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Did birds descend from a single or multiple species of dinosaur?
It seems like there are mixed results because sometimes I read about a single missing link, like an archaeopteryx that somehow single-handedly explains all modern-day birds, but then I see conflicting articles about how different birds are descended from different dinosaurs like a t-rex or a velociraptor and so on. Which theory is correct? Did birds all descend from one common ancestor or multiple?

The answer is "one common ancestor", but I'll expand.
All organisms descend from one common ancestor so that question is not quite well-posed, but what you are actually asking I think is whether birds all descend from one common ancestor that was a bird, or whether their common ancestor wasn't a bird, which implies that different branches of birds became birds independently. In other words, are birds a "polyphyletic" group or a "monophyletic/paraphyletic" one (the difference between the latter is whether all of that common ancestor's descendants are birds, or whether it also had descendants that aren't birds).
The answer to that is that modern birds are monophyletic: they all descend from a common ancestor that, itself, was a bird. (and that common ancestor doesn't have any descendants that aren't birds)
But modern birds aren't the whole story - their group originates in the Cretaceous, and there are many groups of birds that are clearly recognizable as birds but also aren't modern birds - they might have teeth, they have subtle but unavoidable skeletal differences, etc. Like Enantiornithes and Confuciusornis. In other words, modern birds absolutely, unambiguously have a common ancestor that was itself a bird, which isn't hard because animals we would recognize as "birds" were already common by the time it appeared and the ancestor of our modern birds was just one of them. Whether those older, "extended" groups of birds themselves descend from a single species is harder to tell because fossil evidence is all we're going on, and it's even harder to tell when we go closer to the origin of birds and they no longer look unambiguously like birds. But at that point it's not so much a matter of "did this group originate from one ancestor or several" but "are these fossils that we've been putting in this group as closely related as we were assuming?" and "did this trait that these different fossils have evolve in their common ancestor, or did they evolve it independently, and what about those other fossils that seem related but don't have the trait: did they lose it from the common ancestor who had it or are they a sign that the common ancestor didn't have it to begin with?". Like, you might get different answers depending on how you define "bird". BUT paleontologists these days like monophyletic groups, so whichever groups they call "bird", those will have a common ancestor that was a "bird".
The Wikipedia page for Avialae expresses some of the issues with what "bird", or "Aves" means in the context of paleontology. To quote:

Aves can mean those advanced archosaurs with feathers (alternately Avifilopluma)
Aves can mean those that fly (alternately Avialae)
Aves can mean all reptiles closer to birds than to crocodiles (alternately Avemetatarsalia [=Panaves])
Aves can mean the last common ancestor of all the currently living birds and all of its descendants (a "crown group"). (alternately Neornithes)

"Avialae" is one of those "extended groups of birds", in that paleontologists will often refer to any member of that group as "birds", but there's still a wide gap between "Avialae" and "Neornithes"; some stepping stones on that gap:
Neornithes (modern birds) are part of
Euornithes (birds have a certain articulation oriented like modern birds, as opposed to Enantiornithes, or "opposite-birds", who have it the other way, in addition to other differences like having teeth; note this page has a cladogram), which is one branch of:
Ornithothoraces (all descendants of the common ancestor of Euornithes and Enantiornithes), which is part of
Avebrevicauda ("short-tailed birds", to distinguish them from long-tailed Avialans like Archeopteryx) which is part of
Avialae, which as mentioned is basically birdinosaurs that could fly like Archeopteryx but it doesn't stop there because that's part of
Paraves, a group of dinosaurs that by and large had wings and feathers including the four-winged dinosaurs like Microraptor gui, which if we saw today we'd recognize as not like other birds but would we recognize as not a bird, really? That's part of
Pennaraptora, which is the first group to contain names that we definitely think of as not-birds; this group contains birds as well as Oviraptor and Deinonychus, but to quote the page:

The earliest known definitive member of this clade is Anchiornis, from the late Jurassic period of China, about 160 million years ago.

And Anchiornis, as its name suggests, is bird-like, feathered wings and all. This is where we get into "wait, Velociraptors were basically like turkeys?" reactions (Deinonychus is Jurassic Park's "Velociraptors").
(also these points are where the groupings become disputed, or fast-changing, or ambiguous between groups that are defined based on phylogeny, or similarity, or others and you can get different results depending on which group's Wikipedia page you look at; for example the Wikipedia page for Theropods puts Avialae directly under Maniraptora).
Pennaraptora is part of Maniraptora, which also contains your velociraptors, and Maniraptora is part of Coelurosauria which also contains your Tyrannosaurs. At this point we have clear non-bird dinosaurs, although it's likely they all had feathers.
I don't know which articles you read saying some birds would have descended from T-Rex and others from Velociraptor; that seems completely counter to what we know today of bird evolution, even if we extend "birds" to "Avialae" or even "Paraves". In fact the only way it would work is if we call T-rex or velociraptor themselves "birds". What you could have is conflicting articles about how close birds are to T-rex or Velociraptor; that part of the family tree is based entirely on fossils and so new fossils can change our understanding of how things are related... But the current phylogeny that makes, say, Avialae a group that's quite a few nodes away from velociraptors, and both of those a couple of nodes away from T-rex, seems quite robust. We have found many, many bird and proto-bird fossils in the last few decades that have clarified the picture on that scale (you can get an idea of how many by clicking the various links).
One thing those many, many bird and proto-bird fossils also made clear is that the traits of modern birds (feathers, wings, toothless beaks, etc) didn't evolve in a simple line from non-bird to bird. Many of those traits evolved convergently in several lineages, were lost in some, maybe regained in others, and feathers in particular turn out to be a widespread dinosaur feature that cannot be considered a uniquely bird trait anymore (unless we want to call T-rexes "birds"). Still, saying "beaks evolved several times" or "feathers evolved several times" doesn't mean that birds, let alone modern birds, evolved from several different ancestors. It can mean that the common ancestor of birds had lots of variously bird-like more-or-less distant cousins living around the same time.

to add for years one of the definitions of aves was the most recent common ancestor of Archaeopteryx and the common chicken and all of that ancestor's descendants.


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Nucleic acid extractions
Is it fine to leave pulverized plant tissue in CTAB buffer at -80 degrees over night? will the buffer remain effective to generate good quality nucleic acids?

Someone push back but freeze-dried or frozen in liquid N2 is shown to be preferable, typically.

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If I workout, will this inherited trait (of being stronger) not be passed down to my offspring (Lamarck's theory on evolution)?
I'm a student in biology and just recently learned about Lamarck's theory on evolution and how it has been disproved. While I understand that you cannot alter your genes, I'm still having a hard time understanding some parts of it, mainly how inheriting strength (such as working out) will not be passed down to my offspring. If someone was obese, exercised to the point of no longer being obese, will this person's offspring still start off as obese?

You inherit genes for muscle from your parents. What you do with that muscle is not passed on. Your physical attractiveness if you work out may benefit you passing on your gene pool, but that's about all you can do genetically. Obesity may have something to do with gut flora, which can be traded between two individuals, e.g. from mother to offspring. But there is much to obesity which is not understood yet.

Indeed, whether you work out or not will not change how strong your offspring will be. This is exactly why Lamarck's was wrong.

I would note however that Behaviour can be heritable and Your behaviour can affect your kids environment
Behaviour can be heritable
The probability of you working out is affected by your genes and so if you have a genetic predisposition for willing to work out, this will be passed on.
Assuming there are genetic predisposition for liking to work out, the fact that you worked out would not increase the probability of your kid to work out via genetic inheritance but the fact that you have a genetic predisposition for liking to work out will increase the probability that your kid will have the same preference and will work out
By the way, if you want to learn more about the concept f heritability you should have a look at Why is a heritability coefficient not an index of how “genetic” something is?
Your behaviour can affect your kids environment
Working out won't affect your genes but it will likely affect the environment in which the kid will grow. Here are three examples

Teaching

If you eat healthy, you will probably teach your kids to eat healthy too.

Womb environment

Also, if you eat healthy and are a woman, you will likely give the right nutrients to your offspring while still in the womb (assuming you are a lady).

Epigenetics

Your environment will cause epigenetic changes (changes not in DNA but in the very close environment of the DNA such as typically histone tail methylation). These epigenetics modifications will be directly passed to the foetus.
More information
A post your question is almost a duplicate of...

Is it the case that all changes in phenotype during life are not inheritable?

A post on heritability

Why is a heritability coefficient not an index of how “genetic” something is?

And finally an answer that talks about non-genetic inheritance

Why does evolution only involve heritable traits?

"...the fact that you have a genetic predisposition for liking to work out will increase the probability that your kid will have the same preference and will work out..." Can you please support this with a reference? I.e., is there any evidence that points to a genetic predisposition to work out?

I added Assuming there are genetic predisposition for liking to work out [..]. My goal was to explain the basics of inheritance, not to review the heritability of specific trait. Thanks for noticing this potential confusion. I would notice however that given there is very likely heritability for such life style given that many of hormones concentration are heritable (incl. testosterone typically).

There's no evidence that I'm aware of that testosterone levels contribute to a propensity to work out. A propensity towards some things (like hostility, aggression, etc.) but exercise, again, not that I'm aware of.

It is pretty tough to investigate liking independently of an environmental context and of abilities (as many physical properties relating to sport abilities being heritable) but anyway.... it really is not the point of the question nor of the answer. But thanks for clearing the possible confusion.

Also not that it has recently be shown that learned behaviour can be inherited through epigenetic mechanisms. Mice born to parents that were conditioned to fear a certain smell, still reacted to that smell despite never being conditioned (see news article or original paper)

@Nicolai Yes, I did mention that in the answer. Thanks for the references.

@Remi.b Your answer states that behaviour can alter the environment of offspring and thereby affect epigenetic markers on their DNA (which they indirectly inherit this way). What the paper I linked proposes (or shows) is that learned behaviour of the parent is directly passed to the offspring via epigenetic changes in the germline. (The offspring reacts to smell it has never encountered before).

We are saying exactly the same thing IMO. I edited the post to add a single word hoping to make it more clear.

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Why are tumor suppressor genes recessive?
In my Intro. to Biochemistry course, we have been studying cancer. The professor has pointed out that tumor suppressor genes are "recessive" while proto-oncogenes are "dominant". Since only one mutation is necessary to turn a proto-oncogene into an oncogene; while two are needed for the malfunctioning of tumor suppressor genes, why is this not the other way around (i.e. tumor suppressor genes dominant; proto-oncogenes recessive)?
All help is greatly appreciated.

Just for the semantic, a gene is not dominance or recessive. An allele at a given gene (or locus to be more general) can be dominant or recessive in its relationship to another allele. So what you mean by dominant gene, you mean that the wild type allele is dominant over the mutant allele (and vice-versa for what you call recessive genes).

why would they not be, why has a mechanism to sickle cell not evolved a regulator gene, in both cases it becasue the necessary mutations has not occurred. Dominance is a side effect of how the gene and its products function, it is not affect by the whether the allele is deleterious or not.

I was typing out an explanation, but then realized that this text book does a much better job:
Lodish et al. 2000. Section 24.2: Proto-Oncogenes and Tumor-Suppressor Genes in Molecular Cell Biology 4ed. WH Freeman
Proto-Oncogene:

Conversion, or activation, of a proto-oncogene into an oncogene generally involves a gain-of-function mutation. At least three mechanisms can produce oncogenes from the corresponding proto-oncogenes.

Point mutations in a proto-oncogene that result in a constitutively acting protein product
Localized reduplication (gene amplification) of a DNA segment that includes a proto-oncogene, leading to overexpression of the encoded protein
Chromosomal translocation that brings a growth-regulatory gene under the control of a different promoter and that causes inappropriate expression of the gene

An oncogene formed by the first mechanism encodes an oncoprotein that differs slightly from the normal protein encoded by the corresponding proto-oncogene. In contrast, the latter two mechanisms generate oncogenes whose protein products are identical with the normal proteins; their oncogenic effect is due to their being expressed at higher-than-normal levels or in cells where they normally are not expressed. However they arise, the gain-of-function mutations that convert proto-oncogenes to oncogenes act dominantly; that is, mutation in only one of the two alleles is sufficient for induction of cancer.

Tumour Supressor Gene:

Tumor-suppressor genes generally encode proteins that in one way or another inhibit cell proliferation.... Since generally one copy of a tumor-suppressor gene suffices to control cell proliferation, both alleles of a tumor-suppressor gene must be lost or inactivated in order to promote tumor development. Thus oncogenic loss-of-function mutations in tumor-suppressor genes act recessively.

A clarification that would improve this answer: As in Remi.b's comment, the alleles are recessive, not the genes. In the context of cancer, the key point is that cancer-causing alleles of tumor suppressor genes are recessive, not the genes themselves. Often loss-of-function alleles are recessive, because a single healthy copy is capable of performing most of the function.

Thank you! This clarifies things a lot. I am really sorry about the way I wrote my question -- I am aware that what we call recessive or dominant is an allele, not a gene as a whole. If I understand correctly then, in the context of cancer we say that the allele that for instance undergoes a loss-of-function mutation in a TSG is recessive (as canadianer quoted), but then... would the wild-type allele for a TSG be dominant with respect to the mutated allele? (TSG = tumor-suppressor gene). Thanks a lot to everyone!

@Bee You’re welcome! Yes, it would be dominant in relation to the the loss-of-function allele since its activity alone is sufficient for the wild-type phenotype.

Note that while this is generally true - there is also a phenomenon of haploinsufficiency with some tumour suppressors. That means losing one copy is enough to permit tumour development.
See http://www.sciencedirect.com/science/article/pii/S0304419X04000022?via%3Dihub


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Using catalase-test to determine if Staphylo- or Streptococcus
If the microscope clearly shows bacteria of cocci morphology but it is difficult to determine if they are Staphylo- or Streptococcus, are catalase tests a good way to differentiate between the two since Staphylococcus are positive and Streptococcus are negative? Are there any traps/exceptions?
Thanks!

Generally yes: streptococci are catalase negative while staphylococci are catalase positive.

The catalase test is important in distinguishing streptococci (catalase-negative) [from] staphylococci which are catalase positive.

Unlike Staphylococcus, all streptococci lack the enzyme catalase.

However, there are exceptions to every rule:
Catalase negative Staphylococcus aureus.
Catalase positive Streptococcus sp.


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Estimation of cell count of E.coli culture
Can I get some help with an estimation of a cell count in a culture of E.coli cells if we assume we begin with $10^6$ cells, that they divide every 30 minutes and they are incubated for 12 hours?
I do not know how to do the calculation with a start number that is not 2, if it was it would just be $2^{24}$. But how is it done when the starting number of cells is $10^6$?
Is it $(10^6)^{24}$?
Thank you!

You start with $10^6$ cells. After 30 min they double, so there are $2⋅10^6$ cells. After another 30 minutes they double again, so there are $2⋅2⋅10^6$ or $2^2⋅10^6$ cells. After three doubling periods, the number of cells is $2^3⋅10^6$. Doing this, the equation for exponential growth should become evident. All you must do now is determine the number of doubling periods in 12 hours.


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Zinc finger nuclease specificity
If I want to make sure that a ZFN cuts at only a certain position in a genome, how many subunits would I need to ensure this?
If the human genome is roughly 3 billion base pairs, we need a sequence that is 16 base pairs because 4^16 exceeds 3 billion (if my thoughts are correct). But then I don't quite understand how the subunits of the ZFN come into this.

How unique and complex is your cut site?

Hello! I dont have a specific sequence, it is more a general question of how many you would need to really specify a cutting. Can you help?

This sounds like a homework question where you need to find the length of a sequence that has a probability of occurring once in the genome.

@canadianer Exactly, so if the human genome is roughly 3 billion base pairs we need a sequence that is 16 base pairs because 4^16 exceeds 3 billion if my thoughts are correct. But then I don't quite understand how the subunits of the ZFN come into this..

If you want to be a bit cheeky then the answer is that it does not matter anymore as everyone doing real science have moved on to Crispr/Cas9. https://en.m.wikipedia.org/wiki/CRISPR

The human diploid genome is ~6.5 billion bp, so you need to find the length of a sequence that has a probability of occurring only once (assuming the sequence is completely random):
$4^n=6.5\cdot10^9$
$n\cdot log(4)=log(6.5)+9$
$n=\frac{log(6.5)+9}{log(4)}$
$n\approx16.30$
According to this article, each finger of a ZFN recognizes 3 bp, which means you'd need $\frac{18}{3}=6$ fingers to probabilistically recognize a unique site. Interestingly, the article also says:

The requirement for dimerization is a great advantage for this reason: because a monomer is not active, cleavage does not occur at single binding sites. The cleavage reagent is assembled only at the target if the fingers have adequate specificity, and the combined requirement for binding two proteins brings the overall specificity into a very useful range; e.g., two three-finger proteins specify the location of 18 bp, which is sufficient, in principle, to pick out a single target, even in a complex genome.

Thank you once again! You have been very helpful many times! :)

Stupid question: isn't it sufficient to consider the haploid genome because one can approximate the sequence of the second set with the first set of chromosomes? (@O.kth: if you are happy with the answer, please up-vote and accept, thanks!).

@O.kth You're welcome. If this (or other) posts have answered your question, please mark them as accepted by clicking the checkmark next to the answer (and up-vote). It seems I've actually answered several of your questions and you haven't accepted any of them :(

@AlexDeLarge Not stupid at all. I assumed for the calculation that the entire genome was random, which is of course not true (especially when considering homologies between the chromosomes). A more accurate calculation could certainly be made but, fortunately for this question, the answer will be the same.

@canadianer sorry for that, I often forget but I think I have accepted and upvoted all of the good answers I've gotten now! :)


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Are most pathogenic bacteria facultative anaerobes?
I know that S. aureus and most gram-negative rods are facultative anaerobes. In terms of number of species, are most human pathogen-associated bacteria facultative anaerobes?

Most bacteria are facultative anaerobes. There are very few, if any, obligately aerobic bacteria. Wikipedia lists Mycobacterium tuberculosis as obligate aerobe but it can survive in anaerobic conditions.

Thanks. Yes, there are only a few as you mentioned. Moraxella catarrhalis, Legionella pneumophila, and Pseudomonas aeurginosa are some examples.

P.aeruginosa can survive in anaerobic conditions.

In the presence of arginine or nitrate, yes. However, in general terms it is considered aerobic.

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Why does higher venous volume increase atrial pressure?
If the cardiac output stays the same (hypothetically, although obviously it doesn't stay the same), then why does higher venous volume increase right atrial pressure? Shouldn't the flow rate be conserved (with a constant cardiac output) so that the venous return to the right atrium is no different than before, and therefore the pressure is no different?

Read about stroke volume. Cardiac output is not fixed. It's an average.

Imagine the circulatory system is an amusement park ride.  The ride is the left ventricle and the arterial system.  After riding, people go around and get back in line to go again.  The line and the building housing it are the venous system.  Maybe the lungs are some sort of staging area where you get ready to get on the ride.
The right atrium is the end of the venous system.  Venous pressures are right atrial pressure.
When all is well the line is moderate and people wait a short time before riding again.  But now 100 more people arrive.  If the park workers can speed up the ride or loading rate to accommodate the extra riders then great.  But if the ride cannot go any faster then the line backs up.  If you imagine that it is raining out, all the people in line bunch into the building housing it.  Venous pressure increases.  It will stay increased unless the number of riders (blood volume) decreases or the heart improves its output to accommodate the load.
Congestive heart failure is a useful example.  The ride speed (cardiac output) cannot increase because the heart is weak.   If riders increase (blood volume) it backs up into the waiting line or venous system.  This increase in volume occurs if someone with CHF eats a salty meal – water follows salt and blood volume increases, which backs up in the venous system because the heart cannot increase its output to accommodate the increased volume.  These sick folks are said to be volume overloaded.  You can see increased venous pressure as the signs of CHF – for example dilated external jugular veins.
Among many adaptations to deal with increased venous pressure is atrial natriuretic peptide.  When increased venous pressure stretches the right atrium this peptide hormone is secreted which is a cue to the kidney to dump sodium, and with it fluid volume.

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What is the chance a given gene will end up in a given gamete?
Let us say a germ cell had a desired allele. This germ cell was replicated during interphase so that it had two of the desired allele. It then underwent meiosis.
My question then is, what is the chance a given allele will end up in a given gamete that will be involved in conception?
Firstly, there is a 50% chance a chromosome will be assigned to a given daughter cell. This is because of independent assortment. In addition, cross over occurs at chiasmata. Lets assume then that there was a 50% chance that an allele will be crossed over (although this probability may be far from true)
The process during meiosis is that cross-over occurs first. We have two desired alleles, each on one of two pairs of chromatid attached to each other. There is 50% chance for a given allele to cross over. For example, the chance for both desired alleles to cross over is 1/4 (1/2 x 1/2), the chance only one will cross over is 2/4 (since either of the two desired alleles can cross over).
Then there is the first independent assortment during meiosis I which produces the desired daughter cell. In this case there is a 50% chance that a given chromatid pair (containing the desired allele) will be assigned to the desired daughter cell. However, in the case where a desired allele is found in both homologs (2/4 of a chance), then the chance that at least one desired allele will be in the daughter cell is 100%.
Finally, during meiosis II, another independent assortment occurs which produces the desired gamete. The same rule applies with a 50% chance a given allele will be assigned to a given cell (in this case the gamete). However, if the desired daughter cell contains two of the desired alleles, then there is a 100% chance that the cell will have the desired allele.
In conclusion, the chance I estimated that the gamete will have at least one desired allele is 50%. Although, I'm not sure if this is correct. Anyone mind confirming this.

"Let us say a somatic cell... then underwent meiosis"  Somatic cells don't undergo meiosis.

Gametes do not undergo meiosis (at least under normal circumstances). Since you seem to be having ongoing trouble with basic concepts and terminology in genetics I strongly encourage you to take advantage of the many online resources available for making sure you have the background required for understanding this field. Suggestions to follow ...

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

A cell contains two haplotypes (or two set of all chromosomes). One haplotype inherited from the mother, one from the father. A haploid cell, resulting from meiosis, will receive either the maternal (or grandmother if you prefer) or paternal (or grandfather if you prefer) haplotype. It cannot receive anything else. Hence the probably must be 0.5 (or 50%).
Note that you are using the term "gene" incorrectly. You should use the term "allele" instead. And while you are improving your genetic vocabulary you should also check the term "locus". Also, the term "desired gene" is never used. We talk about "beneficial allele" or "detrimental allele".

I think "desired gene" is to mean "allele of interest" for purpose of calculations.

You are making this too complicated.  There is a 50% of any particular allele ending up in a gamete.  The end.


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how can I get stronger staining for my lymph node sections
I am using the same protocol and same antibodies that the literature says but still I cannot get good staining for my lymph node sections, I tried to change the fixation method and I am using now acetone instead of PFA, I also tried with acetone plus ethanol, the antibody concentration used worked in previous sections.
How could I increase the signal and/or remove the noise?
It also happened to work in some sections before but not in others even I did exactly the same, why could that be if I am using the same tissue?
Thanks

could you upload example of microscopic image

Is the tissue you are staining now the same age (i.e., time from initial fixation to staining) as the tissue you used before?

yes I do the fixation just before the staining so I treat them in the same way

I attached the picture, thats the pic of the channel for Madcam which is my interest

Did you try a different fluorophore or fresh antibody? What're you using now? And are you getting signal with other markers like DAPI? What does your staining efficiency look like by FACS? Strong separation from negative or weak? Maybe try digesting some lymph node and see if you get good staining.

the antibodies are not fresh but some times work better than other using the same kind of tissue, so I guess is depending of the tissue and age of animal or sections? the stainning efficiency looks okay. I used Dapi, Cy3, FITC 647 and alexa488.

@bio Okay, and your laser/filter setup are appropriate for your fluorophores? If we rule out hardware and reagents, all that's left the the protocol and the slides.

@bio what's your red laser filter setup?

I can double check on Monday because I do not remember now, but I checked that time ago with my supervisor and it was fine. I upload now another image (first one) so as you can see, doing the same fixation protocol and staining steps I get very big variations within the same tissue. I also tried different ab incubations, different concentration of the primary and secondary ab and all of them look with a lot of noise so Im not sure now what is real signal and how to avoid this big variation between same kind of tissue.


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Is it ok to keep primers at 4 degrees?
I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I am wondering if it will affect to have them overnight at 4 degrees, just for one day.

There is absolutely no problem here. Primers will degrade only very slowly at 4 degrees and even at room temperature leaving them out overnight would not degrade them enough to be of practical consequence. In fact, if you're using them today it's probably better to have stored them at 4 degrees than -20 because repeated freeze/thaw cycles will also degrade primers.

In my experience this is not a problem. I keep my working stocks at 4°C until they are finished to avoid freeze-thaw cycles and better convenience and they work all the time. I also dissolve my primers in pure water, not in TE.
Long-term storage of stocks should be done at -20.


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DNA centrifugation in water
If I have bacteria diluted in water and I centrifuge at max speed for 15-30 min, it is possible that I break the walls so the DNA can scape and I do not get any DNA pellet? or should I get it as a pellet everything togheter (lipids, proteins..) even if the mixure is just bacteria diluted in water?

At which relative centrifugation force (the "g number") do you work? And: Do you use plain water or do you add anything else? Where do these bacteria come from?

I recommend using a proper extraction kit. It may be possible (I mean anything can damage a cell wall) but you may not obtain a high yield.

Not with bench centrifuges.
Bacteria have cell wall and are rather small. This gives the cell wall alot of strength. I am not even sure that ultra centrifuges would work.
What you will likely get is a cell pellet. If you want DNA, pellet the cell and either go for direct PCR or sequencing. Or use a DNA extraction kit to obtain the DNA you want.

yes I use an ultra centrifuge. I am try to up-concentrate the sample but I cannot see any pellet and even when I remove volume and I resuspend the nonvisible pellet, I do real time pcr and it shows the sample was not up-concentrate, any idea why could that happen?

Why aren't you just lysing the cells first? Centrifugation isn't sufficient to lyse bacterial culture to a great degree.

Because I use bacteria direclty to do real time PCR.

Why? You will get more accurate qPCR results with pure DNA anyway. People only normally do colony PCR from whole cells directly as it's a quick and dirty method for checking for transformants and so on. I've never heard of anyone doing qPCR from culture, and I can't really think why you would want to?

because we use samples directly from a collector but maybe we could try to extract as you say. Thanks!


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Combination of different antibodies
How can I know if I can combine anti Cenp-C and anti Rod1 antibodies? I want to use them to label those protein and analysing cells by fluorescence microscopy.
*Cenp-C is kinetochore protein and Rod1 is localized on the kinetochores or spindle microtubules during cell division.
Can I just combine them if they are from different animals? how can I know they will not have cross reactivity?
Thanks

What exactly do you envisage as the potential problem? What do you mean by 'cross reactivity'?

I dont know if the the proteins they recognise can be too similar cause they belongs to the same complex so one ab can regonize a similar ag but not the one I want.

If they are made in different animals you should be fine.  You could do a western with those antibodies though, to double-check.  Looks like Cenp-C is about 106kD and Rod1 is about 60kD.  So on a western, if you see bands at both those sizes with one of the antibodies, you have cross-reactivity between those proteins.  And if you just see the specific band you're looking for, you're good.

Ok thanks. The fact they need to be from different animals is because the secondary antibody would not be specific? I never studied any course of immunology so I am not sure.

Secondary antibodies are made to bind to any antibody from a particular animal.  If both your primaries are from the same animal, the secondary will bind both of them, and you won't know what signal comes from what protein.  If you don't care about distinguishing Cenp-C and Rod1 in your IF, then it doesn't matter.  If you do want to be able to distinguish them (ie, have Cenp-C localization red and Rod1 localization green) then the primaries need to be from different animals so you can use two secondaries.


text:
How is Open Reading Frame (ORF) chosen?
I understand that AUG is the "start codon", and, because of this, most proteins begin with methionine as their first amino acid.
However, this ORF problem on Rosalind.info states that "AUGCUGAC... can be translated as ...AUGCUG..., ...UGCUGA..., and ...GCUGAC".  That is, something (the Ribosome?  The GTP cap mentioned here? Something else?) must cause the translation to be shifted by one or two nucleotides in the sequence.
My first question is :  What mechanism(s) cause(s) this shift in translation to another Open Reading Frame (ORF)?
Specifically, I want to know how the start codon, AUG, can have one ("A") or two ("AU") of its bases ignored in the Ribosome during translation.
My second question is : How often does this happen?  That is, what is the percentage of (known) proteins that start with methionine vs. the percentage that start with something else due to this "ignoring" of the bases of the start codon?
I am interested in the answers for both prokaryotes and eukaryotes.

This is standard material you will find in any modern textbook of biochemistry or molecular biology. Aspects of it have also been discussed here, but I advise you to start with NCBI Bookshelf — a textbook generally provides a better explained and illustrated account of an elementary topic. Here are links in Berg et al. to accounts of prokaryotic and eukaryotic initiation of translation.

I now suspect that you are being mislead by the use of the word "can". In problems of this type "can be translated" refers to the pure informatics conceptual possibility, without any reference to biological reality, except, in this case, that of the genetic code. It is a question of considering the six possible reading frames of any stretch of DNA, and deciding which have the theoretical potential to encode a protein — see my answer to this question. The biology depends on transcription as well as the translation mechanism referenced above.

David the part that confuses me is how the start codon, AUG, can have one or two of its bases ignored (skipped over).  I would expect "AUG" to always get translated.  I don't understand how the "A" or "AU" can be skipped, as the start codon has a specific function in the Ribosome.

@GregThatcher I do not understand what you mean by "A or AU can be skipped". 1) Do you mean at translation initiation? E.g which start codon to choose if "AUGAUG"? 2) Or do you ask what happens when the ribosome encounters a "AUG" in a different frame, e.g. "TAU"G? I feel like Joshua Morris great answer below should answer the second option.

@dtrades, from the Rosalind.info problem statement above, "AUGCUGAC... can be translated as ...AUGCUG..., ...UGCUGA..., and ...GCUGAC".  The first sequence shows "AUG", the second sequence truncates the "A", the third sequence truncates the "AU".

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

It’s the hypothetical “can” applied to the interpretation of a fragment of information written without spaces between each word (codon). Roman inscriptions in Latin are like this, as are the German equivalents of English noun phrases. As an example, suppose such a Roman inscription in English rather than Latin, in which the fragment you have found reads ...MASHIT... You do not know without determining where the sentence begins whether it is referring to a popular recording by a former US President, a call to vandalism,  or maternal faeces. The ribosome decides by the mechanisms I referenced.

@GregThatcher I hope I now understand your confusion. DNA is long. X = "AUGCUGAC" will always have other sequences around it. If there is another 'AUG' before the X sequence it can be read as either "'...'AUG'CUG'...,...'UGC'UGA'... or  ...'GCU'GAC'" depending on the reading frame as explained in Joshua's answer. IF translation initiation happens at the 'AUG' of the X, there is only one possibility: AUG, nothing will be truncated.

I understand now, thanks @dtadres.  It sounds like the Rosalind.info question was written in a confusing way.  They probably shouldn't have used a sample sequence starting with "AUG", when they meant that that particular "AUG" occurred after another start ("AUG") codon.

Question's link  "this ORF problem on Rosalind.info" doesn't seem to be valid? It seem last comment by Greg Tatcher answers the question. Probably it's in the "can", indeed. I bet It's about the theorem that there are 3 and only 3 possibilities to frame, nothing more implied.

Tl Dr: In the rosalind example they are showing the 3 reading frames that stem from the definition of a reading frame(non-overlapping triplets), not an example of open reading frames. Open reading frames are non-overlapping triplets between a start codon and a stop codon.
Its important to step back and understand what is meant by reading frame first.  It has been determined experimentally that translation occurs in non-overlapping triplets.  That is to say that if the ribosome starts reading at position n it will translate n, n+1, and n+2 into an amino acid, then it will start at the next non-overlapping position which is n+3.  For example, in the sequence: ABCABCABCABC if you start at A it will read ABC ABC ABC.... But if you start at B you will have an equally valid reading frame by the definition of a non-overlapping triplet and it will read BCA BCA BCA.  If you start at C it will read CAB CAB CAB.  What would happen if I start at the next A? ABC ABC ABC... See how you are back in the first reading frame?  No matter how long a given sequence it will only have 3 reading frames.
Why does that matter if they all start at an AUG?  You don't know which AUG translation starts at.  Not all AUGs are actually used as the first codon in translation, in fact, most are either internal to a translated protein or not translated at all.  An open reading frame is any sequence starting from an AUG to a stop codon.  An open reading frame can be within another open reading frame. E.g: AUGCTAUGGCGAUGUUAGAUGA. All of the valid open reading frames are:
    AUGCTAUGGCGAUGUUAGAUGACUAACUAA

    AUG CTA UGG CGA UGU UAG
         AUG GCG AUG GUU AGA UGA
               AUG UUA GAU GAC UAA
                      AUG ACU AAC UAA

What do you mean by "triplet pair"? It is a term that I have  never encountered and does not come up in a Google search (except in its chemical meaning) even with DNA appended to the search term. It seems to me that it is incorrect.

Not sure why i put that.  Edited.

A shifting of the reading frame downstream of a given point can occur with either an insertion or a deletion of a nucleotide.  I encourage you to pick a point after aug in my hypothetical sequence and add one nucleotide (A U G C) and see what happens when you group them into codons, then add one more and then another after that.  A change in the reading frame can cause the ribosome to encounter a very early stop codon and produce a non-functional protein. A great early experiment by (Brenner et. all, 1961) carried out this experiment inducing point mutations in viruses.

http://www.ehu.eus/biomoleculas/proteinas/pdf_doc/genetic_code.pdf

Basically one insertion/deletion shifts the reading frame and at some point downstream of that a stop codon occurs far too early.  An additional insertion/deletion (++ or --) it shifts reading frame to the third one and remains disabled.  If you add one more (+++ or ---) the reading frame is back to the original one and functionality reemerges.


text:
How to preserve tissue DNA without using formalin?
Except using formalin to preserve human corpse for autopsy. I heard from the news that technique damages the DNA in the organs
Question:
Suppose corpse will be investigated next by another juridical unit
Do we have any other techniques which are better than this?
For example like freezing in the fridge. Because police office needs all above questions to complete his case.

Welcome to SE Biology. I think this question is off-topic as it's clearly not about biology. I don't think there should be an autopsy tag.

@Michael_A I got it. I just update my question to be more focusing on DNA preservation.

you may want to look into actual police preservation techniques, formalin is only used for certain organs after removal in special circumstances, not the entire body nor all samples.

I'd suggest removing all mentions of investigators and murder; it distracts from your title question about preserving DNA without using formalin. You have provided three numbered questions that an investigator might want to answer but 2 and 3 are not about biology.

@Michael_A I have updated my question and remove 2 and 3 out because it beyonds the scopes of SE Biology


text:
What kind of mushroom is this, and is it edible?

I found these growing on the side of some trees (mostly birch) in my local forest in Gothenburg, Sweden, and was wondering if you could help me with identifying them.
I think they smell of aniseed however my wife thinks they smell of farm animals!
The spore-trace turned out white, if that aids with identification.

Might be oyster mushrooms; look them up. Generally one learns to identify some edible mushrooms and then looks for them. Picking mushrooms and then trying to determine if they are edible is not recommended.

Thanks for the help blacksmith37. Just out of curiosity, why is that not recommended? And by whom is it not recommended? I've always found it more helpful to learn identification with a specimen at hand.

I have several "mushroom" guides , don't remember which ones said it. Pick and examine them with the prospect that the same species may come back in the same spot when you are very familiar with them.

Thanks blacksmith37, I shall keep that in mind. The spore-trace turned out white, so I think you may be right in calling the oyster mushroom.


text:
Want to know which insect it is? I often found it in washroom. Is it dangerous and how to control it
This insect found in the wash room.  Its so fast and disappears once someone enters the washroom.  Is it dangerous?  Whats name of this insect.  How to control this insect

Could you please edit your question and add your geographical location and the size range of this animal? Can you estimate the number of legs?

That is a house centipede, Scutigera coleoptrata https://en.wikipedia.org/wiki/Scutigera_coleoptrata
They are harmless, unless you are a cockroach or termite. People find them unpleasant and creepy, because they run fast, but they are predators that prey on pests in your home.
https://www.familyhandyman.com/pest-control/heres-why-you-should-never-kill-a-house-centipede/

They do seem to have a rather nasty bite. Maybe it is nice to add that to your answer?

No they don't. It may be possible that 1 encounter in a million ends up in a bite, when people are handling them, but I have never heard of it. People have an irrational fear of these completely harmless creatures, and the last thing you would need to say it that there is a minuscule chance that a huge one could bite if you put it in your hands and squeeze it.


text:
Protein electrophoresis
Three proteins A, B and C of equal molecular weight are being investigated in a study. They contain six, four and four cysteine residues respectively. Only Proteins A and B were treated with β-mercaptoethanol (which reduces disulphide bond) and heated in boiling water bath for a few minutes. Which of the following is expected in the SDS PAGE gel run?
a. Protein C will move fastest.
b. Protein B will move fastest.
c. Proteins A and B will move at the same speed but faster than C.
d. Proteins B and C will move at the same speed.
Before knowing the answer the I thought the answer would be b. Because as Protein A has the most no. of amino acids so it will be behind Protein B and C for sure. And for protein B and C, as Protein B has been in a reducing environment it will not form disulfide bridges but Protein C will, so it will be billore and hence will be behind Protein B. So B will be fastest?
But the answer key says C, I am not really sure how?
So the answer is C . Before knowing the answer I thought the answer would be b. Because as Protein A has the most no. of amino acids so it will be behind Protein B and C for sure. And for protein b and c as Protein B has been in a reducing environment it will not form disulfide bridges but Protein C will so it will be billore and hence will be behind Protein B. So B will be fastest? But the answer key says C

Welcome to Biology.SE. Please note that [tag:homework] questions are only on-topic here, if you show that and how you have tried to answer the question yourself. We'll gladly help you with understanding a problem, but we won't just answer it. Please add your own try to answer this question.

I did try it. Sorry I am new to stack exchange. So the answer is C . Before knowing the answer the i thought the answer would be b. Because as Protein A has the most no. of amino acids so it will be behind Protein B and C for sure. And for protein b and c as Protein B has been in a reducing environment it will not form disulfide bridges but Protein C will so it will be billore and hence will be behind Protein B. So B will be fastest?    But the answer key says C

I've made an edit to add your description to the answer (people won't always read the comments, so it's better to update the question), you can accept that edit (I think?) or also add something by yourself.

The problem statement says all the proteins have the same molecular weight but does not say how many amino acids they have.  It does say how many cysteine amino acids each has, but not how many other kinds they have.  Cysteine forms disulfide bonds, holding bends in the protein structure.
BiteSizeBio says:

SDS is a detergent that is present in the SDS-PAGE sample buffer where, along with a bit of boiling, and a reducing agent (normally DTT or B-ME to break down protein-protein disulphide bonds), it disrupts the tertiary structure of proteins. This brings the folded proteins down to linear molecules. SDS also coats the protein with a uniform negative charge, which masks the intrinsic charges on the R-groups.

So the point to SDS-PAGE is to have proteins migrate in the gel according to molecular weight without regard to the natural charges carried by the various component amino acids.  The three proteins should thus migrate at the same rates in SDS-PAGE (not A being slower than B and C, as OP thought).
However, protein C is not treated with β-mercaptoethanol (B-ME) which is an important part of SDS-PAGE, so it retains the disulfide cross-links and thus is not a linear string of amino acids.  Hence C will migrate more slowly than A and B, and the expected result is as stated in choice (c.).


text:
What industry job am I qualified for with a PhD in virology?
I'm considering applying for a PhD studying innate resistance to HCV. I enjoy research but I would prefer to have a stable job, instead of moving from contract to contract and writing grants to ensure that I get more funding.
Would such a PhD enable me to transition into industry? What roles would I be eligible for?

I am not sure if your question should be in Biology S.E. I feel Academia S.E. might be a better place. In addition, it seems you have a preconceived idea of what work in Academia/Industry looks like. I found myself in the exact same situation once and went for the industry. All I would say is that this old adage of job security and higher wages in the industry DOES NOT necessarily hold up in the Life Science industry. My recommendation: Do what you feel passionate about (research/money whatever you want), research companies in-depth (e.g. Glassdoor, salary surveys) before applying.


text:
Does osmosis require a protein channel?
Earlier today, I undertook an exam which featured a question regarding the stickiness of mucus in a person diagnosed with CF's. We had to explain why they had stickier mucus than a 'normal' person, given that CF changes the protein channels used for chloride ions to move through osmosis. This confused me, becuase I thought osmosis was through a permeable membrane, and active transport used a protein channel. I have googled it and I have been proved neither wrong nor right.
Basically, I want to know if osmosis requires or uses a protein channel, or the exam board wrote the question wrong and should have put active transport instead.
(Sorry for the waffle, I just felt some clarification is needed)

Normally, epithelial cells of mucous membranes express a chloride ion channel that allows movement of Cl- down its electrochemical gradient and out of the cell. This increase in extracellular electrolytes draws water out of the cells by osmosis, hydrating the mucus.
In cystic fibrosis, this protein is defective, most commonly caused by misfolding and subsequent degradation. Cl- cannot diffuse out of the cell and thus water is not drawn out, leading to thick mucus.

...given that CF changes the protein channels used for chloride ions to move through osmosis.

Water flows by osmosis, not ions.

I thought osmosis was through a permeable membrane...

Osmosis does occur through permeable membranes, but large, bulk flow of water can be mediated by protein channels called aquaporins. Read more here.

...and active transport used a protein channel.

Active transport of solutes does use protein transporters, but they are not strictly "channels": "channel" is the term used for passive transport, also called facilitated diffusion when a channel is involved.

I hope my edit is okay; I usually try not to edit peoples' posts for content but I thought a little clarification was important.

@BryanKrause How dare you?! But actually, thanks.

To my present knowledge, osmosis will occur wherever there is a solute concentration difference across a membrane permeable to the solvent.  It does not require a protein channel.  Not all cells have aquaporins yet all cells have to control their interior concentrations.  Water can traverse the cell membrane by moving through the phospholipids.  This appears to be the most common form of osmosis in very small microorganisms.  My source for this information is an article which I found online on Jan 10, 2019, Verkman A.S. Aquaporins, Current Biology, 2013 January 21, 23(2).  The url is ncbi.nlm.nih.gov/pmc/articles/PMC(3590904)  I realize your test is long past, but for anyone looking for an answer to the same question (as I was) I hope this helps.


text:
Can someone explain what exactly each score of the BLOSUM62 matrix means?
The descriptions that I've found say it's the log odds ratio (observed/expected) where expected is the assumption that there is no correlation between amino acids.
I'm slightly confused as to what this means? Do we have a database of sequences and if there are 10 A's out of 1000 amino acids is it's expected simply 10/1000 * sequence length for all sequences?
What is the observed? Is the observed different for every sequence so there is a different BLOSUM matrix for each sequence? And can someone explain how this table represents 62% of "kept identity"?
Sorry if these questions seem nonsensical or vague, I'm not of a biology background.

From your bio you appear to have an interest in computing science and mathematics. I am not sure that the answer to this question is mathematically complex (although it is outside my sphere) but it appears quite extensive and may not be suitable for anyone who understands it to present here. For that reason I give you a link to an account I found on line. If someone wants to present an introduction in an answer fine. Likewise if you are still not clear how the blocks are selected (that's the easy part) say. http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf

@David Thanks! This is pretty much exactly what I was looking for. Quick question on expected freq though. Is each sequence given its own BLOSUM scoring matrix and the expected freq is generated for different profiles of proteins?

I have voted to mark this as a duplicate and have modied the overlapping question and my own answer to it to take into account the specific concerns of the Poster her. I think that this is the best way of deal with this. Anyone who wishes to add or extend an answer to the previous question is, of course, free to do so.


text:
What is the proper pronounciation of the scientific name of the ground elder / Aegopodium podagraria?
A audio sample would be great. As a kind of bonus: I would appreciate a kind of database, which contains a lot of botanical plant names.

I'm voting to close this question as off-topic because  it is only about language/pronunciation, not biology. Also scientific species names are pronounced very differently around the world. The only "proper" pronunciation would be the original latin/Greek, but then this is a question about those specific languages.

@fileunderwater for me it is part of biology when you are able to communicate in a proper way to the community. It's like asking for information around biology, like literatur. And I think the probability that question got be answered, is higher in biology.stack exchange as in english- latin- or oldgreek.stackexchange. proper means for me that somebody can understand, to get a idea how it sounds like. thanks for your thoughts.

Here is a american database which offers sound samples for a lot of scientific plant names.

for me the question is now answered. and i will close in 2 days when stackexchange allow me to do. but anyway other sources are still welcome.


text:
How to generate simulated mass-spectrometry data for phosphorylated proteins?
I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are phosphorylated. Could you kindly tell me if there is any good software application to help me do that?
Also, how can I include in the input file (FASTA) that there are 10 modification sites on the protein sequence?
What are the parameters required to be set for top-down and bottom-up MS separately?

I know this is a two years old question... but I recently developed a web application which could be useful for you:
Prot pi
The Protein tool lets you simulate the mass spectrum of the intact protein, while the Peptide tool gives you the fragment ions of peptides. Modifications can easily attached to every site you want.

Have a look at PeptideMass, you can choose to use the "post-translational modifications" option that will output the masses of phosphorylated (among other modifications) peptides.

For peptides (bottom up) mMass accepts a sequence of interest and phosphorylated tyrosine can be specified as a modification after that. The program also performs in silico enzyme digests and in silico MS/MS fragmentation.
There are other tools that attempt to accurately mimic the intensities of the various fragments that could be generated.
The meaning of the final question is unclear. If you want to know which parameters to set for the in silico analyses you need to use those that match the sample processing and analyses that would take place in the real world. Sample processing and instrument setup are highly context dependent, there's insufficient information to help with those.
Obtaining good quality intact measurements from a protein the size of PDGFR-B would be a significant challenge.


text:
Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?
Why do 60S & 40S subunits make an 80S (not 100S) ribosome and, similarly, 50S & 30S make 70S? 60+40 is not equal to 80, nor is 50+30 equal to 70, so why are the subunits of the 80S and 70S ribosomes named so weirdly? I couldn't come up with any other mathematical explanation.

When a complex mixture of particles undergoes ultracentrifugation, they separate based on their shape and mass due to the force applied by the centrifuge and the counteracting frictional force of the solvent. You can read more about this procedure here. S stands for Svedberg, which is a measurement of the sedimentation rate of a particle. This is given by the formula $s=\frac{v}{a}$ where $s$ is the sedimentation coefficient and $v$ is the velocity a particle moves when an acceleration, $a$, is applied.

One svedberg is defined as exactly 10−13 s. Essentially the sedimentation coefficient serves to normalize the sedimentation rate of a particle by the acceleration applied to it. The resulting value is no longer dependent on the acceleration, but depends only on the properties of the particle and the medium in which it is suspended. Sedimentation coefficients quoted in literature usually pertain to sedimentation in water at 20°C.

A 1S particle, for example, would move at 10-13 m/s when an acceleration of 1 g is applied (ignoring diffusion).
What's important to realize is that the sedimentation rate of a particle depends not only on its mass but also on its shape (among other things) since its cross-sectional area determines the effective frictional force it experiences.
When this was done with E. coli extracts, peaks were seen at 32S, 51S, 70S and 100S, depending on Mg2+ concentration. The researchers concluded that the 32S and 51S peaks were components of the 70S peak and that the 100S peak was a dimer of two 70S particles. They also determined that the mass of the 50S particle was about double the mass of the 30S particle which, together, added up to the mass of the 70S particle.

Svedberg unit means 10^-13 sec.... So that means 70s will take 70×10-13 seconds to settle down?

@roxaite I've edited my post to answer your comment.

The other two answers give nice detail, so I want to give a bit more mathematical answer here.
First, the S you are talking about is Svedberg units (of sedimentation coefficient, named after Swedish chemist Theodor Svedberg), used to characterize the behavior of a particle in sedimentation process, especially centrifugation. One svedberg corresponds to exactly 10-13 seconds (see other answers for more details).
Now, lets begin with equations. Sedimentation coefficient is written in equation as:
$s = \frac{v_t}{a}$
where $v_t$ is the terminal velocity. Terminal velocity of a particle in a given medium is constant because the force of gravitation (or centrifugation) is cancelled by the viscous force of the medium. In such case, terminal velocity is calculated as ratio of centrifugal force to the viscous resistance (from Stoke's law) and its equation becomes:
$v_t = \frac{mr\omega^2}{6\pi\eta r_0}$
Also, centrifugal acceleration:
$a = r\omega^2$
Putting the value of $v_t$ and $a$ in first equation:
$s = \frac{v_t}{r\omega^2} = \frac{m}{6\pi\eta r_0}$
As you see, although sedimentation coefficient is the ratio of terminal velocity to centrifugal acceleration, it does not depend on either of them! Now, all other things are constant, and mass would add linearly. So why does the value of $s$ decrease? It is because of non-linear addition of $r_0$ (radius). See the diagram below:

It is clearly visible now that the subunits don't just mix into each other (like two oil droplets joining to form one bigger droplet), the small subunit fits on the large subunit (real shape does vary, but roughly the shape is like this). This makes the average value of $r_0$ of ribosome larger than the sum of average value of $r_0$ of subunits i.e. $r_0 (small) + r_0 (large) < r_0 (ribosome)$. This makes the overall sedimentation rate a bit lesser than expected (remember that $s \propto \frac{1}{r_0}$). I hope this makes the concept more clear.
References:

Sedimentation coefficient - Wikipedia
Difference between 70S and 80S ribosome

@GerardoFurtado I think all 3 answers complement each other quite nicely; it's always good to have different explanations.

@canadianer bringing back the traditional way of answering, something SE missed a lot ;)

@gerardofurtado you mean I need to incorporate more details in my answer? If I do, who would want to scroll down and see other answers? :P

@gerardofurtado I've added all the details I could. What if people say "wow, these 3 answers explain everything so beautifully...here, have my upvote, all of you"! ;)


text:
Which is a good methodology to find out a domestication process?
I just started with my course in genomics and I'm working with domesticated animals (cows, chickens, pigs, etc) and I would like to know which methodology is better to trace the process of domestication since the origin of these species. I'm thinking of using SNPs of a particular gene to identify punctual traits that were selected, but also I was suggested to do a complete screen analysis and identify all the polymorphisms present in each variant and compare them with the species that gave them origin.

Yes, everyone use SNPs today for such analysis. Some RADseq is probably the way to go.
Detecting selection is not an easy task as many technics exist which differ by their assumptions and by the applicability. You should probably try to find papers having done the same type of analysis with the same types of data and eventually talk with authors. Your lab might already be experienced in such analysis.
What test to detect genomic signatures of selection? might help but the suggested algorithms are mainly for the analysis of within species variation. Procedure like mcdonald-kreitman test and other more advanced methodology to detect selection over a phylogeny (such as OUWIE if you have phenotypic traits) might be of interest. You could also simply use some rank tests when having many independent domestication events. The exact methodology you end up using very much depend on your data (how many independent domestication events do you have for example, do you have phenotypic traits, ...).

compare them with the species that gave them origin

Do you really have sample of the ancestor? Most of the time people simply consider a non-domesticated descendant of the non-domesticated common ancestor. Don't make the mistake of considering an extant lineage as if it was a descendant. This extant lineage evolved too!


text:
Where can I find a diagram of cortex connections?
Has anyone come across a diagram (2D, 3D, maybe even interactive) of the connectiontions between cortex regions? Especially, the diagram should display the strength and direction of those connections (but not every single axon). I am interested in information like "Brodmann area 7 receives heavy connections from area 1,2,3 and 17,18", displayed in a neatly arranged way.
If there is no diagram that fulfills my need, is there another source of information, like a table, where I can find that sort of information?
Edit: After some more research I found this paper which contains some interesting diagrams in its appendix. However, this paper does not describe the human brain.

http://www.humanconnectomeproject.org/ might be a good point to start, I have not found a table of the sort you asked for, though.
I don't know whether this information was ever put together in the systematic way you are asking for. At least I never came across it in any of the lectures I've had or conferences I've gone to. For most contexts, it is not just important to know whether two brain areas are connected, but how exactly. Which cell types? Which cells exactly? etc. At this point, the information becomes too complex to be contained in one table. Thus: the connectome project.

Haha that's coool ! My new science project... Pickle brain in paraffin, then robotically slice it into micron thin slices which are imaged with an Epson Perfection scanner at 9600 DPI (2.6 microns).  write a simple computer program which can scan the data and compile a complete neural map of a brain in 3D space so that it can be viewed transparently by a computer in every dimension. every slice would take 3 minutes so that's 200 days to measure a human brain at 2 microns and 10 days for mouse brain. obviously it would not be in vivo.time to buy an epson and pickle a sheep.

The Human Connectome Project looks at imaging the functional pathways in the brain and might include some answers to your question:
http://www.humanconnectomeproject.org
Here is an article in Nature about the project:
https://www.nature.com/articles/mp201792


text:
Punnet Square for Genotype Probabilities
I'm a computational physicist by trade, and today I was working with a student that is coding a simulation that requires the interactions of different genotypes to determine which phenotype will be expressed. This student drew a Punnent Square like so:
$
\begin{equation}
\begin{matrix}
& O & Y \\
\_ &\_ & \_ \\
Y& |YO& YY \\B &|BO & BY
\end{matrix}
\end{equation}
$
and then stated that each genotype should have a 25% probability of being expressed. I remember learning this as well in highschool bio, but since finishing my Bachelor's in Physics (with some focus on complex adaptive systems/chaos theory) I am a bit skeptical that biology really obeys the probabilities of the Punnet Square. Are there examples in biology where the probabilities of the Punnet Square are clearly broken?

Mendelian inheritance is not governed by laws. Mendelian laws are statistically inferred. In reality, by chance it will never be 25% exactly and mutations may mess things up too.

Our germ cells are haploid, while our somatic cells are diploid. The diploid cells of a child result from the fusion of a paternal haploid germ cell and a maternal haploid germ cell. When these germ cells are generated during meiosis, the paired diploid chromosomes of each parent (which they in turn received one of from each parent) are randomly segregated such that for a given chromosomal pair there is an approximately equal chance of a given germ cell containing either member of the pair independent of the what other chromosomes it receives.
In the case of a single gene with a single copy on both the maternal and paternal chromosomes, the Punnet Square accurately estimates the probably of inheriting each possible genotype. (50% chance of getting one of two alleles from dad * 50% chance of getting one of two alleles from mom). In the case of multiple genes on different chromosomes, the 50% chance of any given allele still holds, as all the genes segregate independently. The accuracy of the Punnet Square fails when genes are sufficiently close to each other on the same chromosome. Genes distant from each other on the same chromosome still segregrate independently due to a high level of recombination events between chromosomes in meiosis I, but genes in close physical proximity no longer segregate independently. The closer two genes are physically the more they tend to co-segregate. This tendency is reported empirically as a "distance" in centiMorgans and is related to physical distance in base pairs (kB or mB) but is not completely proportional to physical distance due to the existence of recombination "hot spots."
It's important to note that is accurately predicts genotypic ratios, but not necessarily phenotype. Phenotypes can be less than 100% penetrant, can cause embryonic lethal, epistasis, etc. Such that the observed phenotypic ratio does not match the predicted ratio. (For example, if YY was known to be 100% embryonic lethality, live births -> observed phenotypes instead be expected at 1/3 of each of the remaining genotypes. If Y was instead phenotypically dominant (one copy of Y determines phenotype), then 75% of children would be expected to be phenotypically Y (genotypically, the Y phenotypic children would be expected to distribute evenly between YO, YY, BY).

The clearest example of a Mendelian exception (in my opinion) are lethal alleles.
In your example, let's say that the $YY$ phenotype causes a fatal phenotype in utero (in humans, Achondroplasia is fatal for homozygotes). Your Punnett square might instead look something like this:
$
\begin{equation}
\begin{matrix}
& O & Y \\
\ &\_ & \_ \\
Y& |YO& ☹ \\B &|BO & BY
\end{matrix}
\end{equation}
$
This would also change your observed population proportions, rather than seeing the typical ~25% (1:3 ratio) you'll start to see a ~33% (1:2 ratio) population segmentation, which is a good indication that something fishy is going on. This can happen with both dominant (Achondroplasia) and negative alleles (Hypophosphatasia). In the case of a dominant allele like Achondroplasia, heterozygotes show a phenotype (dwarfism) but only the homozygous genotype is immediately fatal.


text:
What is the best way to block cigarette smoke from the body?
Would it be better to hold your breath after smelling the presence of it or quickly inhale and exhale to get rid of it in your system(body)?
EDIT:
Changed from carbon monoxide to cigarette smoke.

Carbon monoxide is odorless, so you won't be smelling it unless it's mixed with something else. Exhaling won't remove it from your system because it binds to hemoglobin.

You don't smell carbon monoxide in cigarette smoke. It's odorless. (And not exactly the part of cigarette smoke I would be worried about.)
You smell the other components of cigarette smoke. Which are not odorless.
Holding your breath and getting out of the smoke seems the way to go. Even better would be exhaling, then holding your breath until you are clear.[1]
Carbon monoxide, as well as other components of cigarette smoke like nicotine, are very good at getting into your blood stream quickly. Plus, when at rest, we inhale / exhale at only a fraction of our lung capacity. By (deeply) inhaling (your alternative course of action), you would just get more of the smoke into your lungs than you already have.

[1]: The trick with holding your breath is of course that, if you run out of breath while still in the middle of the smoke, you can't help but inhaling deeply...

What is your response to the answer given by @CactusWoman  above ?

@Viv: What do you think I should respond? CO is odorless, I said so myself. Exhaling won't remove any CO already in your blood, that's true as well. But exhaling will remove (most of) the smoke still in your lungs. Besides, the generic advice would be a) a single lungfull of cigarette smoke won't kill you, and b) don't go where there is cigarette smoke if you are so worried...?!? Or is there a different, unspoken question underneath all this?

I do fully agree with your answer that holding your breath is a good option. But the answer of @CactusWoman of the chemicals binding to hemoglobin made me more intrigued that your "better" option of exhaling would clearly not make much difference. So I was pondering if there an actual better way than your general advice/your answer.

@Viv: As I said, exhaling is for getting rid of what's in your lungs, not yet in your bloodstream. Not exhaling gives those molecules more time to cross over into your bloodstream, while at the same time lengthening the time until you need to inhale again, so it's a situational trade-off. Since you can't do an ad-hoc chemical scrubbing of your blood, exhaling while getting into fresh air is your best bet.


text:
Where would the majority of the Indoleacetic acid (IAA) be in the shoot and what would the effect be?
If I propose that a plant is 2D and then a light source was shone on both horizontal side of the shoot, in which direction would positive phototropism occur (or would positive phototropism occur at all?).
I am presuming that light intensity is the same and there has been no modification of the tip.


text:
Does vitamin C decrease after reacting with oxygen free radicals?
From the research that I have done, I know that antioxidants such as vitamin c donate electrons to oxygen free radicals and effectively neutralize them. They themselves do not become free radicals as they are stable in both forms.
So, would it be correct to say that after the vitamin C is oxidized(giving electrons to free radicals) so much that it can no longer give any more electrons(not sure what the actual limit is):

What happens to vitamin C (does it get broken down and therefore
decrease)
Is it any useful in destroying free radicals?

Correct, vitamin C (ascorbate) acts by donating 1 electron to a free radical (reducing them to a stable compound with paired electrons), and is thereby itself oxidized to semidehydroascorbate. This is actually a radical itself, but can be reduced back to ascorbate by thioredoxin reductase or cytochromes, using NADH or NADPH as the reducing agent. A pathway diagram with references is found here.
So to answer (1), ascorbate is continuously recycled after neutralizing free radicals, and is therefore not consumed to any large extent. Therefore, vitamin C is only needed in the diet to replenish the small fraction that is lost from the body (about 1--3% per day; see this book).
And yes, vitamin C is very important in defense against free radicals; it is considered the major water-soluble antioxidant in humans.


text:
List authors (scientists) by various attribute
Is there an easy way to list authors of biology articles by

University
country
number of published articles
sum of citations of all articles he/she wrote
fields of study (population genetics)
...

For example, I want to know who are the 10 most popular/cited authors in population genetics in UK's universities. How can I achieve such search?
For example, do WebOfKnowledge provide such tools?
Please, let me know if this question should be asked on another SE website.

This is not a direct answer to your question, but you might be interested to check out Scholarometer, which aims to compare top researchers within and across scientific fields. This is based on a standardised h-index with data pulled from google scholar.

I don't think that you can do this systematically in Web of Science but you can do it in an exploratory way.
Initial search: Topic - "population genetics" + Address - UK
sort by Times cited is probably more useful than the default (newest to oldest)
open Authors in sidebar - this is a list of the top 100 names
can refine to the top 10, or whatever
For example consider Brian Charlesworth:

Open an item with his name in the author list (he has some single author items)
Click on the link of his name to see his papers
Click on Create citation report to see charts of published items per year and citations per year

It may be that you know all this.


text:
Standardized Selection Ratio (SSR)
In this article the athors used the Standardized Selection Ratio (SSR) in order to infer what is the preferred host (anemone) of anemonefish.
Here is a quotation coming from their methods:
  The “preferred host” of anemonefish was assessed calculating the “Standardized
Selection Ratio (SSR)” (values between 0 and 1) (Manly et al. 1993). Manly’s standardized
selection ratio represents the probability that an individual will use a particular habitat
type, taking into account the different resource availability. For each anemonefish species (i) inhabiting an anemone species (j), SSR was calculated as:

$$SSR = \frac{wi}{\sum{}{wj}} $$
where $wi = \frac{oi}{pj}$
    `Oi` is the relative frequency of the anemonefish species i and `pj` the relative frequency
of the anemone species j. Higher values of SSR indicate a strong preference for the
selected resource. The Log- Likelihood statistic (χ2L) (Manly et al. 1993) was used to
check the significance of the observed distribution under a null hypothesis of a random
host choice.

Here is the book they cite (Manly et al. 1993).
Can you help me understanding basically what they did and how they calculated their SSR and p.values. If $wi = \frac{oi}{pj}$ what does wj equals to?

I can see why you might be confused! The authors chose bad notation, since the way they wrote it $w_i$ clearly depends not just on the choice of anenomefish species $i$ but also on the choice of anenome species $j$. And it is not clear how exactly they are performing their sum in the definition of SSR: sum over all possible anenome-anenomefish species pairs or only over all anenomefish species? The former makes sense but is extremely unclear, and the latter doesn't make sense because there's no way to interpret that as a probability that an anenomefish will choose a particular anenome because the sum of the SSR for all the different anenome species would not necessarily be 1, so the probability of an anenomefish species choosing some species of anenome would not be 1!
NOTE: The reference to Manly 1993 was incorrect (you cited a 1995 paper); they actually cite a book: Manly B, McDonald L, Thomas D (1993) Resource selection by animals. Statistical design and analysis for field studies. Chapman and Hall, London. This would probably be the best place to look to get an exact answer to your question. I think that would be the best place to look first.

Thank you! I fixed the problem with the Manly et al book.


text:
What are 'factors' in biology?
My question is what does the word 'factor' mean in words like transcription-factor or nerve growth-factor? What is similar between these different compounds such that they deserve the word 'factor' in their name?
Edit: My confusion comes perhaps from the use of the word 'factor' in statistics, where it refers to a variable that can take on discrete values (e.g., the factor Gender takes on values 'male' and 'female'). Here a different meaning of the word seems to be used.

I'm voting to close this question as off-topic because it is poorly researched. https://www.google.se/search?q=transcription-factor&oq=transcription-factor&aqs=chrome..69i57&sourceid=chrome&es_sm=122&ie=UTF-8

@rg255 - I think it is fine - your (Swedish :-) google result links to transcription factor. This question doesn't ask what a TF does, it asks for the broader interpretation of 'factor'.

I'd still suggests its poorly researched (https://www.google.se/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=biological%20factors) if the OP has done research and asked about what thye specifically don't grasp it would be on topic

@rg255 - you may be right. I'd say it's borderline. The voting system will tell :)

this is googling-based question. I strongly feel this type of questions should not be dignified with an answer. Otherwise bar is pretty low

@AliceD do you think it is OK to create a question for every entry from a dictionary?

I agree this is off topic. There is no special meaning of the word factor here, a dictionary could answer this question (and did). This is about English language usage.

Yeah you guys are right. Vote2close2

I'm voting to close this question as off-topic because of poorly researched

There are many meanings of "factor" in Biology. In the context where you place it, namely bio-active substances, such as hormones and enzymes I would go for the definition given by the Medical Dictionary:

factor [fak´ter] :
  an agent or element that contributes to the production of a result.

Within this definition, a transcription factor contributes to the transcription of DNA into mRNA, and nerve growth factor contributes to the growth and survival of neurons.


text:
Did any dinosaur molt?
Like snakes or lizards, did any dinosaur molt ?
if yes, have we any proof of it ?

Since dinosaurs had either scales or feathers, and both reptiles and birds go through molting, then dinosaurs probably molted too. However, I doubt the skin came off in 1 piece like a snake, but came off in small parts. Since the skin probably wouldn't fossilize well, we probably have no way of confirming any of this.

Snakes and lizards are a different clade of reptiles altogether (they are Squamata i.e. scaled reptilse). Not all reptiles molt.

Richard Prum (the author of Evolution of feathers) says that ornithology is mostly a science about dinosaurs. He insists that dinosaurs were very close to birds, part of them had feathers and these feathered dinosaurs "shed (molt) them as birds of our days do".
Thus, we can conclude that dinosaurs probably possessed at least one molting-like mechanism, while others are the subjects for consecutive investigations.
sources
Moulting tail feathers in a juvenile oviraptorisaur. Nature, 2010.


text:
What differentiates bound antibodies from unbound ones?
When an antibody is bound to an antigen, it can then stimulate a FcR receptor on a phagocyte etc. to respond to the threat. What stops 'free' antibodies from spuriously activating an immune response?
Even if an unbound antibody won't elicit a response, it can still hog the FcRs of expressing cells or cluster around them and degrade the immune system efficiency.
This article seems to imply that being bound to an antigen causes some change in orientation: "their Fc regions point outwards, in direct reach of phagocytes" but I don't really see how its bound state causes that any more than random movement.
It also states

The low individual affinity prevents Fc receptors from binding antibodies in the absence of antigen, and therefore reduces the chance of immune cell activation in the absence of infection

but I fail to understand the logic in that; let there be low affinity, but as much as a bound ab is somehow able to activate the FcR so can an unbound one, unless the bound/unbound state itself affects the affinity, something the article does not explain.

Keep reading further in that section: ”Many low affinity interactions are formed between receptor and antibody that work together to tightly bind the antibody-coated microbe. The low individual affinity prevents Fc receptors from binding antibodies in the absence of antigen, and therefore reduces the chance of immune cell activation in the absence of infection.” Also keep in mind that soluble antibodies are typically present only in response to an infection.

There are many related questions you can look at here.  Bear in mind that simply phagocytosing an antigen is different from "activating an immune response".  The antibody might be expressed in the membrane of a B cell, bind to a mast cell by its Fc region, or be phagocytosed after opsonization, or cause complement fixation, all with different effects.  But note a cell that engulfs unbound antibody cannot present the antigen it didn't bind to. :)

@canadianer Ii had seen that, but it doesn't seem to have any explaining power re. differentiating between bound and unbound ab's. See my edit. Thanks.

@MikeSerfas you're right that there is not antigen to present, but it should still degrade the efficiency of the system by hogging or wasting FcR interactions.


text:
How much nucleoside triphosphate is required to form one peptide bond during protein synthesis?
I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, specifically during the process of mRNA translation.
I've tried to do some research online, but I could not find a reputable source that will say definitely how much energy is consumed in the process. The best answer I could find is formulated based on 'Molecular Biology of the Cell' 4th edition by Alberts B, Johnson A, Lewis J, et al., which is that at least one molecule of ATP is consumed for every peptide linkage. Is this correct?
I've also read on a science forum that the amount of ATP consumed during translation is different for every amino acid, but I could not find a reliable source to back up that claim. Is this true?

You might want to think a bit about the boundary of your question, which parts of the whole process do you want to include. Loading the tRNA uses ATP as well, do you want to include other aspects or just the peptide bond formation? I'm not sure if there's a single value here, as far as I remember there are also elongation factors and other proteins that require ATP/GTP for protein biosynthesis.

I'd agree with the explanation from Alberts et al from Molecular Biology of the Cell - it may see like a lot, but protein synthesis requires a TON of energy.

Duplicate of http://biology.stackexchange.com/questions/34783/atp-required-for-cell-processes

This is an old question, but as it has surfaced again I have cleaned up the title so it reflects the question better.

Although the question shows considerable effort to achieve clarity, the way it is phrased as:

How many molecules of nucleoside triphosphate… [does] it take to release enough energy

still allows ambiguity, as I would not really regard the NTPs involved in protein synthesis “releasing energy”. So let us consider two reformulations of the question, as the explanation of the answers is of more scientific interest than the actual answers.
1. How many molecules of NTP are hydrolysed in the reactions causing the formation of one peptide bond on the ribosome?

Answer = 3

Formation of each peptide bond involves a cycle consisting of the introduction of a single new aminoacyl-tRNA to the A site of a ribosome carrying a growing polypeptide chain (or initiator tRNA for the first peptide bond), the peptidyl transferase reaction, and than translocation of the extended peptidyl-tRNA from A- to P-site. (See, e.g. Berg et al. online — Ch. 29)
1 ATP is hydrolysed in the aminoacylation reaction:
                Amino Acid + tRNA + ATP → Aminoacyl-tRNA + AMP + PPi

1 GTP is hydrolysed in the aatRNA binding reaction catalysed by EF-Tu/EF1.
1 GTP is hydrolysed in the translocation reaction catalysed by EF-G/EF2
No NTP is consumed directly in the peptidyl transferase reaction — the energy for bond formation comes from the ‘activated’ aminoacyl-tRNA.

2. What is the total energetic cost in molecules of ATP for the formation of one peptide bond?
Here one might argue that:

Answer = 4+

The additional ATP occurs if one considers the total energetic cost of the aminoacylation reaction as 2 ATP, not 1 ATP. This arises from the fact that the ATP is hydrolysed to AMP (+PPi) and not ADP. Recycling of the AMP involves first the use of 1 molecule of ATP in the adenylate kinase reaction to produce ADP:
                                 ATP + AMP ⇄ 2ADP

followed by the energy (from membrane ATP synthase) to regenerate ATP from ADP:
                                 ADP + Pi ⇾ ATP

Why 4+? Certain amino acids (e.g. val and ile) are sufficiently similar to one another that the aminoacyl-tRNA synthetases have evolved a proof reading capacity, in which any incorrectly aminoacylated tRNA is hydrolysed. This only occurs for certain amino acids and at a rate that is difficult to determine, so the wastage of the ATP in this manner cannot be calculated precisely.

Actually it depends on the question. Whether you mean to say: How many amino acids are required? Or proteins?
There is a characteristic difference between amino acids and proteins.
Hence the number. Of amino acids can be determined by the following-
If we consider a  protein composed of "n" number of amino acids,
it takes (4n)-1 number of ATP for the translation process.

You might want to add some reference to your answer. Just a simple answer without any citations wouldn't work.

About 5 ATP molecules are required for the addition of a single amino aid to a growing peptide chain.
I found this answer in Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis by Piques et al.:

The addition of an amino acid to a growing peptide chain requires two ATP molecules for amino acid activation and another two ATP for peptide bond formation and ribosome translation, plus additional costs of about another ATP, for error correction and the synthesis of sequences that are removed during protein maturation.

This is plain wrong and phrased in meaningless terms, e.g. "peptide bond formation and ribosome translation". See the chapter on protein biosynthesis in any standard biochemistry text in the last 20 years.

4 ATP :
2 for activation amino acids to bind with specific tRNA.
1 for initiation
1 for elongation to push tRNA to the p site of ribosome

Please give some references and add some details for each step. A figure could really help clarify your answer.

First, during the initiation of translation, a small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine. And then, this process need one molecular GTP, and GTP--->GDP+Pi, which can provide energy for the assembly.
You can find more details in the book Campbell Biology, by Reece, Urry, et.al..


text:
Practical utility of genes responsible for the biosynthesis of a useful compound in a plant
Assuming a woody plant naturally has a valuable compound, say a kind of sterol. During an RNA-seq analysis, almost all genes involved in the biosynthesis pathway of this sterol were identified in the plant. I was wondering what are the benefits of this finding? If this study was done in a bacterium or fungus instead of a plant, the importance of this finding is clearer, at least for me, since these simple organisms can be the factory of valuable compounds by genetic engineering technology. But, what about a woody plant which cannot be engineered and grown in bulk?

Thank you very much for all your comment, Always Confused!

You essentially gave the answer in your question. By identifying the biosynthetic pathway(s) required to create the compound in the plant, its natural host, those genes can then be cloned and transferred into an expression system like bacteria, yeast, or other plant cells like Arabidopsis thaliana to generate larger quantities of the compound of interest than would be possible from harvesting and processing the original plant itself.

Thank you, that's right. However, I'm looking for other benefits of such finding. In fact, this plant has the highest amount of this kind of sterol amongst nut. How can this information be useful, especially in practical science? Please share me any suggestions if you have.

@Mary your original question did not include this information. Please edit your post and add these additional details. I answered the question as it was posed. For what purpose are you seeking this information? If it is for a class or other educational purposes, please read our homework policy. Briefly, you are required to show your previous research and thinking on the matter, not just pose a question and expect it to be answered in full.