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Does a man contain all the genes needed to make a woman?
This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so forth in the landing. With the artificial "wombs" intact, he populates the planet with clones of himself.
If he wanted to introduce enough variation (without making up new genes, only rearranging) in the population to allow them to be able to reproduce naturally without inbreeding problems, would he be able to? In particular, could he make a woman?
Alternately, could a woman (without a Y chromosome) do the the inverse?
At the risk of introducing bias into the answers, the plot as it stands assumes he is a male and he CAN'T do any of the above and he is restricted to clones.

If they're clones they'd be pretty much identical. He might have better luck making induced pluripotent stem cells and deriving them as gametes, then making embryos. Still have the same genes as he did, but at least the recessive/dominant allele ratios might change and could get some females out of it. Why not get DNA from the dead embryos?

That's a cool idea with the pluripotent cells. Of course exact copies would be clones, the idea is that he could have technology for directly manipulating the genes, he just doesn't know any sequences that are not present in himself. Your point about the eggs can be easily explained away by a fire, but it makes be think of the point that there could be DNA from anyone else who was involved with the building or launching of the ship still aboard

And it wouldn't be hard to keep an electronic database of DNA sequences on a computer.

Another good point.

From a narrow, technical perspective, a man "contains" all the genes to "make" a woman (X-chromosome) while women lack the genes to "make" a man (a Y-chromosome). To actually make use of this is another question (for instance, producing gametes containing X & Y chromosomes), but for a SciFi novel this shouldn't be a problem. Epigenetic effects might also be an issue.

Related: http://biology.stackexchange.com/questions/17410/could-a-sperm-be-altered-to-contain-a-females-genetics/17435#17435

This answer also involves some speculations as the question is about a good theoretical framework for a science fiction.
You can find in this post about how sperm can be used to produce embryonic stem cells. It would still require an oocyte for doing that.
The question now is- Can you produce oocytes from a male?
You may fuse two X bearing haploid spermatids to form a diploid cell with XX. This cell will also have mitochondria and ribosomes — seems like a decent candidate. Gametogenesis has not been shown to happen in-vitro. Moreover a zygote will need a lot more cytoplasmic resources that you can get from a fused spermatid.
Plus there are imprinting issues as already pointed out by Chris.
Conclusion: Next to impossible
For your question "Does a man contain all the genes needed to make a women": yes he has but does not have the biological machinery to do that (exclusive of the womb).
However if you choose to send a female astronaut for this mission then there may be some hope. As Chris said, there are problems with homotypic fusions because of imprinting issues. But with a supply of ova there can be other ways:

Make clones using SCNT: limitation is that there would be very little variability.
Erase imprinting marks and fuse two oocytes: This has not been done yet but this is possible. At this moment we have technology (still incipient for therapy grade), for targeted genome editing. The basic principle involves fusing a DNA-endonuclease with a sequence specific DNA Binding Domain (DBD). Examples include Zinc Finger Nuclease, TALENs and Crispr-Cas. This study demonstrates an engineered system that can deaminate RNA in a sequence specific manner. Based on a similar principle it should be possible to link DNA-(cytosine/adenine)- methyltransferase or DNA-(cytosine/adenine)-demethylase to a sequence specific DBD 1. This system can be used for targeted epigenetic modification. This would have a little more variation than cloning because of meiotic recombination. Limitation is that there won't be any males, this would perhaps become an Amazonian Planet.

Make sure that your space-shuttle has a good biolab facility :P

1 Imprinting is generally implemented by DNA methylation which happens mostly on cytosines.

Thanks guys! All your answers have contributed a fascinating and realistic backdrop with which to write!

A woman (assuming no mosaicism) has two X chromosomes in the nuclei of her cells (except for oocytes). A man, in every cell with a nucleus (except for spermatocytes), has only one, pluripotent or not.
The only way he could make a female would be to either manipulate cells by  duplicating the X chromosome (very difficult to do) or remove/inactivate the Y (giving rise to an XO female). That in itself would introduce problems in the female.
Turner Syndrome XO Syndrome

If he could make pluripotent stem cells he could turn those into egg cells, half of which would carry his X chromosome. If fertilized, half of those would get another copy of the X chromosome and become female. Of course there could also be egg cells with Y chromosomes, which might still function if they get an X chromosome sperm, but a YY embryo probably wouldn't work well.

@user137 - May I ask why you believe pluripotent stem cells are haploid?

@user137 Stem cells are not haploid. Only germ cells are.

The question asks whether a man "...contains all the genes..." to make a woman, while this answer is mostly dealing with chromosomal makeup and the issue of producing haploid gametes. From a strict/narrow gene perspective, I think the answer to this question is yes.

It is possible to make haploid stem cells by injecting a sperm in an enucleated oocyte or artificially activating the oocyte without fertilization. See here

@WYSIWYG - that is wild; I never knew that! I did know there are some nearly-haploid cell cultures, but I did not know the manipulation of genetic material in oocytes was this far along.

@anongoodnurse It was one kickass paper. I was so thrilled while reading it.

@fileunderwater - true enough. I guess the answer would be (for me) even if he could get two gametes with X chromasomes, as a male, how will he introduce the genetic material into a manipulated oocyte? The clone seems maybe better. Some of this is new to me.

@WYSIWYG and anongoodnurse - guys, some interesting gems hidden away in the comments!

@anongoodnurse Here are some more references about making gametes from stem cells Ref 1 ref 2 ref 3

@Chris recently, I saw a paper on haploid pleuripotent stem cells (in Nature, I guess) .

Theoretically this should be possible as men carry both sex chromosomes. You would have to find a way to make haploid cells and then have them form a diploid cell with two X chromosomes. Your population would go through a genetic bottleneck which would soon cause a lot of other genetic problems as there is not enough variety.
But besides this rather theoretical approach, there is a real problem with this kind of reproduction: it won't work because of genetic imprinting. This takes place in the egg and as well in the sperm cell and consists of small modifications added to the DNA. This silences this gene and allows the expression of genes specifically either from the mother's or the father's copy of the chromosome.
An example for this would be the loss of a part of chromosome 15. Depending on which copy is lost, this either causes the Prader-Willi Syndome (inherited from the father) or the Angelman Syndrome (inherited from the mother). This article goes deeper into imprinting.
Due to the missing maternal imprinting, the cells constructed from the father will not be viable since the expression of some genes (which would come from the mother) is missing. Nevertheless it has been shown in mice that it is possible to overcome this problem. The researchers deleted the maternal imprinting on one copy of the chromosomes they used, mimicked the fathers imprinting and where able to breed viable off-springs from two female mice without a father. But this approach is rather technical and also error prone since you have to know the imprinting of the mother. The article can be found here.


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Why do some bacteria have most genes on the leading strand of the genome?
Genes in the (+) strand are black and genes in the (-)strand are red.
The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed regions, as a consequence of (random) evolutionary process. Also, genes don't overlap (it would be highly  unlikely that two complementary strands both carried useful information).
In B. subtilis, on the other hand, there seems to be a preference for one of the strands in each side of the chromosome. What sort of evolutionary pressure could give raise to such a pattern?
I have a guess, but I'm not sure, that this may be related to bacterial transformation.

The pattern we see in B. subtilis is quite common in prokaryotes. The origin of replication is shown at the top of the genome diagram. DNA replication proceeds bidirectionally from this point. In the B. subtilis diagram, most genes are located along the leading strand in each direction. Even in E. coli, by the way, important genes, including all rRNAs, tend to appear on the leading strand.
Why is that? Rapidly growing bacteria are replicating their genomes most or all of the time, so you've got replication and transcription happening at the same time.  If genes are on the lagging strand, RNA transcription proceeds in the opposite direction from DNA replication, and the DNA polymerase will often collide with the RNA polymerase. If the genes are on the leading strand, however, RNA transcription proceeds in the same direction as replication and collisions are minimized. Hence the selective advantage to positioning most genes along the leading strand.
Some genes may also be on the lagging strand in order to target them for mutagenesis (Paul et al. 2013, Million-Weaver et al 2015). This goes back to the concept of transcription-replication collisions where the head-on collisions are worse than co-directional collisions. Head-on genes actually have a higher mutation rate and incidence of convergent mutations which suggests that they are mutated and evolve faster than leading strand genes. This is a controlled process in that it only occurs in lagging strand genes, and only when the gene is transcribed (i.e. when it is needed). It was argued that this is a way bacteria can control and ratchet up or down the rate of evolution in a controlled way. This was argued against by Chen and Zhang based upon computer based modelling. It is an interesting concept that has been hotly debated.
EDIT for additional clarification and references:
This diagram from Chen and Zhang (2013) helps show what is going on:

Caption: "Schematic drawing of a collision between a working DNA polymerase and a working RNA polymerase in bacteria. (a) Codirectional collision when a gene is encoded on the leading strand. (b) Head-on collision when a gene is encoded on the lagging strand. Arrows show the directions of movement." (Chen and Zhang 2013)
A few references

The original idea goes back almost 40 years to Nomura M. and Morgan,E.A. (1977) Genetics of bacterial ribosomes. Annu. Rev. Genet., 11, 297–347.
An early paper about highly transcribed rRNA on the leading strand: Ellwood M. and Nomura,M. (1982) Chromosomal locations of the genes for rRNA in Escherichia coli K-12. J. Bacteriol., 149, 458–468.
A recent overview: Rocha, E. P. (2004). The replication-related organization of bacterial genomes. Microbiology, 150(6), 1609-1627.
Why some genes remain on the lagging strand: Chen, X., & Zhang, J. (2013). Why are genes encoded on the lagging strand of the bacterial genome?. Genome biology and evolution, 5(12), 2436-2439.
Paul, S., Million-Weaver, S., Chattopadhyay, S., Sokurenko, E., and Merrikh, H. (2013). Accelerated gene evolution through replication-transcription conflicts. Nature 495, 512-515.
Million-Weaver, S., Samadpour, A.N., Moreno-Habel, D.A., Nugent, P., Brittnacher, M.J., Weiss, E., Hayden, H.S., Miller, S.I., Liachko, I., and Merrikh, H. (2015b). An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. Proc Natl Acad Sci U S A 112, E1096-1105.

It's an interesting idea; do you have any references for it? Transcription and replication always occur in the same direction (3'->5') relative to a strand.

@canadianer I've added a few references and a diagram -- I hope this clarifies. Yes, both DNA and RNA polymerase move 3' to 5' on the template strand but the 3' to 5' direction of the RNA polymerase can move toward or away from the replication fork, depending on whether you're on the lagging or leading strand.

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How did birds become so intelligent?
I have seen a Discovery Channel video of a bird throwing stones in a pot to raise the water level so it is able to reach and drink it.
A similar experiment in this paper from Current Biology shows the same phenomenon under controlled conditions, and is documented in this video.
This clearly illustrates how intelligent these animals are may well be more intelligent than many mammals. For example, the regular domestic dog will definitely not push stones in a bucket of water to quench his thirst.
How did crows, and perhaps birds in general, became so intelligent, and even more intelligent than many mammalian species?

Birds are animals and, as far as I know, there is no basis for your claim that they are the most intelligent.

@KlaytonThomas - I edited this question as well, but you should try to find an image, a link to a movie fragment or other source illustrating the claims you make on crows increasing water levels

Using a movie scene as an example is not an accurate form of asking a question. However, I have indeed seen documentaries detailing how intelligent crows are. I suggest you youtube it and find a suitable documentary clip.

@TheLastWord - I agree movie clips are not the best thing, but in this case I doubt there are scientific articles that support the claim

some one added "movie fragments" in my question not i, actually i seen this video in discovery channel.

I edited your question as I was expecting it to be put on hold. I voted to re-open as I like the question, but I am afraid it may be too vaguely defined. Give it a thought how to improve it and make it more approachable for folks here.

You should really define what you mean by intelligent... for instance a dog can bring you the newspaper, which a bird can't do.

The basic raise-the-water-level experiment described in this paper has been subsequently repeated and extended with a number of corvid species and also with human children; it is known as the Aesop's Fable Paradigm.

@Corvus Yet another apropos name :P

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History: Building a "Phylogenetic network" of famous evolutionary biologists
Seems like many of the famous evolutionary biologists are somehow related to each others. For example (and I might be mistaken), Ronald A. Fisher was mentored by a descendent of Charles Darwin. Joe Felsenstein did undergraduate research with James Crow and wrote his doctoral thesis under Richard Lewontin. Muller was mentored by Huxley, friend of Darwin. Brian Charlesworth was mentored by John Maynard Smith who was himself mentored by J.B.S Haldane.
Is there anyone who is crazy enough and interested in the history of evolutionary biology enough to draw a network of relationships between most famous evolutionary biologists since Charles Darwin?
An arrow between any two evolutionary biologist might represent a relationship of the kind family, PhD supervision or friendship. Of course there is no limit to the number of famous people to include and there is no good distinction of who should be included. But a network of the 20 (or 50 if you feel courageous) most famous evolutionary biologist would be awesome!

I am not totally sure this question will be accepted on this site but I think it might fall within the history tag. Also, the question has the default to not have a definitive answer and to ask for creating something rather than for pure knowledge.

I bet you could make one using cited/co-authored papers! I'm not sure you could derive specific relationships from that, though. I don't really think this question is really within the scope of this site, though.

This is a really fun question, but probably not within the scope of the site. I'm not where else on the internet would be a good place to ask it, but I sure would like to see it, though!

Thanks for your comment. Following CactusWoman comment: if the post is estimated to be off-topic here. I would love to know where you think I could ask for this question. Do you think they are going to accept such question on history.SE?

Disregarding whether or not it's on topic, I think it's too broad for any SE site.

It also falls under the six degrees theory. There are very few evolutionary biologists in the world, of course they're all related somehow or other. This goes double for the evolutionary biologists of a century ago. There were very few of them so of course, by definition, they mentored each other.

Maybe not exactly what you are searching for, but you should look at the evolutionary biology version of Academic tree. This provides family-tree type relationships between researchers, but mostly (only?) of supervisor-student relationships.
As an example, the tree for Joe Felsenstein includes links to e.g. Dobzhansky, Lewontin and Sewell Wright. You should be able to find much of the information you are looking for at this site.
Here is a small cutout of Joe Felsenstein's tree, just as an example:

Wow this is so cool! Exaclty what I was looking for. As you said almost everything is about supervisor-student relationships but this is really nice. +1

You can add yourself as well - just create a user account.


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Does the metabolic rate determine how fast the telomeres shorten?
In many papers one can read that telomeres may play an important role in longevity. According to Calado et al.1 the telomeres of mice are much longer than the telomeres of humans. However, mice have an average life expectancy of about 2 years and humans about 80 years.
Does the metabolic rate therefore determine how fast the telomeres shorten? Can one say that the higher the metabolic rate, the faster the telomere shorten?

Telomere dynamics in mice and humans

Note, correlation does not imply causation. In other words even if these two values are correlated, that doesn't mean that one determines the other.

The paper is freely available through Pubmed Central, I added the link for you.

@p.s.w.g I'd rather use a phrase suggested by Tufte: Empirically observed covariation is a necessary but not sufficient condition for causality. The usage of implies in this common phrase is a little dangerous, because in one way, correlation does indeed "imply" causation.

@Alex You're right, of course. Correlation does not necessarily imply causation. I was really trying to point out to OP that the title and the body of the question do not ask the same thing.

@p.s.w.g I agree with you, question does indeed to make this distinction. I just try to comment on the usage of this phrase where ever I see it because the word implies have different meanings in its logical and its common usage, and I've seen some signs if confusions in the other direction. Maybe his other suggested phrase is even better: "Correlation is not causation but it sure is a hint.", depending on the situation of course.

Thx for the feedback guys. I ve rewritten the header. Sorry, i am not a native speaker and so may be my expression is not that clear.


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How do researchers map root systems of plants?
For example, here is a picture of the root systems for some prairie grasses:

(Click image for higher-resolution PDF) from: http://www.conservationresearchinstitute.org/educational-offerings.html
How is it possible to follow one root thread 15 feet down? Especially when they are so densely packed in the top foot of soil that you couldn't dig at all without destroying roots.

You originally posted this question on the Garden and Landscaping Section - that's where I'm from, and though it was moved here instead, I'll answer it anyway:
That image you've shown isn't like a photograph, its an impression of what the roots are like. Usual method of working out root patterns on plants is to remove what's known as a monolith, or a block of soil where the plant is - the soil is then either carefully removed by hand, in the manner that archaeologists use, or air blasted, or soaked off in water to reveal as much of the roots as possible. For trees or plants with very large roots, newer methods include geophysical surveying by machine, or electric resistance surveying. Even this doesn't reveal everything - many roots may penetrate too far down, or run along cracks in rocks beneath the soil. The root length and distribution pattern vary according to local conditions, so its hard to be definite about where the roots of any particular plant are in a particular position in the landscape.

Reference and further reading:
Plant Physiological Ecology (ISBN 978-94-009-2221-1; Google books link)
Especially, check the Introduction on page No.367


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Paired-end mapping exercise
Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome.
Then among libraries that had insertion of 500bp, 2kb, 10kb and 40kb which one would you pick to detect the following inversions?
a) an inversion mediated by inverted repeats of 20 kb at its breakpoints
b) an inversion with clean breakpoints (no inverted repeats)
c) an inversion mediated by inverted repeats of 1 kb at its breakpoints

My guesses:
a) 40kb, as if it were to be smaller than the inverted repeats length, the pair ends may align inside and nothing would be detected
b) Medium size, as if it is too small it wouldn't probably cover the area desired, and if it were bigger it would overlap too much (anyway data is needed for and answer is a blind optimization)
c) 2kb. same reasonings as a) and b).


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Inter-codon mutations statistical analysis
I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or CGG... for example).
Is there any articles, databases or others that provide such table?
Please comment if my question is not completely clear.
I searched but didn't find an answer for this question in Google Scholar.

Yes and they are called substitution matrices. You might find some more information in this review.

@cagliari2005 I don't know if you're still active on the site, but this comment is IMO worth converting to an answer.

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How do BCAA's promote faster muscle recovery?
I am aware that ingesting Branched chain amino acids (BCAA's) prior, during, and after workouts has an effect on muscle recovery due to their difficulty of metabolism. However, how much more efficiently do they speed up recovery versus whey proteins for example?

What are BCAAs? Please define acronyms when posting questions (and answers) here.

"Branched chain amino acids" (valine, isoleucine, leucine) is the general understanding.

Branched chain amino acids. @MattDMo


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Given an EC50 value, how do I reproduce the sigmoidal curve from which this was calculated?
All-trans retinoic acid (atRA) is a potent ligand for a nuclear receptor called retinoic acid receptor alpha (RARa). The concentration of atRA at which RARa is half maximal is 19nM. The dose-response curve is sigmoidal, with concentration (log scale) on the x-axis and percentage of maximal activity on the y.
How would I use this information to reproduce the dose-response curve?
Thanks

Depends if the EC50 is given using a constant slope and a max/min that you know. If not then you cannot reconstruct it as you are missing parameters.

Basic sigmoidal curve looks like that: zero at $-\inf$ and one at $+\inf$. All in between should look like an integral of gaussian distribution. Take a look on this wiki page for more information. Now, the question, why sigmoidal curve is integral of gaussian function, I will leave out for now. My understanding is that gaussian distribution tells you how much system response will increase (say, efficiency of treatment) if you increase stimulus by $dx$. E.g., how much response changes when you go from $5$ to $5+dx$ versus from $10$ to $10+dt$.
The problem, as you might realize, that gaussian distribution has two parameters: mean value and width of the function. When you construct your fit, frist one will be 19nM, but second, $\sigma$, is unknown from your question. What you don't know is how rapidly response changes when you increase concentration by little around your EC50. So all your sigmoidal plots will go through same point but with different slope, like that:

Without knowing second parameter, $\sigma$, it makes little sense to plot your sigmoidal curve. However, if you want to, this is MATLAB code. See that cumsum() function effectively integrates gaussian distribution rendering sigmoidal curve.
c = 0:100; % range of concentrations you test
sigma = 1; % unknown parameter
m = 19; % your EC50 19 nM
g = 1/(sigma*sqrt(2*pi))*exp(-((c - m).^2)/(2*sigma^2)); % gaussian
gs = cumsum(g);
plot(c, gs)

If you want, you can plot it with log-scale of X, using semilogx() instead of plot().
NB here I started with Gaussian function and its integral just as a wild guess. You real function might very well be something like $f(x)=\frac{1}{1+e^{-x}}$. "Sigmoid" function is just description of general shape, not mathematical definition.

You answer is correct for a special case of sigmoidal curves. EC50 curves do not necessarily go from 0 to 1 in real experiments. Usually there is a baseline which is non-zero and a maxima which is not 1. To reconstruct the real sigmoidal curve you need those values.

I agree that the case is special, so OP misses even more parameters than I thought. I looked closer on EC50, it seems that it is defined as 50% increase after subtraction of background, that is after you accounted for zero-concentration efficency

Yup. He can approximate it with your method though (given an estimate of the slope). That was my upvote :)

even though I know that "sigmoid" shaped curves have various math definitions, I am a big proponent of link between gaussian distribution and most of sigmoidal relations in biology. Don't have any supporting data so far, unfrotunately

Hi Andrev, this is great, thank you... By slope do you mean the derivative at the point where the function is evaluated or the slope of the straight line bit in the middle? If you mean the latter, then I can work this out from the graph I'm looking at (since my data is from a paper). Essentially I'm trying to build a mathematical model that incorporates this data, so the values of the top and bottom asymptote will be relative - meaning I have to just make them up and see if they fit.

i'd say, 'slope of tangent to mid-point, e.g. EC50'. And yes, that might be a way to go. After that you can stretch and shift curve so it goes not from 0 to 1, but, let's say, from 0.1 to 0.9.


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How does the brain cool itself?
Thoughout life everyone tells you that brain is essentially a computer but just like computers your brain would create immense amounts of heat by being in use, so if that's the case how does it cool down.
Is like liquid cooling where the blood transfers the heat away? and if so what is the critical temperature when your blood can no longer cool your brain? Also at what temperature are you at risk of brain damage?

http://en.wikipedia.org/wiki/Countercurrent_exchange    might be of some help.

You may have to define "critical temperature," because many biological systems do not fail with a sudden transition from "perfectly fine" to "dead."  They usually have several layers of limited functionality.  Consider a nasty fever, which can cause unusual psychological states, but not death until a higher temperature.

At what temperature are you at risk of brain damage.

Brain has liquid cooling. Some liquids like blood or CSF flow around it and cools.

Computers rely on cooling mechanisms like heat sinks( an aluminum alloy mounted over the micro integrated chip) and fan. So far none of these mechanisms are utilized by nature, but analogies like cooling mechanisms in elephants which are in turn considered to be a model quite like the fan.
As the largest land animal, elephant's ears have crucial role in regulating homeostasis. When we see an elephant, it always wave its ears in order to reduce the brain temperature. On the other hand humming birds which are very smaller in size reduces its temperature by flowing blood to its wings. Humming birds wings flutter 90 times a second and it allows them to exchange much of its heat to the environment and the cooled blood is driven back to the brain.
The  carotid rete or rete mirabile in birds have been developed for heat exchange. In mammals, a pool of the cool venous
blood  returns from the nose or
head skin, exchanges the heat with
warm arterial blood of the carotid artery.
These arteries are sub divided into hundreds of
small arteries forming a net like structure which significantly improve the
heat transfer in brain.

Vascular retia mirabilia are also found in the limbs of a range of
mammals. These reduce the temperature in the extremities. Some of
these probably function to prevent heat loss in cold conditions by
reducing the temperature gradient between the limb and the
environment. Others reduce the temperature of the testes increasing
their productivity. In the neck of the dog, a rete mirabile protects
the brain when the body overheats during hunting; the venous blood is
cooled down by panting before entering the net.Reference

In Humans,

The net effect of heat production in the brain and brain cooling
keeps the brain cooler than the rest of the body and is achieved by
surrounding and bathing the brain with venous blood that has been
cooled outside the cranial vault, by bone and fat acting as
insulation, by the veins of the face and scalp through conduction,
convection, sweat and evaporation and by cooled venous blood flowing
through the cavernous and suboccipital cavernous sinuses cooling
incoming blood in the internal carotid and vertebral arteries before
it enters the brain. The combined effect of the brain cooling system
keeps the temperature inside the vault and brain about two to three
degrees cooler than the rest of the body. The effect is important
enough that some physical anthropologists attribute the extra-large
size of the human brain more to its exceptional cooling capacity than
to the increase in arterial blood flow that comes with upright
posture. Anthropologists refer to human encephalization due to
enhanced brain cooling capacity as the "radiator theory".
Reference

Also yawning and panting are considered to be mechanisms to reduce brain temperature.


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Total number of pleura in the exoskeleton of cockroach
Basically as far as i know cockroach consists of 10 terga and 9 sterna but what are the total number of pleura present in the cockroach.
Pleura are situated between tergum and sternum of a body segment and help in the articulation of terga and sterna.
What would that be in the case of the 10th abdominal segment in which sternum is absent ? Are pleura present there? If yes then what is their functions at that place?


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Location of TFBS in genome
I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it.
What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?

Lots of annotated SNPs are located nowhere near  any part of any gene, so you would be quite fortunate to (a) find a SNP that maps close to a gene of interest. It would be even rarer for a public SNP to map in top of a relevant TFBS. If you had some SNPs from an unpublished study that might be cool

I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser.
For the actual question TFBS are located pretty much everywhere, including exons (as described here), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - here a reference).

what about the binding affinities? Is there any tool where I can insert my notrmal sequence and a sequence with snp and it will predict the difference? I know sTRAP(http://trap.molgen.mpg.de) is suitable for that, however the online results differ from r-version results

@Tonja This page contains some suitable software. If you know what TF you are looking at, you might want to look at this page.


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Do DNA repressors exist?
I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am looking for some kind of anti(or reversed)-enhancer equivalent in the genome which would act like an enhancer but reduce gene expression.
I am aware of repressed/poised enhancers which would kind of be that process, even if not really a pure repression of the target gene but rather a "non-overexpression". I also know about insulators but again this would be a different mechanism.
Some intergenic region binding protein repressors which by a folding mechanism similar to enhancers would repress a gene perhaps?

To my best knowledge DNA enhancers are bound by proteins, thus enhancing activity is actually carried out by the activator proteins not the DNA itself. If I get your question well you're asking if similar sequences exist but with inverse effect? Am I right?

@poka.nandor You are exactly right.

OK, thx I just wanted to make sure I do not misinterpret your question and end up having a bad, irrelevant answer. I'll look into it:)

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen.
In the "classical" way the silencer is bound by a  transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the assembly of the general transcription factors. See the figure from paper 1:

Additionally there are non-classical negative regulatory element (NRE), which are usually elements upstream of the promoter which inhibit the binding regulatory proteins. NRE can also be enhancers depending on the proteins bound on them. Some NRE can induce a bend of the DNA, inhibiting the access to enhancer or promoter elements.
References:

Transcriptional control and the role of silencers in transcriptional
regulation in eukaryotes.
Transcriptional Regulatory Elements in the Human Genome

Thanks! How did I forgot about them I don't know :)


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DNA-DNA cross-linking with formaldehyde?
The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding the cross-linking happens only between the DNA and proteins forming a DNA-protein-DNA complex. The "only" is from a DNA stand-point as of course protein-protein cross-links will also occur.
Can formaldehyde cross-link two double stranded DNA molecules? Is the 3C approach also capturing direct DNA-DNA interactions?
I looked at the literature, especially Dekker et al. description of the method, but couldn't find this information. Thanks.

Yes, it can: http://pubs.acs.org/doi/abs/10.1021/ja00074a005

@canadianer Thanks. Had a look at it and some papers they reference but apparently this is only true for single stranded DNA which is not the kind of DNA-DNA cross-link that might happen during 3C.

I've only skimmed the paper, but it constantly refers to interstrand cross links and cross linking of DNA duplexes.…

@canadianer Interstrand cross-linking refers to a cross-link between opposite DNA strands. Not really what I am looking for as in the case of the 3C it is two distinct dsDNA interacting.

years ago my lab mixed plasmid DNA and short polylysine peptides with terminal cystines so the peptides would polymerize on the DNA. Then they mixed in glutaraldehyde to crosslink the peptides. The resulting complex was stable in mouse liver weeks, but of course the DNA itself was useless.

Wouldn't direct double stranded DNA-DNA interactions in any substantial amount make DNA useless as a stable carrier of genetic information. This type of interaction could lead to inaccessibly deep foldings. Just my initial out of the box thought.

@vajra78 Not if those interactions are between two dsDNA regions (in cis or trans) and are not covalent (similar to protein-dsDNA or RNA-dsDNA bindings). Structure influences gene expression and the genomic function, this is actually the whole point of understanding the chromatin structure using 3C and related technologies.

I know structure influences gene expression and the genomic function. I was just thinking significant dsDNA-dsDNA interaction could lead to prion like knots because these types of interaction would be much denser structures.

@vajra78 sorry I actually missed your "substantial amount" point. Interesting, I don't know enough about prions to really judge about how likely would direct DNA-DNA interactions provoke them but nevertheless thanks, this was something I never thought about!

Actually plasmids form super coils, but there isn't covalent bonds formed as far as I know between dsDNA strands. I really shouldn't have jumped in this thread.

@vajra78 actually I am happy you did. That prion story was actually quite interesting. I will keep that in mind.

The fact that there is no inter-strand cross-linking between different double strands might be just because the cross-linker cannot bridge the distance between amines of different bases on different double strands.
The formaldehyde based linking of nucleobases has been described by Chaw et al. (1980) where formaldehyde bridged a gap of app. 3 angstroms (2x 1.3 A for N-C bond).
Even if you take the most condensed form of DNA as in nucleosomes (see X-ray model of nucleosome with bound DNA) you still have at least 20 angstroms between the bases of different double strands.
At the same time there are only 3 angstroms between the nucleobases of the same double strand, agreeing well with the length of a methyl-bridge.


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"Enhancers" of enhancers?
I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to make a Russian doll analogy. I know about epigenetic markings but I am really looking at an example of a DNA region directly acting on a enhancer similar to an enhancer acting directly onto a promoter.
I am asking that because I couldn't find any examples and was wondering if I missed such a report/paper.

Do you care if it's from a viral genome?

@AtlLED If it is a DNA virus then that works. I am interested in DNA secondary and tertiary structures.

It could be possible that certain enhancer regions can bind the regulatory proteins with higher affinity than other enhancer regions, thus surpressing the amount of activation of the genes regulated by the 'lower affinity enhancer region'.

@Wolgast Interesting idea. This would be some kind of gene regulation via competition. I don't know if this actually happens in the cell (i.e. if some TF are in concentration ranges which would provoke such effect) but in any case it is worth looking into this. Thanks.

Yes indeed. I'm am interested where this will lead you. Let me know if you find anything! :-)

@Wolgast Will definitely do!

If you're looking for a strictly and directly DNA-DNA mediated effect (no histones, no transcription involved) I'd look for sequence effects on chromatin remodelling, modulating access of transcription factors (TFs) to their elements. Something about this might be in this paper:
Szerlong, H. J., & Hansen, J. C. (2011). Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochemistry and Cell Biology = Biochimie et Biologie Cellulaire, 89(1), 24–34. doi:10.1139/O10-139


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How to increase the shelf life of yogurt without refrigeration?
When we make yogurt at home and do not refrigerate it, it will become sour because of conversion of lactose into lactic acid by Lactobacillus bacteria, but this does not happen in case of Nestle's yogurt or any other brand until it remains air tight.
I wonder though bacteria is still present in it and continue to convert lactose into lactic acid then why does not packed yogurt becomes sour? How these companies increase the shelf life of yogurt..?

most likely they kill these bacteria after the product is made and / or use preservatives.

high-energy X-rays might help kill a lot of bacteria. But you need to control dose not to overheat sample

@poka.nandor In that case, what about those yoghurts advertised as being "live culture"? It seems incongruous to use preservatives (which are essentially poisonous to the bacteria)

well in those case I think they use bacterial spores that are not active bacteria but under the right conditions can revive them selves. For example: http://en.wikipedia.org/wiki/Bacillus_coagulans

you can get a lot of info from microbewiki. the basic answer is the presense of oxygen results in a diffrent metabolic pathway in the bacteria and thus a diffrent poduct. However the simpliest answer might be that most comercial yogurts add extra sugar after fermentation. https://microbewiki.kenyon.edu/index.php/Yogurt

lactobacilllus (culture) survive at certain temperature, therefore to stop further fermentation after normal fermentation, the fermented youhurt have to be subjected to higher temmperature to kill the bacteria

This article gives an excellent review on yogurt manufacturing, but to summarize:
-Raw milk goes through centrifugation to remove somatic cells and other solid impurities.
-Thermalization is conducted at "60–69 °C for 20–30 s, aiming at the killing of many vegetative microorganisms and the partial inactivation of some enzymes."
After this point, the milk may be inoculated with lactic acid bacteria or other microfloras.
-Then, standardization occurs which for milk refers to the standardization of fat and solid-non-fat content (SNF).  This in short affects the fermentation process ("an increase of SNF increases the duration of the fermentation process").
-The next step is homogenization, which prevents milk fat from rising to the top of the liquid.  This has an effect on the stability of the emulsion.
-I think this step is where "sterility" comes into play, "heat treatment of milk reduces the number of pathogenic microorganisms to safe limits for the consumer’s health. Various heat treatments can be applied, which are classified based on the duration and the temperature. The most common are known as thermalization, low and high pasteurization, sterilization and UHT (Ultra Heat Treatment)."  The review goes into more detail about each type and what they eliminate or don't eliminate (spores, vegetative bacteria, etc.).
-The fermentation process is the most important one for developing flavor and texture.  The two live bacterial strains of Streptococcus salivarius subsp. thermophilus (ST) and Lactobacillus delbrueckii subsp. bulgaricus (LB) are the two most basic strains used in yogurt.  LB is what metabolizes lactose into lactic acid and LB and ST acting in synergy is what causes a decrease in milk pH.  "When the pH of the yogurt approaches 5.0, activity of ST subsides and LB gradually dominates the overall fermentation process until the target value of pH is reached and the fermentation process ceases. Normally, the fermentation period is terminated by lowering the temperature to 4 °C. At this temperature, the culture is still alive, but its activity is drastically limited to allow controlled flavor during storage and distribution."  I think to answer your question, yogurt manufacturers probably have a very sensitive gauge for pH and can control temperature fluctuations finely to maintain yogurt pH and flavor (not too sour).  "After the pH of yogurt reaches the value of 4.7–4.3, the yogurt is cooled to around 5 °C. This inhibits the growth and metabolic reaction of the starter culture and prevents the rise in acidity. Cooling of yogurt can be in one or two phases. One-phase cooling involves the rapid decrease of the coagulum temperature to less than 10 °C, where the fermentation process is inhibited leading to yogurt with low viscosity. Two-phase cooling is initiated by rapidly decreasing the temperature to less than 20 °C and then gradually reaching the storage temperature of 5 °C leading to yogurt with an increased viscosity and limited syneresis. This is quite common in the yogurt manufacture process, especially when fruits are to be added."
You can read about the other innovative methods involved in yogurt making such as: Ultra High Pressure (UHP) which inactivates pathogens and microorganisms that cause milk to spoil, High Intensity Ultrasonication and Pulsed Electric Field (PEF) which all can reduce microbial content.
Edit: Forgot to mention that some DIY yogurt instructions mention that if you ferment longer and/or in warm temperatre the more sour it will be so to reduce how sour it is, either ferment it less and/or start fermentation at a lower temperature (source).
Sfakianakis P, Tzia C. Conventional and Innovative Processing of Milk for Yogurt Manufacture; Development of Texture and Flavor: A Review. Foods. 2014; 3(1):176-193.

Commercial yoghurt usually contains alive Lactobacillus, as exemplified by the fact that you can use them to "seed" your yoghurt at home. I actually don't think they add anything. In France at least it is just pasteurized milk and lactobacillus (ex from Auchan yogurt list of ingredients: Semi-skimmed milk, lactose and milk protein, lactic ferments). Some preparations that are not yoghurt stricto-sensu might have added sugar, starch, pectin or gelatin.
I think they just do yoghurt in an aseptic environment (ex) preventing bacteria other than Lactobacillus to chime in and further mess up the mix. That would go well with your own observation that opening the "brand" yoghurt make them "spoil" faster.

It would be better if you can provide a source to back up your claim.


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Can the absorption of vitamins be enhanced?
Are food additives like vitamins better absorbed when you mix them among fruits?
I heard that secondary substances in fruit promote the absorption.

There are two types of vitamins:

Fat soluble vitamins - Vitamins A, D, E, K
Water soluble vitamins - B complex Vitamins and Vitamin C

Fat soluble vitamins get better abosorbed when fat content of food is good. The bile secretion is also very important. These vitamins form miscelles with the fat molecules and get absorbed as such. The absorption of these vitamins can be enhanced by taking fatty diet.
The water soluble vitamins are absorbed freely and they are also excreted freely - Excess are expelled through urine.
There are inter-vitamin competition and some food biomolecules can inhibit vitamin absorption. For example avidin in the egg would bind to biotin and prevent its absorption. The articles below deal a little with such inhibitions.
For more see:

http://healthyeating.sfgate.com/improve-bodys-absorption-vitamins-2898.html
http://www.ncbi.nlm.nih.gov/pubmed/17023940
http://health.howstuffworks.com/wellness/food-nutrition/vitamin-supplements/body-absorb-vitamins.htm

authors: Саид Файзиев


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Simplified molecular-input line-entry system
This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer.
What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is converted to 1D representation in SMILES(Simplified molecular-input line-entry system)? two properties I found that gets neglected are linkages,interaction properties. By properties I meant isomeric count,isomeric threshold etc. Are there anymore properties that gets neglected?

Hi, could you define 3D biomolecule and provide some reference to SMILES I'm not familiar with these.

http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

http://en.wikipedia.org/wiki/Biomolecule

Shame on me for thinking that biomolecule would refer to something special....

A 3D model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic or aniosotropic B-factor (that models atom fluctuations).
A '1D' SMILES is not a physical 1-dimensional representation, and can be converted to a graph (mathematics) representing the chemical structure. The specification of SMILES CAN retain information about structural isomers, stereoisomers (cis/trans; D/L), but not conformers/rotomers, which, unlike smaller chemical structures, IS restricted to certain favorable regions for larger biomolecules.
By "linkage" if you mean chemical linkage such as a disulfide bond, then SMILES can retain such information. By "interactions", if you mean hydrogen-bonding, salt-bridges and even hydrophobic interactions etc., then SMILES does not code in such information, but neither does a 3D model explicitly -- they are implied from the 3D coordinates for each atom.
Thus, converting from a 3D model to SMILES, you would lose

Unusual bond length and bond angle: they are necessarily specified from the 3D coordinates, but in SMILES (or the subsequent graph), they are taken as 'ideal'.
B-factor or temperature factor
Rotomers: e.g. Proteins have favored dihedral angles in both backbone and side chains, which is not specified in SMILES.
"Interactions": certain intramolecular interaction that is inevitable (e.g. salicylaldehyde) is implied in both SMILES and a 3D model. Most others can only be inferred in the 3D model.

can you please tell me how you came to know about these facts?? I tried to find the properties of a 3D biomolecule but couldn't find it.. Is there any book I should follow?

I happen to be a structural biologist. You could check out some books on 'Structural bioinformatics' or 'Chemical Informatics', and download visualization software to play with the 3D coordinates from one of Protein Data Bank(s). (http://www.wwpdb.org/) RCSB hosts a very good overview http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/intro.html

Okay, I have something to say if you don't mind, can I get your email so that I can contact you when I am stuck with something?

I don't mind. My email is on my profile. There should be many experts here on the forum, too.


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What happen's to a virus's capsid after it injects its genetic material into the host cell?
After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it just falls off. However, since it is now outside of a cell, there are no protein-digesting enzymes -- or are there?
What happens to it now? I'm guessing it doesn't just float around for all eternity.

Interesting question and actually I haven't found a real answer here yet. The phages seem to bind rather hard, since the need to be blended (subjected to relatively high forces) to shear off. This was used in the Hershey-Chase-Experiment to find out what the genetic material of the cell is. It doesn't matter though, since most of the cells which are infected get destroyed anyway. If not, they are most likely taken up and broken down inside the cell, as it happens with other membrane proteins.
This is only valid for viruses which inject their genetic material into the host cell, while the capsid stays outside. This happens mostly for Bacteriophages.
There are a few other possibilities for viruses to enter cells where this is no problem:
Viruses which have a membrane envelope can enter the cell via membrane fusion. To make the fusion happen, either the membranes have to get very close, or the virus first binds receptors on the cell surface and then fuses its membrane with the cell. This causes the interior of the virus to be released into the cell. The picture below shows the fusion (from the Wikipedia article on membrane fusion). An interesting article on this topic is: "Membrane fusion."

Another possibility for a virus to enter a host cell is via endocytosis. Here the virus uses the uptake of material from the surrounding of the cell to get inside. This can either happen together with resources inside a vacuole.
Or it happens via the binding of specific receptors, which are internalized into the cell upon binding of the specific ligand. Here the virus mimics the ligand of the receptor to get internalized into the cell.
In both cases the virus needs to escape from the vacuole before it get broken down because the vacuole is turned into a lysosome.

Thanks! I was talking about viruses which inject their genetic material; I just somehow forgot to mention that. =)

Ah, ok. I answered that, too. :-)

I think the external protein coat is degraded as the virus releases it's nucleic acid into the Host' cell. This is due to the fact that a protein is lifeless without the activity of a gene(one gene-one enzyme hypothesis).Since the nucleic acid is composed of genes, when it is injected into the host's cell, the capsid becomes useless and so it is degraded.

Can you add some references?


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What is the scientific name of such a fungus?
Several days ago, in a bush I found the fungus as attached which is about 25cm in height and does not look like an edible mushroom:

Any one has an idea of its scientific name and other details?

This looks pretty much like a Coprinus comatus (also known as: shaggy ink cap, lawyer's wig, or shaggy mane) to me. You can see the characteristic ring around the stipe of the fungus (see image below from Wikipedia). The fungus is edible and is also cultivated in China for this purpose. See here for more details.


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Understanding the Amino Acids
I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and absolutely, defeated me...
How do I think about the amino acids, without any memorization, and be able to 'derive' all the names, all the categories they fit into, and their important properties? Memorizing some crazy mnemonic is of no help when it says nothing about the amino acids, I can't memorize it without meaning that explains a lot of things. I ultimately just want to be able to read Albert's Molecular Cell Biology and appreciate it, but I can't without conquering this little issue!
On a side note regarding memorization tricks: is there a mnemonic scheme for the amino acids analogous to the thermodynamical Zhao square, (which gives all the info you need about basic thermo by drawing lines and squares)?
Any help is greatly appreciated, thank you.

Sorry, but I don't understand your question. Can you please make this more precise?

This question appears to be off-topic because it is about memorization techniques - maybe academia.SE might be suitable?

My post explicitly says "without any memorization", the entire purpose of the post is that I'm asking for a way to derive all of the properties of the amino acids in a consistent non-memorization way. Said differently: How would you explain the amino acids and all their important properties (for biology on the level of Albert's) to someone in a way that they can reconstruct what you say. e.g. in physics you can derive the entire theory of electromagnetism by postulating an action principle, using one idea and some obvious rules. Apologies if that wasn't completely clear.

I have amended my response to your question however the short answer, to the best of my knowledge, is that it is not possible since thats not how AA nomenclature works.

you can't learn to even spell without some memorization lol

@bolbteppa ok, sorry. My mistake and badly formulated. I guess I read your Q as asking for a way to structure information in general, and not dealing with biological properties. Either way, nomenclatural Qs are on-topic so my mistake.

understand the chemistry. you'll remember the structures

And yeah Albert's a very readable book. I don't think you really need to "know" the amino acids to appreciate the book ! You could also keep a self made chart nearby when you are reading the book, if you feel that's necessary.

Amino acids have different side chains.If you remember the side chains of each amino acids, and know enough chemistry, you can easily derive almost all the properties of the amino acid.

Maybe this will help? (unfinished currently) https://revolutionarymathematics.wordpress.com/2016/12/18/how-to-memorize-the-amino-acids-without-mnemonics-i-introduction/

I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less).  I really wanted to figure out how the amino acids resulted in the resulting protein structure.  So I started to break them down into categories.  The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique way, but it starts to give you a sense of what the sidechains do.

Aliphatic : G A L I V M P
  Aromatic : F Y W H
  Polarizable : F Y W H M C R
  Polar: S T Q N D E K C
  Small: A S T G C
  Large : F Y W H R K
  Strong Structural variation: P G

you still have to memorize them eventually, but you can make it easier to put them in categories and in these groups its easier to bring them to mind.

I don't think methionine and proline are aliphatic compounds, because they don't completely consitsit of Hydrocarbons.

The question is slightly unclear but will do my best to answer it. I'm not a purist as a biochemist and I can tell you when it comes to biology, there are just certain information you have to memorise and one such instance is AA names. You can drive the AA full chemical name (and its properties such as charge, hydrophilic/hydrophobicity) from its molecular structure but such an approach is far far harder than to remember simple names such as A = alanine, S = serine, P = proline etc! There are some odd ones like Y, which is tyrosine but again the only reason they chose letter Y (second letter in tyrosine) was because (the first) letter T was used for threonine. If you want information on AA and their properties look at this page (https://web.archive.org/web/20150302034529/http://www.bio.davidson.edu/biology/aatable.html), but I'm curious as to why you need to know individual AA properties. I don't suggest it is not important but AA property makes more sense in terms of its context in a protein sequence as it interacts with other AA properties and within a 3D protein structure.
Saying that AA names taken at face value do not make sense since it is not telling information about their property, although true, is broadly similar to saying protein names taken at face value do not make sense, again kind of true, because they do not say anything about their function (not true all the time but mostly true). To me this is the wrong way of looking at it. The designations for AA names were made as they were easier to memorise/refer to (and consequently become aware of their properties e.g. Y is capable of becoming phosphorylated) just as it is easier to refer to protein by its name and not its full AA sequence.

Are you telling me that if I derive the molecular structure I can derive all the info on this massive list, as in - if I can picture the structure of Alanine A in my head I'll immediately know a massive amount of info about A? Judging from this page http://books.google.ie/books?id=sZLvdRA_vRgC&lpg=PP1&pg=PA356#v=onepage&q&f=false the molecular structure of Ethylene can be determined by a quantum mechanical variational calculation, can the same thing be done for all 20 amino acids and if I did that would I be able to derive all those properties from knowing the molecular structures?

I do not know much about QM to comment on it but in general, if you know molecular structure of a (complex) molecule and your chemistry is good enough to know what each part entails in terms of its properties towards the entire structure, then yes, you will know many properties of a molecule. That is how people know if a molecule is for example polar or non polar etc. Obviously the more complex a molecule gets, the harder the tasks becomes, which is why we not only use wet experimentations but also computer simulations.


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What does "This variant falls on 11 transcripts in 3 genes" mean in the output from GnomAD?
The gnomAD browser provides information on variants of genes (in this link, for the SAMD11 gene.)   The report on a particular variant, like this one,  includes the information in the header that says (for example): "This variant falls on 5 transcripts in 2 genes."
What does this mean? In particular, how can a variant occur on more than one gene? Isn't such a variant a variant of a particular gene -- SAMD11 in this case?

In this particular case, there is another unannotated gene at the same locus, running in the opposite direction as SAMD11.
http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000268179;r=1:865499-865579;t=ENST00000598827

How can 3 genes turn up?  As in this variant to SAMD1: http://gnomad.broadinstitute.org/variant/19-14198695-C-T

The SNP is in the upstream region of C19orf67, and the downstream region of PRKACA.  http://grch37.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=19:14198195-14199195;v=rs534496627;vdb=variation;vf=67232947


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Mating types in fungi (and somatogamy)
I would have some related questions about the mating types of fungi.

Does a single spore generate a mycelium possessing only one mating type? If it does not in general, do Ascomycota and Basidiomycota possess only one mating type per individual mycelium?
Are homothallism and heterothallism properties of the individual mycelium or of the species? The definitions that I find in my book and on line confuse me. I understand that homothallism is the property of a mycelium (possessing only one mating type or can it possess many mating types in a similar way to hermaphrodite animals? cfr. question 1) that can mate with itself (if it can possess many mating types and it can mate with itself only by using gametes of different mating types, is it still homothallic?) and heterothallism is the property of a mycelium that is not homothallic, but I am not sure I understand, because I read of homothallic and heterothallic species too: is a homothallic species a species where at least some individual is homothallic, where all individuals are homothallic or something else?
I am sure that mating type is a property characterising at least gametes, but is it a property of indiviual cells too? As an example, I know that it is necessary, among many species of fungi, for two gametes to belong to two different mating types in order to produce a zygote. Some fungi, as it is the rule among Basidiomycota, reproduce by somatogamy, i.e. the nuclei generating the zygote are from somatic cells, other than gametes. In such cases, are there species where it is necessary for the somatic cells of a homothallic mycelium to belong to a different type than the type with which they are undergoing plasmogamy? Thank you very much for any answer!

Background:
Most fungi can reproduce sexually and asexually, and some even parasexually. Fungal reproduction is complicated! For one high-level review, see here.
Idiomorphs are alternative versions of the mating type locus on homologous chromosomes that are completely dissimilar and encode unrelated proteins.
Heterothallic - also called outbreeding: male and female reproductive structures are in different individuals. Partners have opposite mating-types with compatible MAT idiomorphs
Homothallic - also called inbreeding: male and female reproductive structures in the same individual. Partners have the same mating type but both MAT idiomorphs are present in the same genome and used in mating-type switching.
Heterothallic species are said to be homogenic incompatible (incompatibility due to the same allele), heterogenic incompatibility (incompatibility due to different alleles) occurs when the offspring of a heterothallic cross between different strainss shows negative heterosis. There are forms of heterogenic incompatibility that appear to act only in the sexual phase. For more discussion of these ideas see here.
Note that mating type and sex are not the same as sex is determined by mating structure and mating type may have no effect on sexual structure only on the nucleic content.
Answers:
1. I am not certain, but my understanding is that a haploid spore will generate a haploid mycelium of the same mating type. Note that things can get more complicated because you can have bifactorial incompatible mating types (e.g. two unlinked mating loci).
2. Homothallism and heterothallism are properties of the species (or at least they are treated as such). Nonetheless, there are some species for which thallic state is variable, mediated by genomic alterations.
3.  I am not entirely sure I understand the question here. In Basidiomycota (Club Fungi) Mycelia of + or - mating type will fuse to form a dikaryotic (two nuclei) mycelium for the majority of the life cycle. Only under unfavorable conditions will karyogamy (the fusing of the haploid nuclei) occur to form diploid hyphae and fruiting bodies where meiosis will take place to create haploid spores with mating types which will generate the new mycelia. Part of what makes the lifecycle here difficult is remembering that diploid somatic cells will have both mating types. (Life Cycle)


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Isogametes and oogametes
I have found the following definitions of different types of gametes:

isogametes: gametes looking and behaving the same;
heterogametes: gametes different in size or in behaviour;
oogametes: gametes different in size and behaviour.

I have some doubts about the exact meaning of behaviour in such definitions. I know that there exist species where gametes of the same mating type can originate a zygote, for ex. in some fungi.
Do differing heterogametes and oogametes always belong to different mating types?
Thank you very much for any clarification!

Where are these definitions from?  Wiktionary defines a heterogamete as "Either of a pair of conjugating gametes that differ in structure or behaviour".

@augurar Thank you for the comment! They are from an Italian language text. It may happen that scientific language usage is different in different countries: edited OP to fit Wiktionary's definition

What do you mean with "Do differing eterogametes and oogametes always belong to different mating types?"? That different individual gametes always belong to different mating types, or that different types of oogametes (e.g. egg and sperm) always belong to different mating types?

@fileunderwater I mean "Do the different types of oogametes (or heterogametes) necessarily belong to different mating types (ex.: + and -) (or can they be produced by the same mating type)?". I'm basically looking for definitions as rigourous and precise as possible. Thank you for the comment!

Allow me to start off with a nice picture showing the differences - note female gametes are on the left while male gametes are on the right in my examples:

Isogametes
For a gamete to be considered an isogamete the other gamete that it meets up with to produce is exactly the same in both size, structure and movement. [2] It is literally trying to find itself. The "male" and "female" are literally no different and it is impossible to tell which is which.
When you look at the picture the two gametes are exactly the same in every way except that they are facing each other in this picture.

The next two are forms of anisogamy:

(source: ulsfmovie.org)
Heterogametes
These gametes differ in at least one of the following:

size
structure
sex

Although it can also be a combination of these three things. [3] As you can see here the female can be structurally the same as the male. (Bottom and top examples of the second picture). From my understanding (although someone can come and prove me wrong) Oogametes are a specific from of heterogamous.
Oogametes
Oogametes differ in size, sex AND function. Females are stationary while males move. [4] Females are also much larger than males. (For instance in humans the cell that divides to make sperm divides equally while the cell that divides in the female divides to make one egg and three polar bodies.)

Very kind answer! What does "sex" mean in the "heterogametes" definition? Does it mean "mating type"? I've read that isogametes undergoing fusion must belong to different mating type at least in some species (ex.: in some strains of Chlamydomonas): must any two (including iso-, hetero- and oo-) gametes undergoing fusion belong to different mating types in all organisms? I've got some doubts because, for ex., of homothallic fungi ( http://biology.stackexchange.com/questions/35057/mating-types-in-fungi-and-somatogamy?rq=1 )... I heartily thank you again!

Male vs female. Like sperm vs egg @Self-teachingDavide

OK: I assume you mean male = motile, female = stationary. Thank you!!!

Yes, exactly @Self-TeachingDavide


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Black/dark-red smooth West African worm, full of red blood
This chap was strolling across my bathtub in Freetown, Sierra Leone, one day after very heavy rains and flash flooding. From its course, it appeared to have come up the bath plug from the drains.

It's about 2mm-3mm wide at the fattest points and 1mm wide at the thinnest points (which vary as it moves). It's maybe around 10cm in length. The picture's not the clearest but (to the naked eye) it looked almost completely featureless - smooth (no visible rings), and no obvious hooks or features at either end.
It was moving to the right from the point of view of the photo, and moved by narrowing and elongating unmarked segments about 2-4cm long each rather than the whole body. I say segments, since it seemed to be the same sections each time, but when it wasn't moving there was nothing to distinguish these segments. Its movements began by elongating the very front 2-3cm, then it'd feel around, come down, and other (unmarked) segments in the body would expand and contract to bring the rest of the body after it.
While I'm pretty sure it's not either of the two most notoriously nasty West African parasitic worms (Loa Loa or Guinea Worm), I didn't want to to take any chances, and we had nothing to isolate or store it in, so we carefully squashed this one after taking photos then cleaned the plug hole with boiling water and cleaner.
On squashing it, it burst in a very similar way to a recently-fed mosquito or bed bug with a splatter of what looked exactly like regular human/mammal blood. I've not seen this before from a worm. Each 5mm or so of worm body contained about as much blood as a well-fed mosquito.
I've done a little browsing of species of bloodworm but didn't find any obvious matches.

This might be unrelated, but the bathroom in which this worm surfaced has for several weeks had a small but constantly replenishing population of tiny flies like this, which I never questioned because they look almost exactly like regular drain flies. There's usually 1-3 of these flies on any given day, even after wiping out all of yesterday's flies, and I've not seen them anywhere else in the country. In this image it's about 3mm from wingtip to wingtip - much smaller than the worm.

There are not so many potential candidate worm groups with similar appearance, namely: (free-living) flatworms, Nemertea and annelids.
While there are several terrestrial and freshwater flatworms, some of which are quite long, they do not approach such an elongated vermiform body shape and their mode of locomotion is different. There are around two freshwater nemerteans in Africa, neither of which looks like your worm, and in any case most nemerteans move by gliding using their cilia.
So the remaining group is Annelida. There are three groups of annelids relevant in this context: polychaetes, oligochaetes and leeches. Polychaeta are predominantly marine and normally have more or less pronounced parapodia ("limbs"). Some of the do behave according to your description, but they are very characteristic in their appearance and you would not expect to find them in a bathtub.
What remains are oligochaetes and leeches. Leeches are more or less dorso-ventrally flattened and have very prominent suckers. Moreover a fed leech (from which you would expect large quantities of blood) would look swelled (the gut in leeches has diverticula).
So, the only worm group I can reasonably suggest is oligochetes. In fact your worm looks and behaves very much like a common earthworm. It is very typical of them to be highly mobile during and after rains and their blood pigment is hemoglobin (i.e. red). The only contradiction is that your worm had no clear true segmentation, but I believe, in some forms it is easy to overlook it.
The fly is indeed some species of Psychodidae.

Great, so nothing to worry about then! Thanks for the thorough answer


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How does current delivered by a neural stimulator propagate in the brain?
I have been trying to find good literature on how a stimulus current propagates through a medium that contains both gray and white matter (like the brain). Is it safe to assume that a current will spread through grey matter more easily than white matter, because of all the insulation provided by the myelin? Is it then safe to assume that, if you stimulated tissue which has white matter on one side of the electrode and grey matter on the other, the current would preferentially flow through the grey matter?
As an example I tried to sketch something that would represent a deep brain stimulation electrode in the subthalamic nucleus (STN) sending pulses through its bottom electrode (let's assume the return electrode is the implant case and far away from the target structure). As the STN is close to the internal capsule, I'm wondering if any assumptions can be made about the tissue activation region. More specifically I'm wondering if the current would spread more easily through the STN and have more trouble getting past the internal capsule (exciting the fibres there if the current is strong enough but maybe not getting past those fibres because of all the myelin?). So could we imagine the activating region of the stimulus pulses to be biased toward the STN rather than the white matter tracts?
Hope this clears things up.

If an electrode is placed in the white matter and current flows, it goes per definition through the white because it has no option to do otherwise. I think it would be good to include a sketch of the anatomical situation you are referring to in question #2. +1 for the nice question.

Hi @Christiaan thanks for your help yet again! I added a little sketch of a hypothetical DBS scenario that started my questioning. But the question is much more generic, basically I'm wondering if some assumptions about tissue activation can be made when the general physiology surrounding stimulus electrodes are known or if overall it's all way too complex to make any such claims and think about it this way.


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How do fish maintain razor sharp teeth?
I was watching a program about Barracuda - they have a front tooth that is supposed to be razor sharp.  My kitchen knife goes blunt if I use it for long periods without sharpening.  Sharks keep on growing new teeth but barracuda don't.
How do fish like Barracuda maintain a tooth that is razor sharp?
Edit News article on how sharp the tooth is
http://www.dailymail.co.uk/news/article-1348152/Barracuda-attack-breaks-womans-ribs-forces-boyfriend-seal-punctured-lung-hand.html

Added wiki link to your post. Adding links to content improves readability for curious and/or competent users, experts and those reviewing your posts.

Fish replace their teeth over time as needed. Thus, they don't maintain the sharpness of individual tooth, they just replace it. This is a passive process not a conscious process.
Source: Barton, M., & Bond, C. E. (2007). Bond's biology of fishes. Thomson.Pg. 414-415.

@cup feel free to accept the answer


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Applying drugs to brain via scalp (transdermal)
Many medications are intended only for the brain, but are taken orally. Hence <10% finds its intended target, while the remaining >90% is at best wasted, and at worst causes unwanted side-effects.
Valproate is a classic example; it is medicated as an antiepileptic, but only a small fraction crosses the brain blood barrier to make it into the brain. Because of this, a large dose is required, and unwanted side-effects are common.
However, certain (small molecule?) drugs (e.g. Ibuprofen) can be applied transdermally.
For a drug intended for brain tissue that allows transdermal application, is there any sense in applying on the (preferably shaved) scalp?
Is this a known mechanism of administration? If so, does it have a name?
Is there any way of correctly scaling the dosage? For example, if experiment shows that 50% of substance X taken transdermally reaches the bloodstream, if it is administered to the scalp is there any way of figuring out how much ends up in the brain and how much ends up in the rest of the body?
Since this is a tricky and obscure question, may I also ask this: how to go about finding an answer to this? Where else can I ask?

If you wanted to deliver a drug directly to the brain, it might be doable with microdialysis, where a tube is inserted into the brain and chemicals can be added or removed for analysis. It's done fairly often for research in mice, but I've never heard of it being used for drug delivery. Here's a review article: http://www.ncbi.nlm.nih.gov/pubmed/19340812

The short answer is no, it will take forever for a drug to pass through skull bones.
The usual reason to apply drugs on skin is if you want them to act right there, on the skin. Acne creams fit here. You need less drugs, you get where it is needed sooner, and you have fewer off-target effects, when compared to taking them by mouth. The brain is not "right there", so this scenario does not apply.
The second reason is convenience. Some drugs cannot by taken by mouth, because they would be degraded by the stomach or guts. In most cases, the drug has to be given through painful, expensive injections. But if such a drug does pass through skin (usually when it is a fat-loving small molecule), you may get away with applying it on skin. Testosterone is one such drug. However, it usually doesn't matter whether the skin you are applying on is close of far from the target organ. The drug will be taken from the skin by blood, get to the heart through veins, and then spread to the whole body, eventually reaching the target. There is no reason to shave your head, since it will go through the same detour before reaching the desired destination.


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What is the core mechanism behind neuroplasticity?
Specifically I am looking at reopening of the critical period of plasticity.
Modern neuroscience has started to unlock the secret of neuroplasticity.
A common experimental setup is with mice. They have a critical period between days 20 and 32 when they learn binocular vision. And if you cover one eye during this period, they never learn to use it properly. Covering the eye even for extended periods outside of this window has no long term effect.
Scientists can then test out various plasticity hypotheses. And they had indeed found several mechanisms that can restore binocular vision to adult mice.
You can find a list towards the bottom of this paper: Autism -- A 'Critical Period' disorder?

enzymatic degradation of PNNs
SSRI
HDAC inhibitors (which are suggested to knock out Nogo-66 receptor)
AcetylCholineSterase inhibitors

It is suggested that there is an underlying pattern of excitation/inhibition (E/I) balance that all of these 4 techniques perturb.
Where can I read about this E/I balance in detail? The Wikipedia page on NeuroPlasticity (here) appears to be a dead-end.
I am looking for an overview, rather than technical scientific papers that explore a particular aspect, already assuming familiarity with the big picture.
How to get the big picture?
EDIT: T K Hensch seems to be a world leader in this research, and his papers answering my questions, for example http://www.ncbi.nlm.nih.gov/pubmed/24439367

a bit strange you call the long wikipedia article with many related links a "dead end". there are probably many different biological mechanisms for neuroplasticity. note that new synaptic changes/ growth are a part of the puzzle. see also growth cone

This is a good first source which suggests further references:
http://www.scholarpedia.org/article/Balance_of_excitation_and_inhibition


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How does Sodium Valproate cause neural plasticity
I have been reading a fascinating paper: Valproate reopens critical-period learning of absolute pitch
18 individuals were given Sodium Valproate (VPA) for a fortnight during which they trained on a pitch-training game. Results suggest that VPA reopens the plasticity window that normally closes by adolescence.
However, the paper seems to suggest that the exact mechanism of action is unknown.

Valproic acid is believed to have multiple pharmacological actions,
  including acute blockade of GABA transaminase to enhance inhibitory
  function in epileptic seizures and enduring effects on gene
  transcription as an histone deacetlyase (HDAC) inhibitor (Monti et
  al., 2009). Of relevance here is the epigenetic actions of this drug,
  as enhancing inhibition does not reactivate brain plasticity in
  adulthood (Fagiolini and Hensch, 2000), but reopening chromatin
  structure does (Putignano et al., 2007). While systemic drug
  application is a rather coarse treatment, the effects may differ
  dramatically by individual cell type (TK Hensch and P Carninci,
  unpublished observations). VPA treatment mimics Nogo receptor deletion
  to reopen plasticity for acoustic preference in mice (Yang et al.,
  2012), suggesting a common pathway through the regulation of
  myelin-related signaling which normally closes critical period
  plasticity (McGee et al., 2005). Future work will address the cellular
  actions of VPA treatment in the process of reactivating critical
  periods. Future MRI studies will also be needed to establish whether
  HDAC inhibition by VPA induces hyperconnectivity of myelinated,
  long-range connections concurrent with renewed AP ability (Loui et
  al., 2011).

So it is saying that the standard use of VPA is to increase GABA levels (which keeps firing rate down -- it is used as an antiepileptic), however it also acts as an HDAC inhibitor, which means it causes unwrapping of chromatin and consequently increased mRNA transcription, maybe even transcription of genes that would normally be entirely deactivated in an adult.
So my guess is that some protein is getting produced that messages neurons to generate new axon/dendrite growth and/or new synaptic connections.
Can anyone clarify how VPA might accomplish plasticity?
EDIT (one month later): I have more detail, but I still can't quite make the connection. Here goes:
Neurites get wrapped by myelin/oligodendrocyte, which produces and exudes some of the chemical messagers {Nogo, OMgp, MAG}. The membrane surface of the neurite contains nogo 66 receptors (NgR-s) that get triggered by these messagers and inform the neuron to inhibit axon-growth. Somehow the 'HDAC inhibition' property of VPA is unwinding DNA enough to alter transcription rates of certain proteins, and one of these must be disabling the NgR.
But how is this happening?

This paper might be of some help http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907704/

As far as I can see this paper is being a little misleading, by saying "VPA mimics Nogo-66 receptor deletion".
The action of VPA doesn't seem to be related to this receptor.
It seems that blocking this receptor and applying VPA both increase plasticity, but via different mechanisms.
VPA seems to facilitate LTP through increased availability of relevant proteins (as an HDAC inhibitor, it "loosens/unwinds" DNA, allowing for increase in protein transcription). And by increasing protein transcription across the board, it may be increasing the availability of proteins that promote synapse formation.
The principal problem with growing new structure is, as hinted at the end of the question, that the adolescent/adult brain secretes a chemical that gets picked up by Nogo 66 receptor, which signals to collapse the axon growth cone.
It's why adult humans can't recover from spinal injuries. The axons won't reconnect.
It so happens that a small molecule Nogo Antagonist has recently been developed by Professor Strittmatter.  He was kind to reply to my query, and I learned that this molecule is currently in the early stages of FDA approval. It's a very exciting discovery!
I would caution anyone considering taking VPA to balance it with a beta-blocker (e.g. omeprazole). It is an acid, and if not balanced with something to reduce the stomach's ability to produce acid, risks acid reflux, which may force a change of diet, and be longterm/permanent. So, DYOR.
Also of note is that (again discovered by Strittmatter) Ibuprofen has been found to also interrupt the signalling pathway that leads to axon growth collapse. But it requires a high dosage, and ibuprofen also causes a similar imbalance.

Can you provide a link to the paper regarding the receptor antagonist? Also, the anecdotal evidence seems to be very unscientific and I recommend that it be removed.

@MarchHo http://www.ncbi.nlm.nih.gov/pubmed/12037567 -- also, that is a terrible idea to remove valuable information (that, as it happens, has been scrutinised by an Oxford educated medical professional). Anyone considering taking VPA should be forewarned and educated.

@Pi anecdotes as basis for medical advice aren't really appropriate for this site - otherwise very good answer that I'd be happy to upvote.

ok 7 years later, I agree. I have cleaned the answer, and also filled in a couple of blanks from memory.

Please add references while you're on it. -1


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What is the evolutionary advantage of red-green color blindness?
Red-green colorblindness seems to make it harder for a hunter-gatherer to see whether a fruit is ripe and thus worth picking.
Is there a reason why selection hasn't completely removed red-green color blindness? Are there circumstances where this trait provides an evolutionary benefit?

Just a general note: evolution isn't a guided process. For a trait to disappear, there must be a strong pressure against that trait - usually either cost (e.g. cave fish eyes) or a more direct danger (e.g. black rabbit on snow). Dichromancy simply may not be disadvantageous enough (just like tetrachromancy, exhibited by some humans, isn't advantageous enough to spread). These kinds of variations are very important for the survival of the species - when the environment changes, that's the pool of adaptations evolution "picks" from :)

Note that the presence of a trait does not mean it's adaptive. Selection is not the only mechanism of evolution and others mechanisms can spread and maintain maladaptive alleles in a population.

Just to to Luaan 's point - and I doubt this is applicable for color-blindness - but sometimes a neutral or slightly disadvantageous trait (like color-blindness) may be bound together with a trait that is clearly advantageous.  So when evolution selects for the advantageous trait, it "accidentally" also gets the neutral/slightly disadvantageous one as part of the "package".

@BaardKopperud yes, a well-known example is Sickle-cell disease protecting against Malaria.

@StéphaneGourichon baard is describing linkage and genetic hitchhiking - sickle cell is an example of heterozygote advantage

It might have been "removed" at specific points in every generation that's ever lived. That won't guarantee that the same or very similar mutation won't happen again and again. There might someday be a clear advantage that isn't obvious today.

Short answer
Color-blind subjects are better at detecting color-camouflaged objects. This may give color blinds an advantage in terms of spotting hidden dangers (predators) or finding camouflaged foods.
Background
There are two types of red-green blindness: protanopia (red-blind) and deuteranopia (green-blind), i.e., these people miss one type of cone, namely the (red L cone or the green M cone).
These conditions should be set apart from the condition where there are mutations in the L cones shifting their sensitivity to the green cone spectrum (deuteranomaly) or vice versa (protanomaly).
Since you are talking color-"blindness", as opposed to reduced sensitivity to red or green, I reckon you are asking about true dichromats, i.e., protanopes and deuteranopes. It's an excellent question as to why 2% of the men have either one condition, given that:
Protanopes are more likely to confuse:-

Black with many shades of red
Dark brown with dark green, dark orange and dark red
Some blues with some reds, purples and dark pinks
Mid-greens with some oranges

Deuteranopes are more likely to confuse:-

Mid-reds with mid-greens
Blue-greens with grey and mid-pinks
Bright greens with yellows
Pale pinks with light grey
Mid-reds with mid-brown
Light blues with lilac

There are reports on the benefits of being red-green color blind under certain specific conditions. For example, Morgan et al. (1992) report that the identification of a target area with a different texture or orientation pattern was performed better by dichromats when the surfaces were painted with irrelevant colors. In other words, when color is simply a distractor and confuses the subject to focus on the task (i.e., texture or orientation discrimination), the lack of red-green color vision can actually be beneficial. This in turn could be interpreted as dichromatic vision being beneficial over trichromatic vision to detect color-camouflaged objects.
Reports on improved foraging of dichromats under low-lighting are debated, but cannot be excluded. The better camouflage-breaking performance of dichromats is, however, an established phenomenon (Cain et al., 2010).
During the Second World War it was suggested that color-deficient observers could often penetrate camouflage that deceived the normal observer. The idea has been a recurrent one, both with respect to military camouflage and with respect to the camouflage of the natural world (reviewed in Morgan et al. (1992)
Outlines, rather than colors, are responsible for pattern recognition. In the military, colorblind snipers and spotters are highly valued for these reasons (source: De Paul University). If you sit back far from your screen, look at the normal full-color picture on the left and compare it to the dichromatic picture on the right; the picture on the right appears at higher contrast in trichromats, but dichromats may not see any difference between the two:

Left: full-color image, right: dichromatic image. source: De Paul University
However, I think the dichromat trait is simply not selected against strongly and this would explain its existence more easily than finding reasons it would be selected for (Morgan et al., 1992).
References
- Cain et al., Biol Lett (2010); 6, 3–38
- Morgan et al., Proc R Soc B (1992); 248: 291-5

I'm red-green colorblind (not sure which flavor) and I can't tell the difference between the full-color image and the dichromatic image :(  that mannequin is wearing some really ineffective camouflage though.

I'm giving +1 for the last sentence. I doubt any selective advantage for colour blindness outweighs the selective benefit for colour vision so it's more likely to be a failure to be selected out of the population than anything that's actively selected in.

I can see the difference between the two images, but it's not clear to me why the man is supposed to be easier to spot in the image on the right.

I have full color vision, and still find the mannequin's camouflage to be wholly ineffective. If the fatigues were green and black, it might have been better than this green and white scheme.

I haven't found red-green color blindness to be as much of a hinderance as many people assume it to be.  A lot of my friends ask me how I tell apart traffic lights. The truth is that I can actually make out the difference, since I'm very perceptive to the difference in brightness between the lights.  Additionally, it's really easy to tell the state of the lights based on context (e.g., which cars are moving, etc.). The same applies to many other situations where normally-sighted people rely heavily on color. So it makes sense to me that color-blindess is not heavily selected against.

Also, tetrachromacy allows women with a heterozygous genotype (carriers) to see more color than an average person. This might be an evolutionary advantage to heterozygous carriers, similar to the sickle-cell gene protecting against malaria.

@jayhendren actually, traffic lights are intentionally designed with a shade of green that also has a lot of blue in it, specifically so that colorblind people can tell them apart from the red lights. Been that way for decades.

There seems to be some evolutionary advantages to red-green colorblindness. The paper in reference 1 (a summary can be found in reference 2) shows that people with red-green color blindness can differentiate between much more shades of khaki than unaffected people. This might help detecting camouflaged food in a green environment.
Reference 2 quotes an expert about this:

For example, it may have helped them spot potential food items in complicated environments such as grass or foliage, he suggests.

This fits with the observation that in a number of new world monkeys dichromatic and trichromatic animals are present in the populations. They found that the dichromatic monkeys have advantages in low light conditions.
References:

Multidimensional scaling reveals a color dimension unique to ‘color-
deficient’ observers
Colour blindness may have hidden advantages
A foraging advantage for dichromatic marmosets (Callithrix
geoffroyi) at low light intensity

Anecdotal evidence: both my brother and I have mild red-green colourblindness and our colourvision in the dark, is much greater than both our sisters. We also, in general, have much better nighttime vision than everybody we know who isn't red-green colourblind, to the point where , when most people can't see anything, we can still navigate comfortably (but obviously not nearly as well as if there's any real light). I can't say if this is due to colourblindness or not.

FYI: Your ref #1 is on deuteranomaly, which is anomalous trichromatic vision.


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harvesting fertilized eggs from Tetraodontidae species?
I would like to know how easy/difficult it is to harvest fertilized eggs from Tetraodontidae species such as Tetraodon nigroviridis or Takifugu rubripes compared to zebrafish? Ultimately, I would like to know how much material would be obtainable from Tetraodontidae eggs to extract DNA from the nuclei.
I know zebrafish lay lots of eggs, and other model fish species like medaka lay much fewer of them, but I couldn't find any information about Tetraodon nigroviridis or Takifugu rubripes after some googling.

For DNA extraction, you would need only a few eggs. PCR would then give you all the copies of your target gene(s). A quick Google Scholar search on Takifugu fecundity revealed a paper by Yang and Chen (2008). They found that T. obscurus produced an average of 320.8 oocytes mg$^{-1}$ ovary wet weight. In comparison, T. ocellatus produced 125.2 oocytes mg$^{-1}$ ovary wet weight. Takifugu rupripes and other species are likely in a similar range, which is plenty of tissue for DNA. Kusakabe (1962) published on the fecundity of T. rubripes but the paper is in Japanese and is not readily available to me.
Beware: T. rubripes ovaries are highly toxic. Why not use other tissue instead?