Design rules for DNA linkers I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism.

I do not expect the nature of the two things to be important for this question, but if it is, let's say I want to link a solid surface and a protein.

Let's say that my only constraint is that I want this crosslinking to be stable at 37°C.

There is a gazillion ways I could design the sequences, and pretty much anything above 20bp without massive self complementarities should work, in theory. But I don't like to pick bases randomly. So my question is this: is there anything I can look for, except for the two constraints above, to design a good linker sequence?

For example, if the melting temperature is 50°C vs. 65°C, I would expect the structure to be stable (infinitesimal dissociation constants in both cases). Would there be any reason to choose one over the other, except for maybe oligo synthesis price? For a given melting temerature, is there any difference between a long AT rich sequence and a short GC rich sequence?

You might want to pick something that has little or no homology with anything that exists in any organism in the databases, just in case.

Gut feeling says to go for balanced oligos in the middle between AT-rich and GC-rich, and not have repeats or homopolymers.  If you go for AT-rich, then your complementary will be GC-rich, and vice versa. I'm pretty sure there would then be a differential in the mechanical properties of the two oligos - maybe this would be something useful to have for other reasons though?

It seems like most of the design principles might be constraints (do nots) rather then goals (dos), so you could do worse than have a generator churn out random sequences, and score each one against the various constraints.  Random seems OK, if you are then checking each randomly chosen pair against some strong rules.  Then pick ten or so pairs that all score well, get them synthesised and see whether any work...


Why do humans lose subcutaneous fat tissue with age? Why exactly do humans lose subcutaneous fat tissue with age?
It appears that we either lose fat cell volume or we might actually be losing the number of fat cells with age.

One hypothesis is that as the vascular system weakens with age, the fat cells on the perimeter of the body shrink and die because they don't have enough blood flow to sustain them.  The problem with this hypothesis is that subcutaneous fat loss is very gradual and starts during young adulthood and continues. It also happens in very fit individuals too.

Another hypothesis I read before was that subcutaneous fat is loss because of a drop in estrogen levels after menopause.  This hypothesis doesn't explain why men lose subcutaneous fat with age.  Also, women start to lose fat on their hands and upper cheeks long before menopause starts.

Short answer
We do not loose fat (cells) as we age; on the contrary - we tend to gain fat by about 1 or 2% per decade. The place where it gets stored does change; instead of going into subcutaneous regions, it gets stored around the abdomen. A sex hormone imbalance might be the cause of this gain in visceral fat.

Background
What a coincidence! I just finished an article in the Sci Am May issue of this year (2018) on exactly this topic, literally just minutes ago.

In young folks, fat tends to accumulate under the skin, while in older folks this tends to shift to accumulation of fat around the abdominal viscera (the internal organs). Bottom line: we don't loose fat overall, we just store it elsewhere. What's more, as we age we store more fat as our base metabolic rates drop.

Why this happens is no known, but there are some interesting findings:

Sex hormones are involved; women in menopause (estrogen levels drop) gain more visceral and belly fat and loose it around the hips (they go from pear to apple);
However, a drop in estrogen is not the cause, as certain ailments lead to belly fat in young women with plenty of estrogen;
Androgen-using females (transgenders) gain more visceral fat.

These findings together have lead to the idea that a sex hormone imbalance might be the cause. However, some findings counter this idea:

Afro-Americans have less visceral fat, while Asians have more;
Blocking FSH results in less visceral fat, which may have other mechanisms of actions than estrogen.

Reference
- Wallis, Sci Am May issue 2018


Why differentiated cells can't "undifferentiate" (under normal conditions)? In a process called differentiation, the cells of the developing organism undergo huge changes, which result in cells, functioning "completely" differently. Two cells are considered to be of different types if they are having different sets of template-competent genes, though most of the genes in the human genome are common even in highly differentiated cells. Being able to produce specific proteins from the same genome is achieved by something called open chromatin state of the DNA. What I would like to ask is why can't this specific conformation of the DNA be reversed as this would likely answer the title of this question? I would also like to have some tips on further reading in the topic of DNA conformations and about DNA generally.

I used Gabor Forgacs's and Stuart A. Newman's book called Biological Physics of the Developing Embryo

This "undifferentiation" is actually possible and it is known as induced pluripotent stem cell (iPSC). The first "undifferentiation" cells i.e. iPSCs were mouse fibroblasts created in 2006 by researchers in Shina Yamanaka's lab who got the Nobel prize in 2012 for this work.

You can find further reading on this topic on the according Wikipedia-Page or more scientific details on the according nature.com topic.


"Immortal Genes" common to all organisms? Author Sean B. Carroll mentions that there are about 500 genes common to all organisms. They have to do with the essential DNA machinery and so forth.
What are these genes? Where can I read more about this fascinating concept?
When you google immortal genes you get mentions of Sean B. Carroll. What term do others use for these genes?

"When we compare the genomes of Archaea, bacteria, fungi, plants, and animals, we find about 500 genes that exist in all domains of life... The functions of immortal genes are central... processes such as decoding DNA ... and making proteins. All forms of life have depended on these genes since the origin of complex DNA-encoded life early in Earth's history." (Making of the Fittest, pg 79)

Introduction
I believe that Sean B. Caroll is confusing:
• the minimum number of genes required for a viable organism
with
• those genes that are present in all organisms — so called ‘immortal genes’
I will deal with each in turn.
The minimum number of genes required for a viable organism
I have not read the book from which the quotation is taken. From its context and my knowledge I think that the author is mistakenly interpreting ‘the minimum number of genes required for a viable organism’ as ‘the genes present in all organisms’. This is because he seems to be referring to work from the laboratory of Craig Ventner on engineering mycoplasma.
Mycoplasma are among the smallest organisms capable of independent life. They have a genome of about 500 coding sequences, but as parasitic organisms they devotes some of these genes to their parasitic mode of life, while they lack others that the host provides.
The number of 500 may actually be too high: a figure of 300 is quoted in this description, who had plans of Ventner’s plans to build an organism containing a minimal genome containing only such essential genes. There is more on this in a Wikipedia article entitled Mycoplasma laboratorium. It should be noted that the word “immortal” does not appear in either account.
‘Les Immortels’ — genes present in all organisms
The poster would like a list of those genes essential to life, but I know of no such list. How would one go about composing one?
First, one has to set the rules. Do parasites, such as mycoplasma, which are dependent on their host organism, count? Do human beings count? We require amino acids and vitamins, but obtain them from food rather than synthesizing them ourselves. So although it is necessary that a self-sufficient organism have the enzymes for synthesizing the 20 amino acids of the genetic code, these are not all present in humans. I would suggest that we have to restrict ‘les immortels’ to self-sufficient organisms.
Second, one has to decide whether one is talking about a set of genes for accomplishing a function, or individual genes with a structural relationship in all living things that suggests a common identity. For example all cellular organisms (i.e. excluding viruses) must have ribosomes to synthesize proteins, but the protein complement of those ribosomes differs among organisms. Thus, the ribosomal proteins necessary to engineer a minimal mycoplasma may differ from those present in a bacterium such as Escherichia coli, and will certainly not be common to humans. I would suggest we would have to go for the latter.
Having made this decision, one  would get a team of undergraduate students to take all the genes in the genome of E. coli (or even of a mycoplasma) and perform BLAST searches to see whether they are present in representative organisms. Unfortunately I am no longer in a position to torment undergraduate students in this way, so I will have to start a list myself and encourage others to add to (or subtract from) it.
The List — a start
The genes for DNA replication, transcription of RNA and protein synthesis constitute the low hanging fruit here. My area is (used to be) protein synthesis, so I will start there:
Protein Synthesis
Large and small subunit and 5S ribosomal RNAs (3)
Ribosomal proteins (≤32)
Protein synthesis factors — EF1, EF2, IF1 and possibly others
Aminoacyl tRNA synthetases (20?)
tRNAs? — but all that is conserved is probably the anticodon (and sometimes not even that)
Accessory enzymes for protein synthesis:
Pseudouridine synthase
rRNA methylases?
DNA synthesis
B-family DNA polymerases?
RNA synthesis
? Evolutionarily related, but complicated because of multi-subunit nature
But if DNA synthesis is a problem, the reactions leading from RNA to DNA are surely not:
Enzymes of nucleotide metabolism
Ribonucleotide reductase (two subunits)
Thymidylate synthase
Uracil DNA-glycosylase?
Tetrahydrofolate reductase?
Enzymes for interconversion of nucleotides — Adenylate kinase? Nucleoside-diphosphate kinase?
Metabolism
This requires some work. One cannot specify either aerobic or anaerobic metabolsm, but in either case one needs oxido-reducto enzymes. Enzymes of hexose metabolism — hexokinase? Enzymes to metabolize key intermediates like glutamate and glutamine, and enzymes for introducing different groups in synthetic processes. This could make an interesting crowd-sourced project, or, failing that, a game for your next Biochemistry Christmas Party.


How can mammalian red blood cells live without a nucleus? Even though they have a shorter lifespan than other varieties of cells, I would think that 120 days without a nucleus is still quite a long time.

It depends on what you call "to live". RBCs cannot divide, for instance. They cannot synthesise proteins either, so they are decaying after their nucleus is expelled. But they produce ATP using anaerobic glycolysis (as they lack mitochondria), which you may take as a characteristic of "living".


What is the effect of the wavelength on the spectrophotometric measurements of protein? Does the wavelength setting affect the absorbance reading of a spectrophotometer? For example, if I am using a spectrophotometer at 550 nm to determine the protein concentration of my samples, would my results be different if I analyze them at 500 nm?

Light absorption happens because of interaction of light with electrons (in a way) such that the energy of the light is transferred to some electrons that moves them to a higher energy state.

As per quantum chemistry (Bohr's model of hydrogen can be referred for a basic understanding), there are distinct energy states (solutions of the Schrödinger equation) and there are no intermediate levels. Therefore, to excite an electron to a higher energy level the energy of the incident light should match the energy gap between the ground state and the excited state.

In a molecule, there are different electrons, that reside in different orbitals and environments; only a few electrons can be exited by the energy that UV-Visible range of the electromagnetic spectrum can provide. These electrons are typically referred to as chromophores. You should refer to a book on spectroscopy for more details. A molecule can have multiple chromophores and each may absorb a different wavelength.

Having said that, there are energy bands (multiple closely spaced energy levels) in the molecule instead of fixed energy state which allows absorption in a range of wavelengths around a value at which the absorption is maximum. The wavelength vs absorption graph will give a peak at the maximum (which usually looks symmetrical but not always necessarily be so).

   From ChemWiki

The width of this absorption band would differ between different chromophores; so in your hypothetical case, some chromophore which has an absorption maximum at 580nm may absorb 530nm while another chromophore with same maximum, may not.

The Beer-Lambert's law will hold for all wavelengths that can be absorbed i.e. the absorbance would be proportional to the concentration of the molecule (unless there are complex phenomena like energy transfers that may be dependent on concentration; this is unlikely in dilute solutions).

As a practical suggestion, I would say that if your spectrophotometer has fixed options then choose the wavelength that is closest to the absorption maximum.

If you see the above example graph and let's say your aim is to quantify nitrophenolate in a mixture of nitrophenol and nitophenolate. Then a measurement at 350nm instead of 400nm would give you erroneous result. In other cases a 50nm difference may not matter (for e.g. measuring at 450 for the nitrophenolate). It all depends on what you are analysing. You should know the molecule that you are analysing.


Does artificial heat (shower/tea) affect diurnal rhythms in humans? I've been reading that over the course of the day, human body temperature follows diurnal rhythm with the lowest body temperature observed some time close to the middle of the sleep episode, while the peak body temperature is observed some time close to sunset.
Circadian rhythm on Wikipedia

I'm interested if humans have internal organ systems or brain "sensors" that "read" the body temperature as a part of synchronizing their own internal circadian clock to the master clock of the human body.

If there are indeed such sensors, then I'm interested if they can be thrown "off track" by artificial heat sources, like hot food, drinks or showers.

Yes, the human body has thermoreceptors that "sense" the current temperature, but these merely help with regulation--you know, shivering to raise internal body temperature and sweating to cool via evaporation. The hypothalamus is primarily responsible for making sure that the circadian rhythm itinerary is adhered to reasonably well. So no, if the thermoreceptors detect that the body temperature is 97 deg F but it's 5 pm, the body will not "get confused" and decide that it is actually 4 am because a human body is about 97 deg F at 4 am.


Why does non-continuous sleep makes you feel tired? Let's say, hypothetically, that you fell asleep at 10PM, and you were woken up by a noise at 1AM. If you went back to sleep immediately and woke up at 6AM, you will feel tired even though you had slept for 8 hours. However, if you sleep for 8 hours straight , your body will feel rejuvenated. Is it because of REM sleep being cut off and restarting again?

Sleep is not homogenous - there are different phases of sleep - REM, NREM-1 to NREM-4. And these different stages may play different roles in 'rejuvenating' the body (as you put it).

When you first fall asleep, you go into NREM-1 phase, which is the lightest sleep, and progresses into NREM-4, and for the first half of your sleep cycle, this cycles so you go from NREM-1 > NREM-2 > NREM-3 > NREM-4 > NREM-3 > NREM-2 > ....

On the first half of your sleep cycle, the NREM3 and NREM4 phases dominates, only on latter half of your sleep cycle are REM phase observed and progressively dominate.

Depending on how much you are waken up by, once you escape your sleep cycle, you may re-enter back at a different stage, which may mean you are no longer able to have much REM sleep. Subsequently, you will not have the rejuvenation that is associated with REM sleep and you feel tired.

Interesting note: There are people who have tried a method called polyphasic sleep, where they nap/sleep periodically and regularly, instead of sleeping once a day for 8 hours, say. People who promote this says that people do not feel tired because as soon as they nap, they go in REM sleep, and so the amount of REM sleep you get per day will still be the same. I'll let you make your own mind up about this one.


Why didn't these scientists restore electrical activity in this pig's brain? This experiment was published in Nature Magazine: Pig brains kept alive outside body for hours after death. The researchers used a system called BrainEx to revive certain metabolic and physiological functions to a disembodied pig's brain, but they never attempted to restart electrical activity.

Why did they stop short of restarting electrical activity in this pig's brain?

Restarting electrical activity would mean that at least parts of the brain become active again and possibly restoration of almost all cognitive functions. While this would be a tremendous scientific and medical break-through, it would also mean that effectively locked-in syndrome would have been induced for these pig brains. Therefore just attempting to restore electric activity in isolated brains has huge ethical problems and was for this reason probably not allowed (or ever attempted).

Whether or not it should be allowed to test this in pig brains (in order to learn how to adapt the procedure to humans) is a different question (and not one for this SE) - the best way to go about would probably be to restore electric activity not in isolated brains, but with the brains still in animals.


Does osmosis take place in prokaryotic cells? As far as I know, osmosis occurs in Eukaryotic cells, and I'm wondering if it could take place in prokaryotic cells too.

Osmosis works across every cell membrane along a concentration gradient as its a physico-chemical principle. Water can cross the membrane (or cell wall), while the substance dissolved in it (for example salts) can not. Because eukaryotic cells only have a cell membrane, they will burst eventually, while bacteria (and also plant cells) have a more rigid cell wall, which will mostly prevent bursting. However the influx (or outflux) of water creates a pressure which is called turgor pressure. How this works is shown below (figure from here), bacterial cells and plant cells work pretty much the same way:


Why are mammals the only animals with pinnae / outer ears? Yes, I know owls have feathery "ear tufts", but these are less suited for hearing and more for display.

And I find it hard to believe that animals like dinosaurs or other cursorial archosaurs would not rely on sound as much as a mammal would. It's just too useful of a sense.

One potential clue is the fact that most non-mammal tetrapods appear to use electrical tuning to discern different sounds, whereas mammals use the hair cells of their longer cochlea to mechanically discriminate sound. I feel like this is related but not completely connected to why a fleshy outer ear structure that can collect and focus in on the direction of a sound.

Why did the pinnae evolve in mammals and why are they the only ones with such a structure?

Short answer Mammalian hearing is unique and amazing.

The mammalian ear is unique and highly sensitive with a built in amplification system that means even minute changes in sound can be detected. The bony amplification is also the reason the mammalian (or at least therian) cochlea is huge, every incremental increase yielded markedly more information, it has to get quite large before you hit the point of diminshing returns. This means mammals can get a lot out of even small investments into improving hearing. The vast majority of other groups just would not get any benefit from an external ear. their ears are not sensitive enough to gain anything the faint echoes external ears collect. The one group that would get some benefit (owls), has something functionally similar to an external ear.

The mammalian ear evolved from the repurposing of vestigial jaw bones no other group had (or more correctly they did not become vestigial in other groups). Mammals are the only group with a single bone in the lower jaw. it is a fascinating story and well worth a look. It kinda makes up for how awful mammalian eyes are.


Function of the alpha subunit in mitochondrial ATP-synthase? Within the catalytic core of mitochondrial ATP-synthase there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so clearly it is in these where ATP is synthesised.

However, I can't find what the function of the $\alpha$ subunit is. A source would be appreciated.

From: Uniprot

  Mitochondrial membrane ATP synthase (F1F0 ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F1 - containing the extramembranous catalytic core, and F0 - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F1 is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Subunits alpha and beta form the catalytic core in F1. Rotation of the central stalk against the surrounding alpha3beta3 subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits. Subunit alpha does not bear the catalytic high-affinity ATP-binding sites.

From: InterPro

  There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha-subunit contains a highly conserved adenine-specific non-catalytic nucleotide-binding domain, with a conserved amino acid sequence of Gly-X-X-X-X-Gly-Lys. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit [PMID: 12745923].

Sources:

http://www.ebi.ac.uk/interpro/entry/IPR005294
http://www.uniprot.org/uniprot/P25705
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278611/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679692/


Detecting cancer or a genetic predisposition based on DNA sequencing I am not by any means a biologist - so go easy.

What would be a method for determining whether or not a patient has cancer based only on a genomic sequence?

Update Thanks for the help in revising the questions.

What information is extractable once a genome has been sequenced?
Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.

When sequencing a human's (i hope im stating this correctly) genome is
  there a difference between the genome before and after the patient is
  found to have developed some sort of cancer.

If you are asking if cancer cells have an altered genome as compared to the rest of the organism, yes, this usually is the case.

  What would be a method for determining whether or not a patient has
  cancer based only on a genomic-sequence.

If you scrape some cheek cells to do DNA sequencing, you will know what the sequence is in those cheek cells, and you can figure that most of the cells in the rest of the body have that same sequence.  But if some, say, brain cells have acquired genetic errors causing them to start going haywire, that won't magically change the DNA in your cheek cells.

A genetic predisposition could be identified...if scientists had determined one.  For instance, Angelina Jolie got a double mastectomy because both her family history and her genetics strongly indicated that she would get breast cancer otherwise.


Global database for patients with rare and important injuries or disease? I was recently reading Christof Koch's The Quest for Consciousness, and several times he mentioned how important some patients with sad and terrible brain injuries were for the understanding of the working of the brain.

It made me wonder how brain researchers as Koch and others find such patients. I expect that only a small number happen to see an expert-brain researcher who understands that this patient could be important for brain research, especially for such people in less developed countries.

More generally, I wonder the same for patients with very rare injuries or diseases, which could potentially be significant for medicin- and biology-research:

  Is there a global database for patients with very rare deseases or injuries, making it possible for medical experts in the field to find them?

Even if the expert can not help the individual person, I imagine that such patients could be very important for future understanding/curing of the injury/disease. I hope to get some literature references or suggestion.

The MatchMaker exchange project is a federated approach that allows clinicians to find matching cases based on genetic or phenotypic similarity, retaining patient confidentiality.


How many chemical species are on average in a typical plant and animal cell? I want to know what sort of range there is on the number of different chemical species in a typical plant and animal cell. Failing that, some specific examples (with sources please).

Thanks

There is no average plant cell.  However this article describes a whole plant flux balance model with 333 metabolites. This won't describe a lot of the molecules plants make.

I seem to remember a natural product analysis of garlic that had scores of sulphur containing compounds that give its distinctive smell for instance.  This model would be a simplified plant which has no special characteristics like that, which probably doesn't exist.  Its probably not less than half the number of compounds that some plants produce or use.


Is there a comprehensive database of fossils (with images) online? Not sure if this is the best stackexchange to ask...

I have not been able to find a decent database of fossils on the web, does one exist?

Here are some of the links I have found through Wikipedia and Google:

http://www.paleoportal.org/index.php?globalnav=doing_paleo&sectionnav=more_submissions&state_id=0&submission_type_id=27&type_id=5
http://www.morphobank.org/index.php/Projects/Index
http://research.amnh.org/paleontology/
http://en.wikipedia.org/wiki/List_of_fossil_sites
http://www.fossilsites.com/STATES/AB.HTM
http://inyo.coffeecup.com/site/ammonoids/ammonoids.html
http://www.historicalclimatology.com/
http://geonames.usgs.gov/pls/gnispublic/f?p=gnispq:3:4473291015495555::NO::P3_FID:354414
http://www.scotese.com/earth.htm
http://www.trilobites.info/biostratigraphy.htm
http://burgess-shale.rom.on.ca/en/
http://www.fossilmuseum.net/FossilGalleries.htm
http://www.kumip.ku.edu/cambrianlife/Utah-Online-Fossil-Exhibits&Collections.html
http://www.ucmp.berkeley.edu/collections/catalogs.html
http://peabody.yale.edu/collections/search-collections?vp
http://books.google.com/books?id=Ezm1OA_s6isC&printsec=frontcover&dq=hartwig+primate&cd=1&hl=en#v=onepage&q&f=false

What are the best places to get fossil data and images of the fossils? Or are museums and textbooks the only alternative?

No. Museums are the traditional repository for fossils, and the process of "digitizing" their collections is slow and labor intensive. Often, the museums only aim to digitize what me might call the "meta-data" associated with the fossil, as was done here:
http://ucmpdb.berkeley.edu/cgi/ucmp_query2?admin=&query_src=ucmp_index&table=ucmp2&spec_id=V8111&one=T

A truly comprehensive database is not feasible in the near future. A single photograph likely would not be sufficient to characterize the fossil -- the interesting components of fossils are often microscopic. For example:

http://www.pnas.org/content/99/14/9117.full.pdf

Even taking a single photograph can be very labor intensive, and fossils can be fragile. Proper photo-documentation would probably require multiple images. More generally, a comprehensive database would probably need to include non-photographic data relating to the fossil -- such as chemical composition of non-visual imaging techniques (X-ray, IR, UV, etc).

For the foreseeable future, "comprehensive" collections will be housed in museums without full digital representation. The only way to know how comprehensive these collections are is to ask the museum curator, who will be aware of the scope and limitations of the collection.


Why does vitamin D need to be exogenous? Vitamin D is a either a hormone or a precursor to hormones. It is very unlike any other vitamins, which are either cofactors or antioxidants, or may be other chemicals necessarily performing catalytic function, just like transitional metal.

But in all sources I found so far it says that Vitamin D doesn't really do anything chemistry-bound, but rather just works as a hormone matching some arbitrary protein receptors or something. E.g. it signals something to the body. But what? And if nothing, then why does not evolution not select out Vitamin D in favor of endogenous chemical or nothing at all?

Vitamin D is vitally important for the uptake of calcium, iron, magnesium, phosphate, and zinc, as well as for bone maintenance:

  Vitamin D promotes calcium absorption in the gut and maintains adequate serum calcium and phosphate concentrations to enable normal mineralization of bone and to prevent hypocalcemic tetany. It is also needed for bone growth and bone remodeling by osteoblasts and osteoclasts. Without sufficient vitamin D, bones can become thin, brittle, or misshapen. Vitamin D sufficiency prevents rickets in children and osteomalacia in adults. Together with calcium, vitamin D also helps protect older adults from osteoporosis.

It also acts as a hormone, binding to the Vitamin D receptor in the nucleus of target cells which then acts as a transcription factor for genes related to multiple processes:

  Vitamin D has other roles in the body, including modulation of cell growth, neuromuscular and immune function, and reduction of inflammation [1,3,4]. Many genes encoding proteins that regulate cell proliferation, differentiation, and apoptosis are modulated in part by vitamin D. Many cells have vitamin D receptors, and some convert 25(OH)D [an inactive form] to 1,25(OH)2D [an active form].

So, the truth is far from your statement that "Vitamin D doesn't really do anything chemistry-bound, but rather just works as a hormone matching some arbitrary protein receptors or something." In fact, a cursory reading of the first couple of Google results for "Vitamin D" shows that it is broadly involved across the body in many different processes ranging from inflammation and cancer to bone maintenance and mineral absorption.

Sources:

Vitamin D - Fact Sheet for Health Professionals. NIH Office of Dietary Supplements. November 2014.
Vitamin D Wikipedia
Effectiveness and safety of vitamin D in relation to bone health. A Cranney, T Horsley, S O'Donnell, et al. Evid Rep Technol Assess (Full Rep). 2007 Aug;(158):1-235.
Vitamin D WebMD


What makes humans omnivores, and not herbivores? Some vegans claim that humans are herbivores, not omnivores, and that we are not physiologically designed to eat meat (see here: http://www.peta.org/living/food/natural-human-diet/).

  "According to biologists and anthropologists who study our anatomy and our evolutionary history, humans are herbivores who are not well suited to eating meat. Humans lack both the physical characteristics of carnivores and the instinct that drives them to kill animals and devour their raw carcasses.
  Although many humans choose to eat a wide variety of plant and animal foods, earning us the dubious title of “omnivore,” we’re anatomically herbivorous."

They go onto claim that we don't have tiger claws and teeth for catching and eating meat, that our jaws and teeth are designed for grinding plants not meat, that our stomach acid is too week to break down meat, that our intestinal tract is long like a herbivore for digesting plants and that it takes so long for meat to pass through that it rots and poisons us causing cancer, that we lack a hunting drive, that meat with it's cholesterol and protein is the cause of all disease so obviously its poison that we are not supposed to eat, that we get food poisoning from meat (like that never happens with vegetables...) and that the only reason humans started eating meat was to survive in times when there was a lack of plant foods available but according to our anatomy it's clear we're actually herbivores not designed for eating meat.

Can this be debunked?

As the answers given already point out, humans are generally considered omnivores that are able to use food sources available to them opportunistically. Apart from that, there actually is not much to debunk in the PETA statement - it is just a slightly one sided view on the history of human diet. Just as one sided as the claims that humans would not have evolved a really big brain without consuming animal products. Especially the canine teeth cannot be seen as evidence for prehistoric hunting, as in great apes the size of canine teeth is ridiculously well explained not only by defensive but mostly by mating behaviour; apart from that, humans do not even have those, and that most likely is caused by the trend towards monogamy which reduces inter-male aggression.

However, coming back to the actual question, in the relative short history (approx. 200-300ky) of our species there is evidence for 'several transitions towards or away from a vegetarian diet in humans' (Nielsen et al., 2017).

And in fact, there even is a human-specific evolutionary derived haplotype (younger than the Human-Neandertal split) that shows signatures of positive selection and is associated with increased efficiency in the synthesis of long chain fatty acid from plant precursor molecules - which would not really be necessary for meat eaters, as these fatty acids are readily available in animal products (Ameur et al., 2012). More specifically, the genes lying on that haplotype belong to the FADS cluster that seemed to have had adaptive value - also for synthesising long chain fatty acids from medium chain plant precursor fatty acids - in African populations even more recently (approx. 85 kya, Mathias et al. 2012).

This finding has been supported by a more recent study by Kothapalli et al. (2016). They investigated a 22bp-indel allele in the FADS2 gene that is associated with both higher blood levels of long chain fatty acids and exhibits high frequency (signature of positive selection) especially in South Asia and Africa where there is long tradition for plant-based diet.

Conclusion:

Modern humans (and this is relevant, as diet varies strongly between species and therefore the species comparison does not need to be very informative) appear to have changed diet frequently but there is evidence for human-specific molecular adaptations towards plant-based diets.


Diffusion across cell membranes I got this question and don't really understand the difference between the answers.

Diffusion is (in cell membrane):

a) passive by nature, no metabolic energy is needed

b) driven process by pressure or voltage

Diffusion is always a passive process that doesn't require energy.  Therefore it would seem that A is correct, B doesn't really make a whole lot of sense.  In the case of the cell membrane diffusion will often be in the form of 'facilitated diffusion' through carrier proteins, however the transport is still not active.


Determining the appropriate bioconjugate I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der Waals radius 5 angstrom) are made between the motifs in these two proteins. I also know that one of the motifs on one protein has a sulfhyryl (Methionine) and for the other motif on the other molecule I (think) can use a primary amide reactive moieties. Now this is where my question is.

Would I be correct in thinking that the best cross linker to use is a heterobifunctional cross linker, with a spacer of 10 (or 5?) angstrom in order to pick this interaction up specifically and stabilise it?

I desperately need a guidance on this. I have used the life technologies crosslinker selection tool and the crosslinking technologies hand book but I can't quite figure out based on the information I have, what cross linker length I need to use. I'm not worried about the cleavability, solubility and membrane permeability parameters.

UPDATE:

I know that the binding motif on the first protein it has Tyrosine, Proline and Methionine.

Looking at the groove contacts, the second protein is interacting with this motif, using Tyrosine and Glutamine BUT the second protein also has Tryptophan, Lysine, Glutamic acid and Methionine.

UPDATE 2:

I found specially close Glutamic acid (E) and leucine (L) on my first protein, specially close to Lysine (L) on my second protein although its not in the consensus sequence for the second protein. They are less than 10 angstrom apart. is that any better? So presumably I can use the homobifunctional linker?

Many thanks in advance

There are general guidelines for cross-linking protein-protein interactions, but specific parameters (i.e. cross-linker sub-types,  spacer length, linker concentration, reaction pH and temperature) are often determined experimentally. Common protein cross-linkers target reactive functional groups that are more likely found on the surface of the protein than in its "active site" or "interface" that is often buried.

Given your relatively hydrophobic, non-reactive binging motif (Tyr/Pro/Met), if you do not need a large amount of cross-linked protein sample, then you could label it with photoactivatable amino acid such as L-photo-Met. Since Met is not often found on the surface, internal cross-linking would stabilize your protein and its binding partner.

If you need a large amount of cross-linked protein (e.g. in mg) for further structural studies, labeling can be costly. You could possibly cross-link the protein (complex) crystal itself (since there were crystals as you mentioned), often just by glutaraldehyde. If the complex is there in the crystal, it would now be as solid as rock.


Different level of toxicity between smoke Has there been studies on the difference between the smoke generated from:

cigarette or cigar manufactured by brands which are proven to contain more than a hundred of dangerous additional components
tobacco/marijuana (more or less pure?)/any-plant-dried-leaves made cigarettes.

Apart from the nicotine both contain naturally, are the latter safer to inhale? in which scale?

The other question Effects of smoking tobacco compared to inhaling other smoke, reminds the danger of all source of intoxication, wall paints are also to consider.. and outdoors gas pipes, etc... But I'm doing a fixation on smoked drugs. I've been living in residences, sharing corridors with flats with more or less important smoke concentration, and had developped fumiphobia (but this is out of topic).

This is probably psychological but I'd never stay in the same room than someone smoking, but if someone take some dried leaves out of a plant,.. roll them in paper, fire it and inspire it. It never happened but I wouldn't be as much scared by the generated smoke. But if a study would show that manufactured cigarettes are between 1.5 and 3 times more 'toxic' then I would consider both cases dangerous.

I am not sure, if any comparisions have been made with other plant leaves, but unless these contain some pharmacologic active substances, I doubt that they are smoked widely.
There are comparisions between normal smoking and the smoking of marijuana and the short version is: Both are harmful. It depends on the temperature at which they are burned, how they where grown and so on. For smoking marijuana it also depends if you mix it with tobacco...
This fact sheet from the University of Washington lists a number of points on marijuana together with proper references.
Then there are some articles about smoking and marijuana in comparision:

A Comparison of Mainstream and Sidestream Marijuana and Tobacco
Cigarette Smoke Produced under Two Machine Smoking Conditions
On the Carcinogenicity of Marijuana Smoke
A possible chemical basis for the higher mutagenicity of marijuana
smoke as compared to tobacco smoke
Is frequent marijuana smoking harmful to health?


Why are males more likely than females to have autism spectrum disorder? The male to female ratio in autism spectrum disorder is around 4:1. However it seems ASD is not a simple X-linked disorder.

Then how is it possible males are more susceptible than females, if the causal genes are located in autosomes?

As the father of two sons with diagnoses of ASD, I think that it is best to think in terms of an extended spectrum which encompasses 'normal' people. We are all somewhere on this spectrum, but there is a threshold zone around where we cross from "normal" to "diagnosable as ASD". Now, if the distribution of spectral position for males is displaced towards the ASD end of the spectrum relative to females (because of some aspect underlying "normal' maleness, such as testosterone levels) then any genetic variation which pushes someone towards the ASD end of the spectrum by some fixed amount will tend to push more males over the threshold than females.


Are humans capable of both anaerobic respiration, and lactic acid fermentation? Are humans capable of both anaerobic respiration, and lactic acid fermentation?

And if so, when do they do each?

I understand that the difference between respiration and fermentation is that respiration takes place in the electron transport chain. I understand that aerobic respiration uses oxygen in the electron transport chain, and anaerobic respiration uses some other molecule in the electron transport chain instead of oxygen, like nitrate. Whereas fermentation doesn't use the electron transport chain at all.

I know humans have an anaerobic metabolic process that produces lactic acid, but I'm not clear whether it's respiration or fermentation, or whether it could be either, in which case when it is which?

added
some further discussion w roland at  the chat link / https://pastebin.com/raw/mkxckeqA / http://archive.is/CwCRL   and on this q at chat link here / https://pastebin.com/raw/9sV38LnQ / http://archive.is/HJVVe     and example of conflicting definitions available https://pastebin.com/raw/3EKGmEb6 / http://archive.is/9sAlY

Humans have no anaerobic respiration, if we define this as oxidation of a substrate with an external electron acceptor other than oxygen. In humans, the terminal electron acceptor in respiration is always oxygen, which is reduced at complex IV in the respiratory chain. Alternative electron acceptors are mostly found in bacteria and archaea.

I would call the anaerobic metabolism of glucose to lactate in humans a fermentation process. It consists of glycolysis, which converts glucose to pyruvate, which in turn is converted to lactate by lactate dehydrogenase. There is no terminal electron acceptor in this case; instead, energy is extracted from glucose by rearranging the molecular structure of the sugar into a more favorable ("low energy") configuration, without any net donation of electrons.

Note: this is how I use the terms, and I believe this is the most common usage in biochemistry today. But I am sure you can find other sources that define them differently. This is rather common in biology and biochemistry, and these terms are very old and fraught with all sorts of historical connotations. But names are not crucial; understanding the biochemical processes is. The important distinction here is that conversion of glucose to lactate does not oxidize the substrate and therefore needs no external electron acceptor; in this way it is fundamentally different from oxidative metabolism.


Please identify this bird Please identify this bird? There are bright red feathers at the bottom of its tail. What do we call these feathers?

update:
Location is North India. Temperature is around 35° C.

I am hesitant to provide 'positive' ID without location information, but this bird strongly resembles a Red-vented Bulbul (Pycnonotus cafer). The species is native to the Indian subcontinent, but is a common invasive species in many other parts of the world.

Key identifying features, with features visible in the photo given in bold (description from NZBirdsOnline):

Red-vented bulbuls are slim, starling-sized songbirds with predominantly dark plumage. They are typically bold and conspicuous, with repetitive, monotonous calls. Their slim build and curved bill are reminiscent of a honeyeater (e.g. bellbird or tui), although they are not closely related. The two most distinctive identification features are a small erectile crest on the crown (giving them a square-headed Roman helmet look when the crest is raised) and the diagnostic bright red patch between the base of the legs and the undertail. The head, hindneck and upper breast are glossy black, with a circular brown patch over the ear. This dark hood becomes streaked or scaly on the lower breast and merges into the pale grey belly. The upper wings and mantle are mid-brown with pale margins when in fresh plumage, creating a scaly appearance. The rump is white, and the tail is long and blackish with a prominent white tip. The bill, eyes and legs are dark. The sexes are alike, although males are slightly larger. Juveniles are dull brown with an orange or pinkish (cf. red) vent.

The red feathers around the vent do not have a special name - you can just call them 'the feathers around the vent'.

edited for the addition of location information

As the photo was taken in Northern India, the bird is almost certainly a Red-vented Bulbul. The Red-vented Bulbul is common throughout India, and there are no similar species in the range that could easily be confused with this species.


I need a site for online courses I need a site which has online courses for anatomy of limb and head and neck and also embryology, so far I have used www.coursera.org and it was really organized and helpful but unfortunately it does not have courses about these subjects, does anyone know a site like that which contains some organized videos in English language, I have searched a lot but it was not successful!

Biology LibreText

Khan Academy

MIT OpenCourse Wave


Why are fish constantly in motion? When I see fish in an aquarium, they never seem to stop swimming. This is in contrast to e.g. the penguins, who spend a lot more time just standing there.

Is this true in the wild or specific to aquariums for some reason? Is there a biological or evolutionary reason this is so? Is it a special case of some more general principle? (It occurs to me that fish are much smaller than penguins.)

A research, detailed in a 2012 issue of the journal PLoS Biology, suggests the fish do indeed take naps and can experience sleepless nights.

Another research with Pacific sand lance species, found them utilize a one of a kind methodology of tunneling into sand to rest and moderate vitality, and to maintain a strategic distance from predation.

Therefore, we can assume that fish sleep cannot be related to a terrestrial. As @Zxyrra has mentioned, with the currents being random in their direction, we can connect the reasoning of the continuous movement of the fishes as an effort to stabilize themselves.

On the aspect of any evolution or biological reasoning, fish sleep is still an ongoing research in marine biology. An interesting research have opened up a case in which through evolution, cavefishes have lost sleep. Information from this research could help you understand the evolutionary relationship of fish and sleep, in atleast, a broad scale.

UPDATE: Unique method of sleep in dolphins.

At the point when it's an ideal opportunity to rest, a dolphin will close down just a single side of the equator of its mind, and close the inverse eye (the left eye will be shut when the correct portion of the cerebrum dozes, and the other way around). Amid this time, the other portion of the cerebrum screens what's going in nature and controls breathing capacities. This process is termed as unihemispheric slow-wave sleep.


Can an octopus survive if one of its three hearts stops working? While reading the book "The Soul of an Octopus" by Sy Montgomery, I learnt that Octopuses have three hearts. This is very fascinating. According to a Wikipedia article,  two of the three are used to  pump blood through each of the two gills while the third pumps blood through the body.

So, my question is can an Octopus survive if one of these hearts stops functioning?

The Wikipedia entry you linked and the other answer both state that...

  ... the systemic heart is inactive while the animal is swimming and thus it tires quickly and prefers to crawl.

I tried to find an accurate source corroborating this (by accurate I mean a paper in a peer-reviewed journal or a zoology book), but I couldn't. The best source (scientifically speaking) I found was this page from the Smithsonian Institute, which says:

  Octopuses have three hearts. Two of the hearts work exclusively to move blood beyond the animal’s gills, while the third keeps circulation flowing for the organs. The organ heart actually stops beating when the octopus swims, explaining the species’ penchant for crawling rather than swimming, which exhausts them.

A much more reputable source is Octopus: Physiology and Behaviour of an Advanced Invertebrate. It says:

  If an octopus is surprised by a sudden movement on the part of an observer, or a thump on the side of its tank, the systemic hear may miss one or more beats.

Which is, evidently, way less dramatic than having one of the three hearts stopping.

The same author says, talking about Octopus vulgaris:

  Together with changes due to exercise and arrests attributable to sudden tensing of the body musculature, any prolonged recording reveals apparently spontaneous changes in amplitude that are not obviously correlated with anything that the animal can be seen to be doing. From time to time the heart stops for several seconds (as it does, for longer periods, in O. dofleini).

Thus, apparently, the maximum we have here is periods longer than several seconds (which the book, unfortunately, doesn't determine more precisely).

In conclusion, despite their circulatory system being very complex and the systemic heart being able to stop beating for several seconds (or during the whole time of swimming, as the Smithsonian says), it doesn't seem possible that octopuses can survive if one of their hearts stops (forever). Have in mind that the hearts are not redundant, that is, one heart cannot perform the function of the other (if that other one stops).

Source: Wells, M. (2013). Octopus. 1st ed. [Place of publication not identified]: Springer.


C1q attachment to antibodies After reading about complement pathway and the complement components, I was wondering, does the C1q component attach to the Fab fragment or to the Fc fragment? The pictures in Janeway's Immunobiology are confusing and the text don't mention about this.

Complement factor c1q binds to the constant Fc portion of an antibody (Duncan & Winter, 1988). Indeed, the constant (Fc) tail of the antibody is where other proteins involved in immune responses typically bind, most notably the Fc receptors (e.g., Clynes et al., 2000) found on immune cells such as B lymphocytes. Fc receptors mediate the recruitment of immune cells to a site of infection. The primary role of the Fab region is antigen binding as it contains the highly variable antigen binding domain. See the following figure (from the site of Invivogen) for the Fab and Fc region showing the constant and variable regions of antibodies:

  Figure legend from Invivogen): The Fc region mediates effector functions, such as antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). In ADCC, the Fc region of an antibody binds to Fc receptors (FcγRs) on the surface of immune effector cells such as natural killers and macrophages, leading to the phagocytosis or lysis of the targeted cells. In CDC, the antibodies kill the targeted cells by triggering the complement cascade at the cell surface. I

The constant regions of antibodies are located on the heavy chain (CH1,2,3) and the light chain (CL). These constant regions are potential binding sites for other immune molecules as they are constant between antibodies, irrespective of the variable region in Fab. Most of the constant regions are found on the Fc region explaining its major role in binding other molecules involved in the immune response, including complement factor c1q. However, the constant regions in Fab (CL) may also provide binding sites for other proteins and indeed some bacterial compounds are known to bind to this region (Bouvet, 1994). However, I have not found evidence of c1q binding the Fab region.


How are PPI networks constructed? I am a CS graduate working in Computational Biology. While the theoretical aspects of both AP/MS (and the various types) and Y2h are quite clear to me, the actual technical aspect of building large-scale PPI networks is not. Is there a machine that can do these experiments? How long would building a network take for say, 2000 proteins? Is there a company that can provide this service?

I would appreciate any help. I have searched a lot but was unable to find an answer for this question.

It depends on the PPI network. Some, like DIP are exclusively experimental, depending on high-throughput robotic AP/MS, Tandem Affinity Purification, Y2H, cross-linking with formaldehyde, clever things involving half-fluorophores, etc. There are a lot of different methods, is what I'm saying. Y2H has a high false-positive rate, immunoprecipitation is expensive (antibodies cost money), others have other drawbacks.

You can also exploit the existing huge body of research using text mining, even though that's really crude. (It boils down to: protein A and protein B or their pseudonyms are often mentioned in the same sentence, they must be related somehow). There are also RNASeq methods, where you just do hundreds of RNASeq experiments and two genes that correlated(or inversely correlated) are probably interacting in some way. If two proteins interact in organism A and they have closely-related homologs in organism B, the proteins probably interact in organism B too.

In short: In a lot of different ways. It would be wise to check the provenance of a link in such a network and handle it differently depending on what kind of link it is if you're working with big networks like this.

I don't know that there are any companies that do this commercially, but the Max Delbruck Center will talk to you about screening something custom. I don't know how long it would take but 2000 proteins would not take a long time, relatively speaking. The human genome has tens of thousands of proteins, so 2000 proteins would only be a few percentage points of the effort. However if they're totally novel there's probably library setup times and overhead, but I don't even have a good guess how long this would take. Depends on who you talk to, I expect.


Advanced books about molecular biology and genetics I'm finishing my third year of biochemistry and doing gene therapy practicals during the summer. I'd like to buy a book that describes flow of genetic information (transcription, translation, replication, splicing...) and its mechanisms in depth (such as transcription factors, regulation, etc). The closest thing I currently own is Lehninger's Principles of Biochemistry, but most of it deals with metabolism. I've also got to know about Molecular Biology of the Gene, but I'm not sure if it's what I'm looking for. I'm not interested in books about heredity or population genetics.

Molecular Biology of the Cell is a great text book, and an older edition is available for free on NCBI bookshelf. However, the book covers a broader range of topics than perhaps you're interested in and may not go into the same depth as others (though I haven't actually done a side-by-side comparison).

Watson, who along with Crick developed the central dogma of molecular biology, literally wrote the book on this subject: Molecular Biology of the Gene. It sounds exactly like the text book you’re looking for, and was one of my favourites as an undergrad. You can check out the contents of the book yourself to make sure it's what you want.


What is the global average BMI? I have been looking for hours trying to find this number, and can't seem to get a straight answer.  I've seen some studies that calculate the change in BMI, but for some reason they don't give you the actual numbers, just the rate of change.  I've also found information for individual countries, but I want the global average, and would prefer not to do a calculation with 196 different sets of data.

The answer might be a little late, but it was published after you asked the question. See the following publication for estimated global BMI averages from 1975 to 2014: http://thelancet.com/journals/lancet/article/PIIS0140-6736(16)30054-X/abstract


What characteristics do living organisms (like humans or plants) have that viruses don't? I am not too sure if viruses are considered living organisms.

I learned that living organism:

-Change their size
-Reproduce
-Heal themselves
-Need energy (by eating)
-React to the environment
-Have a lifespan
-Made of at least 1 cell (some exceptions)

Which features that are listed are not in viruses?

If I need to be more clear, please tell me as I'm not very good at explaining.

Linving organisms have intricate metabolic pathways that viruses donot have viruses stay in equilibrium till they infect host meaning that they they donot exachange matter and energy with surronding when they are outside the body but is a property shown by humans and living organisms.


Confusion regarding the ventricle system in the brain I have a hard time finding out a small detail about the ventricle system.

As the CSF flows into the 4th ventricle, there's a small foramen in the lateral aspect, as well as an open space bounded by the medulla and cerebellum.

Do both these lead the same place? Is the space under the arachnoid matter only accessed through the small foramen, whereas the space between the medulla and cerebellum leads into the spinal column?

I've found the answer. The entire brain and spinal cord is bounded by the arachnoid mater, thus both channels would lead into the subarachnoid space, which also circulates the fluid into the spinal cord region. The CSF exits through the arachnoid granulations, which are like valves, found on the dorsal midline, into the superior sagital sinus, where it returns to the blood stream.


Career progression through biosafety levels? Does a career in infectious disease typically progress through biosafety levels, or do people select one and specialize their training in procedures specific to those hazards?

That is, say Dr. Kliener wants to work on TB (BSL3). Does he first on have to work on MRSA (BSL2), which he has no interest in, just to build up experience? Or could he simply learn everything there is to know about TB and BSL3 lab procedure, don hairnet and gown, and get to work with someone who has experience under those conditions?

My short answer would be no, careers of people who study pathogens requiring biosafety training are not focused biosafety level.

More broadly, the people I know who study infections diseases are not motivated by the biosafety levels of their infections organisms. Rather, they are motivated by biological questions and their research that often require higher biosafty for their labs.

For example, the researchers featured in a recent (July 2015) National Geographic do not study Ebola because they want to work on a BSL-4 level virus. Rather they want to about learn about the disease from both a basic science and applied human heath perspective.

Your hypothetical Dr. Kliener would not work his way up the biosafety chain as a conscious. Let's say a young Mr. Kliener always wanted to study human health. He probably would have started doing research in a BSL-2 facility as an undergrad research assistant (See BSL-2 requirements here. As a grad student, he might have worked at a BSL-3 lab if he choose a good program while spending years focusing on a specific pathogen or system. By the time he became because a PI, he would have needed to find a BSL-3 facility for his research. He worked his way up, but not because he wanted to study dangerous pathogens. Rather his research question guided his path.

Other career tracks could end up using a BSL-3 facility, but not necessarily need the stop at a BSL-2 facility. For example, a hypothetical Dr. Fish may have started off loving the outdoors. She studied limnology as an undergrad and grad student and did not step foot inside a lab. However, when she began working as biologists for a state conservation agency, a novel fish virus emerged. She now is tasked with studying it. Her agency trained her to work in a BSL-3 lab so she could culture fish with their virologists.


How does the body respond to blood donation; are there any possible risks? Can blood donation cause any harm to the donor? I have been told so, but cannot find any references supporting this claim. I have also learned that our body will replace the lost fluids within 24 hours and the RBCs within weeks. Can blood donation still cause health issues for our body?

This is not a personal medication question, and I mainly want to know how the body responds to blood loss and what mechanisms that monitor the altered levels of blood volume? To me, it would also be unethical by medical doctors to withhold the possible risks of blood donation to prospective donors, but it might also be seen as unethical to discourage a person willing to donate blood from doing so, so there might be a conflict of interest here.

My answer below directly (and solely) addresses what I think is the main gist of the question: Are there any adverse effects on one's physiology as a direct result of donating blood?

Blood donation, at the amounts typically taken (200~500mls), will not harm you. A healthy human being produces approximately 100,000,000,000 (one hundred billion) NEW hematopoietic cells DAILY to replenish short-lived blood cells and platelets. All of these ultimately derive from the hematopoietic stem cells residing in the bone marrow within one's long bones.

As you can appreciate, with such a huge amount of turnover daily, the body is constantly churning out new blood cells. Thus, any depletion in blood cells one will experience as a result of blood donation is a fraction of what will be lost normally in daily homeostasis anyway and thus will not affect a healthy individual.

And then there are the knock-on benefits suggested by epidemiological studies, some of which are alluded in this layman article: http://news.health.com/2014/06/13/4-unexpected-benefits-of-donating-blood/

[source: I'm a hematologist]


Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks? I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks:

  Isotopes
  If the mass spectrometer you are working with has sufficient resolution look at the isotopes, a singly charged ion will show isotopic peaks that differ by 1 mass unit, a doubly charged ion will show peaks that differ by 0.5 mass units and so on. This is another way to deduce the charge state of a peak and thus the mass.

So let's suppose the spectrometer has a sufficient resolution to look at the different isotopes. It's not really clear for me at which peak I have to start. So to summarize my questions realted to this topic:

Which peak do I have to look at when determining the charge based on the isotope distribution?
Why would the peaks differ 0.5 mass units (see above)?

update

source: http://mascot.proteomix.org/help/mass_accuracy_help.html

When looking at the above graph, there is a difference of 1 amu between the different peaks.

What do the isotopes have to do with the charge?
What does this charge (and isotope distribution) tells us about the peak on which we zoomed in to create the above graph?

If you have an ion of mass 100 and charge 2, the m/z ratio (let's exclude the root) will be 100/2=50. If you have isotopes, then you expect to find several peaks for a given fragment. For example, the masses of different isotopes of the same molecule could be like: 100, 102, 105 and 107. In this case the spectrometer will detect four peaks, instead of one, for the same molecule (will look something like this): 100/2, 102/2, 105/2 and 107/2. The charge of all that peaks is the same.. it's only the mass that differs.

The page you linked simply makes an example, "singly charged ion will show isotopic peaks that differ by 1" example m=10 z=1 m/z =10, for the isotope m=11 z=1 m/z=11 (difference of 1). If you have a doubly charged ion m=10 z=2 m/z=5 and for the isotope will be 11/2=5.5 (difference of 0.5).

So, if you take the spectra of a compound and you see the isotopic peaks having a distance of 0.5 among each other, you are looking at a doubly charged ion, if the distance is 1, it's a singly charged ion.

What do the isotopes have to do with the charge?
Given that the isotopes peaks are around 1 units far from each other, you can conclude that the ion you are looking at has 1 charge.

The last question is not clear to me.


What is the viability of Intelligent Design as a supplement to chemical abiogenesis and Darwinian Evolution? First of all I am not endorsing Intelligent Design (Wikipedia link); I'm asking this because I (someone who does not have a background in biology, organic chemistry, or philosophy) got into a conversation with someone who does endorse it, and I'm trying to see his point of view as far as rationality can allow. Second of all, I apologize for any vagueness; Intelligent Design isn't well enough defined as a theory for me to help that. I also apologize if this is rehashing content already plentiful on the Internet, but for my purposes I can't simply depend on the likes of Wikipedia or Talk Origins, so what I'm looking for here instead is to take the opposite approach and see, based on your informed minds, if there could possibly be any reasonable likelihood of an ideal ID theory being adopted.

  I'm looking for the most favorable consideration for what ID might be
  if it were best developed as a viable hypothesis or theory to get an
  idea of how far such a discussion is worth taking. An unbiased,
  informed Devil's advocate, if you will.

My cursory investigation of what Stephen Meyers (video link) and Michael Behe (video link) say (correct me if I'm wrong) seems to be that either the first cell was likely designed intelligently judging by the complex code of DNA and that evolution took course from there, or that the first cells were made and many instances of evolution were from some kind of intelligently guided mutations as was needed to make "irreducibly complex" cells or body functions (whether the guidance stops after the Cambrian or continued even to the point of making different types of new bacteria and different types of apes/humans or whether every single mutation and adaptive ability is being guided, I'm not sure if they're at any consensus, and that's why I don't know if I should stop my question at abiogenesis or include evolution). The person I spoke with also brought up some specific claims (everything looks designed, DNA has ordered, complex information, blood clotting is irreducibly complex, ID can and has make predictions like decades ago that "Junk DNA" wasn't junk) that I don't need you to debunk (I have Google).

But if there could be any possible support or truth to any of the above, I would appreciate knowing about that. (Again, Devil's advocate so I can be informed and understand where the points come from.) Reading an ID book alone, it would be in places hard to know where they differ from actual scientific conclusions. After all, when someone who seems to know what they're talking about and can explain something in technical detail says that something is impossible or extremely unlikely, it's hard for me to know why they would be wrong (are they ignoring other possibilities? misrepresenting facts? are they really right and just getting the cold shoulder from an atheistic scientific community because it implies a deity?). So I focus on mainstream sources, even if they don't bother entertaining ID and leave me ignorant of its possible virtues. And thus I'm hoping someone from this informed community might enlighten me to what those possible virtues might be.

I think the issue with Intelligent Design is not so much that its patently proven wrong.  On the contrary, the problem is that it not a scientific hypothesis and so it really isn't a scientific question.

If I may, the basis of the scientific method, as formulated by Karl Popper, but commonly in use today, is that science is the putting forth of theories of cause and effect which are testable (or if we are being precise, falsifiable).

That is to say, you put forth a theory such as 'God/some diety figure made all living things' and then you perform an experiment which can differentiate whether the hypothesis or its null version (i.e. 'no intelligence is the source of life / biology is the result of accidents') is more likely true.

This question will not be testable in a way to answer enough of the reasonable skeptical questions ( or at least so far it has not).  Experiments have been tried, but they are often not acceptable to everyone.  For instance the idea that some biological structures such as the eye or the flagellar motor are too complex to have evolved through a typical Darwinian process which involves a series of small changes are almost biological theology - one can always hypothesize a more inhuman God (probably appropriate) who acts and 'thinks' in such an inhuman manner that anything you see could be created/inspired.  While I think you should feel free to believe either way, I also believe that this is not an argument that can be won or lost.  The tendency for any experiment to confirm both the hypothesis and its inverse seem inescapable.

That is to say, that biology and physics will ultimately fail where philosophy and logic also did in proving the existence of God, besides the less interesting truism that if God does exist, the deity is consistently elusive to proof.

On the other side of the coin, the proof that life has emerged from naturally occurring phenomena such as lighting strikes in a prebiotic environment are interesting since it shows that nucleotides and amino acids might have been available without metabolic pathways to synthesize them.  In its way, the molecular origins of life on earth is a question which is really testable only in theory.

Anyone who thinks they are going to re-create the event of the beginning of life itself is scientifically on thin ice - the prebiotic environment may have extended to the entire surface and atmosphere of the earth as well as down into mud and bodies of water and sat incubating for maybe hundreds of millions of years.  The idea that the fundamental moment of life generation is just going to show up on a well chosen set of conditions in a 500 ml flasks with some electrodes attached is an idea that workers in the field don't even entertain.

Until such an experiment produces life, the work will have to rely upon the idea that there was a moment in time where the necessary elements came together.

This being said, cosmology, biogenesis work has approached the moment of the genesis of life asymptotically with amazing clarity.

The RNAWorld hypothesis strongly supports the idea that an early biotic system might have been very simple - maybe only RNA and its four nucleotides.  Clearly after what Dawkins calls a replicator exists, then the pathway to living things as we know them is pretty easy to envision.

I should add that I'm not one of those people who think that science is everything - the trend that is impoverishing some humanities program is alarming to me.  Its just that some things are not science.


Does a critical mass of infected individuals exist after which mutations will overtake vaccination attempts? As we know, all organisms have a probability to undergo mutations when they replicate. For every infected individual with the Covid-19 their bodies are environments in which the SARS-CoV-2 may mutate beyond existing vaccines.
Therefore, as the number of infected individuals increases, there will come a point where mutations in the SARS-CoV-2 would occur faster, perhaps even concurrently in different countries, than vaccines may be developed and deployed to stamp out the virus once and for all.
So my questions are as follows: is there a critical mass* of infected people, beyond which our existing vaccine development & deployment time frames will not be able to cope with? Do we have an estimate of this number?
*I understand this is not a single, fixed number but a fuzzy, probabilistic range.

Epidemiological modeling
If a virus is able to change so that it renders previous vaccination inefficient, reinfecting those who were previously vaccinated, one could describe this process using epidemiological SIS model (Susceptible-Infected-Susceptible) or its modification that includes a vaccinated group (like SISV model), and indeed estimate how quick should be vaccination in order to eradicate dthe virus before everyone gets infected. One could even add a D (deaths) compartement and study whether the virus may lead to extinction of the huiman species (unlikely, since the survival rate is very high).
Real viruses
In reality we are not dealing with such a situation, since there is no reason to think that mutations make SARS-CoV-2 able to overcome the immune defenses (although they do make it more contagious and more dangerous to non-vaccinated individuals).
To clarify the issue let me outline the scenarios where viruses do escape vaccine resistance.
Influenza
Flu is known to be susceptible to vaccination, and this is a lasting vaccination. What makes this virus to come back every year is gene reshuffling, where it exchanges some of its several genes with similar viruses living in animals (the roles of some of these animals in flu outbreaks gave rise to such names as swine flu, * birs flu*, etc.). This means that every few years we are dealing with an essentially new virus (rather than a virus that has accumulated many mutations), which is not visible to the antibodies created by previously administered vaccines. In this sense, one cannot exclude a possibility of a new coronavirus causing a pandemic in a decade or so, just like the current outbreak follows similar ones due to SARS in 2002 and MERS in 2012.
HIV
HIV is know to adapt very quickly to the new antibodies, evading the immune defenses. This makes it impossible (or at least very difficult) to develop a vaccine against this virus. However, HIV is much less contagious than flu or coronavirus, since it needs to infect specific cells/tissues. In orther words, it is stopped by the barriers of the immune system other than those boosted by vaccination. Coronavirus is a much simpler virus than HIV and will never reach the same degree of sophistication via mutations.
Bacterial pathogens
Bacteria are known for routinely developing resistance to antibiotics, which has been somewhat of a hot issue in terms of antibiotic development. They however share the same weakness as HIV - being less contagious (and far more complex).
To summarize, the devil is in the details: the scenario outlined in the question is good for science fiction, but it has very low probability to be realized in real life.


Is fever a disease or not? I have seen this question where the author is asking why people take drugs for fever. So my question is: Is fever is a disease or not?

I know pretty much nothing in medicine!

Fever is an abnormally high body temperature. Fever is a symptom and not a disease per se. Different medical conditions (incl. various infectious diseases) causes a patient to have fever.

Note that fever might be in some/most situations an adaptive response to a disease. In other words, for infectious disease causing fever, fever might be good for the host and not for the parasite. However this issue remains controversial (see the post linked in the OP's question for more info).

As GoodGravy said in the comments, many people get confused and consider fever as a disease instead of what it really is; a symptom. One likely reason for this confusion is that when one has fever, (s)he very often treat fever directly (taking drugs like Aspirin for example) rather than treating the underlying cause (the virus for example) of the fever.


best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like "biological sequence analysis" by durbin and "fundamental concepts of bioinformatics" by krane, etc. But I wish to read a comprehensive book on biology (genetics) that will help me undertake research in bioinformatics properly. I have been considering 2 books: "molecular biology of the cell" and "molecular biology of the gene". Are these books comprehensive enough? Please suggest some good books as I have almost no knowledge of biology at highschool or graduate levels.

Welcome to Biology and welcome to Biology.SE!

It is hard to answer such a question as the domains you describe are very vast.

If you want a book in an introductory book to biology, then you want to read this post and this post.

If you are more interested in population genetics and molecular evolution then this post will interest you. Still talking about evolution I'd like to attract your attention to this post for the second suggestion in the first answer:  Yang, Computational molecular evolution

You'll probably want to have a look at the post A free book/resource for learning genetics?.

Book recommendations for algorithms used in evolutionary biology and Introductory book in genetics might be a post of interest as well.

Unfortunately I don't know any of the two books you cite so I can't quite give you advice for them. molecular biology of the cell is a very common book among first year biology. It sounds like a potential good reading for you. I know nothing about molecular biology of the gene except what I just read about it on Amazon.

I am hoping one will give you a better criticisms about very general books about molecular biology.


View ABI chromatogram plots with python I would like to view the chromatogram traces from a few ABI (.ab1) files. I would prefer to use python for this, or a function with python bindings, or at least some open source package such as EMBOSS.

If after viewing a plot I could also extract the plotted data in the form of an array, that would be a huge plus.

I have tried the relevant Biopython parser, but it only returns a list of nucleotides (not th actual chromatogram). I have also tried abiview, but I get plots such as this, which makes absolutely no sense:

Could you help me out?

The Biopython 1.65 ABI parser should expose the chromatogram data, as of Biopython 1.66 it should expose everything.

UPDATE: Example using this for plotting here: http://biopython.org/wiki/ABI_traces


What non invasive methods of estimating Body Time are there? I found this article on estimating body time using molecular timetable of 168 genes. researchers looked at gene expressions and plotted them to 24 hour cosines curve with some pretty spectacular results.

Unfortunately the techniques discussed required sampling of liver cells, which may be invasive. Are there non- invasive methods of estimating body time/ biological clock/ circadian rhythm time?

An example of body time: at 8:00 real time, a mouse may exhibit gene expressions more appropriate for 9:30, so the body time of the mouse is 9:30.

For circadian rhythm, the gold standard is melatonin secretion (blood or saliva). Also, core body temperature.

see: Circadian temperature and melatonin rhythms, sleep, and neurobehavioral function in humans living on a 20-h day

James K. Wyatt , Angela Ritz-De Cecco , Charles A. Czeisler , Derk-Jan Dijk
American Journal of Physiology - Regulatory, Integrative and Comparative PhysiologyPublished 1 October 1999Vol. 277no. R1152-R1163


What are the odds of being an albino human and have Down syndrome? I know the odds of a human to be an albino. In Europe and the US it is 1 in 20,000 people (source) and for Down syndrome it is 1 in 1,250 (source). So that means the chance of giving birth to a child that has both albino and Down syndrome is:

$20,000 \times 1,250 = 25,000,000$

i.e., 1 in 25,000,000 correct?

It is correct if (and only if) albinism and Down syndrome are independent events, that is, if albino people is not more nor less likely to have Down syndrome than non albino people (and vice-versa).

However, doing a quick Google search I can't find any source relating albinism and Down syndrome, and therefore independence seems a reasonable assumption unless more information arises and your numbers are right - at least, as right as the sources you are based in.

But beware that your sources are not very representative of what you want to get, or at least not very consistent:

Your source for albinism (and its reference) gives prevalence, that is, number of albino people in the whole population of living people in Europe and USA. Please notice that proportion in living population may differ from proportion of births since albino people may have a different life expectancy.
Your source for Down syndrome gives a "baseline probability" for a given mother age (young) in some unspecified country. For older ages, probability becames larger.

Then, "the chance of giving birth to a child that has both albino and down syndrome" may differ from that you calculated, specially if you want to use it in circumstances that differ from those your data came from.

Anyway, if you just want a rough estimate, you can use your numbers.


What is the smallest known organism with a skeleton? See question title. After doing some looking around on my own I haven't found much so I figured I'd ask some experts.

The smallest vertebrate (if that's what you mean; there are many invertebrates with endoskeletons that are not made of bone) is Paedophryne amanuensis, a Papua New Guinea frog that's about 7 mm long.


Are Zebras white with black stripes, or black with white stripes? I'm not sure it makes sense, but are zebras black or white below the surface?

It is not like someone painted a zebra one color (say white) and then painted lines of the other color (say black) on top. But it does not mean we can't give some thoughts on the question.

What causes these patterns?

The colors are caused by pigments. Melanocytes either produce black pigments or do not and this cause the alternation of white and black stripes. The exact developmental pathway for producing these stripes is still very much unknown. All we know is that several environmental variables seem to affect this pattern. The most important correlate found so far is temperature, where higher temperature lead to darker and better defined stripes (Larison et al. 2015). This pattern can also be observed geographically (although there might have other important covariate driving this pattern, such as genetic typically)

So, are zebras black or white?

According to the Brevard Zoo, under their white or black fur, the skin is always black. This, I suppose, might lead others to rather claim zebras are black with white stripes.

From @iayork's answer, it appears that embryos are first black and then white tripes appear. This an extra reason to claim that zebras are black with white stripes. Note however, that I am not sure whether the skin of zebras are not first white, then turn black and then black fur and then white fur. Under such circumstance, one might want to argue that zebras are white with black stripes.

So if we take your question as phrased

  [A]re zebras black or white below the surface?

If by "below the surface" you are referring to their skin, then they are black (according to the Brevard Zoo)!


Species-area relation graph When species richness is plotted vs area, the graph follows the equation : log S = log C + Z log A where Z is the slope of the line. Z values are usually in the range of 0.1 to 0.2 but if very large areas like entire continents are analyzed, the slope is much steeper. (0.6-1.2).

Why is it so ?

(Here S = species richness and A= area under consideration)

Z value is a fitted constant and it ranges between 0.1 to 0.3 regardless  of the region or taxonomic groups.i.e. the slope is almost similar .Among larger areas like continent,the slope tends to be much steeper.becoz, Larger the area larger will be number of species(species richness),for larger areas the Z values tends to be 0.6 to 1.2.(NOTE:if Z is less,lesser area is enough to capture more species).


Calculating sample concentration factor (opposite of dilution) I am starting up an algae project, and I am getting a bit confused about some details in calculating density. For example, I take a sample of 250 mL, and concentrate it down to 25 mL with a sand filtration apparatus (factor of 10). I am using a gridded sedgwick-rafter chamber to enumerate the density of algal cells on a cells/mL basis using this formula from Standard Methods 10200F: cells/mL = [(# organisms counted)* (1000 cu. mm.)/ (field area)(field depth)(# fields counted)].

Once I calculate cells/mL, should I DIVIDE that result by my concentration factor (10)? My instinct is to multiply, but wouldn't that be appropriate only if I diluted the sample?

Your original sample is more dilute than the sample you counted. The concentration is less and therefore you should divide your counted concentration by 10 to get the concentration in the original sample.


Looking for protocol to produce a drosophila primary cell line I'm looking for a general (and easy, this is going to be for an undergrad class) protocol to isolate and culture primary cells from fruit flies.

This is the original 1972 paper describing the isolation of the S2 cells from Drosophila. However it would be best if you specify what application you are planning to pursue with the cells, which would make it easier to suggest which ones to isolate. I have personally isolated garland cells, which are visible with the naked eye and highly suitable for endocytic assays. It takes a few minutes to isolate them and all you need are two grade 5 or grade 4 sharp tweezers and 2nd or 3rd instar  Drosophila larvae and a dish and some PBS to submerge the larvae in. You don't even need to pin them! If you are interested I can edit this response and write their isolation technique as I can't find a good technique online.

EDIT:

I have not personally isolated S2 cells although I have extensively worked with S2 and S2R+ cell lines (which are embryonic). Garland cells are excellent to work with for endocytic assays using Dextran (fluorescent dye used for bulk endocytosis assays) and Dynasore [dynamin inhibitor] (and infact they were used to characterise Drosophila dynamin homologue, shibire, here and here and its temperature sensitive behaviour in Shi[ts] mutants and shi role in endocytosis) as an example shown here in fig 6 using S2 cells. I have never cultured the garland primary cells so I do not know their PD and how they behave in Schneider+FBS (since I only isolated them and performed andocytic assays with them while they were in schneiders) and I don't think anyone has (but have a look) so it would be a great protocol to stablish and publish in a methods paper. I'm more than happy to share the isolation technique with you, tried looking on jove or youtube for a video but failed to find one, and let you know what to look for if you wish. Just as a cautionary note, garland cells are multi-nucleated (i have seen up to 4) so it might not divide very well or at all so just bear that in mind.


Is female the default sex in humans? I was taught in school that female is the default sex in humans based on the following logic:

Development into a human male requires the activation of the SRY gene in the foetus. If that doesn't happen (because there is no Y chromosome, or for some other reason) then development into a female occurs.

For historical context on the use of the term default, please see this article:

Female sexual development ... was thought to proceed as a “default” in the absence of Sry.
The English word, “default,” means “failure to act; neglect” or “a preselected option adopted […] when no alternative is specified” (Oxford English Dictionary, 2011). In the case of sex determination, “default” became the prevailing model for female pathways—i.e., an ovary results in the absence of other action...

Is it reasonable to say that female is the default sex in humans? If so, is the SRY gene all there is to it?

Summary:

The idea that primary sexual determination defaults to female was proposed several decades ago and is primarily based on the observation that, in the absence of Sry, ovarian development takes hold. However, more recent models suggest that both ovary and testis development require complex genetic regulation and neither can really be said to occur by default. Furthermore, maintenance of sexual determination is apparently a life-long process.

Quote from a Review (Yao 2005):

  We have just begun to glimpse into the mechanisms underlying ovarian development. Convincing evidence challenges us to reconsider the existing paradigm that describes ovarian development as a default system. The default concept was first proposed in the early 1950s when Jost performed the groundbreaking experiments to demonstrate mechanisms of sex differentiation of reproductive tracts (Jost, 1947, 1953, 1970). The term “default” was not originally intended to describe the developmental status of the ovary. Instead, it is referred to the female reproductive tract or the Mullerian duct based on the fact that the female reproductive tract forms in both XX and XY individuals in the absence of gonads. Indeed, now it has become evident that early ovarian development is an active process involving intrinsic cell fate decisions and complex crosstalks between germ cells and somatic cells. Most intriguingly, the appearance of testicular structures in XX individuals where Sry and its downstream components are absent further raises the improbable question: Could the testicular development be default after all?

Some Details:

Sex determination in mammals involves the development of a bipotential gonad into either a testis or ovary. Sertoli cell differentiation and thus testis formation is under the control of the regulatory gene Sry (Koopman et al. 1991). The Sry gene product was later shown to upregulate the expression of Sox9, which is key in testis development (Sekido and Lovell-Badge 2008). On the other hand, ovarian development is centered on β-catenin stabilisation by WNT4 signalling, which is thought to inhibit Sox9 expression (Bernard et al. 2012). Because Wnt4 is expressed basally in the genital ridge and testis development apparently depends on Sry expression, the ovarian pathway has often been described as default; in other words, the pathway that the gonad would take in the absence of Sry.

However, ovarian development is in fact an active process requiring the correct balance of many factors, including a transcription factor called forkhead box protein L2 (FOXL2) (Yao 2005). Studies in mice showed that Foxl2 is expressed in the ovary, both during development and in adulthood. Knockout of the gene prevented granulosa cell differentiation during development, leading to ovarian failure (Schmidt et al. 2004) and increased expression of markers for the testis development pathway (Ottolenghi et al. 2005). Furthermore, mutations of this gene are responsible for XX sex reversal in goats (polled intersex syndrome, PIS) (Pailhoux et al. 2001). Taken together, these experiments indicate that Foxl2 is required for ovarian development and that its absence can favour testis formation.

Many developmental process are dependent on correct timing of gene expression. Sry, particularly, must be expressed within a specific time interval or ovarian development will take hold (Bullejos and Koopman 2005; Hiramatsu et al. 2009). Research by Uhlenhaut et al. (2009), however, shows that this is not necessarily the case for Foxl2 mediated ovarian development, maturation and maintenance. A homozygous floxed Foxl2 mouse strain that expresses Cre under tamoxifen induction allowed conditional knockout of Foxl2. Three weeks after induction, cells of the ovary had transdifferentiated, adopting a morphology and gene expression pattern consistent with Sertoli and Leydig cells (which are normally found in testes). Notably, Sox9 expression increased drastically. Immunostaining showed that, while Foxl2 expression expectedly decreased after Cre induction, the increase in Sox9 was not observed until a day later, indicating that the expression of both is mutually exclusive and that FOXL2 may directly regulate Sox9.

This research presented a novel model for the maintenance of female ovary differentiation. During primary sex determination in females, activation of WNT4 signalling stabilises β-catenin allowing expression of female specific genes and the inhibition of Sox9 (Bernard et al. 2012). In adulthood, FOXL2 actively represses Sox9 expression in gonad cells, maintaining the granulosa phenotype. A similar model of maintenance has been proposed in males due to evidence that the loss of the transcription factor Dmrt1, which normally represses (and is also repressed by) Foxl2 expression, induces transdifferentiation of male mouse Sertoli cells to granulosa cells (Matson et al. 2011). In the case of both males and females, primary sex determination is not just a process that occurs during development but rather requires active regulation for the duration of adult life. This involves collective antagonism between various female and male sex determining factors, including Foxl2 and Dmrt1, and may dispel the notion that ovarian development occurs by default.

Further Reading:

The Genetics of Sex Determination: Rethinking Concepts and Theories

Genetics of sexual development: a new paradigm (Blecher and Erickson 2007)

References:

Bernard P, Ryan J, Sim H, Czech DP, Sinclair AH, Koopman P, Harley VR. 2012. Wnt signaling in ovarian development inhibits Sf1 activation of Sox9 via the Tesco enhancer. Endocrinology 153:901–912.

Blecher SR, Erickson RP. 2007. Genetics of sexual development: a new paradigm. Am J Med Genet A 143A:3054-68.

Bullejos M, Koopman P. 2005. Delayed Sry and Sox9 expression in developing mouse gonads underlies B6-YDOM sex reversal. Dev. Biol. 278:473–481.

Hiramatsu R, Matoba S, Kanai-Azuma M, Tsunekawa N, Katoh-Fukui Y, Kurohmaru M, Morohashi K-I, Wilhelm D, Koopman P, Kanai Y. 2009. A critical time window of Sry action in gonadal sex determination in mice. Development 136:129–138.

Koopman P, Gubbay J, Vivian N, Goodfellow P, Lovell-Badge R. 1991. Male development of chromosomally female mice transgenic for Sry. Nature 351:117–121.

Matson CK, Murphy MW, Sarver AL, Griswold MD, Bardwell VJ, Zarkower D. 2011. DMRT1 prevents female reprogramming in the postnatal mammalian testis. Nature 476:101–104.

Ottolenghi C, Omari S, Garcia-Ortiz JE, Uda M, Crisponi L, Forabosco A, Pilia G, Schlessinger D. 2005. Foxl2 is required for commitment to ovary differentiation. Hum. Mol. Genet. 14:2053– 2062.

Pailhoux E, Vigier B, Chaffaux S, Servel N, Taourit S, Furet JP, Fellous M, Grosclaude F, Cribiu EP, Cotinot C, et al. 2001. A 11.7-kb deletion triggers intersexuality and polledness in goats. Nat. Genet. 29:453–458.

Schmidt D, Ovitt CE, Anlag K, Fehsenfeld S, Gredsted L, Treier A-C, Treier M. 2004. The murine winged-helix transcription factor Foxl2 is required for granulosa cell differentiation and ovary maintenance. Development 131:933–942.

Sekido R, Lovell-Badge R. 2008. Sex determination involves synergistic action of SRY and SF1 on a specific Sox9 enhancer. Nature 453:930–934.

Uhlenhaut NH, Jakob S, Anlag K, Eisenberger T, Sekido R, Kress J, Treier AC, Klugmann C, Klasen C, Holter NI, et al. 2009. Somatic Sex Reprogramming of Adult Ovaries to Testes by FOXL2 Ablation. Cell 139:1130–1142.

Yao HH-C. 2005. The pathway to femaleness: current knowledge on embryonic development of the ovary. Mol. Cell. Endocrinol. 230:87–93.