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Does the Michaelis-Menten equation take in account the non-enzyme formation of products?
I only recently learned about the Michaelis-Menten equation, since I am not studying biology or anything related. Let's write the equation as
$$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [S]}$$
If I'm not mistaken, this equation describes the rate at which products are formed ($\frac{d[P]}{dt}$) as a function of substrate concentration $[S]$ in steady-state. In a translation of Michaelis' paper I read that $V_{max}$ can be written as $k [E]$, where $k$ is a constant and $[E]$ is the total enzyme concentration.
Mathematically one would say that when the total enzyme concentration is zero ($[E] = 0$), the rate at which the product is formed should equal zero. If I recall correctly, in several reactions products are formed without enzymes (Enzymes only enhance the reaction rate?). Is the Michaelis-Menten equation specifically used for situations where $[E]>0$? If so, how does it account for very low enzyme concentrations where product formation from non-enzyme reactions cannot be neglected?

In any study of enzyme kinetics it is essential to subtract all 'blank' rates and to ensure that the measured rate is due only to enzyme catalysis.
That is, in kinetic 'parlance', the velocity vs [enzyme concentration] should be linear and go through the origin.  Doubling the enzyme concentration should double the (enzymic) rate, and halving the enzyme concentration should halve the (enzymic) rate.
Failure to subtract blank rates may give rise to a variety of spurious kinetic effects such as downwardly-curving double-reciprocal plots (Lineweaver-Burk plots).
Downwardly-curving Lineweaver-Burk plots are diagnostic of negative co-operativity, but such a conclusion may be artefactual if blank rates are not subtracted.
A very good reference to this sort of this is Enzymes, (1979) by Dixon, M, Webb, E.C.,  Thorne, C.  & Tipton, K.F. (3rd Edn), Longmans,  in particular pp 461 - 462.

Just for confirmation; the product formation rate would thus be $V_{0} + \frac{V_{max} \cdot [S]}{K+[S]}$ if blank rates were not subtracted? Is there a different notation/name for the rate of product formation when $V_{0}$ is not subtracted?


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What impact do genetic engineering techniques have on seed breeders?
In research of seed breeding, I'm trying to understand the impact of genetic engineering techniques like CRISPR (This is the main one as I understand) on traditional seed breeders. Through searching on the internet, I believe to have found the following two types of impact:

research: increased speed of detection which genes make for which vegetable trait. This is supposed to be used already by many breeders.
Growing: Reducing the breeding cycles by up to a factor 2, by early selection which plants are the good ones in the breeding process (I don't really understand how this would work)

So the main total impact of new breeding technologies would be the shortening of breeding cycles, putting increased pressure on fast innovation.
Am I missing any type of impact? Is CRISPR going to change seed breeding in a dramatic way? For instance, is there a way to take someone else his/her seed, then using crisper (in some way?) to immediately know which genes make up for the desired vegatable traits? Or some increased speed in which one could copy traits of other seeds? Also I'd like to know how the second point works: using CRISPR to reduce the breeding cycles for seeds.

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Is body energy production and consumption cyclical?
If we look into how energy is produced by the humans, it always involves some kind of periodicity: fuel combustion rotates engines, water rotates turbines, nuclear chain reactions heat up water, which rotates turbines, dynamo machines, etc.
So that means that with a few exceptions humans produce most energy (electricity) using rotation or some kind of cyclical rotative movement (as it proved to be the most efficient way of doing that).
Now what if we look at the human body? It is producing the energy from the food that we consume, converting carbs and proteins into glucose, which is then broken down into carbon dioxide, water and ATP. This ATP is then used in chemical reactions that are needed to contract the muscles or to send impulses within the brain.
The question is: Does anybody know – are those chemical reactions also cyclical in their nature? And if not, what's the common dynamical property (pattern) that can be observed in them all, if any?
Thank you and sorry for the long intro, but I thought it's important you know where I come from.

Do you mean a literal cyclical motion i.e a rotation? http://www.youtube.com/watch?v=PjdPTY1wHdQ ATP synthase rotates and takes advantage of a membrane potential to change its conformation. Would you like an expansion on this answer, or have I misunderstood your question?

the enzyme that produces ATP in fact, rotates like a little chemical motor.  not sure if this really answers your question... https://www.youtube.com/watch?v=zOSyGTYCRFw

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How does the human body use energy?
As far as I know the glucose gets processed from carbs and fats and as a result carbon dioxide, water and "energy" are released. The carbon dioxide and water are expelled by the body, and then energy is used by the muscles. But how exactly is it used? What happens to this "energy" and what is it exactly?

Our body does not produce carbon monoxide. It does produce carbon dioxide.

Indeed, there is still one carbon monoxide in your post.

@ddiez :))))))))

You can break down the energy expenditure of the human body in terms of the different organs which use it up: this is done in this biochemistry book for instance, http://www.ncbi.nlm.nih.gov/books/NBK22436/
You can also look at the detailed expenditure of each cell: although the amounts will vary according to cell type (neuron vs. muscle cell, say!), the "budget items" are the same. See this thread: Breakdown of energy expenditure at the level of a single cell

Thanks! So the "energy" is actually ATP, which is then used for different chemical processes? Is there any pattern that's common to all these processes, such as periodicity for example?

Not all energy goes into ATP or GTP cycles, but these are the common way of having ready-to-use energy for molecular processes, e.g. molecular motors (in muscles but also other cells, to exert forces or to carry loads around e.g.). Heat is being produced without producing ATP/GTP, e.g.

I'm not sure what you mean by "pattern".


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5,6-dihydrouracil and 5,6-dihydroxyuracil - how they arise in DNA?
5,6-dihydrouracil can be formed from cytosine after exposure of DNA to ionizing radiation under anoxic conditions [Ref]. What are other ways by which 5,6-dihydrouracil is formed in DNA? What about 5,6-dihydroxyuracil?

Here is the pubmed link to the paper. I couldn't think of an appropriate way to edit the question to incorporate the link.

@WYSIWYG Correction: 5,6-dihydroxyuracil does in fact exist. http://www.chemindustry.com/chemicals/0930310.html

@MarchHo Thanks. I nominated the post for reopen.

Dihydrouracil oxidase can catalyse the reduction of uracil to dihydrouracil in the presence of hydrogen peroxide. The reduction of uracil to dihydrouracil can also be catalysed by dihydrouracil dehydrogenase using NADH.
According to this paper, 5,6-dihydroxycytosine can be formed by treating cytosine or DNA with osmium tetroxide, an extremely strong oxidising agent. Since they are both pyrimidines (and in fact cytosine often spontaneously hydrolyses to uracil), uracil will also be affected by the same oxidation. 5,6-dihydroxyuracil was also detected within the oxidised DNA sample as a result of oxidation and demethylation of thymine.

The presence of 5,6-dihydroxyuracil (peak 11 in
  Fig. 1) can be explained analogously to the formation
  of 5-hydroxy-5-methylbarbituric acid from thymine on
  permanganate oxidation (lida & Hayatsu, 1970, 1971)
  (Scheme 2). The actual oxidation products ofcytosine, i.e.
  structures (I) and (II), were not observed in DNA. As the
  calf thymus DNA used in this work did not contain uracil,
  the uracil derivatives discussed above could not have been
  formed from uracil in DNA.


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ChIP-seq for histone modification not in agreement with RNA-seq for expression
I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at gene A for both of those histone modifications. However, when I run RNA-seq analysis tools (like edgeR or DESeq2) this gene is not marked as differentially expressed (well it has a FDR value of >0.05).
There might be several technical reasons for RNA-seq analysis methods not to find this gene as differentially expressed because

it is really not differentially expressed
or it is not differentially expressed enough for the tools to detect it

However, I am more interested in the biological aspect. If two histones mark gene A as active in treated samples, one would expect that it would be expressed in RNA-seq. What mechanism could lead to the result that however the genes is marked as active by histones, it will not be differentially expressed in RNA-seq?

Your statement that those two post-translational modifications of histones mark active genes is not supported by your experimental evidence (in every case). Perhaps a more accurate statement would be something like "often mark active genes" or "are typically associated with active genes?"

It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators. Some histone modifications like the ones you are mentioning are also a bit dicey and there can be bivalent modifications too. However, if there is a strong reason to speculate that these marks are associated with repression then you can try these:

You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition. Repetition will help you to know if the observation is indeed correct (a biological replicate); possibly you may end also up concluding that these marks are actually dicey.
If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.

Which statistical test are you talking about? I have about 40 genes that are not supported by RNAseq, also I have genes that are supported by RNAseq but not by those histones. Sp, I have king of venn diagram of number of genes RNAseq vs active histone modification.

@Tonja 40 genes discordant: how many agree with the RNAseq? I am not sure about which statistical test to use here. Basically you have to see what is the probability of RNAseq not agreeing with Histone modification.

ChIP-seq isn't perfect. Even between technical replicates, you get a fair amount of variation, especially for broad marks like those you're using. It's rather uncommon to see people use H3K79me2 and H3K36me3 to determine if a gene's expressed or not. Using H3K4me3 and H3K27ac or H3ac is a more common method of marking promoters of transcribed genes.
40 genes discordant wouldn't worry me much unless you really have low reads for either set of sequencing experiments. @WYSIWYG's suggestion to use RT-PCR to verify your RNA-seq data for a few genes is a good one.

I checked the promoter histones as well and I have also some genes that are not supported by RNA-seq. I know I could validate the results but that is encode data. So, I would like just to know the theoretical reason for that.

What is encode data? The RNA-seq?

@JaredAndrews I think Tonja is referring to the TFBS ChIP-seqs..

@WYSIWYG If that's the case, I'd suggest looking at different marks, as they certainly have them if they also have H3K79me2 and H3K36me3. The epigenome is complex, flexible, and variant. As such, you should look at the pieces as a whole whenever possible.


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Notation for repetitive nucleic acids
With regard to nucleic acids with repeating residues, could anyone provide a description of what the following sequences are, and the key differences between them:

Poly(dA)
Oligo(dA)
Poly(A)

Oligo means "few" in Greek, Poly means "many". If you look at the article on Oligonucleotide in Wikipedia, you will see that this is about as precise as you'll get. Another real world definition of oligo would be the size of synthetic DNAs that you can buy or have made at reasonable price, which judging from the article would seem to be at least 25 and not more than 200. I'd put an upper limit lower (e.g. 50), but it's quite subjective.

Although the Wikipedia article on polynucleotides says that according to the US NLM these latter start at 13. Hee hee.

dN denotes deoxyribonucleoside (where N can be A, T, G or C). If there is no d prefix, then it denotes a ribonucleoside.
Regarding the difference between poly and oligo:
The former refers to having a large number of monomeric units whereas the latter means having a few monomeric units. There is no strict definition of the boundary between poly and oligo. Poly-A tails are typically about 70-80nt long in yeast (Eckmann et al. 2010). So it logically follows that anything shorter than that should be called an oligo-A. Chemically synthesized stretches of DNA are often referred to as oligos even though nowadays one can synthesize more than 80nt long DNA/RNA. Moreover, a stretch of As in some mammalian mRNAs smaller than the usual length of ~150-250 is still referred to as a short poly-A tail instead of an oligo-A tail (Jalkanen et al. 2014; there are many more examples).
Additionally, even if the cutoff is, let's say, 100 units, it doesn't apply to proteins. A protein with 100 amino acids is still considered a polypeptide and not an oligopeptide. For peptides, the cutoff is generally around ~30.
So, I would conclude that the usage of these prefixes is quite contextual.

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Does a gene that regulates itself necessarily be a transcription factor?
I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? E.g. given a system of 3 genes {g1,g2,g3} where only g1 and g2 are TF, then in a gene regulatory network, what are ALL possible parental sets of g3 (where in this GRN, you put a directed edge from the regulating gene to the regulated gene)? Will it be {{g1},{g1,g2},{g2},{}} or {{g3,g1},{g3,g1,g2},{g3,g2},{g3}}

There is no one answer to this question. Some non-TF proteins signal through negative feedback loops to eventually downregulate their expression when they're no longer needed/there is a lack of substrate/etc. Others don't, and are regulated through other means.

First of all you need to clarify what exactly is the output that needs to be regulated. We often say regulation of expression of a gene but what expression ultimately leads to is the activity of the gene (whatever it might be: enzyme based catalysis, cytoskeletal rearrangement, response to an extracellular signal). Activity of course depends on the expression level of the gene but it also depends on other factors such as covalent modifications, interactions with other genes (like dimerization) etc. Moreover, for genes which code for proteins, expression also has two stages.
Coming back to your question:

If a gene is NOT a TF gene, can it regulate itself?

Yes it can. There are many modes of gene activity regulation as I already mentioned. Examples where a non-TF gene can regulate itself:

Feedbacks in cell signalling which happen via activity modulation by protein phosphorylation [1].
Regulation via post-transcriptional regulation via RNA binding proteins (RBP) or regulatory RNAs such as miRNA. MAPK signalling pathway has a feedback via the RBP, Rnc1, which upon phosphorylation binds to and stabilizes the Pmp1 mRNA. Pmp1 is a phosphatase which dephosphorylates Rnc1[2]. This loop contains regulation by both post-translational modification and post-transcriptional mRNA stabilization. There are many other examples involving RBPs. An miRNA, let-7 is post-transcriptionally regulated by Lin28 (promotes degradation) which in-turn is post-transcriptionally repressed by let-7 [3].

There are many examples of metabolic feedbacks too which operate via allosteric regulation of the enzyme activity.
If you are only interested in regulation of gene expression then you can ignore phosphorylations and allosteric regulation but there are several examples of post-transcriptional regulatory interactions which also contain feedbacks.

References

Dougherty, Michele K., et al. "Regulation of Raf-1 by direct feedback phosphorylation." Molecular Cell 17.2 (2005): 215-224.
Sugiura, Reiko, et al. "Feedback regulation of MAPK signalling by an RNA-binding protein." Nature 424.6951 (2003): 961-965.
Rybak, Agnieszka, et al. "A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment." Nature Cell Biology 10.8 (2008): 987-993.

I don't understand your system of 3 genes regulatory network question, but I can answer your general question regarding transcription factor self-regulation of transcription/gene expression.
Yes, in biology, there are transcription factors that bind to their own gene's promoter-proximal region (on DNA) and regulate their own gene's transcription. There are examples of positive feedback loop transcription factors (e.g. FOXL2) and negative feedback loop transcription factors (e.g. Oct4, Nanog, & FoxD3; also Irf8 with Cebpb).


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Genetics and blue eyes
Blue eyes are a recessive trait in humans. I read an article recently which stated:

People with blue eyes have a single, common ancestor, according to new research.
A team of scientists has tracked down a genetic mutation that leads to blue eyes. The mutation occurred between 6,000 and 10,000 years ago. Before then, there were no blue eyes.
"Originally, we all had brown eyes," said Hans Eiberg from the Department of Cellular and Molecular Medicine at the University of Copenhagen.

Which appears to be a mainstream hypothesis today. My question is, if there is a genetic mutation that occurred in one individual which made their eyes blue, and the rest of the population is brown eyed, how does this make so many individuals blue eyed? If the blue eyes are recessive, the individual's children would mix with the other brown-eyed individuals and their offspring will be brown-eyed. How does anyone treat this theory seriously?

I think you just stopped at the F1 generation, just take it a step further and you have your answer (I know I am using the terminology miserably)...

"The blue eyes are recessive in humans" - This is not fully true; there is one recessive blue eyes allele for one gene but eye color is actually polygenic. That said, the answer below covers clearly why recessive alleles don't just disappear which is the more important part of your question.

This single-mutation theory seems over-simplified.  What about people with other eye colors, like gray or green?  Or two eyes of different colors, or even two colors in the same eye?  (Hetereochromia)

@another 'Homo sapien' is basically correct, and what they were getting at, is that in just the F1 generation, you're right, any recessive traits are masked. However, if you continue this onward, in subsequent breeding, recessive traits are unmasked. (This is basically why inbreeding is a bad thing).
If we use the traditional Punnet square method for determining genotype:
if A is a Brown-eye dominant allele, but a is a blue-eye recessive allele:
F1:

You can see that a single recessive allele is now present in 50% of the offspring of a given pair of parents.
Now, if in F2, we assume that 2 of those recessive offspring were to mate, the recessive gene would be unmasked in 1 quarter of the offspring (statistically speaking), and 50% would be carriers.
F2:

Now it gets a little more complicated. Our double recessive F2 member has blue eyes phenotypically, they aren't just a recessive allele carrier.
F3:
So, if in F3, our aa mates with another aa, (ignoring spontaneous mutation for simplicity) it should be obvious that all of their offspring in F3 would have blue eyes (and I can't quickly find a Punnett square in Google showing this).
However, if our aa now mates with an AA (homozygous dominant brown), we will get 100% offspring with a heterozygous Aa genotype - in other words, all blue eye carriers, but with brown eyes phenotypically.
If aa mates with a heterozygous individual though (Aa), we have the following:

And thus, 50% blue eye individuals, with 50% brown heterozygous dominant. And so on and so forth, ad infinitum.
Hopefully that explains how a recessive allele can go to fixation despite only occurring once.


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Do both ends of a muscle contract?
I was under the impression that both ends of a muscle contract. For instance, the fibers of the biceps run parallel to the humerus so I thought they pulled toward the middle.
But now I'm confused because it sounds like the contraction of the fibers doesn't necessarily have to parallel the motion of the muscle itself. In other words, just because the fibers contract doesn't mean that the muscle lengthens or shortens in a particular direction.
Can someone clarify if muscles contract in both directions?
Or perhaps a better question is do muscle contract in a particular direction and is this the same direction that the fibers contract or does the muscle as a whole move in a different direction in comparison to the direction the fibers are contracting?

fibres contract towards their centre thereby generating equal force on both ends.

Thank you! I have been using that assumption for years so I'm glad to know it's correct.

The nerves link to the muscles at the center. So contraction is from center to periphery. So the upper half and lower half contract in opposite directions.

The muscular fibers (or more exactly the actin and myosin filaments) are contracted towards each other. This makes them "move to the middle" and you build up a force on both sides of the muscle. See this image (from the Wikipedia), which illustrates this process:

There is also an animated picture available, which illustrates this process even better (from here):

The process of the contraction applies a equal force to both endpoints of the muscle.

I like the moving GIF! Nice answer overall +1

@ChrisStronks I sometimes regret that we cannot embed videos. Sometimes moving pictures make things easier to understand.

Man, when following Biochemistry and Human Biology classes I struggled for hours at those static pictures of filaments doing wacky stuff. This tells it all in one glance :)

It is difficult to understand what happens at the full muscle level with this description. But the OP is asking about that

@Chris wait for HTML5. It would be much easier to embed videos then.

Muscles do contract in both directions. To understand this better you need to know few things:

The smallest unit of a muscle is called myofiber or a muscle fiber. It is basically a multinucleated elongated cell. Each muscle fiber is covered by a layer called endomysium
A bunch of myofibers arranged linearly is called a fascicle. The fascicles are covered by a sheath called perimysium.
A muscle as you see in a cadaver or a picture is a group of fascicles surrounded by epimysium.

source: classconnection
A single muscle fiber is made up of numerous myofibrils which are basically the sarcomere arranged side-by-side.
The junction between the neuron and muscle fiber is called motor end plate. A single motor neuron innervates a group of muscle fibers. The whole assembly of muscle fibers innervated by the axon from one neuron is called a motor unit
The Key:
The key to understand muscle contraction on a macro level is in the fact:

Typically, an axon makes a single point of synaptic contact with a skeletal muscle fiber, midway along the length of the muscle fiber.1

So when an action potential arrives at the neuromuscular junction (another name for end plate), the muscle starts depolarising and contracting from the center towards the periphery. In other words both the ends of the muscle contract toward the center.

source:encrypted-tbn1.gstatic.com. Image has been cropped and edited to illustrate the point
tl;dr:
Every skeletal muscle contracts toward its center, such that the proximal and distal ends act in opposite directions causing tension generation. The proximal end pulls the tendon down and the distal end pulls the tendon up thus generating tension.

1: Medical Physiology A Cellular and Molecular Approach, 2nd Edition, Boron and Boulpaep p.217

The above answers are correct, I just want to add a distinction between the different muscle types.
There are 3 types of muscle tissues:

Skeletal muscle (locomotion)

Striated
Voluntary

The skeletal muscle has visible striations under the microscope, because the myofilaments are aligned: they are all parallel. During contraction, the thin filaments slide over the thick filaments - at the end of the contraction the Z lines will be closer together. The filaments stay the same length, they just slide over one another, shortening the muscle. The muscle doesn’t contract by “going” in a particular direction, it shorts everywhere and the alignment of the filaments enables the muscle to shorten in only one dimension. The muscle is connected to the bone by tendons. When it shortens, it pulls on the tendons which pull on the bone, bringing it closer. A skeletal muscle cell can be up to 30cm long (Sartorius muscle).

Cardiac muscle (in the heart)

Striated
Involuntary

Cardiac muscle cells are very similar to skeletal muscle cells, however the fibers are interconnected via intercalated discs, which enables them to work in an even more synchronized way.

Smooth muscle (in the vascular system, the gastrointestinal tract, etc.)

Not striated
Involuntary

Smooth muscle filaments aren’t as organized as the ones in skeletal muscle. Therefore, the shortening can occur in all directions within the cell. It results in the shortening of the cell in more than 1 dimension.

Also, many organs such as the stomach have more than one layer of smooth muscle, providing constriction in many different “directions” (longitudinal layer, circular layer and oblique layer).


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Is cyanocobalamin toxic?
I see that cyanocobalamin is not naturally occurring, and is synthesized in vivo to methylcobalamin. As part of the synthetic pathway, cyanide is broken off. All opinions I can find are that this isn't a problem as cyanide is naturally occurring in many foods anyway, and is safely detoxified via the the Rhodenase pathway.
However, given its synthetic creation and vast prevalence as the primary B12 source in nearly all supplements, I was curious if any actual studies did exist to rule out potential (albeit minor) long term cyanide toxicity for this synthetic form of B12. I'm unable to find a single study where cyanide toxicity  was directly tested for, only studies stating that RDA in excess of 1000 times the daily dosage isn't lethal.
I understand no evidence currently exists for cyanocobalamin toxicity, but this wouldn't be surprising if there aren't any studies done in the first place.
Would anyone be able to reference an actual study that directly measured levels of potential cyanide toxicity for cyanocobalamin in any animal or humans?

What is the reference to carcinogenicity? Cyanide is not carcinogenic. You can check here for doses of cyanide that are considered safe.

Mistake in the title sorry, corrected now.

The NIH RDA for vitamin B12 is 2-3µg/day. Cyanocobalamin has an $M_r$ of 1355, of which 26, or less than 2% ($CN^-$) is cyanide.
Since the Minimal Risk Level for cyanide is 50µg/kg/day, your studies are correct in that 1000x the RDA of vitamin B12 in the form of cyanocobalamin is not lethal, and furthermore is expected to not cause any negative effects even in the most sensitive of individuals.
This holds true even if 100% of the cyanide ligands dissociate from cyanocobalamin, which is unlikely to be the case in practice due to cyanide being a very strong binding ligand.
Cyanocobalamin contains too little cyanide, and is consumed in too low an amount, to cause cyanide toxicity. The dose makes the poison.

A common mutation in the Methylenetetrahydrofolate Reductase gene (hetero & homozygous), implicated in a vast array of diseases, is prevalent in some populations as much as 38% Source* - and requires excess supplementation of B12 & folinic acid in order to complete the pathway for homocysteine -> methionine. A vast quantity of anecdotal reports show dosages up to 5mg B12 per day alleviate symptoms. Surely at this level the cyanide would start to matter if cyanocobalamin was supplemented, even if just 1% did break down?

@user4779 It seems that there is no issue, even in your case of extreme overdosage of cyanocobalamin (100µg cyanide daily). Assuming 60kg body weight, one has to take 3mg cyanide daily to reach the MRL.

I guess there's no arguing with the current numbers and evidence, given the studies of the MRL in rats. Thanks to you and WYSIWYF for providing the link to the cyanide toxicity.

Potassium cyanide is added to the cobalamins produced by bacteria to give rise to cyanocobalamin. CN is strongly bonded to Co and will not easily dissociate, thereby making this form of B12 inactive. Therefore, it has been argued that cyanocobalamin is not a good vitamin supplement and other variants such as hydroxycobalamin or methylcobalamin should be used. Displacement of CN from the complex would be energy expensive and even if the reaction is efficient the amount of cyanide released would not be in the toxic concentration. The CN-Co bond is so strong that hydroxycobalamin is used as an antidote for cyanide poisoning; it forms cyanocobalamin by displacing OH with CN.

 Source: Wikipedia and the cross references.

Interesting, but for the molecules of B12 that are bioactive, I believe the cyano group dissociates as free cyanide. Just curious if any such effects have been studied, as free cyanide also breaks off in Amygdalin and that has been linked to cyanide toxicity in comparable dosages I believe.

@user4779 Generally the bond between the Transition metal and cyanide is very strong.  It would not easily dissociate. Even if it does, the minuscule concentration would not be toxic. For all practical purposes you can assume that CN- does not dissociate from the metal. Even potassium ferrocyanide K₄Fe(CN)₆ is non-toxic.

I believe CN- does in fact dissociate from cyanocobalamin, as otherwise it would not be bioavailable as vitamin B12.

@MarchHo It should to a little extent but CN is much stronger ligand than others. And B12 bioavailability of cyanocobalamin is very low.

@user4779 In case of amygdalin the CN is not complexed with a metal. It is covalently bonded with carbon and is close to a hydrolyzable group.

Wouldn't an enzyme be able to easily perform this synthesis regardless of how tightly bound it is?

@user4779 enzymes are not magic molecules. If enzymes could do that easily then why should cyanide poisoning happen at all? Cyanide can be and is removed from cyanocobalamin when it is converted to active form but I assume that it would be very energy expensive and therefore won't happen in a large scale.


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determining meaning of basic biological keywords about C. elegans
First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with bioinformatics (modENCODE and NCBI-GEO). Currently, I'm searching RNA-Seq data and I have found the following one in modENCODE website which is stored in NCBI-GEO database.RNA-Seq data
In the description part of it, it is written that:

Synchronized L1 worms cultured at 25degC for about 91 hrs to a point
  at which ~100% worms are resistant to 1% SDS treatment. Illumina
  sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1
  polyA+ RNAseq random fragment library This sample is available through
  the modENCODE DCC (www.modencode.org) as: DauerDAF2-2-1 Local library
  name: DauerDAF2-2-1 Quality values are ASCII encoded Phred + 33.

Regarding with this paragraph, I want to ask that, what is C. elegans dauer daf-2(el370) . I've searched on the internet and I have found that dauer is kind of development stage of C. elegans. However, I could not find any information about the daf-2(el370) part (Actually all I found was that daf-2 is name of a gene of C. elegans). Actually, my primarily concern is whether this RNA-Seq data contains the C. elegans' whole transcriptome or it contains only mRNAs related with daf-2 gene.

I might be wrong here, but daft-2(el370) looks an awful lot like a nomenclature of a transgenic worm. And RNA Seq doesn't do it on a gene by gene basis if I remember my basics. It does it on the whole transcriptome.

@RoverEye Although I have limited information, I agree that RNA-Seq does it on the whole transcriptome, I just wanted to be approved. Thanks for the information.

I think it is daf-2 mutant which prolongs dauer stage. Did you read the corresponding paper??

@WYSIWYG corresponding paper is not available to publicly access therefore I could not read it.

@stackunderflow Here you go: http://genome.cshlp.org/content/19/4/657.long

Have you discovered wormbase yet? It will become your new best friend. In worms gene names reflect the loss-of-function (lf) phenotype. Daf means "abnormal DAuer Formation," so daf-2 was the second daf gene identified (ref). The mutations are called alleles and each worm lab has their own allele designation. e was for England and in that lab's strain list the daf-2 allele was the 1,370th on their list. So daf-2(e1370) designation means that the strain carries a lf mutation in the daf-2 gene, and the specific allele is one that was isolated in Cambridge, UK. I believe that allele is temperature-sensitive (ts) dauer-constitutive.
So at 25⁰C 100% of the animals were dauers. That is when they harvested RNA. It is the entire transcriptome. It sounds like you may be familiar with modENCODE Data Warehouse. You can still ask questions about modENCODE datasets at help@modencode.org. While the modENCODE Data Coordination Center was mothballed at the end of the NIH funding period, there are a few people who still field queries like yours, to the Helpdesk. Also, moving forward the new ENCODE DCC has taken over curation of archival modENCODE metadata.


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enhancers in cell-type-specific signatures
I was reading an article in nature : Epigenomics: Roadmap for regulation and was confused by the definition or/and interpretation of enhancers.

Enhancers are activated through interactions with transcription
  factors, which recognize and bind to specific DNA sequences within the
  enhancer region. Bound transcription factors recruit co-regulators,
  many of which deposit or remove modifications on histones. […]
  Enhancers that are active in cell-type-specific epigenomic signatures
  are typically highly enriched in DNA sequences to which
  lineage-determining and signal-dependent transcription factors bind.

As far as I know enhancers are the DNA sequences to which TFs bind, and then everything including co-activators complexes bind to basal TFs on the promoter.
I am confused by the last line:

Enhancers that are active in cell-type-specific epigenomic signatures
  are typically highly enriched in DNA sequences to which
  lineage-determining and signal-dependent transcription factors bind.

They state, that in DNA sequences to which TFs bind the active enhancers are highly enriched. For me it sounds strange because the definition of enhancers says that these are the DNA sequences to which TFs bind. And of course enhancers are enriched there because otherwise they would not be called enhancers. As for me they are trying to say that active enhancers (by definition TFs bind to them) are highly enriched in enhancers region to which TFs bind.
Does it make sense or not?

You nailed down what enhancers are (canadianer give a good explanation too, while not answering the question in my opinion).
For understanding the authors statement you first need to know that:

Lineage-specific and signal-dependent transcription factors are specific classes of transcription factors. Those are TFs that require external signals for activation.
All enhancers are not always accessible. This depends on the epigenetic marks, and subsequently histones binding, around those regions. If, for example, an enhancer is in a region of tightly packed DNA (i.e. heterochromatin) it will not bind any TFs and is therefore not active.

What the authors where trying to convey is, in my opinion, that active enhancers are highly enriched in DNA sequences specific for signal-dependent TFs. In other terms, the cell's identity is given by a combination of 1) epigenetic regulation of gene expression via a) a certain pattern of active enhancers and b) chromatin state of genes in conjunction with 2) signal-dependent transcription factors.
In summary this means that the cell identity is not only described by signal-dependent TFs but also by the active enhancer pattern. And this therefore implies that one might be able to predict TFs necessary to determine a specific cell's identity as stated in their next sentence:

Therefore, the delineation of a particular cell's active enhancer repertoire provides a powerful means of predicting the transcription factors required for that cell's identity.

I hope this helps.

Enhancer is a just a term for a regulatory region distant from a gene that contains specific sites where transcription factors bind. As it happens, a single enhancer can contain DNA binding sites for multiple transcription factors.
For example, an enhancer called TESCO, which regulates a gene called SOX9 (involved in sex determination) has binding sites for many different proteins (confirmed or putative): SRY, SF1, SOX9, ESR1, FOXL2 and likely many more that I haven't heard of. This allows complex regulation of SOX9 through protein-protein interactions.


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Article or answer to whether "blood volume pressure" and "electrodermal activity" have any correlation to stress and or feelings overall
As the title suggests, I would like some help finding if there is any correlation between between blood volume pressure and electrodermal activity?
The paper I'm writing is about measuring stress and engagement levels of the subject by comparing the levels of electrodermal activity and blood volume pressure during media consuming. This can be anything from music, movies, tvshows etc.
But the papers im looking for can be about the correlation only. Not by measuring the same type of things as I do.
If you know any good articles, I don't really care much about the publication date.
I have full access to ieee articles through university.
Thanks.

Questions should be specific and not lead to discussions. Also, please minimize the use of acronyms. I'm very interested in skin conductance and stress, so I would be happy to look into your issue, but as it stands this question does not meet this site's standards. Please edit and refine the question if you would like to receive input. The help center contains info on what a proper question format is. Have a look!

Okey, updated the answer now.

@SimonNilssonGuldstrand What Christiaan pointed out still stands. What correlation are you looking for? Do you want background on how the two are linked, or interpretation of stats from a certain paper?

@James i would prefer both, but one of them is enough. I'm writing a paper myself that include these points of measure and need to have facts that back up how they are linked. So a graph or short text describing it would be superb.

@SimonNilssonGuldstrand If you could incorporate that into your question and explain specifically the information you are looking for and add the reference request tag. If you don't make it clear, the question is likely to get closed.

Please see the tag wiki for reference-requests and provide the necessary information as mentioned there.

I have updated this question as much as I can. Are you guys still interested in helping me find an answer? @Christiaan


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Research papers that demonstrate work done on other species with honey bee pheromones
I found research where Queen mandibular pheromones (QMP) emitted by queen bees were used to find their affects on Drosophila melanogaster. However, I am curious to see if the QMP from bees have been used in other social insects like wasps or termites. Can you please guide me to any research papers on the same?
Since the eusocial queen pheromones among different species are more or less composed of the same hydrocarbons, treating wasp workers with honey bee QMP should have the same effect on worker wasps as it would have had on honey bee workers.

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


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Cross species effects of Apis mellifera queen pheromones
I am looking for studies that show effects of Apis mellifera queen pheromones on other species. An example of one such study is where A. mellifera queen pheromones deactivated the ovaries of Drosophila melanogaster females. Similarly queen pheromone from Apis mellifera scutellate can deactivate worker ovaries in a different sub- species, Apis mellifera capensis (however, this is a sub species effect and not cross species). If anyone else knows any other studies of cross species effects, it would be highly appreciated if it could be pointed out.


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Systemic sensory confusion?
Sometimes when a person gets touched on one part of the body they feel it else where and may think it came from a different part of the body. What causes this? Other examples are similar to why you can trick your self into thinking your arms are heavier than they really are. another would be that you can close your eyes and move in circles up and down your arm slowly and then when you guess where u are touching your hand is higher or lower than expected. What causes these things?

The situations you describe involve what is called proprioception or the feedback to the brain of where your arms and limbs are in space. As APengioun mentioned, this is a complicated undertaking and if information is restricted, for example eyes are closed then the sense of where your limbs are gets messed up. As for your title, it's not really neuronal confusion as it is confusion of the sensory system if you can call it that. This includes sensory neurons from your limbs as well as central neurons in the brain that further process your information.

When our brain works out where a part of our body is in relation to another part of our body, or in relation to anything for that matter, we combine:

visual information
information about how much our muscles are contracted
how much our joints are contracted
different forces being applied on our arms/legs or other body parts
where it remembers we used to be
how much force we applied to move where we wanted to move
where we would therefore expect to be
and many other things

That's quite a few things that our body relies on! The one that's most fine tuned is our vision. Let's face it, whatever we are actively doing with our hands requires the most skill and knowledge of where our hands etc. are. It is also the system that we rely on the most. But other systems are helpful to make sure we don't fall, grabbing on to things and making sure we reflexively contract the opposite muscles to prevent falling, stop us dropping things and lot's more. It doesn't matter if they're not accurate, they just need to be fast and in doing so they can't be extremely exact.
When we don't use vision, we rely on these other things. They're made to quickly adapt (e.g. hold a shopping bag for a while and when you let go your arm feels light or when you get out of a swimming pool your body feels heavy) and it is important that they do this to allow their functions as listed in the last paragraph.


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How many RNA-binding proteins can simultaneously bind on a single mRNA?
Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA?
Or said differently, how many "binding sites" does an mRNA have?
What order of magnitude?
I am interested in RNA granules like stress granules or P-bodies. They contain, inter alia, mRNA and RNA-binding proteins. I am not a biologist and I didn't come across this information so far in the related literature.

In what kind of cells? Bateria or eukaryotic cells?

Both kinds can be of interest to me, as long at is relevant to RNA granules.

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq.
Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.
They show number of protein protected sites (PPS) per transcript but that is not a proper metric in my opinion. The number should be normalized with transcript length so that you get density of protected sites. From figure 4 (see below) you can roughly estimate that average PPS density is close to 0.6 which means that 60% of any RNA is expected to be protein bound.

Figure 4

Other points to be noted:

Highly translated mRNAs will have multiple ribosomes on their CDS and
are likely to be more protected.
Sequestered RNAs in stress granules will also have high density of PPS
Footprint of different RBPs will be different. So number of proteins that can bind to a mRNA will differ between different RBPs.

Further reading:

http://dx.doi.org/10.1186/gb4153
http://dx.doi.org/10.1016/j.cell.2012.04.031
http://dx.doi.org/10.1016/j.molcel.2012.05.021

HTH :) You can also have a look at ribosome profiling -  sequencing experiments.

@David I added some more links to studies on RBP binding sites


text:
Kinetic binding / unbinding constants of protein + mRNA ⇌ mRNP
I wish to find an order of magnitude for the binding/unbinding constants of mRNA and RNA-binding proteins.
Suppose molecules A and B reversibly associate to give the complex C. Assuming the diffusion is large enough such that no concentration gradient exist, the reaction equation at equilibrium is:

➕[A][B] — ➖[C] = 0
with ➕ the binding constant (units: concentration-1.time-1), ➖ the unbinding constant (units: time-1), and [A], [B], [C] the concentrations of the molecules.
I found many papers assessing the equilibrium constant K = + / ➖ but I am interested in + and ➖ independently.

It's hard to separate the on and off rates, but one approach I've heard of is affinity chromatography. You'd need a column of immobilized protein or RNA, then fluorescently labeled and unlabeled counterpart. You load the column with labeled compound, then pass unlabeled compound through and measure how the labeled compound comes off.

Thanks for your answer. I am not doing experiments so I was searching the literature for some order of magnitudes.

The keyword that you're missing is kinetic. You want the kinetic binding constants/rates. And @user137 is right, this type of data is sadly uncommon, but if all you're interested in is OOM it might be possible... maybe. I'll take a look.

@user137 for future reference, there are many experiments that can be used to determine kinetic rates. Surface plasmon resonance (SPR), stop flow spectroscopy, kinetic ELISA, and many others. There's even a lab in my department working on getting binding/unbinding rates from single-molecule microscopy data.

@tel The only reason I was aware of the affinity chromatography method was because my dad did that for his PhD in the 80's. He had to make his own FITC, label his own antibodies, pour his own column, then build his own fluorescence detector for their HPLC using an automobile halogen headlight bulb and then run hundreds of HPLCs at different protein concentrations and salt concentrations and pH. It makes me appreciate working in a lab with funding.

@user137 build his own fluorescence detector for their HPLC neat

Katsamba PS, Park S, Laird-Offringa IA. 2002. Kinetic studies of RNA–protein interactions using surface plasmon resonance. Methods 26(2):95-104
There are many methods for studying kinetics, I only mention this one because the lab I'm in has used it for studying protein-ligand interactions. That article has a good explanation of SPR and how it works, so I won't offer to much detail other than to say it basically measures the change of refractive index as one molecule binds to another, which is immobilized on a chip. This allows direct measurement of on- and off-rates.
The researches studied two RNA binding proteins: HuD and U1A, as well as several mutants. Here are their results (Table 1 in the article):

I really couldn't tell you if those rates are generally representative of RNA-protein interactions, but I suppose that's not what you're asking.

Ridgeway and coworkers designed a really neat microfluidic device for making these kinds of kinetic binding measurements on RNA and protein (Ridgeway et al. 2009). Their device works sort of like a stop-flow, and they used a FRET based scheme to detect binding and unbinding events. They took measurements for one particular rRNA/ribosomal protein pair and got (6 ± 0.4) × 105 M-1s-1 for the bimolecular on-rate kon and  (5 ± 0.9) × 10-3 s-1 for the unimolecular off-rate koff.
Ridgeway cites references 23,24,26, and 33 when talking about experiments with "similar constructs and buffer conditions", so those would probably be a good place to start looking if you want to assemble a diverse set of kon  and koff  values.


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Are the DNA codon mappings arbitrary?
I am a Biology novice so I apologize in advance if I state anything incorrectly....
My question is, are the DNA codon mappings arbitrary? I understand that the DNA code is made up of codons which each consist of 3 base pairs. There can be 64 codons which map to 20 amino acids (some are duplicated and others act as stop codons). So was there a reason why one particular codon mapped to one particular amino acid - or is the mapping completely arbitrary?
Thanks!

"the assignment of codons to amino acids seem to be an advantageous one (most likely not the optimal one)" - so why didnt the optimal one appear at random ?

The code is for RNA, not DNA. As a novice you need to understand this basic point.

There is no reason for why a certain codon came to represent a certain amino acid. But some reason is attributed to similarity of degenerate codons. Usually the degenerate codons only differ in their last (third) nucleotide. The corresponding first anticodon in tRNA usually bears a modified nucleotide such as inosine which can (promiscuously) pair with A, C and U.
You can see the wikipedia page on wobble base-pairing.

Evidence suggests that the correspondence between DNA codons and amino acids (i.e. the genetic code ) is not random. A good place to start with this interesting topic is the Wikipedia article about the genetic code, in particular, about its origin:

Many hypotheses on the evolutionary origins of the genetic code have been proposed. Four themes run through the many hypotheses about the evolution of the genetic code:

Here I summarize the four themes (adapted from wikipedia).

Chemical principles governing specific RNA interaction with amino acids.
Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of "biosynthetic expansion".
Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations.
Information channels: Information-theoretic approaches models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources.

Other models combine some of these hypothesis.
Selected references:

The genetic code is one in a million. Freeland SJ, Hurst LD. J Mol Evol. 1998 Sep;47(3):238-48.
Selection, history and chemistry: the three faces of the genetic code. Knight RD, Freeland SJ, Landweber LF. Trends Biochem Sci. 1999 Jun;24(6):241-7. Review.

I see your point and have read some articles in this direction too. So as you say rare amino acids like Trp have less codons. But why a certain codon came to represent an amino acid is in my opinion a chance event. Just like any evolutionary process

So it sounds like there are a bunch of theories on how this codon to amino acid mapping came about - but none of these are supported by specific evidence - its all speculation. Is that correct?

@WYSIWYG, yes, evolution is random. But here the point is that some outcomes are more advantageous than others. In this case, the assignment of codons to amino acids seem to be an advantageous one (most likely not the optimal one) based on several considerations.

@MichaelScott, the many research papers on this topic present supportive evidence. As with any research trying to demonstrate the past, it is very difficult to find irrefutable evidence.


text:
Why do cats like enclosed spaces (e.g. boxes) so much?
A recent article doesn't reach a firm conclusion, but offers two possible explanations.

Hiding is a behavioral strategy of the species to cope with
  environmental changes and stressors.

It keeps the cat at a comfortable temperature.

Can you expand on the tentative explanations (i.e. give some background), and explain what you think is lacking?

I just updated the OP. I'm looking for some more credible source to reach a firmer conclusion using better evidence.

"Cats like boxes because they are cryptic animals; they like to hide,"And a box gives them a place of safety and security."
While inside a box, cats feel that they cannot be snuck up on from behind or the side — anything that wants to approach them must come directly into their field of vision. In effect, such hiding spaces allow them to watch the world around them without being seen.
And if something interesting passes in front of the cat — be it prey or a toy — it can dash out to get the object, and then quickly return to its safety spot.
Boxes also provide cats with a cozy, safe place to sleep, which is very important given that the felines sleep for up to 20 hours a day.

authors: user1205901 - Слава Україні


text:
Loss in DNA band size extracted from polyacrylamide gel
I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR  but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. I always extracted the precise bands.  I repeated with both pre and selective primers with the same PCR program before done for amplification of digested cDNA and same size bands observed in agarose gel.I wonder maybe secondary structure causes losses in band size (before running in polyacrylamide samples treated in 94 degree for 5 min), but how I can recognize?  i should notice 350 bp band i mentioned above is very sharp. what other thing I'm wondering is can dye uses in agarose gel alternate the DNA charge and reduces the speed of movement . The big  matter is the rate of losses in band size almost is same for almost all of the bands for one primer. Is it happened for anyone before? can i trust on my extracted bands for doing cloning?

Urea-PAGE is a denaturing gel. The mobilities are likely to be different from the normal agarose gel. Can you put the gel pictures up?

I ran dna ladder in both acrylamide andagarose gel, if mobilities affected it should be true about the ladder!

What ladder was it. Urea will denature dsDNA

I don't know realy. I always thought ladder is dsDNA. is there any ssDNA ladder. I should check it. I'll let you know soon. however thanks for your help.

Thanks. with your guide I could find the problem, really there was no problem! DNA ladder I used was double strand DNA, and somewhere I read ladder's mobilization profile in denaturing gels differs depending on gel percent. I ran the PCR product of extracted band in polyacrylamide gel again. And I found what I expected, the same size -670bp. I think denaturing gel affected sample DNAs and ladder mobilization but because of their size and sequence (GC content for producing secondary structure)difference the influence was not same and it 's not predictable.


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Is ovum + ovum fertilization possible for human?
In humans is it possible to fertilize a ovum with another ovum from the same female subject?
I already found some works in which the ovum is fertilized by a somatic cell (see e.g.  this ), but I am looking for fertilization specifically by another ovum.
Around a year ago I found in the internet a Japanese (ongoing) study on this, but cannot locate it any more.
I would greatly appreciate any help.

The problem is that in cloning you are inserting a diploid somatic nucleus into an egg cell so that works. in fertilising with a haploid sperm, the sperm brings mechanisms for nucleus fusion. two egg nuclei would require us to manually fuse them, which they would probably refuse.

Wouldn't this only result in female progeny if all the DNA is of female origin?

Using a somatic cell in an a ovum is what is typically done in the process of cloning.  It was the same process used to create Dolly the Sheep. What you're asking about is something very different:
Consider that somatic cells are properly diploid.  Whereas an ovum itself just contains a haploid number of chromosomes. In typical sexual reproduction the sperm fertilizes the ovum which would than bring the chromosome number to to correct tally.  So combining the genetic material in two ovum should bring the chromosome count to the correct tally as well, but scientists would need to somehow motivate the  activities that happen when typical  sexual reproduction occurs. It's likely very challenging to do that if not highly improbable. Should it work, this process could only produce female children.

With identical twins, the cells are diploid and start as one cell, but another breaks away and forms a seperate zygote. In fraternal twins two separate ovums are fertilized separately.  Once you have conception (sperm fertilizing eggs) you have a diploid cell. With the exception of some know genetic disorders (downs syndrome) all humans are diploid, so two diploid cells don't join themselves and start dividing in utero.


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Why is glucose so common in disaccharides, as opposed to a different monosaccharide?
The three most common disaccharides (sucrose, maltose, and lactose) all contain at least one glucose monomer (sucrose=glucose+fructose, maltose=glucose+glucose, lactose=glucose+galactose), and the vast majority of other disaccharides also contain at least one glucose.
The only outliers to this that I have found are xylobiose (xylose+xylose), rutinulose (rhamnose+fructose), melibulose (galactose+fructose), lactulose (galactose+fructose), and mannobiose (mannose+mannose), and these all seem to be relatively niche/uncommon. Glucose is also one of the only monosaccharides I can find that binds with itself to form a disaccharide, and I have not found any examples of a fructose+fructose or galactose+galactose disaccharide.
What property of glucose makes it so that glucose found in (and is so integral to) so many disaccharides instead of a different monosaccharide, such as fructose or galactose, and why is it able to commonly form a bond with itself, unlike fructose or galactose?
(link to wikipedia article containing list of disaccharides with the monosaccharides they are composed of: https://en.wikipedia.org/wiki/Disaccharide)

What property of glucose makes it so that glucose found in (and is so integral to) so many disaccharides instead of a different monosaccharide, such as fructose or galactose, and why is it able to commonly form a bond with itself, unlike fructose or galactose?

Some readers seem absorbed with the notion that glucose can "form a bond with itself, unlike" other monosaccharides. This hasn't been addressed because it's an incorrect premise. To my knowledge this happens in many hemiacetals/hemiketals in water.
Glucose is a fundamental hexose; the metabolism of glycolysis is truly central to cellular life. This explains why it's so pervasive, in disaccharides or other carbohydrates. To use the wording of the question, the property of glucose that it explains its pervasive representation in disaccharides is its metabolic availability.
So why is glucose metabolism conserved across all three Domains of life? I explore two reasons.

Glucose metabolism could be central because of evolutionary history. Another type of aqueous biochemistry could prevail under terrestrial chemistries. So galactose-based terrestrial biochemistry is equally possible, in which case it would be overrepresented in biomolecules instead of glucose.

The aqueous abiotic (organic) chemistry of carbon (under terrestrial conditions) support glycolysis as a central metabolic pathway. So a galactose-based terrestrial biochemistry is thermodynamically disfavored.

(Same arguments go for pentose phosphate and TCA cycles, and the few other pathways that are so close to energetic equilibrium as to be amphibolic and metabolically central.)
Evolutionary biology provides evidence for explanation (1). This is because all domains of life share conserved enzymatic machinery for glycolysis; "The phylogenetic distribution of the enzymes of the glycolytic pathway confirms that it is indeed an ancient metabolic pathway, and was present (at least in part) when eukaryotes and
prokaryotes diverged about 1800 million years ago."From this reference, p. 224
There are also strong arguments for explanation (2). Below is one article detailing how glycolysis could very plausibly preceed cellular life. Glucose would then be pervasive, in part, because it's a pervasively metabolically-accessible (and chemically stable) sugar, under terrestrial conditions.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023395/

"Evolutionary biology provides evidence for explanation (1)." Can you provide a link to support this (completely reasonable) statement? Thanks.

Your answer makes no connection between the composition of disaccharides and glycolysis, indeed disaccharides are not even mentioned.

@Ryan.  Perhaps this is a question of stereochemistry.  Ask a chemist.

@anongoodnurse I added an evolutionary biology reference

@jeremiah my reference includes considerations of stereochemistry

@David my answer doesn't reference disacchararides and glycolysis because they do not exist in glycolysis! the preponderance of glucose in sugars, celloses and chitin, etc, is being explained by me in terms of its sheer abundance as a central metabolite

Aren't you putting the cart before the horse? The question isn't "why is glycolysis universal?"

@anongoodnurse my answer is, glucose is preponderant because it's central metabolically, and i gave two possible explanations for this centrality. you asked for a reference as to my claim that it's central for evolutionary reasons, explanation 1.

@Ryan But the question is about disaccharides! The word “glycolysis” doesn’t even appear in the title. I

The paper is about glycolysis, not the ubiquity of glucose. It's like asking for support for democracy in Ancient Greece, and citing the American Constitution.

not following the above analogy, but your persistence motivated a more explicit answer, @David

@Ryan - What came first, glucose or glycolysis? Glycolysis depends of the production of glucose. The principles of democracy (e.g. in Athens) predate the US Constitution, which was heavily influenced by Ancient Greece. Your answer is teleological.

If you want to answer a question on the reason that glucose is the "king" of hexoses, ask it and answer it yourself. However think carefully. Many such evolutionary "why" questions provoke answers that assume that whatever Nature chooses must be the "best". It ain't necessarily so, and stacking up one feeble argument after another doesn't make it so.

glycolysis can be biotic or abiotic. my position would always be to asume abiotic conditions to be ontologically prior. I don't see how my position is teleologica, as well, I haven't asserted a King hexose" type explanation, but I do see how answer 2 is related to that position

Part of the explanation for this preponderance in disacharides is perhaps the dominance of glucose generally, and the clear necessity for it to be stored in organisms. The intuitive explanation for that preponderance, including in polysaccharides generally, likely involves some stereochemical property which distinguishes it from galactose, and broadly speaking, fructose.  The following is an excerpt from the 'Wikipedia' article on Glucose itself; which seems a good starting point.

Glucose is the most abundant monosaccharide. Glucose is also the most
widely used aldohexose in most living organisms. One possible
explanation for this is that glucose has a lower tendency than other
aldohexoses to react nonspecifically with the amine groups of
proteins. This reaction—glycation—impairs or destroys the function of
many proteins (e.g. in glycated hemoglobin). Glucose's low rate of
glycation can be attributed to its having a more stable cyclic form
compared to other aldohexoses, which means it spends less time than
they do in its reactive open-chain form.
The reason for glucose having the most stable cyclic form of all the
aldohexoses is that its hydroxy groups (with the exception of the
hydroxy group on the anomeric carbon of d-glucose) are in the
equatorial position. Presumably, glucose is the most abundant natural
monosaccharide because it is less glycated with proteins than other
monosaccharides. Another hypothesis is that glucose, being the only
d-aldohexose that has all five hydroxy substituents in the equatorial
position in the form of β-d-glucose, is more readily accessible to
chemical reactions, for example esterification or acetal formation.
For this reason, d-glucose is also a highly preferred building block
in natural polysaccharides (glycans). Polysaccharides that are
composed solely of glucose are termed glucans.


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Can human organs be transplanted indefinitely?
I watched this movie, where they rented hearts to people for a year. I wonder if it is possible to transplant a heart indefinitely from person to person, or does the heart have a lifetime? So, do human organs age and eventually die, or is it possible to transplant organs indefinitely? What is the limiting factor for life of human organs?

Welcome to biology SE! Could you elaborate your question? For example, it is not clear if you are talking about keeping the organs fit for transplantation after the donor has passed away, or whether you are asking whether organs have to be transplanted before the donor reaches a certain age while alive.

@ChrisStronks I am asking about does the organs age, or is it possible to transplant organs indefinitely from donor to donor. See my edit please.

I took the liberty to edit your question - I hope it accurately reflects your question.

First of all, it will be practically impossible to make an estimation of how long a transplanted organ will live and how many times it could be transplanted. However, it is relatively safe to say that it will not live forever.
To be able to receive an organ transplantation, the HLA MHC-complexes of donor and receiver need to be matched very carefully, to limit the host-vs-graft reaction. This limits the number of possible donor-receiver patient pars drastically. So to be able to do a "row transplantation" (one receiver to the next and so on), they need to have matching MHC-complexes.
Otherwise the immune system of the receiver turns against the transplanted organ and will eventually destroy it. To avoid this reaction, transplantation patients also receive drugs, which severely suppress their immune system, thus making other infections potentially dangerous. This reaction will still take place, since you cannot shut down the immune system of the receiver completely (for obvious reasons), though it happens at a much slower rate. Transplanted organs will only live for a certain time (see estimates from a number of transplantations below) and it is possible that people need to receive transplants twice in their life.
For this reason, no doctor will put their patient at risk by giving them an organ which might have a reduced lifetime. The risk of the operation itself is also substantial.  Additionally, the original receiver needs to be dead to do this, as he would otherise need another organ in exchange.
What we can do is to take the average number of a lot of transplantations together and calculate some average life-years for a transplant. According to table 2 in this paper ("The Life-Years Saved by a Deceased Organ Donor") the "average benefit by type of transplant (life-years)" is:

Kidney: 7.2 years
Liver: 16.9 years
Lung: 2.1 years
Heart: 14.5 years
Kidney-Pancreas: 12.9 years

These numbers are not definite, since the life style of the donor and the receiver as well as infections of the transplated patient (who has a severely suppressed immune system – this is critical) also play an important role in determining the lifetime of the organ.

The table you cite refers to average number of years a person on a transplant waiting list will live after receiving a donated organ, i.e. the expected lifetime of the recipient. This is unrelated to the maxium or average lifespan of the transplanted organ, which is what the OP is asking about. It's an outlandish question but this doesn't answer it.

No, you are wrong. What I cite here partly is table 2 from the article which describes "Table 2.  Average expected gain in life-years for wait-listed patients from an extra deceased organ donor".

As I understand the article, the numbers cited in the table represents the average number of years by which a single donated organ will extend the life of a person on the donor waiting list for that particular organ. So if one "extra" liver was made available for donation it would be transplanted into a recipient who would then go on to live for an additional 16.9 years. The 16.9 years refers to the expected remaining lifetime of the recipient, not the transplanted organ. Theoretically the organ could be once again transplanted upon the death of the first recipient. [ctd]

Of course this is incredibly unlikely for the exact reason you specify: it will have been damaged by the recipient's immune system. Regardless, the OP is asking how long or how often such an organ could be transplanted in a functioning state, which you did not directly address.

What they did was to calculate the additional livetime gained by a transplated organ which they calculated from a large number of organs. So if you are on the transplantation waiting list or a liver and get a transplantation before you die, this can result in up to 16.9 years.

Even if the numbers listed here are not for the lifetime of the organ, an organ can't be used forever, I suspect the lifetime of an organ can't be much longer than the lifetime of the average person in ideal conditions. Add in stress from immune rejection, lifestyle, infections, and multiple surgeries and the organ lifetime will be even shorter.

@user137 Agreed, but that's precisely what the OP is asking. Ideally this answer would state that explicitly, provide a source for the claim that organs are (almost) never retransplanted and then the table is a good indicator of the practical lifetime of a transplanted organ.

@Chris Apparently we both understand what that table means perfectly, but my point is that it's not actually the number the OP is looking for, unless you preface it as being the average limit to an organ's lifetime in practice (see above comment to user137).

@Lilienthal I have edited the answer, is this clearer now?

@Chris Perfect. Thanks for clearing it up and nice find on the article itself. +1

The median lifetime of an organ transplant is some 5 to 10 years mainly due to chronic rejection mediated by host-versus-graft immune responses.  Hence long-term transplants definitely have a limited half life. However, this graft rejection is relatively slow and early explantation and re-implantation in a new host may actually "reset" this process? With re-setting I mean that the new host's immune system must start the slow graft rejection process (immunization) all over again, including antigen recognition and build up of the humoral and cellular immunity (see wiki on graft rejection). So in theory the organ-lifetime may actually surpass the recipient lifetime as mentioned earlier when grafts are explanted and re-implanted. As this scenario has never been tried as far as I am aware - due to the obvious risks associated with repeated complex surgeries - it becomes speculative at this point.

I don't understand, is it possible or not, or unknown?

@matthew he is saying its unknown.

I tried to improve the clarity of my answer - but indeed it is unknown what happens with repeated re-implantation

It really depends on the primary disease of the transplant recipient and the organ transplanted. Some diseases cause organ failure and will do damage to the transplanted organ and shorten its survival. There are rejection process in the host that will do all sorts of damage to the graft. There is also surgical complications when trying to ex-plant a transplanted organ and re-implant it into another recipient. However, if you want to know the record of how long an transplanted organ has survived please check this out:
http://www.bbc.co.uk/news/uk-england-tyne-37025389


text:
Calculating number of amino acids in mRNA
Assuming there were 20 different amino acids and less than 40 types of different tRNAs found in this alien organism. How many amino acids would be found in the translational product of a 600-nucleotide mRNA?

I am very confused over how I should solve this question.
If we assume 1 codon = 1 nucleotide,
20 amino acids require 20 different codons = 20 different nucleotides < 40 different tRNAs.
If we assume 1 codon = 2 nucleotides,
20 amino acids require 20 different codons = 5 x 5 combination of nucleotides? (considering A, T, C, G, U)?
5 x 5 = 25 < 40 different tRNAs.
The correct answer is to consider 1 codon = 2 nucleotides.
My question,
Since both 1 codon = 1 nucleotide and 1 codon = 2 nucleotides fit the requirement of this question, why is 1 codon = 2 nucleotides the correct answer?

You could have more than 1 tRNA for each amino acid, as well as stop codons. Both of these features are found in Earth's genetic code.

Wait, are we supposed to assume that this alien uses both T and U in it's RNA? To solve this we need to know how many types of nucleotide it uses.

@user137 thanks for your reply, that is the exact question, no additional information  given. I am assuming the organism uses all 5 different nucleotides.

The problem is I don't know how you could use both U and T and tell them apart because they both bind to A. Furthermore we can't assume an alien biochemistry would be at all similar to Earth biochemistry and their "RNA" could use entirely different bases.

If this is the original question accurately and in full it is meaningless and unanswerable. If, as your answer about codon length implies, it is a garbled version of the question, please present it carefully and word for word. As it stands, If the question means how many amino acids in the peptide produced you can't tell because it doesn't tell you where the start and stop codons are. If it means how many different amino acids there are, you cannot tell because you do not know what the sequence is. In either case the number of tRNAs can have no bearing on the answer.

I think I have this figured out. Had to do some math. With our 4 nucleotide system, the number of possible codons is 43 = 64. That is number of nucleotides to the codon length power. The question asks us to determine codon length while giving us the number of amino acids and an upper limit on tRNAs. Using the same formula,  #Nucleotides(Codon-Length) = #Codons, we must find a combination of nucleotide number and codon length that gives between 20 and 40 codons.
                               Codon Length
Nucleotides    1         2        3        4        5
     2         2         4        8        16       32
     3         3         9        27       81       243
     4         4         16       64       256      1024
     5         5         25       125      625      3125
     6         6         36       216      1296     7776
     7         7         49       343      2401     16807

So using this table we see that a few different combinations of Nucleotide number and codon length will fit in that range. A 2-nucleotide system could work if each codon was 5 bases long. A 3-nucleotide system could work with 3 base long codons. A 4-base system cannot work, it goes from less than 20 to more than 40. A 5-base system can work with 2 base codons. A 6-base system can also work with 2-base codons. 7 or more bases fails because even a 2-base codon will make more than 40 codons.
A codon length of 1 nucleotide would require at least 20 nucleotides, so it would not be a good answer.
5 is probably the correct answer because it works with the shortest codon length, though I don't know how you'd get base pairing with an odd number of bases. Perhaps the 5th base pairs with itself. A 6 base system can also work with the same codon length and wouldn't need a self pairing base. However that table shows several combinations could work, so this question might have been to see how you defend your answer.


text:
Burning fat transferred from one part of the body to another
While doing some research on cosmetic surgery, I discovered that there are several ways of doing breast enhancements, one of which was using body fat. While I haven't researched this method, I assume they transfer the patients body fat from one part of the body to another.
Would the body use this transferred fat for as energy, or would it ignore it as it wasn't stored there in the first place? Does the body differentiate fat cells stored in different parts of the body?

It is hard to answer the question whether after transplantation the breast size will reduce or not. I think it will, but without experiments this is just a hypothesis...

Would the body use this transferred fat for as energy, or would it
  ignore it as it wasn't stored there in the first place?

It would use it as energy source, there is no such thing as "ignored tissue". Fatty acid mobilization is regulated by epinephrine and insulin. These are hormones which are ofc. carried by blood, so every white adipose (fat) tissue is affected by them.

Figure 1 - FFA and glycerol mobilization - source
2003 - Fatty acid mobilization from adipose
tissue during exercise

Does the body differentiate fat cells stored in different parts of the body?

This is obvious, just check breasts and butts of girls. ;-) (Those are subcutaneous fat depos. They size is probably regulated by estrogen.)
There are other things involved here, we can talk about subcutaneous (fat below the skin), intramuscular (fat in the muscles) and visceral (abdominal fat) white adipose tissue (there are white, brown and beige adipose tissues). The visceral fat is associated with metabolic diseases, obesity etc...

1995 - Pathophysiology and Pathogenesis of Visceral Fat Obesity
2012 - Lower Thigh Subcutaneous and Higher Visceral Abdominal Adipose Tissue Content Both Contribute to Insulin Resistance
2013 - Genomic and epigenomic regulation of adipose tissue inflammation in obesity

The regulation of body fat distribution and amount is complicated and regulated differently by subcutaneous, intramuscular and visceral fat.

The total transmissible variance ranged from about 40 percent for the
  amount of subcutaneous fat to 60 percent for the pattern of
  subcutaneous fat distribution. Biological inheritance accounted for
  only 5 percent of the variance for subcutaneous fat and the body mass
  index, but 20 to 30 percent for the percentage of body fat, fat mass,
  fat-free mass, and fat distribution. These data suggest that the
  amount of internal fat is influenced by heredity more than the amount
  of subcutaneous fat. Furthermore, we consistently found that
  nongenetic influences are quite important in determining the amount
  and distribution of body fat in the population.

1988 - Inheritance of the amount and distribution of human body fat

These data suggest that adiponectin concentrations are determined by
  intra-abdominal fat mass, with additional independent effects of age
  and sex. Adiponectin could link intra-abdominal fat with insulin
  resistance and an atherogenic lipoprotein profile.

2003 - Relationship of adiponectin to body fat distribution, insulin sensitivity and plasma lipoproteins: evidence for independent roles of age and sex

The FFA storage pathway, which had remained undetected in
  postabsorptive humans until recently, can have considerable,
  long-term, and sex-specific effects on body fat distribution. It can
  also offer a way of protecting the body from excessive circulating FFA
  in obesity.

2011 - Storage of Circulating Free Fatty Acid in Adipose Tissue of Postabsorptive Humans
Quantitative Measures and Implications for Body Fat Distribution

Different colors (white, brows, beige) and orgin (subcutaneous, intramuscular, visceral) originate from different progenitor cells.

These results reveal a major ontogenetic difference between visceral
  and subcutaneous WAT, and pinpoint the lateral plate mesoderm as a
  major source of visceral WAT. They also support the notion that
  visceral WAT progenitors are heterogeneous, and suggest that
  mesothelium is a source of adipocytes.

2013 - Visceral and subcutaneous fat have different origins and evidence supports a mesothelial source

Brown and white adipocytes have been shown to derive from different
  progenitors. In this study we sought to clarify the molecular
  differences between human brown and white adipocyte progenitors cells.

2014 - Comparative gene array analysis of progenitor cells from human paired deep neck and subcutaneous adipose tissue

The regulation of fat distribution is under research, and not fully understood yet.

Fat distribution differs in men and women, but in both sexes, a
  predominantly gluteal-femoral compared with abdominal (central) fat
  distribution is associated with lower metabolic risk. Differences in
  cellular characteristics and metabolic functions of these depots have
  been described, but the molecular mechanisms involved are not
  understood.

2012 - Distinct Developmental Signatures of Human Abdominal and Gluteal Subcutaneous Adipose Tissue Depots

It would be great if you used some references to support your response! As it stands this is more like a comment!

@Bez Okay, I'll edit soon.

Very complete answer.

@pbond Not really, they needed some references, so I gave them.

You are correct - we suction out subcutaneous fat (fat in-between the skin and muscle layers) which is commonly referred to as "liposuction". Then we make a "slurry" type of solution with the fat and saline-like solution. Then using long needles we inject this 'transplanted' fat into another area. Many times if a woman has a breast reconstructive procedure and needs some contouring done around an implant (i.e. to smooth the surface under the skin where the breast implant and surrounding tissue meet) this can be done. Not all the transplanted fat will grow enough blood vessels in this new area and some of the fat tissue will die. This dying process is called "necrosis" and the body will reabsorb the dead cells and their contents. It works very well overall.

This was informative. Can you also add a note on OP's this question: "Does the body differentiate fat cells stored in different parts of the body?"


text:
Can Hepatitis be caused by Bacteria?
There are many information about viral hepatitis. But it is interesting for me, can bacteria cause the hepatitis too?

Short answer: Yes , they can. Have a look at this Wikipedia article.

@Chris - I would disagree; I couldn't find any mention of hepatitis from bacteria in your linked source. Can you please elaborate?

Look under causes, there you will find the following: "Less commonly some bacterial, parasitic, fungal, mycobacterial and protozoal infections can cause hepatitis." Since a Hepatitis only describes the inflammation of the liver, anything what can cause this causes a hepatitis. You could also have a look here.

Hepatitis just means liver inflammation. The word per se does not indicate any causative agent.

Hepatitis is a condition of the liver where the cells of the liver organ are inflamed. Most often it is caused by a viral infection, hepatitis A, B and C are all viral forms of the disease.
Bacteria (and Fungi) can cause hepatitis of the liver, and two examples would be the Staphylococcal and Streptococcal bacteria. These can directly infect the liver, and are also responsible for some inflammations in other tissues of the skin and heart and elsewhere.
Prolonged alcohol abuse is another cause of hepatitis (as well as cirrhosis) and is not associated with bacteria virus or fungi, but instead from a damaging effect on the liver.

Helicobacter hepaticus is suspected to cause hepatitis.

Thanks @inf3rno you could add that in as a second answer

I don't want to, I don't think it is enough for an answer, maybe to an edit...

http://europepmc.org/abstract/MED/11677423

Hepatitis has two definitions: inflammation of the liver in general, or inflammation of the liver due to one of several viruses.  The viruses are, of course, viral.  However hepatitis can also mean the symptom of an inflamed liver.  That symptom can be caused by bacteria.

The suffix '-itis' (-ῖτις, in ancient greek) usually is added to a word to represent a pathological condition called inflammation.
So, haepatitis (or hepatitis) means generically inflammation of liver (ἧπαρ épar, in ancient greek).
Usually it is  caused by viruses  such as HAV, HBV, and HCV.
An haepatitis can be due also to  toxic agents or be autoimmune .
But, whaterver it is the cause of inflammation of liver cell, it is called haepatites; even if it is caused by less common pathogens as bacteria; protists like T Gondii ; minor hepatotropic viruses, like EBV, CMV, and herpetic viruses in general; fungi, or protozoa and other parasites.
Bacteria can cause haepatitis, examples would be the Staphylococcal and Streptococcal haepatitis.
Ever the excessive intake of table salt (Na-Cl) or cronic alcoholism may cause  haepatitis or even a liver's cirrhosis.
So, though it is less common, but bacteria may cause haepatitis.


text:
Why does caffeine give you so much energy, while being so low on calories?
There's definitely something I'm missing here.
Since calories is a unit of measurement for energy, and caffeine seemingly gives you a lot, how can the labels on caffeinated products have such a low calory count?
I would presume that caffeine doesn't really have as much energy as it seems to give you? In which case, what does it do?
Thanks in advance!

I agree with @inf3rno: caffeine is a stimulant that acts on the brain and various other parts of the body (Snyder et al., 1981) and I wish to elaborate on its psychopharmacology. Caffeine's effects in the brain are mediated through adenosine A1 and A2 receptors (Daly et al., 1983). This results in a variety of actions (Fredholm et al., 1999). Most notably, adenosine inhibits neurotransmitter release in various brain structures including the acetylcholine release in the mesopontine projection neurons. Caffeine blocks these adenosine receptors, in turn leading to an increase in acetylcholine release in the cortex and hippocampus. This increases vigilance and information processing. Increased acetylcholine release in the prefrontal cortex may lead to increased attentional abilities. Adenosine also inhibits the effects of dopamine released by the striatium, ultimately leading to disinhibition of motor output in the brainstem. This in turn increases motor activity (Fisone et al., 1997). In all, caffeine does not exert its stimulant effects through its metabolic energy content, but due to its pharmacologic effects on adenosine receptors.

Excellent answer. I had to look up most of the words, but the bottom line summed it up nicely.

Caffeine is a stimulant, which helps you release the energy your body stored.

Caffeine is a central nervous system and metabolic stimulant,[12] and
  is used both recreationally and medically to reduce physical fatigue
  and to restore alertness when drowsiness occurs. It produces increased
  wakefulness, faster and clearer flow of thought, increased focus, and
  better general body coordination.[13] The amount of caffeine needed to
  produce effects varies from person to person, depending on body size
  and degree of tolerance. Effects begin less than an hour after
  consumption, and a moderate dose usually wears off in about five
  hours.[13]
Caffeine has a number of effects on sleep, but does not affect all
  people in the same way. It improves performance during sleep
  deprivation but may lead to subsequent insomnia.[14] In shift workers
  it leads to fewer mistakes caused by tiredness.[15] In athletics,
  moderate doses of caffeine can improve sprint,[16] endurance,[17] and
  team sports performance,[18] but the improvements are usually not very
  large. Some evidence suggests that coffee does not produce the
  ergogenic effects observed in other caffeine sources.[19] High doses
  of caffeine, however, can impair athletic performance by interfering
  with coordination.[20] There is also evidence that caffeine may be
  helpful at high altitude.[21]

wikipedia - Caffeine
1980 - Caffeine and coffee: their influence on metabolic rate and substrate utilization in normal weight and obese individuals.
2010 - Green tea catechins, caffeine and body-weight regulation
1985 - Influence of caffeine on the resting metabolic rate of exercise-trained and inactive subjects.
2004 - Effect of a Dietary Herbal Supplement Containing Caffeine and Ephedra on Weight, Metabolic Rate, and Body Composition
2006 - Metabolic effects of spices, teas, and caffeine
2004 - Enhanced Stimulant and Metabolic Effects of Combined Ephedrine and Caffeine
2006 - Changes in caffeine intake and long-term weight change in men and women

Two excellent and sourced answers. I can only pick one as accepted, but I found a lot of value in your citations. Especially the 2006 one, which inadvertently also answered an unasked question about caffeine intake possibly increasing one's metabolic rate.


text:
How does intron retention make the alternative transcript non-coding?
I faced with a non-coding transcript that specified as one the isoform of BIN1.
It sounds that this isoform generated as a result of alternative splicing with a intron retained; am I right? However, Ensembl reports that the transcript has 5 exons, could you please let me know more about this event? How does the transcript have 5 exons and all are non-coding?
Also, I'll glad to hear why the organism or cell has retained such a transcripts? they have any function?
Thanks

An exon is just a sequence that is retained in the mature RNA. It doesn't have to be protein coding.

I could not find the sequence of this transcript but it must have become non coding most probably because retention of the intron must have caused a frameshift leading to loss of the ORF (there are no stop codons).

Some changes could also destabilize RNA and make the turnover so fast that it does not code. As an example, the intron could add a target for interfering RNA (siRNA) that both blocks translation and forces the degradation.


text:
What is the evolutionary purpose of the topology of the human ear?
What is the evolutionary purpose of the topology of human ears? I understand why the ears may have a funnel-like shape but if the various "hills and valleys" do not amplify incoming sound, what purpose do they have?

Humans do not have the ability to move their outer ear in response to sound. Many animals can do that, and use it to determine the source of the sound waves. Thus, human outer ears are equipped with many "hills and valleys". It does not provide amplification (because the waves can lose their energy bouncing around the ridges), but rather gives the brain more information about the sources' location in space. The brain calculates that location by determining minute differences in the time it takes for the sound to reach sensory cells in the inner ear on both sides. The shape basically attenuates the raw information. That way you get different properties of the sound wave that enters your ear depending on the angle at which it fell on you outer ear.

Could you support your answer with references? Have the effects of different pinna morphologies been tested in humans?

Different ears are shaped differently. Does that mean the brain is aware of the topology of the ear and aware of how sound is affected by it?

Humans can localize the horizontal location of sound ("azimuth") using temporal cues (sound reaches the 'closer' ear first') and level (the head blocks some sound so it louder at the 'closer' eat) cues, depending on frequency.
For detecting the "height" or "elevation" of a sound, other cues are necessary. "Pinna cues" refer to a pattern of level distortions at different frequencies that, combined with predictable elements of natural sound (such as harmonics), allow the listener to determine elevation. The head also contributes, so these cues are grouped together as a "Head Related Transfer Function." Importantly, the two ears are never perfectly the same, so these cues can be differentiated from the azimuth cues I described earlier. One can measure these pinna cues by placing a microphone in the auditory canal.
The Wikipedia article on sound localization has some more information, as do several online course postings and textbooks, for example this one, or by searching for terms like "sound localization elevation pinna".

I'm guessing this is the same as spectral filtering for sound localisation?

Yes; "spectral cues," "head related transfer function," "pinna cues," - these are all related terms with varying levels of application/specificity but they effectively refer to the same thing.

One possible advantage is that's it's probably the best adapted to being able to hear a very low volume source of sound no matter which direction it's coming from. A horse ear on the other hand, is probably the best adapted to being able to hear an even lower volume source in only a very narrow range of directions. One reason for being able to hear well in any direction is to avoid predators. Maybe in our evolutionary history, we sometimes went into a jungle and there was a dinofelis lurking in it with silencers on its feet and we couldn't see it so we evolved ear the shape we did so that we could hear it from really far away if it started walking no matter which direction it was from us and prepare to fend it off with spears. Maybe we always had ears the shape we do then we just started evolving to have horse like ears so that we could keep moving our ears until we locate the dinofelis and then in response to that, the dinofelis evoled to stop walking a very short time after it starts when it's in the jungle so that we can't hear it from further away anymore so it became advantageous to hear as far as we can in any direction so we stopped further evolving horse like ears and that's why some people can move their ears a tiny bit. One reason for being able to hear such a low volume source in any direction is to catch prey. Deers probably evolved ears shaped the way they are so that they could keep turning them until they hear a prey animal and then keep their ears pointed towards it so that they can keep hearing it so that they can hunt it.

Evolution doesn't have a purpose. In that light, it's quite possible for an ear to be poorly adapted to hearing - which in fact it is compared to other species.
Stereo hearing (two ears, so you can better detect where the sound is coming from) is heritage from our ancestors, and I know for a fact it didn't evolve further in humans because there was no evolutionary pressure.
In any case, the topology isn't exclusive to our species and is heritage from our mammalian lineage. At some point in our lineage, the species/individuals who had this topology of the ear were able to gather sound waves better and that affected their survival so they passed on the trait to their offspring. Ear topology didn't evolve in humans.

Can you provide citations to support your assertions? What makes you certain that the ear in humans has not been subject to selection? I'm not suggesting that it has, but I would like to know if there is evidence to the contrary.

Just take a look at the ear(s) of any great ape. Clearly ear hasn't been changed much within our species and the development took part much earlier in our lineage.

But we don't know what the ear of the most recent common ancestor of humans and chimpanzees looked like.

No, we don't, because we don't know what the common ancestor is, when it lived, and what it looked like. No fossil has been found. We can only presume ears of this shape are a shared trait derived from the common ancestor, otherwise we'd be saying it evolved independently at least four times. That's next to impossible.

This answer is misleading and takes the conversation in an unnecessary direction - the question doesn't include an explicit misunderstanding of evolution. I don't believe the question needs to be read as "what are the unique adaptations for hearing in the human ear." I read the question as "Ears look funny. Is there any reason applicable to survival/fitness for ears to look the way they do?"