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Is it possible to purify antigens from a vaccine and to separate them from the adjuvant?
I need to separate the antigens from several vaccines in order to use them for coating microplates to run an indirect ELISA. I at least need to remove the adjuvant from the vaccines. Is this possible to do and if yes, how do I go about it?

The major component of a vaccine is the adjuvant, and according to Wikipedia the most commonly used adjuvants in human vaccines are aluminium salts.
Here for example is the composition of Recombivax HB, a hepatitis B vaccine produced by Merck Frosst and used in Canada (source of information is a Canadian website)

RECOMBIVAX HB ® [hepatitis B vaccine (recombinant)] is a non-infectious subunit viral vaccine consisting of surface antigen (HBsAg or Australia antigen) of hepatitis B virus produced in yeast cells. A portion of the hepatitis B virus gene, coding for HBsAg, is cloned into yeast and the vaccine for hepatitis B is produced from cultures of this recombinant yeast strain according to methods developed in the Merck Research Laboratories.
  Two formulations are available:
   •  10 µg/1.0 mL formulation: each 1.0 mL dose contains 10 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;
   •  40 µg/1.0 mL formulation: each 1.0 mL dose contains 40 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;
  Thimerosal (mercury derivative) 1:20,000 (50 µg/mL) has been added only to the preservative-containing formulations. All preparations have been treated with formaldehyde prior to adsorption onto amorphous aluminum hydroxyphosphate. The vaccine is of the adw subtype.

As explained in   Exley, C. et al. (2010) The immunobiology of aluminium adjuvants: how do they really work? Trends in Immunology, 31:103-109:

The vaccine preparation is primarily micrometer-sized clusters of nano-sized primary particles of the aluminium salt with which the antigen is associated by adsorption and entrapment. The avidity with which the adjuvant associates with the antigen will depend upon multiple factors, including the form of aluminium salt (usually oxyhydroxide or hydroxyphosphate), the physico-chemical properties of the antigen (including its overall charge and molecular weight), the mode of preparation of the antigen-adjuvant complex (for example, ratio of adjuvant to antigen), and the final solution pH. The latter will usually be around neutral (pH 7.0 +/-0.5), and, along with the highly super-saturated state of the aluminium salt, this will ensure that the concentration of soluble aluminium in the vaccine preparation remains below ca 2 mM. Similarly, there will be a variable proportion of antigen, often <1% of the total antigen load, that is not associated directly with the adjuvant, and some of this ‘free’ antigen may also be in a complex with aluminium., what this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material.

What this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material. The antigen itself has of course already been extensively purified before being incorporated into the vaccine, so the task of purifying the antigen from the Recombivax vaccine is one of releasing it from the inorganic adjuvant. The obvious thing to try first would be to isolate the particulate material by centrifugation, and then attempt to release the antigen from this in a soluble form: things to try would be extremes of pH, high salt concentrations, and detergents. SDS-PAGE would be used to monitor how much was released by these treatments.
Now the example that I gave above (Recombivax HB) is fairly straightforward because it contains a single protein antigen. Compare this to Pentacel, given as first vaccination to babies in Canada (same source as before).

Act-HIB ® Reconstituted with QUADRACEL ®Haemophilus b Conjugate Vaccine (Tetanus Protein – Conjugate) Reconstituted with Component Pertussis Vaccine and Diphtheria and Tetanus Toxoids Adsorbed Combined with Inactivated Poliomyelitis Vaccine.
  Each single dose (approximately 0.5 mL) after reconstitution contains:
   •  purified polyribose ribitol phosphate capsular polysaccharide (PRP) of Haemophilus influenzae type b covalently bound to 20 µg of tetanus protein 10 µg
   •  pertussis toxoid (PT) 20 µg
   •  filamentous haemaglutinin (FHA) 20 µg
   •  fimbrial agglutinogens 2 + 3 (FIM) 5 µg
   •  pertactin (PRN) 3 µg
   •  diphtheria toxoid 15 Lf
   •  tetanus toxoid 5 Lf
   •  poliovirus type 1 (Mahoney) 40 D-antigen units
   •  poliovirus type 2 (MEF1) 8 D-antigen units
   •  poliovirus type 3 (Saukett) 32 D-antigen units
   •  aluminum phosphate 1.5 mg
   •  2-phenoxyethanol (not as a preservative) 0.6% v/v
   •  polysorbate 80 10 ppm (by calculation)
   •  bovine serum ≤50 ng
   •  trace amounts of formaldehyde
   •  trace amounts of polymyxin B and neomycin may be present from the cell growth medium

This vaccine is clearly much more complex, so in this case, once the desired antigen(s) were freed from the adjuvant there would be a need to use standard protein purification techniques to separate the various contaminants.
Finally it's worth pointing out that unless you have access to large amounts of vaccine, you are going to be starting with quite small amounts of antigen (see above) so it will probably be quite a challenging purification.


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Regeneration capabilities in humans?
To what extent can humans, (mammals in general), theoretically regenerate, and is their a way to speed up and/or exceed this original extent.

What do you mean by "theoretically"? Regenerate what? Toe nails, for example, are easily regenerated. Livers, less so. As it stands, this question is too broad for this site.

Regeneration - or actions perceived as regeneration by popular culture - depend highly on age and specific type of cells (epithelial tissue cells are a fine example). But you can't regenerate a leg-bone once removed.
But to get a more specific answer you to make a more specific question and define the terms you're using.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Why do we squint?
Recently, I was having an eye exam and admitted to squinting my eyes to sharpen blurred edges. Later, while waiting for the dilation to set in, my brother (a would-be pharmacist fresh off an anatomy course) was telling me about how vision works.
As a non-scientist, here's as much as I gathered:

The pupil allows light into our eyes.
The lens bends and shifts to focus that light against our retina.
The retina translates this light-information into signals via the optic nerve.
Something about brains, and then sight!

So, my question is, if the lens being bent and shifted inside of our eye by muscles is how our eyes focus, why do those of us with poor vision squint? Surely it can't be that by narrowing my field of vision I'm consciously bending my lens.

When I was younger (before I got glasses), I sometimes used to pinch four fingers together to make a tiny square hole and look through it. Same principle as squinting; you decrease the aperture size.

Actually it's a bit physics and biology,
It works, all right. In fact, the word "myopia" (near-sightedness) comes from the Greek words myein (shut) and ops (eye). When you squint, it's like reducing the aperture of a camera lens: You reduce the diameter of your visual lens. This gives you a longer depth of focus.
Shortly you can say, Yes by squinting your eyes you actually bends the eye lens with the help of Ciliary Muscles present in your eyes which reduce it's focal length and helps you to see with a better vision

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Breathing water vapour
Normal air consist of oxygen, CO₂ and nitrogen, with traces of water etc.
Now imagine displacing all gasses except oxygen with water vapour. By water vapour I don't mean hot steam or fog. Just gaseous water.
The question is would it be beneficial or harmful to human, and how much so?
And assuming it's not deadly, in which circumstances could it be useful?
One thing I am wondering in particular is deep dive and high altitude applications. Having no/low content of nitrogen in such an artificial air mixture would help to avoid decompression sickness. And one would think water vapour is at least cheaper than pure oxygen (also might be safer and have less side effects).

Just because you have removed the Nitrogen and CO₂ won't help you keep a higher vapour pressure of H₂O in the air. You Could REMOVE all the other gasses and just have O₂ at its normal partial pressure at 1/5 bar total pressure and breath fine, but there would be a fire risk in this environment due to no non O₂ molecules to quench excited O₂.
The only way to have a high enough vapour pressure of H₂O for something like diving would be to heat it, but I don't think a lungful of very hot water vapour would be terribly good for you.
You can't just pressurise water vapour to any pressure you feel like; it will condense fairly easily.
To avoid Nitrogen's toxic effects, divers often use Helium to replace it as pure Oxygen is deadly at high pressures.

If $O_2$ is at its normal partial pressure, that means there is still the same amount of "non-$O_2$" molecules. Can you expand on how there would be a fire risk despite having the same amount of $O_2$?

Indeed, it was pretty stupid question now that I've recalled some physics :-/

What if we consider saunas? From some off-the-cuff calculations it appears water vapour can actually fully displace nitrogen and CO2 at about 60°. So bring down temperature a bit, bump up oxygen -- would it be a usable sauna option?


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What signals histone methyl transferases to function?
I wanted to find out if anyone knows what stimulates histone methyltransferases to function?  I know that it is a process still trying to be understood, but I can't find anything that seems to direct the activity of the enzymes.  Additionally, where do the methyl groups come from that the enzymes transfer onto the histones?
Thanks!

The proximal source of the methyl group is S-adenosyl methionine.

Histone methylation is regulated by a variety of of events, including transcriptional activation and repression, relative location of the histone in the chromatin (pericentric or not, hetero- vs. euchromatin, etc.), X-inactivation, the cell's point in the cell cycle, and others. A variety of signaling pathways can lead to the (in)activation of HMTs. I found this table at cellsignal.com listing known methylation sites, along with literature references. Elsewhere on the site is this graphic, which shows some of the same info in a different way, and also has links to data at PhosphoSitePlus with links to the protein of interest. If you dig around, you can find all sorts of pathway and experimental information. For example, if you look up PRMT1 (human), you get a brief description of the protein and what pathways it's involved in, as well as links to all sorts of other info. On the histone side, a look at Histone H4 (human) allows you to look at individual modified residues (I picked K21-m2) and find all sorts of literature links and information about experiments used to determine its function.
PS: I'm not affiliated with Cell Signaling, I just think they have a ton of useful protein information, kind of like NEB for mol bio stuff...


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What causes Acne?
What exactly is going on biologically at the molecular level with acne and causes breakouts? Hormonally, there is a lot going on but I'm curious about what is going on chemically.

What are you looking for beyond wikipedia? That seems to cover your questions.

Acne is caused by blockage of hair follicles by oils (sebum) from your skin and dead skin cells. Hormonal changes in puberty cause your skin glands to produce a lot of oil.
Blocked follicles are visible as a small black dot (blackheads).
The recognizable pimples occurring during normal puberty acne form because of bacterial infection (the sebum/skin mix forms a good growth medium for bacteria). The immune system responds with inflammation (the red "base"). The pus (the white "middle") is a dead bacteria, skin and white blood cell mix.
Most treatments for acne focus on either killing the bacteria or removing the dead skin or sebum. Professional medical treatments might also focus on altering hormonal levels. This is also why the COCP , the birth control pill, usually lessens acne in women. Popular over-the-counter remedies for acne (e.g. Clearasil) usually contain a lot of alcohol which both kills the bacteria and removes the sebum, but also makes the skin dry. This in turn causes the skin to produce more sebum thus making the problem worse.

Good answer but it could do with some citations and expansion of "COCP" abbreviation.

And you could've explanded the COCP in your comment @GriffinEvo so that I don't have to google that it means Combined Oral Contraceptive Pill - birth-control pill.

@TomášZato I didn't look it up - I was asking the OP to do it so the correct meaning of COCP was used (if there is more than one). The responsibility lies with the OP, not me, I was just asking for clarification on the abbreviation and other points to make the post meet the guidelines.

You know, you you could've just edited the answer... I added an explanation

I don't like to perform edits that change contents of the answer. I think editing other's posts should merely to improve grammar, formatting and general readability. However this attitude can individually differ.

The anti-acne activity of the combined oral contraceptive is dependent on the type of pill taken. Some pills actually have the opposite effect of worsening acne. This is depending on the type of progesterone in the pill.


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Why do people have antibodies against other blood types?
The ABO blood type divides each blood type according to whether they have the "A" and "B" antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.
Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)

The only reasonably satisfying exploitation I've ever heard is that human gut flora contains the A and B antigens and thus antibodies are created in a reaction to that. But I've never found satisfying reference material or sources for that explanation.

I am not sure I understand your question fully.  The specific immune system has the potential to make antibodies for lots and lots and lots of antigens it has never come in contact with.  Essentially every time you get a cold it is the specific immune system producing antibodies for an antigen that it had not encountered.  If it had encountered it before, then you would have memory cells and likely wouldn't get sick.  In reality it is amazing that we have so few blood antigens and that we can transfer blood as easily as we do.

@DQdlM The difference is: normally you will not have antibodies for antigens you have not come in contact with. E.g. when first encountering a specific type of influenza you will start making antibodies against it. This is why vaccination works. But blood antibodies are special: you already have antibodies for blood antigens even if you've never come into contact with other blood.

interesting.  So the antibodies are present in the blood even w/o exposure to the antigen?  I always assumed that we just had the potential to make the antibodies if the antigen was encountered.  I will have to look into this a little more.

It is written in "Biology - Campbell and Reece " that development of the antibodies occur due to microbes living in our body having antigens similar to other blood group's antigens.

According to the Wikipedia entry for the ABO blood group system:

Anti-A antibodies are hypothesized to originate from immune response towards influenza virus, whose epitopes are similar enough to the α-D-N-galactosamine on the A glycoprotein to be able to elicit a cross-reaction. Anti-B antibodies are hypothesized to originate from antibodies produced against Gram-negative bacteria, such as E. coli, cross-reacting with the α-D-galactose on the B glycoprotein.

The cited reference is Van Oss, CJ (2004) Letter to the Editor: "Natural versus Regular Antibodies The Protein Journal 23:357, available here. This source contains this statement:

..."we have known for more than four decades that these bloodgroup (antibodies) arise out of minor infections occurring very early in life..."

The cited references are:
Pettenkofer et al. Z. ImmunForsch. 119: 415-429
Springer, GF (1960) Klin. Wschr. 38: 513-514
Unfortunately I have access to neither of these articles, and besides they are presumably written in German.

We each inherit either A, B, AB or no antigens from our parents.
The current thought is that when you're between 0-6 months old you are exposed to bacteria/viruses that contain very similar antigens (A or B). These antigens are similar enough to the A and B antigens found on red blood cells that any antibody created against these bacterial antigens would also react against the corresponding red blood cell antigen. Seeing as you can't produce an antibody against your own antigen (except in rare circumstances), you always produce the opposite antibody to what antigen you have.
I hope some of that makes sense. Feel free to point out any glaring mistakes I've made, wouldn't be the first time! ;-)
Source: I'm a biomedical scientist.

I am posting so long after the initial question as I replied to a more recent similar question that was marked as a duplicate. On being redirected here I was surprised at the answers as the question (and certainly that of the supposed duplicate) did not give any indication that he was aware that the situation for non-compatible blood-group antigens was any different from any other foreign antigens. I think it appropriate, therefore, to append the following (@KennyPeanuts has also commented in this vein) for the benefit of those unfamiliar with the idea of clonal selection.
To put it simply, clonal theory of antibody selection assumes that the antigen-specificity of antibody-producing cells is random, so that all types of specificity will exist. On encountering an antigen a particular cell will be stimulated to divide and hence allow the production of a greater amount of antibody against the antigen.
Immune tolerance requires that cells producing antibody against self antigens be eliminated at some stage. Hence people of blood group O, lacking blood-group antigens A and B, will not have become tolerant to them, and will have antibody-producing cells capable of producing antibodies against them, should they encounter them in an incorrect blood transfusion.

I think your answer does not invalidate the others, but it is a requirement? The existence of A/B antigen specific naive B cells is necessary, but those B cells will not produce antibodies until exposed to the antigens (in the context of an inflammatory response). The above answers argue that the "exposure" comes from infection with pathogens that have antigens similar enough to the A/B antigens as to cause cross-reactivity. So the activated B cells will produce antibodies against the pathogen antigens that also recognize A and/or B antigens in blood cells.

@ddiez — OK. I've modified my answer taking your remarks into account. I still suspect that one of the questioners (the one who posted the supposed duplicate) had no knowledge of the special situation for blood group antigens (I certainly didn't) and that my answer forms a basic introduction which the other answers lack.


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position of cell penetrating peptide
I'd like to add a cell penetrating peptide to my custom peptide (30aa). Can I just add it to the end of the peptide sequence or does it have to be positioned on an outward facing external chain?

This papers tables shows that cell penetrating peptides are placed before their cargo peptide and do not need to be on a side chain.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1576229/table/tbl1/


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Why are mosquitoes repelled by smoke?
A well known way to have a rest of mosquitoes during camping is to stand in the fire's smoke. Moreover, I learned recently that shepherds in certain regions of Africa use the same tactic for cattle. They make smoky fires and cattle gathers in smoke to get rid of mosquitoes.
Why humans and cattle can stand smoke, but mosquitoes can't? Does this technique work for other kinds of insects?

Remember mosquitoes have very sensitive CO2 sensors. They track their prey using CO2, and smoke has lots of CO2 which makes mosquitoes blind, I presume.

Sorry but mosquitoes aren't attracted towards the smoke. This is because they get attracted toward Carbon Di Oxide

There is little hard evidence on whether smoke acts as a mosquitoe repellent. A literature review done by the WHO (Biran et al, 2008) on smoke and malaria show that evidence is mixed, at least when it comes to long term protection and protection from blood meals from firewood smoke. Their review also notes that few scientific studies have been done on the topic, and they report results from one experimental and a couple of observational studies. However, they do note that burning particular plant materials (based on traditionally used plants) may be effective (see e.g. Pålsson & Jaenson. 1999).
These results also doesn't preclude that very heavy, temporary, smoke may be effective to get rid of mosquitoes ("... during camping is to stand in the fire's smoke...") - that this can be effective is certainly my personal experience as well.

I imagine almost all insects would be repelled by direct signs of active fire.

Mosquitoes have olfactory receptors. Certain chemicals acts as repellent.
See this wikipedia page for an explanation about insects repellent mechanism.

Can you possibly elaborate on the mechanism? And the linked page doesn't even contain any information about smoke or its constituents.

citronella oil page on wikipedia here says : Consists of geraniol (18-20%), limonene (9-11%), methyl isoeugenol (7-11%), citronellol (6-8%), and citronellal (5-15%) for one type and Consists of citronellal (32-45%), geraniol (11-13%), geranyl acetate (3-8%), limonene (1-4%) for an other. The mechanism can be elaborated by following the cited sources like [number 9 for example](http://link.springer.com/article/10.1007%2Fs00018-011-0745-z]()

Mosquitoes aren't actually repelled by smoke. They are repelled by burning citronella oil. Citronella contains certain chemicals that naturally repel the dengue fever mosquito.

that's a probable mechanism, but not the reason. Why are they repelled by citronella oil?

All insects have a mortal fear of smoke because it is a harbinger of flames and flames - for an insect - means instant death. They have no mechanisms at all that are capable of regulating their body temperature sufficiently to survive direct flames.
Added:
Consider a population of mosquitoes (or any flying insect for that matter) that successfully develops a smoke-avoidance response. In an environment where forest fires are common and smoke is therefore a clear precursor - would this population have a better chance of survival than another that does not? I think you could only answer yes.
It merely remains to prove that it is possible for a population I have described to develop. Well - the presence of this question on this board proves that it is possible. I realize this is a slightly weird form of proof by induction but you have to admit it works.
Sorry - no references or citations - just a "because evolution".

Is there any scientific evidence to back up this claim?  It's plausible, but "fear" is a bit of a stretch.

Less "fear" - more "death follows swiftly". Kinda like "I smell almonds ... should I drink this or put it down?"

Yes, but you (or the cyanide drinker) have more than just a couple of ganglia strung together and a lifetime of experience (i.e., would someone not knowing the fact about that odor actually be repulsed by it).  Anyway, again, like I said, a plausible explanation, but evidence always helps.

Perhaps my additions will help.

Lots of species of insects are attracted by fire and smoke (forest fires), since their larvae develop in burned wood, e.g. the longhorn beetle Acmaeops marginatus

Unfortunately, this is an example of a just-so story https://en.m.wikipedia.org/wiki/Just-so_story.


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How can you test what color different people perceive?
If I would show someone a yellow object and ask them, "is this object yellow?"
 That person would say "yes".
But I could never know if my perception of the color yellow is the same as that other person's.
Because he or she could actually be seeing, what I know to be the color green.
But then tells me that its the color yellow because that has been taught to him or her from young age.
So how can you test if people are really seeing the same color?
(originally posted this question on physics.stackexchange but was advised to try it here)
https://physics.stackexchange.com/questions/48731/how-can-you-test-what-color-different-people-perceive

This is a philosophical question, not biological. More exactly, it belongs to metaphysics. http://plato.stanford.edu/entries/qualia/

I wonder why many people ask themselves "is another guys perception of color X same or different than mine" but nobody is wondering "is mine perception of 440Hz sound same or different than other guy perception of 440Hz sound". Why ? Why color perception seems fundamentally different than sound perception ? Behcause one can reproduce the sound one hears, back ? But then you can give him set of color pencils and he can reproduce the color he sees, back. If "reproduction" test works, then it CONFIRMS what person is REALLY SEEING, no ?

One way we can get evidence qualia are the same or very similar for different people is by reactions to it, beyond just the word.
For example, beyond the word "pain", we have other strong reactions to pain. So nobody
suspects other people might experience pain as pleasure and vice versa. Obviously not!
There are no obvious signs for colour qualia, so it makes sense to suspect some people experience red as blue and vice versa.
Still, there are weak reactions to colours, like sometimes certain colours are associated with certain emotions. But, this is very weak evidence and could easily mismeasured, or be bound up with culture rather than biology.
We could test it: take pairs of identical twins at birth (so that they haven't learned words for colours yet), re-wire optical nerves of one of each pair so that red and blue receptors were switched (and perform a placebo operation on the other one, so they don't know who is who), and see whether there is any statistically significant change in the attitudes to different colours or the like as they grow up.
The experiment has various technological and ethical problems :-) But it could be done in principle, so to me this shows the question isn't meaningless, just that it's hard to find the answer.

I have often wondered this myself and have never found a way this could be asserted.
In fact we know that not all people perceive color the same way: up to 5% of humans are colorblind and about 2-3% of the women are tetrachromates, they have an extra cone type in their eyes (usually somewhere near the red spectrum). So it would be logical to assume that those people perceive colors in a different way. We know this for a fact in colorblind people because we can create images which appear different to colorblind and non-colorblind people.
The evolutionary reason for the common prevalence of red-green color blindness might be because they are less affected by camouflage.

It's impossible to be sure how another individuals brain represents the world. For all we know, they way they sense depth and up and down might be completely different. The representation of colour could be completely different. Both individuals could explain it as images, but if it were possible to move another individuals representation into another individuals brain - it's likely the other individual would experience an abstract sensation that would be difficult to compare to anything else that individual has experienced.
It could well be like having a compass attached to your body, sending nerve signals to your brain. You would not understand how to interpret it unless your brain has plenty of time to associate the stream of signals of direction with other signals such as your balance, vision and audio.
The brain is a very complex organ, and it probably starts out like a tiny, one celled blank sheet of paper. That blank sheet of paper is receiving continous streams of electronic signals from the various sensory organs of the body. Over time, synapses between your neurons will bond with other synapses, due to both of them receiving signals simultaneously. For example, if you are listening to music, you will hear various frequencies. Usually there will be a drum beat, which you will also sense as vibrations in the floor and your stomach. The neurons handling those two different signals will then bond together, so that at a later time - when you sense bass signals in the floor, but not in your stomach and by your ears - your brain will still recognize that drum beat in the floor as music. Some people might even feel like they hear the music.
The nerves are then going from the sensor to the brain in various ways and paths, and those connections are different for everybody.
Your brain will visualize stuff your way, and other people will visualize stuff their way and I believe those representations of objects and things are completely different for everybody. The representations will be compatible among different people, in such a way that physical laws are obeyed - but that is because the brain alters representations according to previous experiences.
So, knowing that it is impossible to be sure, I really do believe that everybody represents sensations completely different. They will be handled in similar regions of the brain due to physical similarities of the body, but within those regions in the brain there will be huge differences in representations.
I believe that if a human, unknowingly had a compass operated into his body at birth and connected to an arbitrary nerve, then that human would experience a heightened sense of direction that it could not explain as an adult. If another human had an identical compass attached to a completely different part of his body and connected to perhaps the nerve going from one of the ears, then that human would experience the same sense of direction.
Disclaimer; I am a computer programmer with a keen interest in virtualized intelligence - I have no education in the area of biology. :-)


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Do hormone drugs affect whether a person feels sexual attraction to males or females?
I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.
But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not?
Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?
The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.

Testosterone injections do not increase libido in healthy adult men: http://www.eurekalert.org/pub_releases/2001-11/aps-tdr113001.php (at least not more than a placebo)

@dtech what about teenagers? It is often said that they want more sex because of hormonal boom.

There is no evidence that postnatal hormone exposure can change the sexual sexual preference of an individual. However atypical hormonal stimulation of the fetus can induce homosexuality.
Homosexuality does not develop without a variety of social factors which are up-to-date mostly unexplained. But can develop without hormonal stimulation.
As real life examples there are a androgen antagonists for the treatment of of prostate cancer, which reduce the testosterone level in males. Under treatment the men often turn softer and more emotional, as described by their wifes. And there is beer which contains oestrogens and can induce the growth of female breasts in men. But none of this mechanisms has been observed to turn males homosexual.

Further Reading (second text is free fulltext):
[1] http://www.ncbi.nlm.nih.gov/pubmed/23397798
[2] http://endo.endojournals.org/content/152/8/2937.long

People suspect that hormones for have an effect, but there are also genetic and biological factors. Hormones have caused some animals, such as frogs, to change sexes. Also, both genders have testosterone and estrogen in their bodies. Men just have more testosterone and women have more estrogen.

Can you expand on that, possibly putting some references? For instance, although it is true that the balance T/E2 is higher in men, but testosterone, in men also act (especially in the brain) after being aromatized to estrogen and local concentrations can be very high.

Suppression of testosterone activity is correlated with lowered sexual desire in both men and women...


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Does difference in expected life duration between men and women have biological nature?
It is known that men in most countries live less than women. I wonder whether it is due to different life conditions or because male and female organisms differ?
For example, I heard that testosterone may cause cardiovascular deceases. Is it true? Are there other biological mechanisms that can shorten men's lifespan?

There are several explanations. Probably these are all true to some degree and thus combine to give the general longer life expectancy of females.
Most of these statistics are from Annex 2 of the WHO Health Report 2004 (found through Wikipedia)

Males are more likely to get lung cancer, liver damage and other drug-related illnesses (implied would be that males are more often alcohol/tobacco/drug users).
Males also die more often as a result of work-related injury, especially as soldiers
Males are usually larger. There seems to be a small inverse correlation between size and life expectancy
Mitochondrial DNA is passes from mother to child. As such, mutations harmful for men are less effected by natural selection.
Men have one X chromosome, while women have 2. The y chromosome is very small and contains almost no genes. Thus if there is a genetic defect on the X chromosome the female might have a healthy X chromosome to compensate while the male does not have one. Among others this makes males more likely to have hemophilia or color blindness.

Does it mean that hormones do not affect the lifespan?


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How is respiration an unbalanced equation
The equation for respiration is C6H12O6+6O2→6CO2+6H2O+36ATP. The chemical formula for ATP is C10H16N5O13P3. How is this possible, since it violates the law of conservation of mass because it is unbalanced?

The ATP is not actually produced from the respiration. It comes from ADP and free phosphate ions.
The production of ATP in cellular respiration happens in all parts of a series of chain reactions, and you can read more about those here: https://en.wikipedia.org/wiki/Cellular_respiration#Aerobic_respiration


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What evolutionary reason is there for having the urinary duct and reproductive organs so close together?
As the old joke goes, "God must have been a civil engineer. Who else would put a waste facility straight through a recreational area?"
But maybe it wasn't God. Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?
To be clear, I'm not asking why isn't it elsewhere. I'm asking where the original "design" came from that spread everywhere.

Looks to me evolution aims to minimize the number of holes in a body since these are - in general - the parts with the largest risk of getting an infection.

Yes, there is.
In order to reproduce, material has to leave one organism and enter another and, in species with internal fertilisation, the eggs need to leave later. Think back to a worm-like organism: it's basically a tube with an opening at either end, those two openings are the easy options for where you can locate your reproductive transfer (and possibly egg-laying). Positioning it at the head end has obvious drawbacks in terms of accidentally consumption, so that leaves positioning it at the excretion end.
Once evolved, there is no compelling reason to fundamentally alter this bodyplan, particularly as other animals show little or no sign of sharing our revulsion at bodily excretions.
Edit: It's been a few years since I wrote this answer and I'm not really sure it is correct anymore. I've moved to working with C. elegans, which is the kind of organism that would meet that "worm-like organism" idea I was talking about, but here's the thing: they don't have their reproductive opening near either gut opening, but with its own opening located half way down the organism. If extant organisms don't follow the bodyplan I suggested, does the argument really hold?

Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?

Because it works.
Evolution doesn't grow things or remove things because they might be funky or useful, Evolution is dictated by the survivability of organisms. If a change helps an organism survive to pass on its genes, it's kept. If it doesn't, it's eliminated from the gene pool over time. As long as a change doesn't significantly help or harm, it can be kept for hundreds, thousands, even millions of generations.
Evolutionarily speaking they are where they are because we're mammals that were formally quadripeds that became bipeds. The stereotypical quadripedal design has the reproductive organs located near the pelvis. Probably because they're best protected there. Powerful hind limbs for kicking, and nasty teeth and claws up front. It also gives easy access for mating, which is pretty important if you want to continue the species. On quadripeds it could be pretty darn awkward if the genitalia were located near the ribcage
Really, you could come up with a lot of reasons why the organs are located where they are. There are a lot of advantages, and a lot of disadvantages, but in the end the simplest explanation is going to be "Because we can survive with them there." The advantages have outweighed the disadvantages for our species' history thus far, and until that changes they'll probably just stay where they are.

your middle paragraph explains why the reproductive system is located where it is.  But why is the urinary system located here as well, not say on the abdomen of the quadruped.

@Chris Could you clarify? The kidneys and bladder are located within the abdomen of quadrupeds (and us).

Yes I meant urinary duct, not system, which is located where the reproductive system is.  That is, why are these located in the same spot as each other.  Your second paragraph explained for the reproductive system, but not the urinary duct.

Nice job giving an answer that avoids the pitfalls of naive adaptationism. The presence of a trait doesn't mean it's a good idea, just that it's not bad enough to kill anyone (and/or kill their chances at reproducing).

I was asking where it came from in the first place, not why it didn't change.

@JoeZeng - That's fine. Next time make that your first question instead of the question that's asked nearly three weeks after the fact via an edit. We can only answer what's on the page, we're not psychic.

I thought it had been clear enough in the initial ask, but apparently I was wrong.

The reason lies within our wormy chordate ancestors - an orifice used to eliminate waste can also function as an orifice to eject eggs. My vertebrate zoology is a little bit rusty so I would suggest picking up any first-course book on the subject, most of them cover the evolution of urinary/reproductive organs extensively.

I actually like this answer best - the body plan is ancient and mostly hasn't changed...

Human body has three channels for excretion of substances, one for each of the three physical phases of matter: lungs for gaseous substances, such as CO2, anus for solid substances such as feces and urinal channel for liquid substances.
It turned out that sperm is liquid, so it uses the same channel as liquid urine.

Excretion of substances is a great reason for them to exist, but not for their positioning. Just because sperm is a liquid isn't a great reason for the penis to be located between the legs.

Anixx, one word - beans.

@MCM, the question doesn't ask why the penis is located between the legs, but rather asks why the urinary duct is close to the reproductive organs.  Anixx is trying to say that it is more efficient to utilize the one pipe for both liquids, just as we use our lungs to both breathe in oxygen, and expel carbon dioxide, rather than have two separate systems.

@Chris - I understand your point, but my critique was that there are pretty common examples of organisms that don't put the excretion of phases of matter together, so I didn't find Anixx's argument as full as it could be.

Then why when one vomits, do we use our mouth? Looks to me that vomit is liquid as well.

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


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Endocannabinoid Transporters - which ones are Likely to Exist and what is the Evidence for their Respective Existence?
Endocananbinoid = Endogenous Cannabinoid or CB1 and CB2 ligands.
I'm asking which endocannabinoid transporters exist and could the one answering show all the evidence for the existence of the transporters they mention. For instance anandamide is suspected to have a transporter and there is some evidence for its existence, and paracetamol's chief active metabolite, AM404, appears to work by inhibiting the actions of the anandamide transporter.

Could you clarify your question a bit? I'm having a hard time understanding what exactly you are looking for as you provide no context to your question.


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What is the extent of the effect of Tris on E. coli?
I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane permeability of cells. I was curious to what extent this actually influences experiments.
Tris(hydroxymethyl)aminomethane buffer modification of Escherichia coli outer membrane permeability.

The cited article describes effects of Tris on the outer membrane of E. coli. Like all Gram negatives E. coli has an inner (or cytoplasmic) membrane which is a typical phospholipid bilayer membrane containing many membrane proteins including transporters and, of course, an electron transport chain. Surrounding this there is a layer of peptidoglycan, and then the outer layer of the cell envelope is the outer membrane, which is a special (highly atypical) bilayer structure containing phospholipid and lipopolysaccharide as well as a number of proteins including the porins. The space between the two membranes is the periplasm, or periplasmic space which contains a number of small secreted proteins.
The outer membrane is susceptible to disruption by a number of treatments including EDTA treatment. For example, many cell lysis procedures for E. coli use EDTA to disrupt the outer membrane sufficiently to allow lysozyme to gain access to the peptidoglycan.
Cells with destabilised outer membranes could display increased fragility, but in general I would imagine that this would not normally cause any specific problems: obviously this would depend upon exactly what your experiments are.
Finally it is worth noting that the concentration of Tris that you will be adding with your kanamycin must be pretty low. Even if you have used 0.1 M Tris you are presumably using a 1000x stock, so the final concentration of Tris will only be 0.1 mM. The work in the cited paper looked at cells resuspended directly in 0.1 M Tris. I don't think that you need to worry about this at all.

Thanks! I had the same conclusions in regard to the dilution factor so I wasn't too worried. However, it's always better to have a good idea of the mechanism.


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Can a tumor produce something not currently found in our own bodies?
While speaking with my co-workers, the topic of tumors growing things came up.  The examples were (and backed by images) of tumors growing a tooth, hair, and sometimes even more complex objects such as an eye.
My question is, could a tumor reproduce something that isn't typically found in the human body?  Could it grow something that maybe a very distant ancestor would have had?

I doubt it - tumours usually originate from differentiated cells where a few growth-restricting genes are turned off by mutations - I'd consider it extremely unlikely for them by chance to mutate and turn on the whole patterns of genes that work in alternation and conjunction to cause correct differentiation and produce tissues other than lumps. But I can't refer to any papers so I might be wrong and hence this is only a comment :)

@Armatus but we do see tumors in one place in a body grow something from a completely different place in the body.  I know that isn't as drastic as something not currently found in the body, but it's still mutating far from what the cell was supposed to be.

can you post links to your examples?  just mentioning them is not as clear...

Isn't a tumour by nature something not inherently found in our body?

@shigeta http://en.wikipedia.org/wiki/Teratoma

@Armatus Take a look at teratomas for examples of crazy "whole things" growing in/from a tumor. That first paragraph (with the references) will surely pique your interest.

Would a mutated protein be a good example of something produced by a tumour that is not normally in our body?

If you look at a cancer textbook (eg. Robert A. Weinberg's The Biology of Cancer), you'll find that by definition, a tumor arises from tissues normally found in the patient's body. There's a great deal more to it than just that simple statement, but given the context of the question, I think that answer should suffice.
In writing, "...tumors growing a tooth, hair...", I think you're talking about teratomas. These contain "normal derivatives of all three germ layers". These arise naturally from cells "...typically found in the human body..."
Cancer is a process where mutations in a single cell transform that cell into something that is by definition not "typically found in the human body." But a human cell transformed by mutation into a tumor (benign or malignant) is never (to the best of my knowledge) going to magically become a cell from another species or a very distant ancestor (ie. something that is not "typically found in the human body.").

Teratomas are thought to be a particular type of cancer, present from early development.  As cells which are essentially developmental cells, they seem to have a fairly unique ability to develop hair follicles, teeth and even structures like organs. Indeed malignant teratomas often require chemotherapy or radiation therapy.
I think this bizzarre quality of producing organs or hair etc, is the result of the fact that the origin cells are programmed to develop into these organs before they become tumorous.  Later in life, we have no developmental stem cells in the body which will differentiate into organs and so other sorts of teratomas would seem to be unique.
Cancer cells are still cells programmed to perform the roles they started with, but they are usually not capable of generating whole functional tissue or organs. If they do they would normally be found amongst the tissue they would grow (e.g. liver cancer might produce tissue that looks like liver) so it would not have the unusual quality of teratomas of producing differentiated and specific tissues in isolation.

Sometimes cancer arises when you have crossing over between non-homologous chromosomes. In the process, a chimeric protein arises. A chimeric protein is a protein that consists of parts of two separate proteins spliced together. In this way, cancer cells end up producing a substance (in this case a protein) that is absent in a healthy person. A good example is the fusion gene bcr-abl whose product leads to chronic myelogenous leukemia.
See http://en.wikipedia.org/wiki/Philadelphia_chromosome for more details on bcr-abl.

Definitely NOT for cancer.
What you are speaking about are teratomas - results of incorrect development of stem cells. Stem cells are the type of cell that can become any other cell type. That way the growth of stem cell tissue may result in production of any organs.


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What type of cell do you start with in Meiosis?
Okay, I was learning about mitosis and meiosis in school and had a question. I know in Mitosis you first start off with a Diploid (2N) cell and then end up with two daughter cells that are also Diploid. However, in Meiosis, I know you end up with four Haploid Cells (N), but what exactly do you start off with? Is it like a single egg makes four more eggs or something? Or does it start off with a Diploid Cell and then end up with the Haploids? If so, what exactly is the starting cell called?

Meiosis starts with a diploid cell and produces four haploid cells.  In animals, the starting diploid cell is usually called a germ cell and the surviving haploid cells become gametes (sperm and ova).  (In animals, the female mitotic sequence produces only one ovum; the other three haploid cells become "polar bodies".)
In other organisms such as plants, the starting diploid cell is typically not called a "germ cell" as it is not distinguished early in the organism's life.  Instead the starting cell can be any undifferentiated diploid cell that finds itself in the appropriate location (e.g. in a flower) at the appropriate time.

During mitosis a diploid cell (2n = two copies of each chromosome, one from each parent) replicates its DNA so that it now has four copies of each chromosome. Then it divides, each daughter cell receives two copies of each chromosome and is again 2n.
In meiosis a diploid cell (2n) replicates its DNA so that it now has four copies of each chromosome. Then it divides, each daughter cell receives two copies of each chromosome and is again 2n. Then each of these divides once more without replicating DNA so that there are now four cells each with one copy of each chromosome (1n).
You might be tempted to think of a diploid cell which has replicated its DNA as tetraploid, but this word is not normally used in this context, since this is a transient 4n state.
This is a very broad overview. Have a look at the Wikipedia entry for meiosis to get a more detailed view and extended terminology.
@mgkrebbs (in comments):
If we are considering the meiotic divisions that create gametes, then in spermatogenesis the cell which undergoes meiosis is a primary spermatocyte, and in oogenesis it is a primary oocyte. Primary spermatocytes and primary oocytes are both diploid cells which undergo DNA replication before entering meiosis I.

Unfortunately, this answer does not answer the main question, stated in the title as "What type of cell do you start with in Meiosis?" and in the last sentence of the question body as "what exactly is the starting cell called?".

Meiosis starts with a somatic (diploid) cell. To make a long story very, very short, this one cell undergoes cytokinesis twice. You end up with four haploid cells, called gametes or sex cells.

I just want to say that this I believe is incorrect. Meiosis indeed does start with a diploid cell, however, this is not a somatic one and is rather a gametocyte. I recommend that you refer to this website: https://www.azolifesciences.com/article/Differences-Between-Stem-Cells-and-Somatic-Cells.aspx# which explains this concept.


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What is the inbreeding coefficient for the female offspring of a sib-mating in a haplodiploid system?
The inbreeding coefficient of a sibling mating for a diploid organism is 0.25 (each allele has a 25% of being identical by descent in the offspring).
In haplodiploid organisms, males result from unfertilized eggs, so they don't have fathers (they get half of mom's diploid genome, and that's it). Females have both a mom and a dad, and are diploid in the standard way (dads give their daughters their entire genome).
What is the inbreeding coefficient for the daughter of a sib mating?

I think the answer is 0.25.
Here's how I arrived at it:
The only way a daughter of a sib-mating can have an IBD (identical-by-decent) genotype is by being homozygous for one of the two alleles belonging to her grandmother (her mother and father's mother).
There is no way for her to be IBD for the allele that her grandfather has, because that allele can never end up in her father (who only gets an allele from his mother, because he's haploid).
Let's trace the path of an allele from the grandmother to the focal grand-daughter:
This allele has a 50% chance of being passed from the grandmother to mother, and another 50% chance of being passes from mother to focal. It has a 50% of being passed from grandmother to father, but then a 100% of being passed from father to focal (it's the only allele that father has to give). So, the probability that ALL of these things happen is 50%*50%50%%100 or (1/2)^3 = 1/8 = 0.125 or 12.5%.
Since this can happen for EITHER allele from the grandmother, this must be multiplied by 2, giving our final inbreeding coefficient of F=0.25 or 25%.

From the same article on wikipedia:

The inbreeding is computed as a percentage of chances for two alleles to be identical by descent.

Now let's draw a family tree for such mating and sign chances for having each allele:

You can see, that the "brother" has a 50% chance of receiving A allele and the "sister" has a 50% chance of receiving A from their mother, but the "brother" will not have the C allele that the sister certainly has. Their daughter will have the allele from her father and one of mother's alleles. Therefore, her chances of having a C allele are 50%, and for a A or a B allele each 75% (remember, she needs two copies, so we need to end up with 200%; furthermore, she may have two A alleles but not more than one C allele). Chances of her having two A or two B alleles are 56,25% $$0.75 * 0.75 = 0.5625$$
Now we have the percentage of chances for two alleles to be identical by descent, her inbreeding coefficient is 56,25%.
The son will have only one allele, 50% for C, 25% for A and 25% for B. Because he does not have two alleles, by definition there is no inbreeding possible.

http://en.wikipedia.org/wiki/Inbreeding
I'm thinking that the answer is not defined as there is probably an explicit or implicit assumption about both parents having the same ploidy (brother (haploid) and sister (diploid) in your question) in both the path and tabular methods used for calculating inbreeding coefficient.


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Why human body cannot defend against HIV?
Some says that HIV destroy IRF3, and some says HIV overruns T-cells.

This question really needs some extra work, you can use more than one sentence.

There are two main components of the immune system that are involved: Antibodies and T-cells.
T-cells are responsible for activating white blood cells to help fight off infection. These are the cells the HIV infects. Antibodies bond to the HIV virus and try to neutralize them before they can infect more cells. Unfortunately as the HIV virus replicates, there is too much virus and not enough antibodies to neutralize.
When a T-cell becomes infected with HIV, the virus takes over and causes it to start replicating more HIV. This eventually causes the T-cell to die. So T-cells keep dying while HIV loads keep increasing. When enough T-cells die, the infected person is considered to have AIDS.
It is particularly difficult for the immune system to fight off HIV infection for a number of reasons, including the following:

HIV attacks the immune system itself, weakening its ability to fight back.
HIV replicates in large quantities that are more than the compromised immune system can handle.
HIV has the ability to mutate (change itself) very quickly, making it more difficult for the body to fight the infection.

So conclusion, our bodies can fight HIV for awhile. It's just a matter of time before the viral load outweighs the capabilities of our immune system.

For an understandable explanation: The human body can defend against HIV - hence why an HIV infection does not immediately develop AIDS, and in fact for a long time the virus cannot be detected in blood. This is because the immune response is keeping them down, but slowly the virus works its way through the cells, proliferates and kills more and more T cells, until the immune response is too weak. That's when AIDS develops.


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Effects of exercise on the brain
I am well aware of the phenomenon of neurogenesis induced by exercise, as well as the dopamine release that results from exercise. I am really interested in neuropsychology and the effects of exercise on personality. What are some other biological processes that are stimulated by exercise, does it activate our parasympathetic nervous system? Is there any cool research out there for me to read? I am grateful for any input. Any information about exercise and its effects on human biology is appreciated.
UPDATE
While this answer was appreciated, i'm interested in other biological processes... What happens to stress and anxiety? Do our adrenal glands stop secreting as much corticosteroids? What effect does exercise have on circadian rhythms? With exercise, can you circumvent the problem of not getting enough light in the winter? What effect does exercise have on memory? It should probably help, since it would lead to decreased damage to the hippocampus. How does exercise effect sleep, learning, memory, metabolic processes??? I'm searching for the comprehensive list of different primary and secondary effects of exercise from a biological standpoint. I'm really interested in what the short term and long term effects of exercise are on the brain.

There's one thing I can add, I'm pretty sure any dopamine release would be catalysed by a endorphin release seeing how beta endorphin is well known to be released during exercise.

Although current research has little to say about the effects of exercise on personality, there has been recent correlations demonstrated between personality and the "drive" to exercise--specifically, aggression as a personality trait has been linked to higher metabolic rate. See http://phys.org/news206006380.html for more information about this.
The causation in exercise-induced neurogenesis is not well understood. A correlation that has been found (in mice) is the presence of a hormone called beta-endorphin, which is attributed to positive affect (a boost in mood). Exercising mice that demonstrated the presence of beta-endorphin in their hippocampal region did experience exercise-induced neurogenesis, while those that naturally lacked beta-endorphin did not experience neurogenesis.
The basic worth of circulation should not be overlooked, either. Anything that gets your blood pumping more efficiently means that the more distal parts of the body will appreciate an influx of nutrients. A smoker with poor circulation (as a result of lowered oxygen in the blood -- carbon monoxide competes for hemoglobin-binding) will have cold hands and brittle fingernails, and this is just a simple example of this phenomenon. The value of increased circulation to the brain shouldn't be overlooked -- the blood is our main transportation system, and the brain gets nothing that is not delivered via circulation. It's akin to watering a plant -- sure, it may grow it you give it 30 minutes of sunlight and 1/4 cup of water a day, but it will certainly grow to its full potential if it is fed as much as it needs.
Exercise is important, but it's easier to think about the questions you pose if you consider exercise more as a physiological stressor on the body. Muscle tissues are torn and damaged by exercise, but the body recognizes that it must need these resources (because of some present danger in the environment that caused you to run/strain yourself) so you begin to see the typical skeletal muscle hypertrophy. The heart is also made stronger through this strain, which is why regular exercisers have a lower resting heart rate -- it takes their heart less effort to pump the same amount of blood.

Exercise stimulates various hormones which have impact on brain as well as other parts of the body. In psychological perspective, endorphins and serotonin released during exercise, are responsible to feel good feeling or act as antidepressants. Endorphins are produced by pituitary gland in the brain. Serotonin is also produced in brain to some extent during exercise. An increased level of serotonin could lead to nausea and vomiting. The other hormone released significantly is dopamine which is responsible for increasing blood pressure but it also helps in focus, attention and increase memory.

Note that the pituitary gland is not part of the brain. Also, I would refrain to say "release of  does XYZ". Dopamine has many different effects depending on what part of the brain releases it and where.


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What is the cannabinoid autoreceptor?
"Is there a cannabinoid autoreceptor? And if so what is the cannabinoid autoreceptor?"
(i.e. is the cannabinoid autoreceptor CB1, CB2 or is it one of the G protein coupled receptors, GPR18, GPR55 or GPR119?)
Where:

An autoreceptor is a receptor located presynaptically that sends back negative feedback that inhibits the synthesis of the neurotransmitter to which the autoreceptor belongs and this negative feedback also inhibits the release of the neurotransmitter from storage vesicles into the synaptic cleft.
The CB1 and CB2 receptors are respectively called the first and second cannabinoid receptors and are a pair of G protein coupled receptors.
GPR18, GPR55 and GPR119 are G protein coupled receptors that are also activated by some lipid messengers including a few of the endocannabinoids and their related compounds.

CB1 and CB2 are indeed particular genes which are present in neurons, but also liver and other tissues.  The HGNC website is a good resource for questions like this - HGNC is the international organization that tries to unify and track gene names.
The official gene names are CNR1 and CNR2 respectively.  Gene names are a bit of a mess, since many genes have been found by different experiments and so have many names.
CNR1 has other aliases, I see:
CANN6, CB-R, CB1, CB1A, and CB1K5.
CNR2 has only the one alias: CB2.
I also searched the HGNC website for those alternate gene symbols and they appear to be different genes, although CB1 and CB2 are GPCR class receptors, humans have hundreds of these genes.  Most cell scientists would not be surprised if cannabinols bound other receptors - the fact is probably only that CB1 and CB2 bind strongest and were found first.  Often weak binding is important to specific pharma/neuro responses.
That is to say there shouldn't be any single Cannabinoid receptor in the animal repetoire.  CB1 and CB2 almost certainly have a primary function other than cannibinol binding.  Primates evolved in the old world and cannabis is thought to have originated in the Himalayan regions.  From an evolutionary standpoint, the activity of cannabinoids is as much coincidence as anything, so you would expect that a single receptor gene is unlikely.


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Cooking with sawdust
In a book about post-war Japan (Embracing Defeat, Dower) the author mentions a process for making sawdust at least partially edible, so it could be used in recipes in a 1:4 ratio with flour for cooking. The author says the sawdust was "fermented," as I recall.
My question is whether this is anything more than marginally possible. After all, kimchee, yogurt, beer, and other fermented foods aren't necessarily easier to digest. Is there a fermentation process involving bacteria that break down cellulose that might make wood even slightly nutritious?
My impression is that in forests the process of breaking down wood does not initially involve bacteria but other microorganisms; on the other hand, ruminants such as cows use bacteria to help them metabolize.
Thanks for any insight.

Be careful about wood preservatives, some of which double up as pesticides. For example 2,4-Dinitrophenol, something you definitely don't want to eat. https://en.wikipedia.org/wiki/2,4-Dinitrophenol

Yes. I think it would certainly be possible for raw sawdust to be made digestible by humans through some sort of fermentation process with some kind of microbe or another.
Pickling (as is done with kimchee and cucumbers and lots of other fruits) uses naturally occurring bacteria that are artificially selected for by using a strong brine solution so that most microbes die but the ones that naturally survive in strong brine also convert the organic materials they find (raw cucumber or cabbage) into different organic materials (pickled cucumber or pickled cabbage in the case of kimchee).
If you could find a microbe that could digest wood (there are many I'm sure; the gut bacteria in termites provide evidence of at least one or some), and if you could find a way to select for that particular microbe, then fermenting sawdust for nutritious human consumption becomes feasible. The only remaining problem is finding that particular microbe whose excretions were digestible to humans.

Was hoping for something more particular, but +1 and will accept after decent interval if nothing appears.


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Photosynthesis - Light Intensity
Say I was conducting an experiment for photosynthesis. If I moved light closer to the plant, what effect would this have on the process of photosynthesis?

Could you list a few ways that you've tried to research this question before asking here so we know that you've put effort into the question?

The rate of photosynthesis varies from plant to plant. Some plants require more light and some require less. If you move light closer to the plant, in most scenarios the rate of photosynthesis is likely to be increased. For some plants a minimal light is enough for their photosynthesis, so for those plants, moving light source closer or further will have less effect.

yes - Individual genetic composition often trumps the typical assumptions of physics in biology.


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At what age do babies begin to synthesize their own antibodies?
When babies are first born, they receive their antibodies from their mother (I assume because they do not yet have the capacity to synthesize their own).  So my question is, at what age do babies begin synthesizing their own antibodies?

In the graph above the darker blue line refers to the antibodies the baby receives from the mother in utero, as you mentioned in your question.
As you can see, the red line indicates that babies begin to produce low levels of their own antibodies between 3 and 6 months before birth.  However, these are IgM antibodies, immature 'rough draft' versions.  These have much lower affinity for antigens then their mature IgG counterparts which are the classically thought of antibody.
Levels of an infant's own IgG start to rise after birth, however don't reach a reasonable level until after the child is roughly 1 year old.  Maternal antibodies start to tail off at around 3 months leaving a period highlighted in blue on the graph where infants are particularly prone to getting infections.

I don't think that is correct to say that IgMs have lower affinity. When a cell shifts from making an IgM to an IgG via class switching, the variable domains remain the same, there is no change in affinity - affinity maturation has already occurred during proliferation of the IgM-producing cell line. In fact IgM will bind well to weakly cross-reacting antigens because of its high avidity (due to the pentameric structure of the IgM molecule).

@AlanBoyd this is perhaps a shortcoming in my notes, I was under the impression that affinity maturation has two 'sub-processes', class switch and then somatic hypermutation however I could have easily got the order reversed.

B cells undergo isotype switching AS WELL AS affinity maturation, under the direction of T cells. So, when a B cell shifts from making IgM to IgG, it is simultaneously altering its antigen binding site in the variable regions to increase the affinity of the antibody being made. Ref: Janeway's Immunobiology

If the fetus gets infected, can it produce antibodies intrauterine to fight the infection ? If yes; is it effective ? Can it be used to test if the infection has traveled from mom to fetus ?


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Why aren't D-amino acids used in proteins?

Possible Duplicate:
Why are amino acids in biology homochiral?

Why are only L-amino acids used in protein construction, and not D-amino acids?

We already have a question about the number of amino acids used in proteins, so I edited your question to be only about the second part of your original question.

We also have Why are amino acids in biology homochiral?

I personally (not base on Lab works) think, maybe structure of  translation related proteins and RNAs, is the cause of these. I'll carefully read your suggested links.

I could give citations of where D-amino acids are in fact used in proteins; however I'm not sure that would count as an answer to this question.


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What kinds of arousal can a human brain experience?
I've been reading about the new phenomenon called "arousal addiction". The context in which this term is used is Internet, Porn and/or video game addiction(cummulatively Internet Addiction Disorder - IAD). Dopamine and Dopamine receptor D2 are sometimes mentioned, as being affected by exposure to a new, novel stimuli.
I'm interested if there are other forms of "arousal" that may involve more than just Dopamine. For example, I know that there are 4 neuromodulators in the human brain:

Dopamine
Serotonin
Choline
Noradrenaline

For example, if a person likes horror movies to the point of addiction, is it Dopamine, or is it Noradrenaline that the person enjoys? If a person is addicted to comfort foods, is it Dopamine or Serotonin?
Thank you!

Depends on what you mean by "addiction": defined, addiction usually requires both psychological and physiological dependence, but conversationally we sometimes only talk about psychological dependence (as in here, your muscles won't cramp up if you NEED a horror flick).
If a person enjoys horror movies, is it the suspense? Such a rush is caused by the well-known fight-or-flight catecholamine epinephrine (also known as adrenaline). This is the short-term stress response at play. Comfort foods are a whole other story, because it depends on the food as well. Carbohydrates can contribute to serotonin levels, yes, but I read a super-interesting study a couple years back about saturated fat causing a decrease in corticosteroid levels and this sought to explain why people eat fatty foods when they are stressed (I'll try to find this article for you). Tryptophan, an amino acid, is converted to serotonin, which is why turkey, milk, and other sources of trp can make one sleepy.
Awesome question! I'm going to try to learn more about this and find that article for you. Dopamine is the primary player in most conventional addiction-talk, as it's crucial to the reward circuitry that is usually discussed.

Thanks! The way I can clarify the question is - exposure to a new arousing stimuli (ex: new sexy female) stimulates release of dopamine in response to the stimuli. I'm interested if there are other neuromodulators that are elevated or lowered in response to stimuli.


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How would ecology be affected if 100km² of an ocean surface was covered by a floating object?
Assume that we planted floating solar cells on the ocean surfaces. Assume a 100km² solar cell field in the middle of the Pacific Ocean. All of the sunlight will be blocked by them. How would that affect the life in oceans?

The vast majority of light only penetrates the top 200 metres of the ocean, the euphotic zone, so your answer is roughly "what ever lives in the euphotic zone which requires light." In all likelihood I would expect this to cause:

anything  which is not highly mobile but, is dependent on sunlight (phytoplankton etc.), would die.

the more mobile ("free swimming") which rely on either sunlight or the (now dead) slower resources would move out of the area.

reduced flow of nutrients in to the lower parts of the ocean - biomass from the upper regions dies and sinks to the lower levels, if it no longer grows in the upper 200m then there will be less down flow after time.

Overall, the impact would be low because the area of the pacific is >165,000,000 km2 so the density of biota would only increase marginally in the top 200 metres of the pacific (the sunlit water volume decreases from 33,040,000,000,000 cubic metres to 33,039,080,000,000 cub. metres). Also, if we assume that the platform is free floating that means it would drift thus only causing short term loss of sunlight for the less mobile organisms.
EDIT:
Upon reading @Kotatsu's answer I feel they have made a very good point and I should add the following:
By providing a solid surface it could also benefit oceanic life by increasing area available to live for sessile organisms (just like shipwrecks, oil rigs etc.). Further if the panels were broken up (I assume this would be the likely design because sitting a huge sheet across the ocean will leave it prone to twisting by wave motion) light would be able to pass between the gaps. I agree with @Kotatsu, and this "floating panel" could even be beneficial to the ocean ecosystem.

note: I am not an expert on this so it is purely an application of logic and my best guess

It might, however, result in an increase of macrofauna, especially if the solar plates were anchored somehow at the bottom of the ocean. This may seem paradoxical, but for most groups of sessile macrofauna (cnidarians, tunicates, bryozoans, brachiopods, some molluscs, and so on), the limiting resource in the ocean is space, and any solid or semisolid surface is a good surface to live on, so at least along the margins of the solar plates, we should expect to see enormous amounts of macrofauna, in the same way as we see lots of it on the keels of ships, on jetties, oilrigs, and all other man-made structures in the sea.
I would expect that once such a sessile community is established, it would be beneficial to other organisms as well. Many polychaetes, molluscs, arthropods, and other groups are predators of the sessile community, and as the larval stages are often planktonic, I would expect to see these established in this community as well, given time.
This could in turn attract fish, especially if the platform is not too far from land, and is not cleaned, but the various shells and structures built by the sessile community is allowed to remain even after the actual organisms die off. The spaces between and inside dead sea shells are often very important places for egg deposition by fish, which may or may not remain in the area when they grow up.
Now, if the solar plates were divided into smaller connected discs, so that there is sunlight reaching the water between the discs, this margin effect would be even more profound, I would expect, as there would be sessile macrofauna around all the margins, and if sunlight comes down between the discs, that would allow some primary production even within the solar field.
So while rg255's answer is certainly also correct, I do not think the situation is necessarily as bleak as depicted in that answer, however, it would all depend on how the structure is built and maintained. Dividing the solar panels into smaller, connected units would be much better than having one solid platform (I assume this would be true also for mechanical and engineering reasons, but I'm not an engineer...), and there are certainly other ways to reduce the impact of such a solar system platform.
I would also guess that any platform placed in the middle of the ocean would have to include some system for keeping oceanic birds away.

I tend to disagree a little.  If anchored, i would think that the dead spot in the middle would still be about 5 km away from any lighted portion of the sea. that's quite a perturbation.  Filtering organisms in the middle of the array would not get so many nutrients, would they?


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ATP utilized in Glycolysis vs. Gluconeogenesis
In glycolysis, the conversion of glucose to pyruvate results in a net gain of 2 ATP molecules. In gluconeogenesis however, the conversion of pyruvate back to glucose requires 6 ATP molecules.  Why does there seem to be an apparent loss of energy?

This energy is not lost, it is dissipated as heat.
And this must happen because of thermodynamics -- the direction of the reaction is simply determined by the difference of energy between substrates and products, and it must be positive for the reaction to happen spontaneously.


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Do adjacent axons in a nerve influence each other?
Suppose I have a nerve fiber consisting of several axons all running in parallel to each other.  When an action potential is generated in a certain axon, this will alter the concentration of sodium and potassium ions inside the axon, and in the extracellular fluid around that axon.
The question is, will this change in ion concentration in the extracellular fluid, alter the threshold potential of an adjacent axon, which shares the same extracellular fluid?

Yes, activity in other cells can affect the surrounding electric field and thereby influence the behavior of nearby neurons. This phenomenon, known as ephatic coupling, can be important but is usually small.
For many cases, it is likely too small to be of physiological importance. Note that individual action potentials are quite transient and, especially in myelinated axons, the resulting currents are local and small. Therefore it's unlikely that a single neuron's activity will have a noticeable effect on nearby neurons.
However, in unmyelinated axon tracts and/or when a larger group of neurons is active, ephatic coupling is more likely. In particular, it seems to play a role in synchronizing cell populations during oscillations. For example, Anastassiou et al (2011) found that firing of cortical neurons could be entrained by the extracellular field and affected the intracellular membrane potential by about 0.5 mV.
Anastassiou, C.A., Perin, R., Markram, H., Koch, C., 2011. Ephaptic coupling of cortical neurons. Nature Neuroscience 14, 217–223.
Also, for reference:
Jefferys, J.G., 1995. Nonsynaptic modulation of neuronal activity in the brain: electric currents and extracellular ions. Physiol Rev 75, 689–723.
Buzsáki, G., Anastassiou, C.A., Koch, C., 2012. The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes. Nature Reviews Neuroscience 13, 407–420. (see pages 411-412)

Edit:
For your particular case, action potential propagation in one axon is very unlikely to affect the other axons in any relevant way in a tract of myelinated axons. This is especially true because the initiation of action potentials does not occur along the axon itself, but where the axon is just branching from the cell body (the axon initial segment). Threshold is important at the initiation site, but is not really relevant in the tract itself, where the axon is just conducting the signal it receives from the initiation site.


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variation in antigen binding site of antibodies
Antibodies or immunoglobulins are proteins made by the immune system in response to alien(!) molecules. Each antibody binds to its specific antigen. This great diversity and specificity is cause of diversity in Antigen Binding Site of heavy chain and light chain of antibody. Although other sections of Antibody are highly stable, Binding sites are very mutant. What is the reason for this difference in mutation rates in different parts of antibodies?

The processes are called gene rearrangement and somatic hypermutation, and are used by maturing B-cells to generate very (very) large amounts of diversity in the antibody repertoire. If your institution has access, this great article in Annual Reviews in Immunology has all the details, or you can read about it in Janeway (slightly outdated edition). Essentially, the genes encoding the B-cell Receptor, or BCR, have many fragments of several different types in them, and through the process of gene rearrangement the final Complementarity Determining Regions, or CDRs (the antigen-binding sites), are generated into one mature sequence for each individual B-cell.
A mature IgG molecule (the soluble, secreted version of the BCR) contains four chains - 2 heavy (each of which are identical to each other) and 2 light (also identical). There are Constant or C regions in each chain that essentially don't vary much, and are not really involved in the process of antigen binding. On the "business end" are three regions (or types, from above) called V, D, and J in the heavy chain, while the light chain just has V and J. Those letters are from Variable, Diversity, and Joining, if you're interested.

Figure 4.3 from Janeway shows the number of "fragments" or gene segments of each type in humans. So, when the heavy chain is being made, 1 fragment out of 65 Vs is picked, 1 of 27 Ds, and one of 6 Js, then each is joined together in a process that can also introduce an additional amount of randomness at the joins. Combine this with an only slightly less complex process in the light chain (as there is no D region), and the fact that a single insertion/deletion of a base pair can drastically effect the resulting protein sequence, and you get a protein with a huge number of possible sequences, potentially in the range of 1011.
This process of gene rearrangement typically generates immunoglobulins with relatively low affinity for their antigens. During affinity maturation, a process called somatic hypermutation randomly changes individual base pairs (translated to amino acids) in the CDR in cells that are descendents of, and bear the same base sequence as, the original. Cells expressing antigen receptors that are of higher affinity are then positively selected and clonally expanded by the immune system, allowing your body to tailor its response to an infection or other exposure to what it sees as foreign material.

I don't understand what this is referring to: "the vagaries of possible frame-shifting during transcription".

@AlanBoyd - I'll edit that. I was referring to the fact that an insertion or deletion of a single base pair can change the frame in which the downstream codons are interpreted, leading to (potentially) very different protein sequences.

Antibody molecules or immunoglobulins (Ig) consist of heavy and light chains (e.g. two of each in IgG). Both heavy and light chains have variable domains at their N termini.
During development of the immune system the pro-B cells in the bone marrow undergo gene segment rearrangements, bringing V and J segments together for Ig light chain production, and V,D and J segments together for Ig heavy chain production. The V gene segments encode the variable domains at the N-terminus of light and heavy chains. There are a few tens of V gene segments in our genome - this is the first source of variability.
The second source of variability is the "sloppy joining" of the V (D) and J segments. This results in frame shifts together with short deletions and insertions. This V(D)J junction corresponds to the third hypervariable region of the variable domain.
Each immature B cell displays its antibody at the cell surface as a membrane-bound form of IgM. If an antigen binds to this antibody the cell is stimulated to divide (clonal selection). During the proliferation of the immature B cell it undergoes somatic mutation due to error-prone replication of the Ig loci. This allows for the production of Ig variants with improved binding affinities which are in turn stimulated to proliferate more rapidly, eventually maturing into antibody-producing plasma cells. This somatic mutation is the the third source of variability in the variable domains of Ig molecules.
See any immunology textbook for details and diagrams.


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What is the state of automated quantitative analysis?
Quantitative analysis of microscope images is essential for many types of studies, but the techniques used most often are very labor-intensive. I have been able to find some literature about using computers to perform the analysis, but do not have a good picture of the state of the art.

Is there a good literature review on the topic?
Is there much use in practice which I have not yet seen?

Nature Methods seems to publish quite a few methods that facilitate this kind of analysis. E.g.
http://www.nature.com/nmeth/journal/v8/n3/full/nmeth.1558.html
And an editorial from them:
http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2102.html
As part of a special issue on BioImage Informatics with some nice examples.
http://www.nature.com/nmeth/journal/v9/n7/index.html

The word to look for is 'Image segmentation'. But also here, it very much depends on what you're looking at. Segmentation and quantification of simple fluorescence images is relatively easy and widely used. It can get very complex depending on how complex the structure is you're looking at. There are machine-learning approaches which are able to distinguish complicated structures from each other, such as different mitosis states.
Segmenting Hematoxylin-Eosin (HE) stained specimens is subject of intensive bioinformatical research. One goal is to assist pathologists in grading tissue lesions, such as in prostate cancer, but this is as far as I know not used clinically yet. Whole-slide scans of histological specimens are becoming more widely used clinically. These images are very huge (1 GB per specimen), so a research focus is also to provide a large-scale analysis of these whole-slide scans.
Also, take a look at CellProfiler (http://www.cellprofiler.org), this free open-source software saved my PhD project.
Literature I found:
Tabesh, A., M. Teverovskiy, et al. (2007). "Multifeature prostate cancer diagnosis and Gleason grading of histological images." IEEE Trans Med Imaging 26(10): 1366-1378.
Petushi, S., F. U. Garcia, et al. (2006). "Large-scale computations on histology images reveal grade-differentiating parameters for breast cancer." BMC Med Imaging 6: 14. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1634843/
I cannot provide you with a recent review, though...


text:
Is Webmedcentral a reputable scientific publisher?
I am a student, and I have written a paper (in drug discovery) which I want to publish. While searching for possible journals I came across Webmedcentral.
Is Webmedcentral a reputable scientific publisher?
What is the impact factor for this journal?

I checked this site and its journals in Scopus.com based on its "ISSN 2046-1690" but nothing was there. they are fast in submitting and publishing but it is not some thing great by it self. I think maybe its better to find some where better to publish your article(s).


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Biological key file format
I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data.
Thanks

Could you give us some more details about what you're looking for? Maybe I'm just not familiar with your terminology, but I'm not sure what biological key data is. I work in Bioinformatics and have done some Android development, so I might be able to help you!

Dichotomous key?

Yes, A dichotomous key. apologies for not being more specific.

@user521469 The Wikipedia page here points to software which may be a source of file format definitions.

I searched a bit and could not find any such format, but I am not a specialist in taxonomy.
From what I understand, the structure you want is that of either a tree or a DAG (Directed Acyclic Graph). Both are straightforward to store in a variety of formats.
One possibility is to use a format similar to other biological data that has a similar data structure. For example, Gene Ontology is a widely used dataset that has the structure of a DAG and has a number of formats including XML listing the parents and additional data of each node in the graph. See here for their formats.

If you mean some thing like .doc .txt .rar or etc. I think there is no special bioinformatics file formats like that, for example NCBI, EMBL, Expasy and others use this common formats in transfering sequence data. BUT there is some thing called file format for introducing data to this data banks for example FASTA file format:

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
  LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
  EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
  LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
  GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
  IENY

As you see, a sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the ">" and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence.
you can learn more things about these bioinformatical formats here and here.

Thanks for your answer. I am familiar with sequence formats. I was wondering if there was any format for storing data for dichotomous biological keys.

Please edit your question.

authors: Соня Бурбыгина


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How to evaluate the efficacy of an antibody for fluorescence microscopy?
I'm trying to evaluate data taken from fluorescence microscopy with antibody staining, and am wondering whether there is any standard way to evaluate the specificity of the antibody for such measurements? In particular, I am interested in evaluating whether there is specific binding of the antibody to the cells in the experiment, or only unspecific binding.
By leaving out the primary antibody or taking a control antibody without specific binding, I can compare fluorescence intensity, and an increase in intensity in the actual experiment towards this control will indicate qualitatively that the antibody binds specifically. But I wonder whether there is a standard statistical test or something to get such a result in a more quantitative way?

When testing an antibody for an imaging application, it is almost always a good idea to test it in another application like ELISA or Western blotting to see if it binds the target of interest. For example, try to find high- and low-expressing cell lines, load equal amounts, and see if there is a difference in signal at the expected molecular weight. Check the company's literature or contact their technical support to see if they have tested the antibody by immunofluorescence (IF), and if so what their results were and how they validated them. Check the literature to see if other people have published with this product. http://highwire.stanford.edu is a pretty good full-text search engine, but they don't have all journals in their database. Google Scholar can help, too.
You can also use your high- and low-expressing cell lines to see if there is a stronger IF signal in the high-expressing line. Look at your images to see if the signal is localizing where you expect it to, and do co-staining with antibodies to other proteins that should co-localize with your target of interest. For example, if your target is expected to localize to mitochondria, co-stain with COX-IV. A quick Google search found this Cellular Localization IF Antibody Sampler Kit that has controls for several different organelles and other specific locations.
Make sure you are following the manufacturer's recommended protocol. Don't crank the gain up too high on the scope, because non-specific background goes up, too. Look at the induction of signal between high- and low-expressing cell lines. Generally you would want at least a 2-3 fold shift, especially if you see a strong change in signal intensity by Western. Try using siRNA or similar silencing technology to knock down the signal in your cells, and validate using Western and IF.
Ultimately, you can never be absolutely 100% certain that an antibody is binding a certain target, and only that target, but you can accumulate a lot of evidence to show that it is likely. Try to put yourself in the mindset of a reviewer, and objectively convince yourself that the signal is real. If you can't, then shop around and try something else. Good luck!

Don't really know if the first point is really so useful... Most of the time antibodies work in IHC but not in WB or vice-versa and not having a signal in WB does not mean that your IHC signal is aspecific. Also, if you are working on tissue (rather than cell cultures) you have many different cell types which may complicate things a lot.

@nico - In my experience (at a certain antibody company) it is perfectly possible to have a great IF or IHC antibody work well in WB, and vice versa. It all depends on how the Ab is screened, and the nature of its epitope. I agree that not having a WB signal would not necessarily disqualify its staining capacity, so that's why I put in the other options like differentially-expressing cell lines and siRNA. It seemed like the questioner was talking about cells, and my mind differentiated that from tissue, which may not have been a correct assumption...

Hmmm... in my experience (in the lab) that is not that common when working with tissue. I don't work on cell culture, so maybe that is different.

Tissue makes for dirty WBs in general, which is why we tried to do as much validation on cell lines (and paraffin-embedded cell pellets for IHC) so we could be sure before moving on to tissue. We wanted to be as damn sure as possible we were staining the right thing before releasing something to market. That meant we didn't quite have the product diversity that some other companies might have had, but the quality and level of trust were a lot higher, overall. If you haven't used their stuff before, I highly recommend it, even though I'm not there anymore.


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Glutamine analysis
I use to run a method to analyse all the amino-acids in a food sample. For that I have to hydrololyse the sample and in the last stage of the method I read the amino acids with a ion exchange chromatography.
However, when using this method, due to the hydrolysis, the glutamine transforms into glutamic acid, thus in my result I get a big peak for glutamic acid and I cannot read glutamine.
My question is if there's a method to quantify glutamine in a food sample.
Edit: it has been a while, thanks for the feedback!
In the kind of samples I have I need to measure the bound glutamine, not free glutamine. This imposes a problem during sample preparation when trying to separate the amino acids. I have made a few experiments and I have almost succeeded by using a 'enzyme cocktail' that does a total enzymatic hydrolysis. Next step will be to find out if I can quantify glutamine.

A Google search for glutamine assay reveals a number of commercial kits. Some of these refer to food assays. I don't know what the basis of these assays is however.

Maybe there's an alternate hydrolysis method that doesn't convert glutamine to glutamate?

I am not so familiar with enzymatic kits for quantifying glutamine, but most enzyme-based analysis kits come with a number of fairly strong assumptions on the enzymology involved, and in my experience they are difficult to use reliably. Commercial kits are hopeless to troubleshoot since their components are not disclosed --- you don't know what you're working with.
Are you at a clinical chemistry facility? If so you may have access to analyzers used to measure blood biochemistry parameters, and some models measure glutamine, for example this one. These instruments are also based on enzymatic assays, but they are carefully tested since they are used in human medicine, and so I would consider them more reliable than the average Sigma kit.
The best alternative I think is mass spectrometry, or NMR. Glutamine is easy to measure on any LC-MS or GC-MS setup (an old triple-quadrupole will do nicely), it ionizes well in positive mode electrospray, is well retained on a typical HILIC column, and isotope-labeled standards are readily available. I'm no expert in NMR but I know glutamine is measured routinely.
Another caveat with analyzing glutamine is that it decomposes spontaneously in water to form pyroglutamate, with a half life of about two weeks at room temperature, as shown in this paper. But I'm sure you're aware of that.