Electricity generated by the body and its applications? I recently came across this article from Nature. In it, it states that the snails have "tiny biofuel cells that extract electrical power from the glucose and oxygen in the snail’s blood", and that the power obtained is dependent on "how quickly sugar and oxygen can be taken from the creatures' blood". They go on to say that the power obtained decreases over time, and that these implants could power future pacemakers in humans.

Would this application in humans require that a patient eats more and "breathes more" than average? Why does the power output decrease over time, and couldn't that potentially lead to the malfunctioning of a pacemaker?

References

Van Noorden, Richard. “Cyborg Snails Power Up.” Nature (March 12, 2012). http://www.nature.com/doifinder/10.1038/nature.2012.10210.

You'd think if such devices were used in humans, they wouldn't require a change of lifestyle.

They don't say the power always decreases over time:

  Katz’s snails, for example, produced up to 7.45 microwatts, but after
  45 minutes, that power had decreased by 80%. To draw continuous power,
  Katz’s team had to ramp down the power they extracted to 0.16
  microwatts.

This is really a chemistry question. The glucose has to be brought to the fuel cell some way. In this case, the glucose is oxydized directly in the hemolymph. As oxygen PP in the hemolymph is always greater than glucose concentration(1), your limiting rate (which is related to the power you can get from the device) is that of glucose intake at the fuel cell. Therefore, the more you oxidize glucose per unit time, the greater intake you need to keep the output from dropping.

The glucose intake at the fuel cell is a function of biological parameters such as quantity eaten, metabolic efficiency, metabolic speed, blood flow, but also diffusion. The kinetics of glucose intake at the fuel cell are such that you can't ask for too much power for too long.

I suggest you read the article to get a more detailed answer. Nature news is good, but there's nothing like reading the real paper.

1 http://pubs.acs.org/doi/full/10.1021/ja211714w


Classifying Polypeptides (and/or Proteins) Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an Alanine, Aspartic acid, Asparagine polypeptide)?

This method of classifying polypeptides would lead to a possible 8000 (20**3) variations just for 3-amino-acid-polypetides (3200000 for 5-amino-acid-polypeptides, etc.) and that there would be many variations; and for longer polypeptides - that is, proteins - there would be even more variations.

Or are only the important polypeptides and proteins named, since not every variation of polypeptides and proteins are found in the body? I would've thought that many proteins (and enzymes, etc.) are incredibly specific and so they could be classified in some methodological way, as opposed to just 'lipase' or 'carbohydrase' which provides no structural information (though it would have a long methodological name).

You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.

  As the largest known protein, titin also has the longest IUPAC name of
  a protein. The full chemical name of the human canonical form of
  titin, which starts methionyl... and ends ...isoleucine, contains
  189,819 letters and is sometimes stated to be the longest word in the
  English language, or any language. However, lexicographers regard generic names of chemical compounds as verbal formulae rather than English words

For more than around 5 amino acids, just the sequence makes more sense. It would be interesting to analyse scientific paper abstracts to see how many have the sequence as the 'name', but anyway.

When we get to proteins, it would be unhelpful to refer to them by their sequence. They usually have names - enzymes are often named by what they act on (like 'alcohol') and how they act on them (like 'dehydrogenase'). In addition, there are structured names called E.C. numbers - sarcosine dehydrogenase is 1.5.8.2, for example.

As you point out, there are a very large number of sequences that do not correspond to proteins found in an organism. To name one of these is tricky, and if someone synthesises one then they would have to come up with some naming scheme to refer to it.


Are there any examples of sudden leaps in evolution? As far as I understand, various abilities like flying, sight, hearing etc. were caused by slow evolution, where those with a greater ability to to these things had better chance of survival. (If this assumption is wrong, then I am happy to delete this question).

Are there, however, any documented examples of by evolutionary leaps being made, over the course of just a few generations? I understand, that some abilities have a tipping point where one gets the ability suddenly, but there is not a lot of physiological change made. An example of this would be the ability to climb a tree, which could suddenly be possible if the body weight is reduced with just a few percent. What my question is about, are sudden changes to the characteristics of a creature.

Zuk et al. (2006) document the rapid evolution of song-less crickets in a population of crickets that previously used song for courtship.

In less that 20 generations, over 90% of male crickets of the species Teleogryllus oceanicus evolved to a novel morphology ("flatwing") that rendered them unable to call to females. They hypothesize that this shift resulted from the presence of an North American invasive "acoustically orienting parasitoid fly."

Basically the flies detect calling males and parasitize them, rendering them unable to reproduce. Were it not for the presence of the parasitoid fly, the flatwing flies would likely not have survived. Non-calling individuals rely on the presence of calling males to bring females near for mating.


results of FgenesH and GenScan Why FgenesH and Genscan don't give good results as I have prdicted number of genes of Chromosome 16 which according to NCBI are 86 but the results I have obtained are 57 genes predicted by FgenesH and only 47 genes predicted by GenScan. why they have done missed predictions. Kindly help me to know the reason?

You would be mistaken to assume that a computer program that is predicting, or classifying, the biological features in a nucleic acid or protein sequence is infallible.

Different programs use different algorithms and will have different parameters for their models of what a gene looks like. Typically they are tested on a learning or training set of features, and optimized to yield the highest score on that training set.  Then when you feed in your novel sequence and ask the program to predict where the genes are it will hopefully give you a list of predictions along with an estimated probability of the confidence of that prediction. However there will always be outliers, actual protein-coding genes that have atypical features not contained in the training set.

In other words, each program is only as reliable as its underlying model, and nobody has a perfect model.


Proof of mechanisms and causal relationships in biology Statistical methods in biology are strongly encouraged: they are quantifiable, unbiased, and usually the only ones that are accepted as evidence.

However, it doesn't seem like the whole picture.

Say, someone wants to prove the hypothesis that wings are used for flight. He (or she) conducts an experiment: takes two groups of birds, ties up wings of all birds in one of the groups, then throws them out of a window and gets statistically significant data that birds with tied wings do not fly.

However, strictly speaking, he didn't prove that birds use wings to fly: only that birds with tied up wings didn't fly when thrown out of window. Or, as they say, correlation does not imply causation.

To tie the hypothesis to the results, he might include a paragraph in the discussion that "wings have large area, there are muscles that can flap them etc" - in other words, explain how wings could be used to fly. However, this explanation isn't statistical, or quantifiable: he just wrote a "story", perhaps used some common sense - but last time I checked, it's not evidence.

And that's pretty much what happens in every paper on biology: when they try to prove some mechanism, they include an experiment results and stats for a single aspect that is related to the mechanism (which, obviously, cannot explain the mechanism on its own), but then, when it comes to discussion, they just drop all the numbers and start explaining the phenomenon "logically" and eventually come to the conclusion. To be honest, they could've done no experiment at all and just went to explanation straightaway.

So what I wanted to ask:

Is there such a method of proof in biology as "proof by explanation", or something like that - when the author just explains the causual effects from, say, physics perspective and comes to a conclusion? Perhaps, even something similar to mathematical proof? Does this constitute valid evidence?
Are there any formal requirements for such proof? Perhaps, some way to quantify it or reduce to a "formula" of some sort?
Say, I wanted to publish a paper about some new protein that affects testosterone production. If I did no stats at all, or experiments like trying to remove the gene for the protein from some individuals and seeing what happens in comparison to control group, but instead just extracted and described the structure of the protein, identified the binding sites to some testosterone precursor, and explained how it can affect the testosterone production chemically, would it be a valid paper?

You are missing a much simpler and more common method. film birds in flight, then demonstrate mathematically that the wings as used are providing the lift that is enabling flight. That is direct evidence for your hypothesis. You can further test it by clipping the wings or putting the birds in a vacuum, or a hundred other strange experiments. You may want to look into biomechanics, the types of studies you are looking for are far more common. How a limb works is not really a statistical question but more of a dynamics one.

Statistics is a secondary way of testing, used when more direct methods are not possible or terribly impractical. to use your last example yes that would be a perfectly valid way to determine a proteins function, there are limitations reasons we don't usually determine protein functions this way, not just becasue often we discover the function before isolating the protein), but even when it is you also want to test it in other ways that is true of anything in science.  This one reason science prefers multiple lines of evidence since one line can compensate for the flaws in a different line.

"Proof by explanation" has specific connotations in biology that may not be what you are really asking about*. Often it refers to unverifiable narrative explanation which is not acceptable in science. Also you never prove anything in science, (even more so with statistics) we shy away from the term proof because it brings to mind absolute proof which cannot exist. In science you can demonstrate something or show it is the most likely known explanation but you do not "prove" it. Research is not one off events but cumulative and constructive, the more lines of evidence the firmer a concepts standing.

What I thinks you are really asking is something much more fundamental to how science works and what empiricism and verification is. You may have better luck with this on a philosophy of science discussion, than a specific field of science since you seem more confused about how science operates. science has both experimental and descriptive research each with its own value.


Can different proteins be produced during translation of a single mRNA in eukaryotes? Is there a translational mechanism that eukaryotes can use to produce different proteins from a single transcribed mRNA?

There are multiple mechanisms that are known to lead to translation of substantially (or entirely) different proteins from a single mRNA. While these mechanisms are more typically seen in viruses, I'm focusing on examples documented within the endogenous transcriptome of eukaryotes.

Alternative translation initiation

One process that can lead to different proteins being translated from the same mRNA in eukaryotes is the use of alternative translation initiation sites.1,2 Translation typically starts with a pre-initiation complex recognizing the 5' cap and loading onto the mRNA. This complex scans until it finds an appropriate start site. The choice of start site depends on the how well the ribonucleotide sequence matches the Kozak consensus sequence.3 If the region around the first AUG is not a good match for that consensus then a process known as leaky scanning occurs and the pre-initiation complex can continue along the mRNA until a "good" start site is found.

While this can result in proteins with different functions, they will typically still have large regions of amino acid sequence in common. One example of this is in a kinase known as MK2, which is "a key regulator of transcription, migration, death signaling and post-transcriptional gene regulation".4

Polycistronic mRNAs

While more common in prokaryotes, in some cases eukaryotes also have polycistronic transcripts5,6.  These transcripts encode multiple separate proteins (i.e. from independent open reading frames). The examples that I have found for mammals are all bicistronic (operons with two genes): LASS1-GDF1, SNRPN-SNURF, MTPN-LUZP6 and MFRP-C1QTNF5. You can search for those gene pairs, but there doesn't seem to be a huge amount of information available and in many cases one of the genes is almost completely uncharacterized. Eukaryotic operons (aka polycistronic mRNAs) are ubiquitous in trypanosomes, appear to be very common in nematodes (round worms), and are also frequently seen in Drosophila (a fly).6

Translational read-through

Translational readthrough aka. stop codon suppression occurs when an in frame stop codon is ignored either stochastically or under specific conditions and translation continues beyond that point. This leads to a C-terminal extension of the protein which in some cases has been shown to have functional implications7,8. An example of this is the [PSI+] prion in yeast, which promotes translational readthrough throughout the yeast transcriptome by inactivating a factor involved in translation termination.7

Translational frameshifts

This is well covered in the answer by @Dirigible.

References:
1: Kochetov, A. V. (2008). Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays, 30(7), 683-691.
2: Wan, J., & Qian, S. B. (2013). TISdb: a database for alternative translation initiation in mammalian cells. Nucleic acids research, 42(D1), D845-D850.
3: Acevedo, J. M., Hoermann, B., Schlimbach, T., & Teleman, A. A. (2018). Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Scientific reports, 8(1), 4018.
4: Trulley, P., Snieckute, G., Bekker-Jensen, D., Menon, M. B., Freund, R., Kotlyarov, A., ... & Gaestel, M. (2019). Alternative Translation Initiation Generates a Functionally Distinct Isoform of the Stress-Activated Protein Kinase MK2. Cell reports, 27(10), 2859-2870.
5: Tautz, D. (2008). Polycistronic peptide coding genes in eukaryotes—how widespread are they?. Briefings in Functional Genomics and Proteomics, 8(1), 68-74.
6: Blumenthal, T. (2004). Operons in eukaryotes. Briefings in Functional Genomics, 3(3), 199-211.
7: Schueren, F., & Thoms, S. (2016). Functional translational readthrough: a systems biology perspective. PLoS genetics, 12(8), e1006196.
8: Loughran, G., Jungreis, I., Tzani, I., Power, M., Dmitriev, R. I., Ivanov, I. P., ... & Atkins, J. F. (2018). Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. Journal of Biological Chemistry, 293(12), 4434-4444.


What happens when the brain is no longer capable of co-ordinating or regulating the heart and breathing rates? Does the heart no longer function? Does it go into ventricular fibrillation?

What happens?

Damage to the brainstem - the part of the brain responsible for controlling breathing and the heart - has different effects on the heart and the lungs.

Every heartbeat is not directed by the brain. Instead, the brain has a "throttle" to the heart, by which it can regulate the heart rate up and down, but the actual heartbeat is initiated by special cells in the heart, called pacemaker cells. In the absence of signals from the brainstem, the heart will continue pumping; this is (one of the reasons) why people who need ventilators to breath for them do not also need their heart pumped for them.

Breathing, however, is directly controlled by the brain. Without signals from the brain, breathing will stop completely (the technical term is "respiratory arrest", but that literally just means "breathing-stuff stopped-ness"). Survival time without breathing depends on a number of factors, but at room temperature, without medical intervention (ie. rescue breaths or a ventilator) and barring any special circumstances, is only a few minutes. Permanent brain damage sets in a few minutes later, even if the person can be resuscitated.

Of course, without any breathing, the heart will stop beating due to a lack of oxygen before long. The general progression will be from sinus ("normal") rhythm, to ventricular tachycardia, to ventricular fibrillation, to asystole ("flatlining").


Why are the genomes of some trees so large? For example, the current largest known genome belongs to a tree: http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree

I have heard that this could potentially be because trees require many duplicates of certain genes because they live their entire life exposed to direct sunlight.

Does anyone know of some specific scientific hypotheses for why this might be the case?

This study of the recently sequenced pine species states that 82% of genome is repetitive. This is characteristic of any complex genome, including humans. Such sequences have often been considered "junk DNA", though any scientist will tell you that just because we don't know its purpose doesn't mean it doesn't have one. That said, a good portion of repeats are due to transposable elements, effectively intracellular parasites, whose only purpose is presumably self-amplification and are more often than not deleterious. These interspersed repeats make up ~45% of the human genome. That paper mentions that, based on sequence homology, ~65% of the pine's genome is made of these repeats (that's 15 billion base pairs).

It's interesting that, even though the pine's genome is ~7 times larger than a human's, it has only twice as many predicted genes. The pine tree has ~50 000 hypothetical genes but only ~16 000 are what the authors call high confidence. When the human genome was first sequenced, there were ~35 000 hypothetical genes but now, some 10 odd years later, there are only ~21 000 predicted genes. It seems too early to compare the two. This also brings up the important point that the number of genes is not necessarily related to organismal complexity: the worm C. elegans has ~20 000 genes.

From the paper:

  The large genome size has primarily been attributed to an extensive contribution of interspersed repetitive content (Morse et al. 2009; Kovach et al. 2010; Wegrzyn et al. 2013). Assembly of the Norway spruce genome has shown that LTR retrotransposons in particular are frequently nested within the long introns of some gene families (Nystedt et al. 2013). In addition, there is evidence for gene duplication, pseudogenes, and paralogs, although the extent of these is not clear (Kovach et al. 2010; Pavy et al. 2012).

I have never heard of the hypothesis you mention (not that that means anything), but it seems to me that it's far to early to tell.


What is the name of this herb plant? I found it outside in the City of South India in the month of May.

Another view:

No guarantee that my answer is the right one but my educated guess that your plant is a species of Acalypha. There are a number of species in this genus and I'm sorry I can't narrow it down further.

The shape of the leaves, the little 'pig-tail' shaped seed (or unopened flower) spike seen in the upper left corner of the first photo, the tinge of pink on some leaves and veins and even the twist or curl on the uppermost group of leaves leads me to think that.

I'm including some photos showing these points. Whether it's a plant in this genus is for you to decide. It would be helpful to know the size of the entire plant and he range of size in the leaves.

Acalypha wilkesiana

Another Acalypha wilkesiana with this one showing the 'pig-tail' flower spikes better.

The flower spikes are very evident in this Acalypha bamentacea here.

The twists and curls can be seen in this cultivar of Acalypha wilkesiana.

Source courtesy of Dave's Garden


In the video, "Inner Life of a Cell", what's the empty space between the molecules? In the video, "Inner Life of a Cell" there's a lot of empty space between the proteins. Is it just a simplification (i.e. they omit smaller molecules)? If so, what are the smaller molecules supposed to be? Or is it just a vacuum small enough to be ignored?

I've done some reading up on it, and found that it's called cytosol which is a complicated mixture of random proteins and molecules.

This is a common simplification of videos and textbook illustrations. In reality a cell is much more crowded and there is hardly any space between proteins. You can find a more realistic drawing here (I linked the pictures, because I am not sure about the license).

Regarding the cytosol:
Quoting wikipedia:

  The cytosol or cytoplasmic matrix is the liquid found inside cells.
  [...]
  Most of the cytosol is water, which makes up about 70% of the total volume of a typical cell
  [...]
  The amount of protein in cells is extremely high, and approaches 200 mg/ml, occupying about 20-30% of the volume of the cytosol


Enlargement of joints in osteoarthrosis If osteoarthritis (osteoarthrosis) is a degenerative condition, where the cartilage in joints wears down, what causes the joints to become inflamed? I'm reading through a book called Understanding Disease: Arthritis by Steven Tiger, and it mentions that Heberden's nodes are caused by osteoarthrosis. if things inside the joint are wearing down, why does it get bigger?

Osteoarthritis results from the gradual degradation of articular cartilage. When the cartilage is damaged extensively, e.g., all the way through the cartilage and into the bone, an inflammatory response ensues in the bone. This often happens when bone is rubbing against bone.

One of bone's responses to injury and inflammation is the production of new bone. In this case, the bone, called osteophytes or bone spurs, is produced pathologically (i.e., not like the bone laid down normally during growth). Heberden's nodes are the names given to these osteophytes at the distal interphalangeal joints, but the process is basically the same at other joints in the digits, ankle, etc.


Do individual (free) nucleotides base-pair with other free nucleotides? I had a student ask me about this and my google-fu let me down. He asked if individual nucleotides (not in a nucleic acid) base-pair with their complementary nucleotides, essentially forming many dinucleotides. I would think this would occur, but have no evidence one way or the other. If it does, how does this impact the usage of nucleotides in nucleic acid synthesis? I'd assume they have to be broken apart first...

The base-pairing in solution only provides 2-3 hydrogen bonds, which the nucleotides could also form with water itself. There are no stacking interactions between bases in water like in a DNA helix. So I strongly doubt that the nucleotides would form a significant amount of dimers in water.
I found a paper confirming my assumption:

Short nucleotide fragments such as mono- and dinucleotides are
generally unable to form stable hydrogen-bonded base pairs or duplexes
in water.
Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts.

An easy way to confirm this would be to observe the proton NMR spectra of free nucleotides. Base-pairing in nucleic acids shows characteristic signals in the imino proton region (around 10-15 ppm), which are not visible in unpaired nucleobases due to chemical exchange.


Do we use 100% of our cerebral capacity? I saw a movie yesterday called Lucy. In this movie, a girl called Lucy absorbs a large amount of CPH4, and her brain capacity slowly increases.

So that brings me to my question which is :

Do we humans use 100% of our cerebral capacity or do we just use 15%?

The idea that we only use 10% of our brain capacity is a myth.  There is a great article at wired.com that discusses the myth and it's history.

There is really no reason to evolve an entire brain of which only 10% is used.  One great point that they make is that minor brain damage can cause devastating effects, not what you would expect if you had 90% spare capacity waiting around.

The entire brain is rarely firing all at once, and it is hard to average how much is being used because it changes with activity.


How can ionized amino acid form be important for the catalytic activity? I can imagine that protonated amino acid form, particularly at the active site, is important for the catalytic activity so hydrogen bonds can be created between the substrate and the enzyme. However, I cannot imagine how the ionized form can be important for the activity?

Both forms are important for the activity as stated in this study:

https://www.ncbi.nlm.nih.gov/pubmed/7306491

  The pH dependence of log V/K for dihydrofolate showed that a group with a pK value of 4.7 must be ionized and that a group with a pK value of 6.6 must be protonated for activity

I cannot understand how the ionized form is important for the activity, could some one help me to understand that?

Enzymatic reactions are chemical reactions. Chemical reactions involve charge ("electron") transfer. Charge transfer occurs more readily if there is a large gradient in charge density between the attacking active site group and the attacked atom of the substrate. Many enzymes (yes, it is really quite common) use ionic forms of aspartate or glutamate as a catalytic amino acid residue.

For example, some enzymes belonging to the alpha/beta-hydrolase fold family (e.g., haloalkane dehalogenases, epoxide hydrolases) use a deprotonated aspartate as the nucleophile (which attacks an electrophilic atom of the substrate); the specific position of the nucleophile within the enzyme and its interaction with other groups in the enzyme enhance the nucleophilic nature of the aspartate, a phenomenon called "oxyanion hole."

Ollis et al. (1992) Protein Eng 5: 197-211.
https://www.ncbi.nlm.nih.gov/pubmed/1409539


How do I clean and calibrate pipettes, and how often should I do it? I work in a lab where all the pipettes are shared. We often have visiting students who come and use the pipettes for a short project. So when I work with them, they might have been handled by other people several times since I last used them. This leads me to worry that they might have been mishandled, or become less accurate somehow.

How do I clean and calibrate pipettes? And how often do I need to do it?

How often you should calibrate your pipettes depends on the tolerances of your application. For some applications, like quantitative PCR setup, one may care a great deal; for general lab work, one can probably be less particular. You can get a sense of how accurate your pipettes are by pipetting DI water onto the platform of a sensitive (and calibrated!) balance. Comparing the random and systemic error you get while doing that over several trials to the specifications published by the manufacturer will give you a good idea of whether pipette calibration will help and help give you a sense of how much you care. Note also that the error may vary with the volume; you should test error over the entire volume range you intend to use the pipette for.

How to clean and calibrate pipettes is specific to each design. Some pipettes, like Gilson's, are not intended to be calibrated by the user. Others are. The pipette user guide published by the manufacturer should tell you.

For some demanding applications, even well-calibrated and well-handled micropipettes may not be sufficiently accurate. In particular, I've made standard curves by serial 10-fold dilution for quantitative PCR both a) relying on my micropipettors to be correct and b) trusting pipettes only to get me into the right ballpark, and intentionally undershooting and correcting volumes with sequentially smaller pipettes until the reading on the balance is correct, if that's at all clear. In both cases I was using 900 ul of diluent and 100 ul of the previous dilution, which I feel are comfortably large volumes to handle. I found that the latter curve gave me noticeably better regressions.


Attachment of muscles during molting in insects Normally, insects' muscles are attached to their exoskeleton but what happens to this attachment when they are moulting?

Sorry if this is an extremely silly question but I have wondered about it for a long time and have tried searching it.

You can find a concise answer here in a section from The Insects: Structure and Function  by R. F. Chapman, eds. Stephen J. Simpson, Angela E. Douglas. 5th Edition. Cambridge University Press.

In essence the source says that the muscle attachment to the cuticle is maintained during the moulting process, while the new cuticle is formed under the old cuticle.

  As a result the insect is able to continue its activities after apolysis during the development of the new cuticle. The connections to the old cuticle are broken at about the time of ecdysis.

Connections to the new cuticle are formed at the same time as the old ones are broken.


DNA topology Linking number vs twist? Background

  Linking number: the linking number represents the number of times that
  each curve winds around the other.
  Twist, called "twist", refers to the number of Watson-Crick twists in the
  chromosome when it is not constrained to lie in a plane

 I read these explanations on Wikipedia and I understand the concept of this (supercoils have to form to compensate the "tension" etc..) however I'm not able to discriminate between these terms while looking at a picture.

   (source)

Based on the formula I can easily calculate the twists in the right image. But I'm searching for a way to see/count the twists.

Question
What is the difference between the linking number and the twists (not from a formula perspective)?

This article (DNA Topology: Fundamentals by Mirkin SM) probably defines and describes linking number better than I ever could:

  The fundamental topological parameter of a covalently closed circular DNA is called the linking number (Lk). Assume that one DNA strand is the edge of an imaginary surface and count the number of times that the other DNA strand crosses this surface (Figure 3). The algebraic sum of all intersections (which accounts for a sign of every intersection) is the Lk. Two important features of the Lk are evident from Figure 3. First, Lk is always an integer. Second, Lk cannot be changed by any deformation of the DNA strands, i.e. it is topologically invariant. The only way to change Lk is to introduce a break in one or both DNA strands, rotate the two DNA strands relative to each other and seal the break... Another characteristic of a circular DNA is called twist, or Tw. Tw is the total number of helical turns in circular DNA under given conditions. Since DNA is a right handed helix with 10.5 base pairs (bp) per turn, Tw is a large positive number for any natural DNA. Take a planar, circular DNA and try to locally separate the two DNA strands, i.e. to decrease the Tw. Since Lk cannot change, a decrease in Tw will be compensated by several positive writhes of the double helix (Figure 4). Writhing (Wr) is the third important characteristic of circular DNA, describing the spatial pass of the double helix axis, i.e. the shape of the DNA molecule as a whole. Wr can be of any sign, and usually its absolute value is much smaller than that of Tw. The above consideration can be formalized by the following equation: Lk = Tw + Wr. Note, that while Lk is an integer, neither Tw nor Wr should be such. Also, neither Tw nor Wr are topological invariants and their values easily change...

Linking number is simply the number of times one strand of DNA passes over the other. Compare this to:

Twist - the number of helical turns
Writhe - the number of superhelical turns

You can, perhaps, think of twist as the passing over of strands within the helix and writhe as the passing over of strands when the entire helix crosses itself. Both twist and writhe involve strands of DNA passing over the other and so both contribute to the linking number. In the absence of writhe, linking number and twist are equal and both describe the same thing: the number of helical turns. However, in the presence of writhe, twist alone is insufficient to describe the topology of DNA because it doesn't account for the passing of the entire helix over itself.

Since twist is the number of helical turns, actually counting it in your image is not necessarily difficult, just time consuming. The image already has the twists numbered, and I've put a red do at every turn of the double helix. I've also circled, in blue, every point where the double helix passes over itself (writhe):

In that image, in may be difficult to visualize (and even understand!) that the strands only cross over each other 36 times (Lk), even though there are 42 helical turns (Tw). While twist and writhe are different modes of strand crossing, it is important to realize that they are interchangeable without breaking the strands. Let's consider a simpler example, where Lk = -1 (Wikipedia: DNA Supercoil):

In the lower image, the strands do not form a helical structure (Tw = 0) but they do both pass over each other together (Wr = -1). Can you imagine that if you were to "unfold" the superhelix (Wr = 0), the two individual strands would still be linked together in a helical structure (Tw = -1)? Neither could I, so I made a video with my shoelaces:

https://www.youtube.com/watch?v=rI3LWIvptf0

I hope that answers your question. Let me know if I misunderstood what you were asking or if anything needs clarification. You may also find my shoelace video on the topology of helicase-mediated DNA unwinding informative.


If wolves (or foxes) are fitter than rabbits, why rabbits have not become extinct? I do not pretend to "demolish" the Darwinian theory of biological evolution and the "survival of the fittest", that's far from my intention.
I have this doubt because of the fact that humanity, as Homo sapiens sapiens, extinguished the Homo sapiens neanderthalensis because we were fitter to survive.

Please consider this question as if the humanity hadn't appeared yet (because we have domesticated rabbits).

Thanks in advance.

Edit: I have assumed that wolves and rabbits (or hares, maybe) live in the same ecosystem.

Simple: wolves and foxes are not fitter than rabbits. If they were, rabbits would be extinct.

This question is like asking "If Gary Kasparov is better than Michael Jordan, why hasn't he won a chess championship against him?"

And the answers are the same:
- "what do you mean, 'better'? Better how? At what?"
- "either way, they've never played in a chess championship against each other, so..."

"Fitter" in evolutionary theory means "better at something"; in general it will be "better at surviving", but better at surviving under what circumstances? There isn't a single "fit" or "fitter". Maybe you thought that wolves are better at surviving than rabbits because wolves kill rabbits and not vice-versa, but I could as easily argue that rabbits are better at surviving than wolves because rabbits would survive fine without wolves, but wolves would go extinct without rabbits (not completely true because they have other prey, but you get the idea). The truth is, as far as we can tell wolves and rabbits are equally good at surviving because both have survived.

So you can only talk about fitness if you focus on one specific circumstance to be fit in. But then there is the other implied idea in your question, which is that fitter species drive less-fit ones to extinction. This is true only if the species are in competition. Two species (or individuals, or anything) are in competition when if one species does badly, the other will do well as a result, and vice-versa. For example, maybe they eat the same food, and there is only so much to go around, so every additional bit of food A gets is less food for B, and vice-versa. In that case it is clear that one species being better at surviving than another is bad for the other species, and can (and, according to theory, will) drive it to extinction. Like fitness however two species can be in competition in some ways but not others. For example, two species might compete for food, but have a mutually-beneficial relationship with respect  to predators, where if there is more of A the predators will go for them which is good for B, and vice-versa.

Wolves and rabbits are clearly not competitors: things that lead to more wolves will indeed lead to fewer rabbits, but things that lead to more rabbits will also lead to more wolves. As such, even if one were measurably fitter than the other by some metric, it would not necessarily lead the other to extinction. For example rabbits being better against the cold than wolves could promote the existence of wolves in cold places, because a lot of them might freeze but the abundance of food might make it worth it.

This does involve an interesting ecological paradox, which is that according to theoretical models, if you have X species in perfect competition, all but one will eventually go extinct. There is a lot of research in how and why our world's massive biodiversity exists despite this. A big factor is that as I have pointed out, perfect competition is extremely rare in nature. Most species aren't competitors at all, and those that do compete usually don't compete on everything, everywhere and at all times. But when they do or close enough, yes, one should drive the other to extinction. Whether this is why the Neanderthals went extinct is another question


Can antimicrobial peptides be called antibiotics? Antibiotic peptides are present in almost all multicellular eukaryotes. So can they be called antibiotics ? ( which are usually defined only for fungi and bacteria )

Antibiotic peptides are definitely antibiotics.  They are often referred to more specifically as peptides because the fact implies that they are less toxic and conveys some important understanding of how they work.  Not sure if they all form pores in the target cell, but that's how magainins work.


Do mucous membranes surround visceral organs? Wikipedia claims that:

  A mucous membrane or mucosa is a membrane that lines various cavities in the body and surrounds internal organs.

The first part of that sentence is clearly accurate, but I cannot find any reference from Google Scholar or books that states mucous membranes surround internal organs.

The mucous layer lines the lumens of the body: digestive, respiratory,urogenital tracts, as well as cavities leading to openings such as the ears and nose, and forms the conjunctiva of eyes. The surfaces of internal organs don't fit any of these categories.

I think wikipedia is wrong about the viseral organ part, am I right?

You are correct.

"Serous membrane" might be what the Wikipedia editor was thinking of, for example the pleura of the lungs; other examples include the pericardium and peritoneum.


How was Restriction Site of EcoRI sequenced? The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977)

How was the restriction site of EcoRI sequenced ?

The first determination of a recognition site for a restriction endonulease was reported in:

  Kelly & Smith (1970) A restriction enzyme from Hemophilus influenzae II. Base sequence of the recognition site. J Mol. Biol. 51: 393-409

The enzyme was then called endonuclease R, but is now known as HindII (or HincII).

The method used was to cut DNA with the enzyme and then remove the exposed terminal phosphates with alkaline phosphatase. These ends could then be labelled with 32P using polynucleotide kinase and γ-labelled ATP.

The end-labelled DNA was then treated with nucleases in three different ways to release mononucleotides, dinucleotides, and a mixture enriched for trinucleotides. In each case the labelled products were identified by their behaviour in 2D thin-layer chromatography, and were  further characterised for their total base composition after digestion to mononucleotides where appropriate.

The deduced site was/is

5'----GTY RAC----3'
3'----CAR YTG----5'

Thus the labelled mononucleotides were found to be A and G (purine=R), the dinucleotides were found to be GA and AA and so on.

The EcoRI sequence was determined by essentially the same methodology and was reported by

  Hedgpeth et al (1972) DNA nucleotide sequence restricted by the RI endonuclease. Proc. Natl. Acad. Sci USA 69:3448 - 3452

Addendum:

Although Sanger sequencing (the plus-minus method) may have been developed through the 1970s, it really didn't catch on until the early 80s. So for example the first complete plasmid sequence to be determined was pBR322 in 1979:

  Sutcliffe (1979) Complete nucleotide sequence of the Escherichia coli plasmid pBR322. CSH Symp. Quant. Biol. 43: 77 - 90

  "I have determined the 4362-nucleotide-pair sequence of the plasmid cloning vector pBR322 using the DNA-sequencing technique of Maxam and Gilbert (1977). The DNA structure has several interesting features that lead to testable predictions."

The standard sequencing method in use at that time was chemical sequencing using the Maxam-Gilbert methodology. When I started a postdoc in the USA in 1979 M-G sequencing was the standard method. Sanger sequencing really only took off following the development of the M13 mp vectors (and later the pUC plasmids) by J Messing in the early 80s. And what a relief it was: M-G sequencing was extremely laborious, as anyone who ever did it will testify.


What does ΔC and ΔN mean with regards to a protein sequence? I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement:

Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the
amino-terminal half of Frat (ΔC Frat) localized predominantly to the
cytoplasm of transfected MDCK cells (Fig. 1, A and B, i and iii).
Unexpectedly, the carboxyl-terminal half of Frat (ΔN Frat) accumulated
preferentially in the nuclei of transfected cells (Fig. 1B, iv).

I am not sure why the amino-terminal and carboxyl-terminal half of the Frat protein are referred to as ΔC Frat and ΔN Frat respectively. I know that the amino terminus of a protein is also referred to as the N-terminus, whilst the carboxyl terminus of a protein is referred to as the C-terminus. I am not sure why in this paper ΔC and ΔN are used to refer to the amino-terminal and carboxyl-terminal half of the Frat protein.
Any insights are appreciated.

The Frat/GBP (frequently rearranged in T-cell lymphomas/GSK-3-binding protein) protein is a proto-oncogene that regulates the Wnt signalling pathway. (van Amerongen et al., 2004)
The cited paper (Franca-Koh, 2002) noted a correlation between some forms of Frat and GSK3 cellular localization. Without Frat, GSK3 is cytoplasmic. In the presence of Frat, the heterodimer Frat-GSK3 translocates to the nucleus. As Frat is phosphorylated, it was unclear then what mechanism(s) was(were) involved. To investigate the role of Frat, the authors hypothesized that a region of Frat may be involved, not necessarily the whole protein.
They engineered deletion constructs and added an N-terminal FLAG tag for easy affinity purification. They used the symbol delta (Δ) for deletion. The N-terminal region of residues 1 – 129 encompassing Domain 1, i.e. deletion of the C-terminal region is called ΔC; likewise, the C-terminal region of residues 129-274 encompassing Domain 2, i.e. deletion of the N-terminus is called ΔN. They also engineered a green fluorescent protein (GFP) tag fusion protein variant. Here are their constructs as illustrated on Figure 1 of their paper:

Human ortholog
I aligned the residue sequence of the murine Frat with the human orthologs: it has 79% identity to human Frat1 and 68% identity to human Frat2. mFrat residues 1 – 129 (ΔC) and 129 – 274 (ΔN) correspond to hFrat1 residues 1 – 132 and 132 – 279, respectively.
Added Note
Here is a co-crystal structure of GSK3β (N-terminal lobe in orange and C-terminal lobe in cyan) complexed with Frat1 peptide 197-226 (forest green) and an inhibitor (N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide) (green) as deposited with RCSB as entry 5OY4.pdb . The presence of the inhibitor helps locate the active site in the image of the GSK3b protein kinase.

References
Franca-Koh, J., Yeo, M., Fraser, E., Young, N. and Dale, T.C. (2002) J. Biol. Chem. 277:43844-43848.
Van Amerongen, R., van der Gulfen, H., Bleeker, F., Jonkers, J. and Berns, A. (2004) J. Biol. Chem. 279:26967-26974.


How are CheY, CheA, CheW, CheZ pronounced in speech? This is a quick followup question to this question about proteins that play important roles in chemotaxis:

How does one pronounce the protein names "CheY", "CheW", etc., in English?  My guess would be that they're pronounced like "key why", "key double-u", etc.

(I want to refer to these proteins in a philosophy of science presentation, but don't have much background in molecular biology. I know about chemotaxis only from reading.)

As was mentioned in the comments, these are not real words and there is no authority on their pronunciation. Given that Che is an abbreviation of chemotaxis, I would pronounce it the same as key.


Which fruit compounds affect the speed of fructose absorption? Blood fructose levels are not regulated by insulin in the human body. This means that the body absorbs pure fructose very fast, and it raises the blood fructose levels rapidly.

Do fruits/ vegetation contain compounds, which help the digestive system to regulate the absorption of fructose? If so, what are they?

Yes they do. The answer is glucose.

Let's begin at the beginning: you eat a piece of fruit. The fruit contains many different kinds of sugars, including fructose and glucose. One of the immediate effects your digestion of this fruit has is to raise the levels in your blood of every type of sugar that was present, and the blood levels of many other types of nutrients as well. This has nothing to do with how well your body does/doesn't absorb fructose, it is simply a normal step in digestion.

Next, GLUT2 transporters in the insulin producing cells in your pancreas import glucose. This acts as a signal that tells those cells to start producing insulin. Insulin then diffuses around the body and produces myriad effects, including upregulation of GLUT4  activity across the body. These GLUT4 transporters are present on cells in many parts of your body and are what are responsible for taking up most of the glucose from your blood.

Now on to fructose. GLUT5 is the main fructose transporter. Just like GLUT4, GLUT5 activity is also regulated by insulin, but in a less quick and dramatic fashion than with GLUT4. Although there's a large body of work showing that GLUT5 does not respond quickly to insulin, recent work has shown that, for example, high levels of insulin lead to increased GLUT5 activity in skeletal muscle over a period of 24 hours.

So if what your trying to get at is some reason why eating an apple is better for you than chugging an equivalent volume of Auntie Jemimah's pure corn syrup, it's always going to be some reason like this where you have co-metabolism of several nutrients that tend to show up together in "natural" food. It is unlikely that there are any complex plant substances that would be primarily responsible for the health benefit of fresh fruit in general.


What would be “Sternum-Intermediate” distance? I've asked this question on the English Language & Usage board, not being entirely sure whether this question is strictly medical, or just English knowledge suffices to answer.

Do note I am no native speaker, hence I am afraid to misinterpret the possibly obvious thing.

In an article written by Wheat et al Engineernig for Life - Kinect Report the authors use the scanning device to calcuate distances on the human body.

The measured distances are: Sternum-Intermediate, Inter-nipple and Sternum-nipple (see Table 3.). The latter two are obvious. The first one, however, not so much. Unfortunately, the authors do not provide a definition, probably assuming it is clear to the reader.

What would be the Sternum-Intermediate? Is this the sternum's length or is "Intermediate" some specific body part?

The article states:

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

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


How to compute the regression of individual fitness on individual phenotype Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma:

\begin{array}{c |c |c|}
& C & D \\
\hline
\text{Cooperate (} C \text{)} & b -c & -c \\
\hline
\text{Defect (} D\text{)} & b & 0 \\
\hline
\end{array}
where $b$ is the benefit and $c$ is the cost. The payoffs are to the player on the left. I need to calculate  the regression of individual fitness on individual phenotype, $\beta (w_i, p_i)$, where $p_i = 0$ if $i$ defects and $p_i = 1$ if $i$ cooperates. Note that I need to calculate the regression within groups rather than between groups.

I thought that the right way of calculating $\beta(w_i,p_i)$ would be to vary the strategy of the focal individual while keeping the strategy of the other individual constant (my thought was that the other individual becomes the environment for the focal individual). Because switching to cooperation causes an individual to lose $-c$ in fitness (if we keep the strategy of the other individual constant), I thought that $\beta(w_i,p_i) = -c$. But, to my surprise, $\beta(w_i,p_i) = -b -c$. To show why, McElreath & Boyd ("Mathematical Models of Social Evolution", p. 242) draw the following graph:

Let $V(X|Y)$ be the payoff of individual $X$ when it interacts with $Y$ (in other words, $X$ is the focal individual; $Y$ is the other individual). I understand that McElreath and Boyd calculated the regression coefficient by computing $V(C|D) - V(D|C)$ --- as opposed to $V(C|C) - V(D|C)$, where you keep the strategy of the other individual constant. My question is why this is the right way of calculating $\beta(w_i,p_i)$.

I am not sure I understood the question. Let me know if this helps.

Case: N=2, freq=0.5

Let's assume that the frequency of those who cooperate is 0.5. The slope of the regression line (which R.squared is equal to 1 as we have as many data point than degrees of freedom) is by definition $\frac{\Delta w}{\Delta p}$. You defined $\Delta p = 1$. What is $\Delta w$ then?

Well, given that one cooperate and the other defect (as indicated in the fact that the frequency of cooperators is 0.5), then one will have the payoff of a cooperator that is facing a defector and the other one will have the payoff of a defector facing a cooperator. The cooperator has a fitness of $w_0 + b$ and the defector has a fitness of $w_0 - c$. I think you may misread the payoff matrix. To know the fitness of someone with strategy $i$ when facing someone with strategy $j$, you look that payoff at row $i$ and column $j$.

Therefore, $\Delta w = (w_0 - c) - (w_0 + b) = - (b+c) = -b - c$, and so the slope is  $\frac{\Delta w}{\Delta p}=\frac{-b-c}{1} = - b -c$

Case: N>2, freq=0.5

In such case the slope of the regression will necessarily be lower than $-b-c$ because some cooperators will meet other cooperators, increasing their fitness (=highering the points on the right hand side of your graph) and some defectors will meet other defectors, decreasing their fitness (=lowering the points on the left hand side of your graph)

At equilibrium

The only stable equilibrium is when the frequency of cooperators is 0. In such case, there is no variance and we cannot even talk about regression.

Conclusion

The slope is not necessarily $-b-c$. It is $-b-c$ for the very special case where we have two individuals, one cooperate, the other one defects. In any other scenario the slope $s$ of the regression is lower. More specifically, the slope $s$ of the regression for any $N$ and for any $freq$ is $0 =< s < -( b+c)$


Are acid-fast bacteria Gram-positive or Gram-negative? Both procedures involve using a stain, decolorising agent, and then a second stain. I am tempted to conclude that acid-fast bacteria, which resist decolorisation (eg. by strong carbol fuchsin), also resist decolorisation in the Gram staining test (eg. by gentian violet) and are thus Gram-positive.
After all, there are much fewer acid-fast bacteria than Gram-positive bacteria.

Is this line of thinking incorrect?

Image URL: http://www.scienceprofonline.com/images/science-image-library/microbiology/staining/differential-bacterial-stain-controls-diagram.JPG

Taxonomic Classification:

The most salient acid-fast bacteria are Mycobacterium spp., which are part of a phylum of gram-positive bacteria called Actinobacteria. This classification is based on 16S rRNA sequencing. However, based on genetic conservation, this paper makes the claim that they are more closely related to gram negative bacteria.

Gram Reaction:

Acid-fast bacteria are characterized by cell walls rich in mycolic acids. This characteristic causes both poor stain penetration and high stain retention which forms the basis of acid-fast stains. However, it also means that crystal violet will not penetrate the cell wall efficiently. Thus their gram reaction is variable and they generally stain light purple. The result is dependent on technique as well as mycolic acid content variation between genera (Nocardia spp, for example, are less acid-fast and stain gram positive). Needless to say, their cell walls don't fit well with the classic dichotomy of thin versus thick peptidoglycan which the gram stain differentiates between.

Example Gram Stains:

For comparison, the left image is of Bacillus subtilis, a gram positive, non-acid-fast bacilli. In the middle is M. phlei and on the right is M. smegmatis, both of which are acid-fast but show a weakly positive gram reaction. Images from Napa Valley College.

B. subtilis is again on the left for comparison. In the middle is M. fortuitum staining positive but more weakly than B. subtilis. On the right is N. astroides which is partially acid-fast but stains strongly gram positive. Images from Microbe Canvas.


Are mature erythrocytes prokaryotic? Mature mammalian erythrocytes have all the characteristics of a eukaryotic cell except that they don't have a nucleus, they don't have any cell organelles. Does this mean that erythrocytes are classified as prokaryotic?

No.  Nobody considers red blood cells to be prokaryotic, perhaps most importantly because they are part of a eukaryotic organism.  Red blood cells begin life with the full complement of organelles, including a nucleus and mitochondria, but our RBCs shed their organelles during maturation.  In actuality, though, only mammalian RBCs lack nuclei; other animals' RBCs still hold on to their traditional eukaryotic characteristics.

As an analogy, apoptotic or necrotic cells don't have intact organelles, but they are still considered eukaryotic.


Are Raf, MEK, and ERK MAP kinases? I am trying to make sense of this diagram.  Can Ras activate RAF or MAPKKK, or is RAF a MAPKKK, making MEK a MAPKK, and ERK a MAPK?

Mitogen-activated protein kinase (MAPK) is a generic name for a family of different but related enzymes involved in this specific signalling cascade. RAF is a MAPKKK, MEK is a MAPKK and ERK is a MAPK. This is evident in the Nature article from which your image is apparently adapted:

  Activated RAS triggers the activation of the MAPKKK RAF. Activated RAF then phosphorylates the MAPKK MEK (MAPK and ERK kinase) on serine residues leading to its activation. Subsequently, activated MEK catalyses the dual phosphorylation of the MAPK ERK.


How common is it to be pregnant with periods? As you may know, some women claim that they have their period while they are pregnant. In the arab world they call it "Deer pregnancy", since when the deer gets pregnant, it still gets its' monthly cycle.

Their doctors do confirm that. The appearance of such: The bleeding comes at the times when the period is expected, but is usually without pain, or smell, and lasts for less days. It is also of different color. But many women (and doctors) still call it a period.

(Although we all know, a real period is impossible biologically).

How common is that?

This is, I think, different from implantation bleeding, since it mostly continues to three months and after that.

But many women (and doctors) still call it a period.

It is not a period:

  Pregnant women can have some light irregular bleeding during pregnancy, but it should not be like a “normal” period. Some women can confuse this for their period because often it can come right around the time she was expecting her normal period. [...] It should not be enough bleeding to fill pads or tampons over a few days [1].

It is quite common in the first trimester:

  Vaginal bleeding during pregnancy can occur frequently in the first trimester of pregnancy and may not be a sign of problems. But bleeding that occurs in the second and third trimester of pregnancy can often be a sign of a possible complication [2].

It happens to about 25 % of pregnant women:

  Up to 1 in 4 women have vaginal bleeding at some time during their pregnancy. Bleeding is more commonin the first 3 months (first trimester), especially with twins [3].

Repetitive bleeding is associated with preterm birth:

  Bleeding of multiple episodes, on multiple days, and with more total blood loss was associated with an approximate twofold increased risk of earlier preterm birth, PPROM (preterm premature rupture of the membranes), and preterm labor. In contrast, bleeding in the second trimester only, of a single episode, on a single day, and with less total blood loss was not associated with any category of preterm birth [4].

References:

American Pregnancy Association. Am I Pregnant: FAQs On Early Pregnancy. Available from http://americanpregnancy.org/gettingpregnant/pregnancyfaq.htm (accessed 29.07.2014)
American Pregnancy Association. Bleeding During Pregnancy. Available from http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html (accessed 29.07.2014)
U.S. National Library of Medicine. A.D.A.M. Medical Encyclopedia. Vaginal bleeding in pregnancy. Available from http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/ (accessed 29.07.2014)
Yang J, Hartmann KE, Savitz DA, Herring AH, Dole N, Olshan AF, Thorp JM. Vaginal bleeding during pregnancy and preterm birth. Am. J. Epidemiol. 2004 Jul 15;160(2):118-25. doi: 10.1093/aje/kwh180. PubMed PMID: 15234932.


Is there an organism which has a common English name which overlaps with another organism's scientific name (or vice versa?) Many organisms have their common names identical to their scientific names. For example, there exist apes of the genus Gorilla known commonly as gorillas, and plants of the genus Delphinium known as delphiniums.

However, are there any examples of the common name of an organism overlapping with the scientific name of another organism, therefore causing ambiguity when the organism's name is spoken aloud? If written with correct formatting, this should not cause a problem in any case, due to the formatting specifically describing a genus/species.

One great example I know of is the duck-billed platypus (Ornithorhynchus anatinus),  often simply called a platypus, which shares its name with the Platypus genus of ambrosia beetle.

Wikipedia gives a brief history of the taxonomy of the duck-billed platypus:

  The common name "platypus" is the latinisation of the Greek word πλατύπους (platupous), "flat-footed", from πλατύς (platus), "broad, wide, flat" and πούς (pous), "foot". Shaw assigned it as a Linnaean genus name when he initially described it, but the term was quickly discovered to belong already to the wood-boring ambrosia beetle genus Platypus. It was independently described as Ornithorhynchus paradoxus by Johann Blumenbach in 1800 (from a specimen given to him by Sir Joseph Banks) and following the rules of priority of nomenclature, it was later officially recognised as Ornithorhynchus anatinus. The scientific name Ornithorhynchus anatinus is derived from ορνιθόρυνχος (ornithorhynkhos), which literally means "bird snout" in Greek; and anatinus, which means "duck-like" in Latin.


Are there any examples in nature of two polypeptides joining into a single, continuous, third polypeptide? Are there any examples in nature of two polypeptides join into a single, continuous, third polypeptide like this:

(Where all the indicated  amino and carboxyl groups are on the main polypeptide chain ( located on Cα of the respective amino acids )

And if this exists, is there any term for the phenomenon?

I am not aware of anything precisely corresponding to your diagram, but the somewhat related behaviour of inteins may be of interest in this respect. They are defined in Wikipedia as:

  An intein is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond in a process termed protein splicing.

So, unlike either ribosomal or non-ribosomal polypeptide (e.g. antibiotic) sythesis, they catalyse a peptide bond between peptides rather than an amino acid and a peptide. However these are already part of single polypeptide chain before the intein itself is spliced out.

[Modified from Intein_mech.png to fit page. — The mechanism of protein splicing involving inteins. In this scheme, the N-extein is shown in red, the intein in black, and the C-extein in blue. X represents either an oxygen or sulfur atom.]


Help on reconciling seemingly contradictory evidence about fetal experience Fetal awareness and especially fetal pain are controversial, political issues. However, I do not wish to get into politics and want to merely stick to the scientific evidence. I have found statements about fetuses in the womb that seem to contradict each other, yet there has been no reference to the opponents in either side.

Some believe that fetuses do not have awareness in the womb and cannot feel pain. Here is an argument along those lines, claiming that fetuses cannot feel pain, even when their nervous systems and brain are developed, because the chemical environment within the womb suppresses awareness and experience that shapes the brain only happens outside the womb.

However, some other evidence seems to claim that fetuses can have experience. Twins can interact with each other in the womb as early as 14 weeks of gestation, as stated here. It is possible to learn in the womb, and newborns, even after they are born, can retain this knowledge, as stated here.

I'm not sure what to think. Are some of these statements, such as the idea fetuses are not aware, just incorrect? Or can interaction and learning occur without awareness somehow? (I know pain is distinct from awareness, interaction, and learning. What seemed particularly strange was the idea that fetuses have no conscious experience whatsoever, especially as no one making that claim, as far as I know, even mentioned the evidence about interaction and learning at all).

I know close to nothing about the subject of self-awareness in fetuses.

But learning —and certainly interaction— can occur without anything close to human "awareness", as evident by the fact that systems without a brain (and even without neurons) can learn. Any system that can process and store information is capable of learning. Does your definition of awareness include anything more than this? Conversely, organisms with a very simple brain can display aversive behaviour.

For an example of memory without neurons, see the Wikipedia article on immunological memory.
For examples of aversive behaviour without a proper brain see Zhang, Lu, and Bargmann 2005 and Babin et al. 2014

References
Zhang, Y., Lu, H., & Bargmann, C. I. (2005). Pathogenic bacteria induce aversive olfactory learning in Caenorhabditis elegans. Nature, 438(7065), 179–184.
Babin, A., Kolly, S., Schneider, F., Dolivo, V., Zini, M., & Kawecki, T. J. (2014). Fruit flies learn to avoid odours associated with virulent infection. Biology Letters, 10(3), 20140048–20140048.


Function of carapace Majority of crustacean larvae have expanded carapace drawn out into processes as an adaptation for :

a. Protection from enemies

b. Planktonic habit

The answer given is b but I think it should be (a) as carapace functions as an exoskeleton.

Please help!

Preface:

Any question about adaptation on macro-level has very little meaning and no precise answer.
There are two types of larvae in invertebrates: primary ("original") and secondary (evolved from post-larval stages). Not digging into the details, nauplius (together with metanauplius) is the only type of primary larvae in Crustacea and it never has a carapace.
"Majority" is by far too strong term, even if we are talking about all larval types. If we just take the largest crustacean orders with species numbers > 1000, together comprising 92% of crustacean species (species numbers are from Ahyong et al, 2011, they seem to be largely correct):

Decapoda - 14.7 k species - rarely have nauplius, marine forms do have planktonic carapaced larvae (principally - zoea)
Isopoda - 10.7 k - no carapace
Amphipoda - 9.9 k - no carapace
Podocopida - 6.2 k - no carapace
Harpacticoida - 6.0 k - no carapace
Cyclopoida - 4.2 k - no carapace
Calanoida - 3.1 k - no carapace
Siphonostomatoida - 2.5 k - no carapace
Cumacea - 1.5 k - have carapace, but development is direct
Mysida - 1.2 k - have carapace, but development is direct
Tanaidacea - 1.1 k - have carapace, but development is direct

So, "majority" could be applied to Decapoda only.

Fabula:

If we substitute "adaptation" with "main biological function" (as you have done) or more correctly "main physiological role":

I would prefer the (a), because carapace does function as a protective structure in those decapod larvae which don't rely on behavioral anti-predatory defenses: see Morgan: "Fishes quickly learned to avoid spined prey, which ... may also increase the rate of evolution of the character". Non-carapaced larvae rely principally on behavior only.

The only contribution of carapace to planktonic life-style in zoea is participation of its spines [when they are pronounced] in parachuting (Chia et al).

[The above should be largely true also for the cypris larva of the cirripeadians, which are enclosed in a non-spined bivalve carapace.]

From the morphological point of view, [at least in adult forms of decapods] carapace creates a chamber for gills, so a morphologist would argue that this is the "main function" of carapace.


Are humans the only species to suffer from impacted teeth? Many humans need their third molars (wisdom teeth) removed due to tooth impaction. Are humans the only species to suffer from this?

According to Wikipedia
An impacted tooth is one that fails to erupt into the dental arch within the expected developmental window. Because impacted teeth do not erupt, they are retained throughout the individual's lifetime unless extracted or exposed surgically.
Now to your interesting question, there are case reports, that yes, animals, other than humans can also have impacted teeth.

Mandibular canine tooth impaction in young dog which was then made to erupt by surgery. Reference

Maxillary canine impaction in a persion cat. Reference

According to this article

Proper growth and development of the oral cavity depends on a series of events that must occur normally and in the proper sequence. Genetic abnormalities or trauma that affects either the developing tissues or the timing of their development can cause abnormalities. Defects that decrease comfort, health, or function require treatment; those that result in only an esthetic problem do not. Common developmental problems include persistent deciduous teeth, unerupted teeth, malformed teeth, malocclusion, and malformed jaws.


Autotrophic and heterotrophic organisms in anaerobic condition Can both heterotrophic and autotrophic organism survive in anaerobic conditions? If an autotrophic organism does not produce carbon dioxide but requires oxygen, it should not be present in anaerobic conditions, instead the heterotrophic organism can develop. Is this correct?

It is not necessary that all heterotrophs are aerobic. Many are anaerobes (yeast etc.)
Anaerobic Heterotrophs

These anaerobes live on glycolysis and fermentation (as far as I know). These two processes don't require Oxygen for release of energy.

Glycolysis

Alcohol Fermentation

Lactic Acid Fermentation

Alcohol Fermentation takes place in yeast (just an example) and Lactic Acid Fermentation in Muscle Cells.

The autotrophs will take care of themselves as photosynthesis require no Oxygen. If place in correct conditions (light and water are available), then they will thrive.

So, the answer to your question would be that both can survive. It varies from species to species. If you select the correct one then, both would survive or only one of them.


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

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

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

Which is great, but there is no connection in this paper between conformation and function - not surprisingly as this is a large part of structural protein analysis!

The way I look at this work is similar to the idea of a "descriptor" from the field of Cheminformatics. The radius of gyration is a descriptor, and so is this hull number. The author claims a correlation between these two descriptors, so... is one easier to calculate than the other?

This is interesting work, but I'm not sure at this point what the significance of hull number is for protein structural analysis. However I can say that the correlation between these two descriptors is not biologically significant - it's just a geometric relationship that would presumably hold for any set of 3D points.


Osmosis- basic questions Hi there,

For the first picture: can someone please explain in simple terms (I started learning biology a few days ago), why the answer to this osmosis question is no?

For the second picture: The answer is left because "the tension of the balloon can resist osmosis". Can someone explain what this means?

Yeah, basic principles of osmosis there, but let me see if I can make it clear.  For illustration's sake, I'll take glucose as a solute and water as a solvent, but recall that the principles are true (though they can have added complexity) for other solutes and solvents (see this post on chem.SE).
Background
The basic principle behind osmosis is that conjoined systems tend toward equal concentrations.  In other words, if you have a more concentrated solution (more particles of glucose per amount of water) on one side of a membrane than the other, the solution "wants" to become equal on both sides of the membrane.
If the membrane is permeable, there's no problem: glucose can flow freely and equilibrate on both sides of the membrane.  So the solution just moves around "mixing" until there's the same concentration everywhere of solutes (ie., glucose) in the solvent (ie., water).
On the other hand, suppose that the membrane is semi-permeable, meaning that the the water can pass through but the glucose cannot.  The system still "wants" to get to equilibrium; a state of equal concentrations on either side of the membrane, but it cannot get the solute across.  What happens instead is that water starts moving from the side which is less concentrated to the side which is more concentrated.  This results in the concentration of particles on less concentrated side going up and the concentration on the more concentrated side going down, effectively equilibrating them.

Now look at Picture 1.  Intuition from all this would tell you that the concentrations would be equal.  However, there's a twist.  Osmosis can only exert so much pressure on a system, and if it has to resist a pressure, it eventually stops, even if the concentrations are not equal.
The assumption in the picture is that the balloons have the same elasticity, meaning that the balloon on the left is more stretched, and is exerting more pressure on the solution than the balloon on the right.  Therefore, it will counteract some of the osmotic pressure and push some water back onto the right side of the system.
Now look at Picture 2. Again, intuition would tell you that the balloons will have equal concentrations at the end of the scenario, but again, the pressure that the balloon on the left is exerting messes things up a bit.  Even though the balloon on the right is pushing water into the balloon on the left, it is unable to push as much as it would like to, because the pressure of the left balloon's elasticity counteracts the osmotic pressure.

Taking it to the next level
They're basically laying the foundation work for reverse osmosis in this question.  In the case of reverse osmosis, we would be artificially applying pressure to the balloon on the left, resulting in water flowing forcibly into the right container.  This can be an advantage if you want to increase the concentration of a liquid - which has hundreds of industrial usages, such as in concentrating maple syrup in Canada and the northern States.


Perception of distant lights without glasses I am fairly short-sighted and wear glasses pretty much all the time. Naively, I would expect that when I take my glasses off, the image I see should look very much the same as as a photograph that's out of focus, or an image to which someone has applied a Gaussian blur filter. In bright conditions this is mostly true, but at night if I look at distant point sources of light, the blurry halos around them appear to have quite a complex structure, and a fairly well-defined edge. Why is this?

To make it clearer what I mean, and at the same time to make a hypothesis about the answer, here is a public domain image of some lights, taken with a camera out of focus:

(image source.) Notice that the image cast by each light is not simply a uniform circle. They are each slightly hexagonal; they are slightly brighter around the edge than in the middle; and there are distinct nonuniformities in the brightness in the interior of each shape.

What I see is actually fairly similar to this but much more extreme. The shape formed by a light is much further from a circle, being very irregular in shape and distinctly elongated in one direction. (This latter is perhaps not surprising given that I have a strong astigmatism.) The bright edge to the shape, and the non-uniformities in its brightness, are much more pronounced than in the camera image.

Now, in the photograph I know that the hexagonal shape is due to the hexagonal aperture in the camera. This can be ruled out in my eyes because my pupils are definitely circular. (Unless some light also passes through parts of the iris?) I would guess that the bright edges are caused by diffraction, and that the nonuniformities are caused by defects in the lens and/or dirt on its surface. I suppose that diffraction and lens aberrations must be the causes of what I see when looking at distant lights without my glasses.

So in the end, my question is mostly just, am I right about this? Are the shapes I see the result of defects in my eye's optics, and which specific anatomical features of the eye are likely to be their main causes?

This phenomenon is known as bokeh.

You are right in the hexagonal shape being produced by the iris (of the camera), and from this, it is clear why this happens: The iris blocks out some of the light travelling into it, and a shape approximating that of the camera's iris aperture is projected onto the CCD.

The same thing happens for the eye. The iris will block out a portion of the light, causing the bokeh to approximate the shape of the iris aperture (aka the pupil), which is roughly circular for humans. Animals with non-circular pupils will perceive differently shaped bokeh. If the lens suffers from astigmatism, it will also result in non-spherical bokeh being projected onto the retina.

This stackexchange link goes into greater detail on Gaussian blur vs bokeh.


Why do people use anti-inflammatory drugs? Why people should take anti-inflammatory drugs, when inflammation is a physiological way to defend our organism?

You are correct in that inflammation is a physiological process. It is vital for the correct development and localisation of a strong immune response, and contributes to tissue healing.

However, the beneficial effects are replaced by dangerous processes when they are prolonged or too intense. This includes both effects of leukocyte attraction and invasion, but also deleterious consequences of the accumulated cytokines. For example, TNF-alpha originally contributes to immune cell activation but in prolonged inflammation prevents tissue healing.

Note that "prolonged inflammation" does not necessarily mean that inflammation has been apparent or noticeable for the affected person for a long time. Often by the time symptoms present, the inflammation process has been persistent and become pathological. At this point, anti-inflammatory drugs need to be used as soon as possible to minimise irreversible damage.

Aside from this, quite often inflammatory and immune processes are triggered without a need for them. Our immune system is quite prone to errors, and cases of misguided immune reactions are actually increasing. Consider for example allergies, which often manifest with skin-symptoms such as eczema that can be treated with anti-inflammatory creams.


Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs? I am new to micro RNAs. I have been trying to find the answer to the question if microRNAs are transcribed from the same DNA strand as the messenger RNAs encoded by the encompassing gene?

From the scientific articles I have read so far, I infer that it is the same strand. If so, does the transcription of microRNA and mRNA occur simultaneously?

Finally, does the strand from which the microRNA is transcribed have any implications for its interaction with its mRNA target?

The following bear on the question of the relationship of the transcription of microRNAs to that of the pre-mRNAs of protein-coding genes:

Some microRNAs (termed ‘intergenic’) do not reside in a protein-coding gene (e.g. Drosophila mir-31a). Here the question does not arise.

Many (although not all) of those that do reside within a protein-coding gene are found exclusively in introns (termed ‘intronic’) — e.g. mir-11 and mir-998 in Drosophila gene E2f1.

For those microRNAs that reside in a parent gene, the direction of transcription is generally, although not exclusively, the same as that of the transcript (ca. 70%, according to this review).
The question arises whether the intronic microRNAs are generated from the spliced introns of transcripts of their parent genes. One of many papers which consider this is by Ramalingam et al. (2014). It appears that in some cases this may be so, but in other cases this appears to be ruled out by a disparity between the expression profiles of parent genes and microRNAs, and between different microRNAs encoded in the same intron.
The co-directionality or otherwise of transcription of ‘parent’ mRNA and microRNA has no implications for the interaction of microRNAs with their, often numerous, ‘target’ mRNAs. This is because (1) there is no genetic relationship between parent mRNA and target mRNAs — the parent mRNA, lacking the intron that gave rise to the microRNA, is not the target; (2) the hairpin loop of the microRNA precursor (imperfect though it may be) in effect represents both strands, from which may be generated either the 5ʹ portion, the 3ʹ portion, or both, depending on the microRNA. The miRBase site contains information on relative abundance of 5ʹ- or 3ʹ-fragments for individual microRNAs, and the microrna.org resource lists potential target mRNAs.


Interpreting qPCR curves: how to find Ct value in my case? I am reading my qPCR results and having no idea why Ct value is returned like this:

This is the qPCR curve of my samples, and the software returned Ct values of most of the curves as seen: 33.99-38.4 for the curves that have lower baseline.
The problem is the 2 curves (navy and black) with higher baseline at the first place. I read Ct values of these curves as 32-33, but the software says that the Ct values are 35.4 for these curves.

What could be the problem and what would be the right answer, my values or the software's?
Thanks in advance!

The software is correct. $C_t$ values are chosen to be sufficiently above background. As you can see, the background level is very different for two of the curves, so you can't use the same signal threshold for determining their $C_t$.


Is there an association between environmental and mutational robustness? The robustness of a genotype is the ability of this genotype to resist (always produce the same phenotype) to various parameters such as mutations and environment. The ability of a genotype to resist to mutations is called mutational robustness while the ability of a genotype to resist to varying environmental variables is called environmental robustness.

Is there a correlation between environmental and mutational robustness?

In other words the above question is: is there a among-species/populations/genotype correlation between mutational robustness and environmental robustness? i.e., Knowing that species $A$ has high mutational robustness, is species $A$ more or less likely than a randomly picked species $B$ to have a high environmental robustness? Or are the concepts of environmental and mutational robustness completely different and involve completely different genes and genetic architecture? Both theoretical and empirical studies that offer insights to this question are welcome.

Hansen (2006) says (middle of page 140):

  A link between genetic and environmental robustness is plausible, because genetic en environmental disturbances may often affect the same functional pathways in the organism, and ny increase in the robustness of a pathway leads to both genetic and environmental canalization. Evidence for a correlation between environmental and genetic robustness has been fund in studies of RNA folding (Ancel & Fontana 2000), in the effects of heat-shock proteins (Stearns et al. 1995).

He also cites Rifkin et al. (2005) who also showed evidence for this correlation. Finally Hansen cites Dworkin (2005) who did not find this link.

Hansen does not cite any theoretical paper and does not offer clear arguments of why this link exist but it is the best I could find


How can I list genes present on a given series of bands? My question is related to this one. My interest relate to this deletion:

  del(7)(q11q36)[12]

as defined by ISCN.

I would like to access a list of the genes found on the bands 11 to 36 of the 7th chromosome in humans. How can I do that?

There's a brief tutorial here on how to search by band. Here is a more extensive help document, and here is a human-specific help page, Basically:

Select the species and annotation release. We're Homo sapiens, by the way...
Select the chromosome you are interested in.
On the left side of the page, it says Region Shown: followed by two input boxes. You can search by band using standard cytogenetic nomenclature: 7q11 and 7q36. Enter these into the input fields and click Go. Here is 7q11:7q36.
There are various links to download data. Perhaps most relevant to you, there is a link on the left of the page which says Data As Table View. Here is said page, a list of genes at various levels of characterization.

Here is a table of different search queries you can use. There are a couple of ways to analyze the data:

Interactive Genome Browser:

Click on Genome Browser.
In the search field, enter the cytogenetic coordinates: 7q11;7q36. Press Go. Here is the resulting page.

Table Browser (for downloading data):

Click on Tools > Table Browser.
There are a lot of options. A tutorial can be found here. Most important for your search is region. Select the position radio button and enter your cytogenetic coordinates. I'll leave the rest of the options to you.


Why are GC-rich regions less condensed than GC-poor regions? As far as I know, chromatin consists of two kinds:

Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC.

Euchromatin is less condensed so translational factors have more access to this region, and this region is rich in GC.

I wonder how GC content affects the condensation status of the chromosome? What is the mechanism behind this relationship?

It is well known that GC and AT pairs differ in the number of their hydrogen bonds. Does this hydrogen bonding play the key role in condensation of chromosomes?

@ThoH.Ho and @Thawn. When banding chromosomes they are first treated with trypsin before staining with Giemsa dye. My understanding, and I have worked in the field of cytogenetics for quite a while, is that chromatin condensation due to gene content IS the reason for differential banding patterns. Gene rich/ high GC content areas, with more open chromatin, are more readily digested by the trypsin enzyme and therefore less protein is then present to stain with Giemsa. Vice versa for the gene poor/ low GC content regions. This is why non coding regions such as heterochromatin stain very dark and gene rich chromosomes such as chromosome 19 are pale. So although chromosomes may be at their most condensed stage of the cell cycle in pro metaphase, there is obviously still a relative difference between chromatin condensation of the GC rich and GC poor regions.


are dead ants returned to colony? Do foraging ants carry dead ants back to colony for disposal or leave them where they died?  I would think they would leave them behind just based on the energy expended that would be needed to transport them.  If they brought the dead back to the nest that might indicate 'feeling' or 'emotion' which everybody seems to say is impossible.

Social insects can respond in different ways to nest mates corpses. They can bury them (sometimes "entombing" is used in the literature, especially in honeybees because they can seal cells or use propolis to build tombs), eat them ("cannibalism"), but most often a specialized group of workers takes care of carrying them outside of the nest, far from the colony. Usually the older workers specialize in undertaking behaviors, it has been hypothesized that this allows to reduce the risks of contamination because older workers are already more likely to die or have fewer social interactions than younger members of the colony.

  Sun, Q., & Zhou, X. (2013). Corpse management in social insects. International journal of biological sciences, 9(3), 313.

What social insects do with the corpses wouldn't be a good indicator of emotions, simply because they may bring them back to eat them, or take them away to avoid contamination. Whether insects do experience emotions is a complex topic, the most advanced piece of work on the subject has been done on bumble bees:

  Perry, C. J., Baciadonna, L., & Chittka, L. (2016). Unexpected rewards
  induce dopamine-dependent positive emotion–like state changes in
  bumblebees. Science, 353(6307), 1529-1531.


Through which mechanisms did the Drosophila Histone Cluster evolve? The Drosophila Histone Cluster is a gene cluster that contains more than a hundred copies of a sequence that encodes several histone proteins. These copies are very similar.

My question is what mechanism are known that could have played a role in the genesis of this cluster?

I'm aware of the possibility of recombination, which might expand the cluster on one chromosome, shortening it on the other. Are there any other mechanisms to expand or change the cluster and are there telltale signs left by these mechanisms in the genome sequence?

Given that in most species histone genes aren't clustered, it would be weird to assume that recombination is the only mechanism to duplicate these sequences. Also, at one end of the cluster bits and pieces of histone genes are mixed with other sequences, a bit like all the broken copies got pushed to one end. It would be interesting to have an explanation for this pattern.

This is the best review I have seen with a comprehensive discussion on gene duplication and amplification mechanisms (and it is also quite recent). It seems like there may be no definitive answers to your question in the literature--perhaps because of a paucity of viable experimental models that would allow one to test various hypotheses.

Also @canadianer is quite correct. Most metazoans with sequenced genomes have some kind of clustering of their histone genes (as well as multiple copies). In Drosophila embryogenesis the early zygotic cell-cycles are extraordinarily brief, on the order of 20 min as I recall, which means the fertilized egg is essentially a bag of DNA polymerase replication complexes.  Therefore there is a very high demand for histone proteins.  The gene amplification you describe is one way to achieve high concentrations of histones in a short time-frame.

Note that not all metazoans undergo this rapid burst of synchronous nuclear division, and therefore not all species have such a high copy number of core histone clusters.


How do plants get carbon? How do plants get carbon? From air or soil? How is it different for aquatic plants and algae?

According to https://en.wikipedia.org/wiki/Soil_organic_matter soil has 3.3 times the size of the atmospheric pool of carbon.

SHORT ANSWER

From the air

LONG ANSWER

Trees are autotrophs, which means that they create their own compounds from inorganic carbon. So, carbon comes from inorganic carbon. This carbon comes from $CO_2$ (carbon dioxide) that is present in the air. The process by which this carbon is transformed into organic matter is called photosynthesis. More specifically, the carbon get fixed through a chain of reaction called the Calvin cycle that are part of the photosynthetic process.

The great cycle of life

You'll note that while plants (and some other things) uses $CO_2$ to build their mass, animals (and some other things) exhale $CO_2$ when they breathe. In other words, respiration frees up carbon dioxide while photosynthesis fixes carbon dioxide into organic matter.

Then you may want to ask where does the carbon we exhale come from. From our food. If you eat a beef burger for example, you'll the carbon that was present in the cow. The beef got its carbon from the grass that she grazed on. The grass got its carbon from the air and there is carbon in the air because animals (and some other things) exhale carbon when we breathe. respiration and photosynthesis are two essential series of chemical reactions that explain the existence of this cycle.

The (very simplified) chemical equation for those two processes are

Introductory sources of information

Here is a video by Veritasium that answers your specific question

Here are a series of videos of Khan Academy to increase your knowledge about photosynthesis


Why should plants transform glucose into sucrose before transporting it to other parts? I've learned that plants transform glucose into sucrose before sending it into phloem. But the process seems to be complex and energy comsuming. Why should plants do it? Is it really necessary?

Glucose, fructose and galactose are the three dietary monosaccharides. Glucose and Fructose are  simple monosaccharides found in plants. A monosaccharide is the basic unit of carbohydrate and the simplest form of sugar, glucose are aldose and Fructose are ketose.

  If the carbonyl is at position 1 (that is, n or m is zero), the molecule begins with a formyl group H(C=O)-, and is technically an aldehyde. In that case, the compound is termed an aldose. Otherwise, the molecule has a keto group, a carbonyl -(C=O)- between two carbons; then it is formally a ketone, and is termed a ketose. Ketoses of biological interest usually have the carbonyl at position 2.
  http://en.wikipedia.org/wiki/Monosaccharide

Whereas Sucrose is a disaccharide composed of glucose and fructose. A disaccharide is more complex than monosaccharide, more complex compounds like oligosaccharides and polysaccharides exists. Sucrose synthesised within the cytosol of photosynthesizing cells is then available for general distribution and is commonly trans located to other carbon-demanding centers via the phloem.

Sucrose and starch are more efficient in energy storage when compared to glucose and fructose, but starch is insoluble in water. So it can't be transported via phloem and the next choice is sucrose, being water soluble and energy efficient sucrose is chosen to be the carrier of energy from leaves to different part of the tree. Another problem exists,   glucose is highly reactive and this may result in some intermediate reactions while transporting glucose. Being a complex structure, sucrose is not as much reactive as glucose. So plants uses the sucrose as a medium to transfer energy. Inside the cells, sucrose is converted back to glucose and fructose. Energy is yielded when it is needed. So plants transfer glucose and fructose in the form of sucrose in order to:

Increase energy storage
Efficient energy transfer
Removing in between reactions

References

Carbohydrates
Sucrose & Starch Biosynthesis
Sucrose Metabolism
Sucrose and starch synthesis
Disaccharide


Should the sum of RPKMs be constant over experiments I have cufflinks data from 18 different RNA-seq experiments.

I've noticed that if the sum all the RPKM values for a particular experiment, are vastly different between experiments. How could this be? I was under the impression that RPKM was normalized by the total number of reads. If that is true then the sum of RPKM values for a single experiment should be the same?

I guess this arises because of the default cufflinks option --total-hits-norm in which it normalizes the FPKMs with total reads including the ones that are not mapped to a known gene or a predicted gene from the assembly. In the genes.fpkm_tracking file the FPKM values are reported for known/predicted genes. It is certainly possible that the number of genes are different in a certain sample compared to the other and perhaps therefore the sums are different. If you are not interested in finding new transcripts then you can run cufflinks with a reference GTF/GFF file provided using --GFF along with using --compatible-hits-norm.

You can also try this:

Assemble with cufflinks, merge the GTFs with cuffmerge and run cuffquant with the merged GTF.

You can subsequently use cuffnorm to normalize the expression values. It has been observed by me and others that the FPKM value reported by cuffdiff and cufflinks are different which is most likely because of differences in default parameters (see this). The inner operations of cufflinks are not very clearly documented; so I cannot conclusively answer your question.