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What is the purpose of DNA?
My very basic understanding is DNA gets transcribed into RNA by effectively replacing thymine with uracil, then RNA is translated to make proteins. Looking at it from an engineering perspective, it would appear that, while the RNA to protein translation is non-trivial, the DNA to RNA transcription process is rather redundant: As it's just a simple replacement, why not start with RNA in the first place? My assumption therefore is that there is something about the RNA molecule (e.g., too reactive, too unstable, etc.) that requires it to be put in "cold storage" as DNA.
I don't have a background in genetics or biology, so could someone ELI5 why DNA is needed?

Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets.
What you would do is to create copies of your blueprint and distribute them to your workers. That way multiple workers can produce the widget at the same time.
DNA is the blueprint, and RNA is the copy. Your workers are the ribosomes that translate the RNA into proteins.
This is of course grossly simplified, and there are other reasons for the specific arrangement, but this is certainly one of the reasons why the intermediate RNA is used.

To make this analogy work, one has to substitute the "DNA is the blueprint" with "every gene is a blueprint".

@har-wradim I intentionally made it only about one widget/gene/protein to avoid making the analogy more complicated than it has to be

An analogy has to be realistic, otherwise it produces misunderstanding and new questions.

RNA was almost certainly the first genetic molecule of inheritance. However, the single-stranded nature of RNA is not particularly stable and thus would not be reliable for the long-term storage of genetic information necessary for reproduction (and ultimately evolution).  The necessary stability is provided by DNA.
The question becomes, how did DNA evolve to replace RNA? This is an area of active research but here is a nice summary.

OK, I found this on Wikipedia. I probably should have checked there first!

DNA has three primary attributes that allow it to be far better than
  RNA at encoding genetic information. First, it is normally
  double-stranded, so that there are a minimum of two copies of the
  information encoding each gene in every cell. Second, DNA has a much
  greater stability against breakdown than does RNA, an attribute
  primarily associated with the absence of the 2'-hydroxyl group within
  every nucleotide of DNA. Third, highly sophisticated DNA surveillance
  and repair systems are present which monitor damage to the DNA and
  repair the sequence when necessary. Analogous systems have not evolved
  for repairing damaged RNA molecules.

"Analogous systems have not evolved for repairing damaged RNA molecules" ..because some of these are impossibilities, e.g. the very common C to U deamination couldn't be detected in an RNA genome. This is also the most likely reason why our genomes are made of DNA instead of U-DNA..

No this doesn't explain, why the RNA step is needed.


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Why has our nose evolved with the nostrils facing down?
For most animals, the whole bottom of their face sticks out and they have a snout with a mouth and nose at the end.  But humans have a flat face and just a nose that sticks out.  We used to have the whole face sticking out, but our jaws got smaller and smaller.  Because our noses still needed space to do their job, they had to stay sticking out.  People who come from very cold areas have bigger noses than people from where it is hot, so they can warm the air up more.
Why has our nose evolved with the nostrils facing down? Is it because we were water animals, and that would help with water coming in?

I don't quit understand how your introduction addresses your question...I may not understand your question. But very quickly I would tend to think that if the nostrils where facing the sky we would probably experiencing much discomfort when raining! Also, we probably tend to smell things that are located under our nose rather than above our nose.

@Remi.b Haha that would be a good evolutionary joke, think of monkey that has nostrils down, there are none. It makes sense that we have extruding noses, but why nostrils are down?

Which mammal has its nose upwards?

@TheLastWord Consider it a joke, An elephant when he is pointing its trunk up.

@TheLastWord The hippopotamus has nostrils pointing upward so they can breathe while mostly submerged. The blowhole of whales and dolphins are the nostrils. They're clearly directed upward.

I have not been able to find any studies that look specifically at the genetic mechanism for nose development. I certainly do not know but I'll offer up two hypotheses.
My first hypothesis is that the elongated nose is a remnant of the elongated lower face of our ancestral species, as you note in your answer. Take a look at this brief YouTube video (1:17 long, the part relevant to this answer begins at 33 seconds) of a time-lapse composite showing the develop of the human face. Our face develops as two separate halves that meet together in the middle. That's what creates the philtrum under our nose.
Watch the especially carefully from the 54 second mark to 1 minute mark. Note that our nostrils are pointing directly forward and the overall region looks somewhat like a pig snout. The mouth is vertical aligned with the front of the nose. The overall face is much more rectangular and the eyes are on the sides of the face.
Then, the face begins to become rounder and flatten. The eyes move to the front of the face and the recesses our our eye sockets recede. The lower face below the nose recedes, becoming flatter. The only part that does not recede is the nose area. The flattening of the lower face may actually cause the nostrils to turn downward.  Our nose does not develop outward from a flat face but instead is left behind as the rest of the face flattens.  This would be my initial thought as the primary reason for the shape of the nose and direction of the nostrils.
My second hypothesis (and honestly independent of the comment by @Remib) is related to our sense of smell and taste. Although our ability to detect flavors is a complex process, the primary sense involved is smell (Shepherd 2006). Therefore, downward-pointing nostrils are located directly above the mouth so we get a good smell of the food just before it enters the mouth, perhaps enhancing our flavor-sensing ability.

Shephered, G.M. 2006. Smell images and the flavour system in the human brain. Nature 444: 316-321.

Note that these two hypotheses are not mutually exclusive. The downward pointing nostrils may be a remnant of our facial development but provides an (adaptive?) advantage for flavour perception.

Wouldn't it rain in ur nose if they were the other way?

We would have just invented baseball caps sooner. :)

@MikeTaylor True. :D

Marc Verhaegen, Putte, Belgium
New Scientist 2782 p 69 Lastword 16 October 2010

Why do humans evolve external noses that don’t seem to serve any
  useful purpose – our smelling sensors are inside the head. Our nose is
  vulnerable to damage, and the majority of primates and other mammals
  manage with relatively flat faces. Traditional explanations are that
  the nose protects against dry air, hot air, cold air, dusty air,
  whatever air, but most savannah mammals have no external noses, and
  polar animals such as arctic foxes or hares tend to evolve shorter
  extremities including flatter noses (Allen’s Rule), not larger as the
  Neanderthal protruding nose.
The answer isn’t so difficult if we simply consider humans like other
  mammals.
An external nose is seen in elephant seals, hooded seals, tapirs,
  elephants, swine and, among primates, in the mangrove-dwelling
  proboscis monkeys. Various, often mutually compatible functions, have
  been proposed, such as sexual display (in male hooded and elephant
  seals or proboscis monkeys), manipulation of food (in elephants,
  tapirs and swine), a snorkel (elephants, proboscis monkeys) and as a
  nose-closing aid during diving (in most of these animals). These
  mammals spend a lot of time at the margins of land and water. Possible
  functions of an external nose in creatures evolving into aquatic ones
  are obvious and match those listed above in many cases. They can
  initially act as a nose closure, a snorkel, to keep water out, to dig
  in wet soil for food, and so on. Afterwards, these external noses can
  also become co-opted for other functions, such as sexual display
  (visual as well as auditory) in hooded and elephant seals and
  proboscis monkeys.
But what does this have to do with human evolution?
The earliest known Homo fossils outside Africa – such as those at
  Mojokerto in Java and Dmanisi in Georgia – are about 1.8 million years
  old. The easiest way for them to have spread to other continents, and
  to islands such as Java, is along the coasts, and from there inland
  along rivers. During the glacial periods of the Pleistocene – the ice
  age cycles that ran from about 1.8 million to 12,000 years ago – most
  coasts were about 100 metres below the present-day sea level, so we
  don’t know whether or when Homo populations lived there. But coasts
  and riversides are full of shellfish and other foods that are easily
  collected and digested by smart, handy and tool-using “apes”, and are
  rich in potential brain-boosting nutrients such as docosahexaenoic
  acid (DHA).
If Pleistocene Homo spread along the coasts, beachcombing, wading and
  diving for seafoods as Polynesian islanders still do, this could
  explain why Homo erectus evolved larger brains (aided by DHA) and
  larger noses (because of their part-time diving). This littoral
  intermezzo could help to explain not only why we like to have our
  holidays at tropical beaches, eating shrimps and coconuts, but also
  why we became fat and furless bipeds with long legs, large brains and
  big noses.

Copying and editing an entire swath of an article is discouraged - please try to answer a question by using your own words and try to synthesize something from multiple sources. -1

As well as the concern over copy-pasting, this seems to be a support of the long-debunked "aquatic ape" hypothesis, coming from a source (New Scientist) that is notorious for its unsupported and over-hyped claims.

Ive found that the study of this feature, the nose is far from complete.Although we see the evolution of other mammals and their faces has a great deal to do with there ability to survive different enviornments I believe it , our snozz is a genetic mutation in which allows us the ability to go from nonaquatic to aquatic with out needing a snorkel. ?.by defying why we have this thing on our face......some so large some so small I dont believe to have much to do with ancestial deviation of the jaw but the defying feature of the human race.....thank you

Could you point to the source please.

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Heterozygosity and the Wright-Fisher model
I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory which I am interested in.
He defines heterozygosity as the probability that two copies of an allele are the same. In theorem 1.3, he derives the expected value of heterozygousity, but what he seems to derive is the expected value of the probability that two allelles have a common ancestor. This does not seem to be the same as heterozygosity to me. Am I missing something here?

The following borrows from Gillespie, J.H., 1998. Population Genetics: A Concise Guide. The Johns Hopkins University Press. It is a good concise guide, and reduces to some extent the mathematics.
Theorem 1.3 is used to show the decay of heterozygosity in a population due to genetic drift.
Consider alleles in a population.  Two alleles drawn at random can differ by state, meaning they have two different DNA sequences. In other words, they are different alleles. Or the randomly drawn can have the same state, meaning they are the same allele. For alleles that are identical by state, they could differ by origin, meaning they are the same allele from two different chromosomes. The two alleles in a homozygous individual differ by origin (sampled from maternal and paternal homologs) but are identical by state.  Or, two identical alleles could differ by descent, meaning they are the same because they trace ultimately back to a common ancestor.
To calculate heterozygosity, you can first account for homozygosity, the frequencies of alleles that are identical by state. First consider two alleles identical by origin.  If you draw two alleles identical by origin when t=1, the probability that the two alleles are copies of same original allele (from the same chromosome) is
$$\frac{1}{2N}$$
because there was only a single copy of that allele on that one chromosome in the population prior to the round of mating, so it is 1 out of the 2N alleles at time point 0 ($t=0$).  The probability that two alleles identical by state are not identical by origin then is
$$1-\frac{1}{2N}.$$
Therefore, total homozygosity ($G'$) in the population (identical by state) after one round of random mating is
$$G' = \frac{1}{2N} + (1-\frac{1}{2N})G,$$
where $G$ is the homozygosity prior to the round of mating.  Of course, anything not homozygous is heterozygous. So, heterozyosity ($H$) is simply,
$$H=1-G.$$
By substituting the formula for $G$ into the above equation, the equation for $H$ becomes,
$$H' = 1-G' = (1-\frac{1}{2N})H$$
where $H$ is the heterozygosity prior to the round of mating.  This formula represents the change in heterozygosity after one round of random mating.  This can now be expanded for several rounds of random mating. For example, the change from $t=0$ to $t=1$ is
$$H_1 = (1-\frac{1}{2N})H_0.$$
The change from $t=1$ to $t=2$ is,
$$H_2 = (1-\frac{1}{2N})H_1$$
Therefore, the change in heterozygosity from $t=0$ to $t=2$ is
$$H_2 = (1-\frac{1}{2N})^2H_0.$$
This can be expanded to any time $t$ with the equation,
$$H_t = (1-\frac{1}{2N})^tH_0,$$
which you will recognize as Durrett's Theorem 1.3.
In short, in the Wright-Fisher model, two alleles that have a common ancestor are by definition identical by state and so cannot contribute to heterozygosity.
I hope this helps. I was a bit rushed and have not explained this often (mostly to myself in my mind) so if I can clarify something, please let me know.

Thank you for the brilliant answer. I think you have one typo though. Just above the second equation, I think it should be the probability of two alleles do not have the same origin is 1- 1/2N, rather than the probability of two alleles with the same state having different origins.

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Why Did 6 Great Ape Species Survive But Only 1 Hominid Species?
My dad asked this question when I explained some circumstances surrounding Homo sapiens survival against all odds.
We know there is only one hominid species left in the world, Homo sapiens. We also know that there are only 6 other species of great apes left: 2 species of chimpanzees, 2 species of gorillas, and 2 species of orangutans. These 7 species are the last remaining in the family Hominidae.
All the other hominids besides Homo sapiens died out tens of thousands of years ago, and we believe the reason our ancestors survived is because we were more "adaptable", meaning we were not restricted to a single environment but could survive in many others. This is the reason we later spread out all over the world, and probably why we gained "sapience" and are able to contemplate these grim circumstances.
At one point, following the eruption of the Toba volcano 70,000 years ago, there were between 1,000 and 10,000 mating pairs of Homo sapiens left, though there may have been other hominid species alive at the time. My dad asked, if the hominids faced such grueling environments and all but a few died, why did the great apes fare any better? Why are there 6 extant non-human Hominidae species left, but only 1 hominid species?

Good question and a great answer below. I think that there are a couple of issues with the question, however: 1) apples and oranges comparison - a monophyletic group (Homo) with a paraphyletic group ('all of the other great apes besides Homo'). 2) taxonomic / taphonomic bias - less effort is put into finding and naming extinct non-human great ape species, and because of their habitats, they also just might not fossilize very well (apparently the first chimpanzee fossil was only discovered in 2005!)

My dad actually asked it when I explained some of this to him. I'm open to suggestions of how to explain it better here and may make an attempt when I get time from work this week/end. Wait, are you saying the first chimp fossil ever found was found in 2005? That's strangely late.

Determining why one species (or group of species survived) while others did not can be difficult to answer, but I can offer one possible explanation for the genus Homo: competition. Competition between similar species is one possibility. Consider for example gorillas or chimps. The two species of gorillas occupy different habitats so they rarely compete with each other for resources (food, water, shelter, etc.). The two species of chimpanzees have non-overlapping ranges (or minimally so) so again they do not compete for resources.
Chimps and gorillas do overlap with each other for parts of their range and even potentially use the same resources, although no competition for resources has been observed (see this primate factsheet and McNeilage 2001). The same applies for the orangutans, which lives on two different southeast Asian islands.
The genus Homo is an entirely different story. As you may know, Homo first evolved in east central Africa. The first species to leave Africa and disperse across Europe and Asia was Homo erectus. This migration out of Africa happened as early as aout 1.8 million years ago. Homo sapiens had not yet evolved. However, while H. erectus was establishing itself across Europe and Asia, populations still in Africa continued to evolve.
Modern Homo sapiens evolved in central Africa perhaps about 250-200,000 years ago and dispersed out of Africa about 100,000 years ago. Homo sapiens also dispersed across Europe and Asia. Both H. erectus and H. sapiens co-occurred across parts of their range. Some have argued (Stringer and Andrews, among others, I believe but I'll have to be at work before I can verify ths reference) that H. sapiens outcompeted H. erectus, leading to its eventual extinction by competition. They occurred together and used the same resources, so H. sapiens could have caused the extinction of H. erectus. This has been called the replacement hypothesis. The later evolving species (H. sapiens) replaced the earlier evolving H. erectus.
However, Templeton (2002) has argued that the two species interbred so the species became integrated rather replaced (if I am interpreting him correctly).  While I don't dispute the possibility of interbreeding, I am skeptical of Templeton's complete dismissal of replacement.
Complicating the picture is H. neanderthalensis. Genetic evidence published by Green et al. (2010) suggests that Neanderthals diverged from H. sapiens (in central Africa) between 800,000-500,000 years ago and also dispersed out of Africa.  They also provided evidence of interbreeding between H. sapiens and H. neanderthalensis in Europe.  Modern H. sapiens may also have outcompeted H. neanderthals.
All of this was occurring during the Pleistocene ice age. Europe was experiencing repeated bouts of extensive glaciation. Thus, it is also possible that climate change caused or contributed to the extinction of H. erectus, H. neanderthalensis, or both.
In summary, the processes that led to the extinction of other species of Homo are complex and likey interactive. Competetion among species is, in my view, well within the realm of possibility but would be extremely difficult (if not impossible) to test. Climate change is also a very likely contributing factor. There are several other hypotheses but I have tried to hit the major highlights.  The debate is certainly not settled.
McNeilage A. 2001. Diet and habitat use of two mountain gorilla groups in contrasting habitats in the Virungas. In: Robbins MM, Sicotte P, Stewart KJ, editors. Mountain gorillas: three decades of research at Karisoke. Cambridge (England): Cambridge University Press. p 265


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Did spiders respond to light for building webs before artificial light was invented?
I have noticed that during summer, beautiful spider colonies grow wherever a strong light is:

I'm wonder whether spiders evolved to seek naturally lighted areas where they build nests (before artificial lights) or if they always had the ability to seek places full of juicy insects - and in cities this ability just leads them to lights.

Here's a null hypothesis based on perception bias: perhaps spiders build their webs all over, but they're a lot easier for us humans to see when they're built next to lights. Consider, for instance, the days when the dew and light is just right and suddenly the forest seems to be full of spider webs – they were there all along, but just harder to perceive. I'm not saying your observation is wrong, necessarily, just offering a null to compare your observations against.

Well, the webs are here when it's day too - still the concentration is around lights. You can see the lights being all dirty because of them.

New Answer, following discussion in comments below.
Spiders are capable of choosing habitats based on the specific requirements of the species (reviewed by Riechert and Gillepsie 1986). Spiders move within and among suitable habitat for a number of reasons, including damage to existing webs, and life history changes that require new habitat types. They point out that spiders are probably choosing the proper habitat based on various cues from the habitat. How the spiders respond to the cues would have been shaped by natural selection. The specific cues used will vary among the different species of spiders but may include wind speed and direction, thermal regime (which affects dehydation foraging time), odor cues, density of competing spiders, and more. The many options are reviewed by Riechert and Gillepsie, which is freely available and not too filled with technical jargon.
Many species of spiders do select their habitat based on prey availability. Gillespie (1987)  lists a number of references. She also studied the long-jawed orb weaving spider, which lives along streams and rivers.  She found that this spider tends to build nests in open areas near water, which prevented dehydration, but the exact site chosen was determined by prey availability. Enders (1973) studied a different orb-weaving species. He found that the juveniles were most often in densely vegetation areas but that the adults were in more open areas at the edges of woods. He suggested that web site selection of adults is driven by light.
Heiling (1999) performed an interesting study on a nocturnal orb-web spider. The spider lives near the water so it will sometimes build its orb webs on the bridges crossing the water. She found that more spiders build their webs near the lights on one particular bridge compared to unlit parts of the bridge that were otherwise built the same. She found that there was more insect activity around the lighted area (no surprise there) and that the spiders that built near the lights caught more of those insects compared to the spiders that built away from the lights.
Perhaps the most interesting result is when she studied the behavior of these spiders in the lab. Spiders that were born and raised in the lab preferentially went to the artificial light source. These had never before been exposed to the artificial lights. She argued that the light-seeking ability of the orb-web spiders she studied is genetic.
These studies suggest that light may have functioned as a visual cue for web location long before humans lit up the night sky with house and street lights, at least for spiders that build webs in open areas. Spiders may identify open areas by light cues (lighter vs darker), perhaps along with other cues such as air movement and humidity. Lighter areas would presumably be more open and thus favorable to large numbers of flying insects. Natural selection would favor spiders that responded to light for web construction. Artificial lights may present a very strong visual cue that attracts spiders, as well as insects.
However, other cues such as olfactory cues (mentioned by Riechert and Gillepsie 1986) may attract spiders. If insect prey are found in high abundance in open areas or near artificial lights, then you would expect higher concentrations of chemical odors emitted by the insects, thus drawing more spiders.
Clearly, more studies similar to that of Heiling (1999) but across a broader range of web-building spiders are necessary to determine whether many web-building spiders are responding to light and if the response is genetically determined.
Citations
Enders, F. 1973. Selection of habitat by the spider Argiope aurantia Lucas (Araneidae). American Midland Naturalist 90: 47-55.
Gillepsie, R.G. 1987. The mechanism of habitat selection in the long-jawed orb-weaving spider Tetragnatha elongata (Araneae, Tetragnathidae). Journal of Arachnology 15: 81-90.
Heiling, A.M. 1999. Why do noctural orb-web spiders (Araneidae) search for light? Behavioral and Ecological Sociobiology 46: 43-49.
Riechert, S.E. and R.G. Gillespie. 1986. Habitat choice and utilization in web-building spiders. In: Spiders: Webs, Behavior, and Evolution (W.A. Shear, ed). Stanford University Press, California, USA.
Legacy answer
Spiders evolved long before street lights were invented. The oldest known spider fossil dates back to between 374-380 million years ago (Coddington and Levi 1991.  Street lighting of any type only goes back a few centuries. So, spiders were spinning webs long before humans evolved, and before we humans began lighting our streets and homes at night.
The spiders are simply taking advantage of the situation. The lights draw insects, the food for the spiders. Webs constructed near light sources may catch more insects than webs constructed away from lights.  Could this affect the current or future evolution of spiders? Perhaps. The spiders that build webs near the lights may get more food, which allows them to obtain more energy, and potentially produce more offspring. This would increase their fitness relative to spiders that do not build webs near lights, which could lead to evolutionary change occurring over the next several thousands of years. However, it may be that so many insects flying around the web end up damaging the web much more often than the spiders away from the lights, so the spiders near the light expend much more energy maintaining the web and removing insects they don't eat.  This is one extremely hypothetical example (of many; see comments) to illustrate the point. We can't actually predict what evolutionary changes might occur, or even if they will occur.
Some of the hypotheses stated in the comments below could be tested to determine whether natural selection is possibly occurring on spider species that build near lights, or if the observation is simply observation bias as noted by @Oreotrephes.

Do you think we can assume no bias in our observation (the potential bias is: we see the webs that are held in the lights much better than the others)?

Assuming no bias, do you think that 1) spiders construct their webs where there is a source of heat because they have evolved in order to construct their webs in these places (as warm temperature attract insects) (you seemed to say no but I am not sure) 2) spiders construct their webs all over but those that are poorly located die 3) spiders construct their webs all over but when they starve they move 4) spiders observe spots of high insect concentration before constructing their web. All of these explanations would explain why there are more webs in the light.

@Remi.b I made no assumptions. I took the question solely at face value. You and Oreotrephes are correct about the potential for visual bias. My hypothetical example was based on spiders building near lights because insects are attracted to light. Your hypotheses are testable but I'm skeptical about whether spiders can scout out spots of high concentration in advance of web building. It's also possible some spider species are themselves attracted to light but benefit from the insect concentration.

Oh my... I didn't ask why spiders build webs near lights! It's damn obvious. I was only curious if they can find a place where flyer insects appear or if their instincts have changed to seek lights automatically - because they're definitely going to attract flying insects.

@TomášZato I misunderstood. Evolution is mentioned in the question and question title. It's still not clear to me what you mean by changed. Do you mean changed due to natural selection?  Changed since when? I wasn't trying to answer why* spiders build near lights. That was just a hypothetical example. I can tell from you question that you understand spiders are feeding on insects. I think we had a miscommunication. :) Perhaps you could edit and clarify your question?

Yeah, I think it's a problem for me to write this question properly in english. I'll try to clarify with another comment and after that I'll take my time rethinking the question. I was asking, whether spiders evolved (due to the natural selection) to seek lights where they build nests or if they always (that means before artificial lights) had the ability to seek places full of juicy insects - and in cities this ability just leads them to ligts. I know, it's almost no difference, but it interests me and I don't know how to find the answer myself.

@TomášZato OK, I think I understand your question. I'll begin working on a new answer.

@TomášZato I've updated my answer to hopefully match the question you were actually asking. I also edited your question somewhat, using part of what you wrote in a comment above. If you don't like my edit or want to use your own changes, you can still edit your question and undo my changes.


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What do you see when your eyes are closed?
If you are in pitch black and you close your eyes, you sometimes can see strange shapes of various colors. A lot of the time these shapes and colors change as you observe them. This phenomenon still occurs if you are not in complete darkness.
I am wondering what this is that you are `seeing'? Is this phenomenon classified as seeing, as how can we be looking at something if our eyes are closed?
If you are not seeing these shapes and colors, then what you observe is pure darkness. What is this pure darkness that you are seeing? Since you are seeing it, is something stimulating the vision parts of your brain? Is it the back of your eyelid?

I'm not asking about floaters, although I have always wondered what those were.

I retracted my vote.

Floaters are different. That's due to collagen fibers in the vitreous "gunk" of the eye interrupting light transmission to the retina (shadowing, basically). Because this requires light hitting the retina, it's not in the category I described below. If you want more info, ask another question (although that one is eminently google-able).

OK, I'm having a huge moment of confusion here... "sometimes" see strange shapes of various colors when you close your eyes ? Don't we always see such patterns (we just don't usually pay attention to them) when we close our eyes or have I just discovered I'm weird ?

This is called a phosphene — the experience of perceiving light in the visual cortex without light actually entering the eye. This commonly happens due to stimulation of the retinal ganglion cells by something else. The most frequent source in normal individuals is pressure to the retina (e.g. rubbing a closed eye.) It is also possible for phosphenes to occur due to neuronal stimulation at the cortical level. Most people have had the experience of “seeing stars” when you stand up too quickly. This happens because orthostatic hypotension results in transiently decreased cerebral perfusion; it is the metabolic shift in oxygenation and/or glucose delivery to cortical neurons that causes the perception of light. Something similar occurs with brief rises in intracranial pressure that occurs with sneezing or coughing.* Magnetic stimuli can also induce this phenomenon.
Phosphenes can also be pathologic (i.e. disease-associated). Migraine headache sufferers may experience a visual “aura” prior to a headache, which is a type of phosphene, likely mediated at the cortical level. There is some evidence to suggest that preventing the phosphene may also reduce headache frequency. Other conditions associated with phosphenes include abnormalities of the optic nerve** and retina — just as stimulation of a peripheral somatic sensory nerve might cause a pain signal to arrive in the brain in the absence of true tactile stimulation, disorders of the optic nerve can generate disorganized signals that the brain perceives as light.

*Increased intracranial pressure leads to decreased perfusion due to the differential between peripheral and cerebral pressures.

**If you read nothing else linked to this question, take a look at that paper (free in PMC). It describes optic neuropathy associated with auditory-evoked phosphenes. The patients perceived sound as light!

Thank you for the great answer. So in layman terms, is it correct to say that the same part of the brain that is activated when your eyes are open gets activated, in some way, when your eyes are closed. This part of the brain being activated is what causes you to 'see' those strange objects?

@JonHerman You got it! The visual cortex in the occipital lobe.

Interesting article on auditory-evoked phosphenes.  I've personally experienced unexpected loud sounds as flashes of light for years (though without any other associated visual issues like the subjects in the paper.)  I do have an epileptic focus in my temporal lobe, however, which perhaps is interacting with the LGN somehow, causing a similar symptom via a different mechanism.  In any case, fascinating read.

I just got another question. If there is nothing stimulating the visual cortex, but you put your attention on what you're seeing, you see pure darkness. What is this pure darkness, it has to be something because I can see it. Is it the back of the eyelid or something like that?

This phenomenon is also known as Prisoner's Cinema

@CoreyOgburn - good point. The pathologic form in optic neuropathy is at least in part due to de-afferentation (lack of normal incoming signals). I suppose the prolonged absence of any environmental light can have something like the same effect.

Retinal implants generate electrically evoked spots of light also called phosphenes. Some of them rely on light entering the eye, such as the alpha-IMS. Hence your definition of phosphene may not be entirely appropriate. Nitpicky. Great answer +1


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Europe: big fly with black/yellow striped body: I'm guessing a horse fly?
This one made a summer night visit to the room and tried to escape by banging against the ceiling. What is it? I found nothing which corresponds, though "horse fly" might be a close match.

Location: Central Europe, Luxembourg
Locality: Where the suburb morphs into the not-yet-conquered countryside
Time: Late August, Nighttime
Weather: Quite warm (~27°C). Dry.

Here is an MP4 of the beast: https://i.imgur.com/F5yqMQ8.mp4
It is about 2 cm (0.8 inch) large. Relatively plump, keels over and likes to clean itself a lot.

Large head, large eyes, a bit hairy, two black stripes

Once it falls on its back it wallows a bit, there is clearly a probabilistic algorithm to get itself out of the predicament:

@BryanKrause Thanks Bryan. I have added some info. And a link to an MP4

Its not a horsefly (Tabanidae), but rather, a flower fly (Syrphidae). I don't know what species.

At first, because of the size and shape, I thought that it was a horsefly, but no horsefly looks like that (at least not in Luxembourg). It turns out that it was a hoverfly, just as Karl Kjer said. The species is Volucella zonaria, or the hornet mimic hoverfly. This hoverfly lives in most of Europe (including Luxembourg) and is 15-25 mm in length, consistent with your 20 mm estimate.
In this image you can see the same coloration and abdominal markings as your insect.

The markings in your photo are very difficult to see but are there.

Wikipedia page
original image source

Thanks. I had forgotten about that question. Good id.

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


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Microarray probe and target
In a microarray, which one is called a target and which one is the probe? the one that is added later , is that the probe or the one present in the slots of the microarray, that is the probe?
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if the question seems to silly, forgive me)

The probes are immobilized on the microtitre plate and the labelled targets are hybridized to them.

In an RNA microarray, a hybridization event between a probe and target sequence would indicate a presence of the transcript within the sample. The probes are oligonucleotide sequences found on the microarray chip. The target sequences are representative of the entire transcriptome. The targets are found within your biological sample and have gone through many rounds of amplification in addition to labeling with fluorescent dyes. The fluorescently labeled target when bound to the probe can then be detected using a scanning laser.


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peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip.
  In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a surface, and population of T cells is incubated with the microarray. The T cell spots act as artificial antigen-presenting cells containing a defined MHC-restricted peptides. The advantage of using peptide–MHC is that it can map MHC-restricted T cell epitope."

These few lines are from Chapter 3 of Immunoinformatics, De, Rajat K., Tomar, Namrata (Eds.).
What is recombinant peptide MHC? What is MHC restricted peptide? How did the advantage get derived?

you might need to clarify what you are struggling with here

The entire paragraph. What is MHC peptide complex?  What is MHC restricted peptide?

Have you tried Google searches? You've already asked similar questions to this before, did you learn anything from those answers? I highly recommend obtaining a good introductory immunology textbook and reading it.

@MattDMo completely agree about reading good immunology books. But I doubt peptide:MHCs are covered in any general immunology book.

@ddiez they were in mine...

Please refer me a good immunology textbook

@MattDMo yes peptide:MHCs are covered, sorry. I meant to say peptide:MHC microarrays, which is the question asked by the OP.

@user3237995 what about Janeway's immunobiology?

According to this paper (Yoav Soen et al. PLoS Biology 2003), peptide:MHC microarrays are a type of cellular microarray (a microarray designed to identify cell types; Wikipedia). These microarrays have attached a MHC molecule bound to a peptide, which allows them to work as artificial antigen presenting cells (APCs) that activate specific subpopulations of T cells.
Another recent paper is here where they specifically use the word recombinant peptide:MHC.
The expression MHC restricted refers to the positive selection (in the thymus) of T cells that recognize MHC molecules of the host but not other self-antigens (Wikipedia).

T cells grows in thymus. So what does "in the thymus of T-cells" mean??

@user3237995 sorry about that sentence, not very clear. I added some parenthesis that hopefully improve readability. Let me know if it is still unclear.

This is an important topic in immunology, especially for vaccine development.
MHC or HLA is a molecule expressed by some cells of the immune system which acts like a "catcher's mitt" and "presents" short snippets of protein to other immune cells. Other molecules act alongside MHC to provide co-signals which promote or suppress immune attack against the peptides that MHC presents.
Basically, it's a protein that holds out chunks of other proteins in order to educate the rest of the immune system. Here's the catch: different people have different genes for MHC which do a better or worse job of presenting certain peptides. This is one reason why different people can respond to different vaccines or different pathogens or cancers: they have different MHCs which may or may not present peptides from the relevant targets.
Thus, one big challenge in medicine right now is to develop good models for which peptides are best to include in a vaccine. The right answer depends on the genetics of the vaccine target (ebola, a tumor, e. coli etc) and also on the genetics of the person being vaccinated (does this person's MHC gene properly present this vaccine?)
So, to datafy this, people sometimes make arrays which allow us to quantify which peptides bind to which MHC genes in high throughput. Then we can use that data to learn which factors are most important for P:MHC binding. "MHC restricted" means that we are talking about a specific genetic subtype of these molecules.
Hope that helps.
Bion Alex Howard


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Difference between sequential and conformational epitope
Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

Yes, the difference is "only" in the 3D structure. This makes some differences when proteins change their shape; antibodies which recognize conformational epitopes are usually not well suited for lab work, as proteins are often denatured here.
The different epitopes are also called linear epitopes (for the sequential) and discontinous epitope (for the conformational). Schematically this look like this:

Nice diagram. Where did you get it from ?

From a book: Immunology for Medical Students.


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In the notch signaling pathway, what is Fringe activating?
Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330

I want to know what is Fringe activating. It is not pointing to another gene or protein, it is pointing to an interaction. What does that mean?

Usually, in such depictions where a species is pointing to a reaction or an interaction, the arrows mean that the species affects that reaction (for example, catalysis by an enzyme ). Generally pointy arrow heads denote positive effect (enhancing the reaction, for example an enzyme) and flat heads denote a negative interaction (repression). An arrow from one molecule to another can be used to depict a conversion (like glucose converting to glucose 6 phosphate).
There are no real standards on how to depict a pathway. So, it can be confusing.
In this case, Fringe actually alters Notch signalling (see below). So the arrow makes sense. However, the figure also has an arrow from Delta to Notch which can be interpreted as Delta getting converted to Notch. They also show an arrow from Notch to NICD which actually means a conversion. I would say that the depictions in this figure are inconsistent.
From NCBI Gene entry on Human homolog of Fringe, LFNG:

This gene is a member of the glycosyltransferase 31 gene family.
  Members of this gene family, which also includes the MFNG (GeneID:
  4242) and RFNG (GeneID: 5986) genes, encode evolutionarily conserved
  glycosyltransferases that act in the Notch signaling pathway to define
  boundaries during embryonic development. While their genomic structure
  is distinct from other glycosyltransferases, these proteins have a
  fucose-specific beta-1,3-N-acetylglucosaminyltransferase activity that
  leads to elongation of O-linked fucose residues on Notch, which alters
  Notch signaling. The protein encoded by this gene is predicted to be a
  single-pass type II Golgi membrane protein but it may also be secreted
  and proteolytically processed like the related proteins in mouse and
  Drosophila (PMID: 9187150). Mutations in this gene have been
  associated with autosomal recessive spondylocostal dysostosis 3.
  [provided by RefSeq, May 2018]

From Shao et al (2002):

Recent studies have demonstrated that O-fucose modifications play an
  essential role in Notch function. Reduction of O-fucosyltransferase
  expression in Drosophila using RNAi (11) or in mice by gene ablation2
  causes Notch-like phenotypes, suggesting that O-fucose modifications
  are essential for Notch function. In addition, we and others have
  shown that Notch activation is modulated by extension of O-fucose on
  Notch with the fucose-specific β1,3-N-acetylglucosaminyltransferase
  Fringe (for recent reviews, see Refs. 12 and 13). Fringe was first
  identified in Drosophila and shown to inhibit Notch's ability to
  respond to Serrate but to potentiate its ability to respond to Delta
  (14). Three Drosophila Fringe homologues have been identified in
  mammals: Lunatic fringe (Lfng), Manic fringe (Mfng), and Radical
  fringe (Rfng) (15). The β1,3-N-acetylglucosaminyltransferase activity
  of Fringe proteins is essential for their biological activity in
  Drosophila (16-18) and in cell-based Notch signaling assays (19), and
  the O-fucose residues are required for Fringe to modulate Notch
  activity (16, 19). Thus, Fringe mediates its effects on Notch
  signaling by the addition of GlcNAc to O-fucose moieties. Nonetheless,
  neither the specific role ofO-fucose in Notch function nor the
  mechanism of how a change in sugar structure alters Notch function is
  known.


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Rules of motif forming
I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead to a particular 3D motif? Are there any such rules? If so, any resources that you can provide me with?

For example, beta-hairpin. What should be the sequence of amino acids or helix/sheet that would result in the formation of beta-hairpin motif?

A motif is a pattern that you discover in a structure by analysis. For example, common sequence motifs are short sequence fragments with parts similar to a regular expression. So, if you have a motif like "A*C" this matches to the sequences "AAC" and "ACC" but not to "ACA". You can reverse the process to discover the motif from the sequences.
Similarly with structural motifs in proteins. A beta-hairpin is :

The motif consists of two strands that are adjacent in primary
  structure, oriented in an antiparallel direction ... and linked by a
  short loop of two to five amino acids.

So first you have to determine where the strands and loops are, then how the strands are connected into sheets, and finally recognise the hairpins. It is the definition of the motif itself that determines how you discover it.
Some resources that might be helpful are:

Motivated proteins (Small h-bonded motifs)
The protein topology graph library (Larger motifs)
The protein geometry database (Not really motifs, but interesting)
PDBeMotif (define and search for motifs in the PDB)

How do I derive from PDB where the strands and loops are and how the strands are connected into sheets?

@Rishika That's a big topic. There are tools out there to do this, DSSP for example. In addition, the PDB file often has secondary structure information provided by the authors. Or you could even just view it in a structure viewer, which will generally show you the strands and loops. Jmol has a DSSP implemention. It depends what you want to do, exactly.


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Degenerate Alignment Analysis
Can someone please tell me what is Degenerate alignment analysis? Could not find a good article on the internet that could help me understand what it means?
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

This would be much easier to answer if you gave us some more context. Presumably you are referring to sequence alignments but where did you read the term? What was it referring to?

First, degeneracy in a basic sense refers to redundancy of the codons in the genetic code.  For example, the amino acid proline is coded for by one of four codons: CCA, CCC, CCG and CCU. The third codon position (the third letter in each group of three) is called four-fold degenerate because it can change without affecting the coding for proline. Phenylalanine is two-fold degenerate because it is coded for by UUC and UUU.
However, this does not account for the alignment part of your question. Without more specific information (such as a reference you saw), I can't be certain of your intent but this paper by Morin et al. (2008) may be helpful. They had a series of small RNA sequences (each about 24 nucleotides long). They wanted to identify DNA sequences in the genome of Lodgepole pine  (Pinus contorta) and rice (Oryiza sativa). To accomplish this goal, they used degeneracy alignment. Here's the relevant section from their methods:

altered to allow searches against genomic sequence. Alignments were kept if they were no shorter than L − 3, where L is the query sequence length. No more than a total of three mismatches or insertions/deletions were allowed within the aligned region.

Their approach was to find genomic sequences that correspond to the small RNAs. They allowed for some degeneracy, either in the genome or the RNA. The sequences could differ in length by no than three nucleotides or mismatches (an A in the query sequence but a C in the target sequence instead of a T; I'm assuming the query is RNA and the target is the genomic DNA). Their degeneracy alignment allowed for a small amount of freedom in identifying potential matches of conserved RNA clusters (high similarity) in the genomes of distantly related plant species.

Morin, R.D. et al. 2008. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Research 18: 571-584.

so basically its like finding common sub sequences even with a few alterations , right??

@user3237995 Yes, basically that is it. Alignments can be found even though some mutations have occurred between the two different species.

Ok Ok, clearly understood!!


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Biological significance of correlation between the radius of gyration and number of layers of convex hull of protein structure
While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, I came to know that there is a correlation between the radius of gyration and the number of layers of convex hull of each proteins 3D structure (convex hull layers are formed by forming the convex hull of a set of points, which forms the first layer, then removing them, and recalculating another set of boundary points, i.i., second convex hull, which form the second layer).
Now my questions is, what is the biological significance of this correlation? Or is there any?

What is a 'layer' of a convex hull? As far as I know, there is just one hull layer (the minimal bounding surface containing all the points)

Never mind I'm guessing that you can nest hulls by removing the points on the outer hull and re-calculating. Still worth describing this in your question, I think

@gilleain I have edited the question. Hope you can understand it now...

From reading the paper, I don't see any obvious biological significance. The abstract says:

Proteins exhibit intriguing diversity in their three-dimensional conformations that enables them to perform different functions

Which is great, but there is no connection in this paper between conformation and function - not surprisingly as this is a large part of structural protein analysis!
The way I look at this work is similar to the idea of a "descriptor" from the field of Cheminformatics. The radius of gyration is a descriptor, and so is this hull number. The author claims a correlation between these two descriptors, so... is one easier to calculate than the other?
This is interesting work, but I'm not sure at this point what the significance of hull number is for protein structural analysis. However I can say that the correlation between these two descriptors is not biologically significant - it's just a geometric relationship that would presumably hold for any set of 3D points.


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What is the significance of cysteine in a protein sequence?
What is the importance of cysteine-cysteine in amino acid sequence? What can I infer if I get a high percentage of C from a protein sequence?

What can I infer if I get a high percentage of C from a protein
  sequence?

A highly stable structure that is likely found in the extra-cellular space.

Cysteine can form a disulphide bond with another cysteine. Cysteine can be found as a lone cysteine, but is often paired with another cysteine in the tertiary structure to form these bonds.
Disulphide bonds play important roles in protein folding and stability (60 kcal/mol compared to around 1 and 5 kcal/mol for a hydrogen bond depeneding on the environment). Notably though, cysteine disulphide bonds are usually only used in extracellular secreted proteins, as they are unstable in the cytoplasm.
As an example, take the structure 2ksk. Look at how the structure is held together by cysteines that are distant in the sequence. If you see cysteines in a sequence, expect interesting folding!
The cartoon is going from blue to red, whilst cysteines are shown with sticks and the S-S bonds are in yellow.

Side note, they are annotated as SSBOND in the PDB.

Cysteine is one of the two sulfur containing amino acids, but far more important than the other (methionine) due to its reactive sulfydryl or thiol group (-S-H). The said sulfydryl group cannot be substituted or replaced by any other amino acid. Importance of these groups lie  on the fact that they involve in the formation of disulfide bonds, the most significant cross linkage in tertiary and quatenary structure of proteins. methionine being more hydrophobic than cysteine and sterically large, acts less reactively and does not participate in disulfide formation.
Cysteine can be easily oxidized (oxidative folding) to form cystine (two cysteine bound by disulfide linkage) via interchain and intra chain bonding. The bonding is covalent and adds stability to the overall protein structure as compared to H bonding (Energy disulfide bond - 60 kcal/mol, H bond - 1-5 kcal/mol depending on the environment). Therefore, energy required to break disulfide bonds are way too high than other covalent bonds. Therefore, higher the number of disulfide bonds a protein has, higher the stability of it.


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Which server to use for volume and accessible surface area calculation of proteins
I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving me different volume and surface area measures as follows:
3vee (vol: 50951 A^3; Surface area: 10837 A^2)
Vadar(vol: 40937.8 A^3; Surface area: 14680.6 A^2)
Can anyone tell me which server to use, which server is more accurate? If you know of any other server giving accurate result, please let me know that too.

Note: Both the publications are from Nucleic Acids Research, I guess I do not need to validate them. 3vee has been published in 2010 with citation of 164 and Vadar was published in 2003 with citations of 416. Is it okay if I take 3vee since it is the latest tool?

How big is the protein/complex? Can you download something like UCSF Chimera or Pymol and calculate it yourself to see if it agrees with either of those numbers? You may also want to check that the surface calculation parameters in both programs are using a similar probe radius. I'd guess from the fact that Vadar has a smaller volume but greater surface area, that it's probe diameter is smaller.

how does pymol calculate a volume ? cannot find any reference , I can generate volume objects but no way to get their value

You can use PDBSum and PDBe-PISA servers for calculating accessible surface area and buried surface area and Castp server for finding pockets within your protein molecule. If your protein is globular, you can measure the diameter in pymol and calculate its volume. Hope it helps.

can you add some references and/or links so that others who are less familiar with your answer and the question can follow along? it would definitely strengthen your answer

The results depend on the atomic radii and on the probe radii.
Without them, it is impossible to have an opinion about the volumes and surfaces values.
Using C=1.75, N=1.55, O=1.4, S=1.8, and adding 1.4 for the probe, running the Monte-Carlo method interactively available in ASV outputs for 10000000 random points (only ATOM records were input):
V = 57335.548996 +/- 1.96*34.439 ;
S = 14887.818374 +/- 1.96*20.345
You can download ASV from:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ;
No installation procedure is required, just flag the binary as executable with the chmod command.
Monte-Carlo f77 source routines are supplied too.
References:
M. Petitjean, J. Comput. Chem. 1994, 15[5], 507-523;
M. Petitjean, Spheres Unions and Intersections and Some of their Applications in Molecular Modeling. In: Distance Geometry: Theory, Methods, and Applications, chap.4, pp.61-83, Springer, 2013.


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Factors on which one compound transforming to another compound depend
Considering the Metabolic Pathway:
http://www.genome.jp/kegg-bin/show_module?M00166
Consider the reaction R01523(the very first reaction). How is it possible to know that the compound  C00199(D-Ribulose 5-phosphate) will get transformed to C01182(D-Ribulose 1,5-bisphosphate)? What are the factors on which this transformation depends?One factor I know is structure but how does structure effect this transformation? Does two similar structured compound means that one of the compound can get transformed to the other one?

From my answer on chemistry:
After looking at the website I found the reaction is based off of an enzyme called: phosphoribulokinase. In biological systems many reactions occur under the auspice of enzymes or proteins. These are incredibly large molecules made of an extremely long chain of amino acids which are a set of 26 or so small molecules that can 'hook' into the chain structure of a protein. Each amino acid has different properties and thus experiences different forces pulling it towards and away from other amino acids on the chain. What this means is the whole chain folds up into an extremely complex structure. For a protein to allow a reaction to occur it has a small region that the reacting molecule can hook into. There are then sets of atoms and molecules that act as scaffolds that allow atoms in the reacting molecule to be moved without the need for nearly as much energy as would be required without the scaffold. Now this is how it changes structure. Now whilst the protein can just as easily allow the molecule produced to be converted back to the original, this may be less energetically favourable which brings us to equilibrium chemistry involving dynamic forward and backward reactions. What makes this more complicated is that proteins often have separate 'hooks' for molecules to disable them. That is if a lot of substance A is around then the protein will be disabled and no longer convert B into A until more A is consumed and thus stops inhibiting the protein.


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What is the meaning and significance of extreme pathways
Can someone please explain me what extreme pathways are? I found this definition in this article:

Extreme pathways are a unique and minimal set of vectors that
  completely characterize the steady-state capabilities of genome-scale
  metabolic networks.

Now, frankly speaking, I did not understand the head or tail of this definition? What is steady state? What does it mean by steady state capabilities? Can someone please explain me in a simpler way?
PS: I am a computer Science student

For any dynamic system defined by different components, the steady state is the state of the system in which the components remain constant over time. If you consider the example of growth (by cell division) the point at which the total number of cells remain constant would be the steady state. This is a point at which birth rate = death rate. Similarly for a multi-component system such as a gene and its activator, the steady state would be the point where the mRNAs and the proteins of the gene and its activator are constant. If only few components are constant then the system is said to be in a quasi-steady state.
A point to be noted that in chemical (or biochemical) systems steady state, as a term, is different from equilibrium (in physics these terms are used interchangeably). Equilibrium is a condition when, for a single reversible reaction, the forward rate = backward rate.
In mathematical terms steady state is a point where the rate of change of components = 0. In an ordinary differential equations based model:
$$\frac{d\bar{X}}{dt}=0 \\$$
where $\bar{X}$ is a vector in which each element is a component of the system. In case of the transcription example, $X(1),X(2)..$ would be mRNA, protein, activator mRNA and so on. In other words $\dfrac{dX(i)}{dt}=0$ for all $i$.
Steady state capabilities should mean the properties of the system at its steady state.
The kind of study described in the question is called metabolic flux balance analysis in which different metabolic reactions are described in the form of linear equations represented by $Sv=0$ where $v$ is the vector of all fluxes (metabolic reaction rates) $S$ is the stoichiometry matrix (which has the stoichiometry of all components in different metabolic reactions). The RHS is zero because we are evaluating the system at its steady state i.e. we are interested in finding out the condition in which the net metabolic reaction flux is 0. In other words all metabolic reactions, balance each other.
You need to read more about this. There are a lot of books on this topic. You can start with this review.
In flux balance analysis, the linear equations are overdetermined i.e. there are many solutions. People generally use linear programming (simplex algorithm) to find optimal solutions. In the space of the optimal solutions, the vertices represent extreme reactions. The entire optimal solution space can be described as a linear combination of these extreme reactions.

Schematic representation of a convex cone characterized by five
  extreme pathways. Extreme Pathways 1–5 (EP1, EP2, EP3, EP4, and EP5)
  circumscribe the solution space for the three fluxes indicated (vA,
  vB, vC). EP4 lies in the plane formed by fluxes vA and vB.
  Consequently, flux vC does not participate in that extreme pathway.
  EP3, EP4, and EP5 are all close and represent different uses of a
  network to achieve a similar overall result. All points within the
  convex cone can be described as a non-negative linear combination of
  the extreme pathways [1].

What is RHS? The RHS is zero

@aaaaaa in S.v=0 the zero represents no net flux.


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Rate of production of enzymes in human
In the metabolic pathways, each of the reaction needs an enzyme(protein) in order to occur successfully. Is there any quantitative measure that can be associated to this enzyme? Like synthesis rate of enzyme, degradation rate, mRNA transcription rate, enzyme activity, amount of enzyme present per unit measure of protein in the cell and if there is rate of generation of the enzyme's product, the rate of production of this enzyme in the human body, etc? I wanted to know the list of features that can quantify enzyme activity in the cell.

Your question is very unclear. There are plenty of quantitative measures when looking at a particular protein - synthesis rate vs. degradation rate, mRNA transcription rate, enzyme activity, amount of enzyme present per unit measure of protein in the cell, rate of generation of the enzyme's product, and on and on and on. Please [edit] your question and explain exactly what you're doing and what kind of data you're looking for. This is definitely an XY problem.

@MattDMo edited the question. Is it clearer now?

This is very broad. Measures of abundance and synthesis rate of enzymes (and other proteins) can be found in proteomics work such as the paper mentioned by @tsttst below. Measurement of enzyme activity is completely different, and is often studied using isotope-labeled metabolites in a technique known as metabolic flux analysis, see for example http://msb.embopress.org/content/2/1/62.abstract  Both are large, active research fields.

Your question already answers a fundamental point: namely that there are several distinct quantitative measures that can be associated with enzymes (the list could also be extended, and you will discover more in biochemical textbooks...).
If experimentally or theoretically accessible, one additional important quantity is the formation of product over time divided by biomass ( e.g.: Jacob et Monod 1961)

I wanted to know all those points and how they are calculated...

Note that the more direct quantitative measures usually require enzyme-specific experimental assays (and measuring the activity within cells usually is even one step up - and something that has only been achieved for very few enzymes). If you want to look at quantitative measures, which can be measured well for most enzymes (and quantities that can be estimated reasonably well by models based on those measures), you could find them (for some cell lines and growth conditions) in Schwannäusser et al. 2011 http://www.nature.com/nature/journal/v473/n7347/full/nature10098.html


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How to find PDB id of an amino acid sequence
Suppose I have an amino acid sequence whose PDB id  is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence?  is there any site that will find the pdb of a protein closest to the query protein?

One way of doing this is to run a protein BLAST search at NCBI in which you specify the Protein Data Bank as your database, as in the example shown below:

The results will be all for proteins in the PDB.

You can also search for amino acid sequences directly at the PDB repository.


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Is there any non-pathogenic gram negative bacteria?
In the category of Gram-negative bacteria, is there any non-pathogenic species? Is such a list of non-pathogenic gram-negative bacteria's available? Can you give maximum 5 examples of such bacteria which has been proved to be non-pathogenic and is gram-negative?

Well, most of them are not pathogenic. It would be quite a long list.

As Canadianer already mentioned in the comments, the majority of bacteria (this includes gram-negative bacteria) are non-pathogenic.
I think a prime example is the human gut flora. You can find loads of bacterial species living in your gut without doing you any harm, if anything they are doing you a favour by breaking down food.
Here some examples of gram-negative genera:

Bacteroides
Escherichia

Most species within those genera are non-pathogenic, however, there are exceptions.

So bacteroides vulgatus is gram-negative and non-pathogenic?

It would appear so.. Here is a study (http://jb.asm.org/content/193/15/4025.full) that refers to Bacteroides vulgatus as one of "the most commonly isolated microbes from the human gastrointestinal tract, and it has been found to constitute part of the core gut microbiota in healthy humans".

I should add, however, that infections may have been reported for said organism. This happens when they grow in environments where they shouldn't be growing. The questions of pathogenicity isn't always as black and white as we would like it to be. Generally, Bacteroides vulgatus is considered commensal.


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Query regarding calculation of survival analysis
According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for the 7th column for the 2nd row is 0.052((square root of 0.003)*0.950=0.052) but in the tutorial it is given 0.049. Am I making any mistake with the calculation?
Many of the values in the table does not match with the calculations given.

"0.003" is rounded up; the exact value is 1/380, which is 0.00263157894... (and some more decimal places).
If you calculate the table entries to a few more decimal places, you get 0.04873397172 (and so on), which rounds up to 0.049.


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What does the term 'epitope mapping' mean?
Epitope mapping means identifying the binding site of antibodies on the target antigen. This means that the site to be identified is part of the antigen and not antibody, am I right?

yes.. you are right. Why the confusion :)

No, just wanted to make sure, actually I am reading immunoinformatics for my phd, and hence i should have crystal clear idea about the things i study. So thats y asked this question. It is not homework. its discussion

i know it is not a "homework" homework.. by homework we mean something that can easily be looked up.

yes,, things can be looked up, but sometimes understanding is a bit difficult more so becoz i havnt touched biology in the past 7 years


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Coordinates of amino acids in a protein sequence
In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL... Where would I get the coordinates of M and K and L separately? Is there any method by which the coordinates of the amino acids can be calculated? I don't want the coordinates of the atoms, I want the absolute coordinate of each of the amino acid in a protein sequence as a whole...

It depends what you want them for. You could take an average of all the atomistic co-ordinates of each residue, you could take the co-ordinates of only the carbon in C-R. It's unclear what you're asking for. Are you asking for a sensible method, an available tool, or are you more broadly wondering what constitutes the center of an amino acid conceptually?

Each atom is annotated in the PDB-file in terms of which aminoacid it belongs to - is this what you are interested in? It might be useful if you would clarify your question, as I think that we are trying to guess at the moment what you actually want to know.

@Gerhard now is the question clear?

Are you saying that you want the 3D-structure of an individual amino acid?  I assume so,  as you have accepted the corresponding answer.

How is this question unclear? To me it's pretty clear that she wants the "pivot point" or "origin" of each individual amino acid on the chain (most likely along with its orientation in space), as if the amino-acid was a single molecule as a whole, not subdivided into particular atoms.

If what you are after are the structural co-ordinates of particular  amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should find them along with other small molecules in the Cambridge Structural Database.

Another way of approaching this problem is to focus on the middle carbon atom between the H2N- from one side and -COO from the other side that make peptide bonds with adjacent amino-acids. This middle carbon has the rest of the amino-acid molecule attached to it, and it's definitely on the chain, so you can use that atom's center as the "pivot point" for the entire amino-acid; perhaps even calculate its orientation in space relative to the chain by looking at the bonds connecting this atom with its neighbors. That would be my answer if the question wasn't blocked ;q

It may not make a lot of sense to consider one amino acid as an indicator of the position of the entire amino acid as different amino acids vary a lot in size. For non-sensitive applications such as plotting the protein backbone you may use the alpha Carbon. If side chains are important you can use what is known as the last heavy atom (What is the last heavy atom of an amino acid?).


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What does high CD4 level means?
I was going through this webpage and I found the following lines:

We hypothesised that despite unimodal distribution of CD4 co-receptor on naïve CD4 T cells they are not homogenous in their function.By testing naïve CD4 population from mice and humans expressing highest and lowest (~10%) levels of CD4 in a variety of functional assays we find that indeed naïve CD4 cells with high CD4 levels respond much better to activation and survive more easily post-activation.

Now what does "CD4 level" means? How is the CD4 receptors distribution obtained? With repect to the value of which feature is it obtained?(If you are not able to understand the last question, let me know, I will try to explain more in details)

In this case, I would email the corresponding author of the article and request that they provide you with a definition of what High means. A scientific text should not use vague qualitative descriptions like that. They should provide you with at the very least a range of what they classify as high, low, and normal expression of CD4 receptors.

and what does just CD4 level mean??

The number of CD4 co receptors on a CD4 T-Cell... when the T-Cell Receptor binds to MHC II the interaction is stabilized by the CD4 coreceptor. It binds to the side of the MHC II receptor on the Antigen Presenting Cell and greatly increases the efficiency of binding. I thought with the second question that you understood that CD4 refers to plasma membrane receptors on the surface of helper T-Cells.

okay okay, it is my fault actually, i was not able to frame it properly

@AMR it looks like the answer is in the question - "high" and "low" were defined as the 10% on either side of the curve...

@MattDMo The problem is that they do not defining what that 10% refers to. Are they talking about the top and bottom ten percent of cells that have been FACS sorted for CD4 receptor levels or is it like you suggested +/- 10% range above and below the mean that differs the highest number of receptors on a T-cell surface to the lowest numbers. I initially thought that Rishika understood what they meant by CD4 levels and suggested the author contact to clarify, but I think that their question was more basic, that CD4 was referring to the corecptor in the plasma membrane.


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Query regarding KEGG KGML pathway files
With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form:

  entry1="46" entry2="41" type="PPrel"
  subtype name="inhibition" value="--|"/
  subtype name="phosphorylation" value="+p"/

In some entries, the reaction "subtype" entries are 2 in number while in some, it is one, as for the above-mentioned interaction. Another entry is as follows:

   entry1="47" entry2="46" type="PPrel"
      subtype name="phosphorylation"
    value="+p"/   relation

Why do some of the entries have 2 interaction types while some have one? What does this signify biologically?
There is an interaction type called "compound". What does a compound interaction signify biologically?

  <relation entry1="17" entry2="16" type="PPrel">
    <subtype name="compound" value="4"/>
    </relation>

have you looked at this description?

@DanHall yes but they have not explained why one entry can have 2 subtypes or how 2 genes are contributing to the formation of a compound...

See the manual:
PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother.
For the first and second example, the subtype(s) give more information about the interaction. They aren't necessarily mutually exclusive. For example, phosphorylation can result in activation, inhibition, something else, or unknown. For the first one, there is phosphorylation and the effect is inhibition.  For the second one, the interaction is phosphorylation but the effect is not characterized.
When compound is under subtype for a PPrel relation, the value is the entry element ID for the compound (so go look for entry element 4), and it refers to an intermediate of two interacting proteins.

Why can't the first one be " it is inhibition and the effect is phosphorylation"?

@girl101 that just happens to be the causal pathway --  phosphorylation of a protein causes inhibition (in some cases... in other cases it is activation).


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How to correlate survival probability to gene expression profile?
I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how exactly is the clinical data and the gene expression data merged?
For example, I have a matrix of clinical data (m by n) where there are m patients and n columns related to followup days, death days etc. I also have an gene expression data (m by t) where m is the number of patients and t is the genes. I first find the survival probability using Kaplan Meier method and plot it. Now how do I related the survival probability to the expression data?

As described in the link, you classify your samples into altered/not altered or high/low expressing (for your gene) by using Z scores (e.g. +/- 1.96) or a median cut-off, respectively. Now that you have a column that gives the expression status of the gene of interest, you can plot the survival for both conditions. The R code is in your link, and you can find how to do the same analysis with Graphpad Prism here: https://www.graphpad.com/support/faqid/1747/

@srao so you mean say out of 500 patients 200 patients will have high expression and 300 will have low, so the survival probability for high expression would involve only the patients having high expression and not those patient having low expression?

Yes, survival probability will be calculated separately for each group, that's how I understand it. In a more complicated example, you could have 4 groups (say 1 group for each quartile of gene expression). There are quite a few papers out there that have done this with TCGA data.

@srao true but how exactly it is done is not mentioned. papers mainly concentrate on results and what is done. detailed description is needed for first timers...


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Do non-pathogenic organism not have PAMPs? Are there any research paper which proves that a certain microbe is non-pathogenic?
According to this

PAMPs are delivered along with additional information that can be
  used by the host to distinguish pathogenic from nonpathogenic
  microbes and thereby guide the ensuing innate immune
  response.

Does this statement mean that non-pathogenic bacteria do not have PAMPs? If yes, then how would the host body differentiate between a pathogenic and a non-pathogenic microbe? Is there any well-known source containing a list of non-pathogenic microbes? Are there any research paper which proves that a certain microbe is non-pathogenic?

https://en.wikipedia.org/wiki/Pathogen-associated_molecular_pattern#MAMP


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How much time does it take for the naive T Cell to get activated?
Suppose a naive T cell comes in contact with an APC. How much time does it take for the T Cell to get activated and within how much time does the T cell move away from the APC due to incompatibility in their receptor structure? What is the probability that there will be activation of a naive T cell by an APC (I mean to ask that how many T cells should come in contact with APC before a T cell gets activated, some number like say 1 out of every 1000 t cell gets activated by an APC at a particular time)? Any resource you can provide that gives a quantitative value of the interaction of T cell with APC, please do if possible.

Do you have any way to access Wiley Online articles? http://onlinelibrary.wiley.com/doi/10.1016/j.febslet.2010.10.010/abstract


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What is the step by step procedure that leads the T cell to release chemokines?
When T cell receptors bind to the receptor of an antigen presenting cell, is this what leads to the release of chemokines? I know that T cell release of chemokines leads to the migration of other T cells to the area of infection. What is the step by step procedure that leads to this release of chemokines from a T cell?


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From a hosts point of view, which comes first, effect of toxins on pathways or identification of toxins by immune system?
From a pure biology perspective, when a pathogen (gram-negative bacteria) affects a host by secreting toxins, what comes first, the effect of the toxin on the pathways or identification of the toxin by the immune system? A generalized overview would be very helpful.

That really depends on the toxin: Some of them are toxic in so low doses that they are never recognised by the immune system (like Tetanus toxin). So it would be good if you could clarify the question towards a specific toxin.

@Chris I have edited the question. Does that help?


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What is a secretion target family protein?
I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398
What is this protein, is it a secreted effector protein or is it something else?
What is the difference between type VII secretion protein (https://www.genome.jp/dbget-bin/www_bget?sams:NI36_12950) and type VII secretion effector (https://www.genome.jp/dbget-bin/www_bget?bmyo:BG05_3891)?

Have you followed up the links you get from an internet search for type VII secretion? I know nothing about the topic, which sounds quite specialized, but reckon I could hack it in a quarter of an hour. Or is the problem journal access?

@David yes I have tried to find the difference between the two types of proteins but could not find any proper explanation....


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Does a bird know it's different?
I live in Northern Virginia, USA. As I am sitting here there is a large flock of small (blackish) birds in a tree. They are quite prevalent here. For the sake of brevity I will call these birds "sparrows." I don't believe it matters what they really are.
There are also several medium-sized blackish birds perched on the eaves of the townhouses. Again, I'll call these birds "crows". (We have a committee of large vultures (yes, really) in the neighborhood as well, which is why I call the crows medium-sized.)
The crows (tend to) lay their eggs in the sparrow's nests. Little crow hatchlings are then "raised by" the sparrow parents, along side thier smaller "siblings".
Does the now adult crow think it's just an oversized sparrow? (IOW, do all of the crows I see have identity issues and feelings of inadequacy due to their extreme gigantism? :) )

Any answer that attempts to directly answer this question would be conjecture.

Could this be not opinion-based if OP says instead: What phenomenon or phenomena does this most resemble?

Crows don't lay their eggs in sparrows' nests - they lay them in crows' nests. What you're describing, though, here is brood parasitism. This relieves the parasitic parent of the responsibility of rearing young, building nests, protecting the eggs, etc.
Brood parasitism is seen in a number of duck species, with females laying their eggs in the nests of others. One example is the goldeneye, Bucephala clangula. Interspecific brood-parasites include the most cuckoos and cowbirds, black-headed ducks, and indigobirds, whydahs, and honeyguides. About 1% of all known bird species are obligate brood parasites (never make nests, need a host).
Here is a picture of a reed warbler feeding a cuckoo which was a parasite, its egg having been laid in the warbler's nest.
Parasite nestlings suffer a relatively high mortality, either from rejection by the host (host bird will not feed the parasite) or rejection before fledgling (once nestling graduates to tree branch, the hosts stop feeding it). However, clearly since cowbirds and cuckoos are still alive and well, enough of them do survive.

Do they think they are of the host species? There was no literature I could find on this. While the parasite messes up the host parents and 'siblings' (when there are surviving 'siblings'), there is much less follow-up done on the behavior of the parasite once fledged. Common sense will therefore need to come into play.
If a cowbird thought it was an indigo bunting, it would not be able to reproduce, as it would try to attract a bunting mate and fail. Since the hosts continue to experience parasitism over many generations, and the population of parasites does not necessarily decline in a given area over several generations (in some areas, it is the host population that declines), I would have to say, yes, the bird 'knows' it's different (probably only on an instinctual - not cognitive - level); the parasite bird feels nothing about its bad behavior, and does not learn their own behavior from their host parents. Instinct takes over; they mate with their own kind, and continue to parasitize the host birds' nests.
Brood parasite
Host–parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird
Brood parasitism by cowbirds: risks and effects on reproductive success and survival in indigo bunting
Brood parasite

When the baby cuckoo comes out of the egg, the first thing s/he does is that s/he pushes the legitimate egg(s) out of the nest! This means that the cuckoo instinctly knows that s/he is different.


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Can microdialysis be made in Drosophila melanogaster?
I've asked this before in stack overflow's cognitive science community, and someone recommended me to ask here:
I've found a couple of studies using microdialysis on insects, but didn't found any in Drosophila. I've found that the membrane diameter are from 240um, and it seems that Drosophila melanogaster brain must be between 200-300um , but I was wondering if the lack of studies of perfused drugs in Drosophila is due to this technical constraint, or is just I'm searching wrongly.
--
Edit: I specified the original target, Drosophila melanogaster, since there are bigger parients like Hawaian D. heteroneura and D. cyrtoloma. that could be subject to MD with current probes.

This is a great question! I was not aware microdialysis was used in Drosophila since most use feeding (compounds dissolved in Drosophila food) to administer different drugs to Drosophila. Is the microdialysis used on the adult Drosophila or larvae? why not inject the larvae?

@Bez , I didn't find microdialysis use in Drosophila but I thought that maybe it could be made on heteroneura and cyrtoloma since they are bigger, that's what I meant to say :P sorry for the missleading comment.

It seems highly unlikely to me. The smallest microdialysis probes I've ever seen are about 250 µm in diameter, so about the size of a Drosophila hemisphere. You can deliver drugs by microinjection (well, I assume you can, seeing as a) you can do it in honey bees and b) you can perform whole-cell patch clamp recordings in Drosophila).


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Identification of this insect
These insects lived inside the wood of my bed in little round holes. They bite, lеаving very itchy red marks. And when crushed stink really bad. In the picture the lines are notebook lines for size comparison.
   I live in Eastern Europe, so I don't think they are fire ants, if they are ants at all.
Any suggestions would be appreciated!

About how large is it? It looks like you took that picture on a piece of lined notebook paper, but that still can't tell us the exact size of the insect. How many millimeters are between the lines of your paper?

The lines are 8mm appart

If the lines are 8mm apart, the ant is about 2.3mm, making this consistent with pharoah ants and ghost ants.

OP states "I live in Eastern Europe, so I don't think they are fire ants". However, Myrmica rubra, the European fire ant, can be found in Eastern Europe. See https://www.antwiki.org/wiki/Myrmica_rubra and https://species.nbnatlas.org/species/NBNSYS0000009343

This looks like an ant, but I cannot say which species. Their small size, colour, bite and being found indoors made me think of Pharaoh ants (Monomorium pharaonis), but I haven't heard that they smell bad. Ghost ants (Tapinoma melanocephalum) are rather similar and have a foul smell when crushed, and have been found indoors in Europe. They usually have a dark head/thorax and lighter abdomen though. They can also be separated from Pharaoh ants by having a one segmented petiole (the Pharaoh ant has two). A closely related species to the Ghost ant is Tapinoma sessile, which also smells but has a uniform colour (usually darker than your specimen though, see picture at bugguide.net). The petiole not being clearly seen in your specimen points towards the two latter species, or other species with a short/hidden petiole (see hidden petiole at antkey.org). However, these are only a couple of suggestions, and there are probably many other possible species.
Termites have larger mandibles (jaws) relative to their size, and no distinct narrow division between thorax and abdomen (your specimen does). Your animal also has eyes (termites don't) and I think you can spot a long first antenna segment, which ants have (hard to see in the picture though).

Good call on the eyes. I had to zoom in quite a bit to finally see them but they are there.  I think I agree more with your answer than mine.

I have attached couple more pictures. I believe it also has a stinger. (Sorry about the quality, but due to the size of the insect and using a magnifying glass and a cell phone I couldn't make better shots)

While there are some wingless hymenoptera species that can resemble ants, I feel pretty certain that this is an ant. I'm not specialized in ants and cannot determine the species. It might be difficult to get a species determination from these pictures, but you should be able to get a genus from an ant expert. Another option could be Tapinoma sessile, which is closely related to the Ghost ant, also smells, but with a uniform colour (usually darker than your specimen though).

The size of this ant is about 2.3mm, consistent with pharaoh ants.

I can't tell you the species but it appears to be a termite. The Australian Museum explains some of the differences between termites and ants. Termites have straight antennae. Ants have bent antennae with a distinct elbow.  Your insect has straight antennae without an elbow. Termites have a broad waist. Ants have a very narrow waist. Your insect appears to have a broader waist. You also find more at The University of Florida. I'm not an entomologist and I do not live in Eastern Europe so consider my answer with a degree of caution.  If you have a pest control company nearby, you can take the specimen to them for verification, in case it is a termite species capable of home damage.