text:
Why is the Hydra Biologically Immortal?
I have heard that the Hydra organism is biologically immortal (later I found that there are more immortal organisms). Now I know that its immortality is related to its telomerase. The thing is that we all have telomerase, but we age and Hydra don't. What are the proteins (especially telomerase) related to aging in humans and Hydra and how do they work differently?

Could you define "hydra" or find a picture of it? The only "hydra" I'm well aware of is the fictional one from Greek myths.

Dear MCM, go to this link

Hydra are just one of the many organisms which are immortal.  That is to say all their cells divide forever - there is no senescence (planned cell death) in any of their cells. Interestingly Hydrae that reproduce sexually age and die, but asexual reproduction appear to be immortal.  Animals that are immortal more often reproduce asexually... this may only be because immortality became unpopular in evolution early on and may have not developed senescence in the way other animals have, or lost it when it was not so integral to life.

Although immortal Hydra also appears to share the (TTAGGG)n telomere repeat, there is as yet no data on how or whether they avoid chromosome end depletion. These data suggest the possibility that senescence or death of asexual individuals and colonies may in part result from a failure to maintain chromosome ends that are restored by going through a sexually reproductive cycle .

So its not clear if the telomeres are protected in hydrae and other immortal animals.  I would guess they probably don't have active telomerase if they are truly immortal, though its possible the telomeres are shortened and are repaired.
There are other factors which are supposed to be important for immortality.  Yeast and single eukaryotes are not individually immortal; an individual mother cell can only divide a limited number of times. While hydrae are not a popular focus of research, there has been a concerted effort in trying to understand yeast mortality and there are more than one mechanism being pointed to.
Since there is no germline in single celled organisms, (they only have one copy of their genome to reproduce from) telomeric shortening would not be a useful mechanism for aging; Calorie restriction has been shown to prolong fission and budding yeast by activating pathways which slow aging by protecting against stress, and slowing down reproduction.  All of these findings have strong parallels in work in aging in animals which is a hot topic now.
Finding these pathways is encouraging strong thought that aging and senescence are an evolutionary adaptation rather than a biological necessity.

Our current knowledge suggests that an apoptotic program has evolved in microorganisms as a survival strategy beneficial to the group. This program is dependent on cellular pathways like the Sch9, Tor1, and Ras/PKA pathways and its activation reduces cell protection and maintenance and raises the level of superoxide production, which in turn contributes to cell damage and death. Superoxide also elevates DNA damage and mutation frequency in the aging cultures ... Aging and apoptosis are intrinsically related in yeast and the mechanisms that cause them have just begun to be elucidated. ...  will provide important information to understand the fundamental biology of aging in other species and investigate the controversial hypothesis that an “aging program” might be conserved in higher eukaryotes.

There is an open question as to whether an immortal yeast could be engineered to be immortal.  A team at Max Planck Institute did a lot of foot work and found a strain which they claim does not seem to experience individual mortality either.
So this does indicates that immortality might not be a necessity for any cell or maybe even for animals.  Occasionally, even animal and human cells can be coaxed to revert to an immortalized state, though usually it is the result of cancerous rearrangements of the genome.
This is a rich field and there are lots of telomerase focused ideas too.  Maybe someone can post something along those lines.

@It isn't correct to say that yeast cells are immortal. See here for example. I spent two years working alongside a postdoc who spent all of her time watching yeast cells age and die!

more complex organisms also have very little senescence - e.g. lobsters (http://www.ncbi.nlm.nih.gov/pubmed/9849895?dopt=AbstractPlus & http://www.fightaging.org/archives/2007/06/ageless-animals-the-lobster-edition.php) - which is linked to constant (near constant) levels of telomerase expression throughout life. From the abstract to the above paper: "We conclude that telomerase activation is a conserved mechanism for maintaining long-term cell proliferation capacity and preventing senescence, not only in cellular models or embryonic life stages but also in adult multicellular organisms.  "

it sounded like this isn't a sure thing yet so I decided not to emphasize it.  there are other wierd cases too.  nobody knows why sharks do not appear to get cancer either, even if they have a more typical planned cell death mechanism.  Lots left to understand.  its certainly possible that some mechainism for immortalizing animals will be discovered.  there is lots of work in that direction.

@shigeta now I have to search those sharks!

here's a start : http://news.nationalgeographic.com/news/2003/08/0820_030820_sharkcancer.html

@AlanBoyd you're right I'd forgotten that.  Did find some exceptions and it turned into a nice section of the post.

Actually, most adult cells do not express telomerase or express it only at a very low levels. Telmoerase is highly expressed only in cells that need to divide (e.g. stem cells), thus "immortalizing" them.
In fact, human cell lines which scientists work with can be "immortalized" by activation of telomerase (along with other things).
So you may ask yourself: why not have telomerase activated all the time in all cells? Well, allowing a cell to reproduce easily can be a pretty bad thing... that is exactly what cancer does. Indeed, one of the things a cancer has to do is to activate the telomerases in order to be able to grow. This is also why cancer cell lines are "immortal". This also suggests a potential cancer therapy - targeting telomerase - which is currently being pursued experimentally.

Thank you, Can you add some reliable articles to your answer please?

@mysky I added a link to the Wikipedia article on telomerase, which has much of this information included. I don't know if you call that "reliable" though and what technical level you would like.

Telomerase activity is just one (probably minor) facet of aging.  It takes a lot more than just basic end repair of DNA to keep a complex organism alive, especially mammals.  Just a few issues off the top of my head:

repairing oxidative stress to DNA and proteins
repairing UV damage to DNA
keeping cells clean of debris like protein aggregate buildup (think amyloid deposits like in Alzheimer's)
replacing dead cells without compromising the tissue they're in

For a solidly scientific, short, but very readable book on the subject, I personally liked "Understanding Ageing" by Robin Holliday.  For being published in 1995, it's still relevant. He had a later book that wasn't quite as good (Aging: The Paradox of Life: Why We Age, published in 2010). In large part it's because it was fairly redundant to the first one; we've known about these problems for a long time and have made fairly little progress on them.
http://www.amazon.com/gp/product/0521478022/ref=oh_details_o03_s00_i00?ie=UTF8&psc=1
Part of how hydra can get away with apparent immortality is their constant proliferation of stem cells and their ability to regenerate entire body parts. This circumvents a lot of the issues above (theoretically, but I'm not an expert on hydras). Many copies of the DNA are separately housed, so if a copy gets damaged irreversibly, it can just get trashed. Most (if not all) human organs have similar reserves of active stem cells. There isn't a single universal source (outside of the sperm and eggs), but this is less important so long as the entire stem cell supply isn't compromised by some gross organ damage.
The second part is much, much harder for humans though. While some tissues (say muscle) can easily replace dead cells, it's much harder in others, like the brain. You don't just have to replace a dead cell, but all of its connections to every other cell. And really, the brain is what this all comes down to, and an identity crisis in humans.  I don't care if you replace my liver and my left arm times, but how do you replace the brain?  I would speculate that we spend a lot more time keeping individual cells alive, because we can't replace them.
If you chop a starfish in half, you get two starfish, and would have trouble saying which was the original. Is it the same starfish if you've replaced the arms 3 times and the body twice?
If you chopped a human in half down the center, and we could magically regenerate everything, you would get two very different people from each other and the original. The problem being that there's no way to reconstruct the connections; you'd just get a blank brain to fill up.


text:
How to determine the direction of regulation of a gene by comparing gene expressions?
I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease.
I am confused about how people can determine whether a gene is down-regulated or up-regulated by its gene expression.
Assume we have a few samples of a gene: some of the samples are normal patients samples and rest of them are disease-infected samples. Do we determine the direction of regulation of a gene by the ratio of gene expression of normal/disease-infected samples?
For example, if the ratio of expressions is a negative value, do we say that the gene is a down-regulated gene, otherwise, it is a up-regulated gene ?

If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated.
Gene expression values are usually measured genome-wide and then normalized before computing the ratios. So you rarely deal with individual raw expression values.

source: Stack Exchange

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

sort: votes


text:
What is the fibre axis in the Watson and Crick paper?
I was reading Watson and Crick’s original article on DNA structure in Nature 171, 737–738 (1953). The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. This axis isn’t shown in modern models of DNA, so what is it?

As this question quotes a paper written in British English, a language acceptable on this list, changing the spelling to US English was neither accurate or necessary. I have corrected the quotation.

Short answer:
The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick referenced to guess their model (performed by Rosalind Franklin).   The fiber axis is the direction along the DNA strand.
Longer:
Watson and Crick created their model of DNA based on the esoteric experiment called X-ray fiber diffraction.  To collect fiber diffraction data ( gathered by Rosalind Franklin actually) DNA is pulled out of a cell lysate and washed with buffer.  It looks like a clear, liquid, string of snot (a technical term that is).  Its stringy though because the long DNA molecules pull out and create viscous fluid where the DNA is pulled along the length of the snot fiber.  Because the DNA is ordered in this one dimension, if you shoot a beam of X-rays through it, it creates a pattern on film that looks like this:

As you can see its got a nice X-shaped pattern.  The DNA in the fiber is mostly aligned along the fiber, in the up and down direction.  Because this is so, the spacings between the different layers is due to the spacings between the DNA bases and the x-pattern comes from the fact that DNA forms a double helix.
Some misc details - you have to use X-rays because their wavelength is about the size of an atomic bond and this is the scale of model Watson and Crick and Franklin and Wilkinson were trying to find.
The fiber axis is along the y axis (top to bottom) because the trail of DNA snot hangs down - it will sag if you hold it an angle.
Rosalind Franklin was a great experimentalist and she realized that the DNA snot trail dries out over time as the experiment would go on for days.  She set up a moist stream of hydrogen gas blowing over the DNA strand during the X-ray experiment and so was the only experimentalist who obtained what we now know to be the true result - double helical DNA.  As it dries out, DNA interconverts to the Z-DNA form I believe, which does not have the x-pattern and also confuses things because the result is a smear of the DNA helix converting from one form to another.
Francis Crick had actually predicted the X-pattern for helices.  The structure actually required these two to come together to get the answer while the American genius Linus Pauling was working hard in California on the structure as well and would have won too if he understood how to keep his snot properly damp.
The reference for nearly all of this is Watson's somewhat self-centered but historically accurate book "The Double Helix".
After some surprisingly difficult Googling, I can't found a picture of DNA fiber... picture below. You can make some yourself from the protocol listed here and some saliva, soap and other common household items.

Your statement "For their experiment (and for Rosalind Franklin who was also doing Fiber diffraction) " implies that W & C were actually doing experiments, but of course they weren't - they relied entirely upon Rosalind Franklin's data, supplied to them by Maurice Wilkins who shared the Nobel prize with W & C.

I adjusted the wording, but didn't feel the need to get into every detail of the story - link to the book is provided.

The obituary of the person who took the key photograph has just appeared in The Guardian "...Freda Collier [was]...part of the core team of Maurice Wilkins, John Randall and Rosalind Franklin (plus Franklin's PhD student, Raymond Gosling) working at King's College London on the structure of DNA. Freda...headed the photographic laboratory at King's that produced the famous "photo 51" seen by James Watson from Cambridge University. Watson immediately realised that the molecule revealed was a double helix."

@AlanBoyd what was your opinion of Maurice Wilkins?  It seems to that Franklin had little or no discussion with him - whether right or wrong - about the work.  I know he's on the paper, but what was his contribution really?  Did he train her in fiber work?  I've not found an answer to that question and certainly sometimes it does not really seem he helped.  I know it was his lab and all, but I mean intellectually or in terms of direct work...

At this date I don’t expect an answer, but why do you term X-ray diffraction of fibres esoteric?  Mainstream molecular biology at the time. That’s how the structures of hair and silk fibres were determined.

Why is Fiber Diffraction esoteric?  relatively few biological molecules are so long.   You are aligning the molecules by pulling snot or a fiber into a string.  In so doing the molecules have to line up.  Hair, spider silk, horn, some kinds of very long virus families (e.g. tobacco mosaic virus) and DNA qualify.  Also the results are often quite low resolution.  Now Electron Microscopy can look at many thousands of particles of arbitrary shape and get low to even medium resolution structures.  A much more useful approach.

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


text:
Are all chromosomes equally susceptible to mutation?
The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old one. Are there any chromosomes out there that may be more susceptible to mutation than their neighbours?

Look into recombination hotspots. Also, for reasons of pure statistics, the larger chromosomes are more susceptible to mutation since they have a larger area in which they can accumulate damage.

Are you asking about the mutation rate with or without the effect of selection?

terdon is spot on with the recombination hotspot comment. Mutations are often associated with recombination (information gets lost during crossing-over, so DNA repair is necessary, which of course can introduce mistakes/mutations). It's a fact that there areas in certain chromosomes where recombination happens much more often than other areas of the chromosome. So it follows that chromosomes with more hotspots would likely have higher mutation rates than other chromosomes, on average. This does raise the point, though, that perhaps it's not the mutation rate of the entire chromosome that matters-maybe mutation rates at a more-local level (such as near a hotspot or far away from a hotspot) are more worthy of consideration for your question.
Also, I imagine that sex chromosomes have much lower levels of polymorphism than autosomes. This doesn't have to be because of a lower mutation rate, though: another explanation would be that deleterious recessive mutations on the X chromosome would be purged more easily than on autosomes because their phenotype appears in males (who don't have a second allele because they don't have another X chromosome, so the deleterious phenotype can't be "hidden" like it would in a heterozygote).

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


text:
Why do red blood cells contain haemoglobin and not myoglobin?
So I am reading about muscles and I come across myoglobin. It has a much higher affinity for oxygen than haemoglobin. So why have animals evolved to have haemoglobin in red blood cells, rather than myoglobin, which would be much more advantageous?

Just to expand slightly on the answer by Jack Aidley:
Have a look at this section from Stryer's Biochemistry text book, particularly Fig 10.17, where you can see that haemoglobin has evolved to have a high affinity for oxygen at the O2 concentrations present in the lungs, but a low affinity at the O2 concentrations present in the peripheral tissues. This is achieved by binding oxygen co-operatively. This means that haemoglobin can release 60-70% of its bound oxygen. Under the same conditions myoglobin, were it be used in red blood cells as an oxygen carrier, would release much less.
Incidentally the Figure linked to shows a comparison between haemoglobin and a hypothetical protein which shows 50% saturation at the same concentration of oxygen but which binds oxygen non-cooperatively (like myoglobin).
A more direct comparison of haemoglobin and myoglobin  - found here -  is shown below:

edit added to respond to shigeta's response
I don't understand some of the statements from shigeta so here are my views - if I am wrong, I would (genuinely) like to be corrected, since I have to teach this stuff.

..."what is particularly useful about Hb's cooperativity is that the last oxygen is harder to pull off the Hb tetramer than the first."

This statement contradicts my understanding of the oxygen-binding behaviour of haemoglobin. In the deoxygenated state the protein is in the conformation known as the T (for tense) state, and this is a low affinity state. The binding of an oxygen molecule to one of the haem groups in one of the globin subunits of the tetramer increases the affinity, so that subsequent binding of oxygen becomes easier. The details of how this happens are still debated, but I think what I have said so far is accepted by everyone.
Here is an equation to represent the binding of the first oxygen molecule to the haemoglobin tetramer:
O2 + [Hb]4 <--> [Hb4]O2
If deoxygenated Hb has a low affinity for oxygen then that equilibrium must lie to the left hand side - in other words the right to left reaction (release) is faster than the right to left reaction (binding). This is not consistent with the idea that haemoglobin hangs on to its last oxygen.

"The heart, which is the first organ in the blood cycle after the lungs uses a lot of oxygen - if hemoglobin were not cooperative, it might take all the oxygen from hemoglobin just after the beat when it uses oxygen when in distress, creating a block of hemoglobin which is completely without bound oxygen."

This is based on an erroneous view of the circulation - it implies that all of the blood passes through the coronary artery before getting to the rest of the body. Oxygenated blood leaves the heart via the aorta. Although it is true that the first branch off the aorta is the coronary artery, most of the blood doesn't enter this branch, but proceeds into the remainder of the circulation. In this sense the coronary circulation (by which I mean coronary artery>coronary veins - the heart's own blood supply) is in parallel with the rest of the circulatory system, not in series with it. At rest, just 5% of the heart's output goes into the coronary circulation.
According to this review, Regulation of Coronary Blood Flow During Exercise, (I am simplifying a lot here, but this statement does appear in the review and is not taken out of context): "Increased myocardial oxygen demands during exercise are met principally by augmenting coronary blood flow." At rest the heart is already extracting most of the oxygen from its blood supply (see here for some interesting data) so again there is no question of the heart extracting much more - it simply needs more blood, and of course the increased heart rate will contribute to this. There is also scope for directing a greater proportion of heart output through the coronary circulation, but I have been unable to find any quantitative statements about that. Interestingly, if you take a look at the data in the 1st table of the data here you will see that, at rest, 22% of the heart's output goes into the renal circulation, but that much less oxygen is extracted from that blood (about one ninth of how much is extracted from the blood going through the cardiac circulation). This represents a source of potential increased blood to be diverted to the heart at the expense of a reduction in renal filtration.

"Also - Hemoglobin is pretty clearly an evolutionary adaptation where four myoglobins came together to form a cooperative oxygen binder, so at one time probably myoglobin was the oxygen carrier. There are some primitive animals which have no distinct hemoglobin, just myoglobin like carriers."

I agree it is clear that haemoglobin and myoglobin evolved from a monomeric myoglobin-like ancestor, and that the appearance of a tetrameric molecule created the potential for co-operative oxygen binding. I am not as convinced by the rest of the sentence. I think we have to agree first on what we mean by an oxygen carrier. What I mean is a protein that is a component of a circulatory system. I know of no evidence that a myoglobin like molecule could perform this function. This arises directly from the shape of a simple binding curve (a rectangular hyperbola). For the protein to be saturable at atmospheric oxygen concentrations it has to have a certain Kd, and this precludes significant release of oxygen at physiologically useful concentrations. You either have a protein which can unload effectively but will not ever become saturated with oxygen, or you have a molecule that is able to become saturated but cannot ever unload except at every low oxygen concentrations. That is the remarkable thing about haemoglobin - the appearance of cooperative binding allowed for a more switch-like interconversion between a high affinity state, for loading up, and a low-affinity state, for unloading.
Now, if you wish to include intracellular oxygen transport in your definition of "carrier" then we enter a whole other debate about the role of myoglobin, but I have gone on for far too long already, so I'll stop there.

See that's a much better answer.

Seems like you have focused on different points than I, which is why I felt I should feel free to pot.  "The oxygen affinity of 3-oxy-hemoglobin is ~300 times greater than that of deoxy-hemoglobin."  Coopertivity creates the shape of the affinity curve, but does not make myoglobin intrinsically higher affinity than Hemoglobin.  The shape of the curve is important adaptation to deal with circulation.  You could define oxygen storage any way you like, I am merely pointing out that the evolutionary history of the molecule.  No need to make a contradictory statement out of it by reinterpreting.

@shigeta Apologies if you think I have reinterpreted something - not sure what you mean by that. As a starting point for comparing affinities of the two proteins for oxygen, if someone didn't know anything about the binding curves they would compare the P50 values and conclude that myoglobin has a higher affinity -if both proteins start off "empty" in the absence of oxygen then, as we raise the oxygen concentration, when myoglobin has reached 50% saturation, haemoglobin is just 2-3% saturated. So I'm not sure what you mean by "intrinsic" affinity.

Just wanted to supplement to the other two answers... I was trying to use comments but ran out of space.
@AlanBoyd s figure tells you a lot - you can see that myoglobin (Mb) has a much higher affinity for oxygen, so it will sit in the muscle and take the oxygen the tissue needs from the hemoglobin (Hb) as the blood flows through the tissue.
But what is particularly useful about Hb's cooperativity is that the last oxygen is harder to pull off the Hb tetramer than the first. As a result, Hb will tend to hold onto some oxygen as it flows through the body, retaining some of its oxygen on each Hb molecule until later in the oxygenation cycle.  This keeps the oxygen concentration in the blood consistent.  The heart, which is the first organ in the blood cycle after the lungs uses a lot of oxygen - if hemoglobin were not cooperative, it might take all the oxygen from hemoglobin just after the beat when it uses oxygen when in distress, creating a block of hemoglobin which is completely without bound oxygen.  As this lot of hemoglobin circulates into the capillaries, you could get some parts of the body with no oxygen at all.
Also - Hemoglobin is pretty clearly an evolutionary adaptation where four myoglobins came together to form a cooperative oxygen binder, so at one time probably myoglobin was the oxygen carrier.  There are some primitive animals which have no distinct hemoglobin, just myoglobin like carriers.  Also some hemoglobins are not tetrameric, but with many subunits, so the cooperativity curves have sometimes been tuned by evolution for different organisms.

Figure above: "Rendering of Hb tetramer and monomeric Mb. Hb is composed of four subunits, two α-subunits and two β-subunits, each highly homologous to Mb" ( from figure in reference )

I have responded to this by editing my answer, since I also needed lots of space.

Blood needs to be able to lose oxygen as well as capture it, the whole point is to take in oxygen in the lungs and then release it throughout the body. Blood that is simply really good at absorbing oxygen would only be an oxygen trap. Myoglobin, having more affinity for oxygen, can take oxygen from hemoglobin and store it in the muscle for the near future use.


text:
Is DNA green viewer carcinogenic?
I use DNA green viewer in Lab to see DNA and RNA bands. Some peers told me it is carcinogenic and is not safe.
Is this correct? If yes, are there better choices to use in working with gel?

Can you please add the exact name of the dye you're using, "DNA green viewer" is not specific enough. I would guess that you mean SYBR Green, but there are probably a lot more green fluorescent dyes for nucleic acids.

I know it is not SYBR but I don't know more about this. It is just name, DNA green viewer on micro tube.

How do you image the dye? SYBR and EtBr use difference wavelengths.

@bobthejoe we have to use a color filter over the gel, orange I think.

SYBR green is designed to be much less carcinogenic than ethidium bromide (EtBr).
All these gel dyes work by intercalating themselves into the DNA stack between the bases specifically which has a great potential for causing mutations and messing with the workings of the nucleus.  My remembrance is that the SYBR and GelGreen/Red etc dyes are large and relatively hydrophilic and can't find their way into the nucleus, greatly reducing their toxicity.  They also do not transfer energy to the DNA itself due to their structure and so also cause less DNA damage when being viewed on a transilluminator.


text:
Where does Taq polymerase migrate during electrophoresis?
Assuming a 1% Agarose gel with TAE.
Follow up questions:

Is there a way to stain for it?
Could the polymerase be captured and reused?

Unlike in an SDS-PAGE, where the SDS adds negative charges to all proteins, in a standard agarose gel for nucleic acids all proteins should move according to their own charge.
You can get a rough idea in which direction Taq would move by getting the amino acid sequence and calculating the isoelectric point at the pH you are running your get at. It might be that the protein isn't even negatively charged at this pH, then it would move in the opposite direction of the DNA out of the gel.
An exact prediction is rather hard, as it depends on the shape and size of the protein, the pore size in the agarose gel and the exact charge. It is not as simple as for DNA. You would have to just try it out to get an accurate value.
You can use any common method of staining proteins like Coomassie.
I think reusing the Taq is very unrealistic. It is still pretty stable at higher temperatures, so it will probably survive the temperatures the gel is running at. I would guess that you lose so much during PCR, gel and purification that it would not be worth the effort. And you would need to purify it extremely well, unless you want to amplify the same DNA in all your future PCR reactions. Any DNA contamination left from your gel might interfere with your later reactions.
If you require a very large amount of Taq and want to cut costs, I'd rather try and produce and purify the enzyme yourself. That should save you a lot of money if you really use a lot of it, but it is likely not worth it on a small scale.

A very good question and a better answer, these were.

The calculated isoelectric point of Taq polymerase is 6.03, and the pH of TAE buffer is 8.0, so Taq is below its pI and is therefore negatively charged, like the DNA.
Taq polymerase is indeed very easy to prepare. There is a protocol here but this requires you to find a suitable strain carrying an expression plasmid. Perhaps another SE.Biol question?


text:
Prostaglandin F2-alpha production in men
I am trying to find information on Prostaglandin F2-alpha, specificaly production in men. Could somebody explain how this prostaglandin is produced? What types of cells are producing it, production signaling? Any books on this subject?

As I know:
One of the most important chemical mediators are prostaglandins that in vivo act on different cell receptors and have different effects on the body. Prostaglandins are twenty-carbon lipid molecules and structurally similar to cholesterol. Prostaglandins have different types, such as F2, E2 alpha, PGI2, and so on.
A phospholipase enzyme converts phospholipids of cell membranes into arachidonic acid. The arachidonic acid within the cyclooxygenase enzyme or Cox (both type 1 and 2) can be converted to prostaglandins.
PGF2alpha has functions in uterus contraction and bronchoconstriction, so I think both uterus and lung cells produce it.
I have no special information about production of PGF2alpha in men.

I think it is incorrect to say that prostaglandins are structurally similar to cholesterol.

PubChem is a good resource for finding out more about compounds of pharmaceutical interest:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280363

This is more of a comment than an answer to the question. To make it an answer you should pick out some key points from the article and include them in your post.


text:
Why people like to see pornographic scenes, but do not feel the same about eating scenes?
This question may seem funny, but I think biology must have good answers.
I think no more explanation is needed.
I really thought about this and searched for an answer, but there is nothing yet.
If you know some thing about or have some thing which may lead to good answer(s) please express.
Also, do animals portray the same behavior in such situations?

:( Please don't be wrong with my question. I really think there most be a good answer to this in biology. thank you

Why do you say they don't feel the same way? Most people enjoy seeing sexual images of attractive people, and seeing these pictures makes them want to have sex. Most people also enjoy seeing pictures of particularly delicious food, and seeing these pictures makes them hungry. Seems pretty similar to me.

Look Octern, There is no eating movies to be like porno movies.

http://www.foodnetwork.com/

I think this could be off topic here unless you want some in-depth details into the biological side rather than psychological.

@MySky: there are plenty of TV shows about cooking, not to mention that there are thousands of food-bloggers.

This would probably be better in http://cogsci.stackexchange.com

@octern And yet I don’t see a multi-billion dollar industry around food videos. Sure there are cooking shows but their economic relevance compared to pornography … is … to say the least … you see?

Sexual arousal, in and of itself, is pleasurable in a way that hunger is not.
As to why this is, perhaps visual stimulation and anticipation improves the sexual function of animals more than it improves eating.  One possible explanation is sperm competition.
Either arousal state can be induced by visual stimuli.  However, the respective hormones work differently.  Ghrelin doesn't affect hunger and feeding(1) the way that dopamine affects arousal and mating(2).  Also, starvation has been found to decrease dopamine concentration(3) in those same areas that sexual stimulation increases it(4).

For these two phenomena to create the same feelings all of the time, the physiology that engenders these feelings would have to be the same.  All I can do is point out that these have been separate and distinct even in yeast and bacteria and invoke a likelihood argument.
The impulse for hunger is almost as old as living things.  In bacteria, cyclic Adenosine mono phosphate (cAMP) mediates hunger, though this does not appear to be universal.
Sexual reproduction appeared much later - in the single celled eukaryotes mating factors for instance are mediated by the MATa/alpha receptors.
In animals like C elegans the differences persist (hunger, mating).  This is not a precise argument, but there is the entropy argument - the odds of these 2 signals evolving together biochemically or genetically is quite unlikely given how separate they have always been.
That's not to say that eating food can't create a sexual arousal, but it does not do so all the time.  The sexual response appears to be plastic and adaptable to nearly any sort of stimulus.  The fact that in primates and many other animals, the pleasure stimulus is related to both mating and eating might make them seem like similar impulses, but when you go deeper it doesn't seem plausible.  So the two could hypothetically create the same feeling, but if you are asking why doesn't it usually... then there are lots of reasons why.
I find it helpful to reverse the question and ask - what would happen to a species where you could suppress the mating impulse by eating?  Probably not an adaptation that would survive long.

Why people like to see pornographic scenes, but do not feel the same about eating scenes?

Well, the whole point of watching porn is sexual arousal. (Or research for the curious, but that's another thing)
Watching someone eat delicious-looking food CAN make people feel hungry. I admit, I have a bad tendency of feeling hungry if I see good food, or if I see someone eating good food.
But I don't get the point of the question. Are you wondering if most people feel this way about watching someone eat, or are you wondering if people are AROUSED by watching someone eat? Lol. Some clarification would be useful.
EDIT: Ok, I think I get it now. You're wondering why aren't there any "food scenes" for food-loving people? Well, it's not as widely prevalent as porn, but it IS there for those who are into it.
Example: http://foodporndaily.com/explore/food/
^ One of my favourite sites, actually.

People can satisfy their sexual urges on their own (that is, without a sexual partner) through masturbating. They cannot satisfy their hunger on their own (that, without food).
I suppose people could eat one food while looking at another kind of food pretending that the food they are eating is the one that they are watching, but where's the fun in that?
Having sex with an attractive person is an indicator of biological desirability ----- namely that another human being wants you in the way you want to be wanted due to your accomplishments or social status. Thus, people watch or read porn to satisfy their need to be accepted or to make them feel as if they are such a person with accomplishments or social status or to compensate for things not going their way in life and subsequently masturbate to such porn.
As for hunger, a better analogy for porn would be taking those kind of drugs that make you feel less hungry.
So yeah, for sex, people watch porn. For hunger, people do not compensate for their inability to eat by looking at food that they cannot have. They would probably take drugs or something. I'm not quite sure if such a thing exists, but I swear one of my grade school teachers said that there was some kind of drug that makes people stop feeling hungry.
I think a better analogy for looking at food they cannot have is looking through pictures of a lustful or romantic interest with his/her romantic partner.
This may sound like a stupid answer that is more philosophical than biological from some loser with 1 reputation. I request commentary along with any downvotes.

Can you please make this a real answer with references?

@Chris This may sound naive, but who needs references to logic? If I prove to you 1+1=2, do you need a reference?

@Chris If I could, I would comment that the question is wrong. OP's analogy is wrong. The analogue of watching porn, falsely satisfying one's sexual desires without a sexual partner, for food is not looking at food but rather falsely satisfying one's hunger without food namely taking drugs.


text:
Why do marine animals have fins?
Why do Marine animals have fins.

Do you mean fish or marine mammals?  I guess it doesn't matter - they both have fins because selection gave the ones with fins huge advantages in their marine environment.

Welcome to the site! You'll get better answers (and generate more interest) if you can provide a bit more context to your question!

Wikipedia has a pretty decent article on fins which seems to answer your question.

Not all marine animals have fins some have flippers like Sea turtles. Flippers are also present in Dolphins.

It is more efficient to use fins than feet, hooves, or other similar body parts. It is the same reason that you can swim faster while wearing flippers. Having a larger surface area allows animals to push against more water, so that they have more force when swimming. Here is a picture of the bones in a dolphin fin. They are extremely similar to the bones in a hand, because dolphins evolved from land animals that had individual fingers.
Amphibians like frogs and salamanders have webbed feet, which is a "compromise" between feet and fins. These feet allow them to push against water with more power, since they have webbing instead is separate fingers. It also allows them to grip the ground on land, since their fingers can move independently of each other.

Dorsal fins also aid in stability. Many marine animals and mammals are fusiform (torpedo-shaped) to reduce drag in the water and make locomotion easier. Without fins for stability, primarily dorsal fins, it would be difficult for animals to orient upright in the water without rolling. The dorsal fin actually increases lateral drag (rolling side to side) to provide this stability. Check out this reference for more information


text:
Is copy number variation dynamic?
Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need to make is that it is static.

the answer to this question depends on the scale you're looking at: individual cells? tissues? organisms? tumors?

@MichaelKuhn Good clarification point, thanks for bringing it up. I'm thinking of changes in the output of whatever technique is measuring CNV--e.g., in situ hybridization, etc.--in a given organism. I assume that data is averaged over multiple cells, but I'm not taking about variance due to the averaging process. You're tumor point is good as well, as I'm interested in variation the cancer genome. Does that help?

Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, ("Is there any evidence showing that [the rate of] copy number variation changes over time?"), then yes, there is indeed.
The rate depends on many factors including which mechanism and which organism and which region of the organism's genome and as @Michael wrote, also what scale (et. al.) is under consideration too.
So your assumption that the rate is static should probably be stated explicitly.
Nature Reviews Genetics 10, 551-564 (August 2009) | doi:10.1038/nrg2593

Thanks, Kevin! That's mostly what I was looking for, and it looks like this review will give me some more information as to how it works. As a side note, I'm interested in modeling regulatory relationships in time series of expression data, but was curious as to whether, if I could get CNV data for my model as well, if those data could be assumed to be fixed over time, or if that would just have to be a limitation of my approach.


text:
Long term effects of "brain freeze" on the cerebral vasculature
According to one theory, ice cream headaches are caused by an increase in blood volume of the anterior cerebral artery:

Another theory into the cause of ice-cream headaches is explained by increased blood flow to the brain through the anterior cerebral artery, which supplies oxygenated blood to most medial portions of the frontal lobes and superior medial parietal lobes. This increase in blood volume and resulting increase in size in this artery is thought to bring on the pain associated with an ice-cream headache.
(from Wikipedia)

Does repeatedly experiencing this phenomenon put someone at higher risk for some sort of cerebral vascular accident, or is it not any more harmful than a small increase in blood pressure that one might experience under exertion, despite the painful nature of the headache?

I do not have a source for the following as it was taught to me in neuroanatomy classes, the explanation given for brain freeze is that it is  referred pain through the trigeminal nerve. The  meninges (the tissue lining the central nervous system) is innervated by the trigeminal nerve in the head. Therefore the pain feels as though it is like a headache from meningeal irritation but is in fact benign.
Given that the mechanism is through referred pain rather than any vascular event it should not put you at any increased risk.
This being said if you experience repeated headaches and are unsure of the cause it would be wise to consult your doctor.


text:
Why is cold water more refreshing than warm water?
Obviously, the temperature of water does not affect its chemical composition. At least not in the ranges we are likely to drink it in. Yet it is clearly far more pleasant and refreshing to drink cool water than it is to drink tepid or warm water.
Is there actually any difference to the organism or is this just a matter of perception? Is cool water somehow more efficient at rehydrating a cell? In any case, surely by the time water reaches individual cells it will have warmed up to body temperature.
So, what, if any, is the difference between drinking cool and warm water in terms of its effect on the human (or other animal) body?
Extra bonus for explaining why the taste of water changes when it is cold.

However, on a hot day an hot drink will make you less thirsty than a cold one.

Care to elaborate @nico? Are you saying that having a drink will make you thirsty?

@terdon: no, I am saying that a hot drink will make you feel less thirsty on the long run. For instance we always bring hot tea when hiking in summer, even if it's quite hot. It's a matter of temperature difference, like having a hot shower in summer, you'll feel way more refreshed then after a cold one.

@terdon: If your drink is cold, your body has to heat the drink up to body temperature. This consumes energy, which leads to a higher body temperature, which leads to sweating. The net fluid balance can probably be negative. :-) That's why desert natives drink hot sweet tea.

@MartinSchröder, yes I understood from Nico's answer. That makes sense. It does not, however, answer the question. Indeed it contradicts it :). Why do we feel more refreshed when drinking cold water? Is it just a question of perception restricted to those surfaces that come directly into contact with the water (mouth, throat etc) or is there a deeper physiological reason as well?

@nico, I understand what you mean and the theory behind it and you are of course quite right. Nevertheless, I have never felt a craving for room temperature water. I often have for cold water. Why not? If drinking warm water makes feel cooler because of the temperature differential with our environment, why then do we not crave hot water on a summer day? Most cravings have a sound biological basis.

@MartinSchröder  Doubtful.  The cold material will absorb energy that's already present.  Your body doesn't have to do any extra work for this to happen.  It might be plausible that a cold drink will increase heat stress on the body in more subtle ways though.

Cultural perception, I know cultures that do not drink anything that hasn't came out of heater

@MartinSchröder, sorry, but you are wrong, it is quite the opposite, actually. Many cultures drink warm or hot beverages in hot days, because the extra heat from the drink increases your core body temperature, which in turn causes sweating. Guess what sweating is designed for. :)

Short answer: Cold is pleasant only when your are not already freezing and cold might satiate thirst better because it acts as enhancer of the "water intake flow meter".

Is cold water more tasty than warm water? No, it is actually the reverse as detailed in my footnote.
Cold is pleasant when your body is over-heating and definitely not if you live naked in the North Pole. Over-heating means sweating which means you loose water and therefore feel thirsty faster. Yet drinking cold water will not rehydrate the body more than warm water and drinking water has only a very small impact on the body temperature. So why do we like it?
A study was actually conducted on the subject and answers most of your questions. Here the reference.
The temperature of the body will indeed not change.

cold stimuli applied to the mouth
  (internal surface of the body) do not appear to impact on body
  temperature and are not reported to cause any reflex shivering
  or skin vasoconstriction that influence body temperature.

As you pointed out, the temperature of the ingested water will not affect the overall hydration of the body as cells are rehydrated mostly via the blood  stream and the blood temperature will not be affected. Someone could argue that, at identical volumes, cold water (above 4C) contains more molecules (i.e. is denser) than warm water but this difference is likely very slim.
In this paper they also define "thirst".

Thirst is a homeostatic mechanism that regulates blood osmolarity
  by initiating water intake when blood osmolarity increases

The problem is that it takes some time before the water reaches the blood stream, and therefore you need a feedback mechanism that tells you to stop drinking independently of the blood's osmolarity. This is where cold might play a role.

The cold stimulus to the mouth from ingestion of water may act
  as a satiety signal to meter water intake and prevent excessive
  ingestion of water

The picture would then be the following

In essence, a cold sensation is pleasant in warm weather, both on the skin and in the mouth, and it apparently helps in reducing thirst by being some kind of an  enhancer of the "water intake flow meter".

Footnote
Reading the comments I just want to clarify some points.
The 5 basic tastes (sweet, salty, bitter, sour and umami) are very distinct from taste sensations (pungency, smoothness, cooling to name a few). The main difference is that taste and "sensation" signals use completely different paths to reach the brain - namely, the facial and glossopharyngeal nerves for the former and the trigeminal nerve for the latter.
Is the temperature affecting basic taste perceptions? The answer is yes. How this happens is quite simple if you understand the fundamental concepts of molecular taste perception. Essentially the temperature affects the response of the receptor TRPM5 which is the main player in depolarizing taste receptor cells in the papillae. To put it simply, higher temperatures provoke a greater perception for taste, and this is not only in term of perceived taste but really modifies the amplitude of the response at the molecular level. As an example this is why ice cream does not taste sweet when frozen but only after it melted in the mouth or on the tongue.

you are absolutely correct. It is the same if you live naked on the North Pole - you will find warm water more pleasant than cold. :)
However please do note that stimuli to the mouth may not affect body temperature but stimuli to the stomach (i.e. almost core of the body) WILL affect body temperature.

I think it's because we are more often thirsty in a warm/hot/dry environment.
Since almost all of us have a house with a household furnace creating that warm/dry  environment.
Thus cold water would be more refreshing since it also cools us off a bit.
I doubt that people that are on a north-pole expedition would still prefer that cold drink over a warm one.
This link contains a lot of information on this topic:
http://chestofbooks.com/health/nutrition/Dietetics-4/Temperature-And-Digestion.html

In addition to cultural preferences and psychological factors, there may be some evolutionary basis in this.
Cooking food is a relatively new development and unique to the Homo spp. line. It makes sense that the tongue/mouth may be more sensitive to cooler temperatures than warm temperatures, given the amount of actual exposure it is given to sunlight and/or objects (across all species).
This is perhaps supported by the concentration of various receptor channels, TRPV1-4, TRPA1 and TRPM8, which are each sensitive/activated across various temperature ranges. TRPV3 operates through a range close to body temp. and has been associated with taste perception. One could hypothesise that in the mouth there is a greater concentration of cold-sensitive channels (such as TRPA1 and TRPM8) than warm ones, thus cold is perceived more readily and the addition of 'taste' channels (TPRV3) may contribute to the preference for cool water over say luke warm/room temp. water. This thinking falls down when we think of the amount of hot food we eat and can of course taste, in addition to the many studies conducted on taste perception, however this entire answer is very rudimentary.
I haven't found literature detailing the relative proportions of said channels, however, this makes for an interesting read: http://www.mnf.uni-greifswald.de/fileadmin/Zoologisches_Museum/Hildebrandt/Dokumente/schepers10.pdf

Welcome to se.biology! Got scooped :). You should maybe modify slightly you answer to introduce TRPA1 and TRPM8 as the cold sensors. TRPV3 senses temperature closer to 37C and TRPV1 noxious heat. I might also just post an alternative answer.

Slightly modified (and hopefully correctly!). Perhaps you might be able to offer a much more comprehensive answer, though.

Ah, so you're suggesting that the difference in taste is down ti the relative concentrations of these receptors, right? OK, any ideas on why one would feel more refreshing (which, presumably, translates to more hydrating) than the other?

@terdon I would be hesitant to offer anything concrete re: taste. I was trying to suggest that there might be a difference in concentrations, maybe weighted towards more cold-sensing receptors (TRPM8) rather than warmth-sensing receptors (TRPV1). The activation of TRPM8 by cold water could induce a more refreshed feeling by association - it is well known to be activated by menthol. This is a leap, but perhaps these pathways stimulate recollection of the feeling after your brush your teeth, use mouthwash, chew gum etc., often one of being clean, refreshed, or fresher.

Here's an armchair evolutionary explanation. In nature, running water tends to be cold whereas tepid water tends to be lukewarm. And for reasons having nothing to do with temperature, running water tends to contain less harmful bacteria. Therefore, our ancestors who preferred to drink cold water over lukewarm had an evolutionary advantage over those who preferred the opposite.

The organism as a thermodynamic machine does need a coolant. The more difference in temperature the more efficiently thermal machine can use energy. Also in all processes in organism it is produced excessive thermal energy, which should be removed.
Thus colder water and air are pleasant.


text:
Can in the case of multiple sclerosis (MS), a too high osmotic pressure in the nerve, lead to a high intracellular concentration of potassium?
Can in the case of multiple sclerosis (MS),
a too high osmotic pressure in the nerve,
lead to a high intracellular concentration of potassium,
and also lead to 'pumping up' of nerve cells,
which then due to the strongly increased internal pressure,
the insulating myelin sheath can be pressed broken,
resulting in a lesion,
or a strong reduced transmission of stimuli ?
If that were to happen,
one can expect in cerebrospinal fluid,
cytokines, which are normally also a component of the nerve cell contents,
and that it wrongly can be interpreted,
as inflammatory reaction to a potential autoimmune disease.
Is there research of this ?

Firstly, demyelination has got nothing to do with membrane integrity of the neuron. Demyelination causes the current to "leak" through the ion-channels and thus causing loss of signal.
There is an old article which reports a study on membrane integrity of RBCs of MS patients but there seems to be no connection.
It has been proven that neurons do secrete some cytokines such as IFNgamma but the signaling is mostly para/auto-crine and I dont think the cytokines will accumulate in CSF.
MS is identified by the presence of anti-myelin antibodies, which might be the exact biomarker for the disease. A general neuroinflammation is not concluded as MS.
So to answer your final question

Is there research of this ?

There is none that exactly talks about neuron membrane dynamics in MS. The most parsimonious assumption is that there is no effect, but any hypothesis has to be proven. It might be experimentally difficult to address this question and how to design the experiment for this study would be an interesting question.


text:
Extraretinal photoreception in mammals?
A Finnish firm Valkee sells light-ear-plugs against thing such as jetlag. I asked a researcher in Aalto university how do they really work and he responded "why would evolution have lead to photoreceptive cells in ears?" -No direct answer. I asked a well-respected professor who said she did not know this area well enough. Now Valkee guided me to the publications such as Penetration of light into the brain of mammals (1963) and Spectral characteristics of visible radiation penetrating into the brain and stimulating extraretinal photoreceptors (1979). Related to the first one, I found this (1980) from the references:

"It  is  now  fully  accepted that  the  perception  of  light  by  extraocular  photoreceptors  plays  a  significant  role  in  synchronizing  endogenous  rhythms  with  the  environmental  light-dark cycle  in  non-mammalian  vertebrates"

Things such as certain birds and lizards apparently have extraretinal photoreception aka photosensitive cells not in eyes (this is how I understand it). Now the publication continues

"The  limited  number  of mammalian  species  tested  to
  date  and  the  near  exclusive  reliance  on  nocturnal  animals  leaves  open  the  possibility  of  extraocular  photoreception  in  some  adult  mammals  (Rusak  &  Zucker, 1975;  1979)."

Now according to a skeptical researcher in my university, there is only one paper supporting photosensitivity in mammals' brains: Wade et al (PNAS 85 (1988) 9322-9326 with rats. My professor in system sciences was extremely scornful when I even asked this question on a seminar course about brain -- he did not specify his reasons and pretty much labelled my thinking as inexperience. Now I am not sure whether researchers are even speaking about the same issues: too large disparities between opposing and proposing teams for the assumed effect apparently through the mechanism called "extraretinal photoreception in mammals". I am very curious.
Helper questions

What are the mechanisms by which a led in ear would affect a mammal such as a homo sapiens? You don't get D vitamin because of no UV light. You get very-very light heat because of tosslink connection. So it cannot sense the heat as antidote against things such as SAD and jetlag. Other mechanism?
Is the "extraretinal photoreception in mammals" just placebo or does there exist scientific proofs for it particularly with large mammals about the size of homo sapiens?
Why would evolution have lead to extraretinal photoreception in mammals?
Do the terms "extraretinal photoreception" and "non-eye photosensitive cells" mean the same thing? Other terms for the same thing?
Now eyes are developed very late in cell-division with mammals. Do born-blind mammals and later-blinded mammals experience extraretinal photoreception differently? If led-light (non-UV light) has an effect on large mammals, then I expect this may be possible to see by analyzing results of mammals with different-developed visual-cortexes.
Does this statement "Light penetrates deep brain areas, eye's receptors have developed from receptors of old CNS." by Humancharger justify the extraretinal photorecetpion?

P.s. I presupposed in this question that extraretinal photoreception is the effective mechanism by which light-in-ear would affect a mammal. It is also possible that there are other mechanisms -- I am not an expert with the terminology here, anatomically and physiologically challenging.

Possible duplicate: http://biology.stackexchange.com/q/700/72

Its pretty well established that there are photoreceptors in cells besides the cones and rods in the retina of the eye.  Humans and most animals have four light receptor genes known (so far).  In addition to Rhodopsin - there are the short, med and long wavelength opsin genes.
While they are mostly expressed in the retina of the eye, they can be found in many other tissues as well. The first image from GeneAtlas below shows the relative amount of RNA found for short wavelength opsin in a variety of tissues - its expressed in immune and nerve cells ( cyan and forest green respectively) relatively well too.   This might imply that neurons are light reactive.  Compare that to that of medium wavelength opsin, which is primarily much more common in the retina.

This is not a psychosomatic effect.  Light receptors in the skin are known to help with seasonal affective disorder - shine a bright or blue light behind your knees.  These receptors are not connected to optical nerves, and so you don't get any image from them, but the information can affect your biochemistry anyway.
The idea of unconscious receptor inputs from other parts of the body probably applies to many sorts of receptors.  This last year there has been a great deal of interest in taste receptors which are expressed in the gut.  They can taste sweetness and other flavors a second time and register the gustatory response in the brain.  Its not a conscious input, but it registers in the brain in MRI.
Why would evolution do this?  It seems to me that this is a new way of looking at the individual life of a cell and makes a good deal of sense.  If every cell has all the genes' DNA why wouldn't a little bit of receptor expression be found in any cell which could use the information?  The conscious processes of the brain probably only take in a small fraction of the information that is sent in and there maybe hundreds of other such senses from various parts of the body to integrate, only a fraction of which we are aware of.
In addition, there are probably lots of cases where receptor signals are only used locally by cells that are sensing their local environment.  It really doesn't make sense that the individual cells must blind themselves.  Individual bacteria and fungi have scores of receptors.  It makes sense that cells that are part of an organism would have as many or more senses as well.

-1. It is well-established that opsins are expressed widely, but their functions are not known. It hasn't been convincingly shown anywhere that human opsins confer light sensitivity to any cells other than those in the retina. The knee study you mentioned has been refuted (see my comment here: http://biology.stackexchange.com/a/704/72). Also, a point of nomenclature, photoreceptors are cells that are sensitive to light, and opsins are called photopigments when they are bound to a chromophore and are sensitive to light.

Do born-blind mammals and later-blinded mammals experience extraretinal
photoreception differently?

This article in Scientific American here where they refer to "Circadian and vision neuroscientist Russell G. Foster of the University of Oxford" outlines:

"In 1999 we found that mice lacking rods and cones were nonetheless
able to synchronize their circadian rhythm to the light/dark cycle.
These observations led to the discovery of an additional
photoreceptor system in the retina of humans and other mammals
consisting  of a small number of photosensitive retinal ganglion
cells (called pRGCs). These cells are most sensitive to blue light,
and, significantly, blue light is most effective in alleviating the
symptoms of SAD." (I added italics to interesting points)

WSJ repeats the blue-light thing and recites:

"In 2002, German researchers isolated one from green algae—a class of proteins called channelrhodopsins—that responded only to blue light. -- Depending on just how researchers tailor the virus that carries the light-sensitive protein, they now can target almost any type of neuron they want to study."

So differently in a way that they lack the cones/rods in retina and some links to visual-cortex but no in a way of SAD: evolution have apparently developed methods for blind-born mammals to survive and to sync their inner clock. This resonates with the earlier facts by shigeta but I don't know whether there is any other thing to light -- perhaps UV radiation -- that could tune the internal clock.
It looks that they are trying to find ways to engineer bionic-visions things similar to dobelle without physical modification of skull. The viruses tries to propagate certain photo-receptive protein into some spot where they try to activate them though external radiation. This is called optogenetics where they are trying to control certain behavioral things with optics.
New puzzles

why do they use protein? Why not other things?

do we have many kind of photoreceptivity? Certain muscles (requires protein) activated by EM radiation? What about other cells such as fat-cells?

P.s. this is pretty fruitless to advance unless someone provides precise power spectrum of Valkee (requires apparently spectrum-analyzer) and polarization experiments. WSJ referred to trials where they use monochromatic light and coherent light in testing while Valkee-light can be pretty much anything.

There may be some light receptor cells at skin (well known, high sunlight cause more melanin in skin and also ultraviolet helps Vitamin-D synthesis). But I can't "see" any trace of light through skin, even if I tightly close my eyes.


text:
Is there a scientific proof that smoking spoils face skin?
I saw that cigarettes-smokers (more than 3 cigarettes per day) often have the skin of the face which is a little bit spoiled.
Is there any scientific proof that cigarette smoke (or the nicotine inside it) is a damaging fator for face skin?
Or it is just due to the skin-smoke interaction casued by the smoke that the person breaths out from the mouth?

This page is pretty complete with examples and references.
In summary a lot of the evidence is empirical - you look at smokers and the quality of their skin and compare to non-smokers and the differences are statistically significant and reproducible.  It seems as if this is old work, dating from the 1970s.
So in many cases these are only observed correlations.  But they are pretty strongly agreed upon by medical people.  Given the fact that we still don't know exactly what causes cancer, I think this is not an unusual level of explanation for medical conditions.
As you can see some theories would include direct effects of the smoke and some indirect effects.

It is not certain exactly how smoking causes early ageing of the facial skin. Theories include:

Heat from the cigarette directly burning the skin
Changes in the elastic fibres of the skin
Narrowing of blood vessels (vasoconstriction), which reduces blood supply to the skin and can cause changes in skin elastic fibres and
  loss of collagen
Reducing Vitamin A levels and moisture of the skin


text:
functional hypocholesterolemia due to very high HDL or low LDL?
Nutritional and medical recommendations about cholesterol seem to focus exclusively on hypercholesterolemia, and as such, they provide only a maximum desirable level for LDL and a minimum for HDL. I've found a little bit of information about hypocholesterolemia caused by inadequate cholesterol in the body (due to overuse of statins, malnutrition, or other disorders), but not about cholesterol deficits due to lipoprotein levels.
It seems like it should be theoretically possible to have so much HDL or so little LDL activity that organs don't maintain enough cholesterol to function properly, even if cholesterol synthesis is adequate. Obviously this might or might not ever occur in reality. Is there any research that has found an upper bound on desirable HDL in humans, or a lower bound on desirable LDL or LDL:HDL ratio?

Upper bound of HDL doesn't really exist. The greeks are known for their incredibly high levels of HDL and the so called mediterranean diet/genetics combination that causes this is only beneficial to health (supposedly - although never been proven that incredibly high HDL levels are beneficial, they're just not harmful).
As for too low LDL levels/cholesterol levels - that's interesting. Unfortunately it isn't possible because any mutations that caused this would be fatal, cholesterol makes up an essential part of cell membranes etc. That's why our body makes our own. A mutation preventing this would not even manifest.


text:
Fibonacci sequence in nature, truth or just wishful thinking?
I'm reading a bit on the Fibonacci sequence in nature, be it the golden ratio or the golden spiral forming over and over again in biological structures, and then I came across this online article by Donald E. Simanek, refuting a lot of these observations as merely optimistic 'flim flam'.
So which is true?
Does the Fibonacci sequence have a place in nature or is it all just a case of vigorously looking for anything that resembles a correlation?

Search for Vi Hart on Youtube. She makes educational and oddly entertaining math videos and she has one about plants displaying both Fibonacci and Lucas numbers as a way to maximize sunlight reception by the leaves.

I mean, I'm curious too, and Vi's video is all I've heard about this correlation. I'm not asserting she's right, just that you might enjoy it. The video is called Doodling in Math: Spirals, Fibonacci, and Being a Plant.

Thanks I'll give them a watch, I remember watching an entertaining one she did on the nature of infinity I think.

Didn't the Fibonacci sequence arise when modeling the dynamics of rabbit populations?

As far as I remember, Fibonacci patterns emerge in plants from hormone gradients. I.e. an apical meristem forms a leaf where the auxin concentration is highest, and already existing leafs lower auxin concentration, leading to some negative feedback.
See e.g.
http://www.sciencedirect.com/science/article/pii/S1360138507000581
or http://en.wikipedia.org/wiki/Phyllotaxis

I'm aware of how these patterns are seemingly formed, what the question is asking is whether these patterns are indeed examples of proper mathematical Fibonacci sequences or if they merely bear resemblance.

The pattern forming processes generate a fibonnachi pattern, but there are other processes that occur as well.


text:
Do mammals develop tolerance to anticholinergics?
I know that first generation H1 antagonists, commonly known as antihistamines have anticholinergic effects. Their sedative side effects go away due to tolerance, but as for their anticholinergic side effects well that's something that is unknown to me at least. You might say use second generation H1 antagonists, but for this application the antiemetic effects that are unique to H1 antagonists that cross the BBB (i.e., first generation H1 antagonists) are desired.

The tolerance to antihistamines is an ongoing debate in the community. Although there were early studies citing that tolerance to therapeutic effects of antihistamines could occur, more recent data, especially studies involving nonsedating antihistamines, indicate that tolerance to the therapeutic effects of these drugs does not occur.
Overall, it seems like the mechanism driving the sedation vs. the therapeutic effects are two separate down stream effects of regulating the inflammatory response. Neuronal tolerance and synaptic transformation is a fairly fluid and ongoing process, whereas the inflammatory response is much more robust. Meaning, the neuronal response is, theoretically, more able to adapt to chronic use of the anihistmaine while still giving the therapeutic effect. This hypothesis is supported by data, but yet to be confirmed, thus creating polarization on the topic.
Also see, Goodman and Gillman Pharmacological Principles of Therapeutics


text:
What prevents a pregnant woman's immune system from recognizing her fetus as nonself (and attacking)?
I'm familiar with the scenario of Rh- mother with Rh+ fetus having complications (more so after her first child), but that's not what I'm curious about. I want to know mechanistically why a pregnant woman's body does not display a reaction similar to what we see with rejection from a mismatched organ transplant. On the most basic level, I feel as though the fetus should be recognized as "nonself" due to paternal genetic contribution.
I feel as though if this mechanism could be understood, it could be harnessed for other situations (e.g., organ transplants).

Right now I don't remember the full story, but part of it is that pregnant women are somewhat immunosupressed and there is something like a layer of NK cells around the placenta making sure nothing attacks it. Not very practical to adapt to organ transplants.

There's a Wikipedia page: http://en.wikipedia.org/wiki/Immune_tolerance_in_pregnancy

Just so that someone answers this question so that the moderators have less work to do:
The fundamental reason why embryos don't get massacred by the maternal immune system is because of the placenta and several of its functions. Three mechanisms are:
1) Secretion of neurokinin B, which is also secreted by parasites to avoid detection of the host.
2) The placenta has developed immunoevasive actions from a virus. It creates a syncytium to limit transaction of mobile immune cells.
3)It only allows specific antibodies,(IgG) to enter and bind infection. (IgG being the only isotype here).
Yay  for biology


text:
Why are 3 nucleotides used as codons for amino-acid mapping in DNA?
DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length?
A related question can be found here: why-are-there-exactly-four-nucleobases-in-dna

I have asked and answered this here because I had posted this answer to the linked question, but that was not truely answering it. There are now much better alternative answers, so I have asked the question I actually answered here!

Your question should be more properly (or rather for clarificational purposes) as nitrogenous bases. I think your query confused me a bit. An article I found online explains this in a more-or-less feasible way: http://www.biologie.uni-hamburg.de/b-online/e21/21a.htm

The central dogma of molecular biology: DNA makes RNA makes Protein
DNA is a reference for proteins*, which are the functional molecules in cells. These are comprised of 20 unique amino acids, and each is coded for by a stretch of DNA known as a codon. Codons are always 3 base-pairs (nucleotides) in length.
DNA is made of 4 unique nucleotides; (A)denine, (G)uanine, (C)ytosine and (T)hymine. This means that there are 64 unique codons that can be made with these 4 bases (4*4*4).
Theory One - evolvability
If codons were only 2 bases in length then the variety of codons that could be created would be less (only 16 unique sequences if there are still 4 nucleotides). More unique nucleotides would be required to get enough unique sequences to code for the 20 amino acids (as well as the STOP codons). For instance, to get 64 unique sequences using a 2-bases-per-codon system there would need to be 8 unique nucleotides.
We cannot ever 'know' what happened in evolutionary terms, but it seems likely that the 3-base (nucleotide) codon system would have arisen after a period of a 2-base system, as the biological systems became more complex. This would have allowed a lot more variation in the amino-acids used, and thus more "evolvability", which would have been very advantageous to early organisms.
However as the 4-unique-nucleotide/3-codon system is ubiquitous to all life we have discovered on earth, it seems likely that, back at the start of DNA (in fact probably RNA), this was the system that worked, or at least, this is the one that survived (although as Kevin rightly points out, we don't know whether there ever were any other systems). Variations may have arisen over the years, but it is this 1 system that has prevailed here on Earth.
See this question for some more interesting info: why-20-amino-acids-instead-of-64?
Theory Two - "redundancy" of codons conveys additional information
This theory is not mutually exclusive to the one described above. In a recent paper D'Onofrio and Abel [1] state that ribosomes pause for different lengths of time at different codons (even if the codon codes for the same amino acid), and that this pausing affects the 3-dimensional structure of the final protein.
Therefore the nucleotide sequence contains at least two "layers" of information: firstly which amino-acid should be added, and second the specific codon used for that amino acid can impact on the final structure of the protein. This could not be done with fewer nucleotides, but arguably even more control could be exerted with more nucleotides, but perhaps this comes back to my first point that this system evolved such a long time ago that more nucleotides were not necessary for life to "work" and proliferate into everything we see today.

D'Onofrio and Abel, 2014. Frontiers in Genetics. Redundancy of the genetic code enables translational pausing

*only around 1% of our genome is actually protein-coding, and many non-protein-coding RNA products have very important functions, but I won't go into this here. Suffice it to say I am referring to the protein-coding regions of the DNA.

Overall, this is a good answer. I take issue though with saying "determined that the most efficient". We have no idea that other combinations ever existed. 4 nucleotides in combinations of 3 did not not work. That's all we know.

@Kevin thanks, and you are absolutely right. I have given the answer a general re-work because I don't think it flowed properly having been adapted from a different question, and have taken your comment into account. Many thanks.

The comment is NOT a criticism toward the answer. I know everybody is talking about the central dogma of molecular biology but it is such a bad name. Dogma has no place in science. Moreover, we now know that retrotranscription exist and therefore the central dogma of molecular biology not always true.

Thank you for posting the theory two part. I've always wondered why CAG trinucleotide repeat in HTT can cause Huntington's, but CAACAG doesn't seem to.

Man, my BSc thesis (8 years ago) was based on the idea of different codons causing conformational change. I compared the codons of structured-regions in proteins with unstructured and found that codon usage was different when coding for the same amino-acid. The guy who marked it gave me 20%. Led to me getting a low final grade. Required I got my masters before my PhD. Probably set me back 2 years. And now it's published in Frontiers in Genetics -_- Academia sucks when you're small-fry.

I think a strong case can be made for three nt codons existing already in the primordial genetic code, which included only eight abiotic amino acids (this is still clearly seen today in translation tables where most abiotic amino acids are defined by four or more codons). However, in this primordial genetic code, the last nt was likely meaningless (this has been reinvented in many mitochondrial genomes where a single tRNA, usually thanks to a modified U in the anticodon wobble position, recognizes up to 4 codons). Assuming the three nt codon primordial genetic code existed, we see that the reason for the three nt codon structure was not that two nt codon structure was not enough for coding everything (4^2 > 9, it would have sufficed), but something else. So what could it be? My educated guess is that it has to do with the A,P,E-site structure of the ribosome not fitting into a smaller molecular configuration (i.e. you couldn't have the adjacent A,P,E-sites within the space limited by just five phosphodiester bonds (six nt, three two nt codons) vs. eight phosphodiester bonds (nine nt, three three nt codons)). So in short, my view is that the primordial ribosomal structure was the key factor to the three nt codon structure of the genetic code, it couldn't have worked with anything less and anything more would have been a waste.

This is very interesting information (sorry for delay in commenting). Could you provide any references/additional reading?

Might I suggest you go directly to the source? Here is a link to a paper published by Francis Crick (et al) in 1957 entitled: 'Codes Without Commas' http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528468/

The source you linked is really good, but simple linking is not exactly what this site is about. Of course it's easier, but please take time and elaborate your answer, explain, interpret the sources you use.

Welcome to Biology.SE. A link only is not sufficient for an answer. Either take time to elaborate your answer or convert your answer to a comment.

For the same reason there are 8 bits in a regular character datatype in old-school programming languages (before internationalization and Unicode).
In modern ASCII interpretations, you have a certain number of characters that need to be encoded, somewhere between 128 and 256. 8 bits would be the minimum sufficient for (modern extended) ASCII encoding. (Unrelated to the question: in computing, it often helps to have the number of bits in various operations be a power of 2. Also, the original versions of ASCII specified 7-bit encoding before it was extended to a full byte in an early internationalization support effort.)
Getting back to nucleotides, there are 20 amino acids. Think of a codon as the equivalent of a "byte" and a base (nucleotide) as the equivalent of a "bit". 2-codon sets would be insufficient except if you plan to custom-build a compact-genome life-form that only supports 15 amino acids, a stop codon, and no wobbles.
Supporting all amino acids plus a stop codon requires at least 21 distinct codon values. In particular, find the smallest power of 4 >= 21, which turns out to be 3.
An added bonus: the number of codon values is roughly triple the number or amino acids (plus a stop codon), allowing for redundancy: some amino acids are encoded by more than one codon, which acts as a buffer against mutations.


text:
Is human face more resistant to cold than other body parts?
Walking outside tonight in -15˚C I realized an interesting observation: While I felt cold on most part of my body, my face (although the only uncovered part) didn't really feel cold. It registered the temperature of course, but it wasn't a negative perception.
I wonder, what is an explanation? Is it simply because our faces are used to the cold, because we almost never cover them? Or is it some evolutionary phenomenon?

I think you should try to measure the temperature of the skin on your face vs. exposed skin elsewhere to determine if the difference is real or perceived. The head receives a disproportionate amount of blood flow when cold, associated peripheral vasoconstriction. So the extra blood could actually be keeping your face warm. Or it could just be a perception of warmth.

specific body parts are adapted to be heat radiators and so have a different role in heat regulation.  i think for humans its the pads of the hands.  http://biology.stackexchange.com/questions/5449/what-is-the-evolutionary-rationale-for-palm-sweating/5464#5464

After 30 years of working outside year round I can verify that my face and hands especially stay far warmer. I can work in freezing temps without gloves without any issues. Right now the blood vessels in my hands are so dilated after spending several hours inside that my hands feel tight ( spent 10 hrs outside working, no gloves at -5 c today) . Short answer is your body is very adept at adapting to the environment .

In response to cold your body causes blood supply to the skin to drop in the whole body. This is to conserve heat, but results in us feeling really cold. Exercising reverses this, resulting in an increased blood supply to the skin in order to remove excess heat and in this case we feel hot.
As mentioned, the head receives a large blood supply, and continues to do so despite other tissues being restricted. This is particularly as a result of the brain requiring a lot of oxygen and glucose. This keeps our head warm.
This phenomenon is why hats keep us warm and are important in cold weather, we lose a lot of heat from our head.
It is also likely that the skin on our head contains less cold receptors, as these aren't likely to be required. However the other parts of our body, particularly the soles of our feet and anterior surface of our hands have many sensory receptors. They are likely to make first contact with anything that may be harmfully cold.


text:
How many organisms have ever lived on Earth?
I've looked for some information on this, but couldn't find anything useful. Has there been any noteworthy attempt to estimate the sum amount of individuals of all species that have ever lived on Earth?

it is impossible to know the exact number so here is my gross ballpark estimate of an upper bound -  i.e. the maximum number of organisms that could have lived on earth in the extreme best case scenario. in practice it is probably much less, but this is to get an idea of what kind of numbers we are dealing with.
The earth's volume is about 1.08321 * 10^12 cubic kilometers =  1.08321 * 10^21 cubic meters
The crust of the earth is 4-8km and the radius is about 6,353km giving around 1% of the total volume available for life.
Hence, the volume available, i.e. the volume of the crust is about 1.1 x 10^19 Meters.
An average-size bacterium such as the rod-shaped E-coli is about 2 micrometers long and 0.5 micrometers in diameter. Hence, the volume is roughly:
(2*10^-6)*(0.5*10^-6)*(0.5*10^-6) = 0.5*10^-18 meters
Hence, if the entire volume of the crust of the earth were entirely filled with e-coli bacteria, there would be:
(1.1 x 10^19 meters)/(0.5*10^-18 meters) = 1.3*10^36 bacteria on the earth.
Bacteria take time until they reproduce. If they reproduce faster than they grow, they will become reduced to zero size, so there must be a balance between growth and reproduction.
Under ideal conditions the E-coli bacterium would divide every twenty minutes. source
Let's say we have the maximum number of bacteria on earth dividing every twenty minutes. Somehow, they divide and then one dies so that the population is stable. (hypothetically)
The age of the earth is roughly 4.5 Billion years. Much of that time, it was not colonised, but just to give an upper bound let's assume it was colonized the whole time.
There are 525600 minutes in a year so this give
4.5 ^ 10^9 * 5.3* 10^5 = 2.385 * 10^15 minutes
Dividing by twenty minutes gives 1.1925 * 10^14 total reproductions.
Hence, the number of organisms that ever lived if the entire volume of the crust of the earth were entirely filled with e-coli bacteria reproducing at the maximum of every 20 minutes would be:
(1.2*10^14) *  1.3*10^36 bacteria = 1.56 * 10^50 bacteria
This is an highly exaggerated gross estimate of the maximum number of organisms that ever lived in the extreme best case scenario. In practice it is probably 5-15 orders of magnitude less than this but we get an idea of the kind of numbers we are dealing with.
UPDATE: A more realistic number
The number of bacteria currently on earth is about 5*10^30 forming a biomass which exceeds that of all plants and animals. source.
According to this source cited by the previous wikipedia article:

Most of the earth’s prokaryotes (bacteria) occur in the open ocean, in soil, and
  in oceanic and terrestrial subsurfaces, where the numbers of cells are
  1.2 × 10^29, 2.6 × 10^29, 3.5 × 10^30, and 0.25–2.5 × 10^30, respectively. The numbers of heterotrophic prokaryotes in the upper
  200 m of the open ocean, the ocean below 200 m, and soil are
  consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5
  yr, respectively. Although subject to a great deal of uncertainty, the
  estimate for the average turnover time of prokaryotes in the
  subsurface is on the order of 1–2 × 10^3 yr. The cellular production
  rate for all prokaryotes on earth is estimated at 1.7 × 10^30 cells/yr
  and is highest in the open ocean.

Hence we have about 1.7 x 10^30 New Cells/year
Multiply this by the estimated 3.5 Billion years (3.5*10^9) when the earth was colonized and we get

5.95 * 10^39 Bacteria that ever lived. of course there were other organisms, but as above even the biomass of bacteria exceeds that of
  all plants and animals combined so their effect on this number is
  negligible. Likewise, the life conditions were surely not ideal at all
  times, so this number may be lower still.

For some perspective, the estimated number of atoms comprising all of planet earth is about 1.33 * 10^50 according to this source.
ESTIMATE OF NUMBER OF MAMMALS THAT EVER EXISTED
The upper bound for mammals is as follows.
The surface area of the land of the earth is 149 million square kilometers.
Let us consider if the entire land area of the earth was completely covered with mice.
A mouse is typically 10cm from nose to base of tail and about 5 cm wide=0.1*.05=0.005 square meters. So we get 200 mice per square meter.
Hence, if the entire land area of the earth were covered with mice the world population of mice would be:
149*10^12 square meters * 200 mice per square meter = 1.788 * 10^15 mice
Mice typically produce a litter of 6-8 young and a female can have 5-10 litters per year. source
Let's say we have this maximum population reproducing in a stable manner. i.e. for every new mouse, an old one dies.
Hence the total number of new mice per year would be:
1.8 * 10^15 * 8 young * 10 litters = 1.44*10^17 new mice per year.
Mammals appeared around 200 million years ago (source), so that makes
1.44*10^17 new mice per year * 200 million years
= 2.88 * 10^25 total mice.
In practice mice need space and resources and compete with other mammals which take up space and which reproduce less frequently. Likewise, deserts and polar regions are less inhabitable, and sometimes there are periods of droughts, and they don't always reproduce at the maximum rate etc. so the total number is probably about around 4-10 orders of magnitude less than this.
So it is probably something like 10^20 total mammals ever existed.

Sorry, but this estimation makes no sense. First, the earth wasn't colonized from the very beginning, as far as I remember the oldest estimates for life go back as far as 3.5 billion years. Then life was different at that point (for example was not dependent on oxygen) and the life conditions were surely not ideal at all time. Not to mention the changes in atmosphere (and biosphere), when the oxygen concentration went up. It also assumes that all organims where from one kind of bacteria, which they were not.

@Chris I am trying to give an upper bound - i.e. a maximum number of organisms that could have lived on earth. this is the best we can do. I updated the answer with your point. primitive organisms were more or less the size of e-coli give or take an order of magnitude or two or three. do you think the upper bound number is higher? if yes, what would you change to increase this number?

20 min for generation time is way, way off. In natural conditions, like for example in soil, your average bacterium reproduces maybe once a week. I imagine generation times are still much longer in e.g. seawater.

@5heikki thank you for the clarification. yes, I wrote in the end, it is probably at least 5-15 orders of magnitude less. this is just an exaggerated upper bound best-case scenario. I updated it with a more realistic number. It's probably still less than this though.

When looking at these numbers, did you happen to see anything similar about viruses?

@Brannon viruses need hosts, so their number is far less than this

This is a hard problem - estimates of total living things in an given environment are usually created by looking at the number of species and individuals found in a sample area and extrapolating.  As far as estimating the number of living things in the world, there are still lots of species which are not known, making this number still unknown for the world today as it is.  Doing a similar survey into past ages adds another layer of problems to the estimate.
EO Wilson has, among others I'm sure, made a serious effort to understand how many species are currently alive on Earth.  Its pretty clear that currently we don't know how many species are currently alive - that would make it nearly impossible to answer your question historically.

About 1.9 million species have been discovered and given scientific names, though the actual number may exceed 10 million. Bacteria and archeans could comprise tens of millions species—once taxonomic units are precisely defined. Knowledge about species and extinction rates remains very poor, and species disappear before we know they existed. We propose that, as scientists are better able to assess the conservation status of the species that compose an ecosystem, the more they will understand the health of that ecosystem. It is time to accelerate taxonomy and scientific natural history, two of the most vital but neglected disciplines of biology.

from "The barometer of Life" Stuart, Wilson, McNeely, Mittermeier & Rodriguez, emphasis mine.
As you can see there are some important technical obstacles to even the question of how many species there are. Bacteria and free living eukaryotes have rules for speciation that are fairly difficult to define, esp since many can transfer just a few genes with many near relatives and do not require sexual reproduction.
Another obstacle is that the animal and plant surveys are not really done yet either.  Plants animals and insects are still being discovered in jungles, deep underwater and at rest stops.  As far as the microbial record goes, an average glass of water from a pond or river probably has undocumented species.
The encyclopedia of life is a resource worth mentioning here. It is self admittedly only a partial record.
For past speciation records, the geographical sampling is not strong - digging down in selected spots where fossil records remain is bound to miss many of the species which had existed.
In 1990, Peter Dodson wrote this review in PNAS holding forth on the taxonomical difficulties in estimating the number of dinosaur species which included a founding period which was as much circus as science as well as the incredibly sparse sampling of prehistoric surveys over time and history. As recently as this year the count of dinosaurs has continued to vary wildly. A pubmed citation list to Dodson's paper shows 7 citing works, mostly from the past 3 years.

The question asked for the number of individuals, which is different than the number of species.  For reproduction by binary fission, would one (and which one--e.g., the longest survivor?) count as the original individual or are both new individuals?  When does a colony or symbiotic collective become a single organism (e.g., mitochondria are presumably not considered distinct individuals but considering the biosphere a single organism seems to be going too far)?  The high and highly variable rate of bacterial reproduction would make estimating this count problematic.

I tried to amend this... but you're right Paul I did misread this. I guess my eyes misled me because the question seems even more impossible. Estimates of bacteria living deep into the earth's crust have seriously multiplied in the past decade or two since they have been discovered and is still being discovered..newscientist.com/article/… Although the question of how many living animals would be more likely, they are hard since only select environments can be surveyed via fossil records. still many dinosaurs, etc to discover.


text:
Which of the nicotinic acetylcholine receptors (nAChRs) catalyse the release of the neuromodulators mentioned below that's caused by nicotine?
Neuromodulators: acetylcholine, norepinephrine, epinephrine, vasopressin, histamine, arginine, serotonin, dopamine, autocrine agents, and $\beta$-endorphin.
I am aware that agonists of the $\alpha_7 $ nAChRs improve cognition in Schizophrenia, presumably by catalysing the release of histamine, norepinephrine and/or acetylcholine.1,2 I also know that $\alpha_7 $ nAChRs antagonists reduce $\Delta^9$-tetrahydrocannabinol (THC) self-administration in mice presumably by suppressing dopaminergic activity in the nucleus accumbens or by inhibiting the activity of the CB1 receptor.3 Selective CB1 antagonists also manage to reduce nicotine dependence.4 Also I know that the activation of the $ \alpha_3 \beta_4 $ nAChRs in the adrenal medulla catalyses an epinephrine and norepinephrine release.

Reference List (Oxford Style)

M Hajós, BN Rogers, 'Targeting alpha7 nicotinic acetylcholine receptors in the treatment of schizophrenia.', Current Pharmaceutical Design, 16/5 (2010), 538-554.
LF Martin, WR Kem, R Freedman, 'Alpha-7 nicotinic receptor agonists: potential new candidates for the treatment of schizophrenia', Psychopharmacology, 174/1 (2004), 54-64.
M Solinas, M Scherma, L Fattore, J Stroik, C Wertheim, G Tanda, W Fratta, SR Goldberg, 'Nicotinic α7 Receptors as a New Target for Treatment of Cannabis Abuse', The Journal of Neuroscience, 27/21 (2007), 5615-5620.
C Cohen, E Kodas, G Griebel, 'CB1 receptor antagonists for the treatment of nicotine addiction.', Pharmacology, Biochemistry and Behavior, 81/2 (2005), 387-395.