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How much does donating blood affect the amount of oxygen in your blood stream at high altitude?
I am a regular blood donor and I am also a skydiver.  We normally go to around 13,000 feet AGL (above ground level).  Depending on how high above sea level the ground is, altitudes could be as high as 15,000 MSL (mean sea level) before a jumper is required to use supplemental oxygen.
At those altitudes hemoglobin is less effective at carrying oxygen, which is why hypoxia is a risk.
The following chart taken from this article about aviation and the body shows how oxygen levels decrease as altitude increases:

What I would like to know is if there is any research into the effect blood donation has on the blood stream's oxygen capacity?  Is it possible to say that x days after a donation, due to reduced hemoglobin levels, operating at 15,000 MSL would be equivalent to operating at 15,000 + x MSL without donation?

The American Red Cross (http://www.redcrossblood.org/donating-blood/donation-faqs) says it takes 4-6 weeks to restore hemoglobin levels.

Right but how much are hemoglobin levels reduced and what does that reduction do to the overall oxygen levels in the blood?  If you lose x% of hemoglobin after donation then being at sea level would be equivalent to being at.... 5,000 feet MSL?  Basically my question is: how much earlier will altitude affect the body after blood donation than without?

The oxygen-carrying capacity of the blood is:

amount of haemoglobin * % saturation

The average blood donation is approximately 10% of total blood volume. . Since the donation will have no effect on the % saturation, the oxygen-carrying capacity at each altitude will go down by 10%.
By inspection of the graph in the question, the % saturation goes down by 10% at 10,000 feet. So I conclude that donating 10% of blood volume is equivalent to ascending to 10,000 feet in terms of the effect upon the blood's oxygen-carring capacity.
Response to OP comments:
1) Anyone living at 5,000 feet will have adapted to that altitude in two ways. First of all the erythrocyte levels of 2,3 bisphosphoglycerate will be elevated to maintain unloading of oxygen from haemoglobin in the tissues. Secondly, the number of red cells per mL of blood will have increased, to restore oxygen delivery. Incidentally this increases blood viscosity which is deleterious in the long term. Tibetans living in the Himalaya have adapted genetically to prevent this effect on their blood viscosity.
2) The effect of air pressure is already included in the graph, since it shows the actual degree of saturation of the blood.

I'm not sure that is right.  If you lived in Denver which is 5,000 MSL then donating blood would be the equivalent of being at 15,000 MSL.  At 15,000 MSL the time of useful consciousness can be as low as 30 minutes or worse depending on things like smoking or general health?

Also the graph shows that the degradation of oxygen saturation isn't linear.  In the linked article it noted that oxygen saturation is also tied to air pressure, so it's probably a more complex formula.

I have responded by editing my answer.


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How was the first ribosome theorized to have been made?
Seeing as ribosomes are what help perform the act of translation itself, and the blueprints for they themselves are in nucleotide sequences, how was the first ribosome theorized to have been made? Also, before there were any ribosome, how was translation theorized to have taken place?

Don't have time to write a complete answer, but you may want to start by reading about the RNA world hypothesis, ribozymes and the central dogma of molecular biology

An interesting take on this question is addressed in Bokov and Steinberg's hypothesis.
They have proposed the ribosome has evolved from a short length (~110bp) of RNA that did not have the translational activity that we associate with ribosomes today.
Instead this short length of RNA carried out alternative functions on RNA in RNA based life. Then overtime the accumulation of mutations occurred, such as duplication events that allowed the RNA strands to fold around one another forming a larger unit. This larger unit may have been able to add building blocks together. Over time natural selection will have guided these strands to be more precise in their building actions.
The details of course aren't entirely filled in yet (it's difficult to do because how long ribosomes have been a staple of life), but it's important to take any seemingly complex structure in organisms, and break them down into potentially useful intermediate evolutionary steps.
Some more reading on this subject here -

An article giving a background of Bokov and Steinberg
Bokov and Steinberg's 2009 paper (believe it's paywalled)
Origin and Evolution of the Ribosome (paper)

source: Stack Exchange

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

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Gas from bacteria that's not methane
Is gas produced by bacteria always mainly methane? Or, are there bacteria out there that produce some biogas composed mainly of hydrogen, natural gas, propane, butane?

synthetic biology is working hard to produce such things, but they aren't found naturally in significant quantities I think.

note that methanogens actually use $H_2$ that is generated by other bacteria.

Isn't natural gas mainly methane?

Microbes can produce several gasses other than methane.

All microbes produce $CO_2$ through the oxidation of reduced carbon

Additionally some metabolic pathways produce other gases.

Photosynthetic microbes produce $O_2$
Sulfur reducing bacteria can produce $H_2S$ (as @ohcanada points out)
Denitrifying bacteria produce $NO$, $N_2O$, and $N_2$
Fermenters produce $H_2$ (as @mart indicates)

There may be others that I am not thinking of but these are some of the major players...

Good answer. Although fermentation can produce carbon dioxide too.

@JackAidley indeed they do... thanks.  I edited the answer.

Well, some bacteria can produce Hydrogen Sulfide gas. For example, Proteus and Salmonella. The presence of $H_2S$ producing bacteria is actually clinically significant and we have a way to test for this, which is via the use of TSI (Triple Sugar Iron) media.
Assume you set up the test correctly, $H_2S$ producing bacteria will generate dark deposit within the media.
In the clinical setting, there are other choices beside TSI, such as SIM media and API20E.

Thanks sviter! This is actually my first time using Stackexchange so I'm still trying to familiarize myself about the word format here.

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Are there predators evolved to eat puffer fish?
Puffer fish is known for having a anti-predation defense mechanism of having toxin-exuding spikes.
Are there predators which evolved specifically to prey on puffer fish? (presumably, by evolving immunity to the toxin)?
I know that sharks eat them, but I doubt sharks evolved to be immune specifically to puffer fish toxin, since their evolutionary development preceded puffer fish's.

Wikipedia has some revealing information here:

Not all puffers are necessarily poisonous; Takifugu oblongus, for example, is a fugu puffer that is not poisonous, and toxin level varies wildly even in fish that are. A puffer's neurotoxin is not necessarily as toxic to other animals as it is to humans, and puffers are eaten routinely by some species of fish, such as lizardfish and tiger sharks. Also, Japanese fish farmers have grown nonpoisonous puffers by controlling their diet.

It seems that susceptibility to tetrodotoxin varies a lot from one animal to another, and so some natural variation might allow a reasonable amount of predation to occur.  I also wonder whether the variation in the amount of toxin in the fish implies that the fish are often depleted.
There are cases of animals who have evolved a resistance to Tetrodotoxin, but for the most part its may the predators you are thinking of.  The toxin is synthesized by a symbiotic bacteria and is found not only in fugu but also blue-ringed octopus, rough-skinned newts and some sea slugs.  These animals probably all began with enough intrinsically low sensitivity to the toxin to take on the symbiont and probably evolved to be completely insensitive.  To find a predator that would have co-evolved a similar resistance you would look for a predator that particularly favors the envenomed animal.  In the case of the rough skinned newt, its suspected that the common garter snake is an example of such co-evolution. Others may be out there to discover - its probably difficult to watch marine animals to know what their typical predators are.

I'm curious if some predator evolved to be immune to the toxin. Is there some data on whether those species that pray on pufferfish evolved this way, or is that purely an accident of environment, as is the case with sharks - which decidedly did NOT evolve to deal with pufferfish?

Added a note on that...

thanks @DVK  I should add that its also possible that Fugu could be a small enough player in its environment so that no predator has selectively pursued it.  It depends on the likeliyhood that an animal can be susceptible to the toxin and how many sources of food there are for those predators in the environment.

I know there are species of sea snakes that actually aren't bothered by the puffer fish's toxins! So they will eat them easily because puffer fish are extremely slow swimmers. Besides that sharks are the only other species, in specific Tiger Sharks don't have any consequences to consuming pufferfish.

Can you provide citations for the content in this post? Otherwise it may be deleted.

It would be an excellent answer with linked references.

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HSL Lightness vs Eye sensitivity
In a monochromatic spectrum, is the human eye equally able to distinguish between lighter colors just as it is in distinguishing between darker colors? I mean is there really a linear relationship between the Lightness property in the HSL color model and the perceived brightness?

Related question

I'm not sure this is really the best possible SE site for this question; my answer below, at least, has very little biology in it. There's no "Colorimetry Stack Exchange", but I'd think this would be on topic e.g. at [graphicdesign.SE]. Alas, they don't have MathJax... maybe [physics.SE] would be a better fit? Or [cogsci.SE]?

No, the L axis in the HSL color space does not really correspond to lightness as perceived by the human eye, except in the very crudest sense that, for given values of the H and S components, increasing L produces an increase in the perceived lightness.
The L component of the standard HSL color space is simply calculated as the average of the lowest and the highest RGB component of the color (in whichever RGB color space in being used): $$L = \frac{\min(R, G, B) + \max(R,G,B)}2$$
This definition alone should make it obvious that the L value cannot correspond to perceived lightness, since it completely ignores the middle one of the three RGB channels.  Thus, the color (R=0, G=0, B=1), i.e. pure $\color{#0000ff}{\rm blue}$, has exactly the same L value (0.5) as the color (R=0, G=1, B=1), i.e. $\color{#00ffff}{\rm cyan}$, yet it's obvious at a glance that the latter color is visually much brighter.
Indeed, the HSL color space doesn't even try to match the perceptual lightness of the colors; rather, the definition of the L channel is chosen because it has the convenient feature that it maps black to L=0, white to L=1, and all the six maximally saturated pure RGB colors (red, yellow, green, cyan, blue and magenta), despite their wide perceptual lightness differences, to L=0.5.

A much better approximation to the perceived lightness of a color is the luma Y', which is defined as a weighted average of the RGB channels.  The precise weights depend on the definition and the RGB color space used, but a common choice (from ITU-R Rec. 709) is: $$Y' = 0.2126\, R + 0.7152\, G + 0.0722\, B$$
The weighs are chosen to account for the different perceived lightness of the different RGB primary colors.  A striking feature is the that the green component alone accounts for over 70% of the luma, nearly ten times as much as the blue component.  Yet a visual comparison of $\color{#0000ff}{\rm 100\%\ blue}$ with $\color{#00ff00}{\rm 100\%\ green}$ does clearly confirm that this choice of weights is justified: the pure green appears much brighter than the blue, and almost as bright as the cyan (which is their sum) above.

However, the definition of the luma still ignores the non-linearity of both the standard RGB color spaces (such as sRGB) and the human eye.  While these two effects partly cancel out each other, allowing luma to be used as a reasonable approximation of perceptual lightness, for truly accurate results they need to be accounted for.  This involves several steps:

Convert the RGB color into a linear color space.  For sRGB, the following formula may be used: $R_L = f(R), G_L = f(G), B_L = f(B)$, where: $$f(C) = \begin{cases}C / 12.92 & \text{if } 0 \le C \le 0.04045 \\ ((C + 0.055) / 1.055)^{2.4} & \text{if }  0.04045 < C \le 1 \end{cases}$$ (Here, $R$, $G$ and $B$ are the sRGB component values, and $R_L$, $G_L$ and $B_L$ the linear ones, both scaled to the range from 0.0 to 1.0.)  Alternatively, a very close approximation to the formula above is given by simple gamma-expansion with $\gamma = 2.2$: $f(C) = C^{2.2}$.
Calculate the relative luminance as a weighted average of the linear RGB component values: $$Y = 0.2126\, R_L + 0.7152\, G_L + 0.0722\, B_L$$ (The weights are exactly the same as for the luma formula above, because that's where they come from; the luma calculation just blindly applies them to the gamma-compressed RGB values.)
Convert the relative luminance value into an approximation of the percieved lightness, using something like the CIELAB formula: $\ell^* = 1.16\, g(Y) - 0.16$, where: $$g(Y) = \begin{cases} \tfrac13 \left(\tfrac{29}{6}\right)^2 Y + \tfrac{4}{29} & \text{if } 0 \le Y \le \left(\tfrac{6}{29}\right)^3\\ Y^{1/3} & \text{otherwise} \end{cases}$$ (Note: In the CIELAB standard, the $L^*$ value ranges from 0 to 100, but for the sake of consistency, in the formula above I chose to define $\ell^* = L^* / 100$, so that its range is also from 0 to 1.)


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Lactose Intolerance
What nutrition is given to infants who are lactose intolerant? I understand, in today's day and that age we have non-lactose formula milk, but what happened, before lactose-free milk was created, to those who suffered from lactose intolerance (Native Americans, Asians, etc.)?

The lactose intolerance Wikipedia page explains the problem fairly well, so I'll refer you to that for a more detailed explanation.
Briefly, the most common cause of lactose intolerance is primary lactase deficiency, which affects the majority of the world's population. This only affects adults: the majority of people do not produce lactase as adults.

Congenital lactase deficiency, instead is a very rare, autosomal recessive genetic disorder that prevents lactase expression from birth.
  [...]
  Congenital lactase deficiency (CLD), where the production of lactase is inhibited from birth, can be dangerous in any society because of infants' nutritional reliance on human breast milk during their first months. Before the 20th century, babies born with CLD often did not survive, but death rates decreased with soybean-derived infant formulas and manufactured lactose-free dairy products. Beyond infancy, individuals affected by CLD usually have the same nutritional concerns as any lactose-intolerant adult.

A couple of good references:
Lactose intolerance in infants, children, and adolescents. - Heyman, Pediatrics 2006
Genetics of lactase persistence and lactose intolerance. - Swallow, Annu Rev Genet. 2003

To expand on the infant thing: lactose is present in most mammalian milk but mammals usually only consume milk as infants so there is no need to preserve functioning into adulthood. It's only our weird fondness for milking other animals that has led to selective pressure on retaining the necessary enzyme into adulthood.

In fact, being lactose tolerant is the mutation. Adult mammals are normally not lactose tolerant, only the still milk drinking babies have the lactose gene activated. Humans developed this mutation earliest in the Neolithic.

Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk.

(citation from Burger et al., PNAS, 2006)
So in fact, people who are lactose intolerant are just plain normal. There is normally no reason to feed babies lactose-free milk. The rare cases where you need to do this are very well described in the post of nico.


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Why seeds won't sprout given excess water?
What would cause a seed to not sprout despite showing signs of germination given excess water? Oxygen, temperature, and light were sufficient for germination and sprouting in seeds of a slightly lesser amount of water.

What kind of seeds are we talking about here - some have special requirements

I think the answer to this question is like this.   Some seeds can sprout with this much water - even germinating underwater. The seed could sprout, but why doesn't it?  Some living things actually have adapted highly specialized conditions for growth - why should this be?  I'll try to come back later and put an answer up if this is right, and nobody else does.

You've stated in your question that oxygen was sufficient for germination, but if there's too much water this probably isn't the case. It's likely given excess water seeds will drown- that is they have not got access to sufficient oxygen to continue germination.


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Can spider silk be synthesized to be used for 3D printing?
With the recent rise in 3D printing, I keep hearing about more novel ways to use the technology: cell 3D printing, liquid aluminum or plastic 3D printing. For example,   this Ted talk deals with printing a human kidney. What interests me is if the current technology can be adapted to print with spider silk. The silk has some amazing properties, and apparently there are multiple types of silk that spiders use.
I found this project: Spiderbot 3D printer.  Can spider silk actually be synthesized in large enough amounts to enable 3D printing?

Just a note, the spiderbot printer you linked to is a multimaterial, but it does not print in spider silk =)

The "...in large enough amounts to enable 3D printing?" part of your question is, I think, still unknown, but spider silk has been being synthesized in transgenic goat milk for quite a long time already, and I suspect that it's now just a matter of time before the answer to your question is an unqualified "yes."
See Macromolecules, 2011, 44 (5), pp 1166–1176, doi:10.1021/ma102291m

Synthesizing spider silk seems to be developing quickly, but for 3D printing we need not just synthetic spider silk, but a liquid form that can solidify once printed. I would imagine it is going to be two or more liquids mixing together at the printhead and then bonding and solidifying with the adjacent layers, like spider silk epoxy.

No, but there is research towards it
there are two methods to look at.
Replicating spider spinnerets and the correct glands is very difficult but not impossible. It is currently a focus of research becasue it would both produce and shape the silk.
The other method is using vat grown silk and pulling it through a printing process, Not yet possible but will probably happen before the first since it involves fewer new processes, possibly. Spider silk can already be added to printer media and printed, but this only makes up a portion of the material. It cannot be printed by itself yet, which is what everyone wants.

spiders silk can't be synthesized very accurately. Carbon is much easier to integrate into 3D prints, it's very commercialized, and only 1-2 3D printers using carbon is available. Silk is much more complex:
They still don't understand the structure and lacing of the proteins very well. milestones of research demonstrate the technical difficulty of the task:
"Solid-State C-13 Nmr of Nephila-Clavipes Dragline Silk Establishes Structure and Identity of Crystalline Regions" 1994
"The molecular structure of spider dragline silk: Folding and orientation of the protein backbone"2002
"Molecular orientation and two-component nature of the crystalline fraction of spider dragline silk"1996
"Stretching of supercontracted fibers: a link between spinning and the variability of spider silk"2005
Spider silk is immensely complex, and contains multiop;e proteins woven together in specific patterns to achieve different elasticity and strength, and the spiders typically have mutliple glands for different types of silk, which use very specific pH gradients and complex chemistry and physics, which we can't match at all.
this page gives some info on recent industrial advances:
https://www.sciencedaily.com/releases/2017/01/170109124957.htm
it sais that you need 1000 protein fibers wound together to make a single spider's silk thread.
this page gives recent advance.
http://cen.acs.org/articles/92/i9/Spider-Silk-Poised-Commercial-Entry.html
For the moment, spider's silk is not commercially available for textiles or fibers, except for stuff taken out of a spider. A spider isn't heavy you can't print much from a spider :)
for the recent spider silk news, see here:
it's all research news as of summer 2017, not sales and business news. so... spiders silk can't be synthesized with volume and accuracy to compete in any commercial fields. Making some of the proteins found in the silk is only the smallest and easiest part of the puzzle.

There are commercial spider silk projects:
In May 2017 Kraiglabs delivered spider silk samples to a US military contractor:

“We are pleased to report that we have delivered the first samples of Dragon Silk to our US Army sponsor for independent performance confirmation,” said the Company’s COO Jon Rice.  “These samples mark the starting point for what we hope will be a long lasting and profound impact on protective equipment for those dedicated to protecting us.  The speed that our Indiana facility was able to ramp up to meet this request helps to confirm, that we have the ability to promptly deliver a top quality, cost effective, fiber to the Army and future commercial customers.”

Bolt Threads presented it's first Spider Silk product at SXSW:

Bolt Threads, a San Francisco-based start-up working on the next generation of advanced materials, is unveiling a limited edition knit necktie, made of its 100% Boltspun spider silk.
  [...]
  More specifically his team of dozens of scientists, engineers, technicians and designers, have developed a way to closely mimic silk created in nature by producing a fiber from corn syrup that was fed to a yeast fermentation, which secretes a 80kDa Major Ampullate (dragline) spidroin protein. Once the protein is harvested and purified into a powder, it is wet spun into fibres, twisted into yarns and knitted into the tie.

Last year Spiber announced a spider silk parka for the Japanese market:

The $1,000 "Moon parka," selling only in Japan, is a gold-colored jacket that uses the same design as typical North Face parkas. However, the item is made from a synthetic spider silk developed by Spiber, according to Bloomberg.

Producing a large amount of the silk doesn't seem to be a key problem. On the other hand, it's not clear that the current companies offer a product that you can use with a 3D printer.


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Why did the urinary bladder evolve?
Sure it's convenient to decide when to urinate but not essential for survival or reproduction, as I understand. But just convenience is not a drive for evolution.
Does the bladder serve any essential purpose? If not why did bladders evolve?

The urinary bladder is not unique to mammals.

Well a Naïve answer for a Naïve question: It's not very "convenient" to leak urine constantly and create a beautiful path leading directly to you when you have lots of predators around looking for you. It's very "convenient" to be able to mark your territory if you're a predator.

The benefits of adaptations can be very small and still be widespread. It doesn't have to be life or death 100% of the time.

apparently mice urinate all the time/as they move

I've changed the question to be more general, without the mammal focus. @Paul A. Clayton's answer is more broadly applicable than just mammals.

@rg255: working with mice every day I can assure you they do not.

@shigeta: although I agree with you for the general case, this is probably a situation where the trait gives you a fairly strong "life or death" advantage...

@nico thanks, I thought that may be a bit of a myth

This is good explanation of a possible role of the bladder
https://link.springer.com/article/10.1007/s42452-019-1692-9

Here are just a few points that might apply:

Urine is used for scent marking by some species, so the ability to store urine could be useful.
At the opposite side, controlling the release of a strong scent would help in stealth for both predators and prey.  (In addition, a single strong scent might temporarily overload a predator's sense of smell making tracking more subtle scents more difficult.)
Flushing an excretion point (single point reduces opportunities for invasion) under some pressure could help avoid blockage and parasitic invasion/accumulation.  (Providing a tube from the extraction organ to the excretion point allows more flexible (and protected) placement of the organ, but also increasing the benefit of a flushing mechanism.)
Flushing could also reduce contact with skin. Urine might act as an irritant and a nutrient source for parasites.
Adding a buffer is a common technique for any pipelined operation to allow smaller resources to handle temporal variation in input and output rate.  Without a such a buffer, all stages have to be sized for the maximum utilization rather than something closer to average utilization.
Avoiding potential contamination of food and water may also be a benefit of controlled urination (or excreting might have a fertilizing or pest-deterrent aspect for plants).

Since terrestrial animals presumably retained urinary bladders developed by their marine ancestors, benefits associated with terrestrial lifestyle would only provide selective pressure to retain such a feature. However, if somehow a line of terrestrial animals abandoned urinary bladders, it is not entirely implausible that even scent marking benefits could increase the selective pressure enough to overcome some peculiar opposing selective pressure.
Initially, the animal might apply scents by scratching at an area of skin irritated by urine release against some surface. Then this scratching might be preferentially located (i.e., a scent marking behavior is developed). Having such a behavior would then obvious bring benefits to storing a significant amount of urine and eventually to being able to squirt the urine (allowing the scratching behavior to fall away).
The above are just somewhat reasonable speculations about what selective pressures might encourage the development (and retention) of a urinary bladder.  Hopefully, someone with actual knowledge will provide a better answer documenting established theory and evidence for how urinary bladders actually developed.

To get rid of excessive liquid as well.

I'd add to this excellent answer that some desert tortoises store usable water in the bladder. They can reabsorb it from the bladder somehow.

I doubt the validity of your first point; I do not see how urine could be used for scent marking until it has evolved. I think it's a case of exaptation of an existing feature for a new purpose.

@JackAidley Does the edit address your concern? (Note that all of the "above are just ... speculations", though I think they are "somewhat reasonable".)

@PaulA.Clayton: Not really. There are grades of speculation, aren't there? And we're free to disagree on what its reasonable and what is not. The rest of your points are good, I just disagree that the first in plausible.

A few observations to add to Paul's:
Urinating on yourself in winter could be a fatal thermoregulatory mistake.
Urinating on your substrate could hinder locomotion.
Having a continual slick of high osmolarity fluid on your skin would be damaging to the epithelium and work at odds to the action of the kidneys.

do you have references for these?

perhaps this is better as a comment on the accepted answer? maybe ask @Paul-a-clayton to add them in if valid

@GriffinEvo Craig didn't have 50 rep.

I'll let you keep the rep and not delete your answer but please put well structured, referenced answers from now on.

Apparently, the urinary bladder is not unique to mammals, and is even found in fish, which one might presume can urinate at any time or even better - expel ammonia out of their gills, so why do they need a bladder?
I found the following article trying to understand what the bladder does in freshwater fish: https://jeb.biologists.org/content/155/1/567.
Apparently they concluded that the bladder is important because the kidneys let too much useful stuff (like Na and Cl ions) out, and letting it sit in the bladder for 30 minutes (as measured in the trouts in that research) allows some of these ions to be re-absorbed by the cells lining the bladder. I don't know if this is why the bladder evolved (which would have been easy - just as an enlarged cavity in front of the kidney holding some urine before it is expelled), or why couldn't a better kidney - absorbing more salts - have evolved instead. I also don't know if mammals still use the urinary bladder in this way. But once it has evolved, it is here to stay, unless it has a negative survival contribution. And as other answers suggested, it probably has positive contribution, if anything - such as avoiding leaving a strong trail of scent leading to you, or avoiding soiling your den with urine.


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Can we use Acetyl Phosphate instead of Acetyl CoA in TCA?
I am thinking Citric Acid cycle and activation of the end parts of Acetyl and alfa-ketoglutarate.
Let's consider only now Acetyl to make things simpler.
I have tried to explain the thing by symmetry - phosphate tetrahedral, while coenzyme A seems to be mostly some V shaped.
However, it does not help.
Can human body use Acetyl Phosphate instead of Acetyl CoA in TCA in some situations?
I know that you can activate acetyl-CoA again by phosphate:
acetyl-CoA + phosphate <-> CoA + acetyl phosphate

Are you asking if acetyl groups can enter the TCA cycle directly from acetyl phosphate? If so, are you asking if citrate synthase can use acetyl phosphate as an alternative substrate or do you envisage the existence of another "citrate synthase".

No, I am not asking if Acetyl group can enter TCA cycle directly. I am asking if Acetyl Phosphate can enter TCA cycle directly. So I am asking if citrate synthase can use acetyl phosphate as an alternative substrate. If no, why?

Enzymes are usually specific to a greater or lesser extent for their substrates. In this case we are looking at citrate synthase which catalyses a condensation reaction in which the acetyl group from acetyl-CoA is added to an oxaloacetate molecule to form citrate. This is the entry point for carbon into the TCA cycle for energy production. The condensation reaction follows an ordered pathway: oxalocatetate binds first and this results in a conformational change which increases the enzyme's affinity for acetyl-CoA by a factor of 20.
Citrate synthase is highly specific for acetyl-CoA as a substrate. The cited reference discusses several aspects of this specificity. The enzyme has a well-defined binding site for CoA, with contacts from both the small and large subunits. This includes the recognition of the adenylyl portion of the molecule.
A relevant quotation from the review:

"Citrate synthase is highly specific towards its substrates. The condensation reaction occurs only with the physiological substrates oxaloacetate and acetyl-CoA."

So, the answer is that citrate synthase cannot use acetyl-phosphate as a substrate because of its specificity for acetyl-CoA.
Wiegand,G and Remington, SJ (1986) Citrate Synthase: Structure, Control, and Mechanism. Ann. Rev. Biophys. 15: 97–117


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What is benjamini
I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some potential pathways the genes belong to(KEGG pathways). However, I have a confusion what this column called benjamini is. What does it denote? Any suggestions?

Probably from Yoav Benjamini and something to do with a statistical test of False Discovery Rate.

please don't cross-post with BioStars without acknowledging it in your question -- http://www.biostars.org/p/64888/

It is a Benjamini-Hochberg q-value, similar to a p-value corrected for multiple hypothesis testing using the false discovery rate.


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Effect of doubling volumes of PCR reagents
We ran PCR with a positive control and two lanes of sample. We used the same sample, but in one PCR mixture we used a total volume of 50μL (25μL Taq, 5μL forward&reverse primer each, 10μL sample, 5μL dH2O) while in the other we halved each volume to a total of 25μL. Pipetting was done by the same person.
The positive control and the 25μL total volume lane gave nice and clear bands, but the 50μL sample showed nothing. How could this be explained?
Edit: We only ran one PCR with all the samples simultaneously, so no second thermocycler or different temperatures or anything. Didn't even consider that option!
Edit 2: In case it's relevant, we were using this: http://www.chemheritage.org/discover/collections/collection-items/scientific-instruments/perkin-elmer-cetus-model-480-dna-thermal-cycler.aspx

Could you attach a picture of the gel? Also, how many times was this experiment repeated? I have used different volumes many times with no difference in efficiency (but with Phusion polymerase)

The thermal cycler adjusts sample temperature based on the volume of the sample. So if you run samples of different volumes side by side, not all of them will cycle through the optimal temperatures of each step. If you were working with a "hot start" polymerase this is even more critical, as the Taq won't be able to amplify at all unless the sample is heated up to a specific temperature.

But presumably, @Armatus used different thermocyclers and he entered the appropriate volume of the sample in the thermocycler options.

@GerganaVandova I didn't presume either that they did or didn't. In both cases it's still a probable reason for this problem. I imagine an ideal set of answers as all probable reasons for a problem. Then anyone looking this up in the future could use the answers to troubleshoot.

Does this apply to very old models? How would the thermocycler test the volume in a tube or the temperature it reaches? We weren't using a hot start.

Older models simply raise the block to the temperature and don't worry about controlling for getting the liquid in the tube to the indicated temperature. In this case, it is possible that the real temperatures were different depending on volume.

That sounds like the most likely problem; I think you should post that as an answer.


text:
Why does Glutamine have the symbol Q?
Spent a half hour googling this and the best I could find was this:

Now for some rhymes: Arginine = R. R we having fun yet?
  Asparagine = N The kNights of Ne say "Ne".
  Glutamine is a cute amine = Q
  I say "glutamate"/a former vice president says "glutEmate" = E
  ditto with AsparDic acid = D
  Fenylalanine makes tasty italien sausage = F
  Theres are two rings in tryptophan, and there are two v's in W = W
  Tyrosine = Y, Y? Because we love biochemistry. Source: One letter codes, rhyme and reason

Because glycine took G?

Did you want a mnemonic or did you want to know why it was assigned that particular code? The cute-amine was the mnemonic I learned.  It may be related to the rationale behind the code, but that could be something else entirely.

@dd3 I want to know why it was assigned that particular code

@Kevin That reasoning makes sense for Lysine (since its the letter before L) but Q is several letters away from G. Though I suppose Q could have been the next available. That may be the simplest answer, thanks.

The Biology Project from the University of Arizona provides the best explanation of Dr. Margaret Oakley Dayhoff's logic for the non-obvious single letter AA abbreviations:
Glutamine ~ Q-tamine therefore, Q

Initial letters of the names of the amino acids were chosen where
  there was no ambiguity. There are six such cases: cysteine, histidine.
  isoleucine, methionine, serine and valine. All the other amino acids
  share the initial letters A, G, L, P or T, so arbitrary assignments
  were made. These letters were assigned to the most frequently
  occurring and structurally most simple of the amino acids with these
  initials, alanine (A), glycine (G), leucine (L), proline (P) and
  threonine (T).
Other assignments were made on the basis of associations that might be
  helpful in remembering the code, e.g. the phonetic associations of F
  for phenylalanine and R for arginine. For tryptophan the double ring
  of the molecule is associated with the bulky letter W. The letters N
  and Q were assigned to asparagine and glutamine respectively; D and E
  to aspartic and glutamic acids respectively. K and Y were chosen for
  the two remaining amino acids, lysine and tyrosine, because, of the
  few remaining letters, they were close alphabetically to the initial
  letters of the names. U and O were avoided because U is easily
  confused with V in handwritten material, and O with G, Q, C and D in
  imperfect computer print-outs, and also with zero. J was avoided
  because it is absent from several languages.
Two other symbols are often necessary in partly determined sequences,
  so B was assigned to aspartic acid or asparagine when these have not
  been distinguished; Z was similarly assigned to glutamic acid or
  glutamine. X means that the identity of an amino acid is undetermined,
  or that the amino acid is atypical. "Nomenclature and Symbolism for Amino Acids and Peptides"

U is the code for selenocysteine.

IUPAC-IUBM add it in 1999.http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1327.1999.news99.x/pdf

I know, it's just that I did my PhD on selenoproteins and everyone forgets selenocysteine and that makes me sad :(.


text:
How long can I store autoclaved disposables and reagents?
I want to stock up on autoclaved disposables, such as Eppendorf tubes, pasteur pipettes etc., and some buffers.
If I don't open the container after autoclaving, how long can I store autoclaved materials and consider them still sterile? Does it make a difference if the material is dry or if it is a liquid?

This is a non-answer, but may be worth checking out for other reasons: http://ohp.nasa.gov/policies/pdf/WFF_Autoclave_Recommendations.pdf

This page for surgical instruments says it's 2  months, or 6-12 months: http://www.research.drexel.edu/forms/compliance/iacuc/pol_autoclaving.pdf.  I imagine that disposables might be less...

@dd3: why would it be less?

@nico: To be honest, I was mostly thinking of degradation of plastics. That's probably not the issue here, though.

Not really an answer I know, but too long for the comments...
This is still too broad a question.  a well sealed, sterile plastic usually has a use by date, but can probably be used more than a year after you receive it.  But these cases are not usually the issue.
Its sterile medium and chemicals, each of which needs to have their own due date.  LB can be used months after autoclaving, but antibiotics break down chemically in weeks (ampicillin 1000x stocks lose their potency in a month).  Even in the refrigerator Agar plates show colonies after a couple of months and dry out quickly.
So more details would be necessary and the case by case policy is the rule.
added in response to comments
Its really a matter of how well they are sealed. An autoclaved bottle will stay sterile forever, until something gets into the bottle - it depends on how well you have sealed things up and the storage conditions.  For stuff sterilized in lab I would tend to use it within a couple of months. For eppendorfs we'd tend to sterilize a few hundred in a beaker and not worry about them...
Our experiments were working with purified protein were only medium sensitive to bio-contamination; they would be done in a few hours and then sterile filtered again.  If you were purifying RNA for instance you would be much more paranoid I'm sure.
If you start to see contamination I would lower the use date and or improve your protocol.
Plastics that come sterilized and sealed by the manufacturer in 3-5 mil plastic bags have really long use by dates and I've used them for up to a year after we received them.

Thanks, I was asking specifically for plastics and buffers, such as PBS. No medium or antibiotics.

I wouldn't use sterilized buffers more than a week after I made them - sterile filtering is easy to do just before you use them.  but that's me.

Great, so from what I gather: sealed autoclaved plastics can be used even after a year of storage. It is safe to presume buffers are good for a week. That pretty much answers my question. I think it outlined clearly in the answer for future reference.

i see - i've added to the response.  this is getting into subjective territory, but I put in some more detail there... there are bound to be those who disagree :) if you are starting to work with animal cells or bacteria it will really vary.  This answer might be enough to get you started...

can you even safely autoclave ampicillin? I would have thought it would degrade in solution at that temperature.

i don't think so.  the general protocol is to make a 1000x concentrated solution, sterile filter it then add after autoclaving. ampicillin goes in solution so freeze the stock solution at -20C and use the plates within a month or so...

http://openwetware.org/wiki/Ampicillin#Stock_Solution describes this fully.

If you work in a lab, there must be a SOP(Standard Operating Procedure) and you can (You should...) follow that. Each lab will have different standard so providing a single definitive answer here may not be beneficial.

Thanks, but I posted this because it's up to me to establish the SOP in this case :)

I expect there to be different established practices. I just need a ballpark of the amount of time I can store autoclaved products - that should be an objective measure.

The question is quite clear: how long autoclaved plasticware stays sterile? Sterility does not in any way depend on SOP. Either something is sterile or it is not.


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Why re-label the strand ends in 3' DNA labelling?
I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.
I took a diagram from my lesson and tried to understand with it; this is what I understood.
If I’m wrong, please tell me and correct me.

We take a restriction enzyme which will cut both strands. The bottom strand will be a 5’ end. So, the top strand is shorter than the bottom strand.
We will add a Klenow fragment which, with its polymerase activity, polymerizes in the 5’->3’ direction the missing part of the top strand, with dNTP α 32P (labelled by a radioactive phosphate in the alpha position).
We get two strands which have the same size, of which one will be strongly labelled.
We finish with a terminal transferase which will catalyse the addition of dNTP α 32P on the 3’OH ends of both DNA strands (in order to label these ends).

But, if I’m right, could you explain the necessity of the last step; why label both ends since we have already labelled the top strand?

Welcome! It will help if you explain the purpose of labeling the DNA according to the lesson: Are you creating a radioactive probe for in situ hybridization? For Northern blotting? Is this a RACE assay?

The goal of this label is not defined ; it is just in the part "how to label DNA " ?   I see that "in situ hybridization", "Northem blotting" are quoted after this part.

Are you asking why it is necessary to label both strands in the final step versus just labeling the bottom strand, or are you asking why it is necessary to label both strands versus labeling only the top strand?

There are many ways to label nucleic acids for probes (Summary of Methods).
While there are cases where Klenow fragment-mediated fill-in should sufficiently label both strands of your probe, there are many others where this would not be enough.  Here are two illustrative, although somewhat contrived, examples:

Example 1: Double digest with 5' and 3' overhangs
  Imagine you did a double digest with BamHI and KpnI to release your probe sequence from the plasmid in which you propagate the sequence.  BamHI will give you a 5' overhang, but KpnI gives a 3' overhang.
Resulting BamHI & KpnI double digest fragment:
  5'-    GATCCNNNNNNNG      - 3'
             |||||||||
  3'-        GNNNNNNNCCATG  - 5'

Subsequent treatment with the Klenow fragment + $\alpha$P32-dATP + cold dNTPs will both fill-in the 5'-overhang (Klenow's 5'->3' polymerase activity) and remove the 3' overhang (Klenow's 3'->5' exonuclease activity).
Post-Klenow reaction (bold = new bases, * = radio-labeled nucleotide):
  5'-    GATCCNNNNNNNG      - 3'
         |||||||||||||
  3'-    CTAGGNNNNNNNC      - 5'
           *

At this point only one strand is radio-labeled so the terminal transferase step is needed to add a label to the top strand.

When using $\alpha$P32-dNTPs, you often pick only one base to be radioactive (eg dATP as above).  Sometimes you also just spike the reaction with radioactive dNTP leaving a population of cold dNTPs to be used most of the time.  In either case you now have the chance of not incorporating only non-radioactive bases.

Example 2: Fill-in reaction that fails to incorporate $\alpha$P32-dATP:
Imagine a digest with PspI and want to fill-in the 5' overhangs using $\alpha$P32-dATP + cold dNTPs.  PspI recognizes CCWGG sequences where W is either A or T so that some fill-ins will incorporate the $\alpha$P32-dATP, but others will not.
Possible digests and fill-in reactions:
   5'-  CCTGGNNNNNNNNNNCCTGG - 3'
        ||||||||||||||||||||
   3'-  GGACCNNNNNNNNNNGGACC - 5'
                 |
         Digest with PspI
                 |
                 V
   5'-  CCTGGNNNNNNNNNN      - 3'
             ||||||||||
   3'-       NNNNNNNNNNGGACC - 5'
                 |
        Fill-in with Klenow + hot dATP + cold dNTPs
                 |
                 V
   5'-  CCTGGNNNNNNNNNNCCTGG - 3'
        ||||||||||||||||||||
   3'-  GGACCNNNNNNNNNNGGACC - 5'
          *

Again you are left with only one strand being labeled (or no strand labeling if the sequence was 5'- CCAGGNNNNNCCTGG - 3') and a need for the terminal transferase step.


text:
Specific enzyme for C. elegans
We are looking for an enzyme that appears in C. elegans but isn't common for: human, Drosophila or mouse.
We need it for a little research project, thanks for your help!

why enzyme? if its any enzyme, why not any gene? loosening up in this regard might make it easier.

what is your actual question?

What level of similarity would be acceptable? What do you mean by "isn't common"? What exactly do you want to do?

Do you just need a unique protein/DNA sequence, and how unique and how long does it need to be? What exactly is the aim of your project? A common problem is that protein/enzyme names may not be identical between species, but their functional domains and/or sequences could very well be, since many processes of life are conserved from one species to the next.

This question would fly rather well if you asked 'how can i find genes that are unique for C elegans?'  Is that what you want to know?

You might explore Li et al (2004) "Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene" Cell 117: 541-552.  (Pubmed Abstract).
Largely the authors focused on comparisons of Arabidopsis, Chlamydomonas and Human genomes, but they did also include C. elegans for comparisons with at least Chlamydomonas (Summarized in Table 1).  Even if they do not give you exactly what you need, you could apply their methods for your particular project.

One way to approach this is to use one of the protein database clusterings available.
Researchers have taken huge protein databases, like UniProt, which basically catalog all known protein sequences regardless of species and clustered the proteins by sequence. The results provide many interesting insights about protein families, but more importantly they are well-fitted for your problem. A cluster would be a set of sequences that are similar to each other but are relatively different from all other known proteins. So, essentially you would be interested in a cluster that is only has c elegans proteins.
I went ahead and used ProtoNet, which is one such tool, and searched for such a c elegans cluster. I found two potential clusters: 4375747 and 4430980, which have mainly c elegans proteins.
Disclaimer: I have been involved in the past in the development of ProtoNet.


text:
Can the sulphur content of biological material be reliably calculated from fat, fibre and protein contents (Weender Analysis)?
An often-used analysis of feedstocks for lifestocks is the Weender analysis, which basically divides the volatile solid content into fats, fibre and protein, as well as N-free matter. I found no English language article on the process.
The individual values and how they are arrived at are:

Fat: anything dissolvable in organic solvents;
Fibre: anything not dissolvable in acids or bases;
Protein: N-content times 6,25 or 6,38 for plants or protein (and the N-content in protein is most of the times close to 16%);
N-free: the rest (sugars, starch, pectines, organic acids ...).

This data is often more readily available than a full chemical analysis.
I want to know the sulphur content - can I reliably say fats contain v mass-% sulphur, proteins x mass-% ... and so on?
If yes, would this be applicable to manure also?

I would say theoretically yes, if you know lots of other information, but practically no, because of all the unknowns.
According to this paper cysteine content and therefore sulfur content of proteins vary depending on what kind of organism your organic material is coming from. Animals have more, bacteria tend to have less.
The sulfur content as a fraction of protein content in a given animal or plant is constant or nearly constant across the entire animal/plant. If a sample's protein content is 50:50 corn protein:sheep protein it's possible to estimate the sulfur content of the protein fraction from the sulfur contents of the sources of the protein.
In addition the sulfur content can be affected by fermentation and sulfur/sulfate-reducing bacteria, many but not all of which are anaerobes. So figures for whatever the source of the feedstock is (as far as cysteine content) can be affected by whatever happens to it afterwards. Chicken waste with a high sulfur content allowed to ferment may give off fairly large amounts of hydrogen sulfide, lowing the sulfur content without necessarily affecting the bulk protein content. The reverse might also happen, where protein is digested and sulfur is released as sulfates but kept in the mixture.
Even if you know for certain the sources of all of the protein(and that no further biological activity has changed them), the unknown amount of organic acids is going to throw off your sulfur estimates if there are sulfur-containing organic acids in the N-free fraction.


text:
Does the Urea Cycle exist in invertebrates?
Do invertebrates (like Drosophila and C.elegans) have a urea cycle?

Questions that ask about "invertebrates" as if they were one group always make me uncomfortable. "Vertebrates" are a well-defined group, but "invertebrates" are just animals that aren't vertebrates. They are diverse, and it is nearly certain that the answer to your question is "some do, some don't".

C. elegans is missing all of the urea cycle enzymes. Drosophila is missing just one enzyme, but there's a shortcut which may enable it to nonetheless complete the cycle. (For comparison, here's the pathway map for human with the complete cycle.)

Perhaps worth adding that the role of the urea cycle in terrestrial vertebrates is the disposal of excess N derived from protein metabolism. Such animals are ureotelic. Arthropods, in contrast, are uricotelic, using uric acid for N disposal, so it would make no sense for them to have a functional urea cycle. (Nematodes - I don't know.)
The importance of avoiding having a urea cycle when it is not needed is illustrated by the situation in yeast (Saccharomyces cerevisiae). In yeast some of the enzymes that would be part of the urea cycle are used in degrading arginine, while others are used in the biosynthesis of arginine. Yeast cells will carry out one or the other of these processes depending upon their metabolic status. If both processes were to be active at the same time this would result in a urea cycle that would waste ATP. This is avoided by having a multienzyme complex consisting of arginase and ornithine transcarbamoylase (in the degradative and biosynthetic pathways respectively), allowing reciprocal regulation so that only one of these is active at any time.


text:
Chromosomes are of different size but why do all chromosomes have similar GC percentage?
When I browsed NCBI I saw a pattern: even if the chromosome sizes, number of genes, and number of proteins are different, GC% in chromosomes tend to be similar. The examples are linked below.
Yeast,
Plasmodium falciparum
If you see Mitochondria genome it is not very similar to chromosome. Why all chromosomes tend adjust their GC% near to the average of total GC%
Is there a specific reason related to metaphase of meosis?
to further clarify I have some images to help

The chromosome size or genes in an organism are not adjusting near the average of their total but GC% does. It has only 3-2% (falciparum) or 3-4% (vivax) variation in GC%. It feel like its balancing like equalizer. Why?

Just to clarify: are you asking why chromosomes of very different sizes each have an average GC content that is similar to the average GC content of the genome?

Yupp you got it... I just want to know why and how at any stage of evolution an organism like [plasmodium vivax] (http://www.ncbi.nlm.nih.gov/genome/genomes/35?details=on&) (43-47%) and faciparum (18-20%) (2 evolved types) try to maintain similar GC% in all chromosome (look a the links given the it feels all chromosomes are maintaining their GC% percent in chromosomes and they dont care for amount of genes or chromosome size)

As @dd3 points out, average GC% indicates a need for stability and coding regions or structural regions of the genome may need to be more stable.  But the largest %GC in genomes are found in thermophiles - organisms which live in high temperature water - in hotsprings and undersea geothermal vents. This review mentions how some thermophiles can be found with 50% GC.  The extreme thermophile Thermus thermophilus can have a GC% content of 69.4%.
But you are asking how does GC content get averaged out over the length of a large genome.  The answer is variation and selection.  When a gene needs to be more stable because of genomic function or because its trying to live in a hotter environment mutations that convert A/T to G/C base pairs will convey an incremental advantage to survival and will tend to be retained in the gene pool as long as no greater disadvantage to the mutation results.  Over time and as the stability creates a greater advantage, GC % will migrate further and further away from the mean.
This works for both thermo-tolerance and because of the biofunctional constraints of being a telomere, centromere or a coding region - stability and coding constraints play against each other to converge on an optimal GC content in any given stretch of the genome.
Conversely most genomes have a GC content below 50% are migrating there because too much stability can have a cost as well.  Breaking up the DNA helix for transcription and other cellular processes must go smoothly as well for example.
Coding regions are significant for bacteria (E coli is 89% coding sequence).  For coding sequences, the genetic code is logically 50% GC on the average, but if you look at the actual codons in the diagram below you will see that except in the case of a single codon case (tryptophan, methionine) the third base always has a GC option, allowing for a GC content in the mid 60 percentiles.  The constraint of allowing coding sequences to freely vary is only an approximation - in some cases substitutions to amino acids with GC rich codons might move the cieling up a bit. And the more frequent amino acids have the possibility of making 2 or 3 bases of their codon GC bases.  Overall it would be remarkable to find a bacteria with GC% greater than 72%.  Mutations and the requirements of proteins being coded for would simply not allow it.

So: over evolutionary periods these GC mutations accumulate where they are helpful, even to the extent of 2/3 of the genome being GC pairs.  The strongest selective force to accumulate a high average GC% for a genome is exposure of the genome itself to a high temperature environment.
Note that this thermo-stability argument doesn't count for many animals because they do regulate their body temperatures.

I liked your line "stability and coding constraints play against each other to converge on an optimal GC content in any given stretch of the genome." It feels more suitable to my question.  Can I get a reference journal please

Thanks.  That thought is a commonly known idea and its rederivable in practice. Let me add to the answer above..

There is significant variation in genomic GC content, both between species and within an individual genome. An average GC content in the range of 35%-45% is common, although there are definitely organisms that fall outside this range. The plasmodium species you link to above is an example of extreme AT richness (low GC content), whereas some bacterial genomes have as much as 70% GC content or more.
For eukaryotic genomes, nucleotide composition is not uniformly distributed. Just because a genome has an average GC content of 40% does not mean you can select any 10kb region in the genome and expect that region to have +/-40% GC content. Rather, eukaryotic genomes are a mosaic of large regions which internally have a very uniform composition, but whose composition is quite different from flanking regions (isochores).
So although all the chromosomes of a particular organism may have similar average GC content, realize this is just an average and that nucleotide composition varies significantly throughout the genome.

Thanks, I truly get nucleotide composition varies significantly (A:T:C:G changes) but still HOW GC% remains similar throughout all chromosomes. To further clarify vivax (V)(43-47% range) and faciparum (F)(18-20% range) are of same plasmodium family. Eg chr 11 of both have almost same size but their GC% percent fall in particular given range(V: 45:1%, F:19%). It feels like differently evolved organism are trying to maintain particular range of GC%. HOW? And journal reference would be much appreciated.

To begin, one might ask "What is the advantage of higher GC content?"
Higher GC content is associated with higher stability of the DNA, and accordingly, people have suggested that this is important for protein-coding regions.  It has been found that there are quite a few protein-coding regions in GC-rich regions, but I am not sure whether the converse is true, which is the important part.
If the converse is true, then one might look at the distribution of protein-coding regions across the chromosomes and correlate it with GC-content. If also the size of the protein-coding regions in a given chromosome is proportional to the size of the chromosome, then you would have a reason as to why the average GC content of each chromosome is similar.
However, I recognize that this is all very speculative.  Does anyone have better ideas?

I liked the idea of proportionality of chromosome protien coding size and genes.. thanks. Why this question made me think it is important to ask because evolution is with random mutation process and with new environmental conditions the orgamism evolves to form new genes & this will cause random huge variations but by looking at GC% information, though there might be huge variation in sequences of chromosomes, a life is conspiring to maintain an equilibrium in AT:GC ratio. life doesnt thinks It has to keep ATG at beginning and poly A tail end for gene. life just checks the equilibrium

Good answer from Daniel. I'd also add that there can be significant differences between chromosomal or nuclear DNA GC content and that of extra-chromosomal entities like mitochondrial and chloroplast genomes or (naturally occurring) plasmids. These DNAs have different constraints on them (replication, sub-cellular location, eg) and that may be reflected to some degree by a GC content different than that of the nuclear chromosomes.


text:
How do amino acids become attached to tRNA?
Is there a protein that catalyzes this or does it happen spontaneously?
In which part of the cell does this happen?

The process to which you refer is called tRNA charging and is catalyzed in the cytosol by a class of enzymes called aminoacyl tRNA synthetases.

...and it happens in the cytosol.

@ohcanada, sorry for blowing off your suggested edit. I should have given the original question and your suggestion more consideration.


text:
Are there any studies of epigenetic difference between twins during their lifespan?
Are there any studies of epigenetic difference between twins during their lifespan ? I ask because I wonder if there exist phases during lifespan, when environmental factors plays major role (expecially in early adulthood) - twins study should allow to distinguish between changes in epigenetic  profile caused by external factors and that from "inner dynamics" of organism.

I would think there have to be, though do you mean collecting samples on a regular basis and plotting out the difference at each point? Or do you simply mean the total accumulated change. If it is the latter, the answer is certainly "yes". You have probably seen the Nova documentary "Ghost in Your Genes" (The US, not BBC one). In it they show comparison of accumulated epigenetic change between a pair of identical twin Spanish women. I'm guessing you are more looking at measuring this change on a regular basis and looking for points of rapid divergence.... I don't know if this has been done for individuals, but it appears that it has been done for sample sets (see the same documentary). They discuss accumulated genetic change in younger twins vs older ones...

Great ! I think similar, regular studies are going to come, but can you write more on the latter case, for example about rate of epigenetic changes ?

I have seen "Ghost in Your Genes". Excellent doc, which, in part, got me thinking about this (yes the Spanish twins in particular). I was meaning more systematically through life (testing at regular intervals). In the documentary, the observations seemed a bit less pre-defined. On a related note, could anyone point me to the specific methodologies for assessing whole-genome epigenetic differences?

good question, ask it but not as a comment


text:
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I realize the term reasonable is subjective, so characteristics, such as skin color, hair color/texture, approx height, eye color, freckles, etc. I came across this article a few years ago, but the company that made the test went bust in 2009. It could detect race (how accurately?). I seem to recall reading an article a few years ago stating that "soon" we'd be able to get an approximation of appearance from a DNA sample that was better than a sketch artist could provide, though I can't recall now where I read it.

In theory it's possible to have an approximation, but not to know with certainty. Identical twins have the same genomes and look very much alike. Whether it can be done in practice depends on how well we can model the relationship between genes and looks and on how much information is necessary for a judge to permit arresting and questioning a suspect.
Scientists know relatively little about how genes influence physical appearance yet. The height of the suspect is controlled by hundreds of genes with complicated interplay between them, so I don't think it's possible to estimate it just yet. Eye color is more simple: it's controlled by only 3 genes. We know weight is partially controlled by genetics but exactly which genes are responsible is not clear. Age is impossible to tell by DNA alone. Skin color should be predictable, since it's caused by melanin production, and we know which genes are responsible.
So to sum up, DNA analysis can tell the gender, skin color, and eye color of the suspect, but very little about height and weight, and virtually nothing about age. That's not enough information to identify a suspect, although perhaps someone with legal knowledge could comment on this.
But let's say in the future we know enough to determine all these traits. Then DNA analysis would be helpful but never enough to identify a suspect. The problem is that different cells in your body undergo different mutations in their DNA with time. That's how one gets cancer. Let's say there's a mutation in the eye color gene in skill cells from a murderer found on a victim's body. It won't affect the murderer's eye color but it will affect the forensic analysis. So it's impossible to know for sure what the suspect's appearance will be.

I agree with most of your assessment. I'd think that some genetic markers could give an approximation on traits like height though. Clearly diet makes a difference too, but working under certain assumptions I'd think a rough estimate could be made. Fair point about mutations, but I'd be curious to see just how significant those turn out to be on the whole. There would clearly need to be all kinds of other traits analyzed as well. Things like cheek structure, lips, nose, hair texture, freckles, widow's peak, etc, etc. Some of these would be easier to glean than others...

@single_digit You're right to point out that one can make a rough estimate, and perhaps it will get more accurate in the future. One of my main points was actually that a judge would not consider the information enough at present to issue a search or arrest warrant, for example, so it's unlikely that these methods would help in an investigation. I have no formal legal knowledge or experience, though. I'm curious for feedback on this from someone who knows more about the law.

For readers coming along later, it appears the remarks in this answer are now out of date with respect to determining age from DNA.  While not a precise measure of chronological age of the individual from whom the DNA same, it appears a Horvath Clock or other epigenetic clocks can actually give reasonable results in many cases. See this Wikipedia summary as one starting point:  https://en.wikipedia.org/wiki/Epigenetic_clock

As far as I know there are ongoing efforts to find genes that affect forensically relevant traits e.g. facial characteristics and fingerprint pattern type/ridge count, and it's definitely a topic of interest to some law enforcement agencies. However as previously mentioned, there are many factors that could influence complex traits, including in utero environments and other, postnatal effects, such as nutrition, as well as the interaction between those environments and genetic influences. Given past literature showing jury-eligible members tend to over-estimate the importance and statistical accuracy of DNA profiling, however, I think even with future technological and methodological advances in genetic research, this type of evidence should be used with caution, explained with extreme care and thoroughness, and never taken as the single determining factor in reaching a verdict.


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Multiplication to formalize Microbiological Processes
I am not from the field, but have a question regarding modeling in biology:

I know that some processes can be modeled with the mathematical multiplication operation, and wondered if anyone could give me an example (or examples).
Especially with regards to axonal growth and the chemical (de-)stabilization taking place which involve microtubuli and actin, I was wondering if these processes again could be formalized mathematically as multiplication of (several) variables.

I have looked through the internet but did not find anything so far,
any help is appreciated

there are mathematical models for each of these things, but i don't think they usually incorporate all possible parameters and its unlikely they are all linear (i.e. resulting from multiplication alone).

can you give me some link, some example of a multiplication?

Here's the quick answer you asked for, too big for comments so sorry if this is not a full answer either.
This paper is an example of cytoskeletal modelling.  the equations are not simple products (that is to say they have exponentials, derivatives and other non- multiplication operations in them).
This example reference is a simple axonal growth model.  You will see derivatives being modeled as products.  Not sure if this is what you are looking for.

oh good - glad that worked for you.


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Can Palisade Cells Survive Independently?
I have been intrigued by this question. Can palisade cells survive independently from its parent plant in a chemical environment? For example, if we were to separate a palisade cell from a plant and place it in sucrose solution, how long would it survive?

Yes they can. In 1902 Haberlandt reported single palisade cell culture from leaves in knop’s salt solution. Now there are many different methods of plant tissue culture
for PLANT TISSUE CULTURE see


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Question about cell signaling pathways (RTK, Jak-Stat, SMAD, etc)
I am in an embryology course right now and we've just started covering cell-cell communication in development. We were talking about the roles of the various cadherins and their discoveries but we got to cell signaling pathways and in reading my textbook I'm finding myself confused by these pathways-- some of those that are mentioned include Notch, Wnt, FGF, TGF-beta, RTK, Jak-Stat, SMAD, integrins, PTHrP, Hedgehog, Discoidin domain receptors 1&2, and the unfolded protein response (UPR).
I know the RTK pathway and I know the SMAD pathway, but the others just seem to be specific ligands that are using these pathways -- is this correct?

In contrast to each and every one that I listed having its own distinct pathway.

Not sure what you mean. Notch has its own pathway, as does wnt and tgf-beta. Don't remember the other off the top of my head. Why don't you check them out on kegg?

see my comment on the post below -- I could have done a much better job saying what I was confused about in writing this question.

@Alexandria Jak/Stat are two families of proteins which mediate signals through phosphotyrosines.
JAK is a tyrosine kinase which binds to cell receptors and STAT is dimerized by JAK action.  JAK specificity seems to be your question.  A specific JAK protein (e.g. JAK1 or JAK2..) may mediate for different receptors in different cells.
There may be hetero- or homo-dimers of JAK, there may be more than one receptor in a cell using the same JAK enzyme, which may result in cross-talk between the two signals.  I think its a pathway dynamic that can vary quite a bit from one cell to another, depending on the receptor and cytokine environment the cell is seeing. JAK action can be modulated by any number of proteins which respond to other pathway signals or the cell state.  The diagram below from a review of heart muscle cell JAK action is not unusual nor is it complete.

With the exception of Jak/Stat, all of the proteins you mentioned are ligands and/or receptors. When a ligand binds to a receptor, it induces one or more cell signaling pathways, which are dependent on intracellular proteins being activated via association with the receptor, then going on to activate other proteins in a signaling cascade that eventually results in the cell doing something - usually involving regulating gene transcription to make proteins that effect the change - such as altering the cell's developmental fate to become more specialized, for example.
Jak/Stat is an example of a cell signaling pathway, that is also fairly straightforward to understand. Various members of the Jak family are loosely associated with a variety of receptor proteins. When those receptors are activated by a ligand binding to them, Jak becomes activated and recruits various members of the Stat family of transcription factors. The Stats become activated and dimerize (form doublets), then translocate to the nucleus and bind specific promoter regions of DNA. They then recruit the rest of the DNA transcription machinery to transcribe these target genes. The gene products then help effect the cell's response to the original stimulation - the binding of the ligand to the receptor.

Thank you, but I do understand that -- I suppose I didn't write my question very well and I was initially confused because my book explains the receptor tyrosine kinase (RTK) pathway in the context of the fibroblast growth factor family of paracrine factors, because the FGF receptors are RTK's. I was wondering how much of this "sharing" takes place -- how many of these ligands use the RTK pathway? My book implies that quite a few do, but isn't explicit about which.


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Can I use PCR buffer instead of cDNA synthesis buffer?
I am using Fermentase First strand cDNA synthesis kit but its buffer is over. I need to work today but I have not access to any sorce currently. I have PCR buffer in the lab. Can I use PCR buffer instead of cDNA synthesis buffer? What are your other suggestions? Thank you

This page has the recipe for 10X M-MuLV RT buffer:

500 mM Tris-HCl
750 mM KCl
30 mM MgCl2
100 mM DTT
pH 8.3

If you have the basic reagents, I suggest making that.


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Plants without bacteria? is it theoretically possible?
I know from school, that all live on the Earth need bacteria as low-level "machines" that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But it is a natural way.
But is it possible to have a world with plants (without mammals or microorganisms and without bacteria) that could exist in the long term. Saying the atmosphere of these world has already enough nitrogen, oxygen and CO2, and of course there is water.
What could break this artificially created world with such conditions (say the world created not from low-level living structures)?
Could bacteria emerge in the world?

This is the sort of question that should be considered from more than one perspective.  Since this is speculation, take it as a given that there is a lot of 'what if' here.
I doubt most animals and plants can do entirely without bacteria - as you say most of the essential nutrients come from bacteria, who fix nitrogen.  If only plants were left on earth, eventually the plants would use up all the nitrogen and they would have to find a way to fix more.
Can bacteria emerge from just a world of plants?  I don't think viruses arise spontaneously, but since genomes often have viruses embedded in them, over the course of a billion years or so, its possible since bacteria and viruses continue to be impressed upon our genomes.  Would it happen in time?  Most would be skeptical whether that timing could work out.
In practice it would be hard to create a world like this.  I would be interested to see whether you could sterilize the microorganisms off of seeds without killing the plant for instance.  If you're asking about a small sterile environment with only plants, you could do it by adding the nutrients the plants need and giving them sunlight.  Such self sustaining systems have been made with cyanobacteria and i'd be surprised if plants could not be included.  But these are closed systems and judged by limited amounts of time, so whether this is an answer to your question is not clear.  Here it looks like some water plants and fish have been done.  If there was a plant that created CO₂ at an adequate rate its possible.
At one time there were no animals at all.  Its thought that for a while there might have only been photosynthetic structures that lay in the water and soaked up the rays.  Its not clear whether as some say there were colony formations of cyanobacteria as we see today, or whether there may have been larger pre-cellular or proto-cellular structures.  But recovering the pre-cambrian configurations of genes from just plant genomes seems like a gambler's bet to me.

thank you for your arguments and broaden answer! the link about the closed ecosystems is interesting. I think the nitrogen will be the most problem. But also it could be possible that some cells will mutate/break and create free components which can transform further. May be then will the microorganisms appear? Hm...what will be the evolution if one take cyanobacteria to another planet with water?...

Thanks.. its hard to tell with things like this - its possible that plants might evolve to fix nitrogen, if there is enough of it around the world for them to survive long enough.  If all the bacteria and animals were digested into the ecosystem its hard to say how long plants could go on - quite a long time I imagine.

Think of it this way: Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.
Early life would be a basic mechanism, trivial in nature, that under the right conditions would kind of replicate itself (kind of, since the replica would be less similar to the original, than when comparing current parent-child similarity). This would basically be a cell. And a cell would remain a cell unless combining with other cells and specializing in functionality would have a certain benefit. Check out this educational video on abiogenesis by cdk007, based on Jack Szostak's work.
But, you know that evolution isn't the process of change of all individuals of a species in a single direction, towards another species. It's a process of forking. So, basic cells of species A could evolve into single cells of species B, but that would only mean the extinction of A if the new environment with the new organisms becomes hostile, if resources are scarce, if species A is less adapted than everyone else, so everyone else occupies A's niche.
Thus, when multicellular organisms evolve, there are A LOT of monocellular organisms already present and occupying important niches. All available sources of energy are being used. If something isn't used - it's a new niche for any accidental mutation that enables the organism to use that niche and prosper as a new species. So anyway you look at it, multicellular organisms won't start existing without single cell organisms surrounding them. So all multicellular organisms will have an environment that includes these "bacteria", so they will adapt to this environment. It's easier to learn to live with something rather than learning to fight with them and then occupy their niche, because the killing and changing to occupy the niche requires much more changes in the organism.
Life on earth is balanced, such as each species occupies its important place in the circulation of substances. This happened not just by chance, but it's the only probable outcome from the process of evolution by natural selection. Having a world that's totally rid of any trace of primitive life forms is next to impossible. On earth we still have species of archaea that are similar to species present on earth billions of years ago. Read this article on Wikipedia about Nanoarchaeum equitans to get a grasp on the diversity of life.

interesting thoghts, and thank you for the links. but this point argues, why such a world could not start existing in a natural way, why it could not appear "by itself", something like our world (as I understood). but what if you have, say, isolated (physically: with all the known forces) giant spehre, where only simple plants exist: would this world survive as is, would it be destroyed by itself, or would it evolution and some day there would appear other types of organisms, due to the spontaneous mutations of plants DNAs and natural selection?

"Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.". That just simply isn't true.

Amory, these are not my words. It was specifically explained, as a solid rule, by Richard Dawkins. And to explain why this happens - any mutation that reduces the likelihood of that individual to reproduce, will not propagate through many generations. That's why all changes go towards better adaptation to the environment.

static, answering your question - I don't think they would. The food chain will have missing links, so it will not be a complete biosphere. The plants might not survive long enough to reproduce, let alone become subjects to evolution.

One of the most important roles played by bacteria is the fixation of nitrogen. Biological nitrogen fixation is carried out primarily by bacteria. There are no known plants that express nitrogenase type enzyme. So plants cannot fix nitrogen.
Without bacteria in the ecology... the ecosystem is in trouble from nitrogen starvation.
That said, denitrification, the removal of fixed nitrogen and conversion back to nitrogen gas is also catalyzed by bacteria. So no bacteria, no lost of nitrogen by biological means.
Nitrogen can be fixed by lightning discharge. About 5%-8% of all nitrogen is fixed this way http://www.biology-pages.info/N/NitrogenCycle.html. However lightning does tend to cause forest fires... which results in the lost of nitrogen.
So where does that leave us? We will have to guess how much nitrogen is lost from forest fires (and burial by sedimentation) vs gain from lightning discharge.
That is is not at all easy to guess. In a world of high rainfall (lots of rain forest)... you can have plenty of lightning and no fires. But a world of swamps would have also plenty of organic matter (and nitrogen) being lost through sedimentation. A drier world would have more fires.
If anything... I would guess that such a world is unstable in the long term, certainly on a geological time scale. Eventually the environment will change to one where nitrogen is lost, and fixation by lightning is reduced... and the ecology will collapse from nitrogen starvation.

Could bacteria emerge in the world?

My guess is no. A second abiogenesis event is unlikely to occur when life is already present. The plant alive on your world would prevent any new form of life re-emerging. Plants are not quiet neighbors minding their own business. Plants secrete toxin to poison other plant. Limit growth. (Walnuts are a great example) Plant root do absorb simple sugars and amino acids. Example. http://link.springer.com/article/10.1007/BF02202082 So the raw material for new life will not accumulate.
That said... there is no reason why plant life cannot simplify itself to a single cell... such extremes have happened to parasitic barnacles of the Sacculina genus.. which look less like a crustacean (ie crab) than barnacles normally do and more like fungus. https://en.wikipedia.org/wiki/Sacculina
So we could have single cell plants.. descended from higher plants.
What is uncertain is if plants could re-evolve an enzyme to fix nitrogen. Nitrogenase (nif) appears to have evolved once in methanogens and by lateral gene transfer was moved to many other bacteria. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733012/#B7

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164190/
Turns out bacteria-free seeds are unable to propagate because root hairs require ethylene to be produced to grow. Secretions that the plant is unable to generate during the seedling phase (it is shown sterile seeds are unable to generate root hairs in the paper). When bacteria living within the plant's roots (endophytes) are fed sugars (by the plant itself), they release ethylene as a byproduct, resulting in root hair elongation, thus allowing plants to grow.
This is fascinating stuff since i too didn't know of this until and always asked "If soil microbes are important for plant growth, why can plants grow even when hydroponic systems would flush away bacteria from the plants roots?"
So no, your hemp plant would literally, physically, biologically, be unable to grow without the presence of bacteria.
You can completely replace the nutrient fixing bacteria, but until you find a way to inoculate plants with a tiny amount of ethylene (nanobubble tech?) without oxidising off the entire plant root system, bacteria are still required.


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What makes a gene dominant or recessive
We all carry two copies of each gene (outside of male sex chromosomes).  If the two differ from each other often one is dominant and one recessive.  How does this mechanism work on a molecular level?  What mechanism determines which gene gets expressed?

It is not the gene but the allele of that gene that is dominant or recessive. In addition, we do not contain two copies of each gene. Some genes exist at zero or one copy and others are somewhat to greatly duplicated - and this is considered normal (copy number) variation.

I don't have time for an answer, but someone should definitely mention haploinsufficiency somewhere.http://en.wikipedia.org/wiki/Haploinsufficiency

Related: Evolution of dominance of alleles

On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.
In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.
On the molecular level a gene can also encode a dominant-negative variant of a protein. In this case the protein cannot do its job and also prevents the functional version of the protein to do its job too.
A third way this could work is by a gain-of-function mutation. In this case, the gene encoding a protein acquires a mutation that gives a new function to the protein. For example, in Huntington's disease, the mutant Huntingtin protein acquires the ability to clump together in large plaques, which are poisonous to some neurons in the brain. Since it takes only one copy of the protein to perform the new function, the gain-of-function allele is a dominant one.
These are only a few examples that deal with simple dominant and recessive inheritance. Most often there are more complex mechanisms of inheritance at play.

Is there an example in which we observe a dominant condition in which  the protein of the mutant allele prevents the functional protein from doing its job?

Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out.
An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment.
Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant.  Phenylthiocarbamide tasting is an example of this dominance.  If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well.
There are other sorts of dominance.  If a variant shows up that inhibits a the other copy this can cause dominance by a variant; it can remove or modulate a phenotype (trait) by turning off or turning down the other copy of the gene.  This would be a case of trans-dominance.
I'm sure there are many other variants on these themes others could post.  Dominance and recessivity are relative and broad terms when you see how traits are inherited.

Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out.
An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment.
Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant. Phenylthiocarbamide tasting is an example of this dominance. If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well. On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.
In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.

A trait cannot be dominant/recessive, only alleles can be dominant/recessive. As a sidenote: There is a extra 3 at the beginning of your answer and you down vote is not really justified.


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A good textbook on Neuroscience
I want to start learning Neuroscience. Can someone give me an advice about a nice textbook for beginners? I'm particularly interested in the application of Neuroscience in programming and AI development. Thanks in advance.

This is too open-ended.  As an aside, it sounds more like you are interested in artificial neural networks, anyway.

Artificial and biological neural network share only the name... Understanding, say, how a neuron fires an action potential, would not really give you any advantage if you are just interested in AI. On the other hand, there are tons of interesting computational neuroscience problems, which instead require deep understanding of biological processes, but are not necessarily related to AI.

"Principles of Neural Science" by Kandel and Schwartz. That was my introductory textbook for neuroscience at Berkeley.

If you are interested in computational neuroscience, I recommend Dayan and Abbott's book: http://www.amazon.com/gp/aw/d/0262541858/ref=redir_mdp_mobile/181-1988504-8834745. This is not a book on neuroscience, not AI, although this particular book has more math than the other introductory neuroscience textbooks I've seen.


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How much food can an average person eat, and which animal is that equivalent to?
When the average person overeats, how much food can he eat in a day? Which animal's average meal would that be equivalent to?
When documentaries are talking about animals feed, they usually say something like "The fish can eat 500kg of prawns in a day!" But when it comes to humans, they calculate in calories. Which animals are we closest to in terms of capacity?
Note: I think I can be slightly loose on the definition of overeating here. It can mean eating beyond the point of feeling full, or the human maximum stomach capacity.


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How does this diagram illustrate carbon cycling in lakes?
Could someone please explain the following process to me:

This process refers to carbon cycling in lakes and is described in the context of $CO_2$ flux from lakes into the atmosphere. GPP is gross primary production, $CO_2$ is carbon dioxide, R is respiration, and OM is organic matter. I realize that this question may be rather simplistic to some but my basic knowledge of any biological/ecological processes is rather limited. So, basically what I am asking is

have I written this process correctly?
how can this process be described?

This shows the major biological transformations of carbon in any system (not just lakes).
On the Left Side:

$GPP$ (Gross Primary Production) is the total amount of $C$ from atmospheric $CO_2$† that is reduced into organic molecules during the calvin cycle of photosynthesis.  This is the process performed by photosynthetic organisms like green plants and algae.

† atmospheric $CO_2$ diffuses into water and develops into several species of inorganic carbon molecules that plants and algae can use but in general you can think of this carbon as being very closely related to atmospheric $CO_2$

$OM$ is a pool of organic matter, which is a general term for reduced carbon molecules.  $OM$ can be living organism tissues (e.g., a fish), dead tissues (e.g., senescent leaves) or biologically generated organic molecules (e.g., sugar that leached from a plant).  $OM$ is the principle pool of energy and raw materials for all living things on Earth so this is a really important pool of stuff.

Since $GPP$ is taking $CO_2$ and converting it to $OM$ as the left side progresses, the amount of $CO_2$ in the atmosphere goes down and the amount of $OM$ in the biosphere goes up.
On the Right Side:

$R$ (respiration) is the oxidation of reduced carbon-containing molecules for the purpose of extracting usable energy.  This may be familiar as "cellular respiration" but there are other metabolic pathways that accomplish the same goal.  In the end when the $C$ in the $OM$ is oxidized and the energy released the $C$ that was in the $OM$ gets converted into $CO_2$.

Note that this is the opposite of the Left Side, so as this occurs, the amount of $OM$ in the biosphere goes down and the amount of $CO_2$ in the atmosphere goes up.
If the Left and Right sides are balanced, then there is no net change in the size of the $OM$ pool or the amount of $CO_2$ in the atmosphere.  However, note that over relatively short time scales these can be very out of balance.  Any time plants or algae are growing (i.e., gaining mass as $OM$) the Left Side > the Right Side or $GPP$ > $R$.  Once those plants die, they accumulate in the system as dead $OM$.  The decomposition of accumulated dead $OM$ by microbes will generally make the Right Side > Left Side or $R$ > $GPP$.
This picture from Wikicommons shows the same cycle in a more realistic setting.


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Do repeated freeze-thaw strip nutrition from vegetables/food?
Some of my family and friends seem to believe that vegetables/food should be subjected to as few freeze/thaw cycles as possible. The rationale put forward is that each such cycle reduces nutrition (sp. nutritive?) value, and accelerates rot.
I'm skeptical; Do repeated (sp. repetitive?) freeze/thaw cycles strip nutrition from vegetables/food?

Not as far as I know, they do however open the frozen foodstuffs to infection. It is not a good idea to thaw and refreeze for that reason.

Repeated freeze-thaw has virtually no effect on macronutrients, such as proteins, lipids, and sugars, because these are broken down to their basic building blocks (such as amino acids and simple sugars) upon food digestion anyway.
According to this paper freeze-thaw has no effect on micronutrients, such as vitamins, as well.
What affects nutritious quality is the length of time the food remains frozen. Most household freezers maintain a temperature of -20°C. At this temperature, the food doesn't get spoiled by bacteria, but degradation of vitamins still occurs, albeit at a slower rate. This is critical for some unstable vitamins, such as vitamin A and C. But elements such as iron, calcium, zinc, and phosphorus are not affected at all.
If you want to prevent vitamin degradation for a very long time, you need a freezer that maintains food at -80°C. This is only if you want to keep the food frozen for many months though.


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What causes XYY Syndrome?
It's obvious how a misdisjunction can result in klinefelter's syndrome (XXY) but I don't see how this can result in XYY syndrome. Your parents have a collective total of only one Y chromosome so how can any misdisjunction result in a child with two Y chromosomes?

It comes from a Y nondisjunction in the father. Anaphase nondisjunction of the Y yields a YY, which goes with one X from the mother to give XYY.

http://en.wikipedia.org/wiki/XYY_syndrome#Cause  during sperm generation