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What is the relationship between migraines and histamine?
A family member suffers from migraines so I have been reading a little around the subject.
There seem to be any number of "triggers", but I have seen mention several times of the role of histamine in migraine activation as an active area of research. The suggestion is that high histamine levels in the body can cause migraines.
Is there solid evidence that histamine can trigger migraines?  How does this mechanism operate?

Yes, this is true.
Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase.  NO is then available to act locally on the vasculature as a vasodilator.
NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to the production of cyclic GMP, which in turn forms phosphorylated protein kinase G. PKG phosphorylates Ca2+ channels, slowing the influx of calcium into the cell, which leads to smooth muscle relaxation, and vasodilation, which leads to migraine.
The only silver lining is that there is a check in place: with the binding of histamine to H3 receptors on c-fibers in the central nervous system, feedback inhibition prevents the further release of histamine from these sites.
References:

Akerman S, Williamson DJ, Kaube H, Goadsby PJ. (2002).  The role of histamine in dural vessel dilation.  Brain Res. 956(1):96-102.
Gupta, S., Nahas, S.J.,Peterlin, B.L. (2011) Chemical Mediators of Migraine:
Preclinical and Clinical Observations.  Headache: The Journal of Head and Face Pain, 51(6): 1029–1045.

This seems to suggest that some sort of antihistamine would be effective in treating this class of migraine. Is that right?

@Poshpaws I didn't run across that information in any of the articles.  Perhaps, but without knowing more about the affinities of the antihistamines for the different types of receptors, the drug might bind to the H3 receptor just as readily and stop that valuable feedback inhibition.

I've experienced migraines for 10 years, and now for the last 14 months that I've taken anti histamine medicine to see if there would be a benifit I've had good results. The frequency has dropped from approx 3 times a month to a migraine approx every 6-8 weeks. For me thats a sizeable drop. The other benifit is the severity is less intense.
 Now I'm trying to find why my body produces too much histamine, so I hopefully can eliminate the anti histamine med's.
 Recently I've greatly reduced foods with refined sugar, also processed foods, and added more whole foods, and I'm seeing excellent results.

james, welcome to Bio.SE. As a science-based site, and one that is NOT for medical advice (please see the first point of the FAQ ) your answer is not really what we're looking for here. Personal experience is certainly appreciated in some types of answers ("this is the protocol I use for PCR, and it works great"), but here it's not really appropriate. Ideally, for this type of question which already has a good answer, you'd add to the science being discussed, and perhaps at the end add a quick personal touch if it's warranted.


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Photosynthetic Pigments vs. Chloroplasts
What is the difference between Photosynthetic Pigments and Chloroplasts? I know plants have both but Prokaryotes (Bacteria and Archeae) only have the former.

Photosynthetic pigments are the chemicals which take part in photosynthesis, in particular they are they ones which absorb photons and fluoresce (emit photons of a different wavelength) or emit electrons. Pigments are molecules, and chlorophyll is a key example. These pigments are required for photosynthesis to take place, as they generate the electrons which create the electrochemical gradients which power photosynthesis, thus all photosynthetic organisms will have photosynthetic pigments of some kind.
Chloroplasts are membrane-bound organelles in plant cells, made up of many hundreds of thousands of molecules including pigments. Plant photosynthesis takes place on their internal membrane, the thylakoid. Specifically, the thylakoid membrane of chloroplasts is the membrane across which the aforementioned electrochemical gradients are created in plants.
Chloroplasts originated from a free-living bacterium, probably a cyanobacterium, entering a eukaryotic cell. So prokaryotes don't have them because the chloroplast endosymbiosis event was one way in which plants diverged from their non-plant ancestors. So you can think of a cyanobacterium as a free-living chloroplast - they have their own internal membranes similar to the thylakoid across which electrochemical gradients are created for photosynthesis. Conversely, you can think of a chloroplast as a small cyanobacterium living symbiotically inside a plant cell.

source: Stack Exchange

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When running gels what is the difference between constant volts or constant amps?
In general, you want to be consistent with running your gels either at constant volts or constant amps. However, it is very clear that during the progression of both PAGE and agarose gels, the free parameter changes due to the change in resistance of the gel.
While there are safety reasons why you run one vs. the other, I'm curious how these difference affect the migration of your gel.

I'll answer only for SDS-Page, which is the system I am most familiar with.
With a discontinuous buffer system, such as the well-known Laemmli system, resistance increases during electrophoresis, as (very mobile) chloride ions are replaced by glycinate (glycine ions).
From Ohms law:

Voltage (V) = Current (I)  x Resistance (R)

and the definition of power (Watts):

Watts (W) = Current (I) x Voltage (V) = I2 x R

At constant current electrophoresis will proceed at a uniform rate, however, as the resistance increases, so too will the voltage and the amount of heat generated.

In some discontinuous buffer systems, such as the Tricine/SDS system due to Schägger & von Jagow, this may be enough to crack the gel plates!
At constant voltage, the current will decrease during electrophoresis; as a result less heat will be generated than constant current electrophoresis, but the rate of migration of the sample will decrease with the decrease in current.

References
Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685. [PubMed]
Schägger, H. & von Jagow, G (1987).
Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166, 368-379.[PubMed]

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effect of background selection on promoter regions compared to distant enhancers?
Has anyone looked at the effect of background selection on the levels of conservation of promoter regions compared to distant enhancers? Do promoter regions have a higher conservation due to background selection from nearby genes compared to more distant enhancer regions?
My attempts to google for this only gave me a 2004 Drosophila paper on a few genes survey:
http://mbe.oxfordjournals.org/content/21/2/374.full
I am wondering if this has been looked at before or if there are any other relevant bits of genetics one should consider first.
EDIT: a bit more of explanation into the hypothesis below, and a reference that could be useful:
Let's start supposing a region near a coding gene that can gain regulatory potential via a new point mutation or small translocation. This new regulatory potential needs to be positively selected after it appears, or it will gradually accumulate more mutations and disappear. But if the region is close enough to the coding gene, recombination rate between the region and the nearby gene body will be low, proportional to their distance. If the gene body is assumed under selective constraint, there will be a hitchhiking effect of the nearby regulatory region by the gene nearby. The background levels of mutation on the regulatory region are then going to be lower (lower background mutation) than in a region that is not near a gene under strong selective constraint. So one way of explaining why close promoter/enhancer regions are more conserved than distant enhancer regions would simply be due to linkage.
A second part of the hypothesis would be about the presence or absence of recombination hotspots in upstream regions of a coding region: if nearby promoter/enhancers are kept via linkage to the closest gene, unbiased measures of cross-over (e.g. PRDM9 experiments in mouse testis) should indicate if there is an increased linkage of functional genomic blocks, like enhancer/promoter/gene blocks (Hi-C, 4C, 3C data), whereas if recombination doesn't play a role, regulatory blocks wouldn't necessarily be kept in the same haplotype block.

So are you suggesting that negative selection (natural selection against a trait) may be stronger on enhancers that are more distant for the gene itself? I haven't seen any, but will keep an eye out! This would probably be a (relatively) simple and interesting bioinformatic/phylogenetic analysis given a proper framework. I expect it will very much depend on which gene/promotion mechanism you are looking at - unless the question is 'any'?


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

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

Thanks every body for answering me. it is an unsual question but anybody working on the it?

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

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

Thanks, for the probability of ovum + ovum conjugation. Please also consider the current model of understanding twin pregnancy. But since it becomes a diploid cell, is it possible to join temselves and can start dividing. Also please consider the cell membrane factors which we see in case of normal fertilization.

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


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SPINAL CORD: Do the axons from white matter synapse with the cell bodies in grey matter?
After wading through a sea of information, I understand the main differences between the white matter and grey matter of the spinal cord.
I know that white matter contains myelinated axons in the ascending and descending nerve tracts from the brain to the spinal cord. I know that grey matter contains somata which contribute to sensory and motor functions from and to the peripheral nerve fibers.
With the differences in mind, I am confused about the relationship between the two.
The main question being: What signaling, if any, takes place between the myelinated axons of white matter and the somata of grey matter? More pointedly, do the myelinated axons from the nerve tracts in white matter ever synapse with dendrites from somata in grey matter?
My guess is yes, that this is a key aspect in how the brain and the spinal cord communicate. But I haven’t yet found any definitive source that addresses this question directly.

This is kind of a big question, as there are lots of different pathways that synapse at different levels and some of the cell bodies send axons over long distances.  Is there a particular tract that you are interested in?

I am studying Excercise Physiology, for the purposes of personal training, from that vantage point I am trying to solidify a big picture understanding mostly. So no i don't have to know the nitty gritty of a particular tract, my texts and resources have illustrated the big differences between the white and grey matter and thier main functions but do not really address what if any signaling takes place between each other. I was guessing and take it from your answer they do. Is there a typical pattern or does each pathway feature a unique setup between the white and grey matter?

That should give you a start.  You can read up on these and some of the other tracts and see if you have specific questions on them.

Here is a great diagram (from here) that outlines all of the different white matter tracts running up (blue) and down (red) the cord.

The portion in the center, as you have found in your research, is the gray matter.  In there are the different interneurons (cells that exist in the network to integrate information from descending controls and do further processing on it) and all of the different motor neurons.  The corticospinal tract descends to the appropriate level (for example, a neuron in charge of moving your arm, to keep it simple, will have a cell body in the brain, and descend to the thoracic level), enters into the gray matter and either synapse on an interneuron or directly onto a motor neuron).
The sensory neurons are a slightly different animal.  Some (pseudo-unipolar cells) have what are basically two "legs", one that runs out into the periphery, which will take the signal from something like a Pacinian corpuscle in the skin, propagates a signal to the cell body, which is outside of the spinal cord in the dorsal root (see below), and the other "leg" runs all the way up the dorsal column into the medulla of the brainstem.

from here
So that should give you some idea of the two major tracts.  To see some of the finer detail, you can look into the different layers (laminae) that the gray matter is composed of, so that you can trace the connections all the way in.


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Is there a detectable amount of bacterial DNA in the blood of infected persons?
With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood?
If any is found it is likely not to be very much, and even difficult to distinguish from human DNA, but presumably recent advances in sequencing should have made it possible.

Even difficult to distinguish from human DNA. Hmmm... a simple PCR for a bacterial-specific gene would easily distinguish human from bacterial DNA.

Yeah I think qPCR is a fairly routine diagnostic for determining a strain.

@nico so which exclusively bacterial gene would you pick out?

@rwst: hmmm... I'm sure there are tons of them. 16S for bacteria vs 18s for human would be easy enough.

Better than DNA detection to show existence of bacteria may be doing a MALDI-TOF of the blood to detect bacterial metabolism products like lipopolysaccharides or extracellular proteins.

Everything depends upon the infection and on the general immune status of the patient.
Generally, the prerequisite for DNA to freely circulate in the blood is the presence of bacteria themselves in the blood (bacteraemia). This means that the infection left its original site (where it is usually kept isolated from the blood flow by the immune system). Depending upon the body reaction to this breakthrough, sepsis and/or SIRS can be the consequences.
Under these conditions (not necessarily as severe as sepsis, but in case of proven bacteriemia), the bacteria cells get attacked by the immuno cells, that leads to their eventual lyzing and releasing their content to the blood.
PCR can be used as a method to prove the existence of bacterial DNA. (Here is a publicly available paper on this topic).

Thanks for the ref. Barbars are they, let the rats gulp CCl4, nasty stuff...


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Calculating Protein Concentration from Kilo Units (KU)
I am looking to purchase Pyruvate Kinase from the Sigma Website, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein.
Does this mean one unit is one protein? so 1KU is 1000 units of protein?
What is the relationship between the KU and mg? and how can I use this relationship to calculate my concentration in um or mg.

EDIT
In this paper (look at the methods section) they calculated the concentration of 25,000 units of calmodulin in 0.5 ml to be approximately 75um which is 40,000 units/mg. How did they calculate this?

if there are 600 units in 1 mg surely there must be more than 1 mg for 1000 units 1000/600 = 1.67 mg?

From the page linked from your link:

Unit Definition
One unit will convert 1.0 μmole of phospho(enol)pyruvate to pyruvate
  per min at pH 7.6 at 37 °C.

So, the unit is defined by activity, and there is no way to know how many molecules or milligrams of protein are included

What about in the paper I referenced? They calculated the concentration of calmodulin to be approximately 75um.

After some serious thinking it is possible to calculate the mg. On the website it states there is 350-600 units/mg protein. So if I bought the 1KU to work out the mg and assuming I receive 600 units I would divide 600/1000 = 0.6 mg. I completely missed the obvious here.

You can obviously calculate the moles or weight by purifying the enzyme and weighing it...

@TomD: sure, but that's the way one would do it!

@TomD: I am not saying HE should do it, I am saying that is one method to do it. The Biuret method would also work, although it only gives you an approximate concentration. If weighting is not an option MS or similar should do.

@TomD: well, I let the nice people at Sigma do the tedious work for me :D

direct protein concentration measurement is a lot easier

The figure of 350 - 600 Units per mg refers to the specific activity of the enzyme.
The Unit is International Unit or IU and is usually defined as that amount of enzyme that will catalyze the transformation of 1 micromole of substrate (or product) per min, under defined assay conditions (such as pH, temperature, substrate concentration, presence of Mg++, etc). It is thus a measure of activity.
When the enzyme is pure (no other extraeneous proteins present), the specific activity provides important information about the catalytic capacity of the enzyme.
It is usually calculated by measuring

the activity of the enzyme preparation under defined assay conditions
the protein concentration of the same enzyme preparation (using, say, the Lowry or Biuret method for protein estimation).
Alternatively, if the E(1%, 280) is known (see below) and the enzyme is pure, measurement of the absorbance at 280 nm gives a very good estimate of protein content (and the enzyme may be recovered 'unharmed' at the end of the measurement).

Thus, taking a figure of 450 Units/mg for the specific activity of pyruvate kinase,
25 KU (25 Kilo-Units, I presume) contains 500/9 mg (~55 mg) protein.
I notice that the Sigma product sheet provides a figure for  E(0.1%, 280) = 0.54.

This means that a 1 mg/ml solution of the protein will have an absorbance at 280 nm of 0.54

E(0.1%, 280) can be used as a very convenient measure of the protein content provided that the enzyme preparation supplied by Sigma is pure.

A 'rule of thumb', useful when the E(0.1%, 280) is unknown, is that a 1mg/ml protein solution has an A280 of 1.

Thus if, say, the A280 (absorbance at 280 nm) of the resuspended lyophilized powder is 1.08 and you have 5 ml of this, the protein concentration is 2mg/ml and you have 10 mg of protein in total.  You may wish to assay the enzyme yourself to determine an accurate specific activity.
The EC (Enzyme Commission) Number may also be of interest.  For pyruvate kinase (EC 2.7.1.40) see here.
For a great ref on PK (pdf may be downloaded) see here (Ainsworth et al.)

For your second question, I do not have access to that paper from home.
However, if calmodulin has a specific activity of 40 000 Units/mg,
 25 000 Units is equivalent to 0.625 mg; this is in a volume of
0.5 ml.  Therefore, the calmodulin concentration is 1.25mg/ml.
Taking the molecular weight of calmodulin to be 16 000,
then 16 000 mg /ml (theoretical) would be a 1 Molar solution.
Thus a 1.25 mg/ml solution is about 78 micromolar.

As far as I can see, "25 000 Units is equivalent to 0.625 mg; this is in a volume of 0.5 ml. Therefore, the calmodulin concentration is 1.25mg/ml."  is correct?


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Why are there exactly four nucleobases in DNA?
Does someone know why DNA is composed of four nucleobases? In particular, is there an explanation for the number? Why four and not two, or eight?

this just in - two new bases added to E coli (X and Y) do reproduce. http://www.wired.com/2014/05/synthetic-dna-cells/  not clear on how much adaptation is needed to make X and Y work to code for genes.

A now deleted answer put this down to an argument based on amino-acid coding in codons but, as pointed out by Konrad Rudolph in a comment, arguments based on codons cannot be correct because the 4-base system likely pre-dates the evolution of protein translation.
So why four?
I suggest that it comes from a combination of factors which make it a 'just right' fit for RNA-based replicators: more would be bad, and less would also be bad. The four bases are able to copy with high reliability because two features combine to exclude mis-pairings: there are two size classes - meaning any purine-purine or pyrimidine-pyrimidine pairing results in incorrect separation between the strands, excluding A-G and C-U bonds; and there are two classes based on number of OH-bonds - which limits the potential for A-C and G-U bonds. More bases must, inevitably, weaken the strength of these exclusionary approaches and increase the number of mispairings. RNA world replicators will have lacked the sophisticated repair and error checking mechanisms of modern lifeforms so this increase in mispairings would likely not be corrected.
Of course, a two base system would be even more capable of reducing errors. I suggest that the advantage of the four base system is that it allows for much more complex 3-dimensional structure to form in RNA and thus enabled a broader range of catalytic capabilities. I've only considered even-numbers because only even numbered systems could use the Watson-Crick style of base pairing.
I'd also suggesting reading Eörs Szathmáry's 2003 paper on this very question.
Addendum
A group in California has just published a paper in which they successfully added a third base pair stably into DNA. I think this could shed some light on why four - you can read about it here or get the full paper here (Nature, so pay walled).

Here is a possible answer given by this paper:
http://www.ncbi.nlm.nih.gov/pubmed/16794952
or
http://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.pdf
It gives a Darwinian explanation to the question. It approaches the problem from Claude Shannon's theory for communication. It treats DNA replication conceptually and mathematically the same as a data transmission. It concludes that the system of four bases, not two, not six, replicates the most genetic information at the shortest amount of time.
The communicational analogy goes like this. If you have two data transmission systems, one can transmit, say, 1 MB per second, and the other can do 2 MB per second but cost less than twice as much. The answer is obvious you will buy the second service for a higher rate per cost. As a data service, it does not care what information you consume -- it can be spam, video, audio, etc. All that matters is the transmission rate. As for DNA replication, it is like a data transmission channel when one base is replicated a time along the mother DNA template. It too does not care whether the process is for a bacterium genome, or a plant, or an animal genome. The pay-off is in information and the cost is in time. Unlike your abiotic communication varieties, time is both the sender and the receiver of all messages of life, and different life forms or species are merely time's cell phones. So if one system can replicate more information in a unit time than another, the faster one will win the evolutionary arm race. A prey operating on a slow replicator system will not be able to compete with nor to adapt to a predator operating on a fast one.
Now because the A-T pair has only two weak hydrogen bonds but the C-G pair has three, A and T take a shorter time to complete duplication than the C and G do. Although the replication time is short in some fraction of nano second, but the time adds up quickly for genomes with base pairs in the billions. So having the C-G pair may slow down the replication, but the gain is in information. One base pair gives you 1 bit per base information. Two pairs gives you 2 bits per base information. But, having more base pairs may eventually run into a diminished return in information replication rate if the new bases take too long a time to replicate. Hence the consideration for the optimal rate of replication measured in information bits per base per time. Without information there would be no diversity, no complexity. Without replication in information there would be no life.
Using a simple transmission/replication rate calculation by Shannon you can calculate the mean rate for the AT-system, the CG-system, the ATCG-system, and for some hypothetical 6-bases, 2n-bases system whose new bases take progressively longer time to replicate. The analysis shows the ATCG-system has the optimal replication rate if the CG bases take 1.65 to 3 times longer to replicate than the AT bases. That is, a base-2 system replicates its bases faster but does not carry more information to have a higher bit rate. Likewise, a base-6 system has a greater per-base information but replicate slower on average to end up with a suboptimal bit rate.

According to a comparison from the paper, the base-4 system is about 40% faster than the  A–T only system, and 133% faster than the G–C only system. Assume life on Earth started about 4 billion years ago, then the A-T only system would set back evolution by 1 billion years, the G–C system would do so by 2.3 billion years. For a hypothetical base-6 system, it would do so by 80 million years. In other words, life is where it should be because the base-4 system is able to transmit information through the time bottleneck at the optimal  bit rate.
In conclusion, life is to replicate the most information with the shortest time, and the base-4 system does it the best. If ever there were other systems they would have lost the informatic competition to the base-4 system from the get-go. Darwin's principle works at life's most basic and most important level.
There are other explanations, all non-Darwinian. Most are based on the base's molecular structures. But these types of explanation border on circular argument -- using observations to explain themselves. They also face this catch-22 problem since there is no way to exhaust all possible bases for replication. However, such lines of exploration are fruitful regardless because more knowledge the better. But without taking information and its replication into consideration it is hard to imagine a sensible answer to the question.

Welcome to Biology SE. It would be great if you can expand your answer to include a summary of the main points. We can't count on the link being there forever.

you can edit your answer. (see the link under your post.)

Cool explanation.

"and for some hypothetical 6-bases, 2n-bases system whose new bases take progressively longer time to replicate." - This assumption seems hard to justify.

There is a chemical dimension to this question too.
If you look at the Watson-Crick Base pairs you can see that there isn't a lot of wiggle room:

The nucleotide bases have 2 or 3 hydrogen bonds.  It's probably not sterically reasonable to have 4.
That means there are only a limited number of ways the base combinations can be complimentary and also specific as they form the double helix.  Since A->T and T->A hydrogen bond patterns take up both donor-receptor combinations there is one possible 2 H-bond pairing.
There are 2 ways to configure the three hydrogen bond bases I think, so perhaps six is possible, but I'm guessing that if you expand the base pairing repetoire, one could start to lose specificity.  As it is, if you play with nucleotides enough, you can make non Watson-Crick base pairs and probably lose some of the confidence you have exact 1:1 matches between complimentary base pairings.   Wobble Base pairs in RNA and  Hoogsteen Base Pairings can already be demonstrated to allow triple helixes and non-perfect match RNA helices.

The 4-bases DNA system with A-T bonds and C-G bonds is the one that evolved to be used by most living creatures on Earth, as mentioned in other answers, because it can encode a triplet table of bases for all aminoacids used, allowing for some aminoacids to have more than one triplet code. There are though slight variations of the system: even though the A-T and C-G bonds don't change, the nucleotides can be modified to mark areas of the genome in what is part of the epigenetic code. The most common modification is adding methyl and 5-hydroxymethyl molecules to the bases, although more modifications are still being discovered.

Theoreticaly from pyrimidines and purines together
they are 6 Base Pairs = 12 Bases possible...
IF the nucleobases are evolved from only pyrimidines and NOT purines
THEN they are only 2 Base Pairs = 4 pyrimidines Bases possible!!!...

Disclaimer: I am not a biologist or a chemist or an information theorist. I just want to toss out a perspective which I've sort of pieced together from the various answers here, but which I don't really see expressed in any one answer.
Namely, I think it's easy to imagine that 4 base pairs is the result of a trade-off between having many base pairs and having few base pairs. That is, it's essentially the result of an optimization problem. There are some advantages to having more base pairs, and some advantages to having fewer base pairs, and 4 is simply the best trade-off between them. As with any optimization problem, the result is likely quite sensitive to exactly how we frame the question -- exactly what environment the 4-base-pair system evolved in, what role RNA played in life at that point, exactly how we quantify the benefits and drawbacks of various base pair systems, etc. And perhaps the 4-base-pair system initially evolved in one environment, while later rising to dominate other competing systems in a quite different environment -- in which case the question is even more complicated.
Likely, many of these modeling questions are uncertain enough at present that it's impossible to confidently "run the optimization problem" and trust the output. But probably the first step would be to try to enumerate as many as possible of the competing factors at play. Let me attempt that, with help from the previous answers here:
Reasons to prefer fewer base pairs

Fewer base pairs means fewer possible "mispairing" pathways, potentially decreasing mutation rate

Fewer base pairs also means that only the "best pairs" need be used, again potentially decreasing mutation rate.

Fewer base pairs simplifies the process of acquiring or synthesizing the base pairs in the first place.

May affect speed of transcription.

Reasons to prefer more base pairs

More information stored per unit mass / volume.

Potentially increases range of structures which can be built directly from the genetic material.

May affect speed of transcription.

I'm sure there are many other factors to consider.
It's unclear to me whether anything quantitative can be said said about these opposing forces with enough confidence to really "run the optimization" and trust the answer.
And of course, there's presumably a lot more to say about the space over which we're optimizing -- exactly which "base pairs" conceivably could be used in the first place, as other more qualified people have already addressed.

Because four is the minimum possible number. If there is no push to make a system more complex, it will never assemble.
One might then argue that a similar system could have been built only using two bases.
Fine.
Try it out.
You will miserably fail. Sure you can make a DNA strand containing adenine and thymine only. But who would be stopping guanine and cytosine from forming and joining some deoxyribose then? How would you manage information storage, preservation and transfer then?
Base pairing - no matter how complex might look - is the simplest way to safely store information at the molecular level so that it could be handled for transfer and translation somewhere else. The spatial combinations of hydrogen bonds that can be established between pyrimidine and purine derivatives are only two.
For replication purposes you need a further symmetry breaking, which leaves you with two bases, one on each strand of a DNA double helix.
Two times two is four.
P.S.: By the way, who on Earth told you that there are exactly four nucleobases in DNA? Tell them they probably forgot methylcytosine! The term "methylation" is just an excuse to avoid admitting that DNA uses five bases instead of four. Open your mind.

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Can rats pass on memories of a maze to their offspring?
A friend of mine told me once about a documentary movie he saw some years ago. On this movie he saw scientists talking about particular experiment. This experiment involved rats and probably electrical traps. The rat had to get to the cheese, there were traps on the shortest route to it, and obviously it got shocked few times. What is interesting is that my friend says that when they took its offspring (probably born later) they avoided those traps.
I'm aware that its not how "genetic memory" works. Its not memory of individual, but of species (so it requires evolution). This is what I'm trying to explain to him, but he says "he knows what he saw".
Anyway maybe someone here is aware of such an experiment. I believe that he is wrong about something (or conclusions drawn where changed later), so I would like to find out more about it.
To sum up:

Its not Tryon's Rat Experiment
It involved: rats, traps (probably electrical), more then one path to cheese, rat's offspring and some sort of memory/learning amongst rats.

This Nature Neuroscience paper published this week suggests that rats can pass on learned smell sensitivities to their F1 and F2 offspring. This is surprising stuff, so I imagine there will be a lot of close scrutiny and good conversation over the next few weeks. Here's a nice summary of the results from a National Geographic blog.

I recall an article in Science magazine, perhaps in the 1950's or 60's that, in essence, claimed that rats who had learned the maze to readily obtain food passed on their ability to their progeny. The progeny were able to learn how to go through the maze statistically quicker than rats whose parents had not experienced going through the maze.

Here is a pop science article talking about "transgenerational epigenetic inheritance." Also, there is good evidence that another smart animal, crows, pass info between generations -- though this is perhaps due to a complex but subtle language that crows have rather than a genetic phenomenon...

The phenomenon you're talking about was a fad in the 60's, called 'interanimal memory transfer'. It started out when James McConnell performed a later-discredited experiment in which he found that if you chopped up flatworms which had been exposed to some stresses, and fed them to other unexposed flatworms, the unexposed worms became wary of the source of stress quicker after eating their dead companions. He jumped to the conclusion that a 'memory molecule' was being transferred, and that the cannibal worms gained the food worms' memories of the stress.
People then started looking to see if they could:

repeat the experiments
find the same phenomenon in other animals

In the first case, nobody could replicate the experiments in worms, but because McConnell was such a PR genius he managed to convince the public that his results were valid (see Rilling, 1996 for more on this).
In the second case, Frank et al. (1970) and others tried working with rats - I think this is the experiment you're talking about in the question. They found various interesting results including that if you trained rats to run through a maze by using particularly stressful negative reinforcement (like electrocution), then those rats' children would be able to learn the new maze much faster. However, Frank et al. didn't make the same mistake as McConnell - first of all they wondered if the parent rats might be leaving a scent trail. So they used duplicate mazes with the exact same design, putting the children into clean mazes. The children of adults who had already learned the maze continued to outperform the control rats - the explanation was not scent trails.
Next they wondered whether it might be that the second generation rats had been born with a higher wariness as a result of the stress their parents suffered; i.e. it could be a hormonal transfer from mother to child (e.g. cortisol, the stress hormone).
Frank et al. tested their hypothesis by torturing some rats for a while (rules about animal welfare were not strict in the 70's). They would lock some rats in a small jar and bash them about for a long time, then kill them, chop them up, and take out their livers. They fed the livers to other rats, and found that after eating the livers the other rats learned the maze much faster. They interpreted the results in what now seems a sensible light: the stressed rats were producing high concentrations of a stress-signalling molecule. When those rats either had children or were fed to other rats, they passed on high doses of the stress molecule. This raised the alterness and wariness of the receipient rats so that they were much quicker to learn which parts of the maze were dangerous.
There is no evidence that the child rats actually 'remembered' the maze - they still had to find their way around, but they were extremely wary of the electrocution plates and so avoided them, finding the safest way to the end. This is not a case of genetic memory.

 Frank B, Stein DG, Rosen J. 1970. Interanimal “Memory” Transfer: Results from Brain and Liver Homogenates. Science 169: 399–402.
 Rilling M. 1996. The mystery of the vanished citations: James McConnell’s forgotten 1960s quest for planarian learning, a biochemical engram, and celebrity. American Psychologist 51: 589–598.

That was probably part of the fad to test Lamarckian ideas, wasn’t it?

@KonradRudolph yeah I think that whole thing was started as a result of McConnell's charade. I came across a reference to this when reading Carl Sagan's Demon Haunted World the other day, where he cited it (the flatwork memory thing) as an example of high-publicity pseudoscience.

It also inspired a scene in THX1138 (early George Lucas film) where children are being fed their lessons through an IV bottle.

Did Frank et al. (or someone else) actually measure concentrations of "stress molecules"? I didn't read the paper, but based on your answer it sounds like a lot of speculation.

This is somewhat unrelated, and for that, I apologize, but I find it truly fascinating, and I believe you will too.
Zebra finches are a song bird that have become a popular model organism for behavioral research. They have a very stereotypical pattern for song learning: at about 70 days after hatching, the baby male song bird starts to listen to his father's song, copy it, practice it, and ultimately learn it. Female birds do not have a courtship song to learn.
Interestingly, if the baby male bird does not learn their father's song, they end up just kind of screeching, and never singing a song. This, in nature, makes them unable to court a female.
But in the lab, this research group did an experiment, where they took these screeching males, let them grow to adulthood, then teach their child as best as they can. The child, wanting to learn a song, takes what it can from the father. After 4 generations of this, the group was able to get de novo song production from these birds.
Unbelievable!
De novo establishment of wild-type song culture in the zebra finch - Fehér et al. - Nature, 2009

Very interesting! I have not had the time to read through the article yet, so I do not know whether they address this, but I wonder what happens if then you expose those 4th generation birds to birds that sing normally. Who would they choose? A screeching one or a singing one?

https://www.facebook.com/ScienceNaturePage/videos/1319435594855362/
I’m not sure if this is the right link, but there was a video on Facebook called “memories can pass between generations DNA” posted by hashem al-ghaili, it is 4 minutes and refers to an experiment where mice passed on maze knowledge to their offspring...

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Aren't antibiotic resistant probiotics dangerous?
Multidrug resistant probiotics are often recommended by doctors in various cases. But since bacteriae can easily exchange genes by conjugation or other means they could promote the drug resistance of other dangerous bacteriae residing in the bowels. (Which could be just "visitors" otherwise causing infections somewhere else)
Or there is something that withholds this transfer? I think not and so my former genetics professor.

I couldn't find a single paper on "multidrug resistant probiotics". What is your source?

I doubt that this is locale to our country but I can't find any international substances. Here is a google translate link for the patient information of such a probiotic. Excerpt from the end of the page: Active ingredient: 2 billion multi-antibiotic-resistant Bacillus clausii spores, 5 ml per bottle Other ingredient (s): purified water

Recommending multidrug resistant probiotics sounds fricking insane. I'm going to stop commenting now lest I start swearing...

Usually, resistance genes are located on plasmids---additional DNA rings in the bacterium that are part of the genome. These plasmids cause their own exchange with other bacteria, even from other species.
B. clausii, the probiotics organism in question here, appears to be special, though, in that it has no plasmids. His resistance genes come with the primary ring-shaped genome and should not be transferred via plasmid exchange to other bacteria. This doesn't rule out other means of gene transfer like phages or conjugation, however. In one study, it was unsuccessfully tried to transfer a macrolide resistance gene to other bacteria. They conclude

A potential hazard is transfer of resistance to microorganisms
  pathogenic for humans. The risk that this event will occur and the
  consequences in terms of morbidity and mortality have not been
  evaluated. Parameters required for risk assessment include studies on
  the nature and mobility of the resistance genes of probiotics.

The only other paper on a B.clausii resistance gene didn't look at its transferability. That clearly shows we don't know enough.
B. Bozdogan, S. Galopin, R. Leclercq: Characterization of a new erm-related macrolide resistance gene present in probiotic strains of Bacillus clausii. In: Applied and environmental microbiology. Band 70, Nummer 1, Januar 2004, S. 280–284, {{ISSN|0099-2240}}. PMID 14711653. PMC 321311.

Thanks so the conclusion is that there is no evidence neither pro nor contra. I think this makes these substances dangerous enough. If anyone can add more, he's welcome.

After all we know now about bowel microbiome destruction it's actually the antibiotics themselves that should be labelled dangerous.


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Are human bodies programmed to die?
Following from this question: What is the evolutionary advantage of death?:
Is there any evidence that human bodies have systemic self-destruction built into their developmental program? I'm not talking about the cell death response, which I know is an important part of growth, development and cancer prevention.
I've read some things about telomere-shortening but don't know if this is a cause or an effect.

From a certain point of view you could argue that our bodies have an inherently limited lifespan;

Telomeres are extensions to the end of chromosomes that prevent damage or loss of genetic information during cell division. Telomeres are not replaced (in normal cells), which gives rise to a replicative lifespan; the number of times a cell can divide before permenantly leaving the cell cycle (senescence).

This is generally viewed as an anti-cancer mechanism to protect against errors creeping in to the genome through many cell divisions. In order to become cancerous, a cell must first overcome its replicative lifespan [ref.]. This is achieved by activating the (normally inactive) telomerase enzyme that extends the telomeres - embryonic stem cells are one of the few cell types that normally express this enzyme.

There are other ways in which you could argue that our lifespans are fundamentally limited, but it is important to note that the objective is not 'to die', but to increase fitness (in a Darwinian sense) earlier in life. This is known as antagonistic pleiotropy; when an advantageous trait early in life is disadvantageous later in life.
Telomere shortening is just one example of antagonistic pleiotropy (protects against cancer when younger, but limits the number of times your cells can divide).
Other traits that inherently limit lifespan include;

Neurons (as a rule) do not replicate, and last for your whole life time. This certainly excludes them from replicate senescence, however it means they are highly susceptible to 'wear and tear'; oxidative stress is a natural by-product of respiration, and the vast majority of damage done by these species (e.g. reactive oxygen species) is repaired by the cell, however some will always remain unchecked, and eventually this leads to neurological dysfunction and cognitive decline. Without intervention this is inevitable in each individual (the rate of aging differs between people, but aging and age-dependent diseases are disorders are a natural part of living).
The same is true for cardiac and smooth muscle - whilst much repair can be carried out, it is inevitable that damage will creep in over a life time, and thus the vast majority of human age-related deaths are due to cardiac problems in one way or another.

So there is no 'programmed' limit to life span, in that we have not evolved to die, but our bodies are inherently limited by the systems that have evolved. Life expectancy a few thousand years ago was ~20 years (if you lived beyond infancy!), whereas now in the developed world this is ~80 years, so our bodies can already survive way beyond our 'natural' life span, and thus we now succumb to age-related disease. Evolution has spent millions of years giving us every possible advantage that leads to reproductive success. Natural selection of traits beyond reproduction are secondary to those beforehand, and thus we have fundamentally limited life spans.

There is an argument for an evolutionary advantage of limited lifespan. This seems at first counter-intuitive, until you consider that natural selection does not act on individuals, but genes. It is proposed to be advantageous (in some circumstances) for an organism to have a shorter life span, as this increases the turn-over of individuals in that population. This in turn increases their evolvability - clearly advantageous for the gene(s) influencing this trait if it increases the likelihood of successful reproduction and thus passing on that gene/allele/trait...
I like this hypothesis, and can see that natural selection may favour it. I think mice are great examples here; they have much shorter lifespans than us, yet they 'age' (biologically) the same (cardiac problems, diabetes, cancer) but at a faster rate to give a higher population turnover). In a high mortality environment, the most adaptable animals will be more successful.
However, I think this is likely to be secondary to the pressures on other survival traits that  more directly increase the chances of successful reproduction.

Great answer, this makes several things clear which I didn't fully grasp before. However, what evidence is there for 'population-level' natural selection (the last section of your answer)? It sounds like the sort of 'group selection' explanation which has been disproved by the modern gene-centred understanding of evolution.

@RichardSmith I'll try to find where I read that last section, but I don't see how group selection can been disproven in that manner. Evolution acts on the genes, not on individuals. If it is advantageous for a group of genes (e.g. the genome of a species) to have a high turnover, giving greater evolvability (i.e. more chance of survival in changing conditions) then it will come at the 'cost' (shorter life) to the individual.

That's exactly what I meant, natural selection is acting on the gene, not the population. It only matters whether any given mutation affecting evolvability leads to more copies of the gene containing it. There is no such thing as group selection, it's a relic of the Modern Synthesis of the 50s and 60s. I think perhaps you were unintentionally using group selection language but you were describing an effect of gene selection. The population doesn't care about the turn-over of its members - it's just an arbitrary group.

So, if something is only advantageous at the population level, it won't be selected for, which is why this sentence doesn't make sense: "This in turns increases their evolvability - clearly advantageous at the population, not individual, level."

@RichardSmith right OK, I see where you're coming from, but not how to re-word what I am saying; that a trait that increases the relative (strictly Darwinian) 'fitness' of a species can be selected for at the 'cost' of a shorter life to an individual organism. This may be disadvantageous in some terms, because they will have less time to reproduce, however higher population turnover will be advantageous in fast-changing conditions.

All you need to do is remove the idea of fitness of a species (or population, or any group) - there is no such thing. Short lifespan would evolve where the risk of death is so high that the best reproductive strategy for the genes of an organism is to make their host reproduce furiously as early as possible in its life. For any given risk of death by accident, disease, etc., there is a corresponding best strategy for investing resources in reproduction, even if doing so puts an upper limit on the lifespan of the organism.

That's because the upper limit is not under selection, because the organism will most likely die anyway before it is reached. So the selection pressure is to ensure the available resources are most efficiently invested in reproduction before the average age of death by accident.

Also I realised I didn't help reword your last idea... In a highly fluctuating environment, there is a high risk that the offspring of any individual will be poorly suited to the environment. Therefore a selection pressure would develop for either individuals with a short generation time (who invested heavily in early reproduction), or individuals with higher rates of mutation. Which one prevailed would depend on the constraints of the organism. In general, K-selected spp. would experience the first pressure, and r-selected spp. the second.

@RichardSmith thanks, that definitely helped. I've changed my answer accordingly - if you feel it is still mis-leading/wrong, don't hesitate to tell me (goes with any of my answers naturally).

I'm not very knowledgeable about evolutionary biology, so I'm going to answer this from the perspective of molecular/cell biology.
The short answer is: No, there isn't any evidence that I know of for a built-in "death".
The long answer:

Telomeres are shortened over repeated copying of chromosomes (so as cells divide repeatedly, the telomeres shorten). Shorter telomeres make chromosomes more unstable, and can lead to some of the symptoms of aging (like limiting organ regeneration). But this is more a side effect of humans not having the most efficient telomerase ever.

In the end, while shortened telomeres contribute to limiting the number of times a cell can replicate (Hayflick limit), we also have stem cells that can then replace those senescent cells. (This is also true in the brain and heart: stem cells are present in the heart and even in highly restricted areas of the brain, and produce neurons throughout life: https://pubmed.ncbi.nlm.nih.gov/10834848/.) So the telomere problem alone doesn't predetermine death.

Other factors that contribute to aging can be divided into two categories, genetic factors and accumulation of damage.

But in both of those groups, the cause isn't that genetically we're programmed to die at a certain time. It is always a case of the systems used to repair or regenerate failing after a time: DNA mutation repair becoming incapable of keeping up with the rate of mutations; failure of clonal deletion leading to autoimmunity; inhibition of autophagy by mTOR leading to accumlation of old and damaged cell parts; failure of senescent cells to undergo apoptosis.
There are many other hallmarks of aging, but the common thread we see is not that there is a set program leading to an organism's death, but rather a failure (through accumulation of damage) of the systems that keep us alive.

In Richard Dawkin's book "The Selfish Gene" it seems that there is a programmed purposeful death of the body. The genes are in control.  They seek out a mate to produce offspring that will be even better suited to pass it's genes on again.  The meaning of life as we have seen and observed it is really for the genes to perpetuate their existance into the future.  Once passed on the body that did the passing is of little use.  The more complex the organism like a human mates may be selected by life span of parents and relatives.  There doesn't seen to be any Newtonian law that states a cell cannot just keep replicating and essentially avoid aging.  Our bodies are doing that for a purpose.  One we just don't understand.

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Can I image Coomassie and GFP in gels at the same time with a fluorescence scanner?
I'm working with a GFP-tagged protein and am routinely using a fluorescence imager (GE Typhoon) and a standard optical scanner to capture fluorescent and absorption images, respectively, of my SDS-PAGE gels.  The Typhoon supports multiple channels, so is there some way that I can scan for the two on the same device (GFP + total protein)?  I assume I can't do absorption on a fluorescence scanner..
I could manually register the two images, but it would be laborious as they are at different resolutions, slightly different rotations, and the gel can stretch ever-so-slightly when placing it on the platens.

Can you explain how you get actual fluorescence images from your gels in which GFP is denatured?

@leonardo the standard running/gel/loading buffers do not seem to be so aggressive as to destroy (all) the GFP; it may be denatured in the loading dye, but when washed out into the gel buffer it seems to recover.  On the other hand, putting the gel into destain or fixing solution is very effective at obliterating the fluorescence.

Coomassie blue fluoresces in infrared when bound to protein, so if your reader has the appropriate filter set, it should be possible.


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Which bacteria have the highest mutation rate?
From my reading on M. tuberculosis, I know that this organism has a pretty high mutation rate due to uncorrected sloppy replication, which leads to a high rate of development of spontaneous resistance to treatment.
Are there species that can beat M. tuberculosis in this degree of mutation, due to polymerase sloppiness or other mechanism?

Do you have a reference for the "sloppiness" under normal conditions, or are you talking about in the presence of antibiotics like Moxifloxacin?

Indeed, the above was from memory. After a second look it appears that it's mainly a sloppiness during DNA repair following UV and especially oxidative stress. (PMID 12705867 and 21516081)

the other way of having a high mutation rate is to be around a lot of ionizing radiation like D radiodurans... it is true that organisms 'throttle' their mutation rate by changing up their dna repair systems. Darwin's gas pedal...  Given that fewer than 0.1% of the bacteria are known that exist (0.001%? the jury is still out), its possible some amazing discoveries will turn up later too.

You seem to be assuming that mutation rates are somehow constant over evolutionary time. They are not. Mutation rates will change according to the stresses a species is subjected to. If you take a bacterial population and place it in a stressful environment (high/low temperatures, oxidative stress, lack of nourishment or whatever) you are likely to see an increase in the mutation rate.
That said, this review and references therein might interest you:
E. Denamur and I. Matic,Evolution of mutation rates in bacteria,Molecular Microbiology 60(4), pages 820–827, May 2006

From my reading on M. tuberculosis, I know that this organism has a pretty high mutation rate

Huh, that's news to me. In fact, Mtb has a rather low mutation rate and rather low genetic variance. See the paper by Sherman & Gagneux in Nature genetics. The paper does state that mutation rate in latent infection is higher than expected or previously assumed, but that's a different story.
That said, mutation rate depends strongly on the genomic context. You can have mutator strains in E. coli or other bacteria that exceed the mutation rates of other strains by orders of magnitude.
A clinical example of a bacterium with mutator strains that help in acquiring resistance is Pseudomonas aeruginosa. More on that in the paper by Ferroni et al..


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What are possible health risks to women having large numbers of children?
What is the possible health issue the women would face in this record?

The record for most children born to a single couple belongs to the
  first wife of Feodor Vassilyev of Russia. In 27 pregnancies between
  1725 and 1765 she gave birth to 16 pairs of twins, 7 sets of triplets,
  and 4 sets of quadruplets for a grand total of 69 children.

Just as a hint so you can go look yourself, the medical term for having more than 6 children is "grand multiparity", or a "grand multiparous" woman, or a "grand multipara".

A common problem for any woman who has experienced pregnancy and childbirth is damage to the levator ani muscle, which comprises a portion of the "pelvic floor."

 from here
This can cause a number of symptoms, including urinary incontinence (due to an increase in pressure on the bladder from less effective muscular support), and possible prolapse of the bladder, uterus, or rectum into the vagina, again due to the weakening of the pelvic floor.

One health risk from going through multiple pregnancies is the risk of a uterine prolapse, also called a prolapsed uterus. The weakening of ligaments basically leads to the cervix and uterus "sagging". In the most severe cases, the uterus ends up in the vagina.

Parity and obesity were strongly associated with increased risk for uterine prolapse, cystocele, and rectocele.

Pelvic organ prolapse in the women's health initiative: Gravity and gravidity
Parity in this context is the number of pregnancies that led to a viable gestational age (pregnancies excluding miscarriages)
Uterine prolapse makes subsequent pregnancies high-risk and can lead to fetal and maternal problems.
The general risk of anything happening increases due to going through multiple pregnancies in a short time span, though. Without sufficient recovery between pregnancies, women are at a higher risk of placental abruptions and placenta previa. For the baby, this leads to a higher risk of premature birth with the associated issues of low birth weight and small size.


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Do cockroaches have less health issues than humans?
Cockroaches are known to live in very dirty places like sewers. Does this cause them to evolve to be stronger against parasites and bacteria? Recently I read online that cockroaches can sustain radioactive harm 6-15 more than humans, so does that mean that cockroaches are less likely to get cancer?
refernece for the radioactive exposure:
http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience

It would be nice if you could add where you read that about radioactive harm.

@Armatus - Is that good enough?

According to Wikipedia, the most common types of cockroaches live between 6 months to two years.  Humans, on the other hand, live about 70 years.  Humans simply have a much longer time to develop cancer than cockroaches do.

@AndrewSalmon - But compare with short-lived cockroach and short-lived human, the human brain stroke rate seems to be higher since never heard of cockroach brain-stroke

Two ways that you can improve your question: 1) "Dirty" doesn't necessarily imply "filled with parasites and bacteria", or imply an increase in radioactivity. What is it that you're really asking for here? 2) Cockroaches and humans have very different physiologies (cockroach cells divide much less quickly that human cells), cell types and of course, size (amount of cells) is definitely an issue. A comparison of generic cancer rates between both would be meaningless.

Note that humans in general get more cancer than other "wild" organisms since they live  much longer then what they would live in the wild. I am guessing this is also why pets have a relatively high rate of cancer.

I have heard that cockroaches are usually infested with parasites.

AndroidPenguin, where did you read that our immune systems are far better than those of 'a cockroach'? This seems pretty strange to me, but I'd be interested in reading a study that compared human and cockroach immune systems if you can provide a reference.
Victor, with respect to cockroaches, there are numerous species of cockroaches. Here's a page about cockroaches with a link to publications on cockroaches and a phylogenetic tree of the families and subfamilies.
http://www.bio.umass.edu/biology/kunkel/cockroach.html
All those species tend to occupy distinct niches with distinct traits. With respect to cockroach evolution, sewers are too new a phenomenon to have had an influence on cockroaches. Rather cockroaches have been successful in adapting to this novel 'habitat'. The same holds for rats and other denizens of sewers. Sewers are a very nutrient rich environment, and as in many nutrient rich environments, a few species tend to possess the right traits (whatever those may be) to survive and out-compete other species. To take an example from coral reefs, when coral reefs suffer from eutrophication, this leads to a growth in phytoplankton and a reduction of the euphotic zone that can lead to the death of all but the most resistant corals. Likewise in the terrestrial environment, only the most tolerant or opportunistic species tend to survive in highly perturbed and nutrient rich environments like sewers. With respect to cockroaches getting cancer, I've never read anything about insect cancer, but I imagine in theory that they could get cancer. I'm not sure, however, of the impact given the much shorter life spans of insects. It's an interesting question though.

Our immune systems are more advanced. Whether that means ours is better is disputable, but specifically older organisms don't have an as well-established adaptive immune system. However of all the insects, cockroaches have one of the most robust adaptive immune systems. They produce primitive antibodies like IgM-like Ig but other immunoglobulins are much more specific to humans and allow us to fight a large range of pathogens more efficiently. Furthermore you can add advances in some of the novel immune cells we possess.

I'm not sure you can call a given cockroach species an 'older' organism. I would need to see a phylogenetic tree of cockroaches, but there may be species, which are younger, that is, evolved later than humans. I don't know enough at present about the immune systems of cockroaches to compare them to those of humans, but you raise some interesting points that I'd like to look into. Any suggestions on relevant publications?

Different pathogens affect different organisms. We live longer because we have an advanced immune system far better than that of a cockroach and because of a hundred other reasons. A cockroach that were to keep itself well fed and clean would live longer, but they can't manage that as well as they could if they had a brain as powerful as ours. Furthermore they're evolutionary suited to live in the environment they do with less consequences than we would. But look at the opposite. A cockroach and a human are in identical locked rooms with a key on the floor. The rooms have no food or water. WHo dies first? The cockroach, because the human simply walks out. For those that will be brutal, the cockroach cannot get out unless it unlocks the door because it's a cockroach escape-proof room :P
Now for your cancer question. Cancer was much rarer in the human population hundreds of years ago than it is now. That's because it's a disease you get due to damage by radiation and other mutagens over time. Cockroaches don't live long enough. But radiation isn't the only mutagen, we could feed them something if we really wanted to give them cancer. As long as cells are dividing, cells can get cancer.


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Why would deer continue to cross a river full of crocodiles even though some of them have been killed?
I recently watched a clip on Discovery Channel, where I saw deer crossing a river full of crocodiles, ignoring the fact that some of them would have been killed doing so.
Is there a possible evolutionary reason for this behaviour?

What's with the down-votes? At least give a reason!

I agree, this is a perfectly reasonable question. If you're going to downvote, have the courtesy to leave a comment explaining why.

Have not downvoted nor upvoted the question, but I surely would say that the formulation is quite "rough" as it stands. It could, however, be a good question if better rephrased.

The question would be better if you replace "deer" with "antelopes" or "bovid" such as the hordes of wildebeest crossing the Mara river each year, feeding a lot of crocodiles.

The reason for their behavior is that exactly the fact that even though some of them do indeed get killed, most of them survive -- what you have said.  The deer cross the river because that allows for the better continuation of the species rather than if they had stayed on the original side of the river. You could think of it this way: If there was a crowd of 5000 people crossing a field of grass and aliens were abducting them one by one, the actual chances of them abducting you are rather little.

The deer do not live for the continuation of the species, but otherwise this answer is correct. The genes which control the urge to cross the river proliferate despite a small amount of predation by crocodiles. Presumably this is because there is a great reproductive or food payoff of crossing the river to better breedinbg/feeding grounds.

@Richard Yes, I agree I could've worded that better.

@Chase Yuan: feel free to edit your question to improve it so to include Richard's suggestions!


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Do cockroaches lay eggs in human flesh when they "bite"?
Recently, I discovered a "bite" by a cockroach, and not only is the "bitten" area red and swallowing, and more specifically, it have a big hole in that area, but when I clean it with hydrogen peroxide solution, something is happening, that is, a yellowish/greenish thing comes out from the holes from each infecting area.
Do cockroaches lay eggs in human flesh when they "bite", and much more importantly, would hydroxide solution kill the eggs and parasites inside those of those holes?

I assume you mean peroxide solution (hydrogen peroxide); not hydroxide (e.g. sodium hydroxide, a strong base).

@NickT - Wow, how do you know?

Because hydroxide solutions are not usually for-sale unless you're looking in the plumbing aisle.

Whilst asking if cockroaches embed eggs in their bites is fine, I'm a little concerned that asking if hydrogen peroxide that I'm putting into the cockroach bite that I sustained is really on the edge of asking for medical advice, which is off topic.

No, cockroaches do not lay eggs into human flesh. You most likely received an infection of some sort from the bug, or it wasn't a cockroach.

the yellow/green liquid is probably pus


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Does artificial high intensity light damage permanently dark ecosystems?
Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor.
E.g. Caves, Undersea
For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1" spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?

Yes, it's possible to damage dark-adapted ecosystems this way, and there are at least a few examples of it happening:

Deep sea Norwegian Lobsters were blinded by being brought to the surface as bycatch by fishermen (or by scientists tagging them). The original paper is Loew 1976, a more recent paper (Chapman et al. 2000) suggests that even a <1 minute light exposure could cause significant harm, which suggests a camera flash could certainly have an effect.
There is evidence that shrimp that live by deep-sea hydrothermal vents have been blinded by the floodlights of exploratory vehicles (Herring et al. 1999).

Chapman, CJ et al. (2000). Survival and growth of the Norway lobster Nephrops norvegicus in relation to light-induced eye damage. Marine Biology 136:233-241 doi:10.1007/s002270050681
Herring, PJ et al. (1999). Are vent shrimps blinded by science? Nature 398:116 doi:10.1038/18142
Loew, ER (1976). Light, and Photoreceptor Degeneration in the Norway Lobster, Nephrops norvegicus (L.) Proceedings of the Royal Society of London. Series B, Biological Sciences 193:31-44

(turned comments by me and @KennyPeanuts into an answer)

Is it known if the blinding is permanent?

Interestingly enough, Chapman et al. 2000 say that for the lobsters, the blinding is permanent, but doesn't seem to be related to growth/survival!

I don't know how harmful the exposure to a camera flash could be to organisms that live in complete darkness. However, since the animals that live in this conditions are usually blind, and the time of exposure is quite short, it's reasonable to assume that the damage produced should be minimal.
In the case of caves, permanent artificial illumination is very destructive to the environment, but the effect is due mainly to temperature changes and the introduction of organisms coming from more illuminated parts of the cave (cave organisms are usually slow and react poorly to light, so they are an easy prey if they're under light). In fact, for tourist activity, the use of lanterns or miner helmets is highly recommended.
In the case of abyssal ecosystems, ecological invasions are less likely, since there still exist a vertical barrier based in temperature, oxygen and carbon dioxide concentration and pressure. However, in this ecosystems there exist many animals which are very sensitive to light, due to the prominence of bioluminescence. Some of this animals could be damaged by the kind of light you describe. However, it's very unlikely that the main functioning of this ecosystems could be affected because of its extensive size. Moreover, the low population densities it has implies that even very long submersions would encounter only a few samples (with the exception of volcanic vents and some other geological curiosities which, in fact, are even more isolated from the rest of the biosphere by physical and chemical barriers), so the global effect should be negligible.


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What is the "lifecycle" of an average eschar and what types of cells are involved in each stage?
(after some deliberation in the comments, I've decided to make the question more general)
An eschar or "dry scab" often forms at a site of injury over a large cut or sore.
It seems as though the healing scab portion binds more strongly to the other scab cells than to those of the surrounding healthy tissue initially, as evidenced by the ability to remove the scab en masse without disturbing the edges of the actual wound (in surgical debridement or when the area is "picked" at).  Then, the eschar bonds then bonds more strongly with the edges of the wounds (so it's more difficult to remove), and then finally, the underlying newly formed skin seems to push it off completely.
Does this accurately describe the "lifecycle" of a common dry scab, or are there other well defined stages in the process?  What types of cells (platelets in the beginning?  epithelials at the end?) are involved with each stage of the process?

What makes you think that it starts binding more strongly?

I thought that scabs were essentially just a protective layer of dried-out and tightly bound platelets (etc) that eventually came-away when the tissue underneath had properly formed/healed, rather than forming the new tissue themselves. Not my field though!

@KonradRudolph Empirical evidence, no, I'm kidding, but just that there seems to come a point between when the healing begins and when it "comes away" (as LukeTheDuke put it) that it adheres to the wound edges more strongly than to itself, otherwise it would just fall off right away.

@LukeTheDuke Yes, not mine either, so I'm struggling with digging out the terminology a bit.

Terminology aside, I don't think there is a distinct point where the scab starts to bind to the wound - this is likely to be an inherent process started when with the initial clotting of the blood. As the clot thickens and binds, the scab will become harder to remove. As the skin underneath heals, the scab is gradually 'excised'(?!). This is purely speculation!

@KonradRudolph Rather than ask an open-ended question about the entire process, I thought that this got more to the heart of my question.  However, if you (or @Luke) have a more general answer, I would certainly take it.

@LukeTheDuke Sounds reasonable, but if you can dig up a source, you should definitely take a shot at answering it.

@jonsca Ah, I misunderstood you, I though you meant that it formed the new tissue, rather than falling off.

@Luke I've made the question a bit more general now

@KonradRudolph I've made the question a bit more general now

Response to cutaneous tissue damage occurs is several distinct but overlapping phases. First an scab is formed as the blood is 'allowed' to clot. A matrix is formed as the platelets adhere to one another, which contracts and 'dries' (forces out the serum) to form a scab. This process clearly happens prior to tissue regeneration/formation to reduce further blood loss.
Fibrinogen
In response to damage to blood vessels a signaling cascade is initated that results in the massive production of fibrin, which is deposited at the site of wounding and subsequently forms blood clots by activating platelets and stabilising the matrix by cross-linking (see PDB's protein of the month 2006).
So this is why clots do not appear to be attached to the surrounding tissue; the fibrin causes the blood to form a matrix that is very tightly bound to itself. Only after clot formation does the tissue remodeling occur, and it is during this stage that the scab will 'bind' more stongly to the surrounding tissue.
The Cell Types and Processes of Wound Healing
This figure (from (Li, 2007)) shows the various stages that occur and cells that are involved in acute wound healing  (wounds such as burns and cuts that heal "in a timely fashion");

Wow, that was perfect. Another great answer.

First, eschar ("es-CAR") is NOT a scab.  They are entirely different, both physically and biochemically.  A scab is made up mostly of blood products and fibrin, and sits on top of the wound or skin.  Eschar is the skin itself (or other tissue), which has died and as a result turns black (or brown).
Scabs will detach from the underlying skin fairly easily, and fairly quickly as the skin heals under it.  Skin eschar heals from the edges inward, and usually takes months to heal, as opposed to weeks for scabs.  It is very hard, leathery, and acts as a natural bandage.  It used to be the "norm" to remove it, with the idea that the skin would grow back faster if it was not "in the way"; however, today that is less common, unless there is an infection at the site that must be treated.  It is considered a "normal" part of the healing process.  (summary of a large number of articles I looked up trying to get answers for myself; facelift patient who had two very rare "hematomas", and as a result developed bilateral necrosis.)

Welcome. Can you add sources to your answer to allow others to background read on your answer?


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Can two protein secondary structures "overlap" in the PDB?
I have a technical question regarding the syntax in Protein Data Bank files.  In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
HELIX    4   4 MET A 255  ILE A  265  1                                  11

SHEET    2   B 2 ILE A 253  MET A 255 -1  N  ILE A 253   O  ILE A 248

Now, as I understand the documentation, this means there is an alpha helix starting from residue "MET A 255" to the residue "ILE A  265".  There is also a beta strand from "ILE A 253" to "MET A 255".  We see that the alpha helix and beta strand share the residue "MET A 255".
The documentation describes these as:

"Name of the initial residue."
"Name of the terminal residue of the helix."

The wording suggests that the "initial" residue is included, but I'm unsure of whether or not the "terminal" residue would be included.

Question:  Should I consider this residue as belonging to both the alpha helix and beta strand?  Or should I consider the "terminal" residue as not belonging to the secondary structure element?  (Or something else?)

ive seen records like this although it does not seem possible as alpha and beta have distinct ramachandran coordinates.  i'll try to look at the structure and post an answer/opinion. a quick way around this is to find the phi/psi values for the amino acids in question and make the call yourself.

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment.

Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful for other proteins.
Default pymol assignment
In PyMol I used fetch 1ae9 and highlighted M at position 255 on the A chain in red. I can see why this isn't a satisfying representation: the beta sheet allocation is very short, and the residue in question is clearly the beginning of a helix.

DSS is more conservative
To run a more conservative secondary structure allocation run dss in pymol (watered down dssp). This reveals that the beta sheets were actually quite putative.

We can see why when we look at the stick model (below). There are only a few (2-4) residue pairs in proximity that would be available for hydrogen bonding, even assuming all 4 form H-bonds, calling this a bona fide beta sheet could be seen as a bit generous.

Dual assignment can be okay.
Looking at this example (1ae9), we see the potential for H-bonding with another putative beta sheet, as well as a backbone angle that starts to form a helix. It's a classic case of ambiguous dual assignment. @AlexanderDScouras draws a reasonable conclusion that both is okay and to directly answer the question: dual assignment is possible, and allowed. I would prefer to rule out beta sheets in this particular case, but on the condition that one highlights that there is plenty of hydrogen bonding in the hairpin loop.
So long as it's reasonable.
So long as you can reasonably justify the assignment it's probably okay. You can manually assign any residue and secondary structure.
# set residue 155 to be alpha-helical
alter 155/, ss='H'

# update the scene in PyMOL to reflect the changes.
rebuild

Evidence is always a good idea to support manual assignments. A quick and thorough way would be to run the sequence through a few secondary structure predictors, or use the genesilico metaserver to save yourself some hassle (you'll need an account) (this does feel like going back a step since you now have a structure, so exercise caution - if the sequence prediction doesn't look correct according to the structure, it's probably not). Another method as suggested by shigeta is running this through a Ramachandran plot (RAMPAGE is a favourite).

If it's very very unclear then discuss it thoroughly and clearly whenever this part of the protein is relevant. These secondary structure assignments have somewhat arbitrary cut-offs after-all, and when things get near the thresholds, it's important to approach the situation with clarity and specificity.

Ramachandran plot image source: By Dcrjsr - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=9105708

A most informative answer! But I'm still surprised PDB allows such overlapping secondary structure markup. Perhaps their attitude is that all that is really important are the coordinates — it's up to the individual how they choose to visualize it.

@David Precisely. The terms α and β are there to help us quickly talk about broad biochemically similar parts of proteins. When the biochemistry get's stretched to the limits of the definition, the biochemical similarities become more vague and perhaps it's time to talk about the specific biochemistry in that protein again. There will be times when this residue example acts more like a helix, and other time when it is more like a sheet.

This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined.  shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP algorithm, i.e. what is their main-chain hydrogen bonding pattern.
The DSSP algorithm is a bit conservative about assignments, often leaving out the first and last residues in  both sheets and helices. In deposited structures, you can compare author annotations to DSSP and STRIDE and see the authors will often assign longer runs than either. And I have certainly seen structures where a residue is annotated as both, especially when it lies at the junction between two secondary structure elements.
Looking at the structure, residues 254 and 255 are clearly hydrogen bonding into a beta-sheet on one side and an alpha helix on the other, so I see no reason they shouldn't be annotated into both.


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Negative feedback in the fructose metabolism in liver
What happens in liver when large amount of fructose is consumed?
I vaguely remember my biochemistry lecturer telling us that the enzymes that process fructose in the liver does not have negative feedback to control the rate of reaction. But I cannot find a reliable source. How is it regulated if it is?

The main reaction of fructose in liver is phosphorylation, catalyzed by ketohexokinase (UniProt P50053). In one paper with rats it was shown that fructose load can deplete the liver of nucleotide triphosphates (ATP, GTP) although ADP and GDP are inhibitors of the enzyme. This shows there is no effective regulation.
M. I. Phillips, D. R. Davies: The mechanism of guanosine triphosphate depletion in the liver after a fructose load. The role of fructokinase. In: The Biochemical journal. Vol 228, Nr 3, Jun 1985, p. 667–671, {{ISSN|0264-6021}}. PMID 2992452. PMC 1145036.

great answer. thanks. It sounds like an important result, but the paper has only been cited 8 times according to google scholar. I wonder why.

I think it's because most of the work was done with cow's enzyme. Human's enzyme was characterized but no inhibition studies are available for that.


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Is there an "evolutionary species similarity calculator"?
Is there a website where I can input pairs of species and get an "evolutionary similarity score"?
E.g. (numbers are completely made up)

Input: Chimp and Human, Output: 97%
Input: Cat and Human, Output: 85%
Input: Is Cat closer to Human or Chimp, or Snake, Output: Cat is closer to Chimp (87%), second is Human (85%) and Snake is last with 50%.

I have no idea what the actual scale should be, but I imagine there is at least one interesting scale, perhaps several.
Cross posted to Quora

Since the simple value of percentage of nucleic acid identity over whole genomes isn't very useful in taxonomy, you won't find these values published in a database, even if they were computed by someone in the process of other work.
One project that provides ready-for-consumption phylogenetic trees based on similarity metrics, by using orthologous genes between species, is OMA. They compute all orthologous genes between two species, and they are now at 1,235 species:
http://www.biorecipes.com/Orthologues/status.html
You could then read off the "distance" between cat and mouse from the eukaryotes tree. This value would then be more meaningful than the nucleic acid identity percentage.
Apart from the trees, using their OMAbrowser you can get for any species pair the number of common orthology groups, i.e., the number of common genes between those two species.

TimeTree gives you an estimate for time of divergence, which is also nice to know. But of course different species have different rates of evolution.


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Does a mydriatic drug neutralize the action of a miotic?
If a person were administered a mydriatic, would the subsequent application of a miotic neutralize the action of the former? If the sequence were reversed would a mydriatic neutralize the effect of a miotic?

The iris has 2 sets of muscles:

The circular muscle (Sphincter iris) - This causes iris constriction and is supplied by the parasympathetic system - Acetyl Choline muscarinic receptors
The radial dilator muscle - This causes dilation of the iris and is supplied by the sympathetic system - The Adrenergic receptors (Alpha 1)

Theoretically speaking, there can be four sets of drugs:

Alpha 1 adrenergic stimulators - will cause midriasis
Alpha 1 adrenergic blockers/antagonists - will cause miosis
Muscarinic blockers - will cause midriasis
Muscarinic agonists/stimulators - will cause miosis

In practice,

Midriatics:

Alpha 1 agonists: Phenylephrine
Muscarinic antagonists: Atropine, Homatropine, cyclopentolate, tropicamide

Miotics (mainly used for Glaucoma):

Muscarinic agonists: Pilocarpine, carbachol, etc...
In practice alpha 1 antagonists are not usually used to effect miosis

There are two ways to achieve either midriasis:

Stimulate the Adrenergic receptors
Inhibit the Muscarinic receptors

Similarly miosis can also be achieved vice-versa.
The answer to your question is yes, when given the proper counter-acting agent, depending on the concentration of the agents and the mechanism of actions opposite effects are achieved. This is primarily because the drugs act on different sets of muscles. If a adrenergic stimulator - phenylephrine is instilled with a muscarinic stimulator - cyclopentolate, both sets of muscles will be acted upon and based on the concentration of the drugs, the decay rate and the efficacy, the iris diameter will either increase or decrease to variable degree. The point is that both the drugs will affect the final diameter of the iris (which is based on the autonomic state of the patient and the strength of drugs administered)
Now the special cases will be to administer a inhibitor of a receptor followed by an stimulator of the same receptor or vice-versa - In this scenario, the duration of action and the affinity of the given drugs to the receptor in question will play a decided role in determining the final action as both drugs act on the same muscle. If the inhibition is permanent or long-acting then inhibition of the muscle action is predominant. This may change if the stimulator has a very high affinity to the receptor - Higher affinity will result in tighter binding of stimulator and remove the chance for the inhibitor to work - i.e. increase the probability of the clearance of inhibitor. As you can see from above statement, if the clearance rate of inhibitor is slow (takes too long to metabolize), then the effect will ultimately be inhibitory effect. Similarly in case of poisonings where the stimulating effect is permanently achieved (Organo Phosphorous poisoning will cause permanent damage to acetylcholinestrase the enzyme responsible to remove acetyl choline) the reversal will depend on the affinity of the inhibitors (in this case, of acetyl choline) to the receptors (muscarinic).
Thus the question must be more specific to get a proper answer, as the effect is totally dependent on the drugs administered.

very comprehensive answer +1

yes, very nice one indeed


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What's in a Name: Statistical Genetics
The novice often performs population calculations using
what is referred to as Mendelian Genetics. Soon after the
publication of Mendel's results; Hardy and Weinberg presented
their results after the interjection of a collection of axioms.
Is there a difference between Medelian genetics and the
Hardy-Weinberg model?

“after the injection of a collection of axioms” – not really, that’s the whole point. Their formula derives directly from Mendelian genetics, but biologists at the time had no formal training in mathematics and therefore had difficulties doing the calculations.

Mendel published his results 1866 but they were rediscovered only in 1900. The Hardy-Weinberg model is an application of Mendel's rules to a population that is not under selection forces. So the one builds on the other, and Hardy-Weinberg is a simplification model-wise, and Mendel's rules are not detailed enough either. It's the same relation as with a physical law like gravitation and a mathematical model of its consequences applied on many entities, like models of a solar system's gravitational behaviour.


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JMol "calculate HBONDS": which atom is the donor/acceptor?
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS".  By outputting the state of the network, we can obtain a lisdt of H-bonds.
Here's one line from an example output (PDB ID number 1a1x):
74    540    4096    0.001    -2.507   hbond;

I believe the correct interpretation of the first two numbers is that atom 74 is H-bonded to atom 540.  (I'm not really sure what the other numbers mean.)

Question: How can we determine which atom is the donor and which is the acceptor?

In the above example, atom 74 is a Nitrogen atom and atom 540 is a Carbon atom, so presumably the Nitrogen atom is the donor.  But, how can we tell in general?

I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go to: Favorites > Reply log
An output of the reply log is below:
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ASP 12.A N    GLU 25.A OE2  no hydrogen  3.012  N/A
HIS 13.A N    GLU 25.A OE1  no hydrogen  3.338  N/A
HIS 13.A ND1  ASP 12.A OD2  no hydrogen  2.835  N/A
LEU 14.A N    TRP 70.A O    no hydrogen  2.934  N/A
TRP 15.A N    ARG 23.A O    no hydrogen  2.866  N/A
...
120 hydrogen bonds found

As you can see the donor and acceptor has been identified as defined in the header line.
If you wish, the information can also be written to a file by selecteing Write to text file in the FindHBond window.

I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds.
Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,
jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS")

Step 2: Only display the hbonds
jmolScriptWait("display connected(hbond)")

Step 3: Export the bonding info to JavaScript array
jmolGetPropertyAsArray("bondInfo")

You will have an array of objects each will contain the atoms connected by this hbond and the bond length.


text:
Are rods/cones rejuvenated periodically?
Pretty much what the title states.
Some cells/structures in the human body undergo rejuvenation periodically by flushing away older cells and growth of new ones.
E.g Skin, Blood
Does this (for want of a better word) 'rejuvenation' apply to Rods/Cones within the eye too? If so, how are the old cells flushed out - or do the old cells become part of the local humour?

The answer can be found in the excellent lecture from 1983 The Life History of Retinal Cells which also has gorgeous microscope fotos. The renewal time of rod outer membrane proteins is less than two weeks. Cells stay indefinitely, as I understand, but are periodically rebuilt in a logistical nightmare/wonder.


text:
Intrinsic apoptosis in erythrocytes
With a lack of mitochondria, can red blood cells perform intrinsic apoptosis and do they have another way of generating cytochrome c to attach to a CARD domain and assemble the apoptosome?
Or are they dependent on killer lymphocytes to bind via the fas ligand and activate procaspase 8 or 10 in extrinsic apoptosis? Do red blood cells even have fas ligand receptors for this process?
Or is there an entirely different method for red blood cells?

No expert, but I thought that red blood cells were relatively inert, and were essentially killed/recycled by the immune system after their useful lifespan. How this is determined I don't know, but I am interested to hear the answer to this question.

Red blood cells (RBCs) don't have nuclei in mammals, so they are usually considered to be pretty inert compared to other cells.
They do have some biochemical activity, and evidently there is some mechanism for cell death  in RBCs when they are induced to degrade or infected by pathogens.  I found this reference that shows caspases -8 and -3 are evident in mature RBCs.  Several other components of the cell death pathway are not evident.
At this time the authors speculate that they don't activate to induce cell death.
It seems that over the broad field of disease research 'apoptosis' and 'cell death' are used equivalently even when the well known apoptosis pathway is not involved.

Senescent red blood cells are cleared by macrophages in a process called eryptosis or is better known as erythrocyte programmed cell death or apoptosis. The mechanism is excellently reviewed here. In summary it is mediated by caspases, phospholipase A and prostaglandin E.

Apoptosis occurs by both external stimuli and internal stimuli.As RBC do not have nucleus apoptosis may occur by external stimuli by activation of caspase8

Can you add references/links?