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Catalytic Triad of Serine Proteases
Is serine considered an acid in the catalytic triad involved in the mechanism of action of serine proteases? It is donating a proton to His but I am not sure if this really qualifies as an acid?

It depends how you define an acid. For what it‘s worth, the chemical definition Google presents when I search is “a molecule or other species which can donate a proton or accept an electron pair in reactions”. On that basis the serine residue in the catalytic triad is acting as a weakly ionizing acid.
Of course in aqueous solution a free serine hydroxyl group is not acidic, but one of the important features of enzyme catalysis is that amino acid residues are operating in a different environment that can enhance their activity. One factor is the proximity of other residues. Another is the effective dielectric constant can be different in the hydrophobic interior of a protein which can exclude water molecules.


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Nomenclature of substrates for DNA synthesis
I have read in my school textbooks that both deoxyribonucleoside triphosphate and deoxynucleotide triphosphate are used in DNA Replication as substrates.
However, it is unclear to me whether the terms refer to the same molecule as one uses the term nucleotide and the other uses nucleoside. What confuses me is that nucleoside is a compound with a purine or pyrimidine base and a sugar and a nucleotide is the same but with the inclusion of a phosphate group.
Is it possible that the “deoxynucleotide triphosphate“ is used in artificial DNA replication as in PCR, and “deoxyribonucleoside triphosphate“ is the natural substrate for the replication of DNA within cells?

The short answer is that one can be almost certain (as certain as possible without seeing your textbooks) that both of these terms refer to the same thing: 2′-deoxyribonucleoside triphosphates. There is no difference in the substrate requirements for synthesizing DNA in vivo or in vitro (as with PCR), but it would be a worthwhile exercise for you to consider what would happen if you added 2′3′-di-deoxyribonucleoside triphosphates to a reaction mixture. If the question is not judged by others to be off-topic I may elaborate on the nomenclature and what parts are important when I have a moment.

Thank you so much sir! We have been taught about ddNTPs, if that is what you are suggesting. I believe that they are used in Sanger's method for determining DNA sequence as they lack an -OH group at 3' which is important for chain elongation and without this 3'OH the chain synthesis is terminated. And I would be very grateful to you if you do get a chance to elaborate on the nomenclature. Much obliged.

Summary
The systematic chemical names of many important biological molecules are too long to write routinely in full, and in any case were preceded historically by abbreviated forms which generally stressed the distinguishing features of importance to those studying their metabolism. Thus, as the poster points out, a molecule such as dATP (image below) has a base-(deoxy)sugar-phosphate(s) structure, and can be termed a deoxynucleotide. Adding triphosphate provides the additional information that there is more than one phosphate. A base-sugar(deoxyribose) combination is, as the poster states, a deoxynucleoside, but by extending this name to deoxyribonucleoside triphosphate, one indicates the addition of phosphates, so that one is, by definition, describing a deoxynucleotide. The reference to ribonucleoside indicates that the sugar is ribose, a specification lacking from the other definition. However, in practice these two terms are used to describe the same entity, one which might a little more completely describe as 2′-deoxyribonucleoside triphosphate (to indicate the position of the reductive change). This answer attempts to explain with precision the aspects of the nomenclature that are likely to be important to the biochemist or molecular biologist.
Disclaimer
The original question might be considered not to represent a biological problem, and one might argue for closing it on that account. However because of the very nature of trivial nomenclature, it is difficult for those without experience of the usage in a field to find the answer. In answering it I have tried to broaden the scope to include the aspects of structure that I feel are most likely to be to biological students.
Answer
It is convenient to start with ribonucleoside triphosphates (rather a deoxy- ribonucleoside triphosphates), and I have chosen a specific example in the molecule that is generally known as ATP:

Alternative names for this ribonucleoside triphosphate, in decreasing order of complexity, include:

[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
9-β-D-ribofuranosyl adenine 5′-triphosphate
adenosine 5′-triphosphate
adenosine triphosphate
ATP

Of interest to us are the three components of the molecule: a purine base (adenine), a sugar (ribose), and three linked phosphates. This is not reflected in the chemical nomenclature (1), so let us focus on the, albeit rarely used, biochemical nomenclature (2).

The ‘9’ specifies the position of the adenine ring that is linked to the sugar. This is not of particular interest in the context of the question.  (The numbering of the ring is, however, relevant to describing differences between or modifications  of the purine and pyrimidine bases1.)
The D-ribofuranosyl is a form of ribose (see below). The ‘D’ indicates that it is D-ribose enantiomer rather than the alternative, L-ribose. However, as all natural sugars are ‘D’ this is generally omitted (although discussions of why all natural sugars are ‘D’ abound2).
Ribofuranosyl indicates that the ribose is in the five-membered hemiacetal ring form (rather than the straight chain or the six-membered pyranose ring), but this is always the case in nucleosides, and so is not of particular interest.
The 5′ specifies the position of the sugar ring to which the phosphates are attached, the prime (′) indicating that the numbering is for the sugar ring (not that of the base). This is important, as it is relevant to the linkage in the (asymmetric) phosphodiester bond made to the 3′-OH:

The image above is for DNA, but before addressing the nomenclature there, we would point out:

The common α, β, γ designation of the three bond phospho-ester bonds. This is very relevant to the formation of polynucleotides (DNA and RNA) from their substrates, and in general to the utilization of the free energy the hydrolysis of these bonds for other processes3.

Finally we come to a structure of interest to the poster, dATP:

In the designation, 2′-deoxyadenosine 5′-triphosphate, the 2′-deoxy indicates that it is the 2 position in the ribose ring (′) that has had the oxygen removed (deoxy), i.e. OH is reduced to H. Although common knowledge, it is important that the student new to the subject understands this, as if it were the 3′ position that was reduced, it could not form the phosphodiester bonds of DNA. And it is relevant in many other contexts. For example the chain-termination method of DNA sequencing uses 2′,3′-dideoxy nucleotides to inhibit such bonds forming4, the single difference between ribose and deoxyribose allows us to understand the profound affect on the susceptibility of RNA to alkaline hydrolysis in nature5, and certain RNA molecules are hydroxy-methylated at this position.

Related information in SE Biology answers
1 Topical example related to base modification
2 Speculation on the origin of biological homochirality — not SE Biology
3 Why does ATP sometimes produce ADP and sometimes AMP?
4 Sanger sequencing by chain termination
5 Difference in stability of DNA and RNA

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Central diabetes insipidus and antidiuretic hormone
Are the levels of antidiuretic hormone in the plasma somehow hard to measure or are the results unreliable, and if so why?
Some countries have moved away from testing for ADH (the national health care systems no longer cover the test so one has to pay out of pocket) saying that it is no longer used either way in medical practice (i.e the test is obsolete).
I wonder whether water deprivation and desmopressin stimulation testing are actually alternatives or why not simply use all three tests. Water deprivation and desmopressin stimulation seem to me less appropriate since one seems to be "cruel and unusual punishment" and the other requires the intake of a substance.
In the National Library of Medicine I have searched for Diabetes Insipidus, Antidiuretic Hormone, Arginine Vasopressin. But at most I could find that the half-life is short (still twice as much as those of the hypothalamic releasing or inhibiting hormones).
Diagnosis and Management of Central Diabetes Insipidus in Adults
Physiology of antidiuretic hormone and the interrelationship between the hormone and the kidney
Above are a couple of papers I read in my search. It seems strange not to test for ADH since it is so central in Central diabetes insipidus (can't understand how the "alternatives" may be more appropriate, more cost effective or have higher diagnostic value).

ADH is highly unstable. This is why it is better to test for copeptin which is much more stable and correlates well with ADH. This is also written in the first article which you linked.
The other problem is that neither copeptin nor ADH levels won't neccessarily give you a definite diagnosis. If a patient has complete arginine-vasopressin deficiency, then ADH/copeptin will be so low that you will be able to diagnose central DI based only on those values and serum/urine osmolality. But if a patient has partial arginine vasopressin deficiency, you have multiple problems. First of all, the levels of ADH/copeptin are highly dependent on fluid intake, so you need controlled environment in order to get relevant measurments. Second of all, a patient might have equivocal results which don't yield a definite diagnosis - for example polyuria with polydipsia and with low normal copeptin, low urine osmolality, normal serum osmolality, normal electrolytes. These results do point towards central DI but you can't be certain. This is why you need the functional tests which may give you new information (though it's not neccessary that they will give you any new information - they might turn out equivocal as well).
Long story short - measuring copeptin is definitely sensible because it can sometimes diagnose central DI on itself. But functional tests are commonly neccessary because they are the only currently known way to formally test the maximum urine concentration a patient can achieve which is an important piece of information when previous results are equivocal.

Considering the question was tagged with biochemistry and proteins (I explicitly included the how so in the question) can you explain why (how) ADH is highly unstable?

I cannot because I sadly don't know why ADH is unstable. I thought the question "how so" was regarded to the reliability of the test and not to the stability of ADH.

@GeorgeNtoulos — Read the question, not the tags. Anyway I have edited it and removed the protein tag. The question is about why a method has been discontinued, not about anything distal to that. The question would have been better posted on Medical Sciences anyway.

@David I think the stability of ADH (and other things that have to do with the protein in itself like the method to measure, the secretion) is crucial to the question. I am not negative to a migration to Megical Sciences. If the community finds the question to better fit there I am all for it.

@GeorgeNtoulos — No. we only allow one question at a time. Your question is why a particular assay has been discontinued — a medical question. If this answer is correct and the reason is the instability of ADH, then a quite distinct question is “why is ADH unstable, from a biochemical standpoint?”  But you would have to do some homework on that topic before asking that separately.

@HinkoPihPih If the unreliability of the results is due to ADH instability the question becomes why is ADH unstable. That ADH is highly unstable is equivalent to yes the results are unreliable.

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If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?
These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing the plasma membrane, which is impermeable to charged molecules (hence the need for membrane proteins).
How do these two statements remain true simultaneously?

which small charges are you referring to? The trans-membrane parts are usually made out of hydrophobic amino acids that don't have a significant charge.

So does the overall charge on the macromolecule not have any effect if part of it is uncharged?

And, building on that, how does the charged element of the protein pass through the membrane after synthesis to create a protein which protrudes through both sides of the membrane?

Just a minor comment on the background part of the question: the net charge on a protein will depend on the pH, and is certainly not always negative. Similarly the charges on individual amino acids will vary, but again are not always negative. So for example lysine and arginine side chains are positively charged unless the pH is very high. This is why histones (rich in these residues) are positively charged at physiological pH, thus interacting with negatively charged DNA.

Transmembrane proteins are inserted into the membrane in the ER in a rather complicated system, there is a whole chapter about translocation of proteins in "Molecular Biology of the Cell".
The proteins are moved through an aqueous pore in the Sec61 complex, which explains how charged parts of a protein are moved across the membrane.
The parts of a transmembrane protein that remain in the membrane are usually composed of hydrophobic amino acids that aren't charged.
I strongly recommend you to read up on the whole translocation stuff in a cell biology book like the Alberts I linked. There's a lot more to it than what I wrote here.

Also, lipoproteins use covalently bound lipids to anchor to the membrane.

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What is the benefit of near-emptying the bloodstream in the mammalian kidney?
In the normal function of the kidney, the bloodstream is near emptied of fluids as it moves through the glomerulus, in which glomerular filtrate is formed.
As it proceeds through the Nephron, a significant amount of this material is returned to the bloodstream, and only a comparatively timy amount goes into the urine.
Why, in evoultionary terms, is it not more favourable energetically to remove only the small number of molecules, perhaph using specialised channels made of protein and activated only by a certain molecules which need removing, at a potentially huge energy saving?

Probably because it's easier to retain what the body wants than get rid of what the body doesn't want.
What does your body want to keep from your Urine? Pretty much water and selective ions (Cl-, K+, Na+, Ca+2, etc.). Maybe a few other things, depending on how healthy you are.
Now, what does your body want to get rid of in your Urine? Well, anything it can't get rid of in your solid waste. That includes pretty much anything water soluble that could harm you, whether it's Urea, chelating agents for heavy metals, ions your body doesn't want (excess minerals), excess vitamins, sugars (to maintain insulin levels), hormones, liver byproducts, and whatever dark horrors mother nature is concocting for us in the forms of virii or whatever else.
That's just the beginning of the list, but already you should start to see the impracticality of having active transport or coupled transport for everything. The list of transmembrane proteins needed to ferry all of the items your body wants to get rid of is a lot longer than the list of transmembrane proteins needed to keep what the body needs.
Then you have the "unknowns" - whatever else your body hasn't encountered yet, but will still be water-soluble. If the body required some sort of transport across membranes for everything it didn't want, then it would need to adapt to every single new compound it encounters. Given the relatively slow generation periods for humans, if a new compound turned out to be significantly fatal then the slow adaptation could spell disaster for any small populations and create serial bottlenecking events.
So, while it may not be energetically favorable to let water and ions pass into the Nephron and subsequent tubules to be reclaimed, Evolutionarily speaking it's probably strongly selected for. We may expend a lot of energy reclaiming water against its concentration gradient, along with whatever else we want from Urine, but at the same time we get rid of everything else we don't need that's filtered through the glomerulus. It doesn't matter what the "everything else" is - but we know we don't need it, and that's the big key.
With my current level of knowledge (B.S. - Biology) this is the best explanation I could think of, but I haven't read any specific papers nor heard any particular theories on why the kidney's components act as they do.

This is a great answer. Usually biological arguments based only on logic are a little questionable, but you make a very persuasive argument that the alternative arrangement is just not feasible.

I've spent a while thinking about this, but it makes a lot of sense, and before I read this answer, I was thinking along similar lines. With the time that changes due to natural selection take, it must make sense to remove everything that isn't exactly what it needs, so newly synthesised or evolved poisons can still be removed, even without the body knowing their sturcuture.

I would argue from an evolutionary perspective: not all kidneys are created equal. The mammalian kidney has a long evolutionary history and potentially a lot of phylogenetic inertia. Mammals do what they can with what they inherited from their ancestors.
The metanephric kidney, which is what mammals have, is thought to have evolved with the first amniotes (terrestrial, cleidoic-egg-laying tetrapods). However, the metanephros, from when the definitive metanephric kidney evolved, was (is) present in most fishes as well as amphibians. These groups live all or part of their lives in fresh water, so their tissues are hyperosmotic relative to the water. Their problem is not retaining water, but getting rid of all the water that enters their tissues via osmosis. (Marine bony fish have small, aglomerular kidneys.) They produce large volumes of urine, and their kidneys are set up to reclaim essential minerals, etc., as @MCM describes.
So the first amniotes, although now living on land, had a kidney that had evolved in conditions where water was in excess. It evolved for filtering large volumes and reclaiming minerals. Amniotes simply adapted it for a water-poor environment.

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Does DNA react in all of the ways most other acids do?
As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of a state of equilibrium in water.
Do these reactions and equilibria occur to DNA (or, for that matter, RNA), which has only ever been described to me as an 'acid', and does this affect the processes DNA goes through, like replication and transcription?

It may seem counterintuitive that deoxyribonucleic acid has nitrogenous bases. Nonetheless, nucleic acids (thus including RNA) were called that way because the phosphate backbone (linked by phosphodiester groups) is a derivative of phosphoric acid.
Phosphoric acid

Image Source
Phosphodiester group

Image Source
Note that the only difference between these two groups is that in the case of the phosphodiester, two O-H bonds are replaced by O-C bonds. This make the last remaining hydrogen atom quite acidic (can quickly be identified by how the conjugate base exhibits resonance). In fact, it is so acidic that at physiological pH, the phosphodiester group is deprotonated, giving that nucleotide a negative charge. This property does have a profound effect on DNA's structure and "behavior" in a cell, and is often exploited in genetics, such as in gel electrophoresis.
An interesting fact is that this acidity of the phosphodiester group actually competes with the basicity of the nitrogenous bases. However, since most often DNA is double-stranded, individuals bases will hydrogen-bond with its partner to make base pairs, which stabilizes and thus reduces this basicity.
TLDR: Although different acids of different molecular composition can act in very different ways, the overall acid-base chemistry is seen in nucleic acids.


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Will lipid molecules 'flip-flop' over a membrane without the use of an enzyme?
All of the references to this I can find refer to enzymes like Flippase making it 'easier' or 'more likely' that the translocation will occur, rather than actually make it possible.
The following is from Alberts

In the ER, however, phospholipids equilibrate across the membrane within minutes, which is almost 100,000 times faster than can be accounted for by spontaneous “flip-flop.”

Does this mean that left unattended, any phospholipid membrane will 'flip-flop' spontaneously, just very slowly, and can this be observed?

Bilayer components will 'flip-flop' at measurable rates, but these are very different for different lipid classes. Here are the results of an experiment using fluorescently-labelled analogues.

Bai, JN and Pagano, RE (1997) Measurement of spontaneous transfer and transbilayer movement of BODIPY-labeled lipids in lipid vesicles. Biochemistry 36:8840-8848 DOI: 10.1021/bi970145r

The authors followed the transbilayer (flip-flop) and interbilayer movement of fluorescently-labelled analogues of various membrane lipids: sphingomyelin (C-5-DMB-SM), ceramide (C-5-DMB-Cer), phosphatidylcholine (C-5-DMB-PC) and diacylglycerol (C-5-DMB-DAG) in a system of unilamellar vesicles consisting of 1-palmitoyl-2-oleoyl phosphatidylcholine.
The results were analysed in terms of a model in which the labelled molecules could move between vesicles and between the two monolayers of the bilayer.
half times:
            interbilayer    transbilayer (flip-flop)
C-5-DMB-SM  >21 s           3.3 h
C-5-DMB-Cer 350 s           22 min
C-5-DMB-PC  400 s           7.5 h
C-5-DMB-DAG 100 h           70 ms

So, for the phospholipid tested the half-time for flip-flop was 7.5 hours.

This answer is a good starting point and gives a flavor of the issue. I think it's worth noting though that there is a pretty big variation between different experiments on flip-flop rates. I think there are orders of magnitude changes, and so a more recent reference would be good. (Anyone interested in this could probably look at the 1997 ref. and see what papers cite it in Google Scholar.)


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Using DTNP to find free thiol groups on a protein
I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA).
After measuring the absorbance, finding the concentration of TNB and calculating the concentration of the BSA, I've come out with a result of around 0.4 free thiol groups per molecule of BSA, which seems unlikely! There is either a free group or there isn't!
Yet, the implication from the demonstrator is that is is the correct result!
How can this be? Is it possible to get a value of less than one in an experiment like this?

This is a perfectly reasonable result. Remember that you are measuring an average value for a very large population of BSA molecules. Essentially what the 0.4 means is that at any one time, about 40% of the BSA molecules have a free thiol, while the rest of the cysteine residues are disulfide-bonded.


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Can a single strand of mRNA form different polypeptide chains?
My book has a statement:
A single strand of mRNA is capable of forming a number of different polypeptide chains.
In my opinion this statement is wrong because a single strand of mRNA will have same sequence of codons. So, every time it gets translated, it produces same polypeptide chain. But, according to my book this statement is correct.
Am I wrong or is my book wrong?

Is your book talking about eukaryotic or prokaryotic mRNAs? You (and anyone answering) need to know as the rules are completely different in the two cases.

And you should also provide the name and edition of your book. We may then be able to check if your are misquoting it or quoting it out of context. (We have ways of finding these things...)

Could you please add some more context to the quote from the book (i.e. what is the topic of the paragraph/chapter, what is the title of the book etc.)

I believe, your book refers to  polycistronic mRNA. This is mRNA where multiple genes are encoded together in one mRNA and are often (but not necessarily) translated one after another. This is mainly found in prokaryotes where the proteins encoded on the same mRNA often form a metabolic pathway together.

I would change 'mainly' to 'only' unless you or anyone else can give a eukaryotic example. The mRNAs that use IRESs only have a single one as far as I'm aware. Polio, for example makes a single polyprotein which is proteolytically cleaved.

@David: There are a few rare cases of polycistronic mRNA in insects.

@David IRESs can lead to production of multiple polypeptides. The mRNA is essentially polycistronic in this case. Example http://www.ncbi.nlm.nih.gov/pubmed/19285701. The proteolytic cleavage is a different mechanism.

Thanks for the links. This stuff has clearly passed me by. It would be interesting to know the mechanism in the case of the insect short peptides — whether it's leaky scanning or what.

You can come at mRNA from two directions. Remember that human genes are largely monocistronic, in other words they often code for a single protein. If we look at prokaryotes, however, polycistronic genes such as those in operons are very much possible. From a single lac mRNA you can get multiple proteins.
For humans with monocistronic genes, you can code for multiple isoforms, however. A good example is protein kinase C: You have PKC-α, PKC-δ, and so forth. So how can this be? In part, you can look at splicing. What gets initially transcribed from your human gene is a pre-mRNA, in that the entire gene contains introns and exons. The spliceosome knows where to cut out introns, and you technically get a mature mRNA that is made of only exons and codes for protein.
In special cases, however, RNA-binding proteins and—at times in concert with, at times to the detriment of—the spliceosome machinery alternatively splice some other combination of introns and exons (sometimes, introns are kept!). And so from the PKC gene, you still get PKC, but a different isoform of it. The different proteins that different types of cells or tissues express that can interact with the splicing machinery are capable of taking the same genetic information, the same pre-mRNA, and make different polypeptides out of it.

Alternatively spliced transcripts are technically different mRNAs.

@WYSIWYG yes, but the OP's book doesn't specify whether this is mature or pre-mRNA.

I don't see how you can assume the book refers to eukaryotic mRNAs. Especially if the book is old, it could quite well refer to bacterial polycistronic mRNAs, which could well be the answer. But without qualification the question cannot be answered, and this point should be emphasized to naive users (and responders). Certainly differential splicing is completely irrelevant and quite misleading, as WYSIWYG might have said if he were as blunt as I am.

I agree that Splicing is off topic and should be removed from the answer.

@terdon the quoted statement in the question clearly states mRNA not pre-mRNA.

@Thawn yes, but it could be misquoted since there is no context and it doesn't seem very trustworthy as a quote to begin with since it claims that mRNA can "form" proteins. I just figure it might refer to polycistronic prokaryote mRNAs or unspliced eukaryotic transcripts. For all I know, the book's authors might even have been thinking of post-translational modifications. Without more context, it's hard to know.

@terdon I just asked the OP to add more context to the quote. Hopefully he complies and we can find out :)

As much as I love Biology SE, I will need down-votes to defend their votes here because I see nothing wrong with this answer. The assumption is that we have mRNA, and unless explicitly noted I've assumed any mRNA to be included, including pre-mRNA.

@CMosychuk I read the question twice and while I understand the criticism, I believe the book is talking about splicing variants as well. It is just badly worded. In any case, I vote to keep this answer here so that both scenarios (1 mRNA -> multiple proteins and mRNA -> multiple proteins) are covered.

@CMosychuk There is nothing wrong with this answer as long as you clarify the premise, which you did. Someone downvoted my answer too, which is certainly not "not-useful" or "poorly researched". Nevermind.

Apart from the polycistronic case there is another possibility of one mRNA yielding multiple proteins. By one mRNA, I mean that the RNA is not in any way altered because of RNA editing or other mechanisms.
Translation can be initiated at alternative sites leading to production of different protein products (Touriol et al., 2003). VEGF is one of the genes that exhibits this phenomenon. However, the precise factors that regulate the choice of the translation start site are not very well known. The basic mechanism, however, seems to be masking of the alternative start sites by different factors such as secondary structures and/or trans regulatory factors.
Similarly a stop codon can be skipped. This is frequently seen in the case of the UAG (Amber) stop codon. This phenomenon is called amber suppression (see this post). Again, the factors that regulate this phenomenon are not well known.
Having said all this, I am 100% sure that your textbook refers to polycistronic mRNAs only.


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What bird is this (found at Alice Springs Desert Park in Australia)?
I was reviewing photographs of the animals we found on our trip to Australia during the past September and I cannot find what is the bird in the picture. It was found inside Alice Springs Desert Park, so it has to be a native bird, same as all the others.

Could anyone please help me?

I'm tempted to say it could be a golden-headed cisticola (Cisticola exilis), but it's a difficult angle to clearly see the head.

Thank you @cezar it totally looks like this one, the habitat matches and I've searched in several photos on flicker and google and it seems like the bird :)

It is a Cisticola exilis as stated by @cezar
If someone has any objection please reopen this.

Thanks and sorry @theforestecologist I'll take that into account next time!


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Why is plasma glucose concentration not double that of whole blood?
It is known that the concentration of plasma glucose is 12% higher than that of whole blood. But since 45-50% of whole blood is red blood cells, shouldn't the plasma glucose be almost double — since it's just the hematocrit that is missing from the denominator.
Obviously something is wrong with this line of reasoning, since it does not meet the observations. Why so? Does whole blood glucose also measure intra-cellular glucose? Is that the reason for the lesser than expected increase?

What units are you talking about — concentration or amount? Please cite values with units, then we can address your question. Otherwise it is unclear and I, for one, will vote to close it on these grounds.

@David I've edited the question, I'm talking about the glucose concentrations in whichever units.

Quoting from the paper: "Within one hour after blood collection protein-free filtrates were prepared from whole blood and plasma according to Somogyi [6] in the following modification [7] : to 2.0 ml of distilled water 0.4 ml of whole blood was added and mixed. Then 0.8 ml each of balanced zinc suiphate and barium hydroxide solutions were added, in this order, slowly and with constant mixing. The mixtures were then centrifuged for 10 minutes at 3000 rpm. (2000 X g). The protein-free filtrates were carefully sucked off with Pasteur pipettes." i.e. the measurements include intracellular glucose.


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Why isn’t Haemoglobin a plasma protein, rather than being encompassed by the erythrocyte?
Erythrocytes (red blood cells) are a common feature of almost all vertebrates. What evolutionary advantage do they provide in containing haemoglobin, rather than it being just a plasma protein? In fact, haemoglobin is dissolved in plasma in a few annelids and haemocyanin in cephalopods.
The only reason I can think of is that haemoglobin is small enough to get filtered into the tubules of the kidney and is renotoxic. Maybe that's why it had to be packaged into erythrocytes. But isn't this a greater cost than reducing the pore size to prevent it being filtered out? Also, doesn't haemoglobin or haemocyanin get filtered into the primitive kidneys of annelids and cephalopods?

I have edited your question a little. Note that haemoglobin may be coloured, but is not classified as a pigment. Also it is a reasonable sized protein (four chains of about 100+ amino acids), although I have not edited that part.

To the man with a hammer, everything looks like a nail.

The poster’s hammer seems to be kidney function. Mine is the biochemistry of the erythrocyte (red blood cell). Others, no doubt will be able to provide yet different perspectives.
From a biochemical point of view the erythrocyte has a limited repertoire of metabolic pathways compared with other tissues. However it does have an extremely active pentose phosphate pathway (not universally found in tissues) and the function of this is to provide the reducing cofactor NADPH, which is needed to maintain glutathione in a reduced state. The importance of reduced glutathione in these oxygen-carrying cells is that it provides protection against reactive oxygen species — something that could not be done — or at least not controlled so well — in the blood plasma.
Another feature of haemoglobin is that the equilibrium between the oxy- and deoxy- forms involves the small triose molecule, 2,3-bisphophoglycerate. This is described in the answer to another question. The ability of the erythrocyte to synthesize this molecule allows the sophistication of this control.
I imagine there are many more examples. (Any added in comments will be added.)
One could argue that these metabolites are not indispensable for organisms (glucose phosphate dehydrogenase deficiency does cause haemolytic anaemia in man), and this presumably explains why the simpler organisms you mention (and about which I know little) can dispense with red cells.
But a question certainly worth asking.

Cool! I'd thought of compartmentalization giving some biochemical advantage but couldn't think of how since G6PD as you mentioned isn't indispensable. But after a little search I found out - absolute deficiency of the enzyme <10% activity leads to chronic hemolytic anemia. Only the moderate deficiencies are 'stressor' induced hemolyses.

But it is important to note that a G6PD deficiency causes anemia by hemolysis - bursting of the RBC. But we are talking of a case when there is no RBC, so the argument doesn't make much sense. Bt yeah 23bpg might play an important role...

@Polisetty — The argument makes a lot of sense. As a medical student you are only thinking about diseases, not the underlying biochemistry. The anaemia is just the end result of the damage caused by active oxygen species resulting from oxygen transport by Hb. In the plasma they would affect the walls of the veins and arteries (or whatever — I don't do cellular stuff) and other proteins.

An additional aspect is that the availability of iron usually constrains the growth of pathogens. Cassat and Skaar in "Iron in Infection and Immunity" state:

Iron is an essential nutrient for both humans and pathogenic microbes.... Given the absolute requirement for iron by virtually all human pathogens, an important facet of the innate immune system is to limit iron availability to invading microbes in a process termed nutritional immunity. Successful human pathogens must therefore possess mechanisms to circumvent nutritional immunity in order to cause disease.

Later they say:

Even in the absence of infection, several facets of human iron metabolism ensure that iron is scarcely accessible to pathogenic microorganisms. First, the majority of iron in humans is sequestered intracellularly, complexed within hemoglobin inside erythrocytes. Some pathogens have therefore evolved mechanisms to liberate hemoglobin by lysing erythrocytes to ultimately extract iron from heme.

Thus, one advantage of sequestering hemoglobin within erythrocytes is that it slows the growth of invading pathogens by making necessary iron more difficult for the pathogen to obtain.

Interesting. I never knew that.

Some pathogens have therefore evolved mechanisms to liberate hemoglobin by lysing erythrocytes to ultimately extract iron from heme.I'm just taking a shot in the dark here but is plasmodium part of these pathogens?


text:
How is the urea cycle regulated with respect to protein deficit?
Proteins cannot be stored in the body. Excess proteins from the diet are deaminated in the urea cycle that takes place in the liver. The liver is the first contact since these amino acids are delivered through the portal circulation.
What I do not understand is what controls the extent of amino acid breakdown in the liver. For example, suppose there is a man who hasn't had protein in a month, and has a net protein deficit, what determines that there shouldn’t be much deamination in the liver?
For carbohydrates and sugars, insulin and glucagon balance regulate the main enzymes controlling the steps in glucose phosphorylation hence maintaining homeostasis. Since this is at an organismal level and not the cellular level, like glucose, I would expect the control of urea cycle also to be hormonal. Since there is no hormone that reflects protein status (at least to my knowledge), what determines the activity of the urea cycle?

Preamble
This question is extremely broad because, rather than there being a ‘one-click’ answer, whole areas of amino acid metabolism need to be considered. This is both inappropriate and impossible to do here — even if I understood everthing about it (which I certainly don’t). However I shall provide a specific biochemical answer (or partial answer, as all is not understood) regarding the regulation of the urea cycle, after commenting on some of the assumptions implicit in the question.
Comments on the assumptions of the question
I am not sure that ‘protein deficit’ is a useful metabolic construct. From the point of view of a clinician, yes, one can say that someone is suffering from protein deficiency or malnutrition, but in metabolic terms protein is a not the highest priority and will be broken down to provide glucose for the brain during long-term starvation. And it is well established that protein synthesis is under the control of hormones and growth factors (reviewed here), and this will affect the fate of dietary amino acids or those produced by protein turnover. In addition, the emphasis on hormones in the question seems to ignore the role of the concentration of amino acids and other intermediates in regulating metabolic pathways. Finally, there is control of the expression of the genes encoding enzymes of the urea cycle, which operates over a longer time period.
The Medical Biochemistry site provides a wider perspective on amino acid metabolism and nitrogen metabolism and the urea cycle.
Regulation of the Urea Cycle
The first point that should be emphasized is that the urea cycle does not exist in isolation from other metabolic pathways, but is intimately connected to them. This is shown in the diagram below:

It should be remembered that ammonia for the urea cycle only comes from the deamination of glutamate by glutamate dehydrogenase, and the transamination of other amino acids to produce this depends on a pool of α-ketoglutarate (2-oxo glutarate). A requirement for α-ketoglutarate also exists in relation to the regeneration of aspartate for the cycle itself.
The entry point of ammonia into the urea cycle is the reaction catalysed by carbamoyl phosphate synthetase:

It turns out that this reaction requires N-acetyl glutamate (NAG) for activity, and it is thought that this plays a regulatory role in the urea cycle, as increased intake of protein has been found to increase the hepatic content of NAG. Although aspects of this remain to be clarified or resolved, it is thought that the regulation occurs at the point at which NAG is synthesized from glutamate in a reaction catalysed by the enzyme N-acetyl glutamate synthase:

This enzyme is activated by arginine, giving rise to a model for regulation described more fully in a review by Caldovic and Tuchman, from which I quote the following:

“… the hypothesis that NAG is a regulator of ureagenesis… If this hypothesis is correct, mitochondrial concentrations of glutamate and/or arginine may reflect the need for nitrogen disposal through their effect on the production of NAG by NAG synthase, glutamate as a substrate and arginine as an effector.”

But how do local intracellular concentrations of amino acids give the big picture of how much to regulate?

The idea is abundance of amino acids means the need to dispose of surplus. You are perhaps worried that this would deprive e.g. muscle tissues of amino acids following return to a protein diet after long-term starvation. I should have mentioned that there appears to be changes in amount of the urea cycle enzymes in the longer term by gene repression. There will also probably lower alpha-keto glutarate because protein and carbohydrate starvation tend to go in concert. It's multi-factorial and quite complex.


text:
I think evolution has goal
Richard Dawkins says evolution doesn't have any goal. But I think evolution has one. At the end evolution creates intelligent being. If we find another earth like planet evolution sould have the same pattern. Evolution is not a chaotic event. Am I wrong?

This is not much of a questions, but only an empty proposition which is not supported by any logical arguments or empirical proofs.

What do you mean at the end? What makes you think we are at the "end" of evolution? If anything can be said to be the "most evolved", that would be viruses, not humans.

Yes you are wrong I am afraid. Evolution is the process of change through time of species by inherited changes. Heritable differences mainly come about from random mutation in the genome. These genetic differences between individuals lead to fitness differences between individuals, ie one individual is better able to produce offspring, thus spreading more of its genes in to the following generation, than another individual. For example, environmental change causes selection for a dark body morph in moths, stabding genetic variation and new mutations affecting body colour is then more favored by selection, and those with the dark body genes survive and reproduce better.
There is no end or goal to evolution. It is often mistakenly said that humans have stopped evolving. This is wrong and to suggest we have is to suggest that evolution is directed and has an ultimate goal. As long as genetic fitness variation exists there will always be some level of evolution because there is a difference between individuals in selection coefficient. Selection is also very unstable, it can change drastically an rapidly, evolution could only then stop if selection was constant and favored one "ultimate genotype" over all others in which case all genetic variation would cease to exist.
If we found another planet which had the exact same conditions and time as earth we may find the same species, but it is not likely. It requires the same mutations and selection processes occurring. Analogous to this is the observation of "many solutions to one problem" where different species use different adaptations to deal with a common problem. For example, geting oxygen is difficult for water deelling species. Sea mammals like whales gather oxygen by going to the surface and breathing and then holding their breath. Fish have evolved gills, a different solution to the same problem, to harvest oxygen from the water. These solutions evolve from random changes with selection acting only on the results (those that could filter oxygen from the water or hold their breath the best survived and reproduce best).

I'm writing this on my iPhone in an airport - if people have some references for examples and reading please feel free to add them.

What do you think what is the next evolutionary step for mankind?
I didn't said we would find same species in another planet. I said we may find same pattern. I think evolution has a pattern and there for it can be said as a goal. You put the initial value you will find the final value. I think it is not a chaotic process.

Just remember that every species is undergoing evolution and few, if any, have evolved intelligence...

@KarziArafatAhmed Just as evolution can lead to different solutions to one problem, as above, it can also lead to similar ones between species. This is called convergent evolution, given the same selection as on our planet, another planet could host similar species as ours. It is not moving towards a goal. How would it know where to go? What is controlling it?

@KaziarafatAhmed On the inherently tricky and mostly unanswerable topic of future human evolution you can look at these earlier posts: Scientifically based theories of future human evolution?, Is evolution possible in contemporary humans?, ...

[cnd]: ...also Medical progress and human evolution? @KaziarafatAhmed


text:
Is there any relation between weight class and extreme lifting performance in O-lifting?
We usually thought that weightlifting is a tough game. It is only for great physique.
There are 6 man in history who lifted  3 times their body weight. Check here.
3 of them are Bantamweight(56kg), 2 of them are Featherweight(60kg), and 1 is at Lightweight(67.5kg).
All of them are light. Is there are fact that light weighted are more efficient in weight lifting?


text:
How long does a tan last?
How long do melanocytes and melanosomes continue to protect DNA after UV exposure? Basically, if skin is tanned, then over the next month it is shed, will melanocytes continue to produce high levels of melanin to keep the new skin tanned without requiring more UV exposure? The cells react by producing more melanin after exposure but will they continue to do this in new skin cells?

The tanning response to UV occurs in two phases:

The immediate response begins at exposure to UV-A, reaches a max at 1-2 hours, and fades between 3 and 24 hours.
This article speculates that this is due to the redistribution of melanosomes rather than additional melanin production.
The delayed response is more durable, occurring by repeated exposure to UV-B, as well as as UV-A and visible light. "It is a gradual process in which the skin starts darkening 48–72 h after irradiation, reaches a maximum ∼3 wk after exposure, and the skin does not return to its original melanin content until ∼8–10 months later."
This source says this is due to additional melanocytes, melanosomes, and more melanin, in general.

Both processes are influenced by genetic factors.
Source for the initial points, which also contains interesting details on the enzymes involved in these processes.

Thanks for the resources, I'll need some time to read them :-D

Not a problem - it was interesting. I might start with the one source I linked to twice in the body of the answer. Although it's older, it is also not written by Avon scientists, and is less likely to be biased.


text:
How exactly does marijuana damage brain cells?
I've heard that THC can cause permanent damage to brain cells. I've also heard this reffered to anti drug propaganda. Another theory i've read is that temporary effects reduce intelligence but long term results are not affected. If Marijuana does cause permanent brain damage how does it do so? How exactly does it kill the cell?

@terdon provides some relevant info in a comment here: http://biology.stackexchange.com/questions/7693/whats-the-difference-between-life-expectancy-of-cigarette-smoker-and-general-po

@dd3 that post is more about smoking.. Marijuana can be consumed in many more ways..

Bear in mind that THC is only the strongest of all the physiologically active substances contained in marijuana (several hundred different ones according to our lecture). Hence, the effect of marijuana can be different from pure THC, especially if the mixture contains toxic leftovers from processing the drug.

There is no damage of brain cells, as in the context of lesions in neurodegenerative disorders. There are, however, two mechanisms attributed to the memory loss associated with cannabis/marijuana and these are purely physiological responses.

Astrocyte mediated: CB1R (cannabinoid receptor) in astrocyte gets activated and promotes glutamate release. This glutamate induces Long Term Depression in post synaptic neuron.
Synaptic currents can cause both LTP and LTD. The properties of the synaptic current wave dictates the outcome. Please refer to review articles on LTP and LTD for more information.
GABAergic interneuron mediated: CB1R activation in GABAergic interneurons (inhibitory neurons) causes activation of mTOR pathway and promotes protein synthesis. CB1R activates mTOR through PI3K/Akt.


text:
How to compare Smith–Waterman algorithm implementations?
Assume that you have two implementations of the Smith–Waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences.
I would like to know if one can be certain that these implementations do a good job of aligning (i.e the program has been correctly written). How do I benchmark this?

Is this a question on DNA? Could you give some more context to the question? Better tagging may help too.

They don't apply any heuristic to speed it up. The essential feature of the Dynamic programming algorithm is it gives you one of the  correct answers. You don't have to speed it up because it runs in real time. This is an important point and I suggest you modify your question.

I am not sure that 'i.e.' is a right word. Alignment quality is a matter of substitution matrices and gap penalties and it has nothing to deal with correctness.

You need to clarify the question. Smith-Watermann is a specific algorithm. There are no other implementations of it. There can be additional steps that are used in conjunction with SW and unless you atleast tell the names of these packages, we cannot comment on how one of them may be better than the other. As far as comparison goes, the one that does your job reasonable well in less time is the better implementation. To check if the program has been correctly written you should look at its source code. That is essentially bug finding.

There are only two possibilities for Smith-Waterman alignment with a given cost matrix. It's either right or it's not.
Honestly, whatever you're using, it's really really unlikely that a pure Smith-Waterman implementation is wrong. It's not that complicated, really. There are a lot of heuristic improvements on Smith-Waterman, but if you're both a) sure you don't want to test them b) sure they're not being used, you can always generate lots of random sequences and align them in pairs. If any pair doesn't align with the same score in the same way, something is wrong and you should investigate further.

I imagine that technically your question can only be answered on a computing science Stack Exchange. The pragmatic biology answer is there is no problem. This is such a well established algorithm that the implementation on any reputable site or from any reputable provider is likely to be OK. No heuristic is involved so if you compare different implementations you should get similar answers. I say similar rather than identical because there may be more than one alignment with the same score but only one is selected. Generally it makes no difference.
I suppose there is one aspect of the Smith–Waterman algorithm that could differ between implementations, but it is one for which you, the user, will have the ultimate responsibility — the scoring system. Your basic assumption is that two sequences are related, and you are asking the program to give you the pairwise alignment that  ‘best’ expresses that relatedness. ‘Best’ in the program translates into the highest score on a system that assigns a different value to the alignment of different pairs of all 20 amino acids (a comparison matrix for proteins) and specific penalties for the introduction of a gap (to allow for an insertion or deletion) and the extension of a gap once introduced. The implementations offer default values (I imagine these are similar in most programs) but its up to you to decide whether they are appropriate for the sequences that you are comparing, and to change them if necessary.
What are your options and when might it be necessary to exercise them? You can choose from different comparison matrices derived from aligning blocks of sequences for the same protein in organisms of different evolutionary separation. These matrices differ because some amino acid changes require only a single base change in the codon, whereas others require changes at all three positions of a codon,. The latter are less likely to occur over short evolutionary time spans (e.g. between mouse and rat) than at longer ones (e.g. between mouse and bacterium). So ideally you should employ the comparison matrix most appropriate to the sequences you are comparing.
Circumstances where you might wish to change the gap penalties or even customize the comparison tables are, admittedly, esoteric, but I would advise that it is better to think about the applicability of the scoring system to your biological problem than to worry that someone might have made a hash of implementing the computer algorithm.


text:
What are the essential criteria for sleep in living organisms?
I was reading this fascinating article about how sleep evolved before brains, and it got me thinking "can plants sleep" and "what is sleep anyway".
A line in the article states:

Studies by a team in South Korea and Japan showed that the hydra
periodically drops into a rest state that meets the essential criteria
for sleep.

But after looking around I am unable to find the "essential criteria for sleep" - Before I am able to answer questions like "can plants sleep" I think I first need to understand what these essential criteria for sleep actually are.
Can anyone here help me out?  Many thanks in advance.

I have edited your question because criteria is a Greek plural (the singular is criterion). This is relevant to your question because the answer to your question is not a single thing. (btw Have you researched this at all? I imagine there is a wide literature on this topic.)

I take it you did not even read the article. The article quite nicely expounds on this question. The whole idea is that sleep used to be considered as a human or psychological phenomenon that could only be studied by EEG, and clearly sleep was a phenomenon that goes deeper and wider in biology than just EEG waves. From the same article, just a little below:

She distilled a set of behavioral criteria to identify sleep without the EEG. A sleeping animal does not move around. It is harder to rouse than one that’s simply resting. It may take on a different pose than when awake, or it may seek out a specific location for sleep. Once awakened it behaves normally rather than sluggishly. And Tobler added a criterion of her own, drawn from her work with rats: A sleeping animal that has been disturbed will later sleep longer or more deeply than usual, a phenomenon called sleep homeostasis.

The keyword is behavioral criteria.
This is cited, I recommend a read-through.
I also recommend reading the rest of the article, it guides you through the status quo in sleep science which may further answer more of your questions. At the end, there is an exposition on animals without brains that seem to be sleeping. The hydra is one of them.


text:
Why are truncations in Receptor Tyrosine Kinases so sommon in transformations?
Receptor Tyrosine Kinases (RTKs) present themselves on the surface of a cell as monomers until a ligand (such as a mitogen) binds and causes the formation of the active dimer. However I do not understand why truncations are so commonly seen in retrovirally delivered oncogenes or in oncogenic mutations. My confusion here is that if mitogen binding of RTKs facilitates the close proximity of two monomers, then simple overexpression should allow for increased transphosphorylation of monomers, and therefore be mitogenic (which it does). But then what advantage would a truncation that removes the extracellular portion of an RTK have in increasing transphosphorylation of monomer units?

I've edited this a little (defined the abbreviation as a start) but the question is so badly expressed I think it should be let die in the absence of a revision of the answer provided by @Mr-Bauer providing references.

As you said the simple overexpression can lead to transphosphorylation and activation of mitogenic signalling. This helps the cancerous cells to survive.
By truncation of the molecule the cell also gains a benefit, because it could prevent inhibition of the receptor from outside the cell.
The truncation furthermore could be induced by treating cancer with inhibitory antibodies against the receptor. For example a treatment with anti-EGFR antibodies could induce resistance by mutation and selection. One of this mutations could be the truncation of the receptor.

Welcome to Bio. References are appreciated here, most notably when making strong statements like anti-EGFR antibodies like Cetuximab could induce an evolution of the cancer cells whereby the truncation of the receptor benefits the cancerous cells.

http://www.nature.com/nrclinonc/journal/v7/n9/full/nrclinonc.2010.97.html maybe

Though I have to agree, it basically says "Hey, nothing wrong, nothing to regulate here" to the outside of the cell, much like truncated NKG2D ligands make it harder for immunosurveillance to do it's job.

Thanks for the comment, I changed my answere a little bit.

The reference from Kendall is very good. Also I would reference this paper link to show annother treatment induced mutation of cancer.

It technically isn't a treatment induced mutation ; K-Ras simply is a subclonal event in those patients that leads cells with it to acquire a selective advantage in the presence of an EGFR inhibitor, but are selectively unfit when the EGFRi is removed.
http://www.ncbi.nlm.nih.gov/pubmed/26030179


text:
Meaning of “gene expression heterogeneity” of embryonic stem cells
What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I have found did not really elaborate on what it meant, and I do not know where else to find the definition.
In particular, I want to understand heterogeneity in the context of stem cells. In the paper by Angarica and Sol, 2016, it reads:

“Experimental studies at the single-cell level have revealed that embryonic stem cells (ESCs), and more generally pluripotent stem cells (PSCs), exhibit significant gene expression heterogeneity.”

“Single-cell studies have allowed gene clustering, depending on the levels of heterogeneity in the gene expression landscape in PSCs.”

Does it have more to do with the variation of its expression in the population?

“In mouse ESCs genes exist that are uniformly expressed in most cells and exhibiting a unimodal distribution (Oct4, Rest, Tcf3, Sal4); other genes exhibit bimodal expression and are expressed in some populations but not in others (Nanog, Rex1, Tet1, Esrrb), and yet another group of genes display sporadic expression (Neurod1, Klf4, Otx2, Pax6) and are undetected in most cells but highly expressed in some speciﬁc subpopulations.”

Reference:

Angarica and Sol, 2016, Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation.

Heterogeneity is a noun meaning:

the fact of consisting of parts or things that are very different from each other

In scientific use the context determines what is differing.
The context here is gene expression in individual embryonic stem cells (presumably single-cell RNASeq). Here the heterogeneity in expression would be for the genes

…(Neurod1, Klf4, Otx2, Pax6)

for which the expression is

…undetected in most cells but highly expressed in some specific subpopulations.

The conclusion is that although the embryonic stem cells may appear to be a homogeneous population (all alike) and do show similarities in many genes that they express, they must, in fact be a mixture of two (or more) types. (This makes the generally accepted assumption that the basis for distinguishing cells is the genes they express and the proteins they make.)
Thus the idea, expressed in the question, that the cells are identical is incorrect. I know little about stem cell differentiation, but I would assume the implication is that the subpopulation will differentiate on a different path to the rest of the population, or that it has already started to differentiate, or something of the sort (which I imagine is discussed in the paper).


text:
Can someone help me identify this larva?
I found this creature in my toilet bowl and very curious as to what it is. The main reason is I want to make sure this wasn't a parasite living in me.  Everything I've researched tells me this is some sort of fly larva, possibly a fungus gnat larva or a drain fly larva.  The fact that it has no long hairy like things makes me think it is not a pet flea larva.  This was in Southern California and it was almost exactly 1cm long.  Any help is greatly appreciated!

Singular larva, plural larvae.


text:
How can the leakage of mitochondrial protons generate heat?
I read the following about thermogenin:

"When thermogenin is
  inserted into the inner mitochondrial membrane, it
  accentuates mitochondrial proton leak and dissipates
  the proton motive force. Since oxidation is no
  longer coupled to phosphorylation, thermogenin is
  said to cause uncoupling. In the presence of thermogenin,
  oxidation and proton pumping continue
  at high rates but with low rates of ATP synthesis. So Thermogenin enhances
  mitochondrial proton leak so there would be heat."

Why does proton pumping without ATP synthesis generate heat?

please add a link to your source. Is it webpage or book?

Hello and welcome to Bio.SE! Take the tour to learn about the site and earn yourself your first badge.

Uncoupling ATP synthesis from the ETC (electron transfer chain; this is where oxidation takes place) by thermogenin or any other method means that the energy used to generate or uphold the proton gradient gets 'lost'.
Since physics teaches us that energy is only transferred and never truly lost, the energy consumed by the ETC must most go somewhere - heat / thermal energy is the easiest and therefore most likely option.
References

Wikipedia article on Uncoupling Proteins
Uncoupling article written in chemical terms
Short general article about brown fat and heat production

Proton pumps just like any mechanochemical process generates heat, normally much of this heat is reclaimed in the production of ATP.  Without thermogenin proton pumps produce a proton gradient, the gradient is used to power atp synthase. thermogenin is a channel protein that creates holes in the membrane preventing a gradient from building up. The pumps never stops or slows so they continuously generate higher amounts of heat, which yields a higher temperature. It is basically the reason an electric motor running full throttle generates more heat than the same one barely running.
Basically brown adipose tissue evolved a way to generate heat by running a "motor" that is not attached to anything. Its not efficient but it is better than not having a way to consistently generate heat.
source 1
source 2
source 3
source 4

This answer is not correct, the ETC/proton pumps don't slow down normally - because they ARE coupled to the ATP syntahse which 'uses up' the proton gradient, thus a stable equilibrium forms. Also the ETC/proton pumps themselves don't generate a lot of heat, that would be pretty inefficient (and  would mean that ALL eukaryotic lifeforms always generate heat, which is not the case).

Its coupled to ATP synthase in mitochondria not primarily used in thermoregulation. In brown adipose tissue which has  mitochondria focused on the production of heat it is not coupled to ATP synthase or has minimal coupling. the proton pumps are indeed the port generating the heat and it is very inefficient.

I still don't believe that the ETC (electorn transfer chain / respiratory chain / proton pump) is generating the heat itself, since that would still mean that ALL mitochondria generate heat. Also non of your sources seem to support that claim, they mostly describe that thermogenin allows thermogenesis.


text:
Is "monosexual" still a valid term in biology?
I read an older article where they talk about species being strictly monosexual as opposite of being hermaphrodite, etc [1]. After an extensive googling and reading about how everybody has to be at least a little bit homosexual, I am still not clear about this. Is monosexual still a valid term to be used in biology? If not, what is the correct term referring to a species that has separate sexes over the entire life-cycle?

After an extensive googling and reading about how everybody has to be
at least a little bit homosexual,

That's not relevant at all.

Yes. It was sarcasm...

I suspect "monosexual" is a term recruited in sociology, psychology and/or medicine. I haven't ever heard of it in application to biological questions. It's a behavioral habit and doesn't seem to be directly related to the (biological) opposition "separate sexes" vs "hermaphroditism".
In biology:
Animals can either be gonochoristic (separate sexes) or hermaphroditic. If an animal species reproduces without gametes it's called asexual (in animals asexual reproduction is rarely the only way of propagation), and if only females are present which give birth without fertilization, they are called parthenogenetic.
In some cases different modes of reproduction are utilized by different stages (alternate generations) or even phases (larva vs adult, young vs old). In other cases in populations coexist males and hermaphrodites or males and parthenogenetic females.
Mammals, including humans, are (nearly) perfect examples of gonochoristic animals: only a male and a female together can produce offspring. If someone is homosexual (it refers to behavior only), he is a dead end in this respect.


text:
A program for cell motility assessment with a batch process function?
Cell motility assessment is a branch of experimental biology or medical science. One example could be an assessment of treatment effects on sperm motility of an animal. The standard procedure involves taking film clips of sperm (or any other moving objects) through a microscope and measuring average linear velocity of particles on these film clips. The program used for measuring these linear velocities is important, and there are not too many choices to my knowledge. However, my knowledge might be limited.
I have previously used CellTrak for measuring sperm swimming speeds. The program works well, but lacks a batch processing function. As the assessment bases on a considerable number of replicates, I end up with 1000-2000 film clips to be analyzed and clicking my way through CellTrak is a tedious and irritating process. Also CellTrak licence costs a lot of money for such a poorly written program.
Therefore, my question is: Is someone aware of a similar program to CellTrak, which includes batch processing option, or even better, which works through command line and can be looped? Are there open source options or extensions to widely used open source programs (ImageJ, Bioconductor, etc.)? Please give a short tutorial/personal experience to the usage of the suggested program (if any).

I wonder if you could adapt Digital Particle Image Velocimetry for your purposes. http://www.holomap.com/dpiv.htm

I don't know of a specific program but the MATLAB file exchange is likely to have scripts for that purpose. It may also help to migrate this to StackOverflow

ImageJ has several tracking plugins, a good one being TrackMate. Most of it's functions can be scripted in various languages and the Fiji distribution can also run in headless mode. It's open source and won't cost you any mony for a much lager feture set.
I personally have used ImageJ in headless mode scripted with its own macro language because it is relatively easy to learn.
TrackMate also should output average speeds for the tracks, if I remember correctly. Otherwise you would have to write a script to measure those from the tracking data. You can use the IJ macro language, Python, Java or one of the other supported languages.
In combination with a bash script wrapper for its headless mode I even use it in Makefiles to convert my tiff stacks to avi and put scale bars and time stamps on everything.
Hope this helps.


text:
What is the acceleration profile of the greyhound?
I'm interested in the acceleration curve over time that's typical of an adult greyhound prior to attaining this peak velocity. My curiosity is motivated by a desire to understand the biomechanical reason why land mammals run so fast.

I'm a little unsure of what you want. I'm pretty sure I know a paper on acceleration of greyhounds specifically, but are you more interested in the physiology and morphology of fast terrestrial vertebrates in general? ( There are studies of cheetah acceleration, too, along with other critters.)

Both of those subjects interest me actually. In fact, in my mind they are inseparable. Would you mind sharing the paper?

I can do that. Give me a day or two.

I might recommend editing your question to make your end goal more specific -- if you're interested in locomotor adaptations for acceleration in mammals generally, as opposed to just greyhounds.

I'm going to try to break this up a bit to address your sub-questions. Most of it is summarized from Williams et al 2008--and almost all of the work I'm referencing comes from the Royal Veterinary College Structure and Motion Lab.
Acceleration Profiles:
So, I can't find an acceleration curve over time for these, but we do know about the potential acceleration range for greyhounds and cheetahs. Greyhounds can reach a max speed of about 17 m/s (Usherwood and Wilson 2005), cheetahs can reach up to 29 m/s (Hudson et al. 2010). Cheetah stride-averaged accelerations have been measured up to 120 W/kg --they can speed up by 3 m/s over a single stride, and slow down by up to 4 m/s (Wilson et al. 2013). Racing greyhounds have achieved 60 W/kg (Williams et al. 2009).  Maximum acceleration decreases with increasing speed
How Land Animals Can Be Fast

Augmentation or hypertrophy of proximal musculature. More than a fifth of a greyhound's limb muscle mass is associated with the proximal portion of the hindlimb (Williams et al. 2008). Muscle power (work/time, important for acceleration) is roughly proportional to muscle volume, so bigger muscles are better in this case.  In cheeetahs, a similarly large muscle mass is devoted to hip extensors (though different specific muscles; Hudson et al 2010). Big muscles = high power and high force production.  In addition, sprinting mammals tend to have longer muscle moment arms than non-sprinters--so they can produce greater torques for a given force.
Longer muscle fascicles. This may also be an adaptation for power output. Greyhounds have longer fascicle lengths in their hamstrings than your average domestic dog (Williams et al 2008), and human sprint athletes also have longer fascicle lengths than endurance runners (Abe et al. 2000).
Long limbs and flexible spines: Longer limbs w/ spinal flexion = greater stride length--and cheetahs have particular elongated hind limbs. A long hind limb also lets cheetahs maintain foot contact with the ground for longer, so lower peak forces are required.

These aren't nearly all of the things involved, but I suppose this is a start.
References:

Abe, T., K. Kumagai and W.F. Brechue. 2000. Fascicle length of leg muscles is greater in sprinters than distance runners. Med. Sci. Sports. Exerc. 32: 1125-1129.
Hudson, P. E. et al. 2010. Functional anatomy of the cheetah (Acinonyx jubatus) hindlimb. J. Anat. 218: 363–374.
Usherwood, J. R. and A. M. Wilson. 2005. No force limit on greyhound sprint speed. Nature. 438, 753-754.
Williams, S.B. et al., 2008. Functional anatomy and muscle moment arms of the pelvic limb of an elite sprinting athlete: the racing greyhound (Canis familiaris). J. Anat. 213:  361–372.
Williams, S. B. et al. 2009. Pitch then power: limitations to acceleration in quadrupeds. Biol. Lett. 5: 610-613.
Wilson, A. M. et al. 2013. Locomotion dynamics of hunting in wild cheetahs. Nature. 498: 185-189.


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Why is a screening process required in selection from a genomic DNA library?
After the process of construction we go for screening process of selecting a recombinant host. Which includes:

DNA hybridisation
Colony hybridisation
Random primer labeling
Nucleotide autoradiography

These techniques are very tedious. So instead of all these tedious process why cannot we just grow them in a minimal media to get the recombinant host and to check which protein is formed?

I have edited your title, first because you should avoid abbreviations in titles and second to improve the English. However I must say I don’t understand what you mean by “recombinant host”. By host we usually mean the organism (bacterium etc.) in which we are propagating some vector (plasmid, phage etc) carrying the DNA. I advise you to set out the problem in more detail, step by step, and this will clarify the question and perhaps provide the answer.

1.) What organism are you referring to? A genomic DNA library from E. coil would be much smaller (have far fewer unique genomic fragments) than a genomic library from a vertebrate (all other things being equal).  So the genomic library you wish to screen for your favourite gene may have between thousands, and millions, of unique inserts. Screening those for protein production, as you suggested, could also be tedious. 2.) Are you dealing with a prokaryote or a eukaryote genome? Many eukaryotic genes contain introns, which need to be removed by splicing, so a library of genomic clones

from a eukaryote would be quite unlikely to produce a protein during propagation in a prokaryotic host. If, on the other hand, you are dealing with a cDNA library, then there are expression vectors designed to express the foreign recombinant proteins. But how do you propose to identify the protein or interest?

The protocol makes sense, if you require to have access to a physical copy of the genomic DNA sequence - and you do not have sequence information about the genomic DNA (or even your probe of your interest). While sequencing service provides will nowadays likely use fluorescence rather than autoradiography, it is wrong to consider the protocol tedious, as you screen many different colonies at the same time with few experimental steps. Selection through media would only make sense, if you already knew what your gene is doing, and you had introduced a cognate inducible mutation in the host.

Actually my question was,  in g dna library we do alot of screening process just to find if the transformation process is successful or not. Instead of that why we cannot grow the sample in a minimal media, we can quickly find the transformed bacteria.


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Apart from nerve cells and muscle cells, what types of cells do not undergo mitosis in adult man?
Neurons and muscle cells in adult humans do not have the ability to divide by mitosis, so they can not repair themselves and their cell cycle remains in the interphase. I’m looking for more cells with this feature. Are there other cells with this inability to undergo mitosis in humans or in plants?
In an adult human:

Do nervous cells ever undergo mitosis?
I wonder if all muscle cells do not undergo mitosis or if this inability only applies to cardiac and skeletal muscle cells.

As I understand no specialized cells undergo mitosis, not even epidermal cells. The difference resides in that certain tissues like epidermis maintain a pool of undifferentiated cells that undergo mitosis and trough this, generate new cells that differentiated into the specific specialized cell. Such a pool exist in certain brain areas like the hippocampus, where it's possible to observe the appearance of new neurons in the adult.

To answer the numbered questions:

In general, neurons never divide by mitosis. However, I believe you may have unintentionally misphrased your question; there are functional neural stem cells in the adult human brain as well, and these are believed to give rise to new neurons throughout the lifespan of an individual. They have only been found in specific parts of the brain, though, such as the SVZ and the subgranular zone of the hippocampus (Gonzales-Perez 2012; Behnan et al. 2017). It also bears noting that following an external insult (such as DNA damage, oxidative stress, hypoxia), even terminally differentiated neurons can re-enter the cell cycle and go as far as to replicate their DNA, but this tends to result in apoptosis or arrest at the G2/M phase; such aberrant re-entry into the cell cycle is more frequent in brains afflicted by neurodegenerative diseases (Frade & Ovejero-Benito, 2015). In addition, the possibility to induce neurons to proliferate and form cancers has been demonstrated in retinal cells in mice (Ajioka et al. 2007).
Correct; as with neurons, muscle cells (myocytes) lack the ability to undergo mitosis. But again, I believe what you really want to ask is whether or not muscles maintain a pool of stem cells that can replace lost cells. The answer to this is yes—there are stem cells within skeletal (Wang, Dumont & Rudnicki 2014)  and smooth muscles (Majesky et al. 2011) that proliferate in response to damage. According to some studies there are stem cells in the adult heart as well, although their regenerative capacity appears to be very low (Bergmann et al. 2009).

If your intention was indeed to ask about which cells are unable to undergo mitosis, then the answer will likely be a very long list, as no terminally differentiated cell type undergoes division under normal circumstances. This would, for example, include all different blood cell types (erythrocytes, megakaryocytes, neutrophils, eosinophils, basophils, B-cells, T-cells, natural killer cells, mast cells, macrophages), most skin cells (e.g. keratinocytes, melanocytes), epithelial cells (such as those that form the intestinal lining) and such. This would likely include most if not all of the cell types listed here that do not have the "(stem cell)" note next to the links (although I did not confirm this by checking the literature on them).
References:

Ajioka, Itsuki, et al. "Differentiated horizontal interneurons clonally expand to form metastatic retinoblastoma in mice."
Cell 131.2 (2007): 378-390.
Behnan, Jinan, et al. "Identification and characterization of a new
source of adult human neural progenitors." Cell death & disease 8.8
(2017): e2991.
Bergmann, Olaf, et al. "Evidence for cardiomyocyte renewal in
humans." Science 324.5923 (2009): 98-102.
Frade, José M., and María C. Ovejero-Benito. "Neuronal cell cycle: the neuron itself and its circumstances."
Cell cycle 14.5 (2015): 712-720.
Gonzalez-Perez, Oscar. "Neural stem cells in the adult human brain."
Biological and biomedical reports 2.1 (2012): 59.
Guo, Dayong, and Lynda F. Bonewald. "Advancing our understanding of
osteocyte cell biology." Therapeutic advances in musculoskeletal
disease 1.2 (2009): 87-96.
Majesky, Mark W., et al. "Vascular smooth muscle progenitor cells:
building and repairing blood vessels." Circulation research 108.3
(2011): 365-377.
Wang, Yu Xin, Nicolas A. Dumont, and Michael A. Rudnicki. "Muscle
stem cells at a glance." (2014): 4543-4548.

Yes, nervous cells never undergo mitosis coz they lose their centriole thereby they are present permanently in G0 phase of cell cycle in which a cell doesn't divide,rather it just carries out it's day to day metabolism.
As far as plants are concerned,they have meristematic cells which are capable of regeneration.But if you know a little bit about plant anatomy then you can say that primary xylem and primary phloem do not divide throughout their lives.
I hope this helps.

Though neurons do not possess the ability to divide in adult humans, glial cells do, and in case of injury or disease, tend to fill up the gaps created by loss of neurons.
Most muscle cells lose their ability to divide after maturation. There are a few cases however, like those in disease or damage, when cells that are lost may be replaced. These are discussed below:

Skeletal muscles:
Each skeletal muscle fiber arises by fusion of multiple myoblasts during embryonic development. Once fusion occurs, the ability to divide is lost. However, a few myoblasts do persist in mature skeletal muscle as satellite cells, which retain the capacity to fuse with one another or with damaged muscle fibres to regenerate functional muscle fibres. So even though our muscle cells cannot divide, they can, in some cases, be regenerated.
Smooth Muscles:
Certain smooth muscle fibers, like those in the uterus retain their capacity for division. Also, new smooth fibers can arise from pericytes, stem cells
present in association with small veins and blood capillaries.
Cardiac Muscle:
These fibers are unable to divide on their own. However, there have been studies related to this, and it was shown that bone marrow stem cells could be used to regenerate damaged heart tissue.
(Refer: Cell transplantation for cardiac regeneration: where do we stand? Neth Heart J. 2008 Mar; 16(3): 88–95.)
I hope this answers the question.
I read this in Principles of Anatomy and Physiology, 12th Edition, Tortora, G. J., Derrickson, B.


text:
Software to model and analyse protein–ligand interactions
I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding interactions and the strengths of bonding regions. I was wondering if there was any type of software that would allow me to analyse this protein and its interactions with swainsonine? I have seen many images like the one below in research papers, but I’m never sure what software the researchers are using to generate these models.

Liberato, M. V. et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci. Rep. 6, 23473; doi: 10.1038/srep23473 (2016).

This appears to be a bioinformatics question rather than one about biology.

I know it is rather dense, but the methods section of the paper you cite indicates how the simulations were performed. If you search this site you will find a number of other questions about straight protein molecular modelling software.

I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things.
For simply viewing, measuring distances, and creating "pretty pictures" like the ones you included with the question, PyMOL and UCSF Chimera are the most popular tools. Chimera is highly scriptable and can perform molecular dynamics simulations (i.e. simulate movement of atoms based on an energy function), though its capability in this regard is somewhat limited. The NAMD/VMD software suite (which was used in the study cited in the question) is more full-featured, as is CHARMM (the latter of which is also the name of an energy function). For prediction of binding sites de novo (without a bound experimental structure), i.e. "docking", there are DOCK and AutoDock (both with long academic histories) as well as more industry-oriented ones like Glide.
Be careful though what you're getting into — while simply viewing structures and making geometric statements by direct observation is well within reach of the average biochemist with reasonable knowledge of protein structure (provided you trust the lab that solved the structure in the first place!), simulation of proteins using energy functions requires considerable computational expertise, though the "black box" nature of some software glosses over this. It may be relatively easy to run a simulation using questionably appropriate parameters, but the adage "garbage in garbage out" applies very much here. This is somewhat true with docking as well.

+1 for the last paragraph alone

A good answer, but be careful about statements of which tools are most popular. You do not mention Jmol, which is one of the viewers available on PDB and is quite powerful. Also, you could enhance your answer with links to the software.

I have edited your answer to add that the NAMD method was used in the study cited in the question. You can revert my edit if you wish, but improving questions and answers is a valid part of the SE model (although should be used with care).

I'm not an expert but a start could be PyMOL https://pymol.org/2/
Unfortunately, you need a license to use the latest version
An earlier (free) version can be found here:https://sourceforge.net/projects/pymol/files/latest/download
A tutorial can be found here:https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners
Hope that helps to start!


text:
Why do musk deer have the smallest red blood cells and amphibians have the largest?
What is the reason that musk deer have the smallest red blood cells and amphibians have the largest? Should they not be proportionate to the size of the organism?

It would be good if you included a reference to your claim that this is, in fact, the case (I personally know nothing about it).

A start would be amphibian red blood cells have a nucleus while mammals do not, removing one of the largest parts of a cell allow it to be much smaller.

In the abstract of (Duke, 1963) we see that mouse deer (Tragulus) have the smallest erythrocytes, not musk deer (Moschus). The paper also explains the origin of the confusion. Mouse deer have 1.5 µm erythrocytes but those of musk deer are 3.6 µm (p. 240). In fact musk deer erythrocytes are the same size as goat erythrocytes at (2.5-3.9) µm (Weiss, D. (2010). Schalm's Veterinary Hematology. 6th ed. pp. 836–842). Whether smaller erythrocytes have since been found, I can't say.
I don't have a definite answer why mouse deer erythrocytes are the size they are but I'd posit a few factors. The size of the erythrocyte needs to approximately match the size of the capillaries so they can press tightly to the epithelium and increase the efficiency of gas exchange. Another factor affecting erythrocyte size is cell number. If you have smaller cells, you need a larger number of them to keep the same sum total volume (as in the figure below). So then factors affecting blood vessel size and the rate of erythrocyte production could possibly affect erythrocyte size.

Size also changes surface area to volume ratio (sa/vol) by the square-cube law and this changes characteristics of diffusion over the cell membrane. A larger erythrocyte may have more plasma membrane, which would allow more diffusion and transporter activity but this may also increase the erythrocyte's volume, which would limit the rate of gas exchange due to solutes needing to work their way out of the middle of the cell. Having a high sa/vol is dependent on morphology (hence, our erythrocytes are biconcave) but Duke claims that mouse deer erythrocytes are actually spherical. So, in theory, the cells' small size could be a compensation to keep their sa/vol high, despite not being biconcave.
Interestingly the size of the cells might not affect the sum total intracellular volume of the cells. In fact, sphere packing density is independent of the size of the spheres. If the cells were made larger, this would increase the size of the gaps between them by the same amount. This could indicate that the the total amount of solutes in the blood is independent of the size of the cells, which could explain the great variation in the size of erythrocytes.


text:
Use of plasmid pXen5 for transposon screening
I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen.
It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409).
Is it a problem to use such a transposon, which contains the transposase within the IR regions?
I am concerned that because the transposase will always be expressed (since its coding sequence is carried around inside the transposon), the transposon will keep on "jumping".
How real is this problem from a practical point of view?
Thanks,
J

There are many natural transposons that are self propogating, hence your plasmid might be derived from one of those.
I can't be sure if it is a problem without knowing more details of the transposon or your experimental goals. However, it might be a good idea to make the transposon inducible, by replacing it's promoter with an inducible one such as pTet or pLacIq, along with including the cognate repressor.
A similar strategy is used in this paper, albeit not with transposons but other integrative and conjugative elements (ICEBs1) from Bacillus subtilis

Brophy, Jennifer AN, et al. "Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria." Nature microbiology 3.9 (2018): 1043-1053.


text:
What metabolically happens when an egg fuses with the nucleus of a somatic cell
In stem cell biology, it is recognized that embryonic stem cells are transcriptionally inactive for the first 3 days of development. However, during somatic cell nuclear transfer, the nucleus is likely to include various polymerases and RNA both coding and non-coding. Does this affect the success rates of cloning?

Somatic cell nuclear transfer is a method for creating a viable embryo from a somatic cell and egg cell. A somatic nucleus is inserted into an enucleated egg, where the somatic nucleus is reprogrammed by egg cytoplasmic factors to become a zygote (fertilized egg).
This requires the use of eggs in metaphase II of the cell cycle. Somatic cell nuclei must be in interphase (G0/G1). Interphase is the portion of the cell cycle that is not accompanied by observable changes under the microscope.
What determines the success rates of cloning
Oct-4 and other yamanaka factor expression is essential for somatic cell nuclear transfer success (Pay-wall).
Outlined here:

"...we now think that the oocyte cytoplasm might reprogramme the somatic cell nucleus too strongly, or that the somatic cell nucleus is more sensitive to oocyte reprogramming factors than are sperm cell nuclei."

Thus, Reprogramming and cloning success is unlikely to be influenced by somatic nucleus polymerases and RNA.


text:
Does the MS2 RNA binding protein have any translational repression effects?
Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects
I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the interaction of the MS2 protein to the hairpin placed upstream of a ORF cause any translational repression?

Why don't you place the MS2L downstream of the ORF? What exactly is the experiment you want to do?

I assume you are talking about the mTAG visualization technique for mRNAs (1). You are probably familiar with it, but the OFR of interest is tagged with MS2L sequence downstream of it and upstream of the 3'UTR. There is also a modified version, in which you can visualize both the mRNA of interest, and the protein that is translated, see the figure below (2). Haim and colleagues found that yeast expressing mCherry and MS2L tagged ATP2 grew on glycerol-containing media, which would require efficient translation of ATP2.

So I would assume that there is no translational repression if you tag the mRNA downstream of the ORF. Unless you have a very good reason to tag the ORF of interest with MS2 upstream of the start codon, I wouldn't do it, because these stem-loop structures would most probably stall translation, as mRNA secondary structure has been implicated in translation initiation efficiency.

The idea would actually be to repress translation via the mecahnism that you suggest. Hence, the rationale of putting the MS2 hairpin upstream of the ORF.

Oh I see now... Interesting idea. Worth exploring. Why don't you use Cas9?

Probably because I asked this question back in 2012 and was more of a curiosity question rather than an actual experimental question. More specifically, I'm concerned more about generating a tuneable analog type of repression system where you can generate a range of repress rather than perform a complete knockdown using CRISPR.