up with regards to humans you should remember the long and ongoing history of badly-justified racism on the topic. So let's ignore intelligence, and just focus on brains and skulls.
If a person has a bigger skull, then they have a bigger volume inside that skull (neglecting the question of thickness). There's not really much inside the skull besides the brain (average volume ~1350 $cm^3$) and the cerebrospinal fluid (average volume ~125 $cm^3$). There's quite a bit of difference in size between skulls (men's brains are on average ~200 $cm^3$ bigger than women's brains, and individual variation large as well). Folks with big heads don't have their brains sloshing around in massive amounts of cerebrospinal fluid (and it would be quite dangerous if they did!): that space is filled with brain.
Bottom line: in humans, a bigger skull generally means a bigger brain.


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How often are diseases caused by more than a single mutation of a gene?
Many genetic diseases are caused by mutations in a gene and often, it is a single nucleotide polymorphism (SNP) that has dramatic consequences (e.g. the E6V hemoglobin mutation in sickle cell disease). Other diseases are the result of multiple mutations, that have occurred within various genes (often in cancer).
My question is, are there also many (or any?) known diseases that only manifest if two or more particular mutations arise in the same gene? My assumption is that they exist, but are rather rare; an ideal answer would point me to a publication with quantitative data: how many known diseases are caused by a single mutation, how many by double, etc.
Regarding alleles: I am not asking whether mutations have to occur homozygously to manifest; I'm talking about mutations in the same copy of the gene; for coding sequences, we would be talking about a double (triple,...) mutant of a protein.

I doubt that such data exist: it would mean a) enumerating all the possible (genetic) diseases, and b) knowing exactly what kinds of mutations are responsible for each of them. There may be also ambiguity in defining what are different diseases and what is not - liek in the case of cancers.

Would Huntingtin mutations fit?

@RogerVadim OMIM is a good database for that but one would have to look at specific diseases. However, I didn't a table of mutations and the associated diseases.

I think that this question cannot be quantitatively answered, because the baseline "non-disease" state is not well defined.
Let's take as a starting point the example that you gave, of sickle cell disease. It turns out there is not actually a single mutation that can lead to the disease, but a number of different mutations. A person with only one of the two copies of their hemoglobin genes affected will be a carried but will not have a sickle cell disease. A person who is affected in both copies will have some form of sickle cell disease, though the specifics will depend on the mixture of mutations present. Does this count as one or two mutations? Would it be counted differently if each copy has the same mutation or a different mutation? What about for the carriers, who have the same mutations, but not the disease?
For another example, consider the case of BRCA1. A person with this gene disabled is highly susceptible to cancer. Should this be counted as a mutation that causes a disease, or should only the mutations on the path to the cancer itself?
It only gets worse when we start considering more complicated questions of susceptibility and potential risk, such as associations between SNPs and heart disease, where the causal relationship becomes extremely murky indeed.
Bottom line: I think that biology has too much fuzziness for a crisp answer to this question in this form.

Updated question to clarify alleles; but question is clear: "are there diseases that only manifest if two or more mutations arise in the same gene". Yes, sickle cell can also manifest with >1 mutation, but one suffices --> not an example of a disease that only manifests if there are >1 mutations. Arguing about disease definitions is also not helpful; there are ressources online that define diseases e.g. here. Ok, there's no IUPAC defintion, but that's okay. For any given definition of a disease: how often are they caused by double mutants?

@Anonymous I still think the concept is ill-defined, because you can't distinguish between "gene with one of two mutations required for disease" and "gene requiring only one mutation for disease"


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Why do different animals have different body temperatures?
Why do different animals have different body temperatures.  For example, humans have 37°C, while dogs have 39°C.
Presumably we have ancestors whose temperature differs from ours.  Why would it change over time?

Because certain species adapt to different conditions by lowering and increasing temperature. Thanks, accept my answer if it helps.

You get pestered by different microbes at each temperature too


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Mutations in a Petri dish overnight
How long does it take for a bacterial culture in a Petri dish to experience all possible single base pair mutations? Can 12 hours be enough?
I want to get an intuition for whether a given mutation is a rare event we can only hope for or something that is all but guaranteed to happen.

Remember that not every mutation is beneficial or conveys some sort of survival advantage, especially in a rich environment like a Petri dish where you are theoretically growing the bacteria on some sort of nutrient agar or in a nutrient-containing solution. Also remember that populations evolve, not individuals.

Sure! Maybe I should delete the last paragraph. The surprising part for me just that mutation is not a matter of "if" but "when". Like in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242871/ I can see antibiotics resistance evolve in a matter of days. Super cool.

A number that gets passed on will be in the non-coding set, I wonder where they get the value for P - presumably from viable specimens, or is it total likely mutations... Question followed.

I don't understand your question, as you give no value for P. Are you saying that the twit quoted some value and you wish to know what it is? In which case your question would appear to be "What is the frequency of mutations per base-pair of E.coli during cell division?" and by extension "How many mutations occur in a petri dish in a period of (say) 24h, and how does this compare with the number of base pairs of DNA in the E.coli genome?". If this is the case please say so explicitly.

@David: Thanks! Yes, that's exactly the case. I've updated the question to be clearer. I'll also try to add an answer based on what I can Google.

It occurs to me that you might be interested also in our sister site, [skeptics.se]. They specialise in challenging notable unreferenced claims in the various media.

@ARogueAnt. Good point! But I can't even find the claim. I decided to cut down the question radically and just ask about how long it takes to get all point mutations. I also cobbled together an answer.

Note that your question, while it takes the usual framing of single base pair mutations, ignores a very large number of possible mutations in the form of structural rearrangements, transpositions, etc., which do most of the real work of changing genomes. Contrary to single-base mutations, there is no way to saturate the space of all such mutations in culture.

We can calculate the number of base pair copy errors in a Petri dish per hour by multiplying the number of base pairs (B), the copy error rate (P), the number of divisions in an hour (D), and the number of cells in a Petri dish (N). (We assume a stable population in a saturated medium.)
$$
B \times P \times D \times N
$$
I've looked up some articles and tried to pull out numbers from them:

B: E. coli has 4.6 million base pairs. [1]
P: Mutation rate per base pair per generation is around $10^{-10}$. [1][2]
D: The doubling time can be as little as 20 minutes. So 3 divisions per hour. [3]
N: Around a billion E. coli per ml. [4] A few billion in a "colony". [5] Let's call it 3 billion for the Petri dish.

$$
B \times P \times D \times N
= 4.6 \times 10^6 \times10^{-10} \times 3 \times 3 \times 10^{9}
$$
This comes out to 0.9 mutations on average per base pair per hour.
Each base pair can change into 3 different base pairs. After 3 hours we will have had almost as many mutations as possible! We can get the same mutation multiple times. But even accounting for that, it's almost certain that a given mutation will happen within a day:

(Click the chart for an interactive view where you can try different numbers.)
Indeed we can see research [6] where selection can give rise to new mutant strains every day:

In general if the inverse of the base pair copy error rate is close to the population size, we will see a large subset of all possible single base pair mutations in each generation.
How likely it is that truly 100% of mutations have happened is known as the "coupon collector's problem". Its solution tells us that the expected number of mutations needed to cover all 3 × 4.6 million point mutations is $3 B \times log(3 B)$. With our numbers above we are doing around 4.1 million mutations per hour, so we would on average need around 55 hours.

Spontaneous mutation rates come into focus in Escherichia coli, 2014 by A B Williams

DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair, 2012 by I J Fijalkowska, R M Schaaper, and P Jonczyk

Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli, 2007 by S Fossum, E Crooke, and K Skarstad

General calibration of microbial growth in microplate readers, 2016 by K Stevenson, A F McVey, I B N Clark, P S Swain, and T Pilizota

Role of the RuvAB protein in avoiding spontaneous formation
of deletion mutations in the Escherichia coli K-12 endogenous tonB gene, 2004 by K Mashimo, Y Nagata, M Kawata, H Iwasaki, and K Yamamoto

Access to high-impact mutations constrains the evolution of antibiotic resistance in soft agar, 2018 by N Ghaddar, M Hashemidahaj, and B L Findlay

The tweet was from an expert and I don't know the first thing about any of this. So I'm pretty sure this answer is wrong. But which part?

I got the whole formula wrong! That's error rate PER BASE PAIR. Then the claim is 100% good. I'll fix this!

All fixed. I'm quite unsure about the number of cells. But https://doi.org/10.1016/j.bbrc.2004.08.078 also gives cell counts in the billions so I hope it's roughly correct.

One needs to compare the total number of mutations, $P\times D\times N \times T$ with the total number of base pairs $B$. If $P\times D\times N \times T > B$, i.e., $P\times D\times N \times T/B >1$, then the mutations explore all of the genome. In fact the condition is even more stringent, if we take into account that it is a stochastic process, i.e., some bases will mutate multiple number of times.

10 mL is a very large volume of cells to be growing on a plate (solid media). Cells do not grow in the medium but on top of it. I would suggest instead using a number of cells in a colony 3.3e9 (https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=6&id=104458). Alternatively, one could instead assume that the culture is in liquid medium of 10 mL, in which case your 1 billion cell number is close (though other estimates are higher, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146540/).

Additionally, on the right side of your equation you still have $T$, but you also have a "3" (?). I think that you meant to remove the last $\times T$.

Thanks for the comments! @RogerVadim: But P is the error rate per base pair. So you will have $B\times P$ mutations for each division.

@MaximillianPress: Thanks, I'll use the colony size. It's the same ballpark. The 3 is there because we have 3 divisions per hour. $T$ is the number of hours.

I'll just drop $T$ and talk about mutations per hour! There are so many variables already anyway!

@RogerVadim: "In fact the condition is even more stringent, if we take into account that it is a stochastic process, i.e., some bases will mutate multiple number of times." I've added a paragraph to address this too. Looks like this pushes out the timeline a bit! Thanks!

@DanielDarabos Another thing that is missing is that the number of cells is treated as a constant, although they divide, i.e., it grows geometriclally (unless we also allow them to die).

Oh man. I was hoping the population stabilizes at some point. ($N$) But maybe they just stop dividing when they go hungry?!

@DanielDarabos it stabilizes, because many mutations are deleterious and/or because there are limited food supplies... in which case they either do not divide or there is strong selection. I think you need to ask a more pointed question: do you want to know how many mutations are there or whether all the mutations have been explored? Under what conditions they grow (in terms of food, selection, growth rate, etc.) - if they do not replicate, why use doubling time?

Yeah. Whether we want to go into that I think depends on why we are asking the question. I edited it now to say that my goal was just to get an intuition for how likely it is to get a specific mutation in a day. On that I'm satisfied even if the answer is lax on population size. I'll also add to the answer a practical example where selection is used to force mutations in a matter of days.

Be careful about what you call a specific mutation. You proved that each site might have experienced a mutation over the night, but it doesn't mean that all the possible genomes were explored: for $B$ base pairs one may have $4^B$ different genomes - it would take much longer to explore all of them.

@RogerVadim: You're right! I forgot this is not binary! I think I've fixed it now. I've also added an interactive thing where you can change the parameters and see how the probability over time changes. Even if we consider 3 mutations per bp, the probability goes up very high in 16 hours or so. Thanks for all the help!


text:
Does surface to volume ratio matter for cold-blooded species with regards to temperature?
While surface grows quadratically with scale, volume growth is cubic. Temperature exchange (gain and loss) of animals is mostly dependant on surface area  (the more area, the faster) whereas heat generation is largely dependant on mass / volume. For warm blooded animals, this implies that specimen in colder climates are usually larger than members of the same species in warmer climates, in order to lose less heat relative to their heat generation.
I'd expect cold blooded animals to approach the environmental temperature faster if they were smaller, having a more suitable surface-to-volume ratio. This obviously is of advantage when warming up, but should be as much of a disadvantage when cooling down. So how does surface-to-volume ratio matter for cold blooded species?

I don't think you understand "zero sum game".

mgkrebbs: What do you mean by that? The point is that while warm blooded species have something to gain by being of larger size, I wonder whether the same is the case for a cold blooded one. Granted, if this was to be a game, who are the players you may ask - and I could only give a rather unprecise answer; so indeed, I'll rephrase.

large size usually offers a gain in savings on food and water needs.  1 elephant eats less than 1 elephant weights worth of mice.

Surface-to-volume ration would predict scaling as multiples of 1/3, which is not what is observed across many domains of life. See this, e.g.: https://biology.stackexchange.com/a/97655/59521

I am a little confused about what you mean in terms of advantage/disadvantage with regard to warming up/cooling down. It seems like it would depend a lot on the environment and the organism in question? Perhaps an illustrative example might help.

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


text:
How to measure the pH of a bacterial species?
I would like to calculate the pH of a certain bacteria species before after an experiment. I was reading about the pH cell of bacteria and I found out about Bacterial Intracellular pH which I different than the pH level outside the cell. I plan to measure the pH Outside of the cell as a method to represent the pH of the bacteria.
My experiment:
I am soaking a piece of paper into a bacteria solution (bacteria + media). After that, I am exposing the piece of paper to different parameters. I would like to measure the slight change in pH if any, due to the exposure. In sum, I would like to measure the pH level of the bacteria on paper before and after exposing it to different parameters to compare the change.
My idea:
For before and after exposure, I will submerge the paper in a neutral liquid suck as DI water or a new sample of the bacteria media for an hour and measure the pH of the solution.
Is that a valid method to measure the pH change or do I have to use a dye to see the color of the cell to quantify the pH?

I think that the only way you'll find this out for this system is to try it. Why not measure the pH directly in the solution rather than putting the bacteria on paper? It may be very hard to get reproducible amounts of bacteria by soaking the paper.

@bob1 Aren't nutrient solutions for bacteria usually pH buffered?

@bob1 I do not know how to take the measurement for the Bacterial Intracellular pH. Therefore, I can not validate my measurement if I took it for the solution or the paper. I was wondering if someone has done both and notice any ddifference.

@AnwarElhadad I don't think this is a great way to measure external pH (just pH the media), and I don't think any measurement of external pH would be a reliable proxy for cytoplasmic pH unless it was first validated in that specific organism. Different bacteria can have dramatically different pH homeostasis mechanisms. For example, E. coli can maintain its cytoplasmic pH within a range of pH 7.4–7.8 over an external pH range of 5.0–9.0. This review discusses some of the measurements and homeostatic mechanisms. https://www.sciencedirect.com/science/article/pii/S0065291109055015

@MikeyC I was thinking of having a very high-density bacteria solution to come close to the PH of the outer layer of the cell

The pH level of the Bacterial Intracellular structure is different from the pH level on the eternal side of the cell. Moreover, there are no studies that suggest that a change in the external pH of the cell will have a linear impact on the Intracellular pH. Therefore, the best methods to measure the Intracellular pH of the bacteria cell are:

microelectrodes ( Escherichia coli intracellular pH, membrane potential, and cell growth. J Bacteriol 158:246–252)

radiolabeled membrane-permeant probes (Escherichia coli intracellular pH, membrane potential, and cell growth. J Bacteriol 158:246–252)

pH-sensitive fluorescent probes (Noninvasive measurement of bacterial intracellular pH on a single-cell level with green fluorescent protein and fluorescence ratio imaging microscopy)


text:
Antibody detection - infection-induced vs vaccine-induced - is it common (or not) for a test to be positive for both?
Given a pathogen and a corresponding vaccine, and given an immune response to either one that results in antibody creation, would it be expected that a clinical test or assay for said antibodies would find it difficult (or SHOULD find it difficult) to distinguish between antibodies generated from exposure to the live pathogen vs a well-designed vaccine?
Or asked another way, would it be the goal of a well-designed vaccine to elicit an immune response that would generate antibodies that are indistinguishable from those generated by exposure to the actual pathogen?  Such that an antibody test would test positive in either case?
Or perhaps more to the point - are there examples of vaccines (prior to 2019) that lead to the creation of antibodies that are not detected by clinical tests for naturally-induced antibodies (where such tests exist) ?

Short answer: no.
Because all vaccines (that I know of) rely on protein or polysaccharide production in some form, whether "natural" (e.g. inactivated virion, subunit vaccines) or "artificial" (purified protein from expressed genes) forms, and the aim is to elicit an immune response that targets the natural pathogen form, so you need to generate an antibody response that covers that form. Vaccines do indeed induce antibodies
Conversely, naturally acquired infections produce antibodies that may not be seen in a vaccine induced response - this is particularly so for vaccines against a single target. For instance, many of the antibodies against SARS-CoV-2 are against the spike protein only, but the natural infection has all the other proteins in the mix, so you get antibodies against things like the Envelope protein and other expressed proteins. If you can detect these antibodies, then you can distinguish between vaccine and naturally acquired immune responses, but not the other way around.
I have however, thought of a mechanism by which a vaccine might induce different immune responses - if the vaccine itself is in a vector that generates an immune response. This is the case for the ChAdOx1 (Astrazeneca) vaccine, where the spike protein is presented on the surface of a non-infectious chimpanzee adenovirus virion. In this case, the adenovirus component could (and presumably does) induce an immune response. However, this is not against the component you are being vaccinated for, rather against the thing carrying the vaccine component.

I was always under the impression that once you get vaccinated against a virus then testing to see if you have antibodies for that virus (to see if you actually have been exposed or infected by it) is meaningless because the test will just pick up on the antibodies to the vaccine so you will test positive from that point going forward.

Is there an example of a human vaccine that will not induce a false-positive test to antibodies produced from exposure to the live / actual virus?

@PeggySchafer - re: your 1st comment - correct that's because the antibodies generated are against the same target. The aim of vaccination is to mimic infection, but in a safe manner.

@PeggySchafer re: 2nd comment - as I said in the post - no, not that I am aware of, because they target things that are the same as the natural infection.

Then I wonder why the FDA says that currently available blood serum covid antibody tests will not detect antibodies produced in response to the vaccines.

Can you link where they say this? Check the "help" link to the right of the comment box to format links properly.

Many vaccines for SARS-CoV-2 use just the S(pike) protein as an antigen; as bob1 notes, those vaccines would not generate a false positive result for serology tests targeted at e.g. nucleocapsid. There's an FDA list of tests with details at https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/eua-authorized-serology-test-performance


text:
How do the lipid nanoparticles in the Pfizer and Moderna vaccines contain and release the mRNA payloads at the right time?
The engineering challenge with mRNA vaccines is that mRNA is fragile and degrades quickly. The solution, then, is to encapsulate the mRNA within lipid nanoparticles that carry the payload into cell.
However, this leads to another problem because mRNA and lipid molecules are both negative and will repel each other. In response, researchers developed cationic lipids that would bind the nucleic acids for delivery into acid. There was yet another problem, because testing found that these solutions were causing undesired side effects. The ultimate solution was to develop a lipid specially formulated to be neutral in at physiological pH, but cationic in acidic environments. This means that the lipid nanoparticles will be stable in blood or extracellular fluid, but once it is absorbed into the cell via receptor-mediated endocytosis, the acidic environment of the endosome will protonate the tertiary amine of the lipid into an ammonium cation, and the mRNA is released into the cell.
It's this last part which confuses me. Specifcally, why does protonating the amine to ammonia cause the mRNA to escape the nanoparticle? Shouldn't doing this cause the mRNA to be more strongly associated with the lipid, since cations and anions attract each other?


text:
How do molecules find their places?
In many molecular biology animations, a molecule just flies in and goes straight to the right spot. It's clearly a useful simplification, but I'm interested in learning more of the full story.

I guess at short distances the electric polarizations of the molecules pull them into the right spot. But I have no idea what is "short" here, on the scale of these animations.
This all is not happening in vacuum. There must be a lot of other molecules crowding around. (Water at least.) How does all that not clog up these mechanisms? I imagine an ATP synthase accidentally sucking in a stray RNA strand.
I understand the animations are also slowed down a lot, foiling my intuition. Do the molecules just randomly bump into each other SO MUCH that hundreds of times per second an ADP randomly flies into the synthase?

Animation of an ATP synthase with ADP molecules flying in:

Source: http://www.mrc-mbu.cam.ac.uk/projects/2245/atp-synthase
Animation of a DNA polymerase with green donuts (DNA primases?) flying in:

Source: https://dnalc.cshl.edu/resources/3d/04-mechanism-of-replication-advanced.html

Apologies for the childish question! I don't know if it's okay to ask such here.

I'm trying to think through the third point. I read that molecules in room temperature water have speeds around 500 m/s. So they can cross a 50 nm distance (roughly the width of these GIFs I think) 10 billion times in a second. The movement of the arriving molecule is much slowed down then.

Another number! The mean free path in air is around 70 nm. In water, 0.2 nm. They indeed are bumping into each other a lot!

I am voting to close this question as a duplicate of the following: Molecular animations of, say, protein synthesis, are simplified, but how exactly?. This is another related question worth consulting.

@David Yes, thanks! I think an answer with more details would be nice, but the question is exactly the same as mine. Sorry I missed it.

You should be aware that the only aspect of such animations that is based on experimental structure determination is the representation of the proteins and associated parts of the nucleic acids. The movement of the proteins is extrapolated from "still" images and the movement of small molecules is completely invented.

Right, thanks! I love Sean Johnson's answer in your second link. It explained everything I wanted to know.

Check  "Fick's law" and "diffusion coefficients"

It depends on the molecule and the type of a chemical reaction. In simple chemical reactions molecules literally randomly collide with the probability proportional to their concentrations, which gives rise to the law of mass action.
However, in a cell, in addition to simple diffusion of the molecules, there are also means of directional transport of molecules from one place to another, such as membrane transport, transport by motor proteins, etc.

I'd add something about concentration gradients to the simple diffusion part.

Thank you! Good point about the law of mass action. When something is burning, I don't go thinking "how do the oxygen molecules find their way precisely into this reaction". I guess as long as the concentration is high enough, random collisions are good enough. Like for ATP? And for rare or unique molecules we have transport molecules.

@DanielDarabos when something is burning a big part is played by convection - the hot air containing the products of burning (CO, CO2) rises, and the fresh air, rich in oxygen, is sucked in. This is not the same as diffusion, which is random motion of molecules. Also, bob1 in their comment above probably meant the osmosis - which is another mechanism of transport governed by concentration difference.

@RogerVadim There's still a lot of diffusion happening at a local scale in that scenario as far as interactions among molecules; the convection portion is best understood as the mechanism for keeping the concentration reasonably high rather than depleting. An important analogy in biology would be the distinction between mass flow, like blood moving in blood vessels, and the diffusion processes by which nutrients/oxygen in blood actually make it into cells.

@BryanKrause I mentioned convection in connection to fire - I am not aware whether similar directed flows exist in a cell. I also agree that diffusion plays a role in fire - in fact, physically they would often be treated together: https://en.wikipedia.org/wiki/Convection%E2%80%93diffusion_equation

@RogerVadim "I also agree that diffusion plays a role in fire" - right, this was my main motivation for commenting. I think your first comment here about convection could have been misinterpreted by someone else (OP in particular) to think that diffusion wasn't as important there. Yes, convection is important in fire, but they were correct to think about the "diffusion part" that matches up molecules for chemical reactions to be effectively the same in combustion/fire and in a cell, and I didn't want them walking away thinking these were fundamentally different.

@BryanKrause I see what you mean, and I agree with this clarification.


text:
How to decipher references in natural history works of the late Renaissance and early Modernity?
Old botany books from the 17th, 18th and 19th centuries (and maybe also some later ones) enumerating lists of species used to give references to their sources as abbreviations consisting of one or few truncated words and sometime numbers.
For example : C.B.Pin.316. or H.Mal.6.79 or Prod.Par.Bat. (see highlighted parts in the following screenshot extract).

Source : https://www.biodiversitylibrary.org/page/502858
The meaning of these abbreviations may have been clear to the scholar of those times, but are quite enigmatic to non-initiated people. And I couldn't find within the books any intelligible list of these references.
I would like to know if there is a somewhat comprehensive list of such abbreviations giving the full wording of the references so that it could be possible to look up for them. Browsing the internet with just the abbreviation mostly gives meaningless results from popular websites (many in social networks ...).
I did find out the meaning of some of these abbreviations:
for instance: C.B.Pin. means Caspari Bauhini Pinax Theatri Botanici, which is this book: https://www.biodiversitylibrary.org/bibliography/713 and the number (here 316) gives the page where the plant was listed in this book.
However, there is a huge number of these enigmatic references, so some help would be really welcome.
I looked at the International Plant Name Index (IPNI), but it does not seem to have results for these abbreviations.
I searched the web for:

"prelinnean book abbreviations", which returned one result of some interest but did not give anything near my desired list.

"prelinnean references", which lead me to this article: C.E. Hutchings, 1903. A supplementary catalogue of the Sturtevant prelinnean library. Miss. Bot. Gard. An. Rep. 1903, pp 233-316. but these are the complete book titles, without the abbreviated forms so that it's quite impossible (or very difficult) to use such material.

I also tried combinations involving such words as "old botany books" "old references in botany books" but could find nothing suitable.

I have found what may be the holy grail. It is a book known as "A Botanical Materia Medica" by Jonathan Stokes. This has several volumes, but the one you want is volume 1, which has no appended "volume X" in the title.
A list of abbreviations can be found on page XIII (or 13 for those not familiar with Latin numerals), just after the introductory letters and dedication.
You can read the volume for free on Google books (let me know if the link doesn't work; I made it into a .com link from my country one...)
I found this by search for "cam hort botany"; "cam hort" being one of the abbreviations in your supplied picture. This lead me directly to one of the Botanical Materia Medica volumes by Stokes, which lead me to think it may well have a list of references somewhere, so I then searched for "botanical materia medica stokes" and working from there.

Thank you so much ! That was exactly the kind of list I was desperately looking for !
I'll keep an "open ear" to possible other lists like this one, maybe of more recent and/or more comprehensive compilation, but as a first result, that's a brilliant one ! Thanks again !

@botaflo no problem. I have come across a similar question before on another site. I'm a former botanist myself (now virologist), so I know the frustration. I also like old texts of this sort, so if you have access to the originals, know that I am deeply envious.

;-) no need for envy : I only access such texts from behind my screen. Yes old texts are cool. It's such a great chance to at least have access to them through internet !

I have found a database which lists some abbreviations, it's on Tropicos.
But it seems quite limited in the search possibilities, for instance: looking for "Hort. ups." does not find the "Decas plantarum rariorum horti upsaliensis" which is abbreviated in this database as "Dec. Prima Pl. Rar. Hort. Upsal.", neither does the search for "Hort ups", nor "hort" nor "ups".
So if you don't give it exactly the correct abbreviated form, it might not succeed. You might have better luck if you have the right beginning and there are not too many options.
Still, it might be of interest for someone, and it does give something like what I was looking for, so I'll leave that link here.
Oh, and there is also this one here.
And the IPNI does provide some search for publications, but no index of abbreviations (but it may be worth to try searching for bits of abbreviations).

I was not so happy with all of these so I made my own list. It's on my Wikipedia sandcast.

[Edition, June 5, 2022] I just found "An Explanation of the AUTHORS Names" in the Gardeners Dictionnary by Philipp Miller (1768), which looks quite close to what I was looking for.


text:
Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?
Any comparable alternatives to linked read sequencing?
I read that 10X Genomics discontinued its linked-reads technologies:

Discontinuation of Linked-Reads
At 10x Genomics, we are committed to enabling your research and providing you with >the best experience to make scientific discoveries. Earlier this year, as a part of >our product life cycle management, we notified you about refinements to some of our >on-market product offerings.
As of June 30, 2020, we discontinued the sale of our Chromium Genome and Exome >product lines. We will not be releasing new versions of these products.
We thank you for your partnership and are committed to providing the highest-quality >technical and software support.
Please contact your Sales Executive, Field Application Scientist, or email our >Support Team at support@10xgenomics.com with any questions.

See here on the 10X Genomics homepage.
This source assumes the product was discontinued due to...

infringed patents held by Bio-Rad Laboratories...

But when searching for "linked-reads" and "Bio-Rad" I cannot find anything. Having worked with ddPCR I assume 10X Genomics problem was the oil emulsion but not the linked-reads approach?
Is there an alternative platform doing what 10X Genomics linked-reads was able to accomplish? I am specifically interested in its role in genome assembly/scaffolding as in the Vertebrate Genome Project (in bold):

The current pipeline (Figure 1) to meet the 3.4.2.QV40 phased metric with the fewest errors currently achievable consists of a combination of the following approaches:

60X PacBio long-reads for an initial phased contig assembly (30X/haplotype);

2. 68X coverage of 10X Genomics-linked reads for intermediate-range scaffolding and further phasing (34X/haplotype);

80X Bionano optical maps to correct scaffolding errors and for further scaffolding;

68X Hi-C linked reads for long-range scaffolding;
PacBio Jelly algorithm to fill gaps using long-reads;

10X Genomics Illumina short-reads for base-call accuracy polishing; and

Thanks for your insights!

What is the specific goal/need that you have that linked-reads satisfied? Is it related to your previous question here? https://biology.stackexchange.com/questions/101425/is-mpseq-more-cost-effective-than-fish-when-looking-for-chromosomal-abberations

This is a question about bioinformatics software, so you will have a better chance of getting an answer on SE Bioinformatics.

@MaximilianPress no I have been reading about the pipeline of the Vertebrate Genome Project. They have been using 10X genomics' linked-reads. I wonder how  the pipeline might change in the future. https://www.rockefeller.edu/research/vertebrate-genomes-project/technology-pipeline-and-policies/
I thought someone might know. Or immediately point out a reason why it might have become obsolete given other technologies on the market.

First, I was just expressing an opinion on the SE group most likely to provide an answer to a valid question. I may or may not be right. As far as ddPCR my guess is that this list might be better as it’s not particularly Bioinformatics, but you’d be expected to research the topic first. Don’t worry too much, if people think you have posted to the wrong list the Moderators can move or help you move your question.

Maximillian provided some good information, but I thought I'd add some practical considerations:

All of the long-read sequencing platforms provide quite contiguous assemblies (scaffold N50s up to 40Mb or so), but those are definitely not chromosome-scale. No matter which platform you use, you will still need a "bigger-scale" method to get to the end. This can be Hi-C, strand-seq or optical mapping.

PacBio Hifi reads are great in that they are high-accuracy and allow high contiguity, but, at least in my experience, you will pay 2-4 times as much to get a comparable result to what you could get with 10X linked reads.

Nanopore can give you a very contiguous assembly with 20-30X coverage (ie about a PromethION flowcell's worth, roughly equivalent in cost to a 10X run on Illumina), but as Maximillian noted, requires polishing with short reads to get the base error corrected. (Note: Nanopore's new Q20+ sequencing is looking promising for this, but costs about twice as much per Gb. It's still cheaper than PacBio though.)

So with that said, it's extremely tragic that the cheapest method for making a high-accuracy, one-step-from-chromosome-scale assembly was killed as collateral damage in a patent war.

And then to answer your question:

MGI have been prototyping a method called stLFR that was supposed to be a replacement, but that seems to still be a work in progress, and also may have been shelved during the pandemic as they shifted towards supporting COVID sequencing.
TellSeq is another possible option, although I can't comment yet on how well it works in practice.

Update:
Answer was transferred to Kieran O'Neill's response, which I think is appropriate. I am not completely convinced that these technologies are necessary, but I am also not as familiar with them.
Original answer
The VGP used 10X linked-reads for 2 purposes, as I have updated your question to reflect:

intermediate-range scaffolding
further phasing

I would argue that both of these purposes have been to some extent rendered unnecessary by advances in technology. VGP protocols seem to be frozen at this point to ensure comparability I guess, but they are now somewhat outdated. For example, the VGP also calls for PacBio CLR technology, which is at this point not preferred for genome assembly. Instead, most would use PacBio HiFi reads, for which an extremely strong suite of tools such as HiFiAsm already exists. HiFiAsm and HiFi tools in general do an excellent job of phasing.
The other component is Hi-C-seq, which provides both intermediate-range and long-range scaffolding information to generate chromosome-scale scaffolds from contigs. The only reason to use intermediate range scaffolding is to simplify the Hi-C scaffolding problem, which is unnecessary with a higher quality of assembly such as that provided by HiFi. Hi-C can also be used for long-range phasing, and is at this point built into HiFiAsm, uniting the two data types.
A similar argument can be made that BioNano is no longer necessary.
In fact, HiFiAsm can use only these two data types (HiFi and Hi-C) in concert to create effectively chromosome-scale diploid human genome assemblies. In my experience it still requires some manual curation to get to full chromosome scale, but the results are still very impressive.
I would say that, at this point, steps 2, 3, and possibly 5 of the VGP are no longer necessary, and step 1 should be replaced by HiFi.
A somewhat lower-cost workflow might be as follows:

60X Nanopore long read sequencing and assembly. For a recent tool see here.
polishing nanopore assembly with nanopore reads using e.g. medaka, possibly diploid phasing.
100X Hi-C sequencing for scaffolding assembly using Salsa2 or RagTag.
Possibly polishing with high-coverage Illumina shotgun.

Additionally, there are a number of service providers such as DNANexus, Phase Genomics, DoveTail Genomics, etc. that will do some or all of these steps for a price. While I was an employee at Phase Genomics, I contributed to a guide for performing genome assemblies that is now almost as outdated as VGP but may still have useful information.
Full disclosure: former employee of Phase Genomics, hold some equity in the company still.


text:
How typhoid fever severe case's intestine perforation occur? (non trauma)
In typhoid severe case, intestinal perforation occurs. As stated here

[4, 6]. Intestinal perforation is a serious complication of typhoid fever

My question here is, how does the bacteria (Salmonella typhi) perforate intestine,like the process?
Does the bacteria somehow weakens the walls of intestine and the pressure cause it to rupture?(Guess)
OR
Due to the bacteria in the intestine, inflammatory reaction occurs which causes thickening of walls and pressure that leads to rupture? (Guess)
Even here, it doesn't state how the perforation occured by the the bacteria
Thank you.


text:
Why does miRNA not get translated?
If miRNA and mRNA are made of the same nucleotides, then why are miRNA not translated like mRNA?
Is it due to miRNA lack of start codon? Or lack of promoters?
Has it got anything to do with RISC?

As you've noted, different RNA molecules are treated differently in (eukaryotic) cells (other common RNAs are tRNAs and rRNAs).  Factors influencing this include the RNA sequence involving both sequence motifs and non-canonical secondary structures, chemical modifications such as caps and poly-A tails on mRNAs, interactions with protein complexes (such as transcription complexes or ribosomal complexes), and localization within the cell.
Regarding translation of RNAs, a useful review is "Principles of Translational Control: An Overview" Hershey et al 2012
Germane to your question, initiation of translation is complex and specific. The authors note

"A conspicuous feature of eukaryotic protein synthesis is the fact
that mRNAs are translated in the cytoplasm, making translation
uncoupled from transcription. Mature eukaryotic mRNAs possess a
m7G-cap at their 5′-terminus and, in most cases, a poly (A) tail at
their 3′-terminus. ... the pathway and mechanism for the formation of
40S and 80S initiation complexes differ substantially from those in
bacteria. For example, a large number of initiation factors (at least
12) promote the binding of the mRNA and initiator methionyl-tRNAi
(Met-tRNAi)—which is not formylated—to the 40S ribosomal subunit. "

Regarding miRNAs, a useful review is "Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation" O'Brien et al 2018
In particular, Fig. 1 is a useful cartoon diagram of the different known pathways producing and processing miRNAs and the subcellular locations of these events.
Later on, they also discuss RISC as one of the mechanisms of miRNA-based gene regulation.
As detailed knowledge of subcellular processes has exploded in the last two decades, it's always good to try to use the most up-to-date textbooks or reviews you can find.


text:
If you catch COVID-19, do you need to be vaccinated after recovery?
When we catch a cold, influenza, or COVID-19, the body starts to produce antibodies against them, so the body becomes immune for a period of time. That means one should not catch them again whilst there is the presence of immunity. Being vaccinated during this period of time seems to be useless.
Imagine someone caught COVID-19 one month ago, should they get vaccinated later?

I don't think the question is suitable under the community rules. Having said that - indeed, in most affected countries vaccination is recommended only a few months after teh recovery from COVID-19. Moreover, as teh sanitary measures go, the certificate of recovery from COVID-19 is usually accepted as an equivalent of the vaccination certificate.

I’m voting to close this question because it is a medical question, more suitable for SE Medical Sciences.

Yes. Studies on reinfections consistently show that a booster vaccination after an infection further reduces the risk of contracting COVID-19 a second time. The recommended time interval is 6 month after the infection.
A vaccination also can reduce the symptoms of Long Covid although the mechanism of this effect is not yet known.

To which studies do you refer?


text:
Can tissue flow apart instead of being tightly attached?
Every tissue of our human body consists on cells and cells are not like static "LEGO bricks". They are highly dynamic and can actively move around, due to myosin-actin networks inside the cell that are fueled by the hydrolyzation of ATP. However, most of the tissue is attached tightly in place. Clearly there is cell migration e.g. in case of wound healing.
But is it possible that tissue flows apart from the body due to the active nature of cells? Under which circumstances this can happen?

Do you mean like placenta separation?

Yes, similar like this.

Blood is considered a specialized form of connective tissue and it can flow.
https://en.wikipedia.org/wiki/Blood

Early in embryogenesis, there are motions which do not flow apart from the embryo, but flow within it in order to shape it.
See e.g. this movie Drosophila embryogenesis
These collective motion are not migration (they don't rely on propelling cells with respect to a substrate) but rather a flow (since there is a change of neighbourhood relations between cells, which is a characteristic of liquid-like flow compared to solid-like deformation), see that other movie at cell scale
Actomyosin is also a crucial player in those movements. The fact that extra-cellular matrix is not yet existent or only nascent during most of these movements is believed to be a key reason why these movements can be much more liquid-like than most deformations in later development.


text:
What is an attenuated virus? What is done to it?
UPDATE: So it looks like I've asked a complex and technical question. I'm going to take @tyersome's advice and study Khan Academy on immunology, and from there, formulate a better question if I still need to.

The question is based on the idea that often a vaccine is based on an attenuated virus.
My understanding is that a virus isn't really alive in the same way a bacterium is, which means they can't be killed. (Correct?)
My (layman) understanding is that a virus is simply DNA or RNA wrapped in a thin layer of protein. (So is it a lifeform, or merely an extremely complex set of molecules?)
I can imagine it's possible, chemically, to obliterate the molecular structure of a virus, and thus "kill" it, but would such a "debris soup" be useful in a vaccine?
I'm not asking how a virus is attenuated, ie, by growing it in certain cultures. I'm asking what it actually means for a virus to be "attenuated"? What's different about it, yet still makes it usable as a method to teach the immune system?

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  Well, everything that came up when I googled described various techniques as to HOW a virus is attenuated. But nothing in layman's terms as to what it actually means for a virus to be "attenuated", except "less virulent."  So why is it attenuated and not, say, just a different strain or variant by that time?

What is the distinction you are trying to make between "attenuated" and "different strain or variant"? Have you read the Wikipedia page? ——— You seem to have multiple questions some of which (especially the last) are much too broad to be answered here. (Both of these are also criteria for closing questions.) ——— To really understand this take/read an introduction to immunology and then post any questions you still have. I have found Khan Academy a good introduction.

Presumably, attenuated means it can't replicate.

@DKNguyen - not necessarily, it may be able to enter and replicate part of the virion, but not the whole genome or perhaps has a packaging defect. Polio and MMR vaccines are both attenuated. The polio one in particular is known to occasionally cause infection and be passed on to others.

@Stewart - you can edit your post with the things that you have found out about how attenuation is done and how this helps make it less pathogenic. Note that the exact mechanisms are specific to the type of virus. Killed (inactivated) vaccines have the structures preserved by fixation or by chemically damaging the genome so that it no longer functions, but proteins remain intact.

@tyersome Thanks for that top tip on Khan Academy

@DKNguyen  That would be a clear well-defined distinction. If factual, that would be the answer I'm looking for.

@bob1 What I found about HOW attenuation is done were long, varied descriptions. None of them went on to explain what actually happens to the virus itself to make it less pathogenic, yet still workable for immune system response.

@Stewart - that's because what happens to the virus is specific to the group of viruses - so changes in an influenza would be different to a coronavirus for example.

@bob1  OK. That sounds like the beginnings of an answer. Does that imply that the functional definition of "attenuated" is different for each group?  And that "attenuated" is therefore a colloquialism for the layman?

Lower entry/binding to receptor, lower replication, lower pathogenicity, sometimes missing proteins or parts of it, and with genetic engineering more curious changes such as lesser replication fidelity, sub-optimal TRS, some proteins replaced by other ones (influenza reassortant). Historically it was just about finding a closely related virus circulating in a different species, giving fewer symptoms and cross-protection (vaccinia virus). Then it was about selecting passaged viruses giving fewer plaques in lab, adapting to eggs so that after enough passages it replicates poorly in human cells.

@Stewart As reuns notes, "attenuated" doesn't really have a technical definition, it just means giving fewer or less severe symptoms while still provoking an immune reaction that will provide protection against the strain(s) of interest.


text:
Coronavirus lineages with amino acid insertions
Is there an overview over SARS-CoV-2 lineages that have some insertions in their genomes? Tools based on GISAID sequences do not show them.
I am aware of a few lineages with insertions

Mu with S:YY144-145TSN (part of lineage definition)
B.1.1.28 with S:ins214ANRN (as I understand, only in a subgroup of the lineage)
B.1 with S:ins214QAS (as I understand, only in a subgroup of the lineage)—now assigned the lineage B.1.639

I'm interested in lineages that occur in the wild, I am aware of some more insertions occurring in lab experiments.

Please check the meaning of Genetic Code in Wikipedia. What you refer to is called the “genome”. I have corrected this.

This is OK with me.

That's because handling insertions is a bit harder than point mutations and deletions.
With covizu I get this, unfortunately it doesn't tell us the insert and the translation. Hope someone can give a more comprehensive answer
    B.1.36.20 ['ins:29594:2']
    B.1.1.373 ['ins:28251:3']
    A.2.5 ['ins:22206:9']
    B.1.214.2 ['ins:22205:9']
    P.1 ['ins:28263:4']
    B.1.604 ['ins:28273:9']
    A.2.5.1 ['ins:22206:9']
    P.1.2 ['ins:28263:4']
    P.1.1 ['ins:28263:4']
    A.2.5.2 ['ins:22206:9']
    P.1.10 ['ins:28263:4']
    P.1.3 ['ins:28263:4']
    B.1.243.1 ['ins:28265:3']
    B.1.621 ['ins:21991:3']
    B.1.1.523 ['ins:26499:3']
    P.1.9 ['ins:28263:4']
    AT.1 ['ins:23599:12']
    P.1.7 ['ins:28263:4']
    A.2.5.3 ['ins:22206:9']
    P.1.4 ['ins:28263:4']
    P.1.10.1 ['ins:28263:4']
    B.1.621.1 ['ins:21991:3']
    P.1.11 ['ins:28263:4']
    P.1.10.2 ['ins:28263:4']
    P.1.8 ['ins:28263:4']
    P.1.6 ['ins:28263:4']
    P.1.5 ['ins:28263:4']

Thanks for the list, this is really helpful.

With the help of the list by @reuns, I was able to hunt down some of the mutations in terms of amino acids:

AT.1 has S:ins679GIAL S:N679K (found in a report from Public Health England)
A.2.5 has S:ins214AAG (usually, the insert can have another point mutation to S:ins214ASG, and it can occur reduplicated as S:ins214AAGAAG
B.1.214.2 has S:ins214TDR (found in a preprint by Gerdol on Recurrent Insertion Region RIR1, the preprint has some more rare insertions in the same region)

The insertions in lines P.* fall in the small gap between ORF8 and N and don't affect AAs, the insertion in B.1.36.20 falls in ORF10 that is probably not coding a protein.

For B.1.621 (Mu) it is ins146N. The insertion in P.1 (Gamma) is at the TRS, duplicating some part of it.

Then the game is to guess where the inserts (including a bit of 5' and 3' context) come from. I didn't find any match in Wuhan-Hu-1 and the matches in human mRNA are not too convincing. `>A.2.5
AGTGCGTGCGGCAGGCTATCTCCCTC

B.1.214.2
AGTGCGTACAGATCGAGATCTCCCTCA
B.1.604
CAAACTAATTTCTTTGGAATGTCTGAT
AT.1
AGACTAAGGGGATAGCACTTTCTCCTC
`

Is it necessary for such short insertions to come from somewhere, can't it be just random? But this is a completely different question ...

For the 12nt one yes, it must come from some mechanism. Most insertions in viruses are unexplained, but sometimes they are, for example some influenza furin cleavage site come from duplication of a motif, others come from host rRNA. It is still a bit mysterious for me and supposedly the 2.5 million SARS-CoV-2 sequences should improve a lot our understanding. The insertion in P.1 comes from duplication of a motif, at the TRS, binding to the 5-UTR, causing the discontinuous transcription / subgenomic mRNA.

On virological.org there are now some insertions with putative origins, either from the virus itself or from host RNA: https://virological.org/t/putative-host-origins-of-rna-insertions-in-sars-cov-2-genomes/761

Another paper on insertions: https://www.biorxiv.org/content/10.1101/2021.04.23.441209v2


text:
How to generate PDB file for custom DNA squence(10 base pairs)
I am trying to study docking of drug-DNA interaction and for that I need PDB file.
How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)?
I will really appreciate if you can please guide me.
Thank you all for your time.

Pymol can build nucleic acids and is free for students.

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.

Further to @canadianer here ins a link that looks as if it might be helpful https://pymolwiki.org/index.php/Builder .

UCSF Chimera is free to use and is very versatile for molecular modeling. It has a Build Structure module (found in Tools->Structure Editing) useful for building proteins or nucleic acid sequences (selections in the left pane).

Clicking Apply performs the build.

It is then saved with File->Save PDB.
Note: the structure is devoid of hydrogen ions, which can be added using Tools->Structure Editing->AddH. I have always used this program because its outputs are readily accepted by CHARMM-GUI (the server adds the hydrogen ions in this case).