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How does Organ Transplant work well despite having Foreign DNA
My question is little bit related to this one Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS but only little bit.
Problem
Suppose the case in which person A got his kidney transplanted (and person B is donor). Now both A and B have different DNAs and how come lung (organ) transplant works well for person A and how does person A's DNA going to "accept" the lung's DNAs and how is replication going to work across the foreign lung?
Question
Will person A's lung contain:

Person A's DNA
Person B's DNA
DNA of both Person A and B (will convert to person A's after some-time having a certain half-life for it)
or
Forever contain both DNAs

Thanks in advance and kindly provide reference for your answer. Thanks

The DNA plays no direct role in organ transplant acception (or rejection), since it is not recognized by the immune system. It is 99.99% identical anyways. Replication works in the normal way it always does.

Replication works in the normal way... So predict the DNA of the transplanted organ after lets say 1 day: Will it have all the DNA (DNA of all the cells I mean) converted into the person A's DNA?

Why should the DNA in the transplant be changed? And how should this happen? Technically you are chimeric after an transplantation.

Chimeric?? Any reference for this point kindly?

After a transplantation you contain the DNA of two different humans.

4. Forever contain both DNAs
Yes, the donor kidney still has (and will remain to have) the donor's DNA. That is irrelevant to the acceptance and continued functioning of the organ, though.
The thing that could make an organ transplant fail is the recipient's immune system. If it detects the organ as "alien", it will attack it like any other foreign particle, and the body will reject the transplant.
To avoid this, two things are being done:

A donor is sought whose organs have similar protein markers to those of the recipient. (Those markers, and not the DNA, are what the immune system looks for when trying to tell friend and foe apart. DNA is inside the cell, the protein markers are on the outside.)
Similar protein markers are usually found in people with similar DNA, which is why close relatives are tested for this kind of compatibility first.

The recipient recieves special drugs that partially suppress the immune system.

If the recipient's body does not reject the organ, it can continue to function normally despite its different DNA. If, for example, there is a genetic defect in there that will lead to some kidney-related issues at a later time, it will be the donor's defect. If there has been a defect in the recipients kidneys that would have led to issues later in his life, that defect would be gone with his kidney. Other cells in his body would still carry the same defect, but those cells are not kidney cells, and thus that particular issue will not manifest itself.
Replication of cells will follow the same pattern: Cells from the recipient will replicate the recipient's DNA, cells from the donor's organ will replicate the donor's DNA.

In case this question was inspired by any novel / movie depiction of "his DNA was changed" and suddenly a person undergoing significant changes in appearance, capability, and / or personality (as in e.g. Star Trek or similar franchises), those are (largely) unscientific. Of course a donor organ could produce a very different mix of hormones, by- and waste products, with all the effects that could have -- but any "change" would be slow, gradual, and basically indistinguishable from naturally occurring changes in a person. With the exception that, without a donor, the recipient would be dead.

(ctd) Also, given that similarity in DNA / protein markers and healthiness of the organ is a basic requirement for organ transplantation, radically unbalanced organ functions are unlikely.

No this question came totally in my mind by chance (as these days all I think about is DNA).


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Why doesn't pure fat taste better than pure sugar?
I mean looking from evolutionary perspective sugar tastes sweet and individuals that had this perception ate more sugar and survived and those that didn't perceive sugar as sweet didn't eat it and died from hunger.
So the better (more caloric) food is - the better it should taste so that one would be more likely to eat it and if choice had to be made between berries or lard (assuming that food is scarce) one should go for lard as this would increase his chances of survival
Out of all foods lard has the highest calorie content (898 cal per 100g) and therefore highest concentration of fat and yet it doesn't taste very nice.
There must be some explanation why fat doesn't taste much better than sugar?

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Can the dead be brought back to life by viruses?
Zombies have been a part of popular culture for decades. The living dead rising up to take over the world is a terrifying concept, worthy of Hollywood blockbusters and television hits. Some of those zombie fiction stories are based on infection by viruses or other organisms.
Is it possible to bring dead tissues back to life by virus infection?

You must tell facts from fiction; viruses need living cells to replicate because they do not have the molecular machinery at hand to generate energy and construct building blocks essential to life. So no, viruses cannot bring back the dead or revitalize dead cells.
One thing that comes close to it are the so-called zombie ants. These ants have been infected by a parasitic fungus that can take over the ant's nervous system (Fig. 1).

Fig. 1. Zombie ant found in Brazil, infested with the fungus Ophyocordiceps. Source: National Geopgrahic.
These fungi eventually kill their hosts, but before doing so they temporarily take over their nervous system. In the case of Ophyocordiceps unilateralis (Evans, 2011), the spores lodge themselves into the ant's head through an exposed part of the ant’s exoskeleton. The fungus then infiltrates and targets the ant’s brain, taking control of the ant. Then it makes the ant leave its colony and head for a leaf that provides the ideal conditions for the fungus to grow. The ant crawls under the leaf and goes into a “death grip”—biting down hard on the leaf's major veins. This allows the fungus to slowly feed on it. When the fungus finishes growing, it eventually kills the ant and releases its spores (Source: Smithsonian).
The interesting thing is that the zombie ant not only provides shade and humidity when hanging under the leaf, it is also positioned directly on top of the ant’s colony, so when the spores burst out they fall on other ants and begin the cycle all over again. There are hundreds of mind-controlling fungi like this one, but the chances of this type of parasitoid fungus evolving to target humans as hosts are unlikely (Source: Smithsonian).
Reference
- Evans, Commun Integr Biol (2011); 4(5): 598–602

While it is possibly a divergence here, does Toxoplasma Gondii fall into the 'brain controlling parasite' category? Yep, not a fungus.  And then there's that tangential symbiotic microbinome and the neurotransmitters that they produce in our gut that might influence our brain...

@MichaelT - organisms infecting the nervous system in general can cause erratic behaviors. They don't control the brain though.

I remember an old BBC documentary-series (1980s?) - I think with David Attenborough - where in an episode, they followed one fungus-infected ant until it's death.  Then there was an episode of X-Files (the original series), where an alien fungus did attack humans and made them seek out other humans - before a mushroom exploded from their chest to spread spores...

Ahh yes...  https://www.youtube.com/watch?v=XuKjBIBBAL8

You have to wonder how a fungus could compel an ant to do something like this. Minor behavior changes? Sure. I guess it could just stimulate an area of the brain making the ant go into a rage or make it docile or something. This is a very specific set of "instructions" that it seems to be able to feed into the ant's brain though. Considering I'm sure all ant's nervous systems develop partly as a result of their environment, how could it reliably control a new ant? It's amazing.

It should be noted that wide range of parasites do influence behaviours of host. Toxoplasma gondi is one of them. However, it should be emphasized that this wide range of parasites does not influence hosts with wide range of behaviour, but one type of behaviour (per parasite). Relatively complex behaviours are possible because one signal (e.g. hormone) can start cascade reaction or influence multiple receptors, thus causing itself complex behaviour. Example might be adrenalin.

Mammals are not immune:
http://phenomena.nationalgeographic.com/2013/04/26/mind-bending-parasite-permanently-quells-cat-fear-in-mice/
There is a parasite that causes mice to no longer fear cats - so the cat can ingest it where it can then reproduce.

Certain parasites including bacteria and worms have been linked to causing obesity by releasing hormones or disrupting our digestive system to make us want to eat more. While not all obesity are caused by parasites, parasites can cause enough behaviour change to cause obesity.

@Carcingenate I asked somebody who researches these ants and fungi that exact question once. From what I remember, she said that ants can't control their body temperature directly to attack an infection, so instead they move to a sunny place to induce a fever. I'm not sure about the clamping reflex.

I recall a snail also which gets controlled, and directed to the tree canopy, where birds then eat it and re-distribute the parasite

Note: This answer is a complement to @AliceD's answer, and is partly reusing stuff from this related answer.

Since you are specifically asking about viruses, I thought that it might be interesting to mention that similar behaviour changes as those mentioned for fungi can also be caused by viruses. See e.g. this quote from Roy et al. (2006):

In many cases the final interactions, or endgames, between a host and pathogen involve complex behavioral modifications such as the infected insect seeking an elevated position where wind currents can effectively disseminate conidia. Elevation seeking by insects at late stages of infection is a common phenomenon that was recognized by early insect pathologists who noted that diseased lepidopteran larvae, such as Lymantria monacha (the nun moth), infected with baculoviruses migrated to the tops of trees where they died (94). This host-altered behavior was named “Wipfelkrankheit” or “Wipfelsucht” (meaning tree top disease in German) for viral diseases (41) and “summit disease” for fungal diseases (24, 57, 106).

Overall, lots of information about the behavioural modifications of hosts caused by fungi and viruses can be found in Roy et al. (2006).
One example of a such a virus that modifies the behaviour of insects is Lymantria dispar multicapsid nuclear polyhedrosis virus, which infects larvae of the moth Lymantria dispar and causes them to climb to high locations (tops of trees) before they die. In another interesting example a parasitic wasp might use a viral infection to control the behaviour of its host, so that the the host beetle is paralysed and is "guarding" the larvae and pupa after the parasitic larvae has emerged from the beetle (see Dheilly et al, 2015 and a popular account in Science).

(Dinocampus coccinellae "guarding" wasp pupa, from http://www.naturespot.org.uk)
References:

Roy et al. 2006. Bizzare Interactions and Endgames: Entomopathogenic Fungi and Their Arthropod Hosts. Annual Review of Entomology 51(1) (pdf)
Dheilly et al. 2015. Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation. Proceedings B 282(1803).
Wasp virus turns ladybugs into zombie babysitters, Science

Even the rabies virus is a good example in case of animals.

@WYSIWYG Rabies is very likely a major source for various “people turning into monsters” folklore, like zombies or werewolves. (“Zombie,” of course, was originally a very specific term for a particular thing in Haitian folklore which does not match up well to rabies, but the broader popular concept certainly gets many nods from the disease.)

@KRyan: Not likely. Rabies is also called "Hydrophobia", furthermore Rabies has quite destructive effect on nervous system. Werewolves are not "rabid", werewolves are people who transform into wolves (or other way around) and there is a LOT about people-turning-into-animals and animals-turning-into-people in every mythology of every nation/ethnics/tribe.

@WYSIWYG Agreed, and there are probably also many unstudied exampes of how viruses can affect human and non-human behaviour.

Stretching the limits of what is known a bit, there is an interesting example of a phage (virus that infects bacteria) infecting a photosynthetic bacterium in the ocean that deserves mentioning.  What is amazing here is that the phage has certain genes that are required for photosynthesis within its genome.  Why does it have these?  The phage extends the life of its host in order to maximize its replication.  It has been shown that while the host metabolism is all but shut down, phage genes for photosynthesis are still being expressed at high levels, giving the phage 'bonus time' to replicate.  Ok so the virus in question here is the reason for the death of the host in the first place.  Also, the host is not exactly living normally during this 'bonus level' of life, as the phage is only trying to produce more of itself.
One can imagine however, that in single celled organisms (for simplicity), a lysogenic phage (one that sits in the genome of its host and waits for the proper conditions to jump out and replicate), could theoretically bring back the organism from death, if it encodes the precise biochemical pathway that was shut down in the first place.  Think of a cell that has lost some necessary gene that is essential to its survival in a given environment.  This new mutation (perhaps because of UV light) would surely kill this cell.  If the cellular components necessary for survival remain intact, and a phage encoding this biochemical pathway (this gene) and the components to express it (yes viruses have many of these genes too), it is conceivable that this cell could return to a metabolically normal state, ie living.  This is just a thought experiment....
Ref:
http://www.cell.com/trends/microbiology/fulltext/S0966-842X(10)00196-4

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Aquarium snail identification
Many of these little snails suddenly appeared in our aquarium from nowhere.  I suspect that some snail eggs hitched a ride with some recently purchased plants.
Can anyone identify the species?  I am not having any luck with googling.
The photos show a baby snail of about 2-3 mm in size.  The shell is asymmetric, with one side looking completely flat (or concave).
These  are not pond snails.  We also have (uninvited) pond snails, but pond snails look different even when as small as these.  This new species has a lighter colour than pond snails, a more transparent shell of a different shape, and moves slower.

You've got me stumped. Are all the little ones this shape? Sort of leaning towards some sort of ramshorn or similar but definitely not sure. You may need to wait until they mature some to get a better idea. The only clear adult snail I can think of is a cave one found a few years ago. I'll bet the shell on this gets some color as it ages.

@Jestep Yes, all of these have the exact same shape, and they all have the exact same size, which is why I think that they hatched from eggs at the same time. The ramshorn photos I found appear to show a more symmetric shell.  I think that the reason why I cannot find anything that looks like this online is that they will change in appearance as they grow up.

I would post the images in some of the aquatic forums. These close ups are great by the way. http://www.aquaticplantcentral.com/ is a good one, there are some others as well.

These are a kind of ramshorn snail, as Jestep correctly guessed.  Now they are grown up and they are clearly identifiable as ramshorn.
I will post photos of adults when I get the opportunity.

Yes but Ramshorn is not an identification. What's the Latin scientific name?

Can you please pray the photos of the adults you mentioned? Thanks.


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

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

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

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

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

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

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

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


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All-or-nothing-law: law or general principle?
The all-or-nothing principle indicates that a nerve cell fires at maximum potential or not at all, based on a threshold on the stimulus.
Is this a statement which is always true, or only mostly-always true?
In electrical engineering, a discipline I have studied, we have a similar rule, a logic signal is responded to as though it is either a high or a low.  However, in the middle are what are known as "metastable states," where the rules of thumb do not apply.  In fact, you can even theoretically lock up a logic circuit by presenting a steady stimulus in between two states.  Needless to say, designers of such circuits take great effort to ensure their logic is never exposed to such stimulus.
Do we have any evidence of neurons exhibiting behavior which defies the all-or-nothing law in some circumstances, or if not, what sorts of metastable behavior are seen when the stimulus is exceedingly close to that of the threshold?

If you only ask if it is always true or not, than here is the answer to your question: http://science.sciencemag.org/content/127/3296/468.short  Unfortunately, I don't know any other example as of now.

That article refers to a bundle of muscle fibers, not nerve cells. Muscle bundles don't exhibit all-or-nothing, or you'd never be able to pick up eggs. It's interesting because heart muscle is similar to nerve tissue in a couple of respects but the all-or-nothing law doesn't apply here.

@Resonating They are controlled via the same mechanism as nerve cells, namely action potential. The strength of contraction is determined by two things: the number of cells activated, and the frequency at which the action potentials are sent. Action potentials are of the same potential regardless of the contraction's strength.

I would argue the all-or-none principle is a rule of thumb. It is generally true if voltage hits a certain threshold then there will be a action potential with the same amplitude regardless the strength of the stimuli. But as you point out with the logic gate example, the threshold is notoriously hard to define mathematically. Furthermore Action Potentials don't always have the same amplitude, but as I will argue that doesn't matter all that much to the function of the neuron.
As most rules in biology we can find exceptions. I'll list some phenomena that confound the all or none principle.

Accommodation is the prime example that not all action potentials have the same voltage amplitude. Accommodation is the when the amplitude of the voltage of successive action potentials drops, and may even stop firing (Depolarization Block). This is usually the result of a too strong of a stimulating current, and occurs under pathological conditions.
Resonating Neurons These neurons fire when a certain frequency of input is achieved and can even fire when hyperpolarizing (negative) currents are injected. The reason I bring this particular neuron  type up is it shows that thresholds are not necessarily more depolarized (positive) than rest. They are complex manifolds (or shapes) relating to the gating variables of Ion channels in the membrane.

Another thing to note, is even though amplitudes of Action potential can change, the difference of a few millivolts in amplitude will not make a difference to the synapse and in that sense the all-or-none principle holds. Recall that voltage gated Calcium entry is required for a synapse to release it's neurotransmitter. Much like the logic gate, it will only enter at sufficiently depolarized (positive values) but the more positive the voltage, does not correspond to more Calcium entry. In other words it saturates at high voltages. In this way, to cause a stronger response at the synapse the neuron increases the firing frequency to stay "on average" depolarized longer. Thus more Calcium entry and thus more neurotransmitter release.


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How do disulphide bonds in hair cause curling?
I understand that there are several characteristics of curly hair which differ from straight hair (such as an asymmetrical distribution of disulphide bonds in curly hair), but really am struggling to understand the root cause of inherent curl on the macroscopic level.
My current understanding of the hair structure is based mostly upon this website
The most relevant part of the hair for our discussion is the cortex, which is made up of many axially aligned macrofibrils, or macroscopic keratin fibers, which are in some filler essentially of lipids/proteins. Inside these macrofibrils are microfibrils. These are also aligned axially and in some filler of lipids/ proteins. Inside the microfibrils are the protofibrils, even smaller fibers which are twisted around each other like a yarn. These protofibrils are made up of 4 keratin chains which are essentially twisted together and connected by disulphide bonds and hydrogen bonds. While hydrogen bonds are easily broken, the disulphide bonds are not. In curled hair, the macrofibril isn't symmetrical but I am unsure as to how this, or what other effects, actually lead to the curling.
I had previously assumed that the reason for curling is that in an asymmetrical configuration of the hair(IE not cylindrical but more oval in cross section), some residual stresses are formed by the disulphide bonds between the keratin, If this is true, it would lead me to believe that it would cause increased buckling of the protofibrils. But, even with straight hair and more symmetrical disulphide bonds, you already have some curling and buckling of the protofibrils, but the hair doesn't curl on a macroscopic level.
As such, it doesnt seem like this buckling due to asymetrical disulphide bonds would necessarily lead to a curled or organized structure on the macroscale, with the macrofibrils. This leads me to believe I am missing something.

Nice question. I must say it took me many hours to get satisfactory answer.
Hairs are made of keratin molecules, which contain cysteine. Cysteine has thiol (-SH) group, by which it can form disulfide (-S-S-) bond with another cysteine of another keratin, causing bending of hair. See this image from here:

Curling of hair can be justified on both microscopic and macroscopic level.

Microscopic level: See this post from here:

Curly hair has to do with the chemical bonds in the protein that makes up hair - $\alpha$-keratin. Keratins, particularly $\alpha$-keratin, have long sequences of amino acids (often more than 300) which forms a helical structure.
Pairs of these helical structures then coil about each other in a left-hand coiled-coil structure. These are then attracted to another coiled coil so two keratin helices will stick together. These four-chain structures then associates with another four-chain structure to form the hair filament. One of the amino acids which make up these chains, is cysteine which has a sulpher group which is able to make connections with other sulpher groups on other coiled coils.
The more interactions a filament has with another filament, the more tightly coiled the coiled-coil becomes. Hence, curly hair has more interactions than straight hair. The process of `perming' hair introduces more accessibility of the sulpher on the amino acid, cysteine, to make these connections. Finger and toe nails have many many bonds between filaments and are thus, very hard.

For example, see how hairs are curled artificially via perming.

Source
This change in location of bonds is what causes curling of the hair (look again at the first diagram and notice the orientation of disulfide bridges). Those vertical strands now get curled due to change in these bonds. Here, the required mechanical tension for bending is provided artificially.

Macroscopic level: Shape of hairs is also determined by its macroscopic structure. Look at this article:

All hair, whether curly or straight, has two major components: the shaft and the follicle. The shafts are the visible, flowing strands that we see on our heads. The follicle is the part of our hair that resides within the skin, or dermis, of our scalp. Each of these structures plays a role in determining our overall hair shape.
Let’s start at the root of the issue (pun 100 percent intended): the follicle. It turns out that the shape of our follicles is a major determinant of our hair texture. If you were to look at the follicle of straight hair, you would find it is perfectly round. The follicle of curly hair adopts an oval shape. The flatter the oval is, the curlier the hair will be.
Another contributing factor to a hair’s curl is the way the follicle tunnels into the scalp. Follicles of straight hair tunnel vertically down from the skin’s surface into the dermis. If the follicle angles into the dermis then the hair will curve as it grows causing it curl. Although, this curving of the follicle can lead to gorgeous curls it causes one major drawback that all curly-haired persons can attest to, dryness. Within the dermis, special glands line the follicle to secrete oil, called sebum, to lubricate the hair. Unfortunately, when follicles curve sebum isn’t able to travel the length of the hair as well leading to dryness of hair that doesn’t get lubricated.

Source
Although how shape of follicle determines structure of hair strand is probably not known, the major contributing factor likely is how hair emerges from the scalp. When it emerges in a bent shape, it faces a lot of tension from the scalp, which causes it to bend in the shape of the follicle to form curls. Since straight-emerging strands don't face such forces, they do not lead to curled hairs.
In this way, hair curls are a consequence of large number of disulfide bridges between keratin molecules and how the hair emerges from the scalp.

Yes, this is an excellent summary of essentially what I had read on the internet as well. However, it fails to fully address the root of the question: why exactly does the disulfide style bonding. We have two obvious contributors to curling: 1) high twisting in the alpha-keratin and 2) asymmetry in the cross section. It seems like 1) may change the elastic modulus of the hair, thus making it more susceptible to bending, while 2) changes the cross section and (assuming the cross sectional area is roughly the same) render the hair more vulnerable to curling.

However, the root cause is still not addressed. There is some cause that is leading to the actual curling. The two factors mentioned previously don't directly cause curling, there must be some residual stress that occurs during the hair growing process. In my mind, this residual stress may occur in several different manners but most likely due to a change in surface chemistry as the hair grows into atmosphere. This change in surface chemistry likely leads to a change in mechanical properties, which in turn induces a mechanical stress and leads to curling.

@user2341 it seems I still have not caught the root of the problem. Apologies, but could you please explain what I have failed to answr here?

As in my previous comment, there is no information regarding the cause of the curling. I went on to speculate as to causes in my previous comment, but I'm not sure that any actual evidence as to the cause or the reason why hair curls.


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Why does influenza sometimes cause GI symptoms?
I'm speaking strictly of influenza, not gastroenteritis which is sometimes mistakenly called "stomach flu." I just read this article on the mechanism through which rotavirus causes diarrhea and vomiting. Since the flu is a respiratory disease, through what mechanism does it sometimes cause diarrhea and vomiting? Does it also release proteins that activate the enteric nervous system in the gut? Is it caused by inflammation from cytokines being washed down the throat in mucus? Or is it the result of a secondary infection resulting from the decreased immune system?

Article: How influenza virus infection might lead to gastrointestinal symptoms Source study: Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation.
The idea is that Influenza virus infection originates in the respiratory tract. In response, the body produces these CCR9+CD4+ Th cells denoted Th17 in the lungs. Gut epithelial cells produce CCL25, a chemokine made to attract cells expressing CCR9 chemokine receptor. Th17 cells are a subset of T-helper cells that produce interleukin-17, more about that here. So what they found, is that the Th17 cells produced by influenza infection in the lungs migrate to the gut through this CCR9/CCL25 interaction, and they secrete cytokines that are meant to defend against infection. Of course, mucosal immunity at the gut epithelium is always active, because there are commensal bacteria there that out-compete pathogens among other roles.
Down in a section titled "Lung-derived CD4+ T cells destroy microbiota homeostasis and promote resident Th17 cell polarization" their conclusion is that IFN-gamma secreted by the lung-derived Th17 cells destroys the homeostasis of the gut microbiota, and cause other Th17 cells to become polarized in a way that they end up producing the specific set of cytokines causing the trouble in the first place. You also have to understand that the other cytokines the Th17 cells are secreting are causing tissue damage, leading to symptoms of intestinal disease concomitantly with what we've been discussing above.
I think that the process is just recently being illuminated so it may not be completely understood, either.

How are the lung-derived Th17 cells getting to the gut?

Generally, leukocytes in the lymphatics enter the blood through the left subclavian vein. Once there, they traffic to vascular endothelium expressing chemokine attractant molecules and utilize a number of adhesion molecules in concert to extravasate into the tissue expressing the attractant. This could mean multiple tissues given the right circumstances. The important thing to remember when i mentioned mucosal immunity is lots of effector cells are already there due to the presence of microbiota at all times, unlike the systemic response where effectors must be generated.
Here's a figure about extravasation, and another about mucosal immunity, and if you look here you can see that the Th17 lineage is under investigation due to it's inflammatory characteristics in autoimmune disease.

That's a complex process! How are the lung-derived Th17 cells getting to the gut? Is it migrating though the bloodstream, being swallowed? I guess I'm confused about how the common mucosal immune system mentioned in the article works.

@Tom I edited the answer to respond to your comment!


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

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

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


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Author statements (Readers) in biological nomenclature
I know that a binomial name may be followed by the name of the reader who has been the first to identify the species and to give it that binomial name.
It is not completely clear to me what the same of a botanist, zoologist etc. means if it is placed between parentheses, as in Blysmus compressus (L.) Panzer. Does it mean that Panzer gave that species the binomial name Blysmus compressus but it was Linnaeus that identified it as a species? I cannot find precise information on line, nor in my books...
Moreover, the pattern may get more complicated if we introduce the subspecies, for example another Cyperacea: Carex ferruginea Scop. subsp. macrostachys (Bertol.) Arcang.. It seems quite trivial to me that Scopoli (Scop.) identified and gave the species the name Carex ferruginea; as to the subspecies,  did Arcangeli (Arcang.) named it macrostachys after that Bertoloni (Bertol.) had identified it as a subspecies?
I thank any answerer very much.

If I remember correctly, a name in parenthesis means that that person (eg. L.) discovered and named the species, but the species was later on re-categorized into a new genus/family/etc. and then given a new name. The person who re-categorized and renamed it has their name appear after the parenthesis (eg. Panzer)

@CactusWoman Thank you very much for your comment! Am I right if I understand it to mean that L. gave Blysmus compressus the name X compressus (where X is name other than Blysmus) and then Panzer identified it as a member of the Blysmus genus? Analogously, I would think that Bertol. gave Carex ferruginea macrostachys the name X Y macrostachys but it was Arcang. that attributed it to the Carex ferruginea species... Or have I misunderstood? Thank you again!

Yes, that seems to be correct. Blysmus compressus, according to the Flora of China, was originally named Schoenus compressus by Linnaeus, then underwent a number of reclassifications before ending up with the current classification.

It is important to note that classifications of species can be very complicated, with the same organism being reclassified many times by many different people. Also, an organism needn't keep its species epithet (the second part of the binomial) after being reclassified. If species Foo barus is later reclassified into the Baz genus, but a species with the name Baz barus already exists, the species will be given a new species epithet, ending up with a name like Baz spamus. Nomenclature can actually get rather complicated!

As @C_Z_ mentions, the double author citation is due to a naming revision. In your case, 'Panzer' has revised the name given by 'L' (Linneus). It can for instance be due to an assignment to a new genus or a change in rank status (e.g. going from subspecies to species).
Note that author citations differ between botany and zoology, where changes in authorship are usually not recognized in zoology (as long as there is a proper and complete species description in the first place), while the botanical code allows for multiple author citations. From Wikipedia: Author citation (botany):

... in contrast to the situation in zoology, where no authorship change is recognized within family-group, genus-group, and species-group names, thus a change from subspecies to species, or subgenus to genus, is not associated with any change in cited authorship

So under the Zoological code, the old author name is kept when a species is reassinged to a new genus, e.g. when Seriola gracilis (Lowe, 1843) --> Cubiceps gracilis (Lowe, 1843). On the other hand, the Botanical code allows for multiple and sequential revisions, so you can have situations as "Dummy species (L.) Thom. emend. Müll.".


text:
Genetic coding question, amino acid to base relationship
I'm studying for a test and I am confused by these problems/statements.

How many amino acids will 18  bases code for? Answer: 6. I got this right.
If a certain complete protein has 33 amino acids that compose it, then exactly how many bases will it take to code the entire thing?

The answer to 2. is 105, but I'm confused on how we arrived at this answer. If possible or if necessary, please explain the related concepts to me!

Think I figured it out.

I don't think that's right.  I think 102 would make sense, because you want 99 nucleotides to code for 33 amino acids and more more triplet to code for stop.  Maybe the question writer didn't quite realize that the starting methionine counts as one of the 33 amino acids.

I realized my own question after a lot more mulling, but yeah, you need to account for the Start and Stop codon. According to my teacher, the Start codon = Start codon when it's the first in the sequence and it codes for Methionine if it's not the first.

No.  It codes for methionine when it's the first.  The first amino acid of virtually every protein is methionine, at least before any post-translational modification.

@biologyflair your teacher is incorrect. Met is START, as well as being the first AA in many proteins. Take this Entrez Protein search for the ribosomal S6 protein, which is conserved across pretty much all species. Pick entries at random and look at the FASTA sequence - the first letter of the second line (beginning of capitalized sequence) is always M. Or, try here for all the proteins in the E. coli chromosome.

Then the question is, should I listen to her and pass the test or listen to this for long term benefit?

Do you have a textbook?  I'd be surprised if the textbook was wrong.  You could try and point out that your teacher is wrong, if you don't think that will work, give them the answer they wnat, but remember the real answer for the future.  That link to all the e.coli proteins is proof.

@biologyflair bring it up after class. Heck give her my contact info, it's not hard to find from my profile. I'm a Real Scientist™, I don't mind talking to her :)


text:
Convert flux value in nmol/min/mg protein to nmol/min/cell?
This is a question about unit conversion. I found an experimental measurement of the saturation uptake of glucose in yeast:
$$V_\textrm{max} \approx 650 \textrm{nmol}/\textrm{min}/\textrm{mg protein}$$
See Table III of Diderich et al. (1999)*. Actually the paper reports a range of measurements, I just picked an intermediate value.

Table III
Maximum velocity (nmol·min−1. mg protein−1) and Michaelis constant (mm)
of glucose transport by cells grown in aerobic glucose-limited
chemostats at various dilution rates and in batch culture on glucose

I want to convert this to nmol/min/cell, that is, to units of flux per individual cell.
These are my questions:

What exactly is the meaning of the units reported?
It wasn't very clear to me after reading the paper, so I suppose these are standard units. I presume that "mg protein" refers either to the milligrams of transporter protein, or to the total cellular protein content, but I don't know which.
If that's the case, what's the advantage of these units instead of
grams of dry weight (which I think are more common)?
Finally, how can I convert this to flux per cell?

* Diderich, Jasper A., et al. "Glucose uptake kinetics and transcription of HXTgenes in chemostat cultures of Saccharomyces cerevisiae." Journal of Biological Chemistry 274.22 (1999): 15350-15359.

I think the reported unit refers to the maximum specific activity of the enzyme.

@WYSIWYG So you guess that the "mg protein" refer to "mg of enzyme", not total protein content?

@WYSIWYG I read the experimental section in more detail. They determine "protein content" using the biuret protein assay, which I looked up and I think only determines the total protein content. That is, it is not specific to a particular protein. But I am not sure, and I still think this is a weird way to measure it? Isn't gDW better?


text:
Question about SAM CIGAR string
My question is about the CIGAR specification.
The documentation states:
M 0 alignment match (can be a sequence match or mismatch)
I 1 insertion to the reference
Q1: If I have a CIGAR string 99M170661N26M, does that mean I have 99 matches. Can that also mean 99 mismatches? What about 98 matches and 1 mismatch? The specification states it could be a sequence match or mismatch.
Q2: Assuming I'm doing an RNA-seq experiment. In my CIGAR string 99M170661N26M, does that mean my read aligns to an intron which has 17066 bases? Can I think like: "I have a spliced read which aligns to two exons and an intron. I have 99 matches to my first exon and 26 matches to my second exon. I have 17066 matches to my intron."?
EDIT:
Can I get the number of matches in my read? Does that even make sense? For example, how do I know if I have 10 exact matches?

Q1: Yes, the CIGAR string operation 'M' means you can have both matches and mismatches. For example if you have a CIGAR string 10M, then you could have 10 bases that matched perfectly or you could have 5 matches and 5 mismatches. In this case, you have what are known as SNPs (or single nucleotide polymorphisms).
Q2: In your case, you have 99 matches, 170661 skipped regions in the reference genome, and 26 matches.
Q3: If you want to find out how many matches or mismatches there were, you'd have to take the reads from your SAM file, align them to their position in the reference genome, and compare them base pair by base pair to see if their nucleotides match. You can take advantage of the positional information found in field 4 of the alignment to accomplish this.
You can write your own code to accomplish this or use  something like Samtools, which I believe comes with a variant caller.

What does that skipped regions mean? In an RNA-seq experiment, can I interpret it as intron?

@Student T for mRNA yes

The MD optional flag gives more details regarding the alignment:

The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means
from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different
from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted
sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.

Don't know how to quote properly in a comment. I quoted footnote 10 of the current sam format specification (page 7).


text:
The evolution of sleep
Are there evolutionary theories as to why we (and most animals) sleep?
Some claimed functions of sleep include: restoration, waste clearance, memory processing, etc. But unless we understand why these functions are necessary (in the sense that the cost outweigh the benefits in terms of evolutionary fitness) and why they cannot be accomplished awake, we won't have a clear evolutionary theory of sleep.
Are there current theories on the evolution of sleep?

What work have you done on your own to answer this question? As it stands, it is quite broad, and would require a very substantive answer. While this is an interesting question, I am voting to close it until it is narrowed to focus on one particular topic, with background detailing what you do and do not specifically understand.


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Whales and cancer
Do whales get  less cancer than they should considering they have a lot more cells and tissue? If a lot of cancer formation is random because of mutations then shouldn't whales receive  a lot of cancerous growths? Is it partly because there's a lot more systems that can protect against pre-cancerous development and apoptosis degradation in the larger mammal than in a human being?

Short answer: Yes/Maybe
More detailed answer: If the rate of cancer was uniform across cells then you would expect large mammals to more frequently get cancer than small mammals, just like buying 10 lottery tickets is more likely to make you a winner than buying one ticket. However, this correlation between mass and cancer rates does not exist, and it's absence is called Peto's paradox.
Some useful quotes from that paper:

The incidence of cancer in humans stands at one in three [33%], whereas it is only 18% in beluga whales....
There are a number of different hypotheses,” says Carlo Maley, director of the Center for Evolution and Cancer at the University of California, San Francisco. “For example, rather than body mass influencing the number of tumour suppressors and oncogenes, maybe there are less reactive oxygen species in larger organisms due to their lower metabolic rate....
Some biologists question whether there is a paradox at all, saying
that variations in cancer rates across species — which range between
20% and 46% — are more similar than different. “All species get cancer
at about the same rate, typically in the latter part of life span,”
says James DeGregori, a molecular biologist at the University of
Colorado in Denver. “We simply don’t have the data yet to back up the
notion that larger animals have come up with a way to avoid oncogenic
mutations.”

Do eels get cancer, or other fish that have certain properties that use an electromagnetic field , like the eel?


text:
Is there any websites that provide the DNA sequences of food samples?
We can get many DNA sequences at NCBI websites for free. Is there any websites that provide the DNA sequences of food especially meat, for free?
When I read papers regarding food authentication, they only stated the exact DNA sequence for the primers only, not the DNA sequence of their food samples. Why primers? Is it because scientists from the same field can guess what the sample's sequence will be?
Alternatively, if there's no site that shares the DNA sequence of food samples, is there any other place where I can get DNA sequence of mixed species or mutation? For free.

They use primers because the DNA of an animal is enormous and they only want to amplify a certain part of the DNA that can help them distinguish one species from another. As far as I am aware, for food fraud purposes DNA sequencing is not routinely done (just because it is quite a resource-intensive process), instead simple electrophoresis is used to separate fragment size. So the sequence itself doesn't matter - it's the fragment length that is used to distinguish species and detect meat/dairy fraud. However I'm sure sequencing will be used more commonly for this purpose in the future.

Thank you for your valuable explanation. Just to clarify that I understand the big picture : first, use primer just for amplification - then amplify (PCR) - then use electrophoresis -  then bands appear - results: band with length A belongs to species X, if length B then species Y, and so on. If wrong please correct me. So they don't need compare the amplification product with any database of species' DNA sequence? That seems nice..or maybe I dont understand its drawback. Why do you said sequencing will be common for food fraud in the future? I'm interested in knowing that.

Yes, you can compare the length of the PCR product to a known database of species, presumably knowing what species to expect. Sequencing is still a relatively expensive and intensive technique, but as it becomes cheaper and easier it will probably become more popular since it's more sensitive than electrophoresis and gives you more information. There are other genetic technologies used in food fraud as well. I don't have time to write this up as an answer now, but will do so later and add more details if nobody beats me to it.

Thank you so much! In my opinion i've read many papers and some books on dna-based food authentication and dna sequencing, but without basic knowledge on biotech (only high school bio). i got confused thus mixed them up..thanks for clearing me up. other than drawbacks, i am interested in how PCR product is compared with the database part also.. thank you for sharing your knowledge even in your busiest time.

I am not aware of any websites that provide full DNA sequences for food products specifically. In the context of your question, by "food samples" I am assuming you are chiefly referring to meat, fish, and dairy products (the headline-making categories of food fraud), although similar principles are applied to plant products, oils, rice, and other natural products.
PCR
There are a wide variety of genetic techniques used to detect food fraud or adulteration. These techniques do not look at the entire genome of the animal or plant from which it is derived – that would be extremely expensive and unnecessary. Instead, scientists look at particular parts of the genome that they know will likely help them distinguish one species from another.
This is where the primers come in. DNA primers are short segments of DNA that are used to initiate replication of segment of DNA, and is the vital component of PCR that determines which part of the genome will be amplified. Once the PCR product is amplified, it can be analysed by a variety of techniques. For instance, if the PCR products of various species are known, they can simply be run on gel electrophoresis which separates the DNA products by size. Thus if a band of an unexpected size appears on the gel you know there has been some contamination. There are also more automated methods of detecting fragment size via electrophoresis.
Examples of where these techniques has been used has been to detect:

cow's milk in buffalo mozzarella cheese (López-Calleja et al., 2004)
king bolete mushrooms potentially mislabelled as slippery jack mushrooms (Moor et al., 2002)
domestic pig meat in wild boar products (Conyers et al., 2012)

From the López-Calleja study on mozzarella, one of the gels looked like this:

The PCR was run to detect cow's milk in buffalo cheese. Lane 1 corresponds to 100% cow's milk (it is a very bright band), lane 2 is 10% cow's milk, ranging down to lane 6 which has 0.1% cow's milk (a very faint band), and lane 7 is the pure buffalo cheese which shows no band. Therefore, this assay could be useful to rule out contamination with cow's milk.
Real-time PCR
Running gels is a somewhat old-fashioned way of doing things, and there are better ways to make use of PCR technologies on a larger scale. Real-time PCR is the technique now routinely done to detect food fraud. This is a variant of PCR, which (as the name suggests) allows one to quickly see which PCR products are being produced, in what quantity, and there is no need to run a gel.
For example, real-time PCR has been used to detect:

horse and donkey DNA in otherwise-labelled meat products (Chisholm et al., 2005)
pork adulteration in commercial beef burgers (Ali et al., 2011)
Atlantic cod, Atlantic salmon, and European plaice in fish products (Hird et al., 2012)
honey containing pollen from a specific region (Laube et al., 2010)

An example of what the read-out from the real-time PCR is given below. This example is from the Ali study on beef burger adulteration. The letter A was 100% adulterated (i.e. contained 100% pork instead of beef), letter B contained 10% pork, and so-on to E which contained 0.01% pork. F had no pork. The more pork contamination there was, the sooner on the plot (in PCR cycles) the contaminant reached detectable levels:

About the sequence
As you will see from reading about these techniques, it is not so much the sequence itself which is important – it is fragment size or other properties of the region analysed by PCR that is most practically useful. Sometimes the PCR product may be sequenced for comparison purposes, although I do not believe this is done as a routine screening for food fraud.
Keep in mind that PCR is just one of a number of genetic techniques used in food safety. For example, DNA barcoding and SNPs are also useful techniques that are used in this field. The technology is constantly improving and evolving and no doubt more refined and efficient methods are being developed to detect food fraud.

This is much better than what I read by myself. Having a great teacher really makes differences. Particularly on how the fraud is detected by each technique. Thank you very much!


text:
Why do bacteria die in a high sugar content environment?
I was reading some questions in the test bank. Then in Chapter 27, I wonder why the answer is A. (undergo death by plasmolysis). Is the high concentration of sugar that kills them or the effects of sugar on bacteria?

Reece et al. Campbell Biology Test Bank. 9th ed. Boston: Benjamin Cummings / Pearson, 2011: 563.

Have you read about osmosis?

@Joseph http://classes.midlandstech.edu/carterp/courses/bio225/chap06/Slide4.JPG

@WYSIWYG yep, i read about it. Actually this question came from a biology textbook (Reece Campbell Biology 9th ed.).

Related: http://biology.stackexchange.com/q/19744/5198

In (very) short: enzymes are necessary for life. Cytoplasm is necessary for enzymes to function. Water is necessary for cytoplasm to exist. Cells have osmotic membranes.
Given a cell in a solution (even a goopy one, like jam) with a very high concentration of sugar, water will move along a gradient of low to high sugar concentration, in other words, water will move out of the cell and into the jam, thus stopping all major activity in the bacterium (basically stopping it from reproducing, if not exactly killing it. The killing actually comes from heating the jam and canning it while still hot enough to kill most bacteria.)
Plasmolysis: The shrinking of protoplasm away from the cell wall of a plant or bacterium due to water loss from osmosis.

In short our environment always tries to maintain an equilibrium, a stable state.
When microbes encounter a surrounding like a high concentrated sugar state or solution (hypertonic), water diffuses out of the permeable cellular membrane of the microbe to its outer environment with high sugar concentration causing dehydration of the microbe and it leads to shrinking of cell. As water is necessary for chemical reactions inside the cell, the natural metabolism is hindered.The phenomenon of contraction of a cell as a result of water loss is called plasmolysis and the food preservation technique is called sugar curing. Actually we can say a different environment created for microorganism (here for the purpose of food preservation)  with high sugar concentration has effect of plasmolysis in microbe resulting inhibition of its natural metabolic activity that results its destruction.

Actually, it doesn't kill them. As far as I am aware people with weak immune responses shouldn't eat honey or jams because of risk of fungal or bacterial infections.
Resource:
http://www.mayoclinic.org/drugs-supplements/honey/evidence/hrb-20059618

I can't find anything in your source about people with weak immune response and a risk of bacterial infection from honey.  Can you point to where it supports that?

In the side effect section, it is mentioned that spore producing microorganisms like Clostridium botolinum have a chance to grow in it.and also I did some research and the reason many microorganisms can't live in high sugar concentration is low water activity level because of sugar molecules which is needed for microorganisms' activity.but it is not simply the case for all microorganisms.

@ShayanKabiri - While you're correct that immunocompromised people should avoid many foods, jams, jelly, syrups (refrigerated after opening) are allowed; raw or unpasteurized honey - and raw soft berries - usually are not, though. See, for example, Diet for Immunosuppressed and other sources.


text:
Can we take advantage of nanopore sequencing systematic errors to predict secondary structure motifs?
One of the methods of single-molecule sequencing, Nanopore sequencing, is based on traversal of DNA strand through a nanopore. Nucleotide is determined by measurement of ion current (when nucleotide passes through the pore, it decreases the current of ions through the pore, which can be measured).
The method is known for producing systematic errors. I.e. if you sequenced the same molecule twice and during the first run Adenine in 255th position was confused with Guanine, it will be confused again if you repeat the experiment.
I wonder, if it's possible to make use of information about location of errors to predict secondary structure of DNA/RNA etc.? It is natural to suppose that presence or absence of errors is determined by the context, where a nucleotide is located. If I want to validate the hypothesis that same errors are produced by the same motifs of secondary structure, where can I get the raw data to validate this theory?


text:
Synaptic pruning and selective elimination during adolescence
How does Synaptic pruning occur during pre-adolescence, adolescence and post-adolescence, after there is blooming overproduction of synaptic connections until the years of late childhood, and how does during this stage of brain development, "selective elimination" of synaptic connections occur, which is depended on the activity of synapses which are involved in  primary functions?
Also, why, how and to what extent does the brain, after approximately age 6, receive the urge to cut back certain synapses?
Update 1: what exactly is triggered before and during adolescence, so that the brain receives the urge to perpetrate synaptic pruning? I know how synaptic pruning is carried out, I am however very intrigued in the specific processes that occur, from the signal that the brain receives to do it, to why exactly it occurs in such an early stage of life

What do you mean with "how does..occur"? Could you specify your problem? It's kind of vague.

@Christiaan I mean "how does... occur"? as in what biological process takes place during synaptic pruning, and what exactly happens to the synapse during the given age range.

Don't you think that makes the question kind of broad? There are many processes going on, from plastic synaptic changes to cellular mechanisms leading to the pruning itself triggered by certain events. I think you cannot expect anyone to lay the full process out for you. Could you specify your issue?

@Christiaan I am in no way expecting anyone to explain the whole process to me, apologies if the explanation of my question is too broad, trying to be more specific: my question would be what exactly is triggered before and during adolescence, so that the brain receives the urge to perpetrate synaptic pruning? I know how synaptic pruning is carried out, I am however very intrigued in the specific processes that occur, from the signal that the brain receives to do it, to why exactly it occurs in such an early stage of life - hope this is more specific

An answer to this question could potentially be found in "Understanding Adolescent Brain Development and Its Implications for the Clinician"

Thanks to research by Jay
  Giedd and colleagues at the National Institute of Mental Health, it has become
  clear that, during the adolescent years, the organization and functioning of the
  brain go through complex changes. Importantly, these changes seem to be unique
  to the adolescent years and not simply the trailing remnants of childhood brain
  development.

Changes in frontal lobes during adolescence

Frontal lobe gray-matter volumes,
  which represent dense concentrations of neurons and their parts, increase
  throughout childhood and do not reach their peak until approximately the age of
  11 (girls) or 12 (boys), at which point they decline throughout the second decade
  of life and into young adulthood.

So why might frontal lobe gray-matter volumes go up during childhood and down
during adolescence?

Recent data suggested that, during childhood, neurons in the
  frontal lobes are allowed to overgrow and form far too many points of communication,
  or synapses, with other neurons. As a result, gray-matter volumes
  increase. As childhood draws to a close and adolescence begins, the brain
  switches from overproduction mode to selection mode. Early in the second
  decade of life, the brain stops overproducing synapses in the frontal lobes and
  puts the synapses that exist on the chopping block. Hundreds of billions of points
  of communication will be sacrificed through the teenage years. Only those that
  form meaningful, useful points of contact will be kept. Guided by a teenager’s
  experiences, the frontal lobes are shaped and molded into a configuration that
  will carry the individual, for better or worse, through the adult years. As this
  pruning process unfolds, gray-matter volumes decrease.

Changes in other parts of the cortex (specifically temporal lobes)

The temporal lobes, which are critical for memory formation as well as processing
  auditory information and seeing detailed patterns and shapes, do not reach
  their maximum levels of gray matter until the age of 16 to 17, at which point they
  plateau. The temporal lobes contain the hippocampus, a structure that is central
  to creating an autobiographical record of what one does and what one learns.

Sources:

White, Aaron M. "Understanding Adolescent Brain Development and Its Implications for the Clinician." Division of Medical Psychology, Department of Psychiatry, Duke University Medical Center, Box 3374, Durham, NC 27710, USA, 2009. Web. 7 Feb. 2016.
Steinberg, Laurence. "A Social Neuroscience Perspective on Adolescent Risk-Taking." Developmental Review : DR. U.S. National Library of Medicine, 28 Mar. 2008. Web. 07 Feb. 2016.


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How are vaccines and inoculations different?
If so are vaccinations more safe? If so how? And how is the vaccine a magical invention?

First: Inoculation and vaccination are synonyms. So what is your question after that? If vaccinations are safe? Yes, they are.

@Jill I've added a possible definition of what you meant by inoculation. If it is not what you meant, feel free to revert back.

Vaccination has nothing to do with magic. Please clarify what you are asking, and what previous research you have done.

If you became infected before the advent of vaccination, you would either live or die. You would also probably die with really good odds. Being said, someone who lived a disease developed immunologic tolerance to the causative agent, that much you could begin to understand. To expose someone to smallpox was to really endanger their lives, so they found that a similar virus known as Vaccinia, which would normally cause cowpox, could be administered to a patient and they would catch cowpox, but now they were resistant to catching smallpox. You can read about all this on the wiki page for vaccination.
Inoculation generally differs because in the case of inoculaton, you could hope for a less virulent strain of a pathogen but you weren't guaranteed it. You ended up with vaccination methods that increased the safety of the process: On one hand, you could infect someone with related pathogen that causes a milder disease for protection from a more dangerous, related pathogen. On the other, you could find a way to disable the agents pathogenicity, such as heat-killing.
Modern vaccinations are much more refined in that we know so much more. Attenuated strains, for example, you take a virus that grows well in human cells and infect monkey cells just as an example. After many generations the virus grows well in the monkey cells, but no longer the human cells. The strain should still retain it's antigens, however, so when you inject a human now, the virus doesn't cause a disease but you produce antibodies to the virus.
In short, you can protect a population from a disease that would normally devastate it with a dramatically improved efficacy.


text:
Incomplete dominance with gain-of-function allele
Can someone cite an example of incomplete dominance with gain-of-function mutation?

As a trivial example, one could use the epigenetic silencing of transformed reporter genes.
Briefly: Genetic constructs are transformed into some organism (in this case, plants). These constructs usually include a "reporter" gene that is expressed at high levels, which allows workers to artificially select successful transformants. Examples might be GFP genes, metabolic genes complementing auxotrophies, or antibiotic resistance genes, all of which would be clear examples of a "gain of function" mutation when integrated into the genome.
After one or more generations, these reporter genes often get "turned off", in that their expression decreases dramatically or ceases entirely (this tends to happen most when the reporter is expressed very highly or is present at high copy number). I'd suggest looking into the linked paper for more information.

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


text:
Can one eye affect the other eye's low-light adaption?
This previous question addresses how long eyes need to adapt to darkness and reach full contrast. My question is how does one eye affect the "transition" and/or efficacy of this "night vision" of the other eye? Specifically:

Are the eyes' adaptation to darkness linked or is it possible for one eye to transition to "night vision" while the other does not?
Would exposure to bright light in one eye slow the other eye's progression toward being adapted to low light?
If one eye had transitioned to low-light vision, can light exposure to the other eye reduce the ability for the first eye to see effectively in low light?

I understand that the dark-adaptation of eyes seems to occur primarily at the rod and cone level, but I'm wondering if perhaps over-stimulation from bright light in one eye would have a saturating effect on the signal being sent to the primary visual cortex (and thus impact the dark adaptation)?

Yes, but not in a really effective manner. Two things occur for an eye to switch to "night mode". The most influential change is that of seeing mainly with the "rod" visual receptors, as you noted. The second, relatively minor change is that of pupil diameter. In the dark, the iris constricts to produce a larger pupil, allowing more light into the eye. This can be done very rapidly, which is why any interruption in this mechanism is negligible.
The important piece of information you need to know is that for most people, each eye's iris acts sympathetically to that of the other. This means that if I were to shine a pen light into your right eye, causing your pupil to constrict, your left eye will do the same, even if no light is entering that eye.
So, if you were to wear an eyepatch over your left eye in a brightly-lit area, and then enter a dark room and remove the eyepatch, you would have far better vision in your left eye because that eye is operating primarily with rods. To answer your question, there was a tiny setback caused by the right eye in terms of pupil diameter, but this would be corrected within a fraction of a second.
Regarding your inference as to a "saturation effect", the answer is yes and no. If you were to wear contacts, with the lens covering the left eye being tinted dark and the lens on the right being clear, then at first it would appear that the light entering the right eye is affecting the vision of the left. This is simply a matter of focus, though. You're distracted by the larger amount of information that needs to be processed coming from the right eye. With proper focus, however, you would see that the left eye is operating independently in terms of light adaptation (aside from pupil diameter, as mentioned).
I hope this answers your question
Edit
I've been asked to add references. I'll not provide a reference for the use of rod receptors in low light as you have already acknowledged this fact, but I will provide a reference for the simultaneous pupil dilation. For the saturation effect, you can easily prove this to yourself at home. Skip the contacts and pop one lens out of a dark pair of sunglasses.
https://en.wikipedia.org/wiki/Pupillary_light_reflex

Can you please add some references.

Done. If you need more, let me know.


text:
How is e-value calculated in BLAST 2 sequences (BLAST+)?
In the BLAST+ packages, you can align two sequences instead of searching a database:
tblastn -query seq1.fa -subject seq1.fa
The web BLAST documentation states that e-values are calculated from the nr database:

Because BLAST 2 Sequences uses the size of the current nucleotide or protein nr database to calculate Expect values, you may need to significantly increase the Expect threshold in order to see shorter alignments.

However, the command-line documentation explicitly states that you cannot provide both a database and a subject sequence:
-db <String>
BLAST database name
 * Incompatible with:  subject, subject_loc
-subject <File_In>
Subject sequence(s) to search
 * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask

How is the e-value calculated when using BLAST-2-Sequences on the command line? (I am fairly certain I do not have the nr database downloaded.)
Thanks!

You do not need the nr database for BLAST to calculate an E-value.
It will be calculated based on the alignment of n sequences.
The exact procedure is mathematically complex but if you want to read the original paper it is here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/pdf/pnas01031-0226.pdf
a simplified version you will find here:
http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf

BLAST does need a database to calculate the E-value. A database should first be made out of the n sequences and then, as you said, BLAST will calculate E-value from that.

Well yes in the sense that you need sequences to look after but the database can be as numerous as one other sequence

You should first understand what the meaning of E-value is. E-value is the likelihood of a random match having a certain score in given database. So, you are right that a database is required to calculate E-value. The online algorithm calculates it from not necessarily the nr database but any selected target database which could be RefSeq or organism specific databases (nr is the default).
When you are just aligning two sequences, E-value does not make any sense and there is no need to look at E-value at all. If you are aligning a sequence with a list of many sequences then you have to first make a database of your selected sequences using makeblastdb.
Now, when you do the alignment, E-value will be calculated from this database.


text:
Do fish increase or decrease pH of aquarium water?
If I understand it correctly, aquarium fish produce NH3 as their waste product and CO2 due to respiration. Producing NH3 increases water pH due to its equilibrium with NH4+. Producing CO2 decreases pH due to its equilibrium with H2CO3 and its equilibrium with HCO3-. My question is: Which of these effects is more important in most common aquarium fish? Do fish increase or decrease water pH?

Like a glass of beer going flat, any excess CO2 that your fish produce will quickly and irreversibly escape into the atmosphere. Thus, at least in terms of the pH battle between NH3 and CO2 that you describe, NH3 would win.
boilerplate "science is complicated" disclaimer
That said, it's likely that the total environmental effect that fish have on a tiny non-circulating volume of water will be much more complicated than the interaction between two basic chemicals. For example, say one of your fish sheds some scales and they start to rot. All sorts of things would be happening at that point which could affect the pH.


text:
What does "~mitochondrial DNA ~bp linear DNA" means?
I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project.
My question is related to the title of a DNA sequence below:

Sus scrofa mitochondrial DNA, D-loop region, isolate: Europeanwild boar 3
1,045 bp linear DNA

I thought a mitochondrial DNA is different than a linear/nuclear DNA, especially that a mitochondrial DNA is circular while a linear/nuclear DNA is linear. So what does the above title actually means (in simple terms)? Is it still linear or not?

Well, Mitochondrial DNA CAN be linear (in some organism), see the wikipedia page on this

In most multicellular organisms, the mtDNA - or mitogenome - is
  organized as a circular, covalently closed, double-stranded DNA. But
  in many unicellular (e.g. the ciliate Tetrahymena or the green alga
  Chlamydomonas reinhardtii) and in rare cases also in multicellular
  organisms (e.g. in some species of Cnidaria) the mtDNA is found as
  linearly organized DNA. Most of these linear mtDNAs possess telomerase
  independent telomeres (i.e. the ends of the linear DNA) with different
  modes of replication, which have made them interesting objects of
  research, as many of these unicellular organisms with linear mtDNA are
  known pathogens.[19]
For human mitochondrial DNA (and probably for that of metazoans in
  general), 100-10,000 separate copies of mtDNA are usually present per
  cell (egg and sperm cells are exceptions). In mammals, each
  double-stranded circular mtDNA molecule consists of 15,000-17,000[20]
  base pairs. The two strands of mtDNA are differentiated by their
  nucleotide content, with a guanine-rich strand referred to as the
  heavy strand (or H-strand) and a cytosine-rich strand referred to as
  the light strand (or L-strand). The heavy strand encodes 28 genes, and
  the light strand encodes 9 genes for a total of 37 genes. Of the 37
  genes, 13 are for proteins (polypeptides), 22 are for transfer RNA
  (tRNA) and two are for the small and large subunits of ribosomal RNA
  (rRNA). This pattern is also seen among most metazoans, although in
  some cases one or more of the 37 genes is absent and the mtDNA size
  range is greater. Even greater variation in mtDNA gene content and
  size exists among fungi and plants, although there appears to be a
  core subset of genes that are present in all eukaryotes (except for
  the few that have no mitochondria at all). Some plant species have
  enormous mtDNAs (as many as 2,500,000 base pairs per mtDNA molecule)
  but, surprisingly, even those huge mtDNAs contain the same number and
  kinds of genes as related plants with much smaller mtDNAs.[21]

https://en.wikipedia.org/wiki/Mitochondrial_DNA
In the case of your sequence, it only means that it has been entered in NCBI as a linear piece of DNA (it is usually the case when you sequence only a piece of a circular DNA for example)
It does not mean that within the organism it is linear !
I hope this answers your question !


text:
Advantage of GCPRs over RTKs or other receptor protein kinases
My book lists two important differences between GCPRs and receptor protein kinases:

GCPRs do not directly activate a signal transduction pathway. It only does so indirectly, via a G protein. On the other hand, RTKs directly activate a signal transduction pathway, bypassing the mediation of a G protein. (Any G proteins involved with RTKs act as relay molecules in  themselves and are part of the signal transduction pathway.)
GCPRs only activate one signal transduction pathway, while RTKs can activate many pathways.

From what I can tell, receptor protein kinases are faster and more versatile than GPCRs. They do not require as many intermediate steps and can activate many pathways at once. However, GPCRs make up the most largest class of ligand receptors in human cells. This leads me to think there is a great advantage GPCRs have over RTKs that I’m not seeing.
If RTKs are more advantageous than GPCRs, why are there more GPCRs than RTKs?

I think GPCRs are evolutionary more older since tyrosine kinase signalling is relative recent evolved system. This could be one explanation for why their is more diversity in GPCRs
By the way GPCRs can actually signal g-protein independent, for example via B-arrestin. Also their are many types of g-proteins witch can all induce signaling via different signaling pathways. So GPCRS are actually quite versitile.
And then their is also a lot of crosstalk between GPCRs and RTKs

Since both systems are widely distributed, they are both evolutionary pretty old. I would rather say "RTKs are evolutionary newer than GPCR" and not that they appeared relatively recently.

Thats is indeed what I ment


text:
Growth factors vs. mitogens
According to Campbell Biology,

A growth factor is a protein released by certain cells that stimulates other cells to divide.

and according to Wikipedia,

A mitogen is a chemical substance that encourages a cell to commence cell division, triggering mitosis.

What’s the difference between them? I suppose a mitogen specifically refers to mitosis, but if something is stimulating mitosis, isn’t it stimulating growth? Are mitogens all growth factors? Are all growth factors mitogens?

There is a lot of confusion and conflicting / imprecise definitions of these terms. It's biology after all :)
A mitogen is an agent that causes a cell to enter mitosis. This definition is pretty clear, and there is a good consensus about it. (Well technically, mitosis is not the same as cell division, but we will gloss over this distinction.)
The term growth factor has at least two different definitions: (1) a factor that causes growth of tissues, organs or entire individuals; or (2) a factor that causes growth of cells (increase in cell size). These two versions are often mixed up, and this causes no end of confusion. Let's consider them both in turn.
Definition (1) is more common and probably older. Since growth of whole tissues usually (but not always) implies both cell growth and division, according to this definition, a growth factor is also a mitogen. But the reverse is not true: there are cases where cells divide without growing, for example the first few cell divisions of a fertilized egg. But note that, since this definition concerns the level of tissues or individuals, it's meaning is not entirely clear in terms of cell growth and division. Muscle growth in the adult stage usually does not involve cell division, for example.
Definition (2) is better suited to cell biology (in my opinion), because it actually concerns cells, not tissues. This definition is more common when studying cell growth and division; see for example this review. Cell growth is a separate phenomenon from cell division: cells can grow without dividing (fat cells, muscle fibers and neuron do this, for example), or divide without growing (as mentioned above). So with this definition, growth factor and mitogen are two completely unrelated concepts. Now, it is certainly true that many proteins can act both as growth factors and mitogens; Matej Pribis gives some nice examples in the other answer. But that is an empirical fact, not a question of definitions.

What about PDGFs? Are they both mitogens and growth factors?

Yes, most of the classic proliferation-promoting proteins are both growth factors and mitogens, since in most cases cell growth and division go together. But to be precise, it depends on the target cell as well: a given protein may be a growth factor for one cell, a mitogen for another, and have no effect on a third. Not all cells respond to PDGF. Nerve growth factor is a good example of a "pure" growth factor (for neurons).

You can find a great article about this here.
basically, these two groups are very similar in their effects, however they work through different pathways.
Mitogens directly promote cell to get through G1 checkpoint through highering the activity of cyclin D/cdk4 (the complex needed to get through the checkpoint.) and according to the article above, also the cyclin E/cdk2 complex (which helps cell to get into S phase). By activating the MAPK (mitogen-activated protein kinase) pathway leading to production of transcription factors (Elk-1, jun, fos), which then promote specific transcription of proteins needed to get through cell cycle.
The mitogen pathway also causes phosphorylation of Rb (Retinoblastom) protein, which then dissociates from E2F transcription factor. This activates the E2F, which in turn helps synthesise proteins needed to promote S phase.
Growth factors usually stimulates mTOR receptor, which is a "serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription." Source
mTORC complex generally promotes translation. It plays role in "cell growth via the modulation of protein synthesis in yeast and mammals, it and its yeast homologs strongly stimulate transcription from all genes involved in ribosome biogenesis, transcription of rRNA genes by RNA polymerase I (Pol I), transcription of ribosomal protein genes by RNA polymerase II (Pol II), and transcription of tRNA and 5S genes by RNA polymerase III" and many other effects. Source.
Although all of this, in practice, I've seen many people use this categories interchangeably or referring to mitogens as a subgroup of growth factors.
I hope this helps.

Nice with some examples, but I think you miss the point of the classification as growth factors or mitogens. These terms do not refer to individual proteins, it's a theoretical classification of function. And they are not "very similar in their effects", on the contrary they are completely unrelated, by definition --- cell growth and cell division are very different things. That some people use the two terms interchangably is just wrong.

Please note that mTOR is not a receptor, it is just a kinase, and also that it can signal through the MAPK pathway as well.

@Roland I definitely agree, and I might have misstated what I meant. These processes (cell growth and proliferation) are distinct, but I wouldn't say completely unrelated. They can affect each other e.g. the progression of cell cycle inhibited by too small cell size. Moreover, GFs (or rather the mTOR) have some effect not only on growth, but also on proliferation and cell cycle progression. According to this article


text:
Can heritability be deduced from a correlation coefficient?
I am trying to understand the concept of heritability and from what I can gather, the heritability of a factor (say birth weight) must be closely related to the correlation coefficient of that factor when you do a linear regression of the factor between parent (say mother) and child.
So my question is this - is it possible to calculate the heritability from the correlation coefficient, and if so, what is the formula.

No. But a strong correlation may nevertheless be an indicator for heritability (it makes it more likely).
The reason is, that the correlation in the phenotype (birth weight) is not only due a correlation in the genotype but also a correlation in the environment of the child and its mother (culture, economical situation, genes, etc of their respective mothers).
If you were able to remove the association of the environments and of the genotypes and the environments by an intervention (eg. shuffling the zygotes (ideally of parents who were shuffled as zygotes as well)) then the correlation coefficient of the phenotype between one of two parents and the child would be half the heritability. $corr=\frac{1}{2} H^2$

Phenotype ($P$), Genotype ($G$), Environment ($E$)
$P_{parent}=G_{parent}+E_{parent}$
$P_{child}=G_{child}+E_{child}$
$
\begin{eqnarray*}
corr(P_{parent},P_{child}) &=& \frac{COV(P_{parent},P_{child})}{\sqrt{VAR(P_{parent})}\cdot \sqrt{VAR(P_{child})}} \\
&=& \frac{COV(P_{parent},P_{child})}{ VAR(P)}\\
&=& \frac{COV(G_{par}+E_{par},G_{chi}+E_{chi})}{ VAR(P)}\\
&=& \frac{COV(G_{p},G_{c})+ COV(G_{p},E_{c})+ COV(E_{p},G_{c})+ COV(E_{p},E_{c})}{VAR(P)}\\
&=& \frac{\frac{1}{2}VAR(G)+ COV(G_{p},E_{c})+ COV(E_{p},G_{c})+ COV(E_{p},E_{c})}{VAR(P)}\\
&\overset{(1)}{=}& \frac{\frac{1}{2}VAR(G)}{VAR(P)}\\
&\overset{(2)}{=}&\frac{1}{2}H^2
\end{eqnarray*}
$
$(1): \,\,\,$if you managed to get $COV(G_{p},E_{c}), COV(E_{p},G_{c}),COV(E_{p},E_{c}) = 0 $
$(2): \,\,\,H^2=\frac{VAR(G)}{VAR(P)}$ - the definition  of heritability

In other words, the answer is Yes, if you manage to get rid of confounding variables (just like with any correlation)

@Remi.b: so if I could guarantee that the environments were the same for all the animals, then what would the relationship be, between the correlations coefficient (call this cc) and the heritability (call this H2). Would H2 =cc? or H2 = cc squared, or H2= sqrt cc or something else?

Heritability is the slope of the parent-offspring regression. Have a look at wiki > heritability > regression.


text:
What would be “Sternum-Intermediate” distance?
I've asked this question on the English Language & Usage board, not being entirely sure whether this question is strictly medical, or just English knowledge suffices to answer.
Do note I am no native speaker, hence I am afraid to misinterpret the possibly obvious thing.
In an article written by Wheat et al Engineernig for Life - Kinect Report the authors use the scanning device to calcuate distances on the human body.
The measured distances are: Sternum-Intermediate, Inter-nipple and Sternum-nipple (see Table 3.). The latter two are obvious. The first one, however, not so much. Unfortunately, the authors do not provide a definition, probably assuming it is clear to the reader.
What would be the Sternum-Intermediate? Is this the sternum's length or is "Intermediate" some specific body part?

The article states:

Markers (blue stickers, approximately 1 cm in diameter) were attached
  to a point approximating the suprasternal notch and an intermediate
  position on the dorsal aspect of the left breast. The position of
  these markers and the two nipples of the model were extracted from the
  point cloud scan of the breast model through manual digitising using
  Meshlab...Three straight line distances were analysed (1. internipple,
  2. sternum-to-right nipple and 3. sternum-to-intermediate marker).

One can infer that the sternum-intermediate distance is from the sternum to the intermediate marker on the dorsal aspect of the left breast. It is not, I believe, a widely measured anatomical distance, rather one 'invented' for the purposes of the study.


text:
Short dated spontaneous ringing in ear
What causes very high pitched sound in one's ear?

Someone mind telling me how is this a "personal medical question" which is just something experienced by everyone?

Spontaneous ringing is caused by When the outer hair cells put energy back into the vibration, which is known as positive feedback. The process is meant to amplify very quiet sounds more so than loud ones. Normally this works, and you would not notice the sound. But occasionally, the amplification level of one or more outer hair cells will go awry and as a result, the whole system will erupt into spontaneous oscillation.

When this occurs, it becomes audible to us. We perceive it as a ringing in the ear, or “sudden-onset ringing tinnitus see here”. As with most of our biological systems, there are quite a few homestatic control mechanisms (negative feedback) which exist to correct the problem and get rid of the oscillation. It takes about 30 seconds for this mechanism to begin, and then sends messages which suppress the ringing. After the message is sent and received, the tinnitus percept begins to fade away.  You can tell when this reaction has taken place as its often accompanied by a slight reduction in hearing sensitivity (like background or ambient noise we hear suddenly getting quieter), followed by a feeling of fullness in the ear. It usually takes about a minute for this process to fully complete.
Sources:

Wikipedia. Wikimedia Foundation. Web. 30 Jan. 2016 (https://en.wikipedia.org/wiki/Tinnitus)
"What Causes Spontaneous Ringing In Our Ears?" Zidbits. Web. 30 Jan. 2016.
"What Causes That Spontaneous Ringing in Your Ears?" Sciencedump. 2015. Web. 30 Jan. 2016.
"Tinnitus." [NIDCD]. Web. 30 Jan. 2016. (http://www.nidcd.nih.gov/health/hearing/pages/tinnitus.aspx)

When you add sources to an answer, please link to them. It's great you used Wikipedia - which freaking page? I'd also stay away from "popular science" Buzzfeed-type websites and look for actual medical literature. Maybe google "tinnitus" or use PubMed instead.

@MattDMo apologies for that – I edited my sources