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Is it possible to create a restriction map using python?
I have some fragments of DNA from single and double digests using three different restriction enzymes. I'm trying to construct a restriction map of a linear fragment of DNA. The map needs indicate the relative positions of the restriction sites along with distances from the ends.
Can this be done using python at all?
DNA Sizes of Fragments (bp) - uncut DNA = 900
DNA cut with EcoRI = 500, 350, 50
DNA cut with HindIII = 600, 300
DNA cut with BamHI = 400, 300, 200
DNA cut with EcoRI + HindIII = 350, 300, 200, 50
DNA cut with EcoRI + BamHI = 300, 250, 200, 100, 50
DNA cut with HindIII + BamHI = 300, 200, 100

I've updated the description so hopefully it is more clearer

Perhaps pointing in the right direction? Like where to find possible modules that do this? We're not all experts.

I'm voting to close this question as off-topic because this is about programming in python and not really about biology or bioinformatics.

First I'll answer this question on the assumption that you are learning or about to learn python (perhaps because you have heard it's become popular in bioinformatics) and you wish to know whether it can be applied to this problem. The answer is: almost certainly, yes. Python is a programming language of the type that can be used to automate the solution of this sort of problem, just as C, C++, Java, Perl could.
How would you go about it? You would first solve the problem by hand, analyse the logic of your solution and then try to devise a general algorithm based on this logic that can deal with a variety of cases. Then you would code this in python (or whatever). The program would have to deal with inaccuracies in real values of fragment lengths (your data are obviously contrived) and the possibility of more than one fragment of the same length (see below).  If you used python and wanted graphic output you would need to use a library that provides graphics as python does not come with graphics like Java does. I gather there are some. However this is certainly not the easiest of programming tasks for a beginner, as you'll see when you try to analyse the logic of manual solution. And of course the data might be insufficient to provide a unique solution.
However as this is a homework assignment you may also be wanting to find a program to check your answer and perhaps be unsure of how to go about it. I don't know of any packages to do this — it's perhaps not 'cutting edge'. So how to go about it?
What I would do is start with the single digests and draw a set of diagrams for each of the possible arrangements of the restriction sites in each case (pencil and paper work well here). Then I'd look at the simplest double-digest, identify unique fragments that were also present in the single digests and thus not cut by the second enzyme, and again draw diagrams of the possibilities for the pairs of restrictions sites. Be careful; the HindIII/BamHI double-digest doesn't add up to 900, so there must be two fragments of the same size here. When you have all the possibilities drawn out, there is presumably only one final restriction diagram that is consistent with all the data.
On second thoughts, devising an algorithm for solving this general case would be quite a demanding task. If you are starting programming I'd tackle easier algorithms first. And an effective algorithm might adopt a brute force approach rather than the semi-intuitive way we solve these by hand. For example your algorithm might generate all possible maps for each of the the three single digestions, and then generate all possible maps for the double-digestions, together with a calculation of the size of fragments the double-digestions would generate. These would be compared with the size of the actual fragments from double-digestions, eliminating those possibilities that don't fit. Coding it would involve writing methods/functions (or whatever they are called in python) to generate these maps, storing the coordinates of the sites in a data structure such as an array, and writing other methods to make comparisons etc.

Thanks for the advice David. It was a homework assignment and I did manage to figure it out. My inquiry to whether it was possible using python is one of interest as I've just started learning it

OK. I'll edit my answer to take account of that.

Python has good string functions, as do Java and C++. You could make a list of restriction enzymes, probably a map or hashmap. Then you load your DNA sequence as a string and iterate through the list of enzymes, searching for the restriction site in the DNA string, and returning the position of the site in the DNA sequence. If the strings do not match, a -1 will be returned. So if you just want a list, you can print to console or a text file. If you want an image, you need to make a list of restriction sites, with enzyme type and cut location, then use pygame or something to draw the map.

Drawing the map isn't hard either. If linear, the DNA of B bases is a line of P pixels long. So the restriction site at position b is drawn at pixel p where p = P * b/B. When circular, you'll need to calculate the pixel from an angle, where the angle is 360 * b/B.

I agree with the previous answer. You can certainly write a solution in python, but have to formulate it as an algorithm first. Doing so will enable us to suggest an actual solution.
Also, I wanted to suggest that posting this questions on a forum with bioinformatics focus (biostars.org) may yield better feedback.


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Is viral single-stranded RNA in the absence of reverse transcriptase infectious?
In a medical microbiology textbook I'm reading (Murray et al, 1994), the authors state the following:

The retrovirus genome has a 5' cap and is polyadenylated at the 3' end. Although the genome resembles a messenger RNA (mRNA), it is not infectious because it does not encode for a polymerase that can directly generate more mRNA. The genome consists of at least three major genes that encode for the enzymatic and structural proteins of the virus: gag (group-specific antigen), pol (polymerase), and env (envelope). At the end of the genome are long terminal repeat (LTR) sequences

From this, I interpreted that because viral RNA doesn't encode an RNA polymerase, it is not itself infectious. However, if a cell were to be injected with retroviral single-stranded RNA alone, wouldn't this RNA be translated into proteins (including reverse transcriptase) as if it were normal mRNA into a protein? If this were correct, then the single-stranded RNA has all the information in itself to propagate the virus. Single-stranded RNA needs to be reverse-transcribed into the host's DNA before being transcribed into mRNA that can be translated.
Is there something different between viral RNA and the mRNA transcript that makes one translatable and the other not?
Source: Murray, Patrick R et al, Medical Microbiology (1994), Second Edition.
EDIT/UPDATE
I contacted the author of this chapter (Dr. Ken Rosenthal) and gained some more insight into how this hypothetical (injecting plain retroviral RNA into a cell) would play out. His answer is that yes producing new viruses possible but not probable. The reasoning for this is as follows:

The main reason that a new virus would likely not be created is that for the genome to make a new virus, reverse transcriptase is needed. Without reverse transcriptase, cDNA can't be made. Suppose that a ribosome was able to make reverse transcriptase with naked retroviral RNA and this newly made reverse transcriptase stayed near the ribosome. It would have difficulties making new cDNA from the original RNA template. One of those challenges is that cDNA synthesis needs a specific primer on reverse transcriptase.
The translated retroviral RNA would likely be degraded due to their finite lifespan in the cytoplasm.
There would need to be enough viral proteins translated to form a capsid. This would be unlikely considering the lifetime of the RNA in
Even if there were enough proteins in the cytoplasm, these proteins would then have to remove the RNA from the ribosome to encapsidate it. This is also unlikely.

Considering this, the microinjection of naked retroviral RNA would be an inefficient process to cause an infection.

@F16Falcon — Could you indicate what relevance the article you cite has to this question?

@F16Falcon — But retroviruses do not possess self-replicating RNA and depend on DNA for their replication. So as far as I can see the article — which is on "The RNA World" — however interesting, would seem irrelevant to the poster's concerns.

So now compare the author's response to my answer. Despite my current score of –1, I do believe I was right. Perhaps you might consider giving credit where it is due and accepting it.

Thanks. It’s the principle not the points (which I have little need of.)

Sure thing, though I disagree with you on one particular point (namely that I shouldn't focus on hypotheticals and "injecting" RNA). I find hypotheticals a useful way to find interesting questions. All the best David.

As far as I can understand, the poster is concerned about the statement:

Although the genome resembles a messenger RNA (mRNA), it is not infectious because it does not encode for a polymerase that can directly generate more mRNA.

I find this a somewhat unfortunate aside as the infectivity or not of viral RNA “injected into a cell” has no physiological relevance, and would advise the student to focus on the essential details of the actual viral life cycle rather than on this sort of thing.
However, the point it would seem that the poster and the other answer misses is that numbers count. A virus (or viral RNA) needs to generate enough progeny for infection to overwhelm antiviral defences. This entails there being sufficient mRNA generated from the genomic RNA (or DNA) for translation into protein.
In the case of ‘normal’ RNA viruses (i.e. non-retroviruses), this involves an RNA-dependent RNA polymerase, which has to be virally coded as the host cell does not have such an enzyme. Retroviruses, however, produce multiple mRNA molecules from an integrated DNA genome (integrated through the RNA-dependant DNA polymerase — reverse transcriptase) by using the cell’s DNA-dependant RNA polymerase, not from replicating the transcribed mRNA.
All viruses rely on host protein synthesizing systems to translate their mRNAs. But a single retroviral RNA that can act as both mRNA or (part of) the genome can only generate enough coat proteins etc. to encapsulate it (or enough reverse transcriptase to reverse copy it). A situation unlikely to cause retroviral RNA to be infectious in this hypothetical situation. I imagine it is this that the authors of the text have in mind.
The student of this subject would do well to distinguish the different transcriptional enzymes involved in viral replication and learn to refer to them by their full names.
Reference: Coffin et al. Retroviruses (1997), available on NCBI Bookshelf

RdRP is virally encoded, but is not necessarily carried in a virion. Thus, the replication of many positive-strand RNA viruses literally starts with translating their genome on a ribosome and thus generating RdRP. In other words, such an RNA introduced to a cell is literally infectious - which seems to be the premise of the question.

@Vadim — "many positive-strand viruses". But not retroviruses which do not encode an RNA-dependent RNA polymerase, which was the premise of the question.

In other words, what counts is not the numbers, but how virus replicates itself and what genes it carries. Note that RdRP is not a precondition here: if retroviral RNA encoded the reverse transcriptase, the integrase, and the other proteins necessary for initiating the retroviral replication cycle, it would be still infectious.

@Vadim — So you disagree with the authors of the text and regard retroviral RNA as infectious?

I disagree with your explanation of why it is non-infectious.

@Vadim — There may be other reasons, but the authors of the book that the poster is trying to understand say that it is because of lack of a replicase or replication, from which one draws the inescapable conclusion that they regard the generation of many copies of a viral RNA as important for infection. So they think numbers are important, and it needed someone to explain that to the poster and those other six people who share his confusion.

The lack of replication means no copies at all rather than few (vs. many) copies. In other words, it is qualitative rather than quantitative difference. In fact, in your earlier comments you acknowledge that much - it is the total absence of RdRP rather than its low efficiency. But the formulation in your answer is misleading.

In RNA viruses with a single-stranded genome, this RNA can be positive or negative sense. Positive sense RNA is directly translatable by a ribosome, while a negative strand RNA cannot be directly translated and therefore non-infectious. It either has to be converted to a positive strand RNA with the help of an RdRP (RNA-dependent RNA polymerase, carried in the virion) or reversely transcribed into a DNA which then serves as the template for generation of translatable mRNAs. In either case, this RNA is non-infectious in absence of the necessary proteins.
Note that positive strand RNA has to be propertly capped in order to be translatable. This is also not always the case - some viruses generate or steal the cap from the cellular mRNAs once uncoated in the cell.
Another aspect worth mentioning is that positive-sense retroviruses usually code for their genes in multiple reading frames and make heavy use of splicing to produce their proteins. Thus, directly translating their positive sense RNA is not sufficient for infection.
From Chapter 3 in Viral ecology:
For plus-strand RNA viruses except retroviruses, translation of the viral RNA
follows immediately after uncoating. The viral RNA extruded from the capsid is then
used by the host translation machinery for directing protein synthesis (Fig. 9).
For all other viruses, whether of DNA or RNA genome, the step immediately following
uncoating is either transcription of the genome yielding functional mRNAs or
reverse transcription of vRNA yielding proviral DNA (retroviruses).

References:

Viral Ecology
Principles of Virology

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Terminology for quantitative response of T cells to antigen complexes
In the article, there is a statement which is:

Although DCs are
  remarkably efficient in evoking T cell responses with few antigen–
  MHC complexes (1–100 per DC) (1–3), they must first
  encounter a T cell with appropriate antigen specificity (one in
  105 to 106).

What does the part  "Although DCs are remarkably efficient in evoking T cell responses with few antigen– MHC complexes (1–100 per DC) (1–3)" mean?
What is the significance of the value "1–100 per DC"?
What does evoking T cell responses with few antigen–MHC complexes mean?

I've replaced your title by something meaningful (in the light of @PeterCollngridge answer). I appreciate it's difficult to formulate a good title if you don't understand the meaning, but titles are important in allowing people to select questions of interest and for indexing.

It means that a dendritic cell only needs between 1 and 100 antigen–MHC complexes on its surface in order to activate a T cell.

A dendritic cell uses an extrinsic pathway to take whole foreign peptides and cut them into segments of 14-20+ residues that are loaded onto MHC-II molecules. The MHC-II interaction with the T cell receptor is what tells the T cell to activate along with some costimulatory signals from the DC.
The dendritic cell doesn't know how to cut the peptides, though. So when it engulfs a bacterial protein for example, and cuts it up, and presents these extracellularly to T cells, no single peptide loaded on MHC-II are exactly the same. There could be thousands of potential antigens.
T cells on the other hand are specific: Every single T cell receptor on a single T cell clone is specific for the same antigen. It's encoded in their genome during VDJ recombination! So the DC is only efficient in that they probably only need 100 or less unique peptide presentations to find a T cell specific for one of those antigens, which is quoted to be 1:100,000 to 1:1,000,000.

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Meaning of proliferation rate of 3 day−1
The abstract of an article in Journal of Virology contains the following line:

We find that CD8+ cell proliferation begins 1 to 2 days after infection and occurs at an average rate of 3 day−1, reaching the maximum population size between days 5 and 6 after immunization.

What does this figure mean? Does it mean that per day the population after proliferation is 3 times the original population?

I know that but what does 3 day−1 mean?

Its from math. 3/day is the same as 3 day^-1 (Three per day, in words)

@skymningen does it mean that each cell after proliferation becomes 3 cells per day?

I would guess that it means that each singular cell has an average rate of 3 proliferations per day. But I am better in maths than proliferation rates.

I'm voting to close this question as off-topic because it's about English language usage.

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Why is the protein ubiquitin so ubiquitous?
Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect the cell, but is used in concert with the 26S proteasome to degrade proteins in many cells throughout the body. I just want to know why is ubiquitin so ubiquitous?

First, plus points for the pun.
Second, I suppose natural selection is at play. Those cells which don't have proteases like ubiquitin would die, and the ones with the enzyme would survive.
(Just my opinion. I don't have any source, I'm sorry)

when I was in graduate school I worked with a faculty member - https://profiles.psu.edu/profiles/display/112215 - who had done a lot of work in the basic biochemistry of the ubiquitin-proteasome pathway. He had been in the field when it was still very young/early and knew many of the early players in that field of research. He always said that the protein was named "ubiquitin" because in nearly every tissue or cell they looked they found it being expressed - they figured it must be important if it was expressed in nearly every tissue they looked in... turns out they were correct

What do you mean by "why"? It is used by all cells and that's why it is ubiquitous. Just like why actin is ubiquitous.

@MalharKhushu ubiquitin is not a protease, or any other kind of enzyme. It is a small marker protein that is covalently attached to other proteins (and itself) by ubiquitin ligases to perform a number of signaling functions, including targeting their substrates to the proteasome for degradation.

@MattDMo thanks for the heads up, I'll edit my comment

@MalharKhushu Of course natural selection is at play. Isn't it everywhere? ;-)


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Why does human chromosome 19 have the second highest number of protein-coding genes?
While chromosome 19 only is the 19th largest autosomal chromosome, it contains 1440 protein-coding genes, and thus has the second highest number of protein-coding genes of any human chromosome.
For comparison: If one would naively assume the same density of protein-coding genes as on chr1, which has the highest absolute number of protein coding genes (2109), the anticipation for chr19 would be ~540 protein-coding genes.
The x-axis of this graph highlights the increased density of protein-coding genes on chromosome 19;

I don't think there is any answer to "why".

Within any natural population there are going to be outliers. The distribution graph you show has a long tail, which is to be expected. Look for graphs on the distribution of height, for example, and you'll see that 90% of the values are within a fairly small range, but the 5% on either side stretch out quite far, as there are extreme outliers on both ends.

As extreme outliers in natural populations often are somehow special, and as a n of over 1000 genes would strongly argue against as many independent chance events, I was curious if there is something special about chr 19 or its genes, which could favor such a comparatively high gene density.

Well a very rough analogy type answer is that random mutation is not a very efficient way to make the genome, just like randomly tapping the keyboard is not a very efficient way to write computer code, you'll end up with variation in the efficiency of scripts

Paralogous genes normally lie on different chromosomes, which shows that the chromosomal location is not strictly given by the de-novo mutation / formation of a gene on a given chromosome.

I think that OP is correct that there is something to explain here (i.e., the standard null models for gene distribution across the genome would not predict such an outlier), but I think that nobody knows the answer.

@WYSIWYG I think "why" in this case translates to "what events led to".

This Nature paper from 2004, by Jane Grimwood et al. goes at least a long way towards giving an answer to the question of the OP. In short: there were inordinately many duplications, especially during an event 30-40 million years ago, as well as during a much more recent event. These duplications are, uncharacteristically, predominantly intra-chromosomal rather than inter-chromosomal. Also, chromosome 19 contains a lot of immunoglobin-like paralogues: a type of gene for which it is clearly evolutionarily adaptive to undergo rapid duplication followed by random mutation, as they play a role in adapting to potential antigens.

It's interesting that not only the leader 19, but also 16 and 17 follow a similar trend. Perhaps their size could be the best weight/length proportion to ensure a safe replication? Then what would have to be explained would be 18, so far to the left. That could be if 18 is newer, resulting from the split of a larger chromosome or the fusion of two smaller, having yet no time to accumulate a greater number of genes favoured by the advantages of the "genes positional co-evolution" (if such thing exists).


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How do red blood cells survive without a nucleus?
I was reading this question
Why do mammalian red blood cells lack a nucleus?
According to my understanding, a nucleus is the cell's control center (like the brain). All the functions in the cell are carried out according to  the nucleus's command.
Then how can a red cell survive without a nucleus? Why does it still perform all the functions correctly without the nucleus?

I think the loss of nucleous renders the structural protein synthesis of Rbcs but their further survial depends upon the ir initial metabolic process which help them to survive till their periods.

As explained in the previous answer, the RBC loses its nucleus only at maturity. The nucleus contains the DNA and which can in turn produce protein. No nucleus means - no protein/ mRNA synthesis. Also, obviously, the cell loses its capability to divide.
Hemoglobin too is a protein. Knowing that it would lose its nucleus, hemoglobin is synthesized in the precursor stages of RBC. A mature RBC can not synthesize new Hb. Hence, the RBC keeps ready its store of enzymes and structural proteins (not only Hb, all proteins it would need for normal functioning) since it can not form new stuff once it has lost its nuclues.
The lack of a nucleus also limits the cell's repair capabilities. So human RBCs are cleared from circulation once they are about 4 months old. Damage (mostly from oxidative stress) to their structural proteins leads to loss in membrane flexibility. Since, the RBC can't replace the stuff, it gets gulped in by macrophages.
It is not surprising that the cell doesn't have a nucleus. The loss of a nucleus renders it better oxygen carrying capability. Even platelets donot have a nucleus. There too, enzymes are prepared and stored beforehand.
Hope that helps!

Probably worth mentioning that RBCs don't hang around that long - about four months in adults.

@arboviral, I thought so, but then, there are WBCs too which last for just a week! But I'll add in something like that!

True - I guess 'not that long' is subjective...

@Polisetty so the nucleus only produces proteins to help the cell in fuctioning properly? And if the cell already has those proteins then will it function properly and won't need a nucleus?

@Adi Technically yes. At least for cells like RBCs which can be thought of just as a truck carrying around oxygen. For other cells, which need to perform more complex functions and modify their protein synthesis in response to stimuli/hormones, the nucleus is required. And since almost all cells do, RBCs and platelets are considered an exception.

"No nucleus means no protein/mRNA synthesis." Just a technical note: this is not generalizable. No nucleus means no transcription, but translation of (e.g. stored or previously made) mRNA can occur, and this happens elsewhere. RBCs actually lose their ribosomes (translation machinery) later than their nuclei (when they are reticulocytes), and only completely mature RBCs lack both. This suggests that translation, especially of hemoglobin subunits, might be occuring after denucleation - which makes logical sense.

I feel like a fair analogy could be made between a mature red blood cell and a space satellite. Satellites are launched with all the structure and consumable resources (fuel) they're ever going to have. In that state, they can operate for quite a long time, but eventually fuel runs out or key components wear out from radiation damage or micro-meteroid collision, and the satellite is commanded to leave its operational orbit (sometimes, to burn up in the atmosphere).

How are "too-old" RBCs recognized for destruction? I.e. what are the mechanics and what is different about an old RBC versus a new one that other bodily systems could use to distinguish the two?

Frankly, I find 100+ days to be quite long. It's surprising that a lipid bi-layer could be stable for that long, without needing repair. Quick searches show that the RBCs have a lot of actin in the membrane, so presumably this adds strength and longevity.

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Can bacterial RNA be degraded at -80⁰C in a SDS solution?
I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded.
Comes from a pellet of pure liquid culture.

I now that RNA should be freezed in RNAse free water or PBS but this was done accidentally.

I will just store it for 1 week before proceeding to RNA extraction.

It's fine. Your RNA should be stable in the current state. Aside from the fact that it's frozen, meaning that any ribonuclease activity will be minimal (if any), the SDS will have denatured some of the RNase too.
However, the detergent (SDS) might impair some of your downstream activities (especially reverse transcription and PCR), so be sure to clean up the RNA well. I would suggest Qiagen columns, and doing the additional wash steps.

I think it is relatively unlikely that the RNA will degrade under these conditions. For the future, I would handle this differently:

You can centrifuge the cells and snap freeze them in an appropriate
buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing.
Alternatively, you centrifuge them, break them up with Trizol (or whatever you use for this purpose) and freeze them in this solution. This will be
safer as it completely denatures all proteins including all nucleases.

I would choose (and have done this already several times with cell samples that I couldn't process without problems) the second method.


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Can genes change as we age?
Let's say you're a 23-year-old man who impregnates a woman. Will your genes be the same if you were to impregnate another woman at age 35? Will your genes in those 12 years have changed/mutated/become smarter?

Epigenetic changes over time is certainly possible.

I believe that's amazing then...

Yes, there are some differences between the gametes that a parent produces at different ages!
Mutations in the germline during mitosis
Every time a cell replicates some mutations may occur (even through mitosis). Of course, any mutation that occurs in cells are located in your hand or in your brain, for example, will not be transmitted to the offsprings. Only mutations occurring in the germline (cells in the testis and in the ovaries whose descendent or themselves go through meiosis) are possibly passed to the offsprings. Interestingly, because of the developmental pathways of sperm cells and ovules, sperm cells go through a lot more mitosis than ovules do, resulting in more mutations in the sperms than in the ovules. Therefore, if you look at a mutation in an individual and assuming you know that the mutation occurred during the lifetime of the parents, then you are more likely that the mutation comes from the father than from the mother.
As reviewed by Cochran and Harpending (2013), mothers transmit on average a number x of new mutations to their offspring. This number x is independent of the age of the Mother. Fathers, however, transmit a number of new mutations to their offsprings that is very much dependent on the age of the father for developmental reasons.
Of course, as it has been pointed out there are various environmental factors that may increase or diminish the mutation rate (such as the mutagens (Tobacco, X-ray, ..))
Note on the process of adaptation
It is important to know that a vast majority of mutations are deleterious (impact negatively the reproductive success and survival of the individual carrying it). If we assume that no selection occurs between the cells of the germline, then no adaptation is possible. And in average sperm cells of an old guy should have lower fitness than the sperm cells of the same guy when he was younger. This process is referred to as mutation accumulation (mutation accumulation is not a concept that is specific to somatic lines mutations). However, one may argue the opposite! One might think that the cells that carry the new mutations (the mutation that occurred during the lifetime of the man) may be selected for or counter-selected. In such a case, the few beneficial mutations might be enough to make our cell lineages more fit with age. Whether the fitness of cells increase or decrease through our lifetime is dependent on the effective population size, the mutation rate and distribution of mutational effects. One can calculate the critical parameters yielding to one (mutation accumulation and fitness decrease) or the other (fitness increase through age) thanks to the mutational meltdown literature.
It is important to note however that what increase the fitness of a cell might decrease the fitness of its carrier. Knowing the joint distribution of mutational effect for both the carrier and the cells should allow us to calculate if reproducing late in life allows transmitting better genes than reproducing early in life. Intuitively, I would expect that reproducing early in life would allow a parent to transmit better genes.
Epigenetics
We have to talk about epigenetics also. Epigenetics refers to all the modification that occur "around" or "on" the DNA but which are not the modification of the sequence of nucleotides. It is possible that the transmission of epigenetic modification is dependent on the age of the parents. But I have never heard of any case where this happens.

Where do you get that info about parental transmission of epigenetics in order to speed up /slow down the baby's development? You're contradicting yourself here by saying there's nothing, and then saying what there is. Aside from that, telomerase is active in germ cells and thus the transmitted telomere length will not be affected by parents' age (http://jcs.biologists.org/content/115/8/1643.full.pdf - it would be a bit weird if it was any other way)

Thks, I removed the Telomere part. It's been a long I was waiting for someone coming with a reference on the subject. I felt that a part of my epigenetics paragraph was not relevant to the question so I removed it. I didn't get where was my contradiction so let me know if you still see this contradiction (you can copy-past the sentences that contradict). What I wrote was in relation to the hypothetical parental conflict origin of genomic imprinting.

The contradiction is gone now - it was exactly the part after "I've never heard of any case" that caused that (because you then went on to explain a case that you heard of) :)

Pre-sperm cells divide constantly, and will have more mutations in 12 years. Unfortunately, neither the genes (nor the father) are likely to be smarter. There is some evidence that children from older fathers are more prone to diseases like autism and schizophrenia.
A very nice, short overview of the current research is in this (open-source) Nature article.

Genes can get mutated in one's lifetime. They gene altering agents are mutagens. Some common mutagens are X-ray, UV-ray, tobacco.
Recent studies have yielded results which state that some behavioral actions may cause gene mutations.
So, yes in twelve years gene can mutate. Moreover as a man ages his efficiency of meiosis division is affected. So, genes may differently get expressed in his progenies.


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Virus that can enter all cell types
As I understand, each virus type can enter a particular cell type. For example HIV can enter CD4 & CD8 cells, while HBV can enter liver cells, some other viruses can enter other cell types like brain cells and cause brain diseases.

Is there any kind of virus that can enter all mammalian cell type so it can be used as a general gene transfer method?

I have improved the English and removed title second unrelated question.

I don't know if there is any "universal" virus that really gets into every cell type, but lentiviruses come pretty close. Lentiviral transfection vectors have been developed for a wide range of human (or mammalian) cell types, including immune cells and terminally differentiated cell types such as neurons and skeletal muscle.
But these are of course experimentally modified viruses that have been optimized in various ways for transfection; typically, the naturally occurring virus is much less efficient. I would guess it's unlikely that a natural virus can enter any (human) cell type, because this capability would be expensive for the virus to maintain, and there is probably little pressure to do so --- as long as the virus has a working route of transmission, via the airways for example, there is probably little benefit in being able to transfect other tissues.

Unlikely. There are 2 ways for viruses to enter cells - mimic something the cell normally uses and trick the cell into "eating" the virus, or grabbing onto a structure on the cell membrane and forcing its way in. Either way, it's largely dependent on the target cell
Different cell types can have vastly different surface structures and receptors. Viruses that already thrive on infecting a specific type of cell have no need to develop the ability to infect other types of cells.
A virus that could enter every type of cell would look like a completely unfolded Swiss Army knife, requiring latches and grapples for each type of cell. The latches and grapples could interfere with each other, the end result being a virus that's ineffective at infecting any cell. This would actually discourage viral mutation for such multi-infection (as an intermediate form with new cell adapters could decrease its fitness on its main cell targets)

Why couldn't it attach to something fairly universal like the Na+/K+ ATPase, and trigger a calcium influx (e.g. by perforating the cell with a single MAC or similar, something a eukaryotic cell should be able to handle) to induce endocytosis-based membrane repair? AFAIK, virtually all cells have that mechanism.


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Detect which antigen binds to IgE
Assume that a patient has chronic hives (itchy) on the skin. I understand that he has an antigen, which binds to IgE and eventually triggers histamine release, causing an allergic reaction. So is there any method to detect which molecule/antigen has bound to his IgE? (can we capture it with like what we do to obtain a 3d protein/molecule structure?)

Have you any idea how much work is involved in determining 3D structures?

@David I've seen some method to determining 3D structures here but i haven't tried it my self ( I'm just a student learning theory ): https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/methods-for-determining-structure. - "The protein is purified, placed in a strong magnetic field," I'm not sure how many copy of purified protein is needed to determine their structure. Is that possible if I extract these IgE-antigen complex from 5cc blood, purify and determine 3d structure like that?

3D structure determination is a complex expensive specialized procedure that can take months or years. It is not something that can be performed routinely or even purchased commercially. Labs that do this kind of work choose the proteins to work on with great care because of this, the main criterion being biological interest. They live by their resulting publications.

@David  I've never known about that. Thank you very much for this precious information. So this mission is very hard to archive even it may possible in theory. I hope to see a method that widely available on the market on near future.

From what I understand most allergies are detected by a scratch test. from the link below:
"A skin prick test, also called a puncture or scratch test, checks for immediate allergic reactions to as many as 40 different substances at once. ... After cleaning the test site with alcohol, the nurse draws small marks on your skin and applies a drop of allergen extract next to each mark. He or she then uses a lancet to prick the extracts into the skin's surface. A new lancet is used for each allergen. ...About 15 minutes after the skin pricks, the nurse observes your skin for signs of allergic reactions. If you are allergic to one of the substances tested, you'll develop a raised, red, itchy bump (wheal) that may look like a mosquito bite"
More information on scratch tests can be found here:
http://www.mayoclinic.org/tests-procedures/allergy-tests/basics/what-you-can-expect/prc-20014505
After a quick google search,I found a paper from 2014 [1] that seems to speak to the essence of what you are asking, link below.
http://www.tandfonline.com/doi/abs/10.1586/14737159.4.4.539 [1]
In the paper above they propose using a protein microarray technology to find allergies.
I am not sure if there is any way to extract the igE-antigen complex from the patient. But I think it could probably be done with the microarray technology. Although it would be cool to see a picture of the complex.
I hope I have helped answer your question.
[1] Harwanegg, Christian, and Reinhard Hiller. "Expert Review of Molecular Diagnostics." Taylor and Francis Online. Expert Review of Molecular Diagnostics, 09 Jan. 2014.

Thank you for sharing your knowledge. +1 for this answer because your answer covered the only possible method that I've known to predict antigen by skin prick test and microarray. But i won't mark this question as resolved because I would like to see a better method, what happen if an unknown antigen present on our body that skin prick test and microarray cannot recognize it?


text:
How do red blood cells obtain energy without mitochondria?
RBCs don't have mitochondria so there is no Respiratory chain in them. But how does they get energy from Lactate. Because Lactate produce NADH which gives energy only in respiratory chain.

They do not get energy from lactate. We are pleased to welcome you to SE-Biology but expect you to do a little research before posting. Google for red cell metabolism, check Wikipedia and see what previous questions on erythrocytes have been posted here.

What process(es) do you think RBC's would need energy for, compared to the "average" cell? Does a keratinocyte need energy? Does the function of hemoglobin require energy? (These are serious questions, the answer to which I hope will help you make your question better.)


text:
How was Campbell's Model of phage lambda integration into E. coli definitively proven?
In a series of seminal papers summarized in Annual Review in Genetics (2007) 41 1–11, Allan Campbell proposed a model that assumed phage lambda integration in its host (E. coli) genome. This is in contrast to plasmids and (as was shown much later) eukaryotic viruses such as, Herpesviruses, which are in synaptic association with their hosts' genomes but not physically integrated.
What experinets actually demonstrated that lambda genomes are integrated into E. coli DNA, rather than associated with the nucleoid?
Was the confirmation made using blotting techniques or more advanced methods?

This might work here, but if not, then our [hsm.se] site might be worth looking at as an alternative.

Sorry for the confusion. That is why I am looking for the papers that physically demonstrated lambda integration. Thanks

OK. But the reference to herepesviruses (specifically EBV) is misleading, because this only became known much later. A more pertinent comparison would be with plasmids (discovered in the late 50s) as extrachromosomal genetic elements in bacteria. I will answer later unless someone else saves me the trouble.

I remember reading the passage on herpes (and papilloma) in one of Campbell's articles but I can't find it back. I agree on moving the question on History of Science. Thanks

I wouldn't move the question to History of Mathematics & Science. I have posted two useful question/answers there recently and the second got no response at all. If you look at the questions they are all Maths. I am going to start a couple of conversations on Meta to the effect that HMS drop the S and that we have an agreed policy to accept History of Biology questions. In my answer (to come) I will discuss the how (the who is uninteresting), which I think is relevant to this list. But a good answer requires time.

I have edited the question, in particular so it is about biological methodology — which makes it appropriate for this site. In contrast, questions focussed on scientific individuals, would in my opinion, be off topic. They may be suitable for SE History of Mathematics and Science, but that SE is dominated by mathematicians so it is less likely to attract interest or a good answer.

The Landy and Ross (reference 15)1 article in the review leads is an article freely available on PubMed Central.
Within in this review, there are further references, including a further review by Gingery and Echols (1967)2, which suggests that references 2-5 are related to this topic. Reference 2 is Campbell's theoretical paper suggesting the framework of insertion, and references 3 and 4 are both from 1965.
Reference 3 in the paper (and here too) is Franklin et al., The linear insertion of a prophage into the chromosome of E. Coli shown by deletion mapping, Biochemical and Biophysical Research Communications, Volume 18, Issues 5–6, 1965,3
Abstract:

Evidence bearing on the relationship of a prophage to the chromo-
some of its host bacterium has been lucidly reviewed by Hayes (1964),
who considered that a clear decision between attachment and insertion
of prophage could not then be made. Just prior to Hayes' suammation,
Campbell (1962) had formulated a largely theoretical model which would
allow for the linear insertion of phage genetic material into a bacterial chromosome, and would account for the permuted gene sequence of
the prophage as compared to vegetative phage. The permuted gene
sequence had been indicated by comparisons of the gene order in phage
recombination experiments and in crosses between bacteria lysogenic for
genetically marked h prophages.(Calef and Licciardello, 1960). Evidence
in support of the model was subsequently supplied by Campbell (1963) in
studies of the segregation patterns of lysogenic heterogenotes, and by
Rothman (1965) in studies of Pi cotransduction of galactose and 1 markers.
We describe in this paper observations which substantiate Campbell's
model by showing that deletions in particular lysogenic bacteria simultaneously eliminate bacterial genes and segments of a prophage
genome. The missing phage segments are overlapping, allowing sequencing of the prophage genes

Reference 4 is Rothman, Transduction studies on the relation between prophage and host chromosome,
Journal of Molecular Biology, Volume 12, Issue 3, 1965.4
Abstract:

Cotransduction analysis by means of bacteriophage P1 has been used to study the relation between the bacterial genetic markers gal and bio and the prophage λ. The order of a series of markers of the λ prophage with respect to the bacterial gal locus has now been found. This marker order is a circular permutation of the order present in vegetative phage λ, in agreement with Campbell's hypothesis (1962). The frequency of cotransduction of gal and bio is drastically reduced when both donor and recipient strains are lysogenic either for prophage λ or prophage 82, an indication that both λ and 82 are located between the gal and bio markers. Additional evidence is presented suggesting that prophage 434 and the λ-434 hybrid may also be located between gal and bio.
It was not possible to find the order of the λ prophage markers with respect to the bio marker; hence, conclusive evidence for a linear insertion of the prophage into the bacterial chromosome could not be obtained.
The presence of a lambdoid prophage appears to affect the early steps of transduction by phage P1. The possible nature of this effect is discussed.

Thus, Franklin et al, provided the first evidence of the insertion of phage into bacterial genomes. Their work was largely performed by crossing of various mutants with non-replicative deletions on various permissive bacterial backgrounds, which led to the recognition that escape mutants, capable of replication had a homology in sequence between sites, which allowed recombinant excision out of the bacterial genome.
References:

Landy A, Ross W. Viral integration and excision: structure of the lambda att sites. Science. 1977 Sep 16;197(4309):1147-60. doi: 10.1126/science.331474. PMID: 331474; PMCID: PMC1994661.

Gingery R, Echols H. Mutants of bacteriophage lambda unable to integrate into the host chromosome. Proc Natl Acad Sci U S A. 1967 Oct;58(4):1507-14. doi: 10.1073/pnas.58.4.1507. PMID: 4867663; PMCID: PMC223953.

Naomi C. Franklin, William F. Dove, Charles Yanofsky,
The linear insertion of a prophage into the chromosome of E. Coli shown by deletion mapping,
Biochemical and Biophysical Research Communications,
Volume 18, Issues 5–6,
1965,
Pages 910-923,
ISSN 0006-291X,
https://doi.org/10.1016/0006-291X(65)90868-5.
(https://www.sciencedirect.com/science/article/pii/0006291X65908685)

June L. Rothman,
Transduction studies on the relation between prophage and host chromosome,
Journal of Molecular Biology,
Volume 12, Issue 3,
1965,
Pages 892-912,
ISSN 0022-2836,
https://doi.org/10.1016/S0022-2836(65)80336-9.
(https://www.sciencedirect.com/science/article/pii/S0022283665803369)

Yes, but your answer would be more informative if you started with a one-sentence summary: "The final physical proof was the DNA sequencing of portions of the E.coli genome containing the junctions between the bacterial and integrated phage DNA (Landry and Ross, 1977)".

If I understand correctly, restriction mapping provided proof of lambda insertion (as opposed to synaptic association). Thank you; that was a very deep answer; I appreciate it!

@Gigiux — You do not understand correctly. I whole series of indirect experiments were consistent with the Campbell hypothesis, but definitive proof was provided by actual DNA sequencing of the junctions between the bacterial and phage DNA integration sites, as the answer states.


text:
Who demonstrated that phage lamba is integrated into the host chromosome?
In the 1950s, the Lederbergs (Esther and Joshua) demonstrated the presence of phage lamba in Escherichia coli K-12.
But who demonstrated that this virus is integrated into the host's genome? Is there a paper related to this discovery?
Thank you

This may work better on our [hsm.se] site than here, but see what others say.

@JiminyCricket — In principle you are probably correct, but looking at SE HoS for the first time I was not impressed by the biological content, eg Crick & Watson discovering DNA, in a title left unchallenged for years. I have tried in my answer to indicate the science as well as the man, so it falls better within our remit. I should have perhaps extended my answer, but would need more time to read round the subject. Fascinating stuff, though .

Allan McCulloch Campbell (1929–2018)
In brief, Campbell was responsible for the hypothesis that lysogenic phages physically integrate into the DNA of host bacteria (rather than being laterally ‘attached’ or ‘synapsed’, as was the prevailing view at the time) — part of his “Campbell Model” — and he was responsible for identifying a particular gene, h, as necessary for the integration of bacteriophage lambda. This relied to a large extent on observations on mutant phage incapable of lysogeny, and bacterial strains that were resistant to phage.
An excellent place to read about how he established this is his own account in Annual Review in Genetics (2007) 41 1–11 (subscription required). This shows how ideas in science often develop as a result of many experiments and their interpretation within new intellectual frameworks, rather than a single ‘historic clincher’.

If there is anyone who is unable to obtain institutional access to the review and is very keen to read it, I suggest they post a comment and I'll see what can be done to help.

Thank you for your in-depth answer.

Thank you for the hint. I have read the paper, but it states that the Cmpbell model is a model. IS there experimental evidence for the integration of lambda? Southern blot perhaps? or microphotographs?

@Gigiux — Southern published his blotting method in 1975. The Campbell model dates from 1962. The methodology of molecular genetics was initially genetic, with the molecular aspects added only gradually. When direct methods were not available science advanced through the interpretation of indirect experiments.This is not easy for younger scientists to appreciate, but the intellectual beauty of such experiments often makes a stark contrast to contemporary brute-force science. I won't have time to go into this in more detail for about a month, as I shall be away, but I may return to it anon.

thank you, I'll be waiting. In the paper, Campbell stated that Jacob and Wollman proposed a synaptic model where the phage chromosome was closely associated but separate from that of the host, like that of EBV. The question is: who gave the final proof that lambda was indeed integrated?

I found a first mention of southern blot of lamda in this paper (https://journals.asm.org/doi/epub/10.1128/jvi.02177-09)...

@Gigiux — I am not clear of the relevance of this 2010 paper is to your question. As I already commented, the lambda experiments predated Southern blotting by 13 years. It is not surprising to find the method used with lambda as with other DNA viruses or genomes after 1975.

Actually, the 2010 paper is not relevant. Now that I read it fully, it is just a study of how lambda integrates into other cryptic lambda phages. It is not the first proof of physical integration instead of merely association.


text:
How is 16s rRNA used to identify unknown bacteria?
How is 16s rRNA used to identify unknown bacteria?
With PCR the 16S rRNA is amplified and sequenced, but how can you identify the bacteria with this 'piece of knowledge' if the 16S rRNA is conserved and so the same in all bacteria?

Welcome to Biology SE change. The area of this question is valid, but it is very basic. We do expect people to use web resources first to try to answer questions, and I am sure you could have found something by Googling. If the articles you found were still unclear to you, then would be a better time to ask for help here.

It is not conserved, its sequence is not the same in all bacteria. Indeed, it has a slow rate of evolution (mutation) that make it perfect to build phylogenetic trees.
As correctly suggested by David in his comment, here are some references about the 16s rRNA and on how it is used to identify known and unknown bacteria.
http://www.sciencedirect.com/science/article/pii/S1369527499800526
http://nar.oxfordjournals.org/content/38/22/e203
https://www.ncbi.nlm.nih.gov/pubmed/18828852
https://www.ncbi.nlm.nih.gov/pubmed/27388368
https://www.ncbi.nlm.nih.gov/pubmed/27659439
https://www.ncbi.nlm.nih.gov/pubmed/18353221
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760787/

You are correct, but you should provide a reference, even for something so simple, so that the questioner and others can check and find more info. I imagine there is a Wikipedia article or a NCBI Bookshelf chapter you could cite.

That's fine. I've upvoted your answer now.

There are two different kinds of conserved here that people are perhaps using a bit carelessly.
The 16S rRNA is conserved, meaning that it's present in all bacteria (and archea, mitochondria and chloroplasts). However, it's not conserved in the way that the sequence is 100% identical in all bacteria, it just evolves quite slowly (it has a low rate of mutations).
https://en.wikipedia.org/wiki/16S_ribosomal_RNA

See my comment to @alec_djinn.


text:
Size ratio of Drosophila bifurca gametes and implication for the definition of sex
I recently learned that males of Drosophila bifurca species have gigantic sperm cells, 5.8 cm long and they only produce few hundred such cells during its lifetime. This made me wonder if the male gametes are larger than the female gametes in this species? If so, it would mean we are naming males and females incorrectly in that species, as according to definition, males and  females are determined by gametes size [1]. However I cannot find any information about exact size (length of sperm is not enough) or weight of their gametes nor even a picture where both are present next to each other.

Wikipedia definition :P https://en.wikipedia.org/wiki/Anisogamy https://en.wikipedia.org/wiki/Sex

I've honestly never heard of sex solely being defined by the relative size of the gametes. That may be a rule of thumb, but size alone doesn't affect anything downstream, like sexual development pathways. That is determined mainly genetically, and in some species environmental factors such as temperature can play a role.

@David I added link to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031617/

@MattDMo Yes, sex can be determined genetically or by environmental factors... but then how do you decide which one we would name "male" and which one "female"?

I think there is some confusion in the comments. OP is not talking about sex determination, but rather the very meaning of male and female. The meaning of male and female is typically made in consideration of gamete size, where the female sex produces larger gametes.

@David What else would define the sexes across taxa? OP includes a reference to a discussion of the development of sexual differentiation from isogamy, it seems pretty clear.

@David I could dig a bit but I don't know where it originates. My own training in biology came substantially after 1972 :)

Thanks @BryanKrause . I've posted an answer now, and this encompasses the points made in my comments, so I have now deleted the latter. As I mention in a footnote, I would still be interested in information about the origin of the gamete-size definition of sex.

I've edited your title to indicate its broader motivation. I hope this may bring it to the attention of more biologists with knowledge of the history of the definition at issue. You are, of course, free to revert if you are unhappy with the edit.

Relative size of gametes
The relative sizes of the sperm and eggs of D. bifurca can be seen in the scanning electron micrograph below, taken from a 2006 Nature paper by Bjork and Pitnick.

The left-hand frame (a) shows a single, 6-cm D. bifurca spermatozoon dissected from the seminal vesicle, where sperm are individually rolled into compact balls. In the right-hand frame (b) six of these have been reduced to the same scale as a D. bifurca ovum and placed alongside it.
It is clear from this that the ovum is much larger than the sperm. I do not think the absolute sizes of sperm and ovum are the point at issue here, but the poster or interested reader can calculate the volume of the ovum from the micrograph above, and that of the sperm from highly detailed electron micrographs in Fig. 6 of a 2008 publication of Dallai et al.. The latter appear to have a cross-section diameter of approx. 0.7–1.0 μm. (Egg volumes for some other Drosophila species can be found here.)
Even if…
Although I think that the section above answers the question, there is a relevant aspect of fertilization in D. bifurca that should be mentioned. This is that, in contrast to Drosophila species with smaller sperm, only a portion of the sperm of D. bifurca actually enters the egg. This is shown in the image below in which only 1.6 mm of the 58 mm long sperm (about 3%) penetrates the egg (only part of which is shown).

(Visualization of sperm in fertilized eggs of D. bifurca. From Karry and Pitnek (1996) Nature 379, 405–6)
Thus, in principle, a giant sperm with a volume of perhaps twice that of the egg would still be able to penetrate and fertilize the latter. The implications of this are considered briefly below.
Implications for definition of male and female gametes
What would the implications be for a Drosophila species in which the volume of the ejaculated sperm exceeded that of the egg, but by an amount that still allowed penetration of a portion containing the nucleus, which could then fuse with the egg nucleus?

Would it mean — as stated by the poster — that “we are naming males and females incorrectly”?

I assume that, like D. bifurca, individuals of this hypothetical species display similar marked sexual characteristics to other species of Drosophila, genetically, physically and behaviourally. In this case, giving the assignation female to what in other species are called sperm (and by implication giving this designation to the individuals from which they originated) seems patently absurd.

I would say that it is the definition that would need changing, not the sex.

Is the definition absolute?
As a molecular scientist with a chemical background who last studied organismal biology at the age of about 14, I was surprised at this definition. The paper cited in the question (published in 2016) makes the statement

“Even when there are no separate male and female sexes as such (i.e.
simultaneous hermaphrodites), there is dimorphism at the gamete level,
where clearly diverged male and female gametes are produced—male
gametes being by definition the smaller ones”

It may be thought that the implication is that individuals that produce male gametes are male, and those that produce female gametes are female, but this is not always the case (e.g. simultaneous hermaphrodites).
Judging from the Wikipedia article on anisogamy (the phenomenon of different sized gametes) and popular scientific websites, this seems to be generally accepted by biologists, but I have had difficulty finding when and by whom it was proposed, and what justification was given for the definition. The paper mentioned points back to one by Parker et al. in 1972 but that paper does not even state this explicitly — it is merely implicit in mathematical modelling of the evolution of gamete dimorphism.
I can only suppose that the original definition was based on a need to define male and female gametes in circumstances such as simultaneous hermaphrodites. The definition adopted was consistent with the situation observed in clearly sexually differentiated situations where the male sperm enter the larger female ovum, and so must have seemed a neat solution. However, as we have seen, in Drosophila with giant sperm, only a portion enters the egg, and this is sufficient because only the nuclei of the gametes need to fuse and form a zygote. Biology is not one of the exact sciences, and such a case would not be the first time a definition needed to be tweaked or to admit exceptions.

Footnotes
I thank Professor S Pitnek for directing me to the papers with scanning electron micrographs of the sperm and egg of D. bifurca. If anyone can cast light on the origin of the size-based definition of male and female gametes I will edit this answer to accommodate the information.


text:
Where does an organism store reserves of amino acids?
Where does an organism store reserves of the amino acids it needs to build various proteins it needs:

in the liver?
in the blood?
in every cell?

In the sense that you have asked the question, humans have no stores of amino acids. Amino acids obtained from the diet are quickly incorporated into new proteins or are metabolised as fuel molecules.
Proteins are subject to continual turnover, and the amino acids that are released by degradation are either reused or metabolised in exactly the same way.
This is one of the reasons why the diet must contain appropriate levels of essential amino acids (those we cannot make for ourselves) since these are continually being released from proteins and used as fuel - we have no mechanism for storing them in case of future dietary deficiency.
During starvation the protein turnover process releases amino acids from muscle and these are mainly used as fuel molecules. This is why muscle wasting occurs in starvation, although the mobilisation of fat reserves helps to delay this as long as possible as tissues, including brain, switch over to relying on ketones (derived from fat breakdown).

In fact amino acids can't be stored as monomers, As monomers they would generate tremendous osmotic pressure. So they have to be stored as proteins but there is no good way to build an inactive protein without needing specific structure, which would defeat the purpose of storage. the closest we get is converting them to fatty acids and storing them that way.


text:
DNA replication - how many times and when does it occur?
I’m currently learning about DNA replication in both prokaryotic and eukaryotic cells. And my lecturer has mentioned that replication is a once in a lifetime activity. And I’m not sure what this is implying because I’ve searched up that DNA replication occurs during cell division (cell cycles), which occur repetitively as organisms develop.

Perhaps your teacher was talking about unicellular organisms.

This sounds like a difference in perspective of when exactly cells "die". If you consider that, in a cell division, a mother cell "gives birth" to two daughter cells, you could argue that the mother cell has "died". It makes sense to think about cell division in this way because it puts both daughter cells in the same level, without one being "special" due to it being the mother cell itself while the other is considered the "new cell".
If you face cell division like this, any cell (eukaryote or procaryote) will only really duplicate their DNA once: they duplicate their DNA -> they split into daughter cells, in which they "die" -> (eventually) each daughter cell duplicate their DNA -> and so on.
Like I said this is just a particular POV we can adpot when we try to understand and describe cell cycle and cell division (although it is a common one for researchers in the field).


text:
Identification of South Indian plant
I'm from South India and I'm having quite a fuss identifying this plant. It has totally transparent stems, and when I break them, water squeezes out. My local friend tells me that this was used in the olden days to clean slates. It has a bit fat stem. And another thing about this plant is that when you soak it in Ink, you can see the ink travelling up it. That's why it is so transparent.
I heard that it is locally called Mashithandu and I searched all  over the net for it, but can't find a name except that. I'm really sorry I can't add a photo. I'll see what I can do.

I presume you are talking about Peperomia pellucida. It is called  Mashithandu in Malayalam.

Reference: Wikipedia
You might like to go through this.

Description
Delicate, glabrous annual herbs; stems erect, 5-30 cm tall, pellucid,
  branched when well developed.
Global Distribution
Native of Tropical America; now Pantropical
Indian distribution
State - Kerala in all Districts

Common names
It is known as pepper elder, silverbush, rat-ear, man-to-man, clearweed (North America); prenetaria (Puerto Rico); konsaka wiwiri (Suriname); coraçãozinho or "little heart" (Brazil); lingua de sapo, herva-de-vidro, herva-de-jaboti or herva-de-jabuti (South America), ewe rinrin (Yoruba Nigeria), corazón de hombre (Cuba).[11] In Oceania, it is called rtertiil (Belauan); podpod-lahe or potpopot (Chamorro). In the different dialects of the Philippines, it is called pansit-pansitan or ulasimang-bato (Tagalog), olasiman ihalas (Bisaya), sinaw-sinaw or tangon-tangon (Bikol), lin-linnaaw (Ilocano) and "clavo-clavo" (Chavacano). In other parts of Asia, it is known as càng cua (Vietnam);sagar bataing သဂါဗတာင် (Mon); pak krasang ผักกระสัง (Thailand); "krasang teap" ក្រសាំងទាប (Cambodia); suna kosho (Japan); rangu-rangu, ketumpangan or tumpang angin (Bahasa/Malay); sasaladahan (Sundanese); rinrin (Nigeria), "shining bush" (Trinidad and Tobago), and mashithanduമഷിത്തണ്ട്, വെള്ളത്തണ്ട് and വെള്ളപ്പച്ചില (Malayalam); diya thippili දිය තිප්පිලි (Sinhalese). In west Bengal, India the plant is locally known as "Luchi pata". In Guyana the plant is also known as "Soldier Parsley."

Welcome to Biology.SE! You are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. In addition, scientific names (i.e. latin binomials) are much more useful than a list of common names. ——— Please also take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!


text:
Do trees have genes for stopping growth?
Do trees have genetically encoded to stop growing at some height, to keep dividing the cells only to a certain amount, or to pump nutritions only till it's advantageous because they've already overgrown their companions? Or do they just keep growing till they can?
I was inspired by this article, according to which the height limit is about 130 m. Since if the second one was true, it would be possible to grow a 130 m tall tree with enough nutritions.
Also, the evolution of trees wouldn't mean to getting more genes of height, but to use nutrients more efficiently.

mildly related: Why is it beneficial for trees to grow tall?

'Trees' are widely different - are you asking about Redwoods in particular? Also note that the paper is specifically referring to the physiology of Sequoia sempervirens, and tradeoffs in this species, not trees in general. Most tree species cannot grow to be more than 100m, no matter how much nutrients you dump on them.

Yeah, I'm asking about trees in general.

The answer I got from Jan Kolář of Charles University:

Traits of trees like height and mass are a result of the genes and
  environment. The determinative factor for the studied plants and
  animals is a big amount of various genes. When we get to know all the
  functions of all the genes, we should be able to determine the most
  important ones but for now we know just that gibberelin and auxin are
  very important for the growth of the tree, so we'll be looking for those
  genes which control the level of those hormones.
In case of trees, a big part of the height they can grow are utterly
  mechanical factors. The stem and the main branches have to be enough
  strong not to break with their own weight and the roots have to be
  enough firmly rooted in the soil. This limit is determined mainly by
  genes that control the grow of the cell walls, their mechanical
  resistance etc.

also at a certain height it isn't prossible anymore for the tree to transport the water to the top of it

@RickBeeloo If you talk about the atmospheric pressure limit I disagree

Take a look at this article: http://www.nature.com/nature/journal/v428/n6985/full/nature02417.html @Probably

@RickBeeloo Thanks, what's the principle behind this "constrains" (if you have it avaiable)?

What do you mean with "this constrains" which constrains?

In the abstract they say "Current hypotheses of height limitation focus on increasing water transport constraints" which isn't really specific.


text:
Transport of newly synthesized proteins to cellular organelles
In the nucleus the DNA is transcribed and processed to mRNA which is translated into proteins in the cytoplasm. What happens between the time a protein is made and that when it reaches the cellular organelle in which it functions? How is it transported to its destination?

You want to read about transcription and translation. In the nucleus the DNA is transcribed into RNA, which then leaves the nucleus. The processing of the RNA and its translation into proteins happens in the cytosol outside the nucleus.

RNA processing also occurs inside the nucleus because the introns need to be removed (only exons code for the protein)

I have changed your title and simplified (and corrected) the content of your question so that it focusses on the question you clearly wish to ask. If I have misunderstood you, please say. A good answer to this question will, in my opinion cover a range of organelles and cellular and sub-cellular locations, as well as perhaps touching on post-translational modifications.

Mature RNA is translated into proteins by the ribosomes.  Ribosomes bound to the ER (endoplasmic reticulum) translate proteins that are bound for export from the cell.  Free ribosomes, which are found in the cytosol, are used for structures within the the cell (http://www.brighthub.com/science/medical/articles/110037.aspx)
Proteins made on the ER are sent to the Golgi apparatus, and are packaged there for transport out of the cell. (http://www.ncbi.nlm.nih.gov/books/NBK9838/)
As far as I know, the proteins made by free ribosomes remain in the cytosol and are incorperated into certain organelles or pathways upon contact with specific other proteins or signalling molecules.

Mark can you add some references - we always appreciate that on this site... even for things that are very elementray

This answer is very limited in scope, as well as being unsupported by references, as Vance writes. I'm down-voting it until you improve it.

Mark: sort of (on the last point). Maybe worth mentioning https://en.wikipedia.org/wiki/Signal_peptide

Sorry about that, I updated it with the references.

Nucleus: DNA transcribed to mRNA.
mRNA is sent out of the nucleus and into the cytoplasm.
Ribosome: Site of translation. Amino acids are placed in accordance with the mRNA codon (triplet of mRNA sequences). Folding is done as the protein is formed.
Once the protein is complete, the golgi apparatus is responsible for packaging and exporting it.

try adding some external sources to back up your claims - i know it may seem like this is basic knowledge, but it is good practice for others to be able to follow your answer and rationale.

This is an incomplete answer as the Golgi is only involved in the processing of secreted or membrane proteins.


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Chemistry of the phosphodiester bond in RNA
I have been learning about the chemical structure of RNA, but I can't understand why all hydrogen atoms disappear in the phosophodiester bond between the riboses of RNA.
Phosphoric acid is $H_3PO_4$:

However, when it's connected to ribose the hydrogens disappear:

Where did the hydrogens go and why?

I have edited your question and corrected your diagrams in a way that should answer your question. The valency of the oxygen in the original diagram of the phosphodiester bond was incorrect. Addition of the negative charge — shown in any book or web page — makes it clear that a H ion has been lost. This is such a basic question of chemistry that I would regard it as off topic for Biology SE. As you have accepted the answer from @anotherHomoSapiens I will now vote for it to be closed.

Hydrogenation depends on pH

@Christiaan correct, I read somewhere that at cellular pH (~6.8) DNA easily loses H and acquires -ve charge.

Generally hydrogen is not shown in DNA structure. I have made a simple diagram to show where all hydrogens go:

There are 3 hydrogens in phosphoric acid, each of them leaves as:

1 H joins with 3' -OH of previous nucleotide to form H2O during DNA replication.
1 OH joins with H of next nucleotide to form H2O during DNA replication.
1 H is released as H+ (remember it was phosphoric acid), hence giving rise to the acidic character of DNA (remember it is DeoxyriboNucleic Acid).

I think you should first study DNA replication (if you haven't, yet) to get more thorough knowledge about the topic.

If this solves your problem, click the tick mark, below the down symbol to the left of my answer, to select it as correct. If it doesn't, ask your query here or improve the question.


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Why does K+ move out of the cell?
I was reading this page: Equilibrium Potentials when I found the following example at the end of the page: "If the K+ equilibrium potential is –90 mV and the membrane potential is –70 mV, in what direction will K+ move through open K+ channels?".
The site gives the answer, and it turns out that K+ moves out of the cell. I'm not entirely sure if I understand why this is the case.
(1) Because the equilibrium potential for K+ is –90mV, this means that the intracellular region must be negatively charged, at –90mV, to have zero net flux of K+ across the membrane. Therefore K+ would leave the cell, making the interior more negative from –70mV to –90mV.
(2) But the resting membrane potential is still –70mV. Will this membrane potential be established by other ions? If not the case, K+ will be pulled inside the cell again, then we wouldn't be able to tell that K+ goes out.
(3) I find the starting conditions somewhat confusing. "K+" goes out means that there needs to be a potential difference. Is the question assuming we have, as starting conditions, the same concentration of K+ at both sides? Otherwise it is not clear why K+ should stop leaving the cell at any moment (even when it is at the state of equilibrium).
(4) Can we conclude, as a general rule, that if MRP is the membrane resting potential and EP is the X+ equilibrium potential, then X+ leaves the cell if EPMRP. Would the roles be reversed for X–?

The other answer is a bit misleading.

"Another cause is the the intracellular K+ concentration"

No, this is exactly the same cause, the differing concentrations is what causes the equilibrium potential. You can think of the equilibrium potential for one ion as "how much voltage does there need to be to prevent this ion from flowing down its concentration gradient." The Nernst equation gives you the equilibrium potential for any one ion. The equilibrium potential is also known as the "reversal potential" because if the voltage exceeds the equilibrium potential, ions will flow the opposite way, against their concentration gradient.

Don't get confused by the resting potential, because it is only a potential that the cell arranges for itself to maintain a stable environment. This cost a lot of energy and attention in form of protein synthesis to keep this potential. This mechanism is achieved by the Na+-K+ ion-pump

The resting potential is not to "maintain a stable environment" or anything like that. The resting potential is the net potential that a cell reaches due to all of the conductances of various ions and the flowing current of each ion governed by its own equilibrium potential.

This mechanism is achieved by the Na+-K+ ion-pump, which exchanges those two ions

This is partly true, but again, misleading. The Na+/K+ pump establishes the relative concentration of ions, which only leads to a certain resting potential because the conductances of different ions vary at rest. Because the conductance of K+ is higher at rest than the conductance of Na+, the resting potential is closer to the equilibrium potential for K+. If the Na+/K+ pump was functioning exactly as it does, pumping Na+ out and K+ in, but the membrane was more permeable to Na+, then the resting potential would be positive rather than negative. All that matters for resting potential is relative ion concentrations and conductivity. The Goldman equation is the way to calculate this resting potential.
What is happening to K+ when a cell has a resting potential of -70mV but a K+ equilibrium of -90mV?
Because you need -90mV to 'hold in' the potassium against it's concentration gradient, at -70mV K+ will flow out of the cell. However, by definition, resting potential is the potential at which the net current will be zero. That means that, yes, other ions have to be involved. This is where the Goldman equation is very useful.
Although K+ may be the ion with the highest membrane conductance, there will also always be some leak of Na+ and Cl- ions (usually others ions are ignored because these three are the major players; other ions can be important in some situations). Therefore, if -70mV is rest, there must be at least as many Na+ ions flowing in or Cl- ions flowing out as there are K+ ions flowing out.
You can calculate these currents if you know the conductance of each ion and the equilibrium potential for each ion using Ohm's Law: I = V/R, where R is 1/conductance and V is the difference between the current voltage and the equilibrium potential. Try it out with the Goldman equation! If you use the voltage the Goldman equation gives you (the resting potential) you will find that the net current is zero!
Okay, so far we've answered your questions (1) and (2). Now (3): you state "Otherwise it is not clear why K+ should stop leaving the cell at any moment". It is important to note that equilibrium potential doesn't mean no ions are moving: it means the voltage isn't changing. If you just left the cell at -70mV and waited some time, eventually the concentrations of the different ions would change. This is where the Na+/K+ pump comes in: this ATPase is constantly pumping some K+ out and Na+ in to counteract the leak that occurs at resting potential. Cl- ions move, too, but mostly passively. It's also important to note that very few ions have to move for the potential to change on the order of millivolts. -70mV might sound like a lot, but electrical forces are very powerful, so very few ions relative to all the ions available have to move.
I don't quite understand what you are asking with (4) but if you can edit the question I will try my best to answer that as well. It's possible I already answered your question by talking about what "equilibrium potential" means for one ion. For a Cl- ion, if the equilibrium potential for Cl- is -65mV, then Cl- will flow into the cell when the membrane voltage is -60mV (tending to make the cell closer to -65mV), and it will flow out of the cell when the membrane voltage is -70mV (still tending to make the cell closer to -65mV).

.. resting potential is not to "maintain a stable environment" or anything like that.. isn't resting membrane potential established by cell to make ICF isotonic to ECF?

@JM97 No, and certainly not in this context. An electrical potential won't do anything with respect to tonicity because water isn't charged. Where did you get that impression?

Yes, water is not charged but this unequal charge distribution(made by the cell) helps cell in preventing excess accumulation of osmotically active substances at one side. So resting membrane potential is consequence of cell's attempt to maintain isotonic icf.

@JM97 " this unequal charge distribution(made by the cell) helps cell in preventing excess accumulation of osmotically active substances at one side" - I don't understand the mechanism here. The membrane potential doesn't do anything to prevent movement of osmotically active substances or water. Do you have a reference?

Last paragraph of http://www.preservearticles.com/2011083012499/what-is-the-gibbs-donnan-equilibrium.html   To survive, the Na+-K+ pump in the cell membrane continuously pumps out excess cations.

@JM97 By a reference I mean something like a scientific paper, or at least a textbook reference, not a blog site. And the statement "Na+-K+ pump in the cell membrane continuously pumps out excess cations" has nothing to do with the membrane potential being necessary for survival. It would be possible to pump out excess cations and yet still have a membrane potential of zero.

The Equilibrium potential(-90 mV) of Potassium-ions(K+) will drive the ions to flow out of the cell if K+ channels are opened, because K+ ions try to establish this potential instead of the resting potential(-70 mV). Another cause is the the intracellular K+ concentration that is around 140 mM compared to the extracellular concentration, which is only 5 mM.
Don't get confused by the resting potential, because it is only a potential that the cell arranges for itself to maintain a stable environment. This cost a lot of energy and attention in form of protein synthesis to keep this potential. This mechanism is achieved by the Na+-K+ ion-pump, which exchanges those two ions (pumps K+ in and Na+ out to achieve the -70 mV).
If K+ ions flow out of the cell the membrane potential will get lower than the resting potential, also referred to as hyperpolarisation. This event occurs at the end of an action potential when the outflow of the K+ ions "undershoots" the resting potential.


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Identifying a mushroom. (Pyrenees near Gavarnie, France)
Can anyone help me identify this mushroom? (a still frame from video taken in the Pyrenees near Gavarnie in France). Also is it edible or poisonous?

This is almost certainly the parasol mushroom, Macrolepiota procera. The parasol mushroom is edible, but many other often resembling mushrooms are not. Never eat a wild mushroom unless you're an expert or consulted one.
 https://en.m.wikipedia.org/wiki/Macrolepiota_procera

Very helpful. Thank-you very much....and also for the note of caution. :0)

@OrbitRob If you think your question has been answered, please check the checkmark next to the answer.


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Determine whether aromatics originate from polyketide or shikimate pathway
Is there a way to determine whether an aromatic compound  originates from the polyketide or shikimate pathway by looking at its structure? If so, how?

I've modified your question. They are pathways not ways.

Aromatics that stem from the Shikimat Pathway result in a structure like this

Whilst aromatics originating from the Polyketide Pathway have an alternativ structure in the distribution of the OH groups.

If both pathways produce the same molecule, you can't tell: It's the same molecule.
You could knock out some enzymes on either side and see which ones affect output. Or you could spike the cells with a radiolabeled precursor of only one pathway, and then see if the output is also labeled.
However, you say "by looking at its structure", so I'm assuming no additional experiment can be done - then no, except for the trivial case where only one of the pathways produces the molecule (in which case it obviously came from that one).

It's no real world scenario. To clarify, let's say you have an arbitrary aromatic, look at its Fisher Projection for example. Is there a way to deduct from that the origin? Are there some unique properties that originate from the pathway that was used for synthesis. I remember something like that from our lecture. Maybe I'm able to find out what exactly the lecturer meant with that.


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Relative roles of ATP and NADPH in anabolic and other processes
Chemistry isn’t my strong point, but I’m trying to understand why NADPH is said to be the main agent necessary for anabolic reactions, and if NADPH is used for anabolic reactions what is ATP used for? Movement?
An example of what I'm wondering: When skin cells are exposed to sunlight, to synthesize melanin is the free energy of ATP hydrolysis sufficient? For example by catabolizing some protein in the cell and using the amino acids to synthesize melanin? Or is NADPH always necessary?
I have not been able to find an explanation on-line that addresses this, so suggestions of a suitable book would be appreciated.

Welcome to SE Biology. Your question is based on a misconception, so I am using this comment to put you on the right track before suggesting the question be removed. ATP is not a reducing agent, it is "the universal currency of free energy in biological systems and you can read about it in section 14.1.2 of Berg et al.. You are correct in relation to NADPH, but the contrast that you should be making is with NADH, an important use of which is to generate ATP — see Berg et al. 14.2.

I see, thank you, it's a little more clear now.

Hmm. Are you sure? After posting I started to wonder whether you were thinking about some anabolic process that required both NADPH and ATP, such as fatty acid synthesis; or had read that reactions of both of these effectively supplied energy. You may not be "good at chemistry", but understanding metabolism involves only a few chemical principles. However these are fundamental. Do you understand the idea of free energy changes in a reaction, and are you clear what reduction is? If there is a particular area of metabolism that provoked your question, we might use that to clarify things.

I guess so, more or less
a reductant is an elecron donor
an oxidant is an electron acceptor
Reduction means gain of electrons
Spontaneous reactions "generate free energy"
What is getting difficult to understand for me is how this energy will be used.
I'm trying to translate it to everyday life of an organism
What i "think" i understand is:
NADH and oxidative phosphorylation get us mostly free energy without a change of mass as we'll be exhaling carbon dioxide and urinating water.
while NADPH get us both free energy and mass.

An example of what i'm wondering:
Skin cells are exposed to sunlight, to synthetize melanin is the free energy of ATP hydrolysis sufficient? For example by catabolizing some protein in the cell and using the amino acids to synthetize melanin?
Or is NADPH always necessary?

OK. What I propose is later today to change your question slightly to something like "Relative roles of ATP and NADPH in anabolic and other processes" using your clarification and example, and then provide an answer (rather than a comment). You can modify the question if it's not quite on the spot.

Preamble
I don’t know where you read the statement “NADPH is... the main agent necessary for anabolic reactions”, but  out of context it is very misleading, and it is difficult to envisage circumstances in which it would be helpful for students of metabolism.
Put simply, NAPH is only used in anabolic pathways which involve chemical reduction.
You ask for a suitable book, but the book I’m going to quote from (Berg et al., Biochemistry) would overwhelm you (and any other student — it is grossly overweight). However an old edition is available on-line, and by citing specific sections you can read what is relevant (and spare me breaking up my answer with pirated diagrams).
ATP and NADPH: energetic similarities and differences
ATP and NADPH can both be regarded as ‘energy-rich’ in the sense that they can undergo reactions that have a high negative change in Gibbs Free Energy (which is what determines whether a reaction proceeds) and that this can be linked to certain other reactions with a positive free-energy change — including, but not exclusively, those in biosynthesis — to drive an overall reaction. (Incidentally both these compounds are synthesized in reactions powered by solar energy during photosynthesis.) However the nature of this linkage or coupling to other reactions differs between NADPH and ATP, and this difference determines the roles that they can play.
The oxidation of NADPH to NADP+ has a standard redox potential of +0.32V , which is an effective a negative standard free-energy change, but it can only occur in conjunction with another redox ‘half-reaction’ with a redox potential that will result in an overall negative free-energy change. Berg et al., section 18.2.1, presents a calculation to show how NADH (essentially similar to NADPH in this respect) can reduce pyruvate to lactate. The key point is that this overall reaction is a chemical reduction, so that the ‘energy’ of NADPH is only of use in reductive synthesis.
The ‘energy’ of ATP (more properly its group transfer potential) is in fact the negative free energy of the hydrolysis of ATP to ADP (and orthophosphate), or to AMP (and pyrophosphate). If an enzyme can couple this reaction to another with positive free energy of hydrolysis then it can drive the second reaction. This important point is dealt with in Berg et al. section 14.1.3 and it is also worth reading the preceding section. ATP is not a reducing agent so is not limited to oxido-reduction reactions. (The hydrolysis of ATP can also be used to provide e.g. mechanical or electrical or light energy, which is why Berg et al refer to it in section 14.1.2 as “…the Universal Currency of Free Energy in Biological Systems”.)  In synthetic processes ATP (or other nucleotide triphosphates derived from it) is often used in reactions forming bonds (C–C, peptide, glycosidic, phophodiester). In some of these cases the hydrolysis of the ATP is used to generate an activated form of the basic component, which allows it to form the bond in a subsequent reaction.
Example of a synthetic pathway using both NADPH and ATP
In Fatty acid synthesis NADPH is used for two reduction reactions — ketone to alcohol, unsaturated C=C to saturated C–C bond — whereas ATP hydrolysis is coupled to the formation of the C–C bond of the condensing unit, malonyl CoA. This is shown in Figure 22.22 of Berg et al..
Example of synthetic pathways using ATP but not NADPH
The synthesis of the peptide bonds of proteins requires condensation of the carboxylic acid group of one amino acid with the amino group of another. This is not a reductive process and NADPH is not involved. ATP hydrolysis ‘activates’ each amino acid by attaching it to the ribose of a transfer-RNA in a bond that has a high enough free energy of hydrolysis to ‘drive’ peptide bond formation to the growing polypeptide chain at the peptidyl transferase centre of the ribosome.
Melanin synthesis?
This is an area in which I am profoundly ignorant, but from Googling it would appear that the first phase of melanin synthesis is the conversion of tyrosine to DOPA and then to indoles. These reactions are oxidative (using molecular oxygen) rather than reductive, so do not use NADPH, and the bond formation is cyclization to form the pyrole ring. This seems to proceed without ATP — presumably it is energetically favourable overall. There is a Wikipedia entry for the key tyrosinase oxidation reaction.
I suppose the anabolic phase is the polymerization of the aromatic units to form the crosslinked polymeric structure of melanin. This appears to be poorly understood, but there is certainly no indication that NADPH is involved, and it would appear to depend on chemical features of the environment of the melanosome, rather than on ATP. (There is a recent short review in this area by VJ Hearing).
You mention the role of sunlight in this process. Although sunlight in itself can provide the energy for one stage of the synthesis of Vitamin D in the skin, this is a ring-splitting step. A direct role in the polymerization of melanin doesn’t seem to be suggested.

Wow, thank you so much for such a detailed explanation, i'll also surely check the book out.


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RNA processing in eukaryotes
Why does post-transcriptional  processing of eukaryotic mRNA involve addition of a 3' polyA tail, rather than one of polyU, -G, or -C?

Quite interesting question. It also evokes the question of abundance / availability, since ATP (which is also used for poly-adenylation - besides its role in providing energy for many biochemical reactions), also appears to be the most produced and consumed molecule in humans, link

This is likely an evolutionary selection result, with A having won out. Most likely dude to availability and stability. Once addition of As to ends of RNA increased fitness of RNA, it was selected for. Simalar question is why is ATP often a substrate when GTP and CTP and such carry near equiv energy.

@SciEnt Please answer questions as answers, not as comments. That's what it says when you click in the comment box.

@David everytime i amswer like you have without any citation i get downvoted or told to cite. Thus my comment feels more appropriate

@SciEnt — I'm sorry but the text in the comment box means what it says. It is basic to the model that the Stack Exchange network follows. If you answer you have to be prepared for criticism. I accept your implied criticism of my answer as valid, and I have now added a reference.

As others have mentioned poly-A seems to be favoured because of higher concentrations of ATP with respect to other NTPs, due to its ubiquitous role. There is no real proof for this like most "why" questions. However, the ubiquitous presence of ATP is itself an evidence for a random selection of ATP and a subsequent expansion of its role. There is no thermodynamic explanation for this. The selection is likely to have been random.
Polyuridylation is also known to happen in eukaryotic cells (reviewed by Munoz-Tello et al., 2015) and one of the well known cases is that of the let-7 pre-miRNA (Heo et al., 2008). Polyuridylation marks this pre-miRNA for degradation.

And then it's also interesting to ask why GTP has a similar but far less ubiquitous role than ATP and CTP and TTP (to my knowledge) have no such role at all. I like to think about these obviously contingent features evolution brought up ... and expand this idea to the notion of us humans assigning functions to observations that might simply be contingent.

Most probably because the concentration of ATP in cells is much higher than that of the other nucleoside triphosphates and there was no functional requirement for a particular base in the tail. Its main function seems to be to work with an appropriate nuclease system to regulate the mRNA lifetime (see, e.g. Wikipedia article).


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How to use Transect-based sampling to select sample trees
I was wondering if you help me how to use Transect-based sampling to select sample trees

More detail on what your studying, the question you want to answer, and how you want to go about doing it would be very helpful. But I can answer this basic question of how to select tree's with a transect.
You will need:

Forms to fill out for data.
A compass.
A transect tape (really a very long tape measure, about 100 yards or meters).
A sampling design that fits your study. (I'm assuming you already have this, but if you want to talk more about it see above.)
A wooden meter stick.

Once you are in your 1st area and ready to select a random subset of trees.

Pick a random spot. (Usually done by throwing a stick or water bottle over the back of your head and going wherever it lands).
Pick a random number between 0-360. This will be the random direction you go in from your random spot. Find north on your compass, then which way your random number points. In your mind mark a way point in that distance you can walk to (a mountain peak, a distinct tree, anything).
Stick the beginning of your transect tape in the ground and start walking. The length that you walk should be predetermined from your study design.

Now you'll select trees to perform whatever measurement that you've decided on. But how? Most forests are not so dense that a straight transect tape will touch many of them. This is where the meter stick comes in. Walk back down the transect and choose any tree that comes within 1 meter of the tape on either side. Is the forest not dense enough to include enough trees that way? Then simply increase the length of your transect, or length that you measure out from the transect (ie. 2 meters, or 3 meters).
This is technically called a "belt transect". And it used in natural resources to measure things that are abundant, but not very dense. Such as trees in a forest or shrubs in the desert. It is essentially a giant quadrat.
Why all the randomness? Humans are naturally bias. Even if you think you are not being bias, you could subconsciously be choosing a starting point in a dense patch of trees, or a direction that will let you measure your favorite species. A rigorous study relies on a random sample of a population of interest, and small non-random decisions like this means it is not a random sample, but a bias sample.

Thanks for the prompt reply. Some detail about my study I want to investigate the effect of browsing on above ground carbon-stock in boreal forest. I have two treatments browsed and unbrowsed. 20 x20 meters plots are randomly selected to exclosure or unexclosed plot on the site. Each plot has four subplots measure a radius of 2 meters. To measure the carbon stock I need to transfer sample trees to the laboratory. I want to select a total of 80 sample trees. I found out Transect-based sampling will easy method to select my tree sample. let me know if you need more detail.

Hmm, based on what you said you should do it a bit differently. Within each 20x20 meter plot the 4 subplots should be placed either randomly or at equal intervals.
If you will have enough tree's with this will depend on the tree density. You can increase the radius or number of subplots to account for this.