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How to induce a steady increase in cyctoplasmic [Ca2+] in HEK293T cells? And is there any simple marker/method to confirm it?
We are trying to find out whether increase or decrease of cytoplasmic calcium concentration affects the interaction of two proteins, using co-IP in HEK293T cells as a readout.
In different forums and papers I have found that to increase cytoplasmic Ca2+ levels in non-exciteable cells, there are three major categories of compounds. Ionophores (A23187, Ionomycin), Agonists of InsP3-PKC signalling (carbachol, ATP) and SERCA inhibitors(Thapsigargin, CPA).
However, different papers and different people on use  different concentrations and durations of treatments. Since a lot of the drugs generate rather transient spikes, I realize that the timing is crucial here. Since, we do not have the resources for the optimisation of [Ca2+]-sensing dye imaging, I am also wondering whether there is a simpler way of roughly assessing [Ca2+], perhaps by by analyzing a marker protein/RNA using Western Blot or qPCR?
Thanks a lot!

As far as I know, microscopy (be it with dyes like fluor or with genome-encoded calcium indicators) is really your only good bet, especially for getting quantitative sensitivity, which I think is what you're looking for. Changes in cytosolic calcium are incredibly dynamic both in time and space, which is something to consider when asking how calcium affects your two proteins.
I do know of an example where investigators transferred cells to buffers with different Ca2+ concentrations and permeablized them with a mild detergent to raise calcium levels (Borges-Pereira et al 2015). I'm not sure if that would work for your system, but it's worth taking a look, as I think it raises the levels pretty gently and steadily, and you have a better idea of what your intracellular concentration is going to be without directly visualizing it. Considering you won't be able to tell the Ca2+ concentration at any given time without microscopy, things like SOCE and intracellular chelation rates might be important, so you'll want to watch out for when after treatment you start your assay, perhaps trying a few different time points
Hope that was of some help!


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Are dominance hierarchies always maintained through violence?
Is there a species in which a dominance contest cannot escalate to a fight? I don't know of any but I'm not a biologist.

I too cannot think of any such species. I think dominance is simply based on "if you are a better alpha male, then defeat me" rather than "if you are a better alpha male, then be more patient than me" ;)

source: Stack Exchange

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

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How does the snail shells' fertilizer compare to regular fertilizers?
May I ask about the quality of the fertilizer derived from the shells and their effectiveness compared to other fertilizers on the market ?

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


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Does our brain contain an innate function about closing only one eye?
I wasn't sure where to post this, but biology seemed fitting for me. Sorry if I'm wrong.
I was wondering why, when we close both our eyes and look at light, it is clear we can see the light even though our eyes are closed. We can identify where the light is too.
However, when you look at the light with only one eye closed, suddenly you cannot perceive this anymore and you can only focus on the open eye's vision. It's like our brain is ignoring the closed eye's vision somehow. What is triggering this "ignore vision"? Is it the closing of the eye?
I found this intriguing and wondered how this works and/or if there is any research about it.

Look up "Ocular dominance"

I'm only a 17 years old student but i guess this is the answer(its just what i guess, haven't seen it in any books or research):

This is a picture from the book Life.
When both eyes are working they send signals to brain.
signals from things on the left side are sent to right side of brain and signals from things on the right side are sent to left side of brain(coming from both eyes).
as you can see both eyes participate in sending signals to right and left hemisphere.
On the right side of picture you can see visual cortex of right hemisphere , it has signals coming from both left and right and makes the thing we see.
While seeing through only one eye (or when you cut optic nerve from one eye) there is still signals coming to visual cortex from the other eye and that makes image of what you see.(when you close one eye there is still little signal from it if you are facing a bright light source, but signal from the other eye has more effect as its more powerful( try it by closing one of your eyes and put a torch in front of only the closed eye, if the torch is bright enough you can see bright thing there))
when you close both eyes the signals coming from both eyes are almost the same and if you face a bright thing, you almost see it.
i just guess that's the mechanism :)

That's a nice explanation! But there is one thing I'm confused about. So, when closing only one eye: the optic nerve is cut from the closed eye? But when closing both eyes, the optic nerve of both eyes are open? Because when both eyes are closed, you can still "see" the light. But when only one eye is closed, you cannot.

no its not cut from the closed eye, i just meant it is like cutting it, when you close the eye, the signals coming from it become weaker and less as if there is no eye. its like comparing these numbers:1-both eyes open:10000-10000     2-one eye open:10000-10(0 if the nerve is cut)   3-both closed: 10-10  10000 is soo big compared to 10 so brain somehow omits 10.


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From DNA to final traits of microorganisms?
From the answer of this topic, could someone indicate me a book or article about how DNA set the phenotype of microorganisms? For example, showing how DNA changes the shape of such a cell or how DNA sets the concentration of a such mineral inside the cytoplasm.


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how do we prevent restriction enzyme of bacteria to cut and destroy our new recombinant?
Based on cloning principle, the new DNA recombinant will be introduced to host cells, commonly bacteria, how do we prevent restriction enzyme of bacteria to cut and destroy our new recombinant ?

I have a few questions: What do you mean by "cloning principle"? What is a "DNA recombinant" for you, a plasmid?

You're essentially looking for a restriction modification system. You modify the restriction sites with methyl groups in a way that blocks restriction enzymes from accessing them. The DNA methylation should also be maintained through replication. So if you have an EcoRI site, you can use an EcoRI methylase to block the action of EcoRI.


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Why we shiver/tremble/shake while performing some work which requires high accuracy?
Shivering when nervous or anxious is a common thing.
But, shivering or trembling sometimes also occurs when we are performing a work which requires high accuracy. In such case, our whole body doesn't shivers but a part (usually hand) which is involved with that work shivers. The most common example is threading a needle. It requires great accuracy and you might have noticed that when you are doing so, your hands are continuously shaking which prevents you from accomplishing that task flawlessly. Even when we aren't in a state of nervousness, our hands tremble. It's un-resistable.
Yet another quick example - Try to stretch your one arm and try to keep it straight (have it loose, don't try to force it straight), you might notice that your arm is actually shaking a little bit. You can't hold it exactly straight without moving even a little bit.
It's also noticeable when we try to pin-point a small spot with our hand(finger) without actually touching it. (that finger and the hand as a whole starts trembling)
So, what's the reason? It isn't anxiousness as we shiver even when we are calm.
Perhaps, it's gravity which is pulling our hand down and we are trying to lift it continuously which creates a imbalance? But, then we should shiver always?

If you thread needles often - like a dozen times a day for many days - you will eventually be steady as a rock, because practice improves the process (you will also unconsciously maneuver to steady both hands.) It's not inevitable that all people have involuntary muscle movements with very fine motor skills; it's a matter of ability/practice for most.
The steadying of larger muscle groups like the upper arms - especially against gravity - is less controllable (e.g. threading a needle with arms fully extended), but not even closely outside the realm of possibility. Think of what great athletes, dancers, craftsmen are able to do that is "impossible" for mere mortals.

..and what surgeons can do! +1

@Christiaan - D'oh! Great example!

A trivial example : applying an eyeliner flawlessly :P

Norepinephrine (noradrenalin) is a neurotransmitter and hormone released by the body in situations which, among other things, require focus. This may (partially) explain the shaking hands when focusing.

"The general function of norepinephrine is to mobilize the brain and
  body for action. Norepinephrine release is lowest during sleep, rises
  during wakefulness, and reaches much higher levels during situations
  of stress or danger, in the so-called fight-or-flight response. In the
  brain, norepinephrine increases arousal and alertness, promotes
  vigilance, enhances formation and retrieval of memory, and focuses
  attention; it also increases restlessness and anxiety."

The shaking occurs because the body is increasing burning of energy.  There's not many good links online for this (unsurprisingly google searches of "noradrenalin shaking hands" pretty much only returns 'medical' websites trying to tell people they have a brain tumor), but I think what happens is the muscles twitch as a result of the excess energy release.

"When you suffer from anxiety, your body rushes with adrenaline - a hormone that gives your body a tremendous amount of energy, which - when unused - leads to physical agitation. That causes your hands and legs to shake, often visibly."

Beta-blockers are known to reduce symptoms of noradrenalin and are frequently (if questionably and irresponsibly) used to treat anxiety. We may shake less when we practice a process multiple times possibly because with practice anxiety associated with such tasks (I imagine a surgeon is quite nervous the first time they open up a patient) and the level of focus required (intricate tasks become easier with practice thus requiring less focus) both reduce, therefore reducing the amount of focus-related and anxiety-related physiological changes.

While I would certainly agree that doing fine motor activity under intense focus might be stressful (and cause cortisol and norepinephrine release), intensively focused individuals - as @Christiaan mentioned - can perform fine-motor actions without trembling. While I'm not impressed with his political views, Ben Carson was amazing in the operating theater. Intense focus doesn't necessarily cause norepinephrine release, and inability to perform fine-motor actions smoothly is more likely a muscle control issue overcome with practice. Examples are innumerable.

It's (I believe) more related to neuroplasticity, for example demonstrated by the ability of stroke patients in regaining gross and then fine motor function with intensive therapy. Practice.

Perhaps as one gets more practiced they need less intensive focus and becomes less stressful - I know from my own lab work at the start I needed to focus a lot, now I can do it with my eyes closed! Practice makes most things much easier, thus requiring less intense focus (and meaning less noradrenaline release)

I considered that as well. I think it's likely a combination of stress and ability in differing ratios under different circumstances. :)

@anongoodnurse and rg255 , both of your answers were pretty well written and answer my question to a satisfactory extent but both of you are holding slightly different reasons as the cause. Which one should I consider as the actual cause? Ability to control muscle movement or Norepinephrine release? or perhaps both of them? It's hard to decide the correct answer for me :P


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Small non-coding RNA (sRNA) vs. micro RNA (miRNA)?
What are the differences between micro RNAs (miRNA) and small non-coding RNAs (sRNA)? Are these two terms used interchangeably?

miRNA are one member of the small non-coding RNA family.
"Small non-coding" is a pretty broad term that encompasses microRNA and short interfering RNA, among other regulatory RNA species. The key word is 'regulatory'; each type of small non-coding RNA works by binding complementary sequences to exert some sort of regulatory control over gene expression. Someone more knowledgable might correct or add to this, but I believe that a key difference between the various types of regulatory RNA hinges on which other factors they recruit to their site of action.
Structural differences between these RNA are a little harder to characterize. This paper, for instance, discusses how miRNA have been found to play contradictory roles in gene regulation; repressing some genes, up-regulating others. The precise mechanisms behind this are an active topic of investigation, but a lot seems to depend, as I mentioned earlier, on which other proteins they recruit and this in turn, seems to be influenced by things like cell type and developmental stage, among others. Here's another paper , that goes into some of the sequence-based structural features of miRNA. I know that this one is free, but the first one might be behind a paywall. If it is, contact me & I can send you a pdf.
I don't hear the terms used interchangeably, however, at least not in the sense of someone saying "small non-coding RNA" when specifically talking about miRNA.

So sRNA may include miRNA, but not the other way around?

@becko That's right.

Small non-coding RNAs are NOT generally abbreviated as sRNA but as sncRNA, if anything. I say "if anything" because the "small" part is subjective and just a portmanteau descriptor. The straight answer to your question is as Forest has written: miRNAs are a specific type of small non-coding RNA, some of which appear to function in the regulation of gene expression — others remain to be characterized. Another problem with the 'small' epithet is that miRNAs may only be 20 nt in length, but are formed from pre-miRNAs of up to 1000 nt.
Other categories of small non-coding RNAs include:
tRNA (transfer RNA) - originally abbreviated sRNA (for soluble RNA) - involved in protein biosynthesis.
5S rRNA - a component of the ribosome
7SL RNA - a component of the signal recognition particle involved in recognizing the signal peptide of secreted and membrane proteins.
snoRNA (small nucleolar RNA) many of which act as guide RNAs in ribosomal RNA modification.
snRNA (small nuclear RNA) many of which are involved in the splicesome, the ribonucleoprotein complex which removes introns from precursor mRNA (these have names like U1, U6 etc.)
SINE RNA: RNA transcribed from the short interspersed nuclear repeats (SINEs - Alu sequences in humans) which are thought to be 7SL signal recognition particle pseudogenes.
And, no doubt, there are some I (and science) have missed.

Maybe not in general, but I have seen some papers where small non-coding RNA is abbreviated sRNA.

No doubt. But not standard, and not to be encouraged.

@David small-RNAs is a commonly used term and nowadays is more or less becoming standard but the abbreviation as "sRNA" is probably not (in contrast with lncRNA). Generally, "non-coding" is not included in these references. So sRNA when used, would mean small non-coding RNA (sncRNA is hardly ever used). In any case the definition of a small noncoding RNA is also quite loose; RNA <200nt. There are many other inconsistencies too. As of now miRNA in itself is a neatly defined term and any classification would only cause confusion.


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Dehydration Synthesis: Why does a monomer contribute a -H instead of an H atom?
My Campbell's Biology 9th edition textbook says that a dehydration synthesis is a reaction in which water is produced while two monomers are joined together. Specifically, it makes the following statement:

One monomer provides a hydroxyl group (-OH), while the other provides a hydrogen (-H).

Sorry if this is a silly question to ask, but what I'm wondering is how exactly a Hydrogen electron joined with a Hydroxyl will create H2O? Why isn't it a Hydrogen atom (1 proton and 1 electron) rather than just the electron which moves?

The dash ("-") does not represent a negative charge or an electron.  It simply indicates that the group of atoms ( -OH or -H ) are attached (covalently bonded) to other atoms in a molecule.  So they are saying one monomer (molecule) contributes OH to the reaction and the other H.  (A charge is indicated by a trailing superscript minus sign.)

That's what I suspected, thanks for the response and for clarifying!


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Atmospheric gas changes, and their effects life
I was curious how life on Earth, or an Earth-like planet, would be effected by changes in the gases which make up our atmosphere.
Assuming there is a similar level of oxygen in an atmosphere, could other gases be reduced or even replaced and still be able to maintain life as we know it?
Not really biology, but if the following could be kept in mind too that would be amazing:
[To give some context, I would like to ask how a sky could be light blue with a purplish hue, which supports some life larger than what we see on Earth, but still capable of supporting life which we find on Earth.
I am assuming a slightly higher percentage of oxygen is needed, but what other gases which are none lethal, but give a purplish hue?]
Thank you to all who take the time to give an answer, very much appreciated!

This question would be much more on-topic on [worldbuilding.se].

The Earth is blue (at least the non-land mass) because of the light our atmosphere refracts from the sun. A planets color is primarily determined by distance from sun, not from gas components.
Most gas does not refract light. Therefore a planet's gaseous composition can not be identified based on color.
To elaborate on your primary question, gas composition balance is essential to most life on Earth. Carbon dioxide, for instance, is responsible for photosynthesis occurring in plants. Different concentrations will affects photosynthetic rates. Another example is that CO2 levels, CO levels, and hexa-fluoro-carbons affect the amount of heat trapped in this planet.
Gas composition is highly delicate and must stay in balance to preserve life on Earth.


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What is an isolated beta bridge?
DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can somebody please explain what this is in some more detail please? If I google it all that comes up is pretty much the same as what wikipedia gives.

http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2b.html

@rg255 Thanks for the link. This seems to describe beta sheets (which I am familiar with). A quick cntrl+f of "bridge" doesn't return any results? I will have a proper read in the morning if you think it will help.

In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract:
We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.”
It seems from this that they are using the term bridge to mean one hydrogen bond of the type found in a beta-sheet, ladder as two protein strands joined by many hydrogen bonds, and sheets as beta-sheets — more than two protein strands joined by many hydrogen bonds. The term beta-bridge in the DSSP documentation (http://www.cmbi.ru.nl/dssp.html) is presumably equivalent to a bridge in the paper
In the DSSP files residues that are in ladders or beta-sheets are designated E, and B is used for instances where there is a single hydrogen bond. The former are very common, wheres the latter are quite rare — some proteins have none. I have prepared an image of an example for residues 74 and 79 (side-chains omitted for clarity) in a loop in the protein 1PPR.pdb (a light-harvesting protein). The other loop residues 75-78 are designated as T (turn) in the DSSP file, whereas residues 73 and 78 have no structure designation. Hence the hydrogen bond between Ser-74 and Val-79 is an isolated singleton and designated B.

Thanks for this answer David. I agree with you're reasons and I think you're correct. I appreciate you tackling the literature better than I had and the example!

You're welcome. The DSSP nomenclature is not straight-forward and some protein chemists are not too enthusiastic about some of the designations of rarer structures.


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How do major and minor grooves arise in the DNA helix?
I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get how the arrangement of bases really generate the grooves.

@canadianer Though the other question was asked two years from now and 1 year before this but David's answer definitely better explains the concept and since new posts with better answers are often marked as mother questions, I think this should be done with this post too.

"Better" is subjective. The picture in the other answer is crucial to understanding why there are major and minor grooves. Perhaps a moderator can merge the questions.

Sure. Should this be flagged then? @canadianer

Try it. I'm not entirely sure how the merging process works.

First the MAJOR groove. This can be considered by forgetting that the two DNA strands are separate and thinking of them as merged together like a rope or an electric cable in my diagram below. The cable is wrapped around an axis, which can be thought of as an imaginary rod. One could wrap the cable tightly round the axis so it was always in contact with itself and no space in between (as on the extreme left), or one can wrap it round less tightly with space in between (subsequent images). The latter is what happens and the space left by the wrapping of the rope is the major groove (because it's wider than the minor groove we come to next).
So to your question, what causes this winding to be the way it is — which is to say what causes the particular pitch of the DNA helix? This is presumably the most thermodynamically stable conformation, maximizing the strength of the hydrogen bonding between the bases (most linear, not too close or too distant) and minimizes steric and electric replusion (the phosphate backbone is negatively charged).
Next the MINOR groove. We now have to consider that our 'cable' is actually two strands of DNA — a sugar phosphate backbone with the paired bases in the centre. Although the bases are in the centre, the space between the two sugar-phosphate strands is not completely occupied. This creates another groove - the minor groove - less wide and of quite different origin to the major groove, but still able to accomodate certain small proteins. As it happens, this is the case with the electric cable analogy illustrated. The cable is two electric wires, but they are encased in the same plastic inuslator.
So to your question, what causes the minor groove? This is just the three dimensional shape of the DNA double-strand which reflects the molecules that make it up. The large phosphate groups can be considered like wide tubes at either side, whereas the bases between the strands are flat and so lead to a groove, irrespective of whether it is wound into a helix or (in one's imagination) stretched out.
(The 'major' groove is exaggerated in size compared to the 'minor' groove in the cable analogy, but I hope it illustrates the difference between the two.)

Nice explanatory answer with a very good example of an analogy.

@Mesentery — Thanks. This was one of my first contributions to SE Biology, so I suppose I put a bit more effort in than I do now. But I do some of my best thinking in the bath or the shower, and my shaver cord was close at hand ;-)

Nice wire ;). Good illustration!!


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Does RNA serve as the genetic material of some plants and animals along with viruses?
My teacher mentioned that some plants and animals have RNA as genetic material but did not substantiate his statement  with examples. I'm wondering if it is so?
I have searched the internet but have found no such information.

There are no animals or plants with RNA genomes. There was a mistaken belief in the 1920s that plant genetic material was RNA whereas animals had DNA, but this was finally disproved by JN Davidson in the 1940s.


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What is projected to go extinct first?
Though a number of animals have been going extinct at alarmingly quicker rates (so called anthropocene extinction), a number of 'star'  threatened animals are still alive.  Which of the following charismatic endangered species is modeled or expected to die off soonest: polar bear, panda, black rhino, african elephant, mountain gorilla,bengal tiger/ tiger.
Where can I find population projection models for each of these species?
Mountain gorillas  have the current smallest population,  but polar bears are clearly in  a lot of (and quickly widening)  trouble due to melting ice. African elephants are seeing species loss due to poaching,  and drying conditions making food/water scarce,  which could also speed their decline, but they have the largest of the populations.
Since WWF and other conservation organizations use these charismatic species to 'sell' conservation and raise interest, awareness and funding,  losing one (or many) of these species could affect conservation considerably. This will either be positively via a reactionary  disappointment by the public or negatively by losing a "poster species".

Welcome to Biology Stack Exchange. Your question needs some clarification in order to be answerable. The 'species' you have listed are in fact groups of species, each with their own extinction risk. For example, there are five extant species of rhino, of which three are listed as Critically Endangered by the IUCN. The IUCN Red List (http://www.iucnredlist.org/search) may help you to clarify your question.

Need to clarify species (what sort of rhino, elephants etc) and show some research effort (otherwise it's "homework") and the question needs to be leading to far more objective answers (will draw primarily opinion based answers).

@rg255 How's that?

Personally I don't think that's enough, you've just put some extremely rough guess. Get population numbers, trends in population decline/resurgence, show what is causing problems for each species... the fact you don't even know that black rhinos are more abundant than three of those species says you've made no effort whatsoever (it took me about three minutes to find numbers for all of your species).

I understand that black rhinos are not the rarest rhino species. My list is not attempting to be a list of the rarest (as indicated by the inclusion of the African elephant and tiger,  which both are only lasted as endangered with 1000s of individuals), but rather a list of commonly recognized so-called charismatic endangered/threatened species.

Further, I'm fully aware that rough population numbers are readily  attainable via wwf,  Wikipedia, iucn, and dozens of other sites. But again my question is not which is the rarest,  but rather where i can find population projections estimating time of extinction of these charismatic species. The rough guess i added was to show you i am aware of their relative threat level,  but again i didn't go into more detail because their absolute pop size is not important to me. I'm interested in their projected extinction rate/time/outcome

"I understand that black rhinos probably have the current smallest population" - they don't (populations of tigers, mountain gorillas, and giant pandas are smaller). If you make that as a claim then clearly you've not done any research.

To get specific projections for each species you will need to search the primary literature for each species. The best current estimate of extinction risk that is comparable between species will probably be the IUCN Red List classification.

@rg255 just looked at the wrong rhino species when i looked at the numbers. I've corrected.

Black Rhino, status: critically endangered
With around 5000+ black rhinos left in existence, and population numbers seemingly recovering (up from ~2400 in 1995), the black rhino is not really under any immediate threat.* The major threats to black rhinos is poaching (for the rhino horn trade), and, with prices for rhino horn increasing, it looks like it will be a problem for a while to come. Furthermore, corruption, war/civil unrest, easy access to guns, poverty, funding cuts (etc.) contribute to make the battle against poaching more difficult.
African Elephants, status: vulnerable
There are around 470,000 African Elephants left in the wild, and 25-30% of these are the Forest Elephant subspecies, so they aren't going anywhere soon.* Numbers are steadily increasing (~4% per year), although some populations are reducing. Poaching for ivory and bushmeat are signficant problems, but habitat loss and fragmentation is a massive issue. Elephants occupy a large number of habitat types and populations cover vast ranges, it is very difficult to protect an entire population range such that elephants could freely and safely move throughout their range (particularly at national borders), but things are getting better in many cases and efforts are ongoing.

An increasing number of transboundary elephant populations are co-managed through the collaboration of relevant neighbouring Range States. Large-scale conservation interventions are also planned through the development of conservation and management strategies at the national and regional level.

Polar Bear, status: vulnerable
Population estimates range between 20 and 25 thousand polar bears in the wild, and populations are on the whole fairly stable at the moment (in population studies, for populations where enough data was available, 1 grew, 6 were stable, 3 declined over a 12 year period). These animals are dependent on sea ice which, with human caused climate change, is rapidly declining. Climate change poses a more serious threat to polar bears. Relative to many things, like poaching and habitat fragmentation, it will take a very long time to reverse the tide; it may even be too late to prevent fatal damage to the polar bear habitat. They are also at risk from hunting, pollution, and habitat disturbance. Realistically, it is hard to predict when (or if) polar bears will go extinct because there is so much variance in the prediction of climate change and loss of habitat (sea ice).
Giant Panda, status: endangered
Less than 2000 pandas are left in the wild. Hunting and habitat loss remain to be enormous problems for wild pandas; masses of deforestation and fragmentation is occurring in their range. The chinese government has established >50 panda reserves, but this covers around ~60% of the population. The population trend is a decreasing one, which is serious cause for concern, and fragmentation of populations could reduce genetic diversity (increasing inbreeding depression and reducing adaptive capacity). Despite popular belief, pandas reproduce fairly well in the wild, it is in captivity that we have struggled, and that causes problems for breeding programs that can boost numbers and restore genetic diversity to sub-populations.
Mountain Gorilla, status: endangered
Fewer than 1000 mountain gorillas are left in the wild and populations are declining. Habitat encroachment, deforestation for the charcoal industry, bushmeat, and poaching are major issues affecting populations, and much has been fuelled by conflict (e.g. the 1990's war in Rwanda) in their range (in the last 20 years, 140 Virunga rangers have been killed trying to protect Gorillas). Also affecting them is human disease including the common cold which is often fatal to gorillas.
Bengal Tiger, status: endangered
Currently with a population of >2500, and with populations stabilising, and even rebounding in many areas (I was in Ranthambore last year, numbers have risen from ~20 to ~60 in the last 10 years), it seems the Bengal tiger is no immediate threat of extinction.* The major threats are poaching, population fragmentation, and habitat encroachment which leads to conflict with (and killing by) humans in the areas. Project Tiger is a major programme in India which has greatly contributed to successful growth in tiger numbers. The range of tigers is under increasing pressure from encroachment.
Summary
In summary, few models will be able to predict when or if any of these species will go extinct. Even if the short-term problems can be overcome, loss of genetic diversity prevents issues for the long-term prosperity of these species. Many of the problems are fixable in a relatively short time but will take a lot of effort and money, (such as poaching, hunting, deforestation) because they are mainly about cultural and social issues.
Climate change is perhaps more concerning because reversing the effects of human caused climate change will be extremely difficult (social and economic pressure), and slow to reverse; by the time we reverse the trend of rapidly declining sea ice it may be too late. Therefore, out of your species I'd say it's a close call between polar bears (despite good numbers they perhaps have the worst prospects of rescue) and mountain gorrilas (because numbers are so low and conservation projects are fighting difficult problems such as poverty and the effects of decades of civil wars and unrest). This article from national geographic suggests mountain gorillas may have as little as ten years left, while polar bears may be able to cope with some amount of warming, but the rate of warming is a major concern.** The WWF has also warned that pandas are not far from extinction.
What happens if we lose these species?
Many of these species are very attractive to the general public. The loss of some species would likely be worse than others; many of these are used to promote ecotourism and this would have varying effects for each. For the cases of black rhinos and african elephants many of these areas have many other species which are of interest to ecotourists (lions, leopards, cheetahs, white rhino, giraffe, crocodiles, buffalo, and many other mammals and birds, even sharks). However, if black rhinos went extinct then there would probably be losses in those species too (they face many of the same problems). Ecotoruism in the relevant areas tigers and pandas on the other hand are hugely important draws, India and China simply don't have the same diversity and abundance of highly sought after species with which to boost ecotourism should either go extinct (there are other nice species in these areas, but few are as highly sought as tigers and pandas). It's much the same for mountain gorillas and polar bears, these areas have less to fall back on should their species go extinct, so in many cases these species are of major economic importance.
That said, losing one or two of these species could cause some good. The outrage at losing some of the most popular animals in the world would be enormous. Funding for conservation and social pressure would likely swing massively more in favour of conservation efforts, making the fight to protect other species easier. Personally I don't hope we will ever have to rely on this strategy.

* Relatively speaking
** Strong selection may not get adaptive responses to occur quickly enough because generation times, standing genetic variation etc. such that while populations may adapt they don't adapt quickly enough.


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How many species of mites live on the human body?
How many known species of mites regularly live on the human body?
I've always heard that most people have eyebrow mites. This source  mentions 2 species of face mites, Demodex folliculorum and D. brevis,  that also regularly live on humans, but I'm wondering if there are in fact other species of mites that also call human bodies home. If so, how many? And where do they live?
Note: I'm not talking about disruptive mites such as scabies,  but mites that go less detected.

Mites like all living things require an energy source. Demodex and lice are parasite. Other mites can be ectoparasites but are not permanent residents of the human body

The answer is 2-3 human mites.
This page says that 2 mites specialize on humans:
http://www.bbc.com/earth/story/20150508-these-mites-live-on-your-face
https://link.springer.com/article/10.1007/s10493-009-9272-0
Another page I found said there are 3 common human mites, adding scabies to the list.
This page talks about bites from a variety of dust and house mites:
https://link.springer.com/article/10.1007/s10493-009-9272-0
My biology lecturer from university of Edinburgh told us that we have hundreds of species of detrital nematodes living on and inside us and that nematodes can be a few microns long. About 800 million humans have a 30cm large nematode inside them according to the WHO.


text:
Formula for number of divisions required to form x number of cells (Mitosis and Meiosis)
In case of Mitotic Division, we say that if the total number of cells formed by mitotic divisions are $x$, then counting from the first cell onwards, we get $x-1$ divisions ($N$)
$N = x-1$
This is fairly logical to me

However, to find total number of meiotic divisions for $x$ cells, we use the formula
$x/4$ (In questions where we are supposed to find total number of divisions required for forming some number of seeds or pollen grains)
Shouldn't the formula be $N = (x-1)/3$ (Using the same logic as used for the mitosis formula)?

there will always be even number of cells unless a daughter cell has not divided. Binary fission/continuous mitosis will yield 2^n cells after n divisions

For a male, one primary spermatocyte produces two secondary spermatocytes through meiosis I, which in turn produce two spermatids each through meiosis II. So one primary spermatocyte produces four spermatids. That means that $x$ spermatids are produced after $x/4$ meiotic divisions consisting of once meiosis I and twice meiosis II.
However, we don't count the first cell here because a primary spermatocyte is fundamentally different form a spermatid. So in meiosis, the first cell isn't counted, and four new cells are produced.
In mitosis, we do count the first cell. Note that there are two cells produced form one, so there is only one new cell. Hence we get the formula $x-1$.


text:
Can we say the 'goal' of Mullerian mimicry is a 'decrease in the number of sacrificed indivials'?
Can we say that Mullerian mimicry allows two species to decrease their number of sacrifice individuals because:

Originally, one species needs to sacrifice some individuals to allow predators to recognize the warning signals (e.g., 10% of the population);
Another species, with a different set of warning signals, would also need this same population sacrifice (i.e., 10%);
Now, is the benefit of mimicry that, when two species share the same warning signals, each of those two species only loses half of the otherwise sacrificed number of individuals (i.e., 5% in the example)?

What is Müllerian mimicry?
Proposed by Fritz Müller, is when two or more species, which are both unpleasant to eat, poisonous, toxic, harmful etc. have similar colouration and patterns. A key point to note is that they have common (shared) predators. A classic example is the Heliconius genus of butterfly.
Why does it evolve?
The argument you make is kind of along the right lines, but it is a group selection argument, and is worded slightly badly as it insinuates that evolution is a goal driven process. I will use a toy example/thought experiment to explain why it's evolution is adaptive.
In this example there are three species of butterfly are toxic. We will call these species Butterfly-1, Butterfly-2, and Butterfly-3 (yeah, I'm not feeling very creative today). We also have a predator, a bird which likes to eat butterflies. We will call this species Bird.
Butterfly-1 and Butterfly-2 are very different to look at; they have different colours, shapes, and patterns. An individual Bird then eats one of Butterfly-1 and becomes sick. That individual learns to avoid Butterfly-1. Our Bird is then hungry again, and eats Butterfly-2, and again gets sick, and learns to avoid Butterfly-2. Two individuals die before Bird can learn to avoid both species.
Butterfly-1 and Butterfly-3 are very similar in appearance; they have similar colours, shapes, and patterns. An individual Bird then eats one of Butterfly-1 and becomes sick. That individual learns to avoid Butterfly-1, but also to avoid the similar looking species Butterfly-3. Likewise, if it eats a Butterfly-3 then it learns to avoid both Butterfly-1 and Butterfly-3. This is Müllerian mimicry. Survival is higher in one or both species because of more rapid learning by predators, fewer individuals will die compared to the non-mimicry scenario.
The essence of this is captured in the following statement from this paper:

"Müller provided what could well be the first formal mathematical model to support an evolutionary hypothesis. Following Müller’s original argument (1879), let $a_1$ and $a_2$ be the numbers of two approximately equally unpalatable (or otherwise defended) species in some definite district during one summer, and let $n$ be the number of individuals of each distinct unpalatable species that are killed by predators during a season before their distastefulness is generally known. If the species are distinct in appearance, then each species would lose $n$ individuals in the course of educating predators. If, however, the two species were exactly alike in appearance, then the first species would lose only $a_1n/(a_1+a_2)$ and the second would lose only $a_2n/(a_1+a_2)$. Under these conditions, a mimetic mutant of species 1 that perfectly resembled species 2 would tend to spread from extreme rarity"

Note that there may be caveats and complexities which I haven't discussed, this is a simplification to try and explain the general reasoning

I agree the wording issue; in the linked paper they talk populations, not species-level. +1

Is there a model that tries to simulate this? Although it seems obvious as the OP also noted, a mathematical (dynamical) model would provide a better explanation. I can see a mathematical expression. If possible can you add the full model description?


text:
How many residues can a reliable ab initio structural model contain?
A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be reliably modelled.
7 years after that paper: I just attended a pre-publication presentation in which a 400+ residue structure had been modelled using I-TASSER. The speaker claimed it was reliable and it did fit well in the biological context, but it still needed experimental validation. Unfortunately they had no in silico validation scores to hand so I had no handle on how seriously I should take the model.
Ultimately, my question is how many residues can I-TASSER (other modern ab initio brands available!) reliably handle for a typical globular domain with today's technology?

Year on year reliable ab initio predictions are becoming more common for longer proteins. 400 residues is not an unfeasible length. Of course, loops still remain more of a challenge than helical and sheet secondary structures.
At CASP13, the Google DeepMind team used AlphaFold to produce a good quality model (T0594) of a 774 residue protein which is a WD40-repeat of RFWD3 (6CVZ).
All of their CASP13 entries are here.

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


text:
What gives diarrhoea caused by Cholera its milky colour?
The diarrhoea caused by the Cholera bacteria is a milky colour, also known as 'rice-water' like. Why is this? I have a fairly good understanding of how Cholera acts on the body.

The color of our feces is caused by the breakdown products of the hemoglobin, namely Bilirubin and Stercobilin, which depending on the concentration, cause a yellow to brown color. See here for details.
Since the amount of liquid lost by the cholera diarrhea with up to 250ml/kg bodyweight is really high, there is only very little to nothing of these breakdown products available in the feces. This causes an absence of color.


text:
Is "aggregate percentage" still a valid term in ecology?
Martin et al. 1946 define "aggregate percentage" as a metric that describes the mean percentage contribution of a group to the total mass/abundance of all samples. The metric is useful in datasets that are plagued by outliers and non-normality, something that is a commonplace with most ecological community and diet studies in my experience. Aggregate percentage is calculated as follows:
$AP_i = \frac{100\%}{N_y} \times \sum\limits_{j = 1}^{N}(\frac{a_{ij}}{\sum a_j})$
Where i is the i$^{th}$ taxon, j the j$^{th}$ sample, N total number of samples, a$_{ij}$ the abundance or mass of i$^{th}$ taxon in j$^{th}$ sample, and $\sum a_j$ the summed abundance or mass of all taxa in j$^{th}$ sample.
Martin et al. 1946 illustrate this as follows:

I am sure that "aggregate percentage" is a standard method in ecology, but I cannot find many studies using this term by googling. Probably the method has synonyms and there might be a more accepted term for the method nowadays. My question is what is the valid term to use for the method?

The formula of "aggregate percentage" that you show is just the arithmetic mean of percentages, and I suspect that no special term is used in most studies that use mean percentages as a measure of e.g. prey composition in a certain predator (as seems to be the case in your example).
When searching for studies I think you will have more luck with using "mean prey percentages", "prey percentages" or "mean percentage composition". For instance, see Shoup & Lane (2015) which includes the text (with my emphasis):

Results of regressions correlating Secchi depth (mm) with prey percentages by weight in the stomach contents of Largemouth Bass sampled from Boomer.

Also (Ahlbeck et al, 2012):

For each of the 25 individuals in each size class, the diet composition was calculated as the mass percentages of different prey, and then the average mass percentages were calculated for the size class.
  [...]
prey percentages were first calculated for each fish separately and then averaged over all individuals in the sample (Hyslop 1980).

Finally, Ledger & Hildrew (2008):

Mean percentage composition (food category area as percentage total particle area) of faecal pellets of N. pictetii nymphs fed biofilm from four acid streams and four circumneutral streams.

Thanks for clarification. It certainly seems that there is no standardized name for this method (which is just a mean of percentages, as you say). I suppose I was thinking about "frequency of occurrence", also a simple method that had several names until people settled to that term. I'll wait for some days and accept this answer unless someone comes up with a better one.

@Mikko I agree that it's not entirely obvious, and people come up with all sorts of terms for basically the same thing (which can be a big problem). Personally, I hadn't heard of "aggregate percentage" before, and my main point is that most that use it as a statistic are probably not calling it that (or any other specific term necessarily).


text:
Pathogenesis of Cardiac Atypia?
I am studying the pathogenesis of atypia in cardiac cells where the etiology is most commonly irritation or infection and where the precancerous risk depends on the context of diagnosis.
This fact motivates me to think how they can generally arise, from superficial or stromal origin, and how - multifactorial and/or polygenic.
Cardiac tumours are mostly secondary (30x1) in comparison to primary tumours.
I am thinking the sources of these metastases.
I did not understand if benign tumours can be secondary such as myxoma. Therefore, I assume now that myxomas (superficial) and stromal origin can be secondary.
I am mostly interested in superficial changes of the heart in atypia.
It is interesting to notice that benign cardiac tumours originates from the left side of the heart mostly, while the malignant from the right side.
I am thinking the mechanisms here and how the myxoma could be related to the pathogenesis of stromal procesesses in the right part of the heart and the pacemakers' function (AV, SA).
It would be nice to understand the links between myxoma, AV and SA.
Myxoma in the left chamber

Benign.
Origin - superficial mostly in left atrium.
Pathogenesis - polygenetic and/or multifactorial. Mobile mass obstructs blood flow in chambers and cause an increase in pulmonary capillary wedge.
Myxoma (benign tumor of connective tissue containing mucus and gelatinous material) most commonly in left atrium, fossa ovalis in septum.
Imaging DX sound after S2 in ECHO and sometimes ECG; ECHO heterogenic mass.
Differential DX lipomas, rhabdomyomas, teratomas.

Stromal Processes

Malignant diagnostically mostly.
Right side of the heart mostly.
Most commonly haemangiosarcoma (= angiosarcoma).
Pathogenesis. There can be some pathways which are activating atypia such as lymphoma.

Myxoma and Stromal Processes?
I did not understand the link between these two processes.
The former resides mostly in the left side of the heart, while the latter in the right side of the heart.
Their link or their individual links to the pacemaking (SA, AV) would be nice to understand.
I am not sure if we can exclude Purkinje cells, although they reside physically far from the atrias because their low conduction frequency and because the myxoma is about benign tumor of connective tissue which would well reside there, probably even better energetically than in SA/AV.
Sources

DynaMed Plus Lymphoma, sarcoma, ..., visited 25-February 2016.
Orlandi A, Ferlosio A, Angeloni C, et al; Cardiac tumors. Pathologica. 2005 Jun;97(3):115-23.
Patient.co.uk. Visited 30.12.2014. URL: http://www.patient.co.uk/doctor/cardiac-tumours
Cleveland Clinic. Visited 30.12.2014. For Diagnosis. URL: http://my.clevelandclinic.org/services/heart/disorders/cardiac-
tumors
http://www.learningradiology.com/lectures/cardiaclectures/insideoutflash.swf, visited 13.1.2015.
Emilsson, Medscape. The Characterisation and Risk Factors of Ischaemic Heart Disease in Patients With Coeliac Disease.
P. e. a. Whorwell, DEATH FROM ISCHMIC HEART-DISEASE AND MALIGNANCY IN ADULT PATIENTS WITH CLIAC DISEASE. Institute of Cancer Research, Sutton, Surrey, United Kingdom: The Lancet, 1976, volume 308, Issue 7977, p. 113 - 114.

How can you describe the pathogenesis of Cardiac Atypia?


text:
Why does ESR have to be waited for one hour?
It is said that the length of the column of clear plasma in a narrow tube left by erythrocytes which gradually sediments after one hour is the measure of ESR(erythrocyte sedimentation rate). Its normal values are found to be 3-5 mm after 1st hour for male and 4-7mm after 1st hour for female. What I want to know is why "1 hour" has been chosen. Why not 30min, 2hr, 3hr etc?

Does it really make a difference how long they settle, or why they chose that amount of time? At one extreme, you haven't really given them adequate time, at the other, there's no more useful information to gather.
The tubes in which Sed Rates (or ESR) are measured are 200 mm in height. Why wait three hours for the result (which is still expressed as a rate, i.e. mm/hr)? In three hours, they may (depending on how quickly they settle) have all settled an hour and a half ago. (If an ESR is 100mm/hr, it will hit the settled cells at the bottom before it finishes settling if two hours is the length of the test.
The test is simple, cheap, easy, with good sensitivity and specificity. And the results come back in a little over an hour. The sooner the diagnostician gets the results back, the sooner the answer helps in the decision tree needed for the treatment of the patient. Longer wait times aren't helpful and may not be accurate with very elevated ESRs.
Acute Phase Proteins Molecular Biology, Biochemistry, and Clinical Applications By Andrzej Mackiewicz, Irving Kushner, Heinz Baumann, 1993


text:
Understanding common identifier codes (IDs) in biology databases
I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database.
I have the output:
sp|Q9NZT1|CALL5_HUMAN

However I'm not sure exactly what this is referring to.

Is Q9NZT1 q unique identifier?
Is CALL5_HUMAN unique too?
Should one use both together to get information?
How many types of ID are there?

Hi and welcome to Bio.SE! I've made a few edits to your question just so that it's clearer what you're getting at. Feel free to roll back those changes :)

@James thanks, everything is good. i appreciate any comment and help :-)

Glad I could help. I wasn't sure exactly what you were asking when you said "How many types of ID are there?" Did I answer your question, or were you talking more generally "how many databases use different IDs?"

@James your answer was very good but I appreciate if you make it more general about databases etc. so that I can accept it

If you open the question up to general databases it becomes far too broad to answer in any meaningful way. I would suggest you edit the question to make it clear what you want to know. I've updated my answer with a bit of information relating to some of the most popular databases.

Common biology ID codes.

PDB: 2BIB for example. 4 letter code for a specific structure.

Uniprot: Q9NZT1 for example. A six letter combination of numbers and letters for either a TrEMBL or Swissprot record. This record contains information on domains, and Uniprot links out to lots of useful things like interaction databases, redundancy datasets etc.

Pfam: X1WG39_DANRE A uniprot ID followed by an identifier. Tightly linked with Uniprot, but with an emphasis on domains.

NCBI: NP_000108.1 For example. These IDs link to either a gene, transcript or protein in refseq. In an NCBI record there are two main distinctions in prefix of the ID code: hypothetical/automatic assertions (XM_, XR_, and XP_) and manually curated assertions (NM_, NR_, and NP_). This is followed by a 6 digit number, and sometimes followed by a "." and a number, indicating an splice isoform.

Uniprot IDs
I'm not sure where you got this output so this seems a strange concatenation of Uniprot information.
Q9NZT1 is indeed the unique Uniprot ID. This is specific to uniprot.
CALL5_HUMAN is the "gene name" or "Identifier" and often spans across different databases for that gene. It's a little more back end, but is essentially not unique due to splice isoforms.
There are many IDs in uniprot, and many types. Already below you'll notice some are swiss prot, others are Trembl. These are the main types. Swissprot are manually reviewed, whereas Trembl is an automatically compiled collection.

There are many many different accession code types with each database using it's own nomenclature that you'll come across. Unfortunately, there are too many to list here comprehensively.


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Why aren't plants and animals capable of assimilating $\ce{N2}$ directly from the atmosphere?
From a E-book  written by Hungary scientists, the reason is $\ce{N2}$ is inert.

Is this correct?
How does the chemical properties of gas species ($\ce{SO2}$, $\ce{O2}$, $\ce{NH3}$, etc) influence the assimilation process by organisms?

You can read about nitrogen fixing: https://en.wikipedia.org/wiki/Nitrogen_fixation. Most plants that "fix" nitrogen are symbiotically associated with nitrogen-fixing bacteria (Rhizobia, https://en.wikipedia.org/wiki/Rhizobia). Also some diatoms (algae), Rhopalodia gibba, are able to fix nitrogen as they have cyanobacteria in their cytoplams.

Thanks for your reply! I have read about the content of nitrogen fixing. I just curious about the chemical nature why assimilation process select certain gas species.

By the way I think this does not have a direct relation with geochemistry or atmospheric chemistry, e.g. asking about how these processes affect the atmosphere or Earth, or things like the whole nitrogen cycle. Rather you are focusing on the specific processes that occur in the organisms (and nothing about environmental interaction), that's biochemistry. That's all just IMHO tho, you can ignore me if you don't agree :-) .

Thanks for your insight. The tag I set  is inappropriate.

But since we're already here: "inert" simply means that it does not readily react with other molecules, i.e., that the activation energy is very large before it reacts with anything else. Plants and animals have simply not evolved the very strong reagents you need to break the N-N triple bond.

As @Wolfgang Bangerth commented, inertness just means that nitrogen gas doesn't undergo reactions because the NN triple-bond has a very high bond energy and the activation energy for reactions that break the bond (even though thermodynamically favourable) is therefore high. So I suppose that you could say that a major chemical factor in the reactivity of gases is their bond energies.
The key reaction of biological interest for nitrogen is reduction to ammonia, as referenced by the comment of @aretxabaleta. Stryer makes a couple of points that seem chemically relevant (http://www.ncbi.nlm.nih.gov/books/NBK22522/). He says that the reaction pathway for the reduction of nitrogen involves unstable intermediates, and he also mentions that the nitrogenase enzyme in Rhizomium is extremely sensitive to inhibition by oxygen. I am no expert, but I presume that the instability of the intermediates is related to their ease of oxidation. Leguminous plants maintain a very low concentration of free oxygen in their root nodules by synthesising the protein, leghaemoglobin, which mops oxygen up.
So the answer to the question in the title — why animals (at least) don't fix nitrogen — could well be because as aerobic organisms they would find it very difficult to provide an oxygen-free environment to do this. And the fact that animals can get their metabolizable nitrogen second- or third-hand means that there is no evolutionary pressure to develop such a mechanism. (Most bacteria and plants manage without too.)


text:
50:50 sugar/fat mixture
A couple of years ago I saw a BBC Horizon television documentary about sugar and fat. One section mentioned three experiments in which rats were given their ordinary rat food plus and unlimited supply of:
Experiment A. Unlimited sugar
Experiment B. Unlimited fat
Experiment C. Unlimited sugar&fat mixed together (50:50)
The stated results were that in experiment A the rats did not put on any weight, in experiment B the rats put on weight but not much and in experiment C they put on loads of weight and would eat the 50:50 mixture to the exclusion of their ordinary food. I also remember the documentary said the 50:50 ratio was critical and if the ratio was shifted too far in either direction then the weight gain effect reduced sharply.
I have two questions. 1. What was the original research paper. and 2. Have there been any related new results with other mixtures like sugar/salt fat/salt?
EDIT: I have just found this related paper. I don't know if its the exact one relied upon by the documentary, but it's certainly close... perhaps the documentary employed the results from multiple papers.
EDIT: You can see the whole documentary here: https://www.dailymotion.com/video/x1arpze - the rat experiment discussion begins around 46 minutes in.
EDIT: years later... I found this and this.

Are you interested in other studies about sugar/fat mixtures or in other foodstoof mixtures?

@Jan: I am interested in any food group mixtures where the combination induces greater calorie consumption than either one in isolation.

OK, you may also make clear what is your exact question. I guess, you are asking for a mechanism by which certain food/combination leads to increased food consumption. Or you just want to stick with the basic facts: this and this food combination --> greater food consumption.

@Jan: Ultimately I am looking for followup research along the same lines. If I knew the exact paper(s) the results presented in the documentary were based on then I could search for papers that referenced the originals.

@xusr: you should put that as an answer rather than a comment - so far it's the best answer I've seen.

1. What was the original research paper?
This one appears close: Hyperphagia in rats produced by a mixture of fat and sugar (PubMed, 1990)

Experimental groups were fed sugar (sucrose), fat (corn oil), or a
  sugar-fat mixture as an option to chow; options were in the form of
  water solutions or emulsions. The control group was fed only chow. The
  sugar-fat group displayed a robust hyperphagia (greater than 36%),
  relative to the control group; the hyperphagic response was greater
  than that observed in the fat group but not in the sugar group. The
  sugar-fat group selected more calories from the option than the other
  two experimental groups. Body weight gains were also greater in the
  sugar-fat group than in the fat and sugar groups. Addition of
  saccharin to the fat emulsion increased fat and total intakes to
  levels close to those of the sugar-fat mixture. In a second
  experiment, the relative palatability of the plain and sweet fat
  emulsions was assessed with two-bottle preference tests. The sugar-fat
  mixture was preferred to the saccharin-fat mixture, which in turn was
  preferred to the plain-fat emulsion. These results suggest that the
  sweetness of the sugar-fat mixture contributed to the pronounced hyperphagia and obesity obtained with this diet option.

2. Have there been any related new results with other mixtures like sugar/salt fat/salt?
A free-choice high-fat high-sugar diet induces changes in arcuate neuropeptide expression that support hyperphagia (PubMed, 2010) (a study in rats)

Our data suggest that the specific combination of saturated fat and
  a 30% sugar solution results in hyperphagia-induced obesity.

Snack food intake in ad libitum fed rats is triggered by the combination of fat and carbohydrates (PubMed Central, 2014)

Thus, it can be concluded that the combination of fat and
  carbohydrates is a major molecular determinant of potato chips
  triggering hedonic hyperphagia.

Fat/carbohydrate ratio but not energy density determines snack food intake and activates brain reward areas (PubMed Central, 2015)

We conclude from our behavioural data that the ratio of fat and
  carbohydrates, but not the absolute energy density, is the major
  determinant of the palatability and intake of snack food during
  short-term two-choice preference tests in rats.

Which Foods May Be Addictive? The Roles of Processing, Fat Content, and Glycemic Load (PubMed Central, 2015) (a human study)

In summary, the current study found that highly processed foods,
  with added amounts of fat and/or refined carbohydrates (e.g., sugar,
  white flour), were most likely to be associated with behavioral
  indicators of addictive-like eating. Additionally, foods with high
  GL [glycemic load)] were especially related to addictive-like eating
  problems for individuals endorsing elevated symptoms of “food
  addiction.”

In conclusion, it can be either a combination of fats and sweetness (due to sugar or non-sugar sweeteners) or a combination of fats and high glycemic carbs (sugar, white flour, potatoes) that can induce overeating.

Thank you. That's exactly the kind of thing I was looking for.

It is easier for the body to use carbohydrates as energy source rather than lipids.
When the food is full of fat, the mouse will use fat as a source of energy and only a little part of it is stored.
Furthermore, when the food is full of sugar, the mouse will use the sugar as source of energy and as above, only little part of it is stored.
When the food ratio is 1:1 sugar and fat, the mouse uses sugar as energy source and stores fat so it gains more weight than the other two.
Salt is not an energy source and cannot be stored in the way sugar and fat is stored.

I think the comments that applied to rocc's answer, also apply to this.

I have to apologize at first, we had that phenomena in a lecture but I am not a native speaker and some of the processes are maybe wrong translated.
Despite the other answers, I have learned that the primary cause has a chemical reason :
Your adipose tissue is made out of triglyceride. When you eat Triglyceride your body won't use them like this. Your body breaks them down and is synthesizing its own triglyceride to be saved as fat tissue. Triglyceride synthesizing  needs glycerol - this is where the phenomena appears : Your body can not use glycerol from food,  it has to use its own synthesized glycerol  from sugars and amino acids. So only if you consume fats and sugars/proteins simultanously your body can transform it into fat tissue.
Short way of fat when you eat it : Triglyceride > Monoglyceride+2 fat acids > if energy is needed those fat acids will be used for metabolism, if no energy is needed your body wants to save those acids for a later moment by resynthesizing them to triglyceride. Your body needs sugar or amino acids for this process.
It seems worthful to mention that other factors propably play a role like  preview answers already mentioned. But the biochemical principle is this one. Another aspect is the efficiancy - it is not mentioned where the amino acids or sugars come from, if they are saved ressources or fresh molecules from food. But if the phenomena doesnt appears - like my professor said - when you seperate those, it seems reasonable to assume that the body won't use stored sugars.
Edit/Sources:
I was trying to get some sources due to request in the comments: The problem that appears to me is that the medicine books,  where this pathway is described,  are not in english at our local library. Since this is a common known pathway in medicine you should be able to find it in every standard biochemistry book for  medical students. But I can give you some keywords:
Lipogenese on Wikipedia, in the introduction the pathway is already mentioned https://en.wikipedia.org/wiki/Fatty_acid_synthesis?wprov=sfla1
This is the pathway in form of a picture from a great german publisher for medical books

I have mentioned that aminoacids can also be used for synthesizing glycerol for triglyceride : https://en.m.wikipedia.org/wiki/Glyceroneogenesis?wprov=sfla1
this is an article I havent read but it seems accurate
https://www.sciencedirect.com/science/article/pii/S1043276008001379
hope these keywords help :)

It would be great if you had some even more official sources that you could reference for further reading.

is the Bounty Still on?

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


text:
Can we taste electrons?
Why does licking a 9-Volt battery elicits a taste sensation? Can taste be stimulated by electrical stimulation?

I'm assuming stimulating a taste receptor generates a "taste", and there are no taste receptors on your knee. This could be relevant: https://en.wikipedia.org/wiki/Digital_lollipop

Short answer
Yes, taste sensations can be generated electrically. However, we cannot taste electrons themselves, as taste-receptor proteins on the taste receptor cells are not activated by electrons. Instead, electrical currents stimulate taste receptors directly by depolarizing the cell membrane, without the need of activation of the proteins that normally bind ions or molecules.
Background
There is a medical device called the BrainPort that electrically stimulates the tongue (Fig. 1.) The device is marketed as an electrotactile vision substitution device. Basically, it captures images of the outside world with a glasses-mounted camera and these images are translated into electrical stimuli presented on a 20 x 20 electrode array. That array is embedded in the tongue display unit (aka intra-oral device, IOD). The IOD is worn on the tongue.

Fig. 1. BrainPort V100. source: TuWindowsMundo
It typically generates electrotactile sensations, like champagne bubbles. However, some subjects do report metallic taste sensations when using the device. In fact, Lawless et al. (2005)* investigated the electrically evoked metallic-taste in response to anodic stimulation of the tongue directly and confirmed the anecdotal reports obtained with the BrainpPort device that electric stimuli evoke metallic-taste sensations.
Physiologically, taste receptor cells sense certain compounds (salts, acids etc.) due to activation of receptor molecules on the cell's surface. In turn, activation of receptor molecules depolarizes the cell membrane which eventually lead to neurotransmitter release and activation of secondary neurons that transmit the signal up to the brain (Fig. 2). Electrical stimuli bypass the receptor molecules and directly depolarize the taste receptor cells.
Given the anatomy of the taste receptor system in the tongue (Fig. 2), I am inclined to believe that the taste receptors are stimulated directly, and not the secondary neurons, because they are situated in deeper layers.

Fig. 2. Neural pathway of the taste buds on the tongue. Note that the secondary neurons transporting the taste information to the brain are situated in deeper layers than the taste buds. Source: Universe Review.
Note that taste receptors do not sense electrons. Rather, larger ions or molecules may stimulate them and cause a depolarization of the receptor cell, in turn activating the secondary neuron via a chemical synapse.
Reference
- Lawless et al., Chem Senses (2005); 30(3): 185–94
Acknowledgment
*Credits for the Lawless et al. (2005) reference go to @CMK

I have also heard of some device that can produce tastes of different foods via electrical stimulation. I am not sure if this is the same device.


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How to name a case of convergent evolution where the same mutation is involved in both lineages?
Definition of Convergent evolution - from Wikipedia > Convergent Evolution

Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function, but that were not present in the last common ancestor of those groups.

Examples
-- Lactase --
Humans have evolved the ability to digest lactose at adult age twice; once in Europe and once in Africa. Different mutations are involved in European lineage and in African lineages.
Source: Tishkoff et al. (2007)
-- White fur --
Beach mice and mammoths have both evolved white fur independently. The same mutation is involved in both lineages.
Source: Römpler (2006)
Question
Is there a term to differentiate convergent evolution that involves the same mutation in different lineages from convergent evolution that involves different mutations in different lineages?

This is really a question of semantics, as there are not universally accepted definitions of these terms. The first example (lactase) is by the given Wikipedia definition not really "convergent evolution" since it states that it occurs "in species of different lineages" - not within one or very closely related species. This is a mutation that occurred twice in lineages of one species, and might be better termed genetic parallelism. I am not sure it is useful to speak in vague macroscopic terms like "convergent evolution" when discussing subtleties at a genetic or molecular level.

I have to say I really enjoyed this question, it was a new thought for me and it's great when biology SE gets to poke around in these sorts of very academic areas! Enjoyed reading for it and scouring literature for an answer - nice one @remi.b thanks for posting such a good question!

As you already know convergent evolution is when two separate lineages evolve the same (or similar) trait, and this is generally assumed to be a result of similar selection. For example, if flying helps both birds and bats catch insects to eat, then convergent evolution of flight is somewhat unsurprising. Other examples include those of mimicry where the convergence on a common colour patterning reduces predation rates.
The wikipedia page on convergent evolution does a pretty good job of explaining the subtle difference between parallel and convergent with its illustration. In convergent evolution, two lineages have dissimilar starting points and arrive independently at similar end points. In parallel evolution, two lineages have similar start points and arrive independently at similar end points.

"...a convergent change at an amino acid site refers to changes from different ancestral amino acids to the same descendant amino acid along independent evolutionary lineages ... It is distinguished from a parallel change, in which amino acid changes along independent lineages have occurred from the same ancestral amino acid (see fig. 1A for examples). Both convergent and parallel evolution, if verified, suggest adaptive evolution."

This, and other sources (page 113), suggests that convergent and parallel evolution/change/mutation are relevant terms. In your context you are looking for a term to differentiate two cases.

Case 1: convergent evolution of a trait, by different mutations; either different nucleotides at the same site, or mutations at different sites. This is seen in your lactase example.
Case 2: convergent evolution of a trait, by the same mutations; the same nucleotide changes at the same site(s). This is seen in your white fur example.

A key point is that your are looking at convergence at two different levels, phenotypic and molecular. In both cases you have convergent evolution at the phenotypic trait level. The cases differ at the molecular level where you have convergent and non-convergent mutation respectively. I have found one term being used in this paper.

"In some cases it has been shown that different loci are involved in phenotypic convergence (e.g. Refs [8,25,26]), demonstrating that similar phenotypes can be reached through alterations of distinct enzymes. However, other studies have traced phenotypic convergence to modifications of homologous genes (e.g. Refs [3,5,6,26,27]); in this paper such phenomena will be further referred to as convergent recruitment (Glossary)."

I think the term you are looking you are looking for would be  convergent recruitment to describe case 2, and some form of antonym* for case 1, perhaps you could say non-convergent recruitment. However, non-convergent could make it sound like no convergence is occurring so I'm not a fan and you should be careful in any papers to clarify. I'd say something like:

"Phenotypic convergence by the recruitment of different genes and/or mutations is herein referred to as non-convergent recruitment, in this case convergent evolution is occurring but through non-homologous changes at the molecular level."

You would then have to be consistent in your writing, talking about the phenotypic level as (non-)convergent evolution and molecular level as (non-)convergent recruitment. E.g.

"The convergent evolution of flight occurred as a result of non-convergent recruitment."

* I couldn't find an established antonym term, and as I suggest in the post, I don't think non-convergent recruitment is a perfect antonym, we could discuss it in chat or the comments to try to come up with some new terminology. Perhaps "non-homologous convergent evolution" or "non-genetic convergence" would work? In this paper they simply refer to it as "convergence through different mutations".

I'm not aware of a specific term for this. In the places I can find the concept discussed in the literature (here and here), the authors simply describe the pattern as "the same [...] mutation in two lineages" and "parallel mutation in two lineages".


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How can I make a protein interaction/protein-complex network?
Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated.
An example input is what you see below. What can I do with the following list of protein IDs? These IDs are from human.
P41182,P56524, P41182,Q9UQL6, P41182,Q8WUI4,Q92793,Q09472,Q9Y6Q9,Q92831

Could you clarify what you mean by "complex"? Do you want to know if they are part of an oligomeric quaternary structure, or how they interact with other proteins?

@James if they are part of oligomeric quaternary structure

This question is not a homework question. It is not a trivial, easily google-able task. I buy the "too-broad" argument, but closing this for homework seems a bit naive. Even if it's an assignment it's a tough one if you don't know where to start!

Without a pairwise mapping between interacting proteins, you cannot make the network. Do you have a file that contains this information?

@WYSIWYG No I don't have such info, do you know how to get that ? please make another answer if you know a better way

@Mol you need to somehow know which proteins interact with which others. This can be experimentally found out using techniques such as Co-IP (it can also show indirect interactions though). Whatever techniques or predictions you use, you would need to know the individual edges of the network to actually build it. Otherwise, it is impossible.

@WYSIWYG If I know that these proteins are coming from the same sample, then I can assume they interact , no ?

@Mol no you cannot assume so. In a protein extract from a eukaryotic cell actin and cyclin would both be present but they do not interact.

This is not a trivial task depending on how well studied your network is or what information you want to gather. It sounds like an interaction dataset is what you want rather than scouring the PDB for static structures (that would be such a hit and miss process I'm not sure it's worth bothering).

Upload you list of gene codes to string-db.

You'll see the network here, and structures are made clear of known complexes in an expandable thumbnail.
It's a limited web-server tool, and whilst very powerful, isn't very flexible. Cytoscape might be needed for a more novel study because it is scriptable.

You can probably stop here and investigate your network.
From string-db download the .txt file (TXT - simple tab delimited flatfile). I think it's an old-school save icon on the web-server, although if you're uploading multiple identifiers, it is simply the "save" button at the top left.
Download Cytoscape here.
Then use File>Import>Table>From file.
This will build an interaction network and you'll see which genes/proteins interact with one another.

Catch: whilst this provides spacial information, you can't get a picture of temporal information: i.e you know what is interacting, but not when nor for how long.

how to get the .SIF ? how to give all the ID together ? i tried to save it but it did not give me any .SIF

Did you manage to get string-db to display an interaction network?

not for all IDs together but when I use one ID, it works

Have you tried uploading them all at once under the multiple identifiers tab?

both txt files are the same ?  also can you please give me some hint related to the CytoScape? what to study and where to study so that I can get an idea how to build the network and visualise it

@Mol if cytoscape is a bit overkill then just stick to string-db. All the nodes and connection show interacting partners.

I know but seems more flexible than String-db. both txt are similar ?

@Mol The tab delimited txt file is the one you want. Cytoscape is more flexible you're right. But that flexibility comes at a cost; a steep learning curve. There may even be a way to query from within Cytoscape. What I like about string-db is the direct links to pdb structures which is probably very useful for you.


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What do the negative and positive signs mean in the rotation angles of DNA helices?

Does it mean clockwise and anticlockwise?

The signs refer to the direction of rotation. Anticlockwise (right handed helix) is positive whereas clockwise (left handed helix) is negative. The direction of rotation is observed from the side where the helix is ascending towards you (perpendicular to the ascent of helix).
In other words, curl your right hand and extend the thumb out. When viewed from above (thumb points towards you), the fingers curl anticlockwise. This is a right handed (RH) helix. Conversely, you can use your left hand to understand left handed (LH) helices such as that of Z-DNA.

Obtained from http://biomedapps.curtin.edu.au/biochem/tutorials/prottute/helixfigures.htm. Which, in-turn is modified from Lehninger et al (1993) Principles of Biochemistry 2nd Edition Worth Publishers

 This figure depicts a RH helix. Taken from Wikipedia.

These definitions can be defined in a converse sense too and you would find many web sources that do like that. For example, if you look from below your hand such that the thumb points away from you, then the fingers curl clockwise. However, in physics and mathematics, positive angles are conventionally measured anti-clockwise. So my definition here would be suitable with respect to your question.


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Help analyzing SDS-Page gel
In this experiment, we transformed a truncation of the NFAT protein sequence into a plasmid vector to be expressed in E.Coli as a fusion protein with GST.  We also attempted to transform the normal plasmid without NFAT so that we could get GST alone.  After growing up these colonies and selecting positive colonies, we lysed the e.coli.  We collected some of this lysate for SDS-PAGE.  We then put the lysed GST and GST-NFAT solutions in separate columns with glutathione beads.  GST binds glutathione.  We washed the column and collected some of the wash for SDS-PAGE.  Finally, we eluted the GST and GST-NFAT off the column and saved some for SDS-PAGE.
I have attached a picture of a successful version of the SDS-PAGE.
You want to direct your attention to the first lane, the Molecular Weight Marker (MWM).  The rest of the lanes should be interpreted in sets of 3.  The first of the three is the crude lysate, the second of the three is the first wash, and the last is the eluted protein of interest.  The important lanes for my analysis are 8-10 and 11-13.
I will explain what I know from this SDS-PAGE gel so far.  I know the weights of the different bands in the molecular weight marker because I was given a copy of the different proteins in the marker.  From this information, I was able to confirm that I isolated my protein of interest in lane 13 and isolated GST-alone in lane 10.  I also understand the reason why the lysate lanes are darkest, followed by the wash lanes, and then very clean protein of interest lanes.  Also, note that the marker and the elution lanes were loaded with 10 microliters while the other lanes were 2 microliters each. However, there are some things that I do not understand from the gel.
(1) Why are the bands so diffuse/low resolution.  I imagine it may be overloading the wells, but I am not convinced because I followed a set procedure.
(2) Why is there large amounts of streaking, especially in lanes 5, 8, 9, 10, and 11.
(3) I isolated my protein of interest because it was a fusion protein with GST (or just GST alone), and then eluted the protein off the glutathione beads via excess glutathione wash.  Theoretically, the lanes for the elutions should be free of everything except the protein of interest and glutathione then.  This mostly holds true for lanes 4 and 9, which should only have GST and glutathione.  However, lanes 7 and 13 should only have GST-NFAT and glutathione.  The lanes are not as clear however and seem to have stained numerous other proteins.  What is going on?
(4) I was told by a professor that the second band in lane 13 (the GST-NFAT lane) was a degredation product.  How can this be?  The band does not correspond to the weights of NFAT alone or GST alone.  Also, if the NFAT-GST was degraded, wouldn't there be two bands of degredation product?
(5)  Why do the GST-alone lanes have what looks like doublet-bands?  (Lanes 4, 10).
(6)  If we eluted the proteins of interest with excess glutathione, which has a very low molecular weight, why doesn't it show up on the gel?  Is it possible that it ran off before everything else?
(7)  I have a list of the weights of the bands of the molecular marker.  Yet, there is an extra band at the bottom that does not show up on my list.  Is it possible my list is incomplete, or is there something else happening?
Finally, I have attached a picture of a failed SDS-PAGE gel.
The only thing that I definitively know was a source of error is the fact that my buffer level fell during the run (due to a leak).  The results of this gel are accurate (Lanes 2-7 correspond to lanes 8-13 on the above gel, and the results are almost identical) yet the gel turned out horribly.  How can the buffer falling cause this result?  Or is there something else that may have contributed to this weird pattern?  Finally, the lanes are not as distinct in this gel as the first gel, yet the same comb, and thus the same size and spaced wells were used.  So why was there so much bleed between lanes/ lack of space between the lanes?
Thanks in advance for any help.

These are a lot of questions and there is still some information missing to give you at least some answers. 1. Which molecular marker did you use (it would be at least important to know the bands), it would be even better if you could number lanes and buffer in the gel. 2. What did you put in which lane? 2-4 is crude lysate, 5-7 the first wash, 11-13 the elution, but what is in 8-10?

Here are some thoughts based on my own experiences purifying many proteins and running many SDS-PAGE gels:
(1) Resolution--how fast did you run this gel? Often if you run at higher than say 150V or so you can get bands that look like this. The resolution could also be related to..
(2) I would bet the streaking is due to salt in the sample--a lot of the time lysis/wash/elution buffers can have upwards of 500 mM or 1 M salt, and this invariably causes streaking. Load less sample in these lanes and keep the total volume the same to dilute the salt below 250 mM at least. Other things in your buffers could be causing the streaking, but salt is the most common (let us know the composition of your lysis/wash/elution buffers).
(3) Your purification of GST alone looks very good--often your preps will look much more like the lanes you have indicated, which are not entirely clean. This is quite common for a one step purification--often you need 2-3 for certain proteins to completely remove contaminants. There are several possible sources of these bands:

Endogenous proteins: Many bacterial proteins will non-specifically stick to the beads (this is why we wash), but even thorough washing can still leave some contaminants. These proteins also could be bound to your protein of interest and are co-eluted off of the resin.
Truncation products: Depending where your tag is (let's sat it is on the N-terminus), you can sometimes get incomplete translation products--they have the tag, but they are not full length proteins. These will still bind and elute from the beads because they have retained the tag. Ignore this point if you tag is on the C-terminus, as in that case the tag will only be on full-length protein.
Degradation products: This is related to your later questions--often during the purification your protein will be degraded by bacterial proteases. Did you include a variety of protease inhibitors in your lysis buffer? Keeping all of your samples on ice is also important for this reason.

(4) Understand that degradation products do not mean you get only your protein and the fused GST--they can be a variety of truncations due to degradation by proteases.
(5) I would bet this is just due to your running conditions or the salt in your samples. I think this is probably actually your single GST band.
(6) Glutathione will not show up on the gel--it's formula weight is about 300 g/mol if I recall meaning it's about 300 Daltons, so much smaller than anything that you'll retain on the gel. Further, remember than your stain is for proteins--Coomassie blue binds basic residues on proteins.
(7) I'm not sure which band you are referring to, but I think the very bottom band in your marker lane is simply the dye front. It could also be a degradation product of a protein in your ladder.
As far as the second gel goes--it is all due to the buffer level falling during the run. Without buffer covering the top of the gel there is no current flowing. Probably as the leak was occurring you had uneven distribution of the buffer. Strange things can happen when this occurs (unscientific, I know).

Thank you for your detailed analysis.  I have taken the information and used it to help me understand my gel more.
(1) I ran the gels at 120V through the 4% stacking layer and then 200v through the 12% resolving gel.
(2) I will look more into the salt composition and report back.
(3) I still do not understand why the GST alone lanes were more free of extraneous proteins than the GST-NFAT lanes.
(4) If a protease degrades a protein, would there not be two resulting products?  Yet there is only one extra band.
I attached a labelled gel to make things more clear.  Thanks for the response!

Definitely your streaking and resolution is due to the voltage you used--I usually do 80V for the stacking and 120V for the separating. You still get enough information running it that fast, but not great pictures (as you can see!). As for the extra bands--again these could be bacterial proteins bound to your protein (especially chaperones). I think this is the most likely issue--you can increase your washes to try and clean it up. The GST prep might be more pure because you have more GST than GST-NFAT--it could be fully saturating the beads, preventing bacterial proteins from binding.


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Server for protein structure prediction for multiple sequences
Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, sheet and coil? I searched but could not find any. There are servers that take in 1 sequence. I want to get the structure of multiple sequences together...

Why do you want multiple sequences together? What is the problem with doing one after the other? Is there any additional aspect to this that is not evident in the question?

the number of proteins is huge, so I wanted to know if there is any website that allowed batch processing

I am sure some API would exist. What is the server that you are using? Did you check its manual? You can also write a script that can do one-by-one submissions and retrieval.

Also when you have lots of data you should get program not waste time with server.

@Mithoron with this kind of data and computation, that's easier said than done

@Maljam What kind? It's not like OP asks specifically to get native structure with 100% accuracy

Unfortunately it is impossible to predict the tertiary structure of proteins using raw amino acid sequence. The information required to be computed in the construction of the dynamic protein shape is too large for any computer at the moment.
There are actually a list of research facilities that are looking for people to donate their computer's idle CPU time to help sequence proteins.
Here is a list: (http://www.hyper.net/dc-howto.html).

I really am not concerned about who wants idle computers right now. I need to know if such a server exists or not

People are working on it.  So no, they don't.

In other words, what OP should be looking for are protein databases that can be indexed with amino acid or DNA sequences.

It can't be done exactly but such servers do it more or less accurately, OP wasn't asking if protein folding problem was suddenly resolved.

If you are only looking for secondary structure prediction you could try the JPred-server API.
On their website they refer to a script that

provides a JPred user with advanced functionality for an easy submission of hundreds of JPred jobs in a sustainable manner.
  […]
  For full details on the code, how-to, and for download please check Fabian's GitHub repository page.