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Do transcription factors bind to both strands of DNA?
Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. Any reference books, papers or links will be helpful.

possible duplicate of On which strand does the promoter sit?

I don't think this is a duplicate, in fact I might vote to close the other question and link to this one, as the accepted answer is much clearer and nicely illustrated, with links to sources. However, both questions are fundamentally different, and neither necessarily needs to be closed. Yes, they are about similar things, but are not identical.

The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding proteins obviously bind one strand but they do this in a non-specific manner.
RNA-binding proteins recognise the sequence on a single strand by inserting intercalating planar residues between bases! All of this binding is non-covalent.
Transcription factors recognise sites in dsDNA, with DNA-binding domains. The rest of the protein might surround (partially, to varying degree) the negative outer surface of the dsDNA double helix with positively-charged surface, in order to hold it on to DNA as it scans (perhaps) along its length.
DNA-binding domains: major groove

The following domains are found in many transcription factors, and they all recognise both strands. More correctly, they recognise basepairs and their orientation. The first 5 pages of this lecture slideshow demonstrate that the chemical groups on the side of basepairs, accessible in the major groove, allow proteins to distinguish A:T, T:A, C:G & G:C by the order of hydrogen-bond donors, acceptors, and a methyl group.
Hence, TFs recognise a sequence of basepairs - oriented such that one strand is (e.g.) pTpCpApG, and the complementary strand is pCpTpGpA; and the bulk of the protein may 'sit' on one strand or the other - or a nearby gene may locally define one strand or the other as the coding strand but this does not mean that this one strand is read.

Zinc fingers probe the major groove with reading helices.
Helix-turn-helix motifs do much the same.
Leucine zippers also do much the same.

These are common domains that all recognise basepairs in the major groove by interactions with residues on a probing aplha-helix.
TATA-binding protein: minor groove
TATA-binding protein (TBP) is a different, interesting case. It binds the 'TATA-box' via the minor groove, where the exposed chemical groups only distinguish [A/T] from [C/G], but not their orientation. This means that the sequences on each strand cannot be easily read from the minor groove. TBP instead recognises the shape and flexibility of the double-helix at the TATA-box, 'grips' it by the minor groove and bends the DNA, which aids the melting of the strands to the transcription 'bubble'.

The TATA-box sequence is usually pTpApTpApApA on the coding strand upstream of the transcriptional start. This is the convention when giving the sequence of a TF-binding site, but you couldn't say that TBP actually reads TATAAA - it doesn't!
Here is another, similar set of lecture slides.
Even better, here is the same material covered in a popular textbook.

@Teige : Comprehensive answer

Addition to the answer provided by Teige.
Transcription factors bind to both the strands however your question also included proteins in general.
DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) and Rad52 bind to ssDNA during replication and recombination respectively (there are more examples). These are not transcription factors though.


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Recombination-based vs. Sequence-based genetic mapping
Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?
I think that in the past recombination-based genetic maps were used as blueprints for sequencing projects. But since now the entire genome can be sequenced pretty cheaply both in time and money, what is the unique value of recombination-based genetic mapping?
One thing that comes to mind but I am not very sure. It might be suitable for mapping novel phenotypic markers e.g., unmapped diseases.

A couple of months ago I listened to a plant physiologist who strongly recommended recombination-based mapping over sequencing based mapping. The main reason he gave was the error-rate of 2nd generation sequencing. The error rate on Illumina platforms are about 1 % if I recall. In a small genome like that of Arabidopsis thaliana (157 Mbp) that accounts for over 1 million sequencing errors. That can of course be reduced having a proper sequencing depth and using the consensus sequence. But it can still cause problems if you're tracking a phenotype caused by an SNV. In plants like A. thaliana where back crossing can be used to create homozygous plants, recombination-based techniques can be particularily effective.
But he was talking from a plant physiologist's view when working with A. thaliana as a model organism. When working with humans which always are heterozygous, can't be back-crossed, don't have a generation time of six weeks and where samples sizes will probably be small I imagine that the situation is different. The classic geneticists' working with human diseases that I have talked have expressed fear that their work will soon be obsolete due to falling sequencing prices and growing sequence data collections.

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Can the immune system stop plasmodium from being active?
Suppose a female Anopheles infected with Plasmodium bites someone and transmits Plasmodium to their body.
Can that person's immune system be strong enough that it can kill the Plasmodium before it starts entering into red blood cells to rupture them?

There appear to be some references here: http://www.bio.davidson.edu/people/sosarafova/Assets/Bio307/ruturakhia/page03.html

The short answer is yes, at least with P. falciparum. Even if they're not taking anti-malarials, not everyone who gets bitten by an infected mosquito becomes symptomatic (I don't know about RBC entry, that may happen too quickly). Unfortunately I don't have the references handy, which is why this isn't a formal answer, but this information came from a professor studying the immune evasion techniques of the parasite.

@MattDMo hmm!. I always tell my friends who curse the medical science to not to eat anti malarial tablets when they get malaria. I tell them that one infected with malaria will 100% die if they don't eat antimalarial tablets which is a medical science creation. so MattDmo am I right when I say that to support medical science to my friends who it. I mean if malarial patient doesn't take antimalaria, will he die?

@MattDMo why don't you answer it instead of adding comments. I want to upvote you for this answer that I can't unless you answer it

The experience of a former adviser of mine was that some people who are not taking anti-malarial medication can still resist infection with Plasmodium falciparum, one of the parasites responsible for malaria. The parasite's life cycle includes stages inside the Anopheles sp. mosquito, and they are transmitted to human host via the female mosquito's saliva when she bites to have a blood meal:

(from Wikimedia)
There is currently a great deal of research going on to understand the biology of the parasite and how it typically evades the immune system so well. Proteins expressed by the parasite can undergo antigenic variation, meaning that different forms are expressed at different stages of the life cycle, and just as the immune system may be forming a response to one version, it is down-regulated and another takes its place. This is one reason why making a vaccine has proved to be so difficult, as unlike the influenza virus, for example, a single strain of Plasmodium can alter its immunogenic appearance and escape antigen-specific immune responses.
While malaria is responsible for a high degree of morbidity - sickness - it is not necessarily fatal except in some cases, frequently when the victims are young, already ill, or are otherwise immune-compromised, or when the infection moves to the central nervous system and the brain. I can't speak from personal experience (fortunately!), but I have been told by numerous friends that malaria is something you want to avoid at all costs. The sickness can last for weeks in some cases, and apparently is quite debilitating at its worst. Brain fever can be deadly, and in many third-world countries and among the poor the lack of good medical care can lead to complications. There is the additional factor that the family has to care for the sick, and if the ill person is a wage-earner that can mean the difference between food on the table and going hungry.
So, your friends are not going to die (probably) if they don't take their tablets, but there is no reason not to take them unless you have strong side-effects, and in that case the doctor may be able to find you another one. Other common-sense measures include always sleeping with a bed net, putting screens in windows, covering exposed skin during active mosquito hours, wearing repellant if available, and eliminating places where standing water can collect, stagnate, and provide a breeding area for mosquitoes.

This paper estimates the mortality rate of untreated malaria as 1.8% (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021416/).  The lifetime cost in terms of protracted illness are not considered.  There's a good reason that antimalarials are useful and worth taking in the future. If you haven't taken them before, that's another thing.

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How do I get recombinant proteins into the nucleus of mammal cells?
I know that there are Nuclear Localisation Sequencenes (NLS). They can be taken from endogenous or viral proteins and fused to the N or C terminus of my recombinant protein.
Which is the best one? Which the best short one (so that it can be more easily added with a Primer)? Should it be attached to the N or the C terminus?
Do they influence expression?
I have heard that size does matter (Too large wont fit through the nuclear pore, too smalll will diffuse out again). What is the range of protein sizes that can be targeted efficiently?

To use a N-terminal or a C-terminal tag depends on your protein. I can only say that you can try both and see which one does better.

It also depends if your protein has important domains on one of the sides. If so, I would start by using the other end to avoid interference.

Thanks for the general tip. In my case I have seen people putting stuff (including NLS) to both ends of the protein. Here I am really more concerned about transport efficiency.

I've seen people use 3 NLS sequences in a row, I assume this improves transport efficiency, but they never explained their reasoning.


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Is it possible to give a person an allergic reaction in a very specific place?
Can I give a person an allergic reaction at a very specific spot in a tissue?
And if so, how accurate can i get?

You might want to look at the patch test.  Though I'm a little concerned by the motivation of this question.

Thank you this did help :)
Lets say I know a persons allergic reactions will it be possible to do the following? and if so can I change the hypersensitivity level reaction in this proses?

I don't have enough information to make a full answer, but I'm allergic to mangoes. When I eat one, the parts of my skin that the mango touched will get a bad rash, but anywhere it didn't touch will be unaffected.

Depends on the kind of allergic reactions you want to create. If your target tissue is skin epithelium sure you can.
That's actually the way the skin allergy test is all about: The physician tries a wide variety - last time I did it were 28 well known kinds - of substances in liquid form (drops). If an allergic reaction is caused, the physician takes note. Even very small quantities can cause allergic reactions.
These tests are usually made in a secured environment (physician's office, hospital, etc) at a very low level which most of the times, if result is positive will cause just an irritation. The level of irritation will be self-explanatory, so even a non trained patient can understand what is going on.
Not sure if that what you were asking though.
Best Regards,
pa

Funnily, the severity of the reaction does not correlate to symptoms the allergy might cause... of all allergies I have, dust mites gave the weakest skin prick reaction; but it's the only symptomatic allergy I have. The prick test can vary a lot, depending on the purpose; I don't think there's a standard set of allergens they test, apart from ready-made allergen "sets" such as "grasses" or "trees".

Well, yeah I was referring to allergies about trees, grasses, dust, etc.  But sure, allergies are not 100% understood anyway.

Thank you this did help :) Lets say I know a persons allergic reactions will it be possible to do the following? and if so can I change the hypersensitivity level reaction in this proses?

You say "do the following", but there's no "following" sentence, so I don't know what you mean by "do the following". :-) - The hs reaction usually is "linear" but might have more than one variables, so I'd say that it's kind of dangerous to try it out on your own... Better visit a physician.

as in following i mean the patch test mentioned earlier :)
and i wont this is a part of sum recerch Im douing ill go to the universality to figer out more soon thank you.


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Rate of cell division in humans
On average, how many cells divide each day in a human being?
How long does a cell wait before dividing itself ?
I have tried to look on the internet but surprisingly the answer is difficult to find..

Thats pretty hard to answer, since the proliferation rate of cells is pretty different. For example heart cells hardly ever divide while cells of the hematopietic systems do this pretty often.

This is very difficult to answer since the rate of cell division is age and also health dependent.

My first thought was this:
According to Wikipedia (citation provided)

Between 50 and 70 billion cells die each day due to apoptosis in the average human adult. For an average child between the ages of 8 and 14, approximately 20 billion to 30 billion cells die a day.

For every cell that dies a new one must be born, so there must be at least between 50 and 70 billion cell divisions to replenish these cells in an adult human (no net growth).
But then I remembered erythrocytes. Wikipedia again:

Adult humans have roughly 2–3 × 1013 (20–30 trillion) red blood cells at any given time, comprising approximately one quarter of the total human body cell number

and...

these cells live in blood circulation for about 100 to 120 days

So approximately 1% of erythrocytes are destroyed every day and must be replaced. That's 2-3 x 1011 cells formed every day, which dwarfs the cells replenished due to apoptosis (5 - 7 x 109).

Through this process [erythropoiesis] erythrocytes are continuously produced in the red bone marrow of large bones, at a rate of about 2 million per second in a healthy adult.

I like the answer, but there is a problem with the math. 50-70 billion cell is 5-7 x 10e10, not 5-7 x 10e9. It is still larger than the 2-3 x 10e11 number of the blood cells by a factor of about 4, but not by a factor of about 40 which is the result of the original calculation.

Thanks for spotting that Len.  So the sentence that says 'That's 2-3 x 10e11 cells formed every day, which dwarfs the cells replenished due to apoptosis (5 - 7 x 10e9).' should say 'That's 2-3 x 1011 cells formed every day, which is ~4 x the cells replenished due to apoptosis (5 - 7 x 10e10). Not sure about the protocol here, do I edit my answer?

It's also important to note that starting point of this estimate of 50-70 billion cells has no reference in the wikipedia. D'oh! So the whole thing is on very shaky grounds. I've tried to find a paper for this statement but have come up empty so far.

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Meiosis vs. Mitosis
Meiosis is a type of cell division that reduces the chromosome number from 2n to n to make gametes viable for reproduction in humans. I know that during meiosis, there is independent assortment and crossing over that occurs, which help to make more genetically individual organisms.
My question is, why don't haploid gametes go through mitosis to reproduce instead of diploid germ cells going through meiosis to create more gametes, without considering crossing over and independent assortment? This is just my opinion, but meiosis seems like a much more energy intensive process. After the germ cells go through meiosis once to create the gametes, I do not see why the gametes don't then just multiply via mitosis (again, not considering crossing over/independent assortment.)
Is there any specific reason, other than to create more genetically diverse people, that gametes do not undergo mitosis to multiply rather than germ cells undergoing meiosis to make more gametes?
Sorry if my question is confusing, I'm just curious to what the reason is. It's probably something obvious I'm not seeing myself. :)

I think this is a great question, but it is based on two questionable assumptions: (1) that meiosis is more energy-intensive than mitosis; and (2) that energy efficiency is a key driver in evolution.

Couldn't fit in a comment...
To me, your question sounds like "what are the possible advantages of sexual reproduction over asexual reproduction?" but in the meantime you're saying that you're not interested neither in the advantage of recombination nor in the advantage of "independent assortment". I don't quite see what you mean by "independent assortment" in this context.
I just want to say some words about some "proximate" possible explanations of the evolution of sex. It's been suggested that meiosis have evolved in order to repair damage in double stranded DNA. Also, it's been suggested that meiosis is important for the problems of telomere length also.
You might be interested to have a look to the evolution of bi-phasic life cycles and, more globally speaking to the evolution of sex.

I'm not interested in the advantage of recombination because I want to know if there's anything beyond that that makes meiosis more advantageous than mitosis. Also, I was always taught that "independent assortment" referred to how chromosomes line up independently of one another in Metaphase 1 before they split into separate cells. Is that term incorrect? Is it just a term used to help students learn the process? I guess I never really questioned the terminology before..

So, you're interested in what I called "proximate" explanations? Or we could call them physiological explanations. If yes, I'll let someone further develop these kind of explanations.

Yes! Please. Sorry for not being clear initially.

I would suggest that the key here really is the variation produced from meiosis. Every gamete produced from meiosis is genetically unique. This gave rise to variation, which is the raw material for evolution. Meiosis would give a selective advantage in this way, therefore it could have allowed organisms to survive and pass on their genes.


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Why is it that I can understand speech through one ear better than the other ear?
First, I do a lot of music so I'm used to pick up details in sound and I have had hearing tests showing that my ears are quite well balanced, for my age, without any dead spots.
When I am in a social situation, I will hear people's voices equally well on both sides, however I will 'understand' dialog better on one side.
I remember reading many years ago that this is normal and there is a known reason for it, but I can't really find much about that topic.
Does anyone here know why this is happening?


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Eye Brain Mapping
If our eyes are separated by some kind of full proof barrier/isolation, is it possible that our brain can picture/visualize two different pictures at a time?
How the brain will function in this situation?
which are the books to read to understand in depth brain behavior?
I tried to isolate my eyes with hands/paper but i am not able to do it.

I heard about yogi learning to move their eyes independently, this may be a starting point for research.

dd3 answered this already, but here's an idea how to separate your eyes: take a pair of (sun)glasses and put a different sticker on the left and the right piece. Then put them on.

First off, I should note that binocular vision is important for depth perception.
The phenomenon in which you are interested is called binocular rivalry (distinct images are presented to each eye).  You typically switch between the images, and sometimes, both at once (superimposed; this is called binocular transparency) or an averaged picture (binocular fusion).
You can find some good links at the Wikipedia page.  The Scholarpedia page is even better.  If you don't find what you're looking for, I think searching for papers on "binocular rivalry" will give you the best result.


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What are centromeres *really*?
I've gathered that a centromere is a a region*  where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark regarding its physical structure and functioning.
At what point during DNA replication is the centromere created, and how is it created? How does it hold the chromatids together (what are its components)?
Specifically:
When it is being created (presumably during cell division) how is the positioning  of the centromere controlled? Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot: a section of DNA that 'says' "Right part of centromere, to be attached to left part"?
Secondly, after their condensation into chromosomes (e.g. during prophase), are the sister chromatids physically intertwined around each other** for the purpose of joining, or are they simply adjacent?

Is there a 'loop' in the centromere slung over the adjacent chromatids to join them?
If they are intertwined, how is this achieved during DNA replication, whilst the non-centromere parts of the sister chromatids are not intertwined?

How does the centromere break down to allow the chromatids to separate (e.g. during meoisis 2 and anaphase)?
On a somewhat unrelated note, what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?

*(i.e. there is not a separate physical object dubbed 'the centromere', rather it is a collection of objects in a region)
**(That is, considering no other molecules than the chromatids, if you were to pinch the top and bottom ends of the left and right chromatids and pull them apart, could you separate them without them locking together (basically, do they intersect knot-theoretically)?)

There are many questions in your question. I'll try to answer each question pointwise.

Which flags are used by the enzymes in the process of making the
  centromere to tell them that it is the right spot

There are some centromere associated repeats in the DNA which mark the site for centromere assembly. There is no particular consensus sequence of this repeat. However, this study says that in certain cases stable chromosomes are formed in the absence of centromeric repeats.

are the sister chromatids physically intertwined around each other for
  the purpose of joining, or are they simply adjacent?

They are joined by proteins called cohesins. Cohesins looks like rings which form around the sister chromatids. During anaphase, the anaphase promoting complex (APC) activates an enzyme called separase, which in turn degrades cohesin.

what in the centromeres do the spindle fibres attach to, and how do
  the tips of the growing fibres notice it to head it its general
  direction?

Centromeres serve as a site for the assembly of kinetochore. Kinetochore is a multi-protein complex which forms contact with the spindle fibres (specifically, K-fibres. Refer this previous post). An essential component of kinetochore is the motor protein dynein which makes the kitetochore to crawl along the spindle fibres, towards the pole. The wikipedia article on kinetochore is quite descriptive and you can refer that for details.

Thanks you. I put many questions in one place for continuity.

Supplemental

When it is being created (presumably during cell division) how is the
  positioning of the centromere controlled?

The marks of "centromere" is added the G1 (CENPA) and S phase (all other members of the CCAN) of the cell cycle. As for how the positioning is controlled... the answer is unknown. But it does appear that when a centromere sequence is replicated, the proteins from the original centromere are divided between the two new copies of the centromere DNA sequence . So a DNA sequence is a centromere because it was a centromere. But how did it get to become a centromere in the first place is currently unknown.


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Are CoA and CoAS the same thing in a compound?
Is CoA-S-R the same as CoA-R, and is CH3C(=O)CoA the same as CH3C(=O)SCoA? Eg. Above is the compound on the right just coenzyme A or is it actually another compound and not just notation?

To understand the nomenclature here it is very helpful to think about how Coenzyme A works. It has a thiol group (-SH) which can form a thioester bond to an acyl group.
So the sulphur in "CoA-S-R" is part of the CoA, and in "CoA-R" the sulfur is just not explicitly named. Those two mean exactly the same thing: Coenzyme A linked to R via a thioester on the thiol group.
One specific variant that is very important in biology is acetyl CoA. The chemical formula you mentioned (CH3C(=O)CoA) is acetyl CoA, and here the same as above applies and the sulphur is explicitly mentioned in the second one and implied in the first one.


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Is there a difference between NADH and NADH2?
I've been reading a lot about the oxidative dissimilation etc, and often I see different sources use NADH and NADH2 in the same reactions. One source uses NADH and another uses NADH2 in the exact same way. Is there a difference or is it just a different name for the same substance?

They are often used interchangeably to indicate the reduced form of $\ce{NAD+}$.  The overall reaction when oxidizing some molecule $\ce{RH2}$ is: $\ce{RH2 + NAD+ -> NADH + H+ + R}$.  The proper reduced $\ce{NAD+}$ is $\ce{NADH}$ (it accepts two electrons and one proton), but sometimes $\ce{NADH2}$ is used to account for that second hydrogen that gets removed from the substrate being oxidized.  The notation $\ce{NADH2}$ doesn't really take into account the fact that the second hydrogen is charged, and not bound to the $\ce{NAD}$ in the same way that the first hydrogen is, so it is confusing.  The notation: "$\ce{NADH + H+}$" is more correct and is also sometimes used.


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At what cancer stage do tumors release circulating tumor cells into the blood?
And would a very accurate sensitive system for detecting circulating tumor cells (which detects 1 cell per 50 billion) be useful as a screening tool ?

Tumour cells can also metastasise using the lymphatic system. They first need to detach (produce enzymes that break down the extracellular matrix or any adherent molecules etc). Then they need to survive in the blood which is really hard with all the mechanical stress of being pushed around, the completely different nutrients, the different levels of blood gases, the immune cells in the blood and numerous filter mechanisms, then to truly metastasise they need to settle down somewhere and grow in their new environment. That's a lot of things right? So a sensitive assay like one you describe would need to have that tumour cell in the sample (unlikely, and only one cell is required to make a new tumour), is likely to be unable to tell that the cell is a tumour cell, wouldn't be able to differentiate between tumour cells that could or couldn't survive in the blood or differentiate those that could then go on to grow more in a tissue or not. And of course you're missing the entire lymphatic system. Following all of that, why does it matter? See a cancer, cut it out if you can and give chemotherapy to get rid of any possible cells outside of what you cut. If your assay came back negative or positive, treatment wouldn't change.

Screening programs are ruled out following sharp guidelines, like the so-called  Wilson' criteria and subsequent  ones provided by WHO. Specific documents regarding  cancer screening have been published. A good primer on what a screening program in medicine is, can be found on  wikipedia.
Conventionally, a tumor is considered non capable of metastasis (neither through blood, nor through lymphatic vessels), unless it doesn't invade the basement membrane, that is a thin layer of tissue that separates epithelias from the underlying tissues.
In invasive neoplasiae, the surgeon have to cut it until the resection margins are free from tumour cells. This is achieved through real time microscopical examination by a pathologist during the procedure. If an ideal resection can't be performed, often medical therapy (e.g. chemotherapy) is suggested to the patient as neoadjuvant therapy. A neoadjuvant therapy is given in order to transform non optimal resectable tumors in good surgically treatable ones.
Commercial kits like this  1 ,  2 ,  3 ,  4  are available on the market for this kind of test. Although there are this kit to find this cells, this method is not suitable for screening.

First: This doesn't really answer question how to detect circulating tumor cells. Then: The administration of chemotherapy is not only dependent, if tumors can easily be resected but also from the stage etc. It's not that easy.


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Regarding cancer cells and radio-frequency ablation
Are cancer cells destabilized if near a strong electromagnetic field over a long period of time? I read this technique of using radio-frequency ablation and heat shock to kill cancer cells. I don't know if this is viable but maybe a person could wear a device like a pacemaker right over the area of a tumor that emits  strong E.M. pulses over say a month or a year. Could this destabilize the tumor ?

Can you please add a source for this? To my knowledge electromagnetic fields have no proven effect on humans. Otherwise the use of NMR scanners (which use very strong magnetic fields) wouldn't be a good idea.

a separate device could be designed if viable. Doesn't make sense to get a pacemaker as it has another more specific purpose.

There was a story today on the C.T.V. news (in Canada) , on Saturday August 9/ 2014 about using beams of microwave and an M.R.I scanner to kill a tumor ; the patient improved greatly.

I think you're referring to radio frequency or microwave ablation. It works by heating the tissues up with electromagnetic radiation, just like you'd use to microwave food, but it's heating you instead. Healthy cells have better repair mechanisms and survive these treatments better. Cancer cells tend to have poor repair ability and can be killed more easily. I've heard of injecting metal nanoparticles which collect in the tumor due to the enhanced permeability and retention (EPR) effect. The nanoparticles respond to the microwaves much more powerfully than cells do and get hotter, burning the tumor from the inside out.

User 137 said 'cancer cells tend to have poor repair ability'. Could a mild virus that is not harmful to healthy cells kill a cancer cell?

Do cancer cells have poor repairing ability because most of their 'facilities' are committed to growth and repair?


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Regarding inherited fertility in animals
If an animal is fertile does it follow that both its parents of the same species (not necessarily the same species of the offspring)? Was it Mayer who said a fertile male and fertile female of two different species, if they 'reproduce' and the offspring survives it won't be fertile. Reproductive isolation I think this is called. So if an animal is fertile then both its parents should be of the same species, right?

No it isn't necessary that the parents should be of the same species. Mules (male donkey X female horse) have been found to be fertile (reference). The wikipedia page on hybrids lists many inter-species hybrids that are fertile including Beefalo (Domestic male cattle X american bison). There are also many canine hybrids which are fertile. Wholphins have been found to be fertile.

A wholphin or wolphin is an extremely rare hybrid born from a mating
  of a female bottlenose dolphin (Tursiops truncatus) with a male false
  killer whale (Pseudorca crassidens).

So in short, for a hybrid offspring to be fertile, it doesn't necessarily need to be of the same species.

I know this is 'heresy' but if two different species are fertile and have a fertile offspring maybe they are not really different species but different subspecies.

@user128932 I wouldn't call them sub-species but atleast closely related species because a donkey and a horse can hardly be called a sub-species of one or the other. You can read this article. http://www.detectingdesign.com/donkeyshorsesmules.html

Do a donkey and a horse have a common ancestor ( with four legs)?

If a fertile female 'individual' , call it 'A' ,and a fertile male 'B' of a 'similar' but distinct species ; both have important differenses in their respective physiologies ; 'A' might have an important physiological process that 'carries out a certain biological tasks yet 'B' might not have something similar to this. So when passing on their important biological info. to their offspring how are possible physiological-process differences resolved. For Example a cat and a dog must have unresolvable physiological differences ; no one has bred a Dat or a Cog.

@user128932 Yes, they do have a common ancestor and your question here about the resolution of physiological processes in species crossbreeds needs to be asked as a separate question.


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Have we succeeded in building a living organism from inanimate material?
Following the Miller-Urey experiment where we were able to produce organic compounds with basic primitive atmospheric gases, high potential and water in a closed system. Have we been able to create a living organism fully functional with only inanimate material (dead material, or atoms, or anything that is not coming from a living organism such as a clone, or already existing DNA)?
I mean building a living organism from scratch. Are we able to do this?

We have not been able to do this, though whether or not we can in a reasonable time scale is unknown.

We've made organisms with 6 different nucleotides (instead of 4) though.

Do you have a source to support this? I'm guessing it's more prion or virus looking than plant or sheep looking...

https://www.sciencealert.com/new-organisms-have-been-formed-using-the-first-ever-6-letter-genetic-code and https://phys.org/news/2017-01-scientists-stable-semisynthetic.html

The most recent paper on the subject is Feldman et al. 2017. They worked on E. coli. This video by Sciencium (same author of Veritasium) report their findings for the general public.

You will have serious problems defining the "non-animated material" aspect of the question. Does this designed genome of a bacteria made from yeast cells count? Hutchison et al. 2016

I edited your question and replaced non-animated with inanimate. In between, I find an issue in the last part of your post - 'dead material' and  'not coming from a living organism' are contradictory. Also what you meant by 'or already existing DNA' is unclear to me. Did you try to imply, forming an organism only with inorganic substances?

It could be with organic and inorganic compounds as defined in chemistry. I just wanted to know if we are able to take chemicals like H2O, N2, CO2, CH3, etc. and form a life/a living organism.

In short, no https://biology.stackexchange.com/questions/60331/synthetic-life-creation-status-of-attempts

It depends on your definitions.
we have built organisms with an entirely synthetic genome. basically the genome was "printed" from a computer file and inserted in a cell which had its DNA removed, it continued to function and replicate just fine.
We have not built a modern cell from scratch, mostly because even the simplest living cells today need to compete with other more complex cells so they are still extremely complex in their own right. The simplest possible cells would never survive in the current world due to competition and "predations" so we don't know exactly how it has to be arranged to function.
You may want to look at the much more modern experiments like the Urey-miller one, Jack Szostak has been trying to work up to what you are looking for, his lab has created RNA from abiotic (non-life) sources.
This is probably the closest since we know a slightly longer sequences of RNA can be self-replicating. And Harvard scientists have put manufactured self replicating RNA in an artificial lipid capsule and gotten it to function.
 Getting the right sequence of RNA to form by itself is possible but would probably need several billion repetitions of the first experiment.


text:
Why does olfactory sensation need lateral inhibition?
Why does olfactory sensation need lateral inhibition? If it's not helping in spatial discrimination then why is it needed? Don't we just smell the odour which is more concentrated?
My attempt: It is said that lateral inhibition is an important part of olfaction as it aids in odour discrimination by decreasing firing in response to background odours and differentiating the responses of olfactory nerve inputs in the mitral cell layer. But we also know that sensory perception is based on the pattern of receptors activated by the stimulus. So following questions arise:
Why don't background odours laterally inhibit the target odour? Isn't there more chance of inhibition of target odour being inhibited since its concentration is less?

Can you provide references to your claims?

Its in my textbook and some other information is from wikipedia.

Can you tell us about which textbook / chapter it's from, and which wikipedia article / section you are referring to?

About lateral inhibition here https://en.wikipedia.org/wiki/Olfactory_bulb

In the note below action potential https://goo.gl/sFAjqD

Background odours are downregulated. https://en.wikipedia.org/wiki/Olfactory_fatigue

Here is the paper which directly answers your question.
Urban NN. Lateral inhibition in the olfactory bulb and in olfaction. Physiology & behavior. 2002 Dec 31;77(4):607-12.
A few salient points:

It is true that the spatial gradient of sensory attributes is not as clear in the olfactory bulb-neuronal topography as it is at other places with lateral inhibition, but lateral inhibition still seems to serve a similar purpose in all these cases, namely sharpening the perceived stimuli. It is not settled how is this "edge enhancement" brought about in a nontopographical system ( "...Specific inhibitory connections between groups of cells with similar receptive fields may allow for functional lateral inhibition in such nontopographic systems, but no evidence for such specificity has been provided in the olfactory system...").

Unlike say for example in the Retina, where lateral inhibition creates the on/off centres, the lateral inhibition in olfactory bulbs is more widespread. That is, the area inhibited is relatively more expansive. This fact, coupled with the highly localised excitation caused by odours, suggests that "....lateral inhibition will be most effective at suppressing signals with low spatial frequency, in other words, signals that involve activation of broad regions of the olfactory bulb...". This is what I assume was meant by your source while referring to background odours.

The overall neurological effects of lateral inhibition is not settled, and the evidence is scanty. To quote the aforementioned paper, "... A simple prediction for the effects of lateral
inhibition on olfactory behavior would be that impairment
of lateral inhibition should impair performance on olfactory
discrimination tasks, and perhaps that these effects should
be strongest for tasks involving discrimination of very
similar odorants. Such a result has been obtained in experiments
in the honeybee in which inhibition is blocked by
picrotoxin. However, in these experiments, the blockade
of inhibition did not affect the odor-evoked firing rate of
the cells recorded, suggesting that the impairment of discrimination
ability was independent of a broadening of
tuning curves..."

Have a look at the cited paper, and the papers quoted therein, for further information.

Thanks for the link , but what I am unable to understand is how come background odour not inhibit the other odour? Shouldn't the inhibition be equal? If thats true then new odour must be more suppressed but its not the reality. So how can I justify this unfair treatment?

THe suppression of background odors happens by a different mechanism, namely receptor desensitization which is a phenomenon occurring in almost all receptors. After a while, these receptors reduce their firing intensity despite the molecules still being present. If this happens, it won't affect the lateral inhibition profile in the olfactory bulb.

Second, the paper suggests a different meaning of background odors, as odors with wide receptor specificity. These also have a different lateral inhibition effect. And one caveat that always looms overhead while studying neuroscience is that we might not know the thing perfectly well. I couldn't find any other simple papers regarding this, but if you delve a bit deeper, there might be more complicated yet explanatory papers out there


text:
What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?
Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker histones? Also, how do both linker and core histones interact within nucleosomes to ultimately regulate gene expression?

The core histones are H2A, H2B, H3, and H4, and the linker histones are H1 and H5. The structure of the nucleosome is well explained in wikipedia:

Two of each of the core histones assemble to form one octameric nucleosome core particle, and 147 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn. The linker histone H1 binds the nucleosome and the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA separating each pair of nucleosomes (also referred to as linker DNA). The assembled histones and DNA is called chromatin. Higher-order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.

The core histones have a positive net charge, which facilitates the interaction with the negatively charged phosphate groups of DNA.
Apart from defining the nucleosome structure, the function of the core histones is regulatory: it can switch on/off gene expression by histone modifications like acetylation or methylation.
The gene expression is ON when there is:
• DNA demethylation
• histones acetylation
• H3K4 methylation
• H3K36 methylation
• H3K9 demethylation
• H3K27 demethylation
The gene expression is OFF when there is:
• DNA methylation
• histones deacetylation
• H3K4 demethylation
• H3K36 demethylation
• H3K9 methylation
• H3K27 methylation
// H3K4 demethylation is abbreviation for: Lysine 4 of H3 is demethylated.
Berger SL. 2002. Histone modifications in transcriptional regulation. Current Opinion in Genetics & Development 12: 142–148 is also a nice review.


text:
Energy cost of chewing vs production of enzymes
Consider a hypothetical case that you ingest a piece of starch. Which is more costly energetically 1) chewing + reduced amount of enzymes production needed or 2) sole production of all the enzymes for digestion for achieving the same amount of glucose absorption given the digestion time is constant. (There could be different answers for different sizes of starch ingested)

I think an important consideration is the digestion efficiency. Whole food would have to be broken down from the outside-in. By chewing or otherwise mechanically disaggregating the food, the surface area exposure to digest enzymes is increased, which is more beneficial if the endpoint is products liberated over time.


text:
Role of neuraminidase in preventing polyspermy in humans
Neuraminidase is a hydrolytic enzyme present in the acrosome of human sperm. It removes neuraminic acid (salic acid) from glycoproteins. I have read in a book that due to this reason it (the enzyme) prevents polyspermy. Can anyone corroborate both of these statements?


text:
Cooperativity of haemoglobin and oxygen dissociation curve of haemoglobin
Haemoglobin shows positive cooperativity with oxygen. When an oxygen atom binds to one of hemoglobin's four binding sites, the affinity to oxygen of the three remaining available binding sites increases; i.e. oxygen is more likely to bind to a hemoglobin bound to one oxygen than to an unbound hemoglobin. This is referred to as cooperative binding.

Haemoglobin reaches 50% saturation when the partial pressure of oxygen reaches about 28 mm Hg. Now partial pressure had to be increased by about 70 mm Hg for haemoglobin to reach maximum saturation. If haemoglobin is a cooperative molecule, once haemoglobin reaches 50% saturation it should be easier to attain ~100% saturation. But it is taking a difference of 70 mm Hg. Whereas 50% saturation requires only 28 mm Hg.
Hope this makes sense.
Please answer this and correct my understanding.
Thank you

As you may notice from the graph you provided, there actually is no such thing as true 100% saturation: there is always an asymptotic approach to 100%, regardless of cooperativity.
Let's think, though, of what is actually plotted in that graph: $p_{O_2}$ effectively oxygen concentration, versus number of total percentage of binding sites that have an $O_2$ bound.
However, this also means that as you go up on the y-axis, the number of sites available to bind also goes down. So even if those sites have a high affinity for oxygen, there aren't as many of them open!
That's one big problem with the type of plot you show: it doesn't highlight the cooperativity very well. Therefore, people sometimes plot this information in a "Hill plot", with an algebraic shuffling and log scaling like this:

See Wikipedia
...where $\theta$ represents the fraction of receptors bound to ligand, and $L$ is the (unbound) ligand concentration. $n$ is the Hill Coefficient, i.e., the cooperativity.
When plotted this way, you can easily see the effect of the cooperativity of hemoglobin versus myoglobin (which has cooperativity of 1, because it has a single binding site):

http://cbc.arizona.edu/classes/bioc462/462a/NOTES/hemoglobin/hemoglobin_function.htm via Fig. 7-13, Nelson & Cox Principles of Biochemistry, 3rd ed., 2000

I agree with everything in the answer  from Bryan Krause but, in case it helps, here is the explanation that I came up with.
One way to think about this is in terms of the familiar MWC two-state model, which is essentially what you have used to frame your question.
If the concentration of oxygen is high enough for 50% saturation then, to a first approximation, most of the haemoglobin molecules have bound some oxygen and in terms of the whole population of molecules they are mostly in the relaxed, high affinity state in which any unoccupied binding sites will have the dissociation constant that is characteristic of that state. So all you are seeing in the right half of the curve is the usual hyperbolic binding curve for the relaxed form. For any saturation curve this is the behaviour that falls out of the mathematical description of the binding.
In other words, in terms of your word 'easy' it is always less easy to bind the next increment of ligand as you approach saturation because the concentration of occupied binding sites has increased so the rate of dissociation has also increased.

Yes. The basic fallacy is to think that co-operativity implies a sort of exponential increase in rate. One really has to understand that however efficient the protein-ligand interaction is, complete interaction only occurs at infinite ligand concentration. This is the basic idea of the hyperbolic  curve being explained by the Michaelis-Menten model of specific enzyme active sites, and the mathematical treatment that corroborated it. And describing the behaviour of haemoglobin in terms of oxygen binding detracts the student from its importance in the release of oxygen.

@David Agreed, it can be quite a challenge to persuade students that the key innovation in the design of haemoglobin is the reduction in affinity for oxygen that cooperativity achieves.


text:
Can anyone identify this bird?

Can anyone identify this bird: it looks like a zebra finch but they are not native to UK  are they?
Photo taken from my garden in Shoreham, West Sussex on 16/8/2014.

This looks pretty much like a female zebra finch to me (the male have a more prominent feather pattern). See this picture:

These birds are not native in Europe, this is correct. But it is always possible that birds escape captivity (or are released) and the live in countries where they originally not belong. I think this is the case with the zebra finch here. Since the birds are able to live in a pretty broad range of habitats, they can also survive in England.
According to this Wikipedia page (thanks to @Orethrephes) zebra finches which escaped from captivity are quite common in Britain although they usually not survive for long.

Looks like there's a note about feral Zebra Finches in the UK here: http://en.wikipedia.org/wiki/List_of_non-native_birds_of_Great_Britain

Ah, that's interesting. Thanks for the notification.

I think this answer should be accepted


text:
Why is lead dangerous?
Lead is known to be bad for your health for a long time, but I can't find a explanation why is it so.
In school they teach that heavy metals are poisonous, and they are trapped inside our bodies. I can just assume that the liver can't process those elements. But I still don't understand why this happens.
And finally why is lead different from, let's say, gold that is also a very dense metal, but is safe.

Please read http://en.wikipedia.org/wiki/Lead_poisoning and update your question if you have additional specific concerns.

Lead acts as a poison in a variety ways relative to what tissue it is exposed to. For example, lead is able to pass through the blood-brain barrier where it can act act as Calcium homolog to interfere with neurotransmitter release. In the blood, Lead inhibits porphobilogen synthase, an enzyme required for heme synthesis.
Lead's toxicity mechanisms include:

Its ability bind sulfhydryl groups, common to many enzymes
Its ability displace metals in enzyme complexes
Its ability to act as a Calcium homolog

Lead's valence electron configuration is $\require{mhchem} \ce{[Xe] 4f^14 5d^10 6s^2 6p^2}$; which means it has two electrons in its valence shell. This pair of valence electrons contribute's to Lead's ability to act as a Calcium analog and to Lead's tendency to form compounds in which it has an oxidation state of +2. Many such compounds dissolve in lightly acidic solutions. This has created lead exposure hazards when acidic tap water was pumped through lead pipes and when fruit juices have been served from ceramic vessels with lead-containing glazes.
Lead Poisoning
Lead

The part about the elements and their electons is pure speculation. Can you please either correct it or take it out? Following your argumentation gold should be as reactive as other elements which only need one electron to reach noble gas configuration. Gold in fact is so unreactive that it is always found in its elementar form in nature.


text:
How can I determine the purity of cells isolated from rat brains if I cannot use FACS, Immunohistochemistry or SEM anaysis?
Please help.
I know how to isolate the different cells (astrocytes, other glial cells, neurons and synaptosomes) from brain tissue using a Ficoll-based separation but how do I determine the purity of the fractions that I have isolated if I cannot use immunological techniques, FACS or SEM analysis.

You can do qPCR for certain markers from the extract. GFAP for astrocytes, Tuj1 for neurons, Myelin for oligodendrocytes etc and calculate their percentages to have an estimate of the relative populations. If you are quite used to microscopy and studying these cells then you can identify the different populations of cells with normal light microscopy as well; this is not quantitative and is susceptible to bias.

I guess that a Western would count as an example of an immunological technique (excluded in the question).

yeah I meant qPCR only.. @AlanBoyd.. yeah true 'ill correct it

@leonardo.. they are quantitative if there is an automated algorithm for scanning and classification of cells based on the images.


text:
Do plants need sleep?
Turns out that you can do indoor farming these days via hydroponics and specialised LED lights. My mother, who has a large garden, warns me from exploring this as a hobby. She mentions that 'plants need to sleep too' and that having a LED light on them 100% of the time might be bad for them.
Is there any sense in this? Is it true that plants would grow suboptimally if the sun was on them 100% of the time or would they in fact grow quicker? Is there any research on this?

The quote as phrased is a bit non-sensical really because it mostly hinges on what you define as 'sleep' or 'rest'. Plants, like most living things, including us, are far from dormant at night.
It's true that diurnal patterns govern the behaviour of most, if not all, living things that are exposed to them (1). Plants are no exception to this.
For example, photosynthesis is a 2-component process. With the so called 'dark' and 'light' reactions of photosynthesis (more correctly "light-dependent" and "light-independent"). Though both happen during the day and night, it is at it's peak during peak sunlight.
In CAM plants, to avoid dessication, there is differential carbon fixation because the stomata are kept shut during the hot daylight hours.
Respiration however, where the produced food is converted to energy, primarily happens at night.
The Khan Academy has a great 'walkthrough' of the steps of photosynthesis:
https://www.khanacademy.org/science/biology/photosynthesis-in-plants/the-light-dependent-reactions-of-photosynthesis/a/light-dependent-reactions
(1). The diurnal course of plant water potential, stomatal conductance and transpiration in a papyrus (Cyperus papyrus L.) canopy
https://link.springer.com/article/10.1007/BF00379885

The light-independent (or 'dark') reactions take place in the light, not at night. The production of ATP and NADPH by the light-dependent reactions is not separated in time from the fixation of carbon dioxide. How would the plant store all of the ATP and NADPH?  Also carbon dioxide fixation produces carbohydrate not hydrocarbon.

Right you are. Wrote that answer in a bit of a rush, edited it now.

Yes, as long as there is light there is photosynthesis going on. The light/dark cycle allows your plants to process what they created and rest a bit. It is good for them and encourages adequate growth.
http://www.popsci.com/blog-network/our-modern-plagues/do-plants-sleep

Could you please add some sources for this?

Plants need no rest as long as there is a constant source of nutrients and they are kept in the right environment they will not be damaged or die or get "tired". However Plants can be subjected to the seasons where they rest in the winter ect. due to the lack of resources and essential elements.
You can however make them grow better by subjecting them to blue and red light as this is the light they respond to the best out of the whole spectrum of light.
https://www.popsci.com/blog-network/our-modern-plagues/do-plants-sleep
https://homeguides.sfgate.com/24hour-light-schedule-bad-plants-95954.html


text:
Is the CMV promoter active in yeast?
I wish to transfect yeast and want to control my efficiency. So I thought to use pEGFP-N1 as control. The EGFP is driven by a CMV promoter. Can yeast read CMV promoters.
Thanks
Hermann

Yes (reference)
While I found your question interesting this was pretty much the first hit when I typed "CMV yeast" in google scholar. You should really look there first before you ask!


text:
On which part of the DNA will the new DNA nucleotide connect?
My question is:

Where will the new DNA nucleotide connect on the (part of the) DNA shown on the picture? Will it connect to the phosphate group?

What does the 5' --> 3' mean?

Thank you in advance.

The numbers come from the numbering of the carbon atom of the ribose in the backbone of the DNA. The ribose is numbered as shown in the figure below:

In the nucleotides the phosphate groups are attached to the 5' carbon atom and new nucleotide will be added at the 3' carbon atom. See the image below:

First you have a OH-group at the 3' position which is then "replaced" by the new nucleotide.


text:
What is an Ihh-/- mouse?
This one is too basic question:
I just came across $Ihh^{-/-}\ $ mouse. Is that means this mouse devoid of that gene Ihh. What is this sign called and are there other such representations?

These are allele notations or nomenclatures and they refer to a gene, and what changes a particular gene has undergone, if any. In this case, the -/- refers to the fact that the Ihh gene is homozygous for a null mutation as correctly stated by @Alan Boyd. This page has further examples of allele nomenclatures. This page, which can be reached from the previous link provides comprehensive guidelines for nomenclature of genes, genetic markers, alleles, and mutations in mouse and rat. Please note that (if you look at the examples here) a nomenclature can be different in different species for example in the fly field, you tend not to use the -/- sign to denote a null mutation and instead it can be a name or a number for example Rab5(1). The only reason this is called allele 1 is that it shows the most severe phenotype, which is embryonic lethality. You can read this paper here for some of the Rab5 alleles produced in Drosophila.

The IHH gene encodes the Indian hedgehog homolog protein, a member of the family of hedgehog proteins that  regulates bone formation. The ihh-/- notation represents an animal which is homozygous for a null mutation in the gene (i.e. the animal has no functional IHH gene).

Thanks. Can you add the other signs which are used? like for heterzygous it will be +/- or -/+. (Sorry, I know it's too basic.)

@DevashishDas it's generally +/- for hets

authors: ساره هشام الصقور


text:
To what extent do domestic animals understand language?
Note: Please tell me to re-post this in Cogsci or pets if this doesn't belong here.
Hello All,
I want to know how dogs or other domesticated animals differentiate between normal chat and a command. Do they understand their master's language or body language?
If they understand the body language of the master alone, then how come they can do the same trick (in most of the cases) if some other person gives the same command?
And to what extent do they have this understanding, meaning how many words does a domesticated animal understand?

Yes, they can understand some words and even simple sentences.
Here is what Animal Planet says:

Studies show that the average dog can understand about 165 different words, in some cases more if you make a point of training them. This includes the basic commands such as "sit," "stay," and "go," as well as a range of other terms, assuming they're tangible words and not abstract ideas.

Here are some supporting studies:

Some domestic dogs learn to comprehend human words, although the nature and basis of this learning is unknown [1].
A female mongrel dog, Sofia, was initially trained to respond to action (point and fetch) and object (ball, key, stick, bottle and bear) terms which were then presented as simultaneous, combinatorial requests (e.g. ball fetch, stick point). Sofia successfully responded to object-action requests presented as single sentences, and was able to flexibly generalize her performance across different contexts [2].

References:

Tempelmann S, Kaminski J, Tomasello M (2014) Do Domestic Dogs Learn Words Based on Humans’ Referential Behaviour? PLoS ONE 9(3): e91014. doi:10.1371/journal.pone.0091014
Ramos D, Ades C (2012) Two-Item Sentence Comprehension by a Dog (Canis familiaris). PLoS ONE 7(2): e29689. doi:10.1371/journal.pone.0029689


text:
Is there any size limit to the amount of information a human (or other) brain can hold
Im not sure how this would ever be tested but is there a limit to how much the brain can 'hold' before it reaches capacity ?
I guess this could also be interpreted in terms of memory, as how well some one remember something before reaching capacity / forgetting 'old' memories to make way / space for new ones.

Yes. The brain has finite size. You can't keep an infinite amount of information in a finite space.

Yes, there is a limit:

Despite the impressive complexity and processing power of the human brain, it is severely capacity limited [1].

Human brain has 78.82– 95.40 billion neurons [2] and about $3.6 \cdot 10^{14}$ synapses in the cortex [3]. We shouldn't worry about running out of space, because neurons connect with each other to exponentially increase brain capacity to about 2.5 million gigabytes as Paul Reber, professor of psychology at Northwestern University claims for Scientific American [4]:

Each neuron forms about 1,000 connections to other neurons, amounting to more than a trillion connections. If each neuron could only help store a single memory, running out of space would be a problem. You might have only a few gigabytes of storage space, similar to the space in an iPod or a USB flash drive. Yet neurons combine so that each one helps with many memories at a time, exponentially increasing the brain’s memory storage capacity to something closer to around 2.5 petabytes (or a million gigabytes).

References:

Marois R, Ivanoff J. Capacity limits of information processing in the brain. Trends Cogn. Sci. (Regul. Ed.). 2005 Jun;9(6):296-305. doi: 10.1016/j.tics.2005.04.010. PubMed PMID: 15925809. Full text available on http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf
Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S. Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J Comp Neurol. 2009 Apr 10 513(5):532-41. p.535 right column top sentence. Via Bionumbers http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106322&ver=4
Roth G, Dicke U. Evolution of the brain and intelligence. Trends Cogn Sci. 2005 May9(5):250-7. p.253 right column 1st paragraph. Via Bionumbers http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106138&ver=2
Paul Reber. What Is the Memory Capacity of the Human Brain? Scientific American. Apr 2010. Available from http://www.scientificamerican.com/article/what-is-the-memory-capacity/. Accessed 12.07.2014


text:
What signals histone methyl transferases to function?
I wanted to find out if anyone knows what stimulates histone methyltransferases to function?  I know that it is a process still trying to be understood, but I can't find anything that seems to direct the activity of the enzymes.  Additionally, where do the methyl groups come from that the enzymes transfer onto the histones?
Thanks!

The proximal source of the methyl group is S-adenosyl methionine.

Histone methylation is regulated by a variety of of events, including transcriptional activation and repression, relative location of the histone in the chromatin (pericentric or not, hetero- vs. euchromatin, etc.), X-inactivation, the cell's point in the cell cycle, and others. A variety of signaling pathways can lead to the (in)activation of HMTs. I found this table at cellsignal.com listing known methylation sites, along with literature references. Elsewhere on the site is this graphic, which shows some of the same info in a different way, and also has links to data at PhosphoSitePlus with links to the protein of interest. If you dig around, you can find all sorts of pathway and experimental information. For example, if you look up PRMT1 (human), you get a brief description of the protein and what pathways it's involved in, as well as links to all sorts of other info. On the histone side, a look at Histone H4 (human) allows you to look at individual modified residues (I picked K21-m2) and find all sorts of literature links and information about experiments used to determine its function.
PS: I'm not affiliated with Cell Signaling, I just think they have a ton of useful protein information, kind of like NEB for mol bio stuff...


text:
Bacterial chromatin binding data?
I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions.  Can anyone point me to a source?

Well, a byproduct of the fact that prokaryotes do not have nucleosomes, is that they don't have chromatin either. Compaction is achieved through supercoiling of the genophore.
Do you mean binding of a protein to prokaryotic DNA ?

@agrimaldi: That is not exactly the case.  Some prokaryotes have nucleosome-like structures.

A large number of prokaryotes do indeed have nucleosome-like structures.  The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria.  H-NS like molecules have also been found in mycoplasma (Lsr2).  One of its roles is to bind AT-rich DNA and silence transcription.  The binding is usually to suppress the expression of foreign DNA which tends to have a lower GC content than the host organism.  There is a great paper that did ChIP on ChIP with H-NS in Salmonella by Navarre et al in Science (Pubmed ID: 1676311).
As a side note H-NS does compact DNA and there is a paper by Dame et al. that demonstrates it with atomic force microscopy.

@agrimaldi: There's a lot of papers about H-NS and H-NS like proteins, it's very interesting.

I was just reading this paper:  In making the case for chromatin binding, to the bacterial genome, it seems like the nucleate at supercoiling regions but then may migrate.  The GC content idea sounds intriguing, but wondering if there is any more specificity the chromatin exhibits upon binding.   Genome biology, 5(12), 252. doi:10.1186/gb-2004-5-12-252


text:
How much time does it take a human body to replace all of its atoms?
Mikel Vsauce (Vsauce youtube channel) said in his video that it takes about 5 years for the body replace all of its atoms, while in asapscience youtube channel they are claiming that it takes 10 years. I am confused and I can't find anywhere the precise time it takes.
Mikel's video (minute 1:14)
AsapScience video (minute 1:07)

It would have been nice if there were some references/studies for that claim. I'm not sure for example if DNA in neurones in CNS (i.e. brain) get replaced unless its through DNA repair mechanism but still, that claim should be viewed with some amount of scepticism until a study is put forward and the assumptions are clarified!

http://www.quora.com/How-long-does-it-take-for-most-of-the-atoms-in-your-body-to-be-replaced-by-others

I also imagine atoms in the bone mineral that sets in the actual matrix doesn't change too often.

I expect this to have a mathematical model resembling a half life. Bone turnover is significant. Bone remodeling is part of the normal mechanism for responding to physical activity. Bone loss in space is also significant doe to this effect. http://cjasn.asnjournals.org/content/3/Supplement_3/S131.full

I don't think Iron would be totally replaced because we can't excrete it well. The iron in our red blood cells is very efficiently recycled by macrophages, and excess iron is stored in hepatocytes. If you really have too much iron it will accumulate as hemosiderin in hepatocytes, which is almost irreversible. The best way to treat iron overload is through regular blood draws, which is a non-natural way to remove iron, I don't know if men have a natural way to remove excess iron, so if the atoms can't leave, they can't be replaced.

Forever, since some atoms are not ever replaced: https://skeptics.stackexchange.com/q/18427/155

Not all the atoms in the human body are replaced.
Carbon atoms in tooth enamel are not replaced after the enamel is laid down during tooth development. This was demonstrated in the 2005 Nature article "Forensics: Age written in teeth by nuclear tests", where the researchers showed that the amount of carbon-14 in tooth enamel can be used to accurately determine date of birth.

Another good SO answer with more references and details of atomic replacement time for other tissue types is at Are all the atoms in our bodies replaced on a regular basis?


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Can neutrophils kill bacteria inside other cells?
Are neutrophils able to get inside epithelial cells in order to kill bacteria. Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill the bacteria?
Also when the bacteria get into blood stream can neutrophils kill the bacteria?
I am not from a biology background. So, a simple explanation will be helpful

Please do some basic reading on neutrophils (or whatever your topic is) before you post a question. We want to help clear up confusion or solve problems in people with a sincere interest in Biology. But we do ask for evidence (in the question) of what you read about it. Thanks.

Are neutrophils able to get inside epithelial cells in order to kill bacteria.
  Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill the bacteria?

No. Firstly because bacteria (except for very special cases) do not enter epithelial(or other) cells - that's what viruses do. Second, neutrophils recognise bacteria based on markers on their cell wall. These markers can come from the bacteria themselves, or from the innate immune system (see complement system) that 'marks' the bacteria, in any case being inside another cell would protect bacteria from neutrophils. Cases are like these are handled by the CD8+ T-cells of the adaptive immune system.

Also when the bacteria get into blood stream can neutrophils kill the bacteria?

Yes, that's their job and neutrophils are usually inside of the blood(stream), so they could find and kill bacteria there.


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Can yeast ferment maltose directly?
I have been taught that yeast can act only on simple sugars (monosaccharides) and breaks them down into ethanol and CO2
I also know that yeast can break down maltose (disaccharide) and maltotriose (trisaccharide) using maltase from its enzyme complex (zymase) into monosaccharides of glucose and then ferments the same.
My question is whether yeast can directly ferment maltose and maltriose WITHOUT first breaking them down into glucose?  If so how is it done - enzymatically and what is the chemical equation

The statement in your first paragraph is correct: for yeast to ferment a carbohydrate it must be fed into the glycolytic pathway which, in the case of oligomers of glucose (e.g. mannose) simply means breaking the oligomer into its constituent glucose monomers using a single enzyme. This is similar to how yeast processes sucrose: the disaccharide is hydrolysed by invertase to release glucose (fed directly into glycolysis) and fructose (fed into glycolysis via fructokinase).
A separate mannose pathway would require a completely new set of enzymes that somehow processed mannose in a stepwise fashion without breaking the glycosidic bond linking the two monomers - I'm sure that you can see that this is a much less likely option in terms of the evolution of yeast metabolism.


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Understanding what passes through and doesn't pass through the plasma membrane
I have difficulty in understanding the reason why certain molecules can pass through phospholipid bilayers.
Firstly, I understand that the outer layer of the lipid bilayer is hydrophilic - my understanding is that they "like water" and can interact better with water.

Bilayers can absorb hydrophobic substance like N₂ and O₂.

Does this mean - because the hydrophilic surface are capable of hydrogen bonding - that's why they are able to absorb hydrophobic substances like F , O and N ?

They can absorb non-polar molecules.
They can absorb small uncharged molecules like H₂O and CO₂.

I'm not sure of the reasons behind 2 and 3 ...
And of course , vice versa ... (what can't pass through the lipid bilayer easily).
Any help would be appreciated!

Great questions! Your 3 questions can be answered in 2 parts:
1. How do small, uncharged gasses (ie: O₂, N₂, CO₂) diffuse through lipid bilayers?
First it's important to clear up some terminology: Absorbing a compound isn't the same as being permeable to that compound. If you say that a compound is absorbed (or partitions) into a bilayer, you're assuming that the absorption of the given compound by the bilayer increases the entropy of the system (and is thus energetically favorable). For example, lipophilic compounds partition into lipid bilayers because of the hydrophobic effect; by partitioning into the bilayer they break a number of hydrogen bonds and thus increase the disorder of the system.
Small, dissolved gasses like O₂, N₂, and CO₂ are not absorbed into lipid bilayers, they simply diffuse through passively because of their small size and because they are non-polar.
Water is also able to passively diffuse through a lipid bilayer even though it is polar. We might think it should be fairly rare for a polar water molecule to pass through the hydrophobic center of a lipid bilayer, but typically living cells are found in aqueous environments, where concentrations of water outside the cell are extremely high, so this does occur at biologically relevant rates. In fact, the passive diffusion of water in and out of cells is so important that many cells have developed special transmembrane proteins to facilitate the passage of water in and out of cells (most notably aquaporins and pressure-gated channels).
2. How do non-polar molecules pass through lipid bilayers?
This is answered in the related question posted in the comments section of your question. Briefly, it has to do with the same electrostatic problem I mentioned above: Though there is an energetic cost for non-polar compounds to pass through the hydropilic layer of a lipid membrane, in most cases the partitioning of the compound into the membrane still raises the overall entropy of the system (due to disruption of the hydrophobic effect), making it an energetically favorable process.
It should be noted that for the most part, polar compounds do not spontaneously cross cell membranes because of the hydrophobic region of the lipid bilayer. When passage of these compounds into or out of the cell is required for life, cells typically produce transmembrane proteins which can act as either active or passive transporters to allow these compounds through.

Good effort, just a couple of points. It is true that there is some spontaneous water exchange across membranes, but not because water molecules are small, rather because the concentration of water is very high. And still water exchange over membranes is limited, that's why cells have aquaporins. For (2), I think you should rather emphasize that most polar compounds do not cross cell membranes spontaneously. (That's of course the reason for having cell membranes in the first place, to keep solutes inside cells.) Transport proteins are required to move polar metabolites across membranes.

@Roland, good points, I'll fix my answer to reflect them. I had decided not to mention larger polar compounds and transport proteins since they weren't mentioned the original question, but I can add some detail for clarity.


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What is the difference between contig- and read-based sequence alignment?
I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused that if you have read based alignment then what is the importance of aligning contigs on the reference.

I have never heard the term “contig based alignment”, and your question is the only Google hit of this exact query (apart from a 2012 patent application).
That said, and without knowing the exact context, I am assuming that you are essentially right: contig-based alignment probably refers to the de novo assembly of reads into contigs, which are then aligned into a scaffold by use of a reference.


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In which organs is water that we drink absorbed into the blood?
From biology classes I remember that water from food we eat is mostly 'sucked in' (absorbed into blood) in the colon. I guess the same is true for water we drink. But if I eat something, it will reach the  colon after say 4 hours, and if I drink a lot of water, I'd want to go to bathroom earlier than in 4 hours.
So is water absorbed not only in colon?
If it's absorbed in other organs, what % of it would be absorbed in each organ?

The internet is unanimous on this: some absorption takes place in the stomach, but most of the water is absorbed in the small intestine. Try searching Google: water absorption stomach

@AlanBoyd - The internet is not unanimous on anything as far as I know. Which site the information is obtained from matters a lot! (I agree with the small intestine, though.)

@anongoodnurse perhaps unanimous was a little strong, since I didn't check the entire internet (still working on it), but I think you'll find it difficult to find a relevant site that doesn't provide this information.

Role of the stomach in water absorption:
The absorption of much of the ingested water from a hypotonic food already starts in the stomach due to osmotic reasons.
If we study the mechanism of secretion of HCl by the oxyntic cells of the stomach, HCl secretion favours water osmosis from the blood to the lumen both for protective reasons as well as to maintain the osmotic balance of the gastric juice. This is predominantly the phenomenon in a filled stomach.
However, in the empty stomach, absorption of water is relatively more perceptible in the reverse direction upon water consumption.
Furthermore, the pyloric sphincter is usually open to the passage of water and electrolytes to empty to the duodenum. Thus, they may travel to the large intestine for absorption even before chyle. But this too is dependent on the empty or filled condition of the stomach, in which an empty stomach would pass the water and electrolytes in 5-6 minutes whereas in the filled stomach it could take 15 minutes or even more. Thus these factors may cause the early micturition to ensue.
Role of the small intestine in water absorption:
The small intestine, besides the transcellular pathway (through the cells), also facilitates water transport via the paracellular pathway. Thus it is more permeable to water osmosis than the stomach. Furthermore, the small intestinal segments duodenum, jejunum and ileum are differentially permeable to the absorption of different solutes. This facilitates the simultaneous absorption of water according to the osmotic gradient resulting from this differential absorption of the solutes, maintaining isosmoticity with the blood plasma.
However, this also has the implication that, when the digested products from the stomach (chyme) are hyperosmotic, water may flow from the blood in the villus to the intestinal lumen rather in the opposite direction until chyme is rendered isosmotic to the plasma.
Role of the large intestine in water absorption:
The large intestine is the key centre for water reabsorption rather than the stomach and the small intestine because of the following reasons:
a) It prevents most of the paracellular flow of water and electrolytes because of tight junctions, unlike in the small intestine. This prevents the back flow of electrolytes and water from the chyle to the blood.
b) The proximal colon is where most of the water reabsorption occurs as a consequence of major electrolyte intake. This region is highly active in the reabsorption of Na+ and Cl-.
c) It is mainly involved in concentrating the fecal matter, so reabsorption of water and electrolytes becomes its principle function.
For reference:
Textbook of Medical Physiology by Guyton and Hall

Can you recheck your references? Though water absorption does occur from/in the stomach, it is far from the primary site. Also, there is more to the GI tract that the stomach and intestines. There are the duodenum, jejunum, ileum, ascending, transverse and descending colon.


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Large plasmid ligation: do I need alkaline phosphatase?
I have a doubt about a protocol I'm using for a ligation of a very large plasmid (15kbp circa) with an insert: after digestion with a single-cut enzyme (sticky ends), the protocol passes directly to the purification of the plasmid without making any alkaline phosphatase. My doubt is during the ligation, the plasmid will self-ligated without accepting the insert?. Am I mistaken or the protocol is incorrect?

A plasmid vector will always be prone to recircularisation when a single restriction enzyme has been used, but recombinant plasmids will also be formed during the ligation. Alkaline phosphatase treatment can be used as you describe; you can also  simply make sure that the insert fragment is present in high molar excess and be prepared to work harder at the end to find the recombinant plasmids. Neither approach is correct or incorrect, they both have their limitations.
Of course the best approach is to avoid this type of cloning altogether.
Added later
Incidentally, the wording of your question suggests that you think you may have more of a problem because the plasmid vector is a little larger than usual. Not so! Circularisation is favoured because the two ends are tethered so the effective concentration of each is high with respect to the other. As the plasmid gets bigger the tether is longer and the tethering effect will be less.


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Is it true that the human brain has not evolved in 100 000 years?
I read that the human brain has not evolved in 100 000 years and that's why there are no genes for intelligence.

Can you please cite your source for that claim?

Perhaps "there are no genes for intelligence" because intelligence isn't a simple trait like eye color or blood type.  Multiple genes likely control various factors that affect intelligence, and these gene probably affect other things as well.  Then too, there's the nature vs nurture aspect.  How much of intelligence is inherent, and how much is developed?  For instance, my genes might allow some maximum muscle development, but if I choose not to exercise, I will never come close to that max.

tl;dr
Here are the two claims you make

human brain has not evolved in 100 000 years

Wrong!

there are no genes for intelligence.

Wrong!
The claim there are no genes for intelligence. is unclear though (see below) but if rephrased in the most intuitive correct way, then the claim is wrong!
Are there genes for intelligence?

[..] there are no genes for intelligence.

The claim there are no genes for intelligence is unclear. Does that mean there is no genetic variance in the human population for intelligence? To understand why the claim "gene for something" makes no sense, please have a look at this post
Make sure to read this post..... Done? Now you understand why the concept of heritability is key. So let's rephrase the question so that it makes sense and can be answered
Is Intelligence heritable?
Well, the issue here is to define the term 'intelligence' in a way that is non-arbitrary and yet match our intuition of what we like to call intelligent. A number of studies have investigated the heritability of intelligence, often using different definitions / metrics for intelligence.
All these studies agree on one point. Yes, intelligence is heritable! How heritable it is varies a lot from one study to another (because those studies vary in the population studied and in the definition of intelligence). See the wikipedia article on Heritability of IQ for more layman information.
Has the human brain evolved in the past 100 000 years?
First you need to understand how evolution is defined. Here is a commonly used definition

Evolution is a change of allele frequency through time in a population

Have a look at the post What is meant by individuals do not evolve, populations do? to understand what this definition mean.
Well... first. Everything evolve. You can't stop evolution from happening on any phenotypic trait or on any genomic region. So, of course it evolves. But let's not stop there.
There is still one issue with this question. The saying brain characteristics rather vague. But I'll deal with it as I can.
Is the brain still evolving - phenotypic evidence
Spoting changes in brain structure through time is not easy, as brains don't preserve well. Over such a short period of time (100,000 years) it will be even harder to detect much difference on gross metrics we can use such as cranial cavity.
We can compare the volumes of cranial cavity. Neanderthals interbred with humans (see this loosely related post) with Homo sapiens and Nanderthals had a cranial cavity that is bigger than Homo sapiens, so this gene flow would very likely affect H. sapiens cranial cavity.
Is the brain still evolving - genetic evidence
Consider for example Evans et al. 2005 showing that the allele coding for micro-encephaly at the gene MCPH1 is currently increasing in frequency in the human population.
This article from NewScientist also reports the findings of Evans et al. 2005 in layman terms.
Is the brain still evolving - current selection pressures
You should have a look at the post Is intelligence declining due to the lack of selection pressure? and eventually on the wikipedia article for the Flynn Effect.

Every part of the human genome is constantly evolving - but at a VERY slow rate. Therefore there are only a few changes from the last 100k years (This article describes this quite well).
Intelligence is a very complex characteristic, which is therefore influenced by many different genes. Most of these influences are only minor, so that scientists are arguing whether the influence is real or not (pro, uncertain, contra). Additionally there are a lot of genes that are just necessary for the brain to function the way it does - you could argue that all of these are 'genes for intelligence, since without them we would not be intelligent.

Not every part of the genome is evolving at a slow rate. Every part of the genome is evolving, most of them at a slow (although this is relative) rate.

I'm curious to where you read that b/c its simply not true. Remember that evolution is driven by selection pressures. Also known as evolutionary pressures, they drive a reason to evolve. The stronger the pressure the faster evolution takes place. An easy way to spot this pressure is by looking at the range in ability, skill or adaptation of a trait. The larger the range the stronger the pressure.
With that in mind, can you think of any selection pressures that the human brain might had to face over half your given time, lets say the past 50,000 years?
The human brain has had to adapt to entirely new environments in that time frame.
Within that time-frame is all of recorded history. How about the adaptation to formal education? That might be one. Also during this time think of the explosion in languages. Consider how different we all are in our ability to be educated and to pick up languages. Or how some of us can cognitively operate effectively with wildly different amounts of sleep debt or calorie intake.
Also there are many genes that influence intelligence since intelligence is multifaceted and can be expressed in many ways. You also need to remember that  these pressures can influence how genes are turned on or off. This is known as epigenetics. You might have a gene but your cells could simply not use it.
There have been theories of autism being a result of an evolutionary pressure.
With all of this in mind the last thing you need to remember is that the human brain is evolving in other ways than simply via its genes or their expression. The human brain exists in a space shared by other human brains and we have the ability of sharing our ideas with others. This allows for groups of people to share a selection pressure and thus evolve as a group.
Do you know what this is called? I know you know.
Culture. In many ways human evolution has moved on from the biological to the cultural space. And I find that quite fascinating.
https://www.timeshighereducation.com/features/human-evolution-has-moved-on-from-the-biological-to-the-cultural-arena/169440.article


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Do omnivore mammals vary food preferences based on dietary needs?
I'm wandering if mammals that can eat many different kinds of food (omnivores) vary their preference for food not only based on the availability, but also based on dietary needs?
I'm looking at this site Food nutritional content and see that "not all foods are created equal" - the vitamin/mineral and amino acid contents can vary dramatically. Is there some part of an omnivore brain/digestive system that "monitors" the micronutrient density of digested food and adjusts food preferences towards foods that make the diet more complete?

I want to say yes, as I've heard of cases that people starving afloat on the ocean and desperately in need of Vitamins will eat Vitamin-rich portions (eyes, liver, etc.) first, but I haven't the sources yet. There's also Geophagia, which can be common for pregnant women who are starving for the iron content of the dirt.

For what concerns amino acids, mice rapidly reject meals that are not balanced in essential amino acids and continue to look for other kind of foods. This behavior is called aversion response and it is an adaptive phenomena that can be observed already 20 minutes after exposure to the unbalanced food. The mechanism involves brain sensing of uncharged tRNAs. The significance of the aversion response is to minimize depletion of essential amino acids that can not be directly synthethized but are required for protein synthesis. You can find good reviews in PubMed, for instance Gietzen et al. 2007, Annual Review of Nutrition, and Gietzen and Aya 2012, Molecular Neurobiology.

Great answer! Reading the 2nd article, I see that there's "rapid
recognition of Indispensible Amino Acid(IAA) depletion in the rat brain's IAA chemosensor, the anterior piriform cortex (APC)".

Here's a paper that deals with pleasure in the brain, but also mentions that aversion response to salt can be decreased dramatically, and be replaced by "liking" response when brain experiences sodium deficiency: http://www.lsa.umich.edu/psych/research&labs/berridge/publications/Aldridge%20&%20Berridge%202010%20Neural%20coding%20of%20pleasure%20chapt%203%20in%20Pleasures%20of%20Brain.pdf

Yes, but not by monitering  the food.
Its well reported that food prefrences in animals reflect nutrient and micronutrient composition. Animals even show stronger prefrences when deficent in the relevent micronutrient. It appears that they are are responding to the uptick in the micronutrient in the body after eating the food. Basically they are responding to the change in the bodies demand for that micronutrient and its not perfect it can make mistakes esspecially if the animal eats a variety of foods.
It basically goes as follows:
(body)
Day 1 "I need calcium"
Day 2 "I need calcium"
Day 3 "calcium OK"
(brain)
I ate X today and stopped craving calium, so X must fullfill that craving.
Its basically the same pattern recongnition we use for learning anything. Nothing special about senseing the food, just sensing the bodies needs from cell signals. because of this it can be tricked. I would bet money you could trigger a  future food craving in someone by giving them vitamins along side novel foods when they are deficent.
A deficencey can also trigger a prefrence for novel (new) foods as well, likely in hopes of obtaining the lacking nutrient.
Now that said animals do have a lot of smell receptors geared towards detecting micronutirents. But they are also easily lost evolutionarily, so they may not be very reliable compared to craving satiation.
https://onlinelibrary.wiley.com/doi/abs/10.1002/ajp.22059
https://www.sciencedirect.com/science/article/pii/S1751731115001937
https://bmjopen.bmj.com/content/14/3/e078082.abstract
https://www.sciencedirect.com/science/article/pii/S0195666322001465
enter link description here
https://extension.usu.edu/behave/files/Mineral_Nutr.pdf
enter link description here

I found that there are seasonal rhythms in the nutrient intake:
Seasonal rhythms of human nutrient intake and meal pattern
The article's abstract mentions carbohydrates, while I'm more interested in the micronutrients, like amino acids and vitamins/minerals.

not sure amino acids can be considered micronutrients like vitamins.

That is a very good observation! I'll check the articles above to see if they mention vitamins as well


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What are the limitations of commercial-grade DNA genotyping compared to full sequencing?
I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what the modern "commercial grade" genotyping really does.  What are the limitations of commercial-grade "genotyping"?  From what I've been reading, they test DNA against ~100 different markers, but do not really sequence it.
If I understand correctly, if DNA is sequenced, genetic markers and genes can be identified in it, including the newly discovered ones. However, (if I understand correctly) if DNA is genotyped, the genotyping is a one shot operation which states if some genetics markers are present in the DNA. To test against newly discovered markers, it would have to be genotyped again, right?
Thank you for any clarifications!

23andme briefly describes the technology they use here. They are testing the genotype of your DNA at roughly 1 million locations. The technology they use to do this is known as a microarray.
The limitations of using a microarray, as compared to sequencing, is that you will only find what you are looking for -- people often describe the disadvantages of microarrays as compared to sequencing with the streetlight effect/metaphor.
Arrays can only measure regions of the genome that they were designed to probe. Technically, if they probe 1,000,000 million locations, and the human genome is roughly 3.4 billion bases ... you can do the math.
In practice, SNPs tell you a bit more about just the nucleotide being interrogated, due to linkage disequilibrium (cf. tag/proxy SNPs), so the array might tell you more than you expect.
Of course, modulo sequencing errors, whole genome sequencing will tell you "everything" as far as recovering the NTs that make up your genome, but how much information that will provide you is another thing altogether (for now, that is).

+1: on the other hand, 23andme proposes a certain type of analysis to their clients that does not require whole genome sequencing. They say "We will test such and such SNP and tell you that you have x% probability of having an heart attack in your 60s"...

@nico: Yeah, very true. You can also get a copy of the data, though, which is cool. Also, they're also currently offering exome capture for some already existing members ... a look towards what the future may hold, perhaps.

Just to be transparent, I work at a microarray company, but I've also attended high throughput sequencing workshops.  I think this is a pretty fair assessment, but leave me a comment if you see anything out of line...
As pointed out by @SteveLianoglou, Genotyping microarrays are best for revealing whether a particular variant (not only SNPs but short insertions and deletions, copy number variations (CNVs) reliably and cheaply.
High Throughput DNA Sequencing has made great strides and the latest cost estimates are in the few thousands of dollars for a full human genome.  This is better for discovering new variants but currently its not a great way to do do say a medical test to see if you have a particular mutation.  The problem with sequencing right now is that sequencers have systematic biases - the local sequence can give the same error over and over again.  It takes some significant effort to differentiate the error from the real variant data.  In the workshop I attended, the data consisted of 38 full human genomes at 30-40x coverage. Despite this deep level of sequencing, systematic errors were still obvious (the proceedings are in press now - reference should show up at the link provided soon).  So it can be fairly expensive when you have done all your data analysis and validation data to get the variants via sequencing.  All this could change very quickly, but I think this is accurate in the current state of things.

I want to give the OP a slight variation on Steve's answer.
It is important to note that most of the genome is the same between different people. That isn't surprising, since we belong to the same species.
For example, it is estimated that there are about 10,000,000 SNPs (single basepair positions that may vary) in the human genome. So if you check 1,000,000 SNPs with a microarray (genotyping), you are covering ~10% of the possible differences. In addition, variation in some of the SNPs is very common while others are very rare, so if you check the most common 1,000,000 SNPs with a microarray, you might actually cover a very large portion of the differences. It is also possible that if you know in advance some general information about the person you are testing, such as ethnicity, you might be able to eliminate many uninformative SNPs.
This of course only refers to variation in SNPs (but these are the most common variations).

This is a good point - to test only what varies the most