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Are RNA transcripts always synthesised from the same DNA strand?
The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the strands. And even if it were possible to synthesise RNA from the other strand, due to the directionailty of the strands/RNA the RNA transcript would then code for the protein in reverse. Surely the reverse synthesis of a protein, even if containing all of the same amino acids, would lead to dfferent folding and thus only on eof the proteins is correct?
Now that I am considering the origin, it seems likely to me that the strand on which the origin is dictates which strand acts as the RNA template (perhaps both starnds can, however for a given GENE the RNA is always synthesised from the same strand.
Is this the case? I have read this post: Majority of transcripts are from sense strand? however I found it slightly confusing. I think what the answerer said is similar to what I have suggested here, however I am not quite sure. Would greatly appreciate some input.

By "origin" do you mean "promotor"? You might wish to consult https://en.wikipedia.org/wiki/Promoter_(genetics) and then edit your question if appropriate and you feel it not answered in  https://biology.stackexchange.com/questions/39046/how-does-rna-transcription-determine-which-half-of-the-dna-to-use.

@David Thanks I did mean promoter! I realised when I re-read my question now- it is easy to get mixed up with the terms when learning about DNA replication and transcription simultaneously! As it transpires my question was answered in the post suggested by another 'Homo Sapien'. Thank you for your input.


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Tardigrade scaling and survival
Tardigrades have attracted the attention of researchers with their amazing endurance. They withstand enormous temperatures, high doses of ionizing radiation, resistant to harsh atmospheric factors and high pressure, used in experiments in outer space and survive in conditions of many years of lack of moisture.
At the same time, they have tiny sizes (the body of tardigrades has a size of 0.1-1.5 mm) and a very slow speed of movement (only 2-3 mm per minute).
Suppose tardigrades would grow to the size of an average cat. Would they have the same survival rate if everything else (conditions and habitat) had not changed? Would size scaling affect their bodily functions in any way?
Partially, this topic answers my question, but I would like to know if tardigrades have any features here too.
What are some examples of scaling laws in biology?
EDIT: Very interesting topic left unattended

I doubt that this could be answered by any scientific study as it isn't something that is possible to do in science, so would mostly be speculation, which doesn't fit well here. There are giant plant cells (e.g. Caulerpa taxifolia (multi-nucleate) and Valonia ventricosa), and things like island gigantism in animals, but it isn't several orders of magnitude change there. You might look at reptiles (e.g. chameleons) for some animals with an order of magnitude size range.

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Mathematical aspects of the study of dinosaur locomotion
I'm interested in getting a better understanding of dinosaur locomotion. Therefore, I am looking for a book that will cover various mathematical aspects and discuss various mathematical tools for studying dinosaur locomotion. I do not have a basic biological education with a specialization in paleontology. However, I am proficient in some computer algebra packages and I enjoy learning applied mathematics.
Can anyone suggest good names that give a good basic and systematic idea of the problem described above (with examples of the use of computer algebra packages if possible)?
I have tried searching for suitable sources. I came across mostly articles on a narrow specialized issue. And I would like the first sources to give me a general idea of the general methodology, so to speak.
The object of study is clear: the musculoskeletal system of dinosaurs. Subject of study: mass-dimensional properties of dinosaurs, kinematics and dynamics of their movement. I have not fully formed in my head the methods that are used for research. It is clear that these are elements of mechanics and statistical analysis. Well, that's all I know today.
Specialized articles I found:

William Irvin Sellers, Lee Margetts, Rodolfo Aníbal Coria, Phillip Lars Manning. March of the Titans: The Locomotor Capabilities of Sauropod Dinosaurs

Bohun, Sean. Mathematical model of the mechanics and dynamics of the tails in dinosaurs.

Update March 23, 2023:
After a necessary pause, I returned to the study of this topic. An image formed in my head of how the movement of dinosaurs is studied. But some things need clarification. For example, in article 1 that I cited here ("March of the Titans") there is a figure 4. I am attaching a screenshot here.

In the figure, everything is more or less clear to me, except for these red cylinders. The article (in the section Muscle and Joint Locations) describes at length what it is. But neither specific methods nor principles are given.
So my new question is about this. If respected experts will help me figure it out, I will be very happy and grateful.

What research have you done on this already? Have you looked for literature reviews or even primary literature, such as on Google Scholar? That may be a much better (and certainly more up-to-date) resource than a book. For example, look through the results of this search.

@MattDMo see my edit, please

can you edit your question to include some of the specialized articles you found? I'm guessing that you won't find books on dinosaur locomotion/kinematics specifically. However, if you search for/find articles on models for animal locomotion/kinematics more generally, that will probably give you most of the background you need to understand more specialized studies.

@BenBolker see my edit, please. Yes, this is an alternative approach - if I can't find a source where I can get the maximum information in a short time, then I will put together a puzzle from pieces of information scattered across highly specialized publications. I also came across a book by Robert McNeill Alexander. Dynamics of Dinosaurs and other Extinct Giants, Columbia University Press, 1989. I leafed through it, it's a good book, but it's pretty "old" today. And it's not as mathematical as I would like. Therefore, I did not include it in the list of references.

The cylinders will be approximations of muscle groups and/or tendon/ligaments.

@bob1 and on what principles is their calculation based, number, location, etc.?

@dtn Position will be based on anatomical clues - you can see on bones where soft tissue attaches and the size correlates with strength/stressors put on the muscle or bone attached. I don't know much more than that though as I have very little anatomy training.

@bob1 But your comment is really very important, clarifying and confirming. In one of the articles, I came across something like this: it depicted a dinosaur bone, on which possible attachment points for muscles were marked. And that was the starting point. Now I will try to find a specialist who is well acquainted with the mathematical side of the issue. I have a small request for you: the knowledge that you consider significant for the question I asked (at least the biological basis) - could you arrange it as an answer?

At OP's request:
Disclaimer: I don't have any full answers to this question or any training in anatomy beyond the basics from undergrad many years ago, so if any of this is outright wrong, feel free to correct me and either comment so that I can fix it or fix it yourself.
In the update in March 2023; OP asked what is the purpose of the cylinders and how are they determined?
The rods are approximations of muscle groups and their attachment points on the bones. If you look closely at the diagram you will see small bumps or lumps in the bone structure. These lumps are called by various names in anatomy, depending on who named them, how big they are and a range of other factors. These names include things like Processes, Tubercules, and Eminences. These bits indicate the attachment points of tendons (I remember it by: tendons are tenderer and join muscle to bone.) and ligaments (bone to bone) to the bones. There are also other anatomical markings that indicate the attachment points, but I don't know the names of them.
One might presume that, based on what we know of the anatomy of similar animals in the current day, we could use that knowledge to predict what the muscles and joints of dinosaurs look like, and how they behave. Of course, many dinosaurs were much larger than modern animals, but this is not always the case; the smallest dinosaurs that we know of are about the size of a hummingbird1, so this might not be an insuperable problem. In addition, the bones of many dinosaurs are so similar in structure to modern animal bones, that, even with a basic knowledge of anatomy, you can easily identify the major bones such as femurs and vertebrae, no matter how large (or small) they are. This means we can make some extrapolations from current animals to dinosaurs as to how the joints and muscles worked and where they were placed.
As to how the models of the muscles work, I have no idea. I do know that muscle strength doesn't scale with size necessarily, but does with cross-section2, but beyond that I have no knowledge of what this might mean for an anatomical model and how to apply it.
Refs:
1: Xing, L., O’Connor, J.K., Schmitz, L. et al. Hummingbird-sized dinosaur from the Cretaceous period of Myanmar. Nature 579, 245–249 (2020). https://doi.org/10.1038/s41586-020-2068-4
2: Jones EJ, Bishop PA, Woods AK, Green JM. Cross-sectional area and muscular strength: a brief review. Sports Med. 2008;38(12):987-94. doi: 10.2165/00007256-200838120-00003. PMID: 19026016.

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Why doesn't T5 exonuclease have endonuclease activity in Gibson assembly?
Gibson assembly uses T5 exonuclease to chew back the 5' end of dsDNA to generate overhangs. However, T5 exonuclease, in contrast to lambda exonuclease, is reported to have ssDNA endonuclease activity (https://www.neb.com/products/m0363-t5-exonuclease#tabselect0). Why doesn't his cause problems during gibson assembly? Is it just because these don't yield viable assemblies? Or is it because this activity is inhibited somehow, such as the T5 concentration is too low?

The buffer conditions used in the reaction also mitigate against the endonuclease reaction, so it should not be a problem if you stick to the protocols exactly. I've worked on this enzyme since 1988 and was the original "cloner' of the overproducer see http://www.sayers.staff.shef.ac.uk/fen/   for more information on these enzymes
Jon Sayers, University of Sheffield.

I've never actually done a Gibson assembly, but looking over the protocols at the New England Biolabs website, I think the answer must be that the ssDNA exposed by the T5 exonuclease is quickly protected from the ssDNA-endonuclease activity because it (the exposed DNA) anneals with the complementary sequence on the other component of the assembly reaction. Following that, any gaps are repaired and sealed by DNA polymerase and DNA ligase. All of these enzymes are of, course, present at the same time in the one-step assembly reaction.
In summary, under the conditions of the assembly reaction, the low-level ssDNA endonuclease activity of the T5 exonuclease is simply outcompeted by the other reactions taking place.

This idea is supported by the paper that originally discovered the endonuclease activity of T5 exonuclease: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC328551/?page=1 . They report the level of endonuclease activity is low compared to exonuclease activity.

Yes, I found that too, and set off on a search expecting to find that the low Mg suppression of endo- activity would be the key, but apparently not.

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Comparison of gene expression time series in vitro and in vivo
I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days post-partum. The second data set was obtained in a C2C12 cell line, where t = 0 was defined as the day in which 100% confluence was reached.
Is there an optimal way to align the two time series? Simply aligning the two series using the two t= 0 samples as starting point seems arbitrary.

Welcome to Biology! I attempted to clarify the question. Feel free to roll back if it doesn't reflect your question anymore.

I would start asking myself: does it make sense for the two series to be aligned? In other words, do you have any evidence that the events in the in vitro experiment may correspond to events in vivo? It would help if you describe you experiment in a bit more detail, (if possible, this may be sensitive information). Which species, what tissue, what experimental conditions, what is your scientific question.

Hi, yes, it is sensitive information... however thank you for the answer, I will try to find out if there is a best shift that globally maximises the correlation between pairs. If not everything will be traced back to up/down regulation...

This is a mesenchymal cell line that differentiates in vitro after reaching confluence (and serum deprivation). There are likely similar cells in the animals, but they might be a small percentage of the total number of cells. During differentiation in vitro you'd expect to see some genes going down and others going up over time. In the animals that signal would likely be swamped by tissue-specific genes from the dozens of tissues and hundreds of cell types.

Direct comparison of the course would be difficult between tissues and cultured cells. In stead of time scale, you might want to use markers.
For example, Kislinger et al. show the expression peak of SIX1 is 2 days after differentiation; SMAD3, 4 days. I am not a right person who can tell which markers are good, but I believe you could find more information by literature search.
http://www.mcponline.org/content/4/7/887.full

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A request for an overview of the cranial nerves
Is there any resource that contains motor and sensory innervations, or pathways of all the twelve cranial nerves (i.e., cranial nerve I to XII)?
I have found this book chapter on the cranial nerves, but it is too broad for me -  I'm still at high school.

A lot of the information that you are looking for is in the book chapter, but I can understand how it might be overwhelming.  Unfortunately, anything "easier" is probably going to be too cursory and sugar-coated, so you may just have to slog through it and cherry pick what you need.  Also, you're in the perfect spot to ask specific questions about the material already! :)

"Too broad"?  to me that means something lacks detail, isn't specific enough.  It sounds like you find that chapter too dense or too deep.  Can you clarify?
What is the context, what do you already know, and what do you need to know?  (and what do you not need to know)

I am not entirely sure what you are after, but I (as have others that commented on this question) interpret your question as "The linked chapter contains too much technical information". Quite frankly, after scanning the book chapter, I have to agree with you. Therefore I have sought for a quick overview image of all the cranial nerves including their sensory and motor targets.

Encyclopedia Britannica has published all the cranial nerves and their sensory and motor innervations in a single comprehensive figure:

Cranial Nerves and their targets. Source: Encyclopedia Britannica
I can highly recommend this online encyclopedia. Their articles are more concise and better accessible than similar topics on wikipedia. Moreover, this encyclopedia is not freely editable by everyone on the planet, and everything I have seen so far on their website is credible.

This is exactly what I need! Thank you for helping me!

@Ridho - my pleasure! :)

Very nice find!

If you're still learning the names and functions of all 12 cranial nerves, something like this page may help you get ready for more in depth material like the chapter you found.
https://faculty.washington.edu/chudler/cranial.html
I like the fact that they include activities for each nerve to help give you one more way to remember their functions.


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Iron absorption and oxidative stress
Fe2+ is more bioavailable than Fe3+, so it's absorbed more quickly. I read that, for this reason, Fe2+ doesn't give enough time to the organism to bind it to a protein then it stays longer in a damaging free form in blood.
So if we consider 2 persons absorbing (in blood) the same amount of iron via Fe3+ for one and Fe2+ for the other, will Fe2+ generate more oxidative stress?
In response to David:

The bioavailability of a drug product is known as the rate and extent
of its absorption.

https://www.ncbi.nlm.nih.gov/books/NBK557405/
So, high bioavailability means high rate of absorption which means that, for a given duration, a higher amount is absorbed, so it's absorbed more quickly.
By protein I meant ferritin or transferrin.

Ferritin preserves iron in a safe state; thus, it is a direct defense
molecule against redox-active iron.
Non-transferrin bound iron is a candidate for the redox-active iron in
extracellular space.
When a large amount of iron enters cells and overflows the capacity of
iron binding proteins, the iron behaves as a redox-active iron in the
cell.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9324531/
If iron can overflow the capacity of iron binding proteins, it means that it's about time since a slower absorption could help to prevent this overflow. As you can see, it's not a nonsense.
So, is Fe2+ more likely to cause such an overflow and thus more oxidative stress?

Welcome to SE Biology. Please either provide a link or quote the exact text and context of what you have read. That way we can check whether the author is correct and whether your understanding is correct. Statements such as "it's absorbed more quickly because it's more bioavailable" and "Doesn't give the organism time to bind the protein" are scientifically ambiguous at best and meaningless at worst. Which protein is "a protein", and could you check this is about affinity rather than the nonsensical "time to bind"? Are you just asking whether free ferrous ions cause more oxidative stress?

that info seems readily available online, did you check this list of findings: https://www.google.com/search?q=oxidative+stress+fe2+fe3&oq=oxidative+stress+fe2+fe3&aqs=chrome..69i57j33i160l3.7224j0j7&sourceid=chrome&ie=UTF-8

Most of the studies I found were about Fe2+ causing oxidative stress, and since Fe3+ has to be reduced to Fe2+ to be absorbed, Fe3+ may also cause oxidative stress. I didn't find any study comparing Fe2+ and Fe3+ intakes to confirm that Fe2+ generates more oxidative stress.

Please don't refer to me in your question. Edit it instead. 2. If you respond to a comment of mine, you need to leave a comment addressed to @david so I am alerted to it. (I don't have to do this to you as the poster or answerer always gets notified of comments.) Iron is a vital mineral not a drug, and your statements about bioavailability would seem to mean that ingested Fe2+ is taken up by cells less well than Fe3+.The question is why? Is it possible that it might be because transferrin only binds Fe3+. Check if/how Fe2+ can be taken up into cells and edit the start of your Q accordingly.

I know little about iron metabolism but I am an experienced biochemist/molecular biologist. I may be able to help you if you do the work to research your question in molecular and cellular terms. I have glanced very briefly at the literature and it would appear that bioavailability basically means absorption into the circulation. However it is absorption into cells that would appear of interest as that's where oxidative stress occurs. For Fe3+ this requires transferrin, interacting with receptors on the cell. If Fe2+ is not taken up the question is invalid. Is there a mechanism for this?


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Specific Heat Capacity and Thermal conduction of Blood
Is the specific heat capacity and thermal conductivity of animal blood (e.g., steer for beef) and bird blood (e.g., broilers, ducks) [e.g., immediately after slaughter] similar/same as human blood?
I found regarding human blood:
Specific heat capacity = $3300-3900$ Jkg$^{-1}$ $^\circ$C$^{-1}$ (average $3617$ Jkg$^{-1}$ $^\circ$C$^{-1}$) (https://itis.swiss/virtual-population/tissue-properties/database/heat-capacity/)
(For Americans that's $0.788-0.93$ BTUs lb$^{-1}$F$^{-1}$) (average $0.86$ BTUs lb$^{-1}$F$^{-1}$).
Thermal conductivity = $0.49-0.56$ Wm$^{-1}$ $^\circ$C$^{-1}$ (average $0.52$ Wm$^{-1}$ $^\circ$C$^{-1}$) (https://itis.swiss/virtual-population/tissue-properties/database/thermal-conductivity/)
(For Americans that is $0.2848-0.3248$ BTUs hr$^{-1}$ft$^{-1}$F$^{-1}$) (average $0.3$ BTUs hr$^{-1}$ft$^{-1}$F$^{-1}$).
Is this the same/similar for animals and birds? Where can I find this info?
Thanks a ton!

I have no evidence, but I'd suspect so, the compositions are very similar.


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What is the minimum length required for a circular DNA ligation?
What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?

I stumbled across this paper demonstrating it is between 150-200 base pairs.
DNA flexibility studied by covalent closure of short fragments into circles
D Shore, J Langowski, and R L Baldwin
PNAS 1981 78 (8) 4833-4837
http://www.pnas.org/content/78/8/4833.full.pdf

good source - ligation still occurs at 126 bp but much less efficiently... at some point there, the DNA is too stiff to flop around and join in the ligase catalytic site.

Yes, and in the last sentence the authors suggest that the exact number of base pairs will become important at these lengths: "If the number of bp in the DNA fragment is not an integral multiple of the helix repeat,then the need to twist the DNA helix in order to make strand ends meet may [make ligation difficult] for sizes less than 500bp."


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Why do ants raid the house in summer when it is hot, but in cooler months they don't come in?
Over summer the ants invade our house, including our kitchen. In winter and the shoulder seasons they are not to be seen.
I can think of a number of possible reasons for this, including:

they are cold-blooded, and need heat from the outside atmosphere (similar to flies), making winter too cold to go outside for ants
ants need water, and tend to run short on it in summer when the temperature is higher, so travel further for water
the higher temperatures cause aromas from food crumbs to effervesce more strongly, and so ants are attracted to a stronger smell
ants natural natural nest cycle means they run their food supply low in summer and they need more

My question is: Why do ants raid the house in summer when it is hot, but in cooler months they don't come in?


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Can a chicken's lard become liquid depending on its diet?
On Cooking.se, somebody asked a question about the fat in chicken stock sometimes being liquid and sometimes solid once the stock has cooled. The only answer until now suggests that the difference is due to the percentage of saturated fat in the chicken lard, which will vary depending on the chicken's food.
I am not entirely happy with this explanation. I am aware that the proportion of saturated to unsaturated fat in an organism's cell walls will vary with diet, and could imagine that the fat stored within its adipose tissue will be different too. The person who provided the answer also posted references which confirm that part. But I doubt that the effect will be strong enough that, if an animal on low-saturated-fat diet is processed to lard, the resulting lard will be a viscous liquid, as opposed to the usual soft solid. If my memory doesn't fail me, my grandma used to keep her animals on a mostly starch-based diet, and still was able to process them for (solid) lard.
Can somebody confirm or disprove this theory?

What is your reason for thinking that "cell walls" (I assume that you mean cell membranes) composition will vary with diet? My recollection is that the fluidity of the phospholipid bilayer is tightly regulated, and since organisms can saturate or desaturate acyl chains this would be easy to achieve. As far as stored lipid is concerned my feeling is that fluidity might be somewhat less critical so could vary.

@AlanBoyd I have read it as the explanation to why saturated fats are unhealthy: the cell walls membranes of the eater become stiffer and less flexible by incorporating molecules made with saturated instead of unsaturated fatty acids. I don't remember my sources, they were some kind of popular science, not peer-reviewed literature, so it is possible that they were wrong, or that they were oversimplified enough to give me a wrong understanding of what is actually happening.

Without going into the biochemical details of fatty acid digestion, mobilization, and synthesis, the brief answer is that the animal regulates its own fatty acid composition to within a specified range regardless of its food. Lipid metabolism does not differ from the metabolism of other compounds, in that it is a highly regulated, enzyme-mediated process, which ultimately is genetically determined.
It must be stressed that a heterotroph assimilates its food, not as complete macromolecules, but as their base components. For example, the starch-fed chickens you described would digest the starch down completely to glucose, which would then be converted in the liver to fatty acids. These fatty acids would be, of course, those that the chicken had the enzymes to synthesize, which are consequently mostly saturated fatty acids of a certain length that happen to solidify when cooled.


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Do E. coli change color (from white/grey to yellow) when they grow older?
In my experiment, I had white colonies initially and they turned yellow. So I thought it´s natural that mature E. coli colonies are yellow and young are white. But it could be that I had two types of E. coli and the yellow one just dominated the white.
I research the affect of vitamin C on susceptibility of E. coli to H2O2.
First I treat bacteria with vitamin C, incubate for an hour and H2O2.

That is what I have on all of the plates. It really seems like there are 2 species present.

Can you please add more information about the experiment that you are doing?

It would be really helpful if you could attach pictures of experiment results.


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How is chicken egg a single cell
It is unexpected for ostrich or chicken egg to be single cell yet so large.
How could it happen, I thought egg is made up of several single cells.
If not, how is yolk a single cell http://www.alearned.com/egg/

Welcome to the site. Please take [tour] and visit the [help] to learn more about this Stack Exchange.  At this SE, we like questions that show that the person asking has done some research for possible answers for themselves.

Before the egg hatches, there is really only one intact cell inside the egg, that is the yolk. Before fertilization, the yolk is just an egg cell, but after fertilization, it is a fertilized egg. If the egg begins to hatch and the fertilized egg cells undergo cell division, there's not just one cell. A white spot on the surface of the yolk. The unfertilized egg is called an egg, and the fertilized egg is called a zygote, which further develops into an early blastocyst. The disc of the fertilized egg is about 3 mm in diameter, and the ovule of the unfertilized egg is smaller.

Welcome to the site, please visit the [help] to see what makes a good answer. In particular, this site (Biology SE) values answers that have some references to back them up.

But the yolk is too big for intracellular communication and exchange of mayerials @Jeffrey

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

"Hatching" refers to the process of the fully-developed chick (definitely a multicellular organism) exiting the egg casing. It only occurs at the very end of gestation.

Welcome to Biology.SE. Please take the [tour] and then consult the [help] pages for advice on [Answer] effectively on this site. In particular, answers are much more likely to receive a favorable response if they include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Also note from [answer], Answer well-asked questions. Not all questions can or should be answered here. This is an inappropriate (under researched) question (see help) — please delete your post to avoid encouraging such questions.


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Are all the atoms in your body replaced with others over a 30 year period?
I was reading Creation - Life and How to Make It by Steve Grand. (This is the book that inspired Jeff Bezos to start the AWS initiative. ) In it he makes the following statement:

Anyhow, by now I hope you have thought of an experience from yoru childhood. Something you remember clearly, something you can see, feel, maybe even smell, as if you were really there. After all, you really were there at the time, weren't you? How else would you remember it? But here is the bombshell: you weren't there. Not a single atom that is in your body today was there when that event took place. Every bit of you has been replaced many times over (which is why you eat , of course)....

That didn't sound quite right to me. How could the atoms in your bones be replaced? Aren't your nerves pretty much fixed in place?
My question is: Are all the atoms in your body replaced with others over a 30 year period?

Bones, although they are hard, are very dynamic. They are literally in continual resorption and reconstitution, even in adult life when there is no growth. So you shouldn't be too surprised. And, in principle, yes, after a given period of time, all the atoms in your body would be "replaced". If you like that kind of thing, look up the Theseus paradox.

The lens of your eye is not replaced, IIRC.

There is no solid scientific evidence that this is true. It's sensational, and is likely true for much of the body (though I don't know the timeframe.) While many proteins and even some entire tissues turn over, some do not. Tooth enamel, for example, does not regenerate or get replaced. That makes carbon dating - to the year of birth +/- months - possible.


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Why don't chilli peppers taste as hot in space?
The following commentator writes:

Chili peppers don’t taste as hot in space as they do on Earth. Nobody knows why.

We know that the 'hot' feeling of chilli peppers is caused by Capsaicin. We read:

Capsaicin inside the pepper activates a protein in people’s cells called TRPV1. This protein’s job is to sense heat

There appears to be some question about the cause of the 'spicy' taste of chilli peppers.
My question is: What is the reason that chilli peppers don't taste as hot in space?

What atmosphere pressure is used in an orbital space craft?  How does that compare to the pressure in an aeroplane cabin, where food is also comparatively tasteless?   Hypothesis, taste bud efficiency drops with air pressure.  So, how does food taste in a diving bell, or other pressurised vessel ?

Could just a more mundane answer about chilli tasting bland in space...because astronauts are using it all the time?
As an avid chilli eater, I can report that the more you eat, the less sensitive you are to it, and if you are having it all the time in prolonged period of times, you will feel less effects.
As an example, I recently eat raw two of the reportedly stronger chilli of the Philippines without needing drink or food (in Earth), and without it bothering me. I just got a slightly runny nose.


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PedigreeAnalysis Genetics

Hello! I need help with this exercise question. I am not really sure which pedigree diagram is autosomal and which is not. But, is question b 1/2. Can someone give an explanation? Thanks very much in advance? Appreciate any help!!

According to the key given, the one shaded black on the right is autosomal and one on the left is sex linked.
Yes, the answer to b is half because Maria is XhX ans Peter is XY and so the probability of the child having this disease is 1/2.

@ApothemCyte Does this make sense ? Ask, if u need help !

Thanks for the reply! But if the the diagram on the right is concerned with an autosomal disease, shouldn't we use Gg/gg/GG notation in place of XhX (for Maria).

Also, I'm a little bit unsure as to whether the genotypes I have for the diagram are actually correct. So, a brief explanation would help. Thanks in advance!

ApothemCyte, the diagrams are concerned with both the autosomal disease and the X-linked disease; look at whether the person symbol is shaded on the left side or the right side.

@mgkrebbs I filled them up that way but pretty sure it's completely messed up. Can you please check to see if they are right? Thank you in advance! link: http://s837.photobucket.com/user/apothemnew/media/1557562_10152265905761177_608325393_n_zps950a5df1.jpg.html?filters[user]=138960233&filters[recent]=1&sort=1&o=0

The G's seem mostly ok, but you don't know that Maria's grandmother is "GG".  The A/a's are messed up; you're treating the disease allele as recessive, but it's dominant (XA). [but then I have no formal training; I've never had a genetics course or even college biology.]

@mgkrebbs So here is my 2nd attempt. Do they look right now? (even to a person with no formal training) link: http://s837.photobucket.com/user/apothemnew/media/attempt2_zps419409e5.jpg.html

@ApothemCyte U have written Gg for peter's father but he could also be GG !


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Is it possible to identify a kind of scorpion based on a photo of its dried body
Somebody at my university have came back from a vacation trip and brought back a dried body of this small scorpion.
Can you identify it for me?
This is a very tiny (?) scorpion, if I may say so. I can't provide the exact measures right now, but I'd say that the whole body was 7-8 centimetres long. Maybe 10 cm with its tail straighten up.

Is is endangered of extinction? Is transporting it illegal? Can it be dangerous (when alive)? Lethal (I've heard that the smallest scorpions' bite are the most dangerous / more dangerous then much bigger counterparts' bits; but that might be some kind of urban legend).
Unfortunately, I don't know whose belongings is this, so I cannot ask for a location where this dead scorpion was found. It was simply lying in university's kitchen as... I don't know what. A trophy?
All I know is that it is 100% not a native species. I am from Poland, eastern Europe and we definitely have no scorpions here. Due to to too low temperatures and the climate being very unfriendly for that kind of animals.

Definitely not small at 8 cm - that's a large one. No expertise at all, but there are scorpions in Europe (Spain, Italy(?) Greece, even the UK (whether it is Europe or not aside)). Likely to be a common species (as that's usually what people find).

Spain, Italy and Greece are all much, much warmer than Poland so that would fit into my theory. United Kingdom is on the other hand pretty much in the same temperature zone and climate like Poland. So, it seems that I must revise my thoughts and... watch my steps! :) Thanks!


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What do ribbon diagrams mean?
What is the higher order meaning of ribbon diagrams like this one? I know the first order meaning is a graphical representation of α-helices and β-sheets, but what else does it mean? Is the protein's function or behavior encoded in there? Do the α-helices helices and β-sheets form a kind of protein alphabet so that a particular arrangement (a "protein word") always has the same function?
An analogy might help: take the word ox. The zeroth order meaning is a circle followed by a cross; the first order meaning is the graphical representation of the sound oks; and the second order meaning is a castrated male bovine.
An English speaker who sees ox reads it as oks and understands it as castrated male bovine. A non-English speaker just sees a circle followed by a cross.
I'm at the non-English speaker level with ribbon diagrams and would like to get to the English speaker level. What does the protein researcher see and understand where I only see spirals and squiggles? Googling hasn't been helpful.

Source

What is the source of the image?

Added source in edit

@zencraft Nice analogy!

Do some research on "protein secondary structure". The figure you include is just trying to show where probably-relevant amino acid mutations are located in the S protein's 3D structure. For example, since an antibody would normally only have physical access to the outside of the S protein, a neutralizing-antibody-evading amino acid mutation buried inside the interior of the S protein is probably changing the overall 3D protein structure rather than just "disguising" a bit of the outside of the S protein by changing a bit of the surface.

I have, and it's not been much help. Another analogy might help: the stuff I've found by googling is like the quadratic formula, I'm looking for higher order understanding, like Galois groups.

There is no higher order meaning.

Ribbon diagrams are a cartoon representation of portions of a polypeptide chain that are engaged in what is termed the secondary structure of proteins — the regular areas of protein structure formed by hydrogen bonding of peptide bonds. These are either individual helices (α-helices) or adjacent flat pasta strips (β-sheets).
An experienced scientist in the field of protein structure can look at the combination of such features and perhaps recognize combinations that recur in proteins of similar function, but there is no — heaven preserve us — code. Ribbon diagrams are just one device for simplifying a complex object.
There are other types of representation that allow appreciation of surface charge, hydrophobicity or individual side chains. An author representing proteins in a paper will choose one (or a combination) that best allows the reader to understand the information he is trying to convey.
Ironically, in the diagram presented in the question they are merely serve as references to indicate the positions in the protein where mutations have occurred.


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Why don’t all HPV strains cause cancers?
There are roughly a dozen high risk HPV strains responsible for cervical cancer. These strains promote hyperplasia of infected cells by encoding E6 and E7, which potently antagonize tumor suppressor genes RB1 and TP53. Overtime the episomal viral DNA gets incorporated into the host chromosomes by the cellular DNA repair mechanism, which enables stable propagation of viral oncoproteins to daughter cells (according to this paper, about 80% of cervical cancer cases harbor at least one copy of HPV DNA in the chromosomes).
However, there are many more strains causing hyperplasia of infected skins, such as the strains causing common warts, flat warts, and genital warts, but none of them have been found to be associated with cancer. Is it because these viruses encode milder oncoproteins that don’t potently antagonize RB1 or TP53; because these viruses infect wrong types of cells which are refractory to transformation by E6 and E7 compared to cervical epithelium (oncogenes are context dependent. For example, EWS-FLI1 potently transforms mesenchymal stem cells into Ewing sarcoma, but causes senescence and apoptosis in more differentiated cells); or because the viral DNA do not incorporate into the host chromosomes (which sounds unlikely because incorporation of foreign DNA by DNA repair mechanisms is inevitable after prolonged exposure)?


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If guanosine transfer reaction in the RNA capping is reversible, should intermediate reactions be reversible as well?
Guanosine transfer is the second step of RNA capping. The enzyme (GTase) first displaces a pyrophosphate of a GTP molecule, forming an unstable covalent enzyme-GMP intermediate (E + Gppp ⇌ E-pG + PPi). Then the GMP moiety is transferred onto the diphosphate end of RNA (E-pG +ppRNA ⇌ GpppRNA + E) forming a triphosphate bridge. It’s obvious that this reaction is highly reversible, because the GMP moiety is transferred from a diphosphate to another diphosphate. As a result, the two intermediate reactions should be reversible as well. This is indeed the case according to this paper.

Recently a paper revealed that coronaviruses use a distinct reaction to make 5’ caps. The viral enzyme nsp9 reacts with the triphosphorylated RNA, forming an enzyme-pRNA intermediate (nsp9 + pppRNA ⇌ nsp9-pRNA + PPi). Then the pRNA is transferred onto a GDP molecule (nsp9-pRNA + Gpp ⇌ nsp9 + GpppRNA). This reaction is shared with nonsegmented negative sensed RNA viruses, and is likewise reversible (the L–pRNA intermediate is able to transfer pRNA to PPi to produce pppRNA, although less eﬃciently than to GDP to form GpppRNA). However, the paper claimed that “Interestingly, although inorganic pyrophosphate (PPi) was able to deAMPylate nsp9-AMP, it was unable to deRNAylate nsp9-pRNA”, “RNAylated nsp9 was not reversible in the presence of PPi”, which indicates that the first reaction is not reversible. This creates a problem. If the first reaction is irreversible, the covalent intermediate should be very stable and the reaction should be strongly thermodynamically favorable (large ΔG gain), which will make the second reaction strongly unfavorable. Although coronavirus nsp9 is different from the L proteins of negative sensed RNA viruses, the reaction thermodynamics should be irrespective of catalysts.


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Is CRISPR mediated RNA editing less specific and less efficient than DNA editing?
According to this diagram, the high efficiency and the high specificity of CRISPR lies in its reversible binding with the target DNA. The Cas protein unzips the target DNA and have the gRNA to base pair with it, forming a short R-loop. Because the formation of the R-loop doesn’t change the number of basepairs, there is minimal free energy change. If there is a mismatch, the R-loop formation is inhibited which facilitates the release of the Cas from the DNA.

However, RNA are single stranded and can basepair with the gRNA directly. As a result, the formation of dsRNA should be strongly exothermic even with one or a few mismatches. As a result, the Cas assembly will be trapped on the slightly mismatched target RNA, which will greatly reduce the efficiency of RNA editing and interfere with the functions of the target RNA (such as protein translation).


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How does the exposure time affect the potencies of antibodies?
The potency of neutralizing antibodies is commonly represented by their binding affinity for their targets. However, binding affinity is based on the dissociation constants at equilibrium, which can’t accurately predict the potency against intracellular parasites (viruses, bacteria and some eukaryotes). These organisms primarily multiply inside the host cells beyond the reach of antibodies, and are only accessible when new offsprings are released from infected cells, which exposes them to antibodies in the bodily fluids. As a result, the time it takes on average for a new offspring to find another target cell (the exposure time) should have a direct impact on the potency of antibodies.
Here are several good examples. HPV is a sluggish virus. Newly released HPV particles have to spend hours in the bodily fluid to undergo complex conformational changes and enzymic activation to become infectious, which gives ample time for antibodies and phagocytes to neutralize and destroy them. As a result, even a very low antibody titer can provide sterilizing protection. Malaria parasites are on the opposite end. It takes only 30 seconds for a newborn parasite to latch onto a RBC and invade it. As a result, antibody concentration needs to be several orders of magnitude higher to stop them. HIV can spread via cell-free particles or close contact between infected and uninfected cells (virological synapses). The amounts of antibodies required to neutralize direct cell-to-cell transfer are also much higher. So is there a more detailed mathematical model to describe the relation between exposure time and neutralizing potency?

Citations:
Explanations for the high potency of HPV prophylactic vaccines
The RH5-CyRPA-Ripr Complex as a Malaria Vaccine Target


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Does HIV erase the immune memory?
It’s said that HIV selectively infects and kills CD4+ T cells, which disables the adaptive immunity because both CD8+ T cells and B cells need CD4+ T cells to activate them. However, once activated, memory B cells and CD8+ T cells can function independently of CD4+ T cell. Does that mean HIV+ people still retain immunity against previously encountered or vaccinated infections even at advanced disease stage?
Cited from:

As the affinity of surface Ig from memory B cells is increased, their
requirements for reactivation are lower than for naïve B cells: memory
B cells may thus be recalled by lower amounts of antigen and without
CD4+ T cell help.

https://www.sciencedirect.com/science/article/pii/B9781416036111500064

Welcome to SE Biology! It would be helpful to link to/cite sources for your information.

Here: As the affinity of surface Ig from memory B cells is increased, their requirements for reactivation are lower than for naïve B cells: memory B cells may thus be recalled by lower amounts of antigen and without CD4+ T cell help. https://www.sciencedirect.com/science/article/pii/B9781416036111500064

Please edit your link into your question - that way it is more likely to be read, and more likely to persist as comments can and do get deleted occasionally.


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Is it possible to identify a worm being carried by a depicted wasp?
Wikimedia has a picture of a Ancistrocerus trifasciatus / mason wasp carrying a kind of worm:

Is it possible to tell what exactly kind of worm it is, based only on the above image, number of worm's segments, dots on its skin and a correlation in size to wasp's size (or its feeding preferences)?
I am not the author of the picture, I was not present when it was captures, so I can't provide any more details that are usually helpful in species identification (like moment of day and year, geographic location etc.). The image itself doesn't contain any geolocation data, but from its German description in can be assumed that this was captured somewhere in Germany, Europe.

Not too sure but by the general look of it, it seems to be the leaf beetle Chrysomela populi.
This is mostly from the idea that they are very common in Europe and the distribution of the spots on its body. If nothing else it is most likely from the Chrysomela genus.
Here is a link to a description of the species

For species ID questions, we ask that answerers provide a reference for their ID, and preferably a description of what led them to that ID or defining characteristics (such as things that allow you to exclude other possibilities).


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A single leaf in a very strange air current / wind?
Here is my eight years old movie where I have pictured a single leaf moving in a very weird way:
https://www.youtube.com/watch?v=sCjvgdfNCjU
Can someone explain me what is depicted in this movie (what process, event or situation) or otherwise what is causing this single leaf to move there and back in such way / pattern?
By listening to the sound or observing other leaves (barely moving) you can assume that this isn't a wind what is causing leaf to move. There was also nothing in the kind of spider web or no animal around that could influence leaf's movement.
The movie was captured in late September 2011 in southwest Poland, near Jedlina Zdrój in a forest on the hillsides of the "Mały Wołowiec" mountain (approx. 50°44'22.5"N 16°18'28.7"E).
Note: I understand that this question maybe considered a trivia, downvoted or even closed, yet it depicts one of my personal really weird biology-related mysteries, I ever run into. So, I'd really would like to know, what is going on here?


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Interchromosomic vs Intrachromosomic Recombinations
What is the difference between interchromosomic and intrachromosomic recombinations?
I did a research about them and saw some videos (e.g. this and this) with animations on YouTube. But I'm still lost between them and can't differentiate between these two expressions.

Welcome to Biology.SE. It always help to show what you found. Linking to the youtube videos you've watched would be could.

The link should be added in the question (using the 'edit' button) not in a comment and especially not as an answer. I edited your post to add the link. You can now delete your comment and your answer.

The prefix inter- means "between two or more", and the prefix intra- means "within one".
So interchromosomal recombination means recombination between two different chromosomes (for example, it normally and often occurs between each homologous paternal and maternal chromosome pair during the Prophase I stage of meiosis).
Intrachromosomal recombination would mean recombination within a single chromosome.

Thnx alot beautiful explanation


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are the spontaneous generation and evolution the same idea but in a different time scale?
I was in my biology class, learning the history of spontaneous generation and how this idea was discarded. I told my teacher that is the same as evolution but in a different timeline. I Argue that evolution does not explain how life formed, but complemented by abiogenesis. Ultimately it is almost the same thing. Therefore it could not rule out spontaneous generation.
I got an F.
My appreciation is so wrong?

Do you mean to say 'spontaneous generation and abiogenesis are the same idea'?

Yes, ultimately it is almost the same thing.

You are right in the sense the evolutionary biology doesn't try to explain the origin of life as it is not within its scope. Other fields of biology investigate the question of origin of life (abiogenesis).
Now, there is a very important difference between spontaneous generation and evolution. Life originated at some point and the through repetitive speciation events, created the whole diversity of species existing on earth. You could say that what really happens is that there was one spontaneous creation of life (although there is more a continuum from non-living to living things than a sudden switch from non-living to living) out of non-living things.
The main fallacy of spontaneous generation is that under the spontaneous-generation-conceptualization of life, every species are made de novo and independently which is definitely not the case as in reality species speciate (split in two) causing the existence of to two new species. There are tons of fallacies hidden behind the spontaneous generation conception of life, one of which relates to the concept of species and another one is the origin of within population variation.
So, in short spontaneous generation is definitely something different from a single abiogenesis and evolution and the hypothesis of spontaneous generation has been ruled out a long time ago already.
So I am not so much aware of the grading philosophy in your school but your argumentation was wrong and probably the F was worth. Next time, you will probably want to discuss your opinions with your teacher before the test to make sure you agree.

Evolution is about descent with modification.  Spontaneous generation doesn't have that.  It's about modern organisms emerging from raw molecules.  If flies spontaneously appeared from rotting cow meat, why would they have DNA that made them look like they were evolutionarily related to other insects?


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Glycogen vs cellulose-curvature of glycogen molecule?
I was wondering if anyone knows what the degree of curvature is or bond angle between the $\alpha$ glucose molecules in glycogen is. I know that glycogen/amylose/amylopectin have a general curved backbone (as well as branches in glycogen and amylopectin). This is a consequence of the 1,4-glycosidic bond between $\alpha$ glucose molecules. On the other hand cellulose has straight molceules, which is a consequnce of the 1,4-glycosiodic bond between $\beta$ molecules with alternating orientation. However I cannot find anywhere what the degree of this curvature is in glycogen backbone, or the bond angle between molecules in $\alpha$ 1,4-glycosidic bond?

Interesting question. Here, the question actually comes down to how the bond actually looks vs how we depict the bond. In detail, see this image of maltose from here:

Pay attention to the geometry of the glycosidic bond. From how it is depicted, one would conclude that it is straight in geometry. But how it actually looks is like this:

Now, the obvious conclusion is that the glycosidic bond does have an angle.
Now, with introduction over, lets come to the main point. After searching a lot, I found the value of this angle. It is 109°, much closer to the general tetrahedral angle (109.5°) of sp3 hybridized oxygen atom (deviation could be due to steric hindrance). See this article:

300 alpha-glucose units, bonded by $\alpha$-1,4 glycosidic linkages, making a 109 degree angle between 2 C-O bonds
causing the polymer to twist into a helix. -OH group of C2 projects out into the middle and form H bonds with each other, stabilising the shape.

Yes, the glucose molecules in amylose form intermolecular hydrogen bonds which stabilize the molecule. See this article and in the diagram, notice that the hydrogen bond is formed between adjacent glucose units (to the left and right of the glycosidic oxygen atom):

Although the $\alpha$-(1$\rightarrow$4) links are capable of relatively free rotation around the ($\Phi$) phi and ($\Psi$) psi torsions, hydrogen bonding between the O3' and O2 oxygen atoms of sequential residues tends to encourage a helical conformation. These helical structures are relatively stiff and may present contiguous hydrophobic surfaces.


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Recombination frequencies
I have been learning about recombination frequencies, but an still getting a bit confused despite having gone over many of the links in Google regarding them. I was wondering if someone could verify whether the following is correct.

To calculate recombiation frequencies and thus create a genetic map from this, you have to have true breeding parents for two or more different genes.
You have to cross these parents, so that you have an F1 generation consisting only of heterozygotes
You then have to backcross the F1 individuals with either of the parents. If these genes are all located on different chromosomes you will just get independent chromosome segregation and therefore a 50/50 chance of each allele occuring with the other one in the progeny. Whereas if they occur on the same chromosome, then in the F1 heterozygotes the alleles from each parent will only segregate differently into the gametes if recombination occurs.
To calculate the recombination frequencies we therefore take the number of offspring for which the combination of these two alleles is different from that observed in the parents- we call these the recombinants.

Is this correct?

This answer is mainly copy-pasted from my answers here and here.
The importance of polymorphism
To understand what generation to backcross, it is central that you understand why we need polymorphic loci.
If at least one locus is homozygous
If a recombination event happens between two loci where at least one is homozygous, then you would not see anything. Consider for example the following strand sequences in a diploid individual
-----A-----B----
-----a-----B----

Whether a recombination event occurs or not, the two possible chromosomes passed down to an offspring are
-----A-----B----
-----a-----B----

Therefore, you cannot tell whether recombination has occurred.
If both loci are heterozygous
Now consider the following individual
-----A-----B----
-----a-----b----

If no recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are
-----A-----B----
-----a-----b----

If on the other hand a recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are
-----A-----b----
-----a-----B----

Therefore, you can tell whether a recombination has occurred or not.
Statistics of recombination
There is a tiny bit of maths below. These equations are mainly for curiosity as one can understand the answer without understanding the maths behind it.
Definitions of $r$ and $M$
You are getting confused between two different statistics

The rate of recombination $r$ between two loci

$r$ is the probability for two sequences found at two loci to remain in the same gamete after recombination occurred. This probability cannot be greater than 0.5 ($0 \le r \le 0.5$).

The distance in Morgans $M$ (or more commonly in centiMorgans) between two loci

$M$ is the expected number of cross-over that occurs between the two loci.

Morgans and centiMorgans
You will note that I talk in Morgans rather than centimorgans which is unusual in the literature but it helps at conveying the intuition of what it means. if $M= 150$ centiMorgans $= 1.5$ Morgans, then the expected number of cross-over between the two loci is 1.5. Below are some more explanations on these two definitions with some drawing :)
Case study with loci A and B
While $M$ and $r$ are closely related, they are not exactly the same thing. Consider the following sequence with the loci A and B
---[A]------------------[B]---

Let's assumed the two loci are very far apart and $M=2$. The probability of having exactly $k$ crossovers is therefore given by a Poisson distribution with rate $M=2$
$$P(k) = \frac{e^{-M}M^k}{k!}$$
Let's say for a given case that $k=1$ (a single cross-over occurred). This cross over is represented by a "/" below
---[A]-------------/----[B]---

Here clearly the two sequences at loci A and B will be separated. Let's say now that $k=2$ (two cross-over occurred).
---[A]---/-----/--------[B]---

Here, even if crossovers have occurred, the two sequences at loci A and B will remain together. Only the sequence in between the two cross-overs will come from the homologous chromosome.
Relationship between $r$ and $M$ - in words
You might see it coming from the previous section. The probability $r$ of these two loci A and B to be separated via recombination is the probability of an odd number of recombination events to occur between them (knowing that $M$ is the expected number of cross-overs).
Relationship between $r$ and $M$ - in equation
Let's calculate first the probability $p_{even}$ that an even number of cross-overs occur. This probability is just
$$p_{even} = \sum_{k = 0}^{\infty}{e^{-M}M^{2k} \over (2k)!}$$
, where I just added the constant $2$ before $k$ at both the numerator and denominator. With some algebra and trig, one can show that
$$p_{even} = \sum_{k = 0}^{\infty}{e^{-M}M^{2k} \over (2k)!} =
e^{-M}\sum_{k = 0}^{\infty}{M^{2k} \over (2k)!} = $$
$$e^{-M} \: cosh(m) = e^{-M}\left ( \frac{e^{M} + e^{-M}}{2}\right ) =
{1 + e^{-2M}\over 2} $$

As, $r = p_{odd} = 1 - p_{even}$,
$$r = 1 - {1 + e^{-2M}\over 2} = {1 - e^{-2M}\over 2}$$
Here we go! We have our relationship between $r$ and $M$! Let's graph it
Relationship between $r$ and $M$ - on a graph
I just graphed the above equation in Mathematica (Plot[y = (1 - Exp[-2 M ])/2, {M, 0, 5}])

Here is the same graph but zoomed on lower values of $r$ and $M$ (Plot[y = (1 - Exp[-2 M ])/2, {M, 0, 0.1}])

We clearly see from the graph that for low values of $M$, as $M$ increases $r$ increase quasi linearly ($M≈r$). For greater values of $M$, $r$ still increases but slower and slower until reaching an asymptote / plateau at $\frac{1}{2}$. $r$ is indeed bounded between 0 (when $M=0$) and $\frac{1}{2}$ (when $M=\infty$).
Note, the fact that the sum of probabilities of every even $k$ in a Poisson distribution is always lower or equal to 0.5 is an interesting math fact in itself!

Yes that's how it works as far as I know
Because the theory part is pretty straightforward.of the genes are on the Same chromosome, the chance of them being separated in segregation during meiosis is lower
Consider a simple example
---------A--b--------------c----d-e---------------------------------f
Let this be a rope with 6 point a b c d e f
If I were to make a random cut anywhere here, the chance that a,b will get separated is much lower than a,f....because a and f are so far apart that any cut in the middle will ensure them to be separated.
If u look at it again...the chance of d,e to be separated is EXTREMELY low
This is the principle of LINKAGE
Now let me say gene a stands for tall, b for blue and f for bushy...(don't judge the characters)
Now if this is a part of a chromosome on the parent, and meiosis is taking place
We all know that crossing over too is a phenomenon involved here
Now during crossing over.....a and f are bound to get separated for sure, so they will be independently assorted, obeying the law of Mendel
But when we talk about a and b, they may or may not get separated in the various gametes
The closer they are, the lesser chance of them being separated and thereby, higher chance of them occurring in the same gamete and therefore, higher chance of them being expressed in the same offspring(assuming they are dominant)
lets assume we cross blue tall(dominant) with green dwarf(recessive)
As you know f1 will be blue tall(no incomplete or co dominance please)
Now if I take this blue tall and cross it with parental green dwarf
You will have very high number of blue tall and green dwarf(remember, there are alleles of SAME GENE....AND OCCUPY SAME LOCI)(therefore.....high chance of both occurring together in the same gamete)
Therefore the number of recombinant you get will be very low(blue dwarf and green tall........as the chance of these characters entering different gametes is very low)
Therefore we can conclude that higher the number of recombination....higher the chance of the genes segregating which implies a greater distance between the genes)
Therefore a higher recombination frequency implies a higher distance between the 2 linked genes
I hope u have understood the concept and are not struggling to byheart it as a force
Thanks


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Are there any cases where broadening the tissue tropism decreases the virulence of viruses?
Broadening the tissue tropism often increases the virulence. For example, poliovirus normally replicates in the guts and causes minor febrile illnesses. In rare cases (1%) the virus invades neurons and causes paralysis. But are there any cases that broadening the tissue tropism decreases the virulence? Imagine that we have two strains. One specifically infects the upper respiratory tract while the other specifically infects the lungs. The first strain is easily transmissible but very rarely fatal (few upper respiratory infections kill people as far as I know), while the second strain is difficult to transmit but highly lethal. Now imagine what will happen if there is another strain which can infect both the upper respiratory tract and the lungs. It’s intuitive that the new strain will combine the high transmissibility and high lethality. However, infection of the upper respiratory tract does little help to kill the patients, but can alert the immune system to neutralize the infection in the more critical part (lungs) especially if the virus invades the upper respiratory tract first. This is just my thought experiment. Are there any papers supporting this hypothesis?

This is a good question, but I would recommend changing pathogenicity in your title and text to virulence. See https://pubmed.ncbi.nlm.nih.gov/15707863/ -- "Specifically, pathogenicity is the quality or state of being pathogenic, the potential ability to produce disease, whereas virulence is the disease producing power of an organism, the degree of pathogenicity within a group or species. Pathogenicity is a qualitative term, an 'all-or-none' concept, whereas virulence is a term that quantifies pathogenicity."


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If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold?
Do they fold independently of each other or synergistically? If we express these globular domains separately, would their structures remain the same?
I came up with an easy way to test it. Many RNA viruses like HIV and coronaviruses encode multiple proteins in one peptide which folds into a polyprotein with multiple globular domains. The globular domains are then separated by the viral protease. Can we express these proteins separately and compare their structures with native ones?

This question is not a mere curiosity. Many proteins have multiple globular domains which makes structure determination difficult because these domains are very loosely joined together. It would be much easier if we can solve the globular domains individually instead of solving the whole protein at once.

I don't think there is any one answer, it probably varies. One data point is the capsid protein of phage p22. If its "I-domain" is removed, the rest of the protein fails to fold. That is maybe more of an intrinsic part of the protein than you meant, though.

Do they really fold into a polyprotein with a structure that has been determined? I thought that autoproteolysis occurred rapidly. And please provide examples of proteins with multiple domains that make structural determination difficult? In any case, expression and crystallization of parts of proteins is widespread. I certainly wouldn't draw any general conclusions from the polyproteins of RNA viruses.

Many proteins are shaped like a sausage. For example, the L proteins of nonsegmented -ssRNA viruses have a large RdRp/capping core and a flexible CD-MTase-CTD tail. The L proteins of VSV and rabies are tightly packed which enables us to solve all 4 domains with cryo-EM, while others’ only have the core resolved because the tail is too floppy. https://www.annualreviews.org/doi/abs/10.1146/annurev-virology-111821-102603

So I came up with an idea. If the CD-MTase-CTD tail can’t be resolved, would it be a better idea to remove it? Cryo-EM solve protein structures by averaging millions of images of identical particles, while the flexible tail only add noise to the images. If the flexible part is removed, the remaining is must easier to align.

Yes, as David mentioned, it's common to perform x-ray crystallography or Cryo-EM on a truncated version of the protein of interest. NMR is also done on smaller fragments or domains.

A broad interpretation of the question
The question refers to the “folding” of proteins. This term — and the associated biological problem — is often used in the rather specific sense of the attainment of a structure with a particular thermodynamic minimum free energy. I take the intent of the  OP (original poster) to be whether, or to what extent, one component of a polyprotein influences the structure adopted by another by physical association. I shall extend the question to that as I think an attempt to answer it will be more interesting and rewarding.
The general and the specific
I do not think one can assume that there will be a single answer to the question that will be true for all polyproteins. Nature is seldom so obliging, and there is no guarantee that what may be true for a polyprotein translated from a viral RNA will also be true for one translated from a cellular RNA. Even within these categories it would be prudent to consider things on a case by case basis.
The answer in summary
Comparisons of the sort suggested have been made in certain cases or are implied by the accumulated work in others. In the polyproteins of both RNA virus and cellular biosynthetic complexes the evidence suggest independent folding in many cases. However in some viral polyproteins, particular pairs of protein domains may be have as a single folded protein in precursors to proteolytically cleaved subsequent forms.
Viral polyproteins
Comparisons of the sort suggested by the OP have, in fact, been performed, although not on complete viral polyproteins — rather restricted to examining possible interactions of particular subsections of the latter. I can see two reasons for this:
Practical Difficulty. I am not aware of any viral polyprotein that has had its total structure determined. This may be because large protein assemblies are generally difficult to crystalize, or because the flexibility of the linkers may mean most do not adopt a single structure, or because even if they do they may not maintain it for any length of time before proteolysis occurs.
Insufficient interest in the question. I suggest that most virologists would assume that the sole or primary reason for synthesis of RNA virus proteins as a polyprotein is that the mechanism of eukaryotic translational initiation precludes polycistronic mRNAs (in all but a few cases not relevant here), and the way the linkers space the protein domains suggests that they fold independently of one another. Furthermore, the unrelated nature of many adjacent protein domains (polymerases, proteases, structural proteins) — and the non-conserved organization of neighbours — gives no reason to suppose that they interact in any way. There is a long history of the crystallization of individual RNA viral proteins expressed from artificial constructs including only the open reading frame of the viral RNA, as exemplified most recently by the expression of Covid proteins for research and vaccine development. This also suggests that individual proteins fold independently.
Comparison studies on partial viral polyproteins
Nevertheless, it has been recognized that — and there has been considerable interest in the fact — the viral polyprotein system has been refined and adapted to the infection. In some cases, for example, there is a process of protein maturation by successive proteolysis, with intermediates having functionally different properties to the mature end-product. For this and other reasons structural analysis and comparisons of parts of the polyprotein have been performed with different viruses and proteins, some of which were reviewed by [Yost and Marcotrigiano in 2013].(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660988/)

One example (from this review) is the 3C/3D precursor of poliovirus, in which the two components are well separated (above) and, to quote, “Overall, the structures of 3C and 3D alone are very similar to their counterparts in the 3CD precursor.“
The preceding result may be the one anticipated, but the nsP2/nsP3 precursor of Sindbis virus illustrates a quite different situation. Here the two proteins components interact strongly in the precursor (below), suggesting that after proteolysis a rearrangement of the structures or interaction with some other protein might occur. Suffice it to say that the situation is complex and remains to be resolved. However a comparison of with the structures predicted by alphaFold might be informative.

Cellular Polyproteins
The situation with cellular polyproteins is rather different. These relate synthetic pathways in which the enzymes catalysing successive steps are organized into a pipeline. In the (relatively few) examples the eukaryotic version is a polyprotein, whereas the prokaryotic equivalent is a multi-enzyme complex of similar, but distinct, components. In contrast to the viral polyproteins, there seems no a priori reason for a polyprotein in this case, and, indeed, this is not subject to (natural) proteolytic cleavage.
Polyproteins of this type have been crystallized only relatively recently, although there are several structures of individual components and prokaryotic equivalents. I shall consider two examples.
The first is enzymes of the shikimate pathway, responsible for the synthesis of aromatic amino acids. In bacteria, such as Escherichia coli, this comprises seven individual enzymes, but in lower eukaryotes such as Neurospora crassa a polyprotein of five of these, the arom complex, is employed. (Higher animals lack the ability to make aromatic amino acids, and plants use separate enzymes encoded by the chloroplast genome.)  The structure of the arom complex polyprotein was determined for the thermophilic fungus, Chaetomium thermophilum, by Verasztó et al. A feature of this polyprotein is that the individual enzyme domains move and function independently of one another with little effect from their linkages. Although many structures have been reported for the individual enzymes of the complex, these differ between species, and I can find none for C. thermophilum in the protein data bank. Hence the exact test proposed by the OP has not been carried out, but the indirect evidence suggests independent folding. A structure, from Candida albicans, has subsequently been reported.
The second example of a cellular polyprotein is the enzymes of the fatty acid synthase pathway in mammals, and the homologous  polyketide synthases in bacteria (only few of which synthesize fatty acids). The first such structure was reported by Maier et al. in 2008. The porcine complex is shown below, and has a more open and flexible design than the arom complex, that seems to have allowed insertion and deletion of different catalytic domains during evolution. Again, this argues in favour of independent folding of individual components, although I am not aware of direct comparison with individually expressed fragments. I suspect that there might be structures available to do this, although I haven’t had the time to examine this further myself.

I would conclude by noting that although the individual components of these cellular polyproteins interact with one another to cooperate in the biosynthesis, the flexibility they exhibit allows transfer of the growing substrate from one component to another.

This is a much more extensive update to my initial answer, now, I think justifying acceptance. However criticism and additions are welcome. I would like to look for structures of individual FAS enzymes, and do some work with alphaFold, but do not currently have the time.


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How does HIV assemble its capsid correctly?
HIV’s capsid is very unusual. The capsid is made of around 1200 identical CA proteins (p24). These CA proteins first assemble into either pentamers or hexamers, which assemble into a fullerene like polyhedron containing 12 pentamers at the vertices and about 200 hexamers filling the bulk. Compared to other viral capsid, HIV’s capsid is unusually big (with an equivalent triangulation number of T=1200/60=30) and highly asymmetric. Instead of a perfect icosahedron made of 20 equilateral triangles, the edges are of different lengths (as well as the h and k numbers https://viralzone.expasy.org/8577) in HIV’s capsids, and even two HIV can have slightly different capsids.
It should be difficult for such complex structures to be assembled correctly because the structural environment is very different among the subunits. For viruses with small and symmetrical capsids, the symmetry is guaranteed by the fixed binding angles between subunits (because the structural environment is equivalent everywhere). More complex viruses can encode multiple types of capsid proteins taking different positions. For example, the capsid of poliovirus can be modeled as a soccer ball, with each pentagon made of 5 VP1 and each hexagon made of 3 VP2 and 3 VP3. However, HIV’s capsid is solely made of CA, which means the very same CA need to adapt to the highly variable structural context. Some complex viruses like herpes viruses encode scaffold proteins to guide the capsid assembly, which is unlikely true for HIV as HIV’s capsid is self-assembled. Despite its irregularities, HIV’s capsid is perfectly sealed off, which is unlike murine leukemia virus with large gaps in its capsid (https://www.pnas.org/doi/abs/10.1073/pnas.1811580115?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed). How can the seemingly simple CA proteins assemble into such complex structures accurately?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300640/

How capsids self-assemble isn't fully known for any virus, but it's been studied a lot and there are a number of principles we can apply. First, HIV isn't as unique as you assume. 30 is a fairly large triangularization number, but Faustovirus has T=277, and Mimivirus is estimated at over T=1000. The conical shape of lentiviruses is indeed very unusual, but if we look at how that shape is constructed, it seems less exotic. Hexagons can tile infinitely on a 2D plane or cylinder. However, if a hexagon is replaced with a pentagon, the tiling is distorted such that the plane becomes curved. The geometry works out so that replacing 12 hexagons in a lattice with pentagons will create an enclosed shell, regardless of size. If the pentagons are evenly spaced, the shell is an icosahedron. However, many bacteriophage build a cylindrical region between two half-icosahedral endcaps, with 6 pentagons at each end. This type of capsid is called "prolate", and the well-known T4 phage uses it, as well as the elongated "corndog" phages shown below:

Negative-stain transmission electron micrographs of the C. crescentus phage phiCbK and five phiCbK-like phages. All five exhibit Siphoviridae morphology and prolate heads. Scale bars are 100 nm.

The conical capsids of lentiviruses like HIV have a similar geometry to these corndog phage, except the two endcaps are asymmetric; with 7 pentons at one end and 5 at the other. If HIV was like many large icosahedral viruses and encoded different proteins for the pentons, arranging them correctly would be difficult. However, the current theory is that the overall geometry is imposed on the maturing HIV capsid, and CA protein simply changes into a pentameric arrangement where the local curvature of the immature lattice is too great for hexameric arrangement. From Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly, referencing Nonequilibirum Assembly, Retroviruses, and Conical Structures:

Levandovsky and Zandi used tapered triangular prisms to represent CA units and were able to recapitulate spherical, conical, and tubular shapes.26 Tapering caused growing sheets to curve, and as the curved sheets grew, inclusion of pentamers became necessary to relieve accumulated stress. Opposing edges of the growing sheets eventually curled around toward each other and connected and then the top and bottom ends sealed. Conical shapes therefore emerged not as a result of template interactions or membrane enclosures but through simple nonequilibrium growth of elastic sheets.

The overall shape of the CA immature lattice before the conical core forms is guided by two forces that mimic the "scaffold" proteins used by other viruses. These are the outer membrane and the inner RNA payload, to which CA is stuck via the MA and NC subunits of the Gag polyprotein, respectively. This figure from Assembly and Architecture of HIV illustrates how the constraints of the membrane and RNA leave the Gag units organized in a way that allows the CA units to organize into the required shape once they are cleaved free:

Wow, mathematics is beautiful. I didn’t know that a fullerene structure is always enclosed no matter how the 12 pentons are spaced. It is now clear that the perfectly enclosed capsid of HIV is quite natural for fullerene structures, while the gaped capsid of MLV is unnatural and may need some mechanism to disrupt its continuity.

The formation of pentons is also very interesting. I once thought that CA proteins first assemble into hexamers and pentons, which then assemble into capsids. But there is a serious flaw in this model. A capsid contains 200 hexamers and only 12 pentons, which means the equilibrium should strongly favors hexamers. However, a slight fluctuation will greatly change the number of pentons. If pentons are not enough the assembly will fail. If there are too many pentons, they may compete with each other.


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How do B memory cells provide immunological memory? Do they differentiate into plasma cells?
My text book doesn't say anything about how B memory cells actually ensure a faster response the second time the antigen is encountered. My guess is that they differentiate into plasma cells which produce antibodies, and release cytokines to cause clonal expansion of the correct T killer cells, but I'm not sure...
Thanks in advance for any responses ^_^

This 2005 review in the Annual Review of Immunology entitled "Antigen-specific memory B cell development" would be a great first resource in answering your question in great detail. Briefly, memory B cells (MBC), upon re-exposure to the same antigen, very rapidly expand and differentiate into antibody-producing plasma cells (PC), with the help of memory T helper cells (Th). However, more MBC are still produced by this reaction, so that a second challenge with antigen doesn't deplete the memory population.
PC are geared towards producing gobs of antibody, and not much else. Upon stimulation with antigen, MBC will produce some cytokines to attract the Th cells that are required for costimulation and regulation, but to my understanding it is the Th cells that manage the whole response, activating effector T cells ("killer" T cells), NK cells, dendritic cells, etc., and not the MBC themselves.


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Protein PTM site prediction
Is there any in silico analysis method to predict post-translational modification sites on a given protein?

There are actually a lot of these sites available, I have used some of the one listed below. Additionally there are some huge list of other services available in this field from ExPASy, you can find it here and the Center for Biological Sequence Analysis, which can be found here.

ExPASy - FindMod
The Eukaryote Linear Motif resource for Functional Sites in Proteins
Phosida


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Conserved acetylation sites in a given protein
I want to identify potential conserved Acetylation sites in protein X. As it is known, acetylation happens in Lysines (K), thereby I would like to identify conserved K residues for protein X during evolution. Eventually I would use different Acetylation site prediction tools to further filter the results, but initially I need the other data, does anyone know a user friendly but trust worthy bioinformatic tool to do so?

You can use the NCBI subpage HomoloGene
Halfway down page on left you can choose to show Multiple Alignment as seen in this screenshot.

I think you will then see what you are looking for as in this screenshot:


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Difference between CDS and cDNA
What is the difference between Coding Sequences (CDS) and cDNA?
Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured mRNA?

The difference boils down to UnTranslated Regions. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (almost) always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG).
The transcript however (note that I am referring to mature transcripts that have already been spliced so introns have been removed) will also contain the UTRs which are not actually translated into protein. A cDNA sequence is derived from the transcript by reverse transcription and will, therefore, also contain the 5' and 3' UTRs. For example, see this schematic diagram of an unspliced transcript:

The CDS of the gene depicted in image above will only contain the ATG, the STOP and the two green regions (exons). The cDNA will contain all that and, in addition, the two UTRs. Of course, both the cDNA and the CDS will not contain the introns.

Actually, exons include 5' UTR, CDS and 3'UTR. And CDS should not include STOP codon as it's not translated into an amino acid.  Your diagram isn't very accurate with where you draw Exon 1 and Exon 2.

@olala that's just a simple diagram to illustrate the existence of UTRs. Yes, of course they are exonic but that is not really relevant here. As for the CDS, no it also includes the stop codon. First because the stops are recognized by specific tRNAs, just like any other codon, and because that's the convention in the field. See, for example, the CDS described here: http://p53.iarc.fr/p53Sequence.aspx

i have to disagree on CDS and stop codon. If you look at at GTF format annotations, they listed stop codon separately from CDS, see an example from this post at the bottom of the page: http://mblab.wustl.edu/GTF22.html, also see this post Istvan's answer https://www.biostars.org/p/65162/

The definition of coding sequence is, to my mind, a little confusing. It is actually the sequence of DNA in the gene which has the same sequence as the corresponding mRNA (except it has T instead of U). Now, you will often see definitions that say that the coding sequence is the DNA that is transcribed, but this isn't really correct because during transcription the RNA polymerase actually copies (transcribes) the other strand of the DNA (i.e. the one that is complementary to the coding sequence). And I would go one step further and say that the coding sequence excludes introns. You could also refer to the coding strand of the DNA, to encompass the entire transcriptional unit including introns as a way of referring to the strand which carries the coding sequence.
You are correct in your definition of cDNA (except its reverse transcription not reverse polymerisation). The the full-length cDNA sequence for a protein-coding gene will encompass the CDS but, as @terdon points out in his comment, will also include untranslated regions at the 5' and 3' ends.

so the difference in sequence to a given gene among its CDS and cDNA would be?

The CDS sequence is not identical to the cDNA sequence. That will only be the case for genes with no UTR regions.

Yes, @terdon is correct - I'm so protein-oriented I overlooked this. So the cDNA sequence will encompass the CDS. Will add a correction to the answer.


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Ethidium bromide and mutagenesis on cloning
When performing a DNA cloning, sometimes PCR amplicon is run in agarose and it is detected by ethidium bromide marking under UV light. After that, gel is sliced, DNA extracted from gel....... until eventually you have your transgenic organism. The thing is that when doing so, you use the very same DNA sample that was "contaminated" by ethidium bromide, so does this DNA you are using for transformation contain ethidium bromide? if so, how can it affect in numbers to mutation risk?

Purified DNA contains negligible amounts of ethidium bromide. PCR and gel clean-up kits remove it quite well. There is, though, a risk of mutation from the fact that you're visualizing the gel in UV light with ethidium bromide. The risk of mutation from UV is minimized by exposing the gel as little as possible, and by using "preparative" transilluminators that come with a low-light setting for cloning purposes. If you work well and quickly, the chance of mutagenesis isn't higher than the chance of a polymerase incorporating the wrong nucleotide.

The ethidium bromide stays in the solution when the DNA is purified (either with a column or with precipitation).

While it is possible to get mutations from the ethidium bromide, this is hardly the only source of mutations in the process.  Taq itself will introduce mutations fairly frequently, so sequence sensitive procedures typically use a higher accuracy (but slower and more expensive) polymerase, like Pfu.  As stated before, the UV can also cause mutations.  The PCR process iteself can result in primer dimers and other "funky business".  Inappropriate sequences can be picked up from environmental contamination, particularly if you frequently use the same restriction enzymes in the lab, because sequences with appropriate "sticky ends" will be all over the place, no matter how much you clean.  If inserting into a plasmid, multiple inserts can get ligated into the final product, depending on how homologous the sticky ends of the insert are.
The solution is to accurately sequence the final transgenic product before you put it in the transgenic organism.  I usually have the plasmid (I work with plasmid transfections) sequenced, as well as cleaving the plasmid insert from the plasmid and running it on a gel.  The sequencing catches any base swaps/indels and the gel makes sure there is only one copy of the insert in that particular plasmid.
You would be surprised how often you get mutations and other "garbage" in the final product, which is why it's important to make multiple batches together.  I make mine in batches of 8, so that at least a couple will be exactly what I intended to produce.
Reference: My own research/experience with site-directed mutagenesis and construction of plasmid vectors for transfection.


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First documented beneficial mutation?
I've been reading up on beneficial mutations, and am curious when we discovered and documented the first one.
Can anyone point me to the first documented beneficial mutation?

Per request, let me try to clarify my answer a bit.
I know that we've been aware of mutations perhaps as long ago as the 1930s (I believe it was R.A Fisher who was one of the first to talk about them??).
I have read various documented beneficial mutations since then, such as lactase example in humans, or cit+ in E.Coli.
What I'm curious about is when it was that we first identified and documented (scientific paper or article) an observed beneficial mutation, in any organism (not just humans).
So yes, Remi.b, your wording would have been what I was looking for:
"what is the first article that has documented a beneficial mutation, in any organism"
Does this clarify it enough?

You think about things like the mutation which activates lactase in people of european ancestry permanently?

Do you mean the first documentation (no matter if mutation was earliest exactly known), or earliest exactly known such mutation (which has been documented at any time)?

I am not really sure what kind of observation you are interested in? If we see a sweep just like for the lactase example in humans? Or are you looking for a mutation that appeared in a lab and that has directly been shown to be beneficial? And as Hyde said did you actually mean "what is the oldest beneficial mutation we know" or "what is the first article that has documented a beneficial mutation". In both case, the question needs editing I think, to make clear what kind of observation you are interested in.

I'm not even sure if you mean in humans or ever. This question is unclear. As others have said, it really needs to be narrowed down in its scope. This could mean nearly anything.

E. coli using citrate might be the best document beneficial mutation.

@user137 - there are many examples of beneficial mutations. The problem is that it's unclear what the OP is asking.

It's a valid question, just needs refinement and then it can be re-opened for sure

Earliest beneficial mutation discovered by humans is what I guess OP is interested in, which I think is of no great relevance. Mutations happen all the time and beneficial mutations are selected in the evolutionary process. Which was the first example in the textbook doesn't make any great sense to me.

What search parameters have you tried to find the paper?

Good Gravy:  I didn't save my exact search text, but a lot along the lines of 'history of beneficial mutations', and 'first discovered beneficial mutations'.  I was getting no-where.  I figured I'd turn to a place like this, hoping someone here could point me in the right direction.

I found a list of documented beneficial mutations by typing in google "beneficial mutations". It was the fourth link. (http://www.gate.net/~rwms/EvoMutations.html)
Check the years and find the one which interests you. All of them are very well vulgarized and all their sources are cited.

authors: Àñùj ģàmìñģ AK 33


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Bowtie: cannot read fasta file?
I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows:
bowtie2 -x $REFERENCE -f $TARGET -S $TARGET.sam

The version 2 of bowtie complains with the following:
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because length (0) <= # seed mismatches (0)
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because it was < 2 characters long
Warning: skipping read 'ORIGINAL: GGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAG' because length (0) <= # seed mismatches (0)

Note that bowtie (version 1) is pleased by my FASTA! Here's a snippet and what bowtie says:
>ORIGINAL: GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
>ORIGINAL: ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
>ORIGINAL: GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGCT
AATGGGAGTGAAAATCTCCGATGAGCAGC

# reads processed: 471409
# reads with at least one reported alignment: 464583 (98.55%)
# reads that failed to align: 6826 (1.45%)

Now I'm at loss. Can anyone see what I'm doing wrong here? Can I trust anyway bowtie2 when it finishes and outputs how many sequences are aligned?
Thanks!

Since I apparently don't have enough reputation to comment, I'll post this as an answer and let someone move it.
Firstly, try to ensure that the order of the arguments are correct. You should be typing bowtie2 -f -x $TARGET -U $TARGET -S $TARGET.sam, since bowtie2 (as with many other programs) can be a bit picky about the argument order.
Secondly, it's usually advisable for the example input to include lines that are causing the problem (since it's apparently not complaining about the lines you posted, we can only assume that it's aligning them).
Thirdly, you'll typically only get those warnings if they're true. For example, if you were to grep -A 1 -w GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT $target then my guess is that you'd find it to have no remaining sequence. Presumably these are the result of you trimming adapters or something like that, so just have your trimmer discard really short results (they won't align meaningfully anyway).

it makes a fine answer @DevonRyan

Yeah even bowtie-1 doesn't take the argument bowtie -f $target.fa ..<other options>

Apparently, bowtie2 when reading headers will try to understand if the string is a DNA sequence: it does not ignore the content. However, it processes fine. Why it complains about headers, remains to me unknown.