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Why does the chance of having a baby with Down's syndrome increase with the age of the mother?
Down's syndrome occurs when either the egg or the sperm cell contain on extra chromosome 21. To my understanding, women are born with all the egg cells in place already, so there's no further cell divisions, and thus no further chance of having one cell with an extra chromosome.
Now, the chance of having a baby with Down's syndrome increase with age:

At maternal age 20 to 24, the probability is one in 1562; at age 35 to 39 the probability is one in 214, and above age 45 the probability is one in 19

Why is this so, when the egg cells are complete at birth?

It is true that woman are born with all the eggs they will ever release , meiosis is not completed in the egg. There will be a meiotic cell division. Now this might sound confusing to you how there can be cell division without increase of egg number. For this - I will recommend that you read any basic bio textbook covering both the meiosis and gamete formation in females.

I think by this discussion it is clear that there is a chance of having one cell with extra chromosome.

The frequency rises with maternal age due to a peculiarity of meoisis
  in female mammals.  Meiosis is originated in the fetal ovary,
  arresting at metaphase I with the homologous  chromosomes aligned for
  segregation. Cells remain in this state until the time of ovulation,
  often  decades later in humans. The longer cells remain in the
  arrested state, the greater the chance  that there will be a
  nondisjunction event when meiosis resumes.

Source : http://www.madsci.org/posts/archives/2005-07/1121714807.Ge.r.html
I think you have the misconception that egg cells have completed meiosis by the time female is born. This is not true ( as indicated above in the answer). At birth, they are in metaphase I , after puberty, each month some of them divide further but only one survives and get arrested at metaphase II . Only after fertilization is the meiosis complete.

If you are not familiar with some of the terms or have any other confusion , ask !

If you expect folks may have difficulties with jargon, linking appropriate pages in your answer may help. Great answer here btw +1

no need to be careful! Just a hint :)

It isn't right that in Metaphase-I oogenesis gets arrested until puberty but actually in diplotene stage. The secondary oocyte after having completed Meiosis-I enters Meiosis-II and gets arrested in Metaphase-II until fertilisation(not syngamy). Source Besides madsci.org is not a reliable source, it's a Q&A site.

@biogirl Even I was wondering this for a long time then. Very fluid, biogirl. PS: just checked your bio(profile) and it seems(seemed) to me like I was reading something that I had written long back. Akin :) kudos and best of luck to your future endeavours. Sorry for this redundant praise incase if it doesn't fit in here but take my kudos ;)

@biogirl I would like to add 1 thing I think primary oocytes get arrested at prophase -1  of meiosis and stays in this state till puberty,  after ovulation begins in ,it gets arrested at metaphase-2 until it gets fertilized by sperm

The chance of having a child with Down's Syndrome does not only have to do with cell division, but the mechanism that allows spontaneous abortion to occur within the uterus of the mother.

There is strong evidence for uterine selection against genetically disadvantaged embryos.  However, as women approach the menopause and the risk of future infertility increases, this selection, or filtering stringency, is expected to relax.
Neuhäuser and Krackow’s paper provides evidence that older mothers, who give birth to children with Down Syndrome, have a relaxed stringency of quality control of embryos (or relaxed filtering stringency), which increases the probability that these women will bring children with developmental defects to full term.  They believe that this relaxed filtering stringency is an adaptive maternal response and it might explain why the rate of Down Syndrome accelerates with increasing maternal age.

Basically, the mechanism that allows for the uterus to select against 'genetically disadvantaged embryos' (which can be Down's Syndrome, or other genetic deficiencies) is not as good at detecting these problems, OR as this paper suggests, is 'less picky' about the genetic quality of the fertilized egg, and will allow it to implant in the uterine walls.
It is also important to note that these studies are all ongoing, and many different reasons for the development of Down's Syndrome are unknown.
Literature Cited
Neuhäuser M & Krackow S (2006).  Adaptive-filtering of trisomy 21: risk of Down Syndrome depends on family size and age of previous child.  (Naturwissenschaften, DOI 10.1007/s00114-006-0165-3)

That's a very interesting finding. Are there any models for relaxed filtering stringency (RFS) in animal models?


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Definition of species - location of gene
I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.
Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of classifying this way ?
Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.
But I think this isn't valid for bacteria as there is so much recombination going on.

The position of gene is not always fixed within a species. There are Copy Number Variant within species for examples. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles. CNV, position of genes, regulatory sequences and other stuff are important too. The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. You won't find the perfect objective definition of what is a species.

@Remi.b Yes , but are CNVs genes ? Are there variation in no. of genes in population ?

CNV's are DNA sequences of any length that are present at several different number of copies along individual in a population or along species. THese sequences can contain one or several genes. So the answer to your question is yes! There are variation in number of genes within a species. Here are two references that might interest you: http://adsabs.harvard.edu/abs/2006Natur.444..444R and http://genome.cshlp.org/content/16/8/949. You will as well find some information about CNV on the [wikipedia page] especially under "identification". (http://en.wikipedia.org/wiki/Copy-number_variation)

@Remi.b Hello! I think you have answered my question in the comments. Would you like to write an "answer" ?

The position of a gene is not always fixed neither within nor between species. There are Copy Number Variation for example. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles though. CNV, position of genes, regulatory sequences and other stuff are important too in the description and the functionality of a lineage.
The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. For french speaker people this podcast(Follow: Biodiversité: Plus qu'une simple histoire de conservation/Pierre-Henry Gouyon) is of interest. You won't find the perfect objective definition of what is a species. Here and here are posts that discuss the definition of species.

As Remi points out you are generally incorrect but the locality idea is specifically ok. The positions and types of mutations and divergence for specialization in certain genes regardless of their place in the genome is key in determining homology which is used for species determination at the molecular level. The drawback is: its rather expensive when most species differences are obvious at the phenotypic level.

I would add:
Most categories in sciencie (species, order, living, planets, moons, stars, organs, fruits, etc.) are not "real". We (humans) create categories and attach objets to them in order to make general assumptions, so we can say things like "Most objects of category X have Y property."
Then, the way we define categories it's mainly the most practical way. And sometimes we addapt definitions, when there are practical motivations.
I think the motivation to define species related to the usual intra reproduction hability (and usual inter reproduction inhability) it's because that mantains certain homogeinity. Maybe a better definition would be something like "two groups of individuals belongs to the same specie if the rate of fertility among their individuals is > x %".

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Were early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?
I found that many friends of mine are quite easy in sexual relationship. Ex, I knew a lot of girls went to the night club & met a stranger & brought home to sleep  with him even she had never known his name. The next morning, the guy left her & she starts to do the same way to get another guy maybe in 3 days or so.
So that triggered my thought. I wonder "Are early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?"
My hypothesis is "Yes", that is "Early human beings are far more promiscuous than we are now". So how i came up this? Cos Human came from Chimpanzee right?, so if we want to know early human, then we could study Chimpanzee. The early human & Chimpanzee could have some similarities.
There is a research saying that "Chimpanzees are far more promiscuous than humans" http://www.nature.com/news/specials/chimpgenome/interactive/chimp_interactive_graphic_pf.html
So, that proved my hypothesis.
Also, when human evolved, they started to realized that promiscuousness wss not healthy & not good for society so they started to develop some regional/society (ex,  monogamous relationship) codes to prevent that.
Do you approve my hypothesis?

i'd be surprised if there weren't some time when sex was not socially regulated in the way it was and then the typical human would have more partners than they do on the average (though modernity has definitely increased the maximum number of partners someone can have).  people did not live very long though and sizes of human groups were small on the other hand..

Your question is interesting but I just want to make some comments about basic stuff that sounds weird in your question. The article you found is not a prove neither an evidence for your hypothesis. But it is an interesting fact that should be considered in the discussion. Humans does come from chimpanzee but they both share a common ancestor. If you observe two different phenotypic trait in two sister lineages you cannot quite know which of the two trait had the common ancestor.

My hypothesis is "Yes", that is "Early human beings are far more
  promiscuous than we are now". So how i came up this? Cos Human came
  from Chimpanzee right?

No.

Also, when human evolved, they started to realized that
  promiscuousness wss not healthy & not good for society

I'm sorry, what ancient society are you claiming cracked down on male promiscuity?

I guess you meant that chimps are not human ancestors, because the claim regarding human promiscuity is much harder to disprove. 2. Jewish?

Well, your logic is flawed because it is not proven that humans evolved from chimpanzees. not trying to start another debate with the whole evolution, but even if I did believe in evolution I would suggest before making up your hypothesis of researching a lot more than monkeys. Research things like: ancient brothels, traditional marriage views/ cohabitation views, {things that humans practiced and accepted back in the day} and you will have much more evidence.

Humans did not evolve from chimpanzees. Both evolved from a common ancestor some 5 Mio years ago (which is an important difference).

even if I did believe in evolution?? So you don't now??

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Is there any evidence telling us what the oxidation state of early earth's atmosphere was?
I ask this question in relation to the origin of life. I realise it would probably be better suited to a geology stack exchange, but it does not yet exist.
The Miller-Urey experiment gives a lab based demonstration of how organic compounds may have been produced. It recreates that conditions that are thought to have existed in the early atmosphere (Hadean period).

What this experiment relies on however is an assumption that the atmosphere lacked oxygen (reducing). The Miller-Urey experiment does not produce proteins if it is conducted in a oxidizing environment. I've seen that there is some debate over the oxidation state of the atmosphere, and the main evidence for a reducing atmosphere is that life wouldn't have been able to begin without it. Is there evidence supporting an oxidized early atmosphere, and if so, how did life come about?

There are wikipedia pages on Geological history of oxygenation and on Great Oxygenation Event
I don't know much about geology and someone else might be able to give an exhaustive list of evidence (and method of measuring) concerning the oxygen concentration on earth but that would be a very long answer I guess! Rather than a full answer, I give you a list of wikipedia pages below that will interest you and should help answering your own question.

Banded Iron Formation
Evolution_of_dietary antioxidants
Huronian Glaciation
Ice core


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Why is Thermus aquaticus and Taq Pol stable?
What is the molecular basis of the stability of the bacterium Thermus aquaticus and the enzyme Taq Pol it produces ?
I have tried googling this but did not get a good answer.

By the way, does Thermus aquaticus belong to archea or bacteria ? Wikipedia says bacteria but I have read somewhere else that it is archea

Here is an article from Razvi and Scholtz that help you understand the thermostability found in thermophilic proteins. They compared protein stability of thermophilic proteins and their homologous versions in mesophilic bacteria (i.e., bacteria that grow in more normal temperature ranges), and compiled these proteins into a database. Their method was to make estimates of protein stability curves for each of these proteins through a model of free energy based on the known physical parameters of these proteins. From the article:

[...] the most common way to attain a higher [melting temperature] in proteins from thermophiles is to raise the stability curve to higher values of ΔG (higher intrinsic stability) at all temperatures."

This is achieved through mutation of just the linear sequence of the protein. Fundamentally,

"...each of the methods of stabilization are results of features like an increased number of hydrogen bonds, salt bridges, improved core packing, shorter and/or tighter surface loops, enhanced secondary structure propensities, or oligomerization."

Also, everything I have seen about the genus thermus places them as Gram negative bacteria.

Razvi and Scholtz. Lessons in stability from thermophilic proteins. Protein Science, 15(7) 2006.

How can oligomerization help in this ?

While I doubt that oligomerization is used to stabilize Taq DNA Pol, oligomerization (usually through C- or N-terminal tails) can help stabilize larger, quaternary, structure. For example: hemoglobin, insulin.

I just know what oligomerization means. So I am not able to understand what it exactly does to help stabilize proteins.


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Double mutant analysis with null mutants
My professor was talking about double mutant analysis with null mutants, and how double mutant analysis won't work with hypomorphs.  I really don't understand the concept of double mutant analysis.
He was talking about pathways - if A and B are in the same pathway, then you would mutate A and he said something about the phenotype being identical.  If A and B are in different pathways, you could mutate both of them and there would be a "stronger" phenotype.
He also said it would only work with null mutants, not with hypomorphs, because with hypomorphs some of the pathway would still be active, not completely shut off.
I really don't understand any of this - what a double mutant is, the whole pathway thing, why the phenotype is "identical" or "stronger", or why you use hypomorphs.  I would really appreciate a rundown on the idea of double mutant analysis because my professor's explanation was so unclear.  Thanks in advance.

Do you mean why you DO NOT use hymomorphs ?

you may also want to see this

Basically your professor was saying some hypomorphs (weakly expressing phenotypes) do not necessarily show their phenotype since they still express some of the gene products and there are other pathways that might compensate for their lack of expression of that gene to an extent. So if you want to see a phenotypic effect then you got to have a null in those situations since that will be harder to compensate for specially in organisms that do not have that many redundancies such as Drosophila. But even nulls are not exempt to the above rule if there is another pathway compensating for them!

What is a double mutant ?

See this image.
In this mutant 1 has one mutation, mutant 2 has another mutation while the double mutant has "double"  or 2 mutations.
Key : A,B means double mutation , A means mutation in A and B means mutation in B.

Types of double mutations

a)Additive phenotype:  A, B = A + B   Implies that A and
  B function independently and on different processes.
   Eg.  A =
  short roots, B = no root hairs A, B = short roots with no root
  hairs.
  Conclusion: A and B function independently on different
  aspects of root development (A is required for normal root growth
  and B is required for root hair development.
b) Epistatic phenotype: A, B = either A or B
i) If A = B = A, B   then epistasis implies that both genes function in the same pathway and that each gene is essential to the process.   Eg. A = short roots, B = short
  roots A, B = short roots.  Both A and B are  required for
  normal growth of roots.
ii)         If A is opposite in phenotype to B, and A, B = A, then epistasis implies that  A and B are in the
  same pathway and B is a negative regulator of A.   Eg. A = long
  roots, B = short roots A, B = long roots.  A is required to
  suppress root growth and B is a negative regulator of A.
c)
  Synergistic phenotype: A, B >>> A or B.
Implies that A and B contribute independently to the same process.   Eg. A = long roots (wt = 2 cm, A = 4 cm)    B =
  long roots (B = 4 cm)  A, B = very long roots (20 cm).  A and
  B negatively control root growth independently of one another and
  are performing partially redundant functions.

When your professor was saying that if A and B are in same pathway and you mutate A and phenotype comes as if both A and B have been mutated, then he was probably referring to the epistatic phenotype.
When he was talking about having a stronger effect by mutating them both, he was talking about Synergistic phenotype.
Source : Double mutant analysis

I do not know about the hypomorph thing. Maybe someone else will help you !

Feel free to ask anything u do not understand. These things are tricky !

Hypomorphs (now commonly termed 'dominant negative') have a reduced (hypo) phenotype as compared the wildtype. Null (knockout) mutations, however, have the phenotype removed, so to say.
The reason that you would use null rather than hypomorph mutations to do double mutant analysis is because with the hypomorph, you would still see some effect of the phenotype you are trying to have eliminated.
Why do you want to eliminate a phenotype? Let's say you want to try to find the pathway for the genetic interactions between A and B. You have 2 animals you want to cross (I work with C. elegans worms, and use double mutants often). If we look at the wildtype homozygous of both animals, they will be the same. Animal 1: +;+/+;+. Animal 2: +;+/+;+. (where + denotes wildtype, and ';' means they are not linked, so the genes are independent of each other).
We will use 'a' to denote null mutation A, and 'b' to denote null mutation B.
Animal 1 will have mutation A. Animal 2 will have mutation B. So now Animal 1 will look like a;+/a;+, and Animal 2 will look like +;b/+;b. Notice that each locus is corresponding with itself - ie: in the region where Animal 1 is still +, Animal 2 is b, and vice versa (for null mutation 'a').
So then we cross Animal 1 with Animal 2 and get a;+/a;+ x +;b/+;b which will segregate in a 9:3:3:1 ratio (according to independent assortment of 2 independent genes - just draw a 4x4 punnet square to convince yourself).
We are interested in achieving the 1/16 a;b/a;b animal (also can be noted aabb, btw). And THAT is our double mutant.
Because we use a null allele, there is no chance of the wildtype phenotype "leaking" within our cross, giving us a false ratio or false assessment, as would be the case with a hypomorph (reduced, but not gone).
Now, when talking about genes in a pathway: I think this is what your professor was referring to. When we are mapping how genes interact, and in what order, we can either have the genes interacting in redundant or sequential pathways.
Redundant pathways: A -> C and B -> C. So either A or B can have an effect on C, meaning that having both is redundant, because one can do the job.
Sequential pathway: A -> B -> C  OR  B -> A -> C. So both are existing in the pathway in sequence, and both are needed.
Just as a side note, whenever you are using double mutants to find out if your pathway is redundant or sequential, you MUST compare it to a single mutant!!! Otherwise you WILL NOT be able to tell the difference between your results.
In a single mutant (A, for example), when using in a redundant pathway, you will still get phenotype C, since B is available. Just note that your C phenotype will be weaker.
When you then use a double mutant, knocking out both A and B, you will see NO expression of phenotype C. The same will apply if you knock out B instead of A.
Now, for a sequential pathway. If you use a single mutant (again, let's use A as the example) you will have no phenotype C, since A is needed to interact with B (whether upstream of downstream) in order to have an effect on C. And, if you use a double mutant (so knock out both A and B), then you will also have no expression of C, since both A and B are gone. (again, same applies if you use a B single mutant first)
So, for a redundant pathway: single mutant will have C phenotype, double mutant will not have C phenotype. There IS a change!
For a sequential pathway: single mutant will have no C phenotype, and double mutant will have no C phenotype. There is NO change!
If you would have used a hypomorph to do these experiments, then you would probably see some percentage of C expression in your double mutant experiments, making your results inconclusive.
--
I hope this helps!
[source: you can find this information in any genetics textbook (in my case, since i study worms, WormBook is a great source); I have given this information from my own experience. I have an honours degree in Genetics (Biochemistry and Medical Genetics) and am currently continuing my education in grad school (biochemistry and molecular biology).

Null mutants are not necessarily KO! they can for example be substitutions causing a premature stop codon. Hence it would be great if you made that clear in your response!


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How well do we notice asynchronicity?
I'm stopped at a stoplight and, with nothing to do, my thoughts wander to the timed don't-walk sign that governs any pedestrians who might wish to cross the street I'm driving along.
I can see two such signs, one on my side of the cross street, and one across the way. They are synchronized: each counts down the seconds at exactly the same time as the other, as far as I can tell, lighting up as "5", then a second later as "4", etc. Nothing's wrong with my ocular nerve or brain, as far as I know. Can you fill in the blanks please?
I can be …% sure that the lights are synchronized within … seconds of one another. (Not something trivial like "100" and "1", of course.)

I'm only familiar with human perception of audio-visual asynchronies, but in that case it is highly context-dependent and varies by individual. Under best-case scenarios, humans can detect an audio delay of 100 milliseconds. Under more normal conditions, 200-300 milliseconds is the threshold for perception.  I would imagine we'd be better at detecting asynchrony between two visual stimuli in general, but the fact that you can't look at both lights at once probably makes it harder to detect asynchrony. So it's probably hard to know what the result is on balance without testing it specifically.

Thanks for the info, @seaotternerd. I figured it varies widely by individual, which is why I asked for a confidence interval rather than a straight answer.

The lights are probably working off the same controller, so actually are synchronous to within maybe the few nanoseconds it takes electrical impulses to travel through different length wires.

Can I add something to the question? What about audio delay in audio visual clip?

@DevashishDas - your added question is about intersensory asynchrony; for the answer see the answer on this question: http://biology.stackexchange.com/questions/31505/latency-differences-between-our-senses/31666#31666

@jamesqf Well, assume we don't know that: assume it's not necessarily true.

Short answer
I can be 75% sure that the lights are synchronized within 0.02 - 0.2 seconds of one another.
Background
Interesting question, but hard to answer! Because it has been unanswered for quite a while I will try to formulate an answer that may provide an approximate value for the minimal asynchrony perceivable.
The temporal resolution of the visual system can be quantified in a number of ways. As you are referring to relatively simple stimuli, the critical flicker fusion frequency is probably the most relevant. At a certain critical frequency, a flickering stimulus will appear as a continuous stimulus (Holcomb, 2009). For example, the good old CRT screens can sometimes seem to be flickering. The mains is 50 Hz (US) or 60 Hz (Europe, Australia), and indeed the critical flicker fusion frequency is 5 - 50 Hz, dependent on the lighting conditions (Kalloniatis & Luu). Hence, stimuli separated by 200 ms (low lighting) to 20 ms (high lighting conditions) can be temporally resolved.
I am aware that your question is different, as you ask whether two stimuli on the retina can be perceived as being asycnchronous. Flicker fusion testing is mainly done with flash stimuli, i.e., a single stimulus per image, not two. However, from the various measures of temporal resolution of the visual system that have been used to date, the critical flicker fusion has the most conservative value, in that it provides the top-value of temporal resolution. Higher-level processing is much slower and values of around 4 Hz are obtained. For example, when subjects are tested on a stimulus of dots that are white when moving right and black when moving left, and they change directions/colors at a certain frequency, it becomes hard to tell whether the color change and direction change are synchronized at alteration rates of ~5 Hz and higher (Kalloniatis & Luu).
As to your question what the percentage chance is that stimuli separate by 20 -200 ms are separable, I can say that in general, psychophysical procedures determine the threshold defined as halfway between chance and 100% correct. Assuming a typical yes/no tasK (are the traffic lights synchronous yes/no?), chance would be 50% (guessing), and threshold would thus be defined as halfway between 50% and 100%, i.e., 75% correct.
References
- Holcomb, Trends Cog Sci 2009; 13(5): 216-21
- Kalloniatis & Luu, WebVision, chapter "Temporal Resolution" 2007

authors: محمد الخثيميً

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Under what conditions does the body burn fats, proteins and carbohydrates?
Searching the internet, I have found lots of conflicting information from various fitness sites concerning when the human body burns fats, proteins and carbohydrates.
My basic understanding was that the body will first utilize glucose and glycogen stores, followed by fats and finally proteins once the fat and glycogen stores become depleted.  Also I believe there is some overlap in this process.
However many fitness websites claim that during high intensity physical activity, the body will prefer to burn protein over fat.
Scientifically speaking, when does the body ordinarily burn the following food groups (proteins, fats and carbohydrates) and how does exercise influence this process?
If you are able to provide graphs or data to back up your answer this will be extra helpful because I am bored of all the speculation I see on other sites.

I do not know about exercise but I can tell you that in case of starvation, body first uses glycogen/other carbs as energy source and then fat and lastly proteins(as proteins have other important functions,too). I also want to point out that proteins might be used for the first week of starvation but then fat takes over and only after all the fat has been consumed is protein utilisation started substantially.

Even though I am not sure, it seems ridiculous to me that "protein is used during heavy exercise" as proteins are generally the last resort and they have other more important functions.

Introduction
The system that regulates body energy store consumption is hugely complicated, but is mainly a cooperation between hormones released by the pancreas (insulin - lowers blood sugar and glucagon - raises blood sugar) and the liver (as the bodies main glycogen store and factory for various energy related tasks).
Fed State
In the fed state (high blood glucose e.g. after a meal), the body produces a large amount of insulin.  When the ratio of insulin:glucagon is high (≈0.5):

Dietary glucose is absorbed by the liver when glucose concentrations are over 8mM.  This glucose is then either

used in respiration by the liver
converted to glycogen to be stored in the liver
converted into fatty acids which are then transported out to the periphery in very-low-density lipoproteins (VLDLs)

Adipose tissue (fat tissue) takes up glucose in the blood.  This glucose is then:

used in respiration by the adipose tissue
converted into fatty acids then tri-acyl-glycerols (TAGs) - fat.  VLDLs from the liver can also be absorbed by adipose cells to be used for this.

Skeletal Muscle again directly absorbs glucose from the blood

During contraction glucose is used directly in respiration to fuel the activity
In preparation for future contraction it is converted into glycogen and stored in the cell
Amino acids are incorporated into cellular proteins though if they are superfluous then they can be used in respiration

The brain directly absorbs glucose and uses it in respiration

Early Fasting State
Where the insulin:glucagon ratio has dropped to around 0.15

In the liver

Glycogenolysis is activated to release glucose from stored glycogen to compensate for falling plasma glucose levels (signalled by elevated glucagon)
Triglycerides in the liver are preferentially broken down for hepatic respiration - fatty acids are transported in from the blood to meet the livers own energy demands
The liver begins the process of gluconeogenesis - making glucose from non-carbohydrate precursors

Adipose tissue

Rapidly starts lipolysis - stored fats are broken down into free fatty acids and glycerol.
Some of the free fatty acids are used for the adipose tissues own respiratory demands
The majority is released to the periphery to be utilised by other tissues
The glycerol released can't be used by most tissues, but is taken up by the liver where it can be used to make glucose by gluconeogenesis

Skeletal Muscle

Uptake of glucose from the periphery is reduced to preserve glucose for cells that can't easily use other fuels - e.g. the brain or red blood cells
Free fatty acids become the main fuel for skeletal muscles to conserve the glucose for elsewhere
Unlike in the liver, glycogenolysis is not activated as there are no glucagon receptors in muscle tissue.  This means glucose is only produced from glycogen when muscles are actively contracting, as before.
At this point proteins can start to be broken down,  their skeletons used as an immediate source of energy and amino acids released to be taken up by the liver and used in gluconeogenesis

The brain directly absorbs glucose and uses it in respiration.  Fatty acids can not be used as these do not cross the blood brain barrier

Late Fasting State
If there has still been no glucose intake, the insluin:glucagon ratio falls even further, to around 0.05.

Liver

No further glucose has entered the liver and within 24h all hepatic glycogen stores have been depleted
Gluconeogenesis becomes the principle source of all plasma glucose - the liver creates new glucose from:

Amino acids - muscle & liver protein breakdown
Glycerol - from adipose tissue
Lactate - from red blood cells and muscles

High amounts of fatty acids are converted into Acetyl CoA to be used in respiration by the liver, but too much Acetyl-CoA is produced.  The remainder is converted into ketone bodies that are useless to the liver, so jettisoned to be used by other tissues (esp. the brain)

Adipose tissue

As the fast continues into a few days, adipose tissue adapts to producing large amounts of free fatty acids.  This becomes sufficient for most body tissues
These fatty acids are used preferentially by all tissues that can use them, conserving glucose for the brain

Skeletal Muscle

Fuelled almost entirely by fatty acids and ketone bodies from the liver and adipose tissue
Protein breakdown continues to release carbon skeletons and amino acids for gluconeogenesis - but this is inhibited in the presence of high levels of ketone bodies to prevent unnecessary muscle wastage (still allowing the human to hunt)
Amino acids are incorporated into cellular proteins though if they are superfluous then they can be used in respiration

The brain

Once ketone levels reach a critical level, they can cross the blood brain barrier to be used as a supplementary energy source
However, it is not sufficient alone, so a net source of glucose is needed from somewhere in the body

Progressing to starvation
This process can continue for a number of weeks, with the body eventually exhausting fatty acids in adipose tissue and being unable to produce ketone bodies in the liver, losing the inhibition of proteolysis causing a last ditch response of muscle breakdown for energy.  Death is usually from heart failure resulting from cardiac muscle breakdown.
Summary
This chart might be useful in summary, it shows where the glucose levels in the blood are coming from at various stages, the gluconeogenesis line indicating protein and fatty acid breakdown:

Exercise
Exercise has to be very intense to have any effect on this system in normal situations.

Resting Muscle metabolises stored fatty acids for its own energy.  Glycogen stores are replenished from glucose ready for more vigorous contraction.
Brisk Walking fatty acid metabolism again provides almost all the energy
Sprinting Glycogen stores are used, respiration is almost entirely anaerobic as blood vessels are constricted by the muscle activity and ventilation has not had time to increase.  Lactic acid is produced, which can be used by the liver for gluconeogenesis
Middle distance running: aerobic metabolism takes over as the body adjusts to the higher oxygen demand.  Lactate is still the major end product

One example of where this may be more noticeable is during a marathon.

0 Mins - Muscle is resting at the start line, as above.
10 mins - Muscle and liver glycogen released to power muscle contraction
2 Hours - A marathon requires roughly 700g of glycogen to complete, however the liver can only store around 500g.  This is largely depleted after roughly 20 miles.  Blood glucose levels fall rapidly and the body switches to fatty acid metabolism.  This only provides around 60% of the power output and pace falls off (known as hitting the wall).  At this point, virtually every reserve power source is being used simultaneously to keep the body going.
Finish - Muscle and liver glycogen are entirely depleted. If glucose levels haven't been maintained by other means, hypoglycaemia results causing confusion, hallucinations and even coma and death.

Thanks for your informative answer.  Let us say someone is on a calorie deficit diet, and undergoes exercise that night.  They would supposedly have low glycogen stores, and would rely on gluconeogenesis.  What proportion of gluconeogenesis will be fatty acids, and what proportion will be from protein?  Is this ratio always the same or is it dependent on intensity?

@Chris I would anticipate greatly more from fatty acids than protein breakdown until one runs out of fat.  You'll be able to release enough energy through fatty acid usage for any intensity of exercise assuming that you still have fat stores available.

@Chris The only gluconeogenesis that is possible from fat breakdown is that derived from the glycerol of the triacylglycerol. Fatty acids are metabolised to acetyl CoA, and it is not possible to synthesise glucose from them because for every acetyl group that enters the TCA cycle, two CO2 molecules are lost before the 'start' of gluconeogenesis (oxaloacetate). A starving subject would rely on fatty acids (directly and as ketones) and glucose derived from glycerol, lactate and amino acids. Despite the switchover to using fat, a net loss of protein is unavoidable.

Dear @RoryM i really liked your answer and just want to kindly ask you further readings (even technical) about this field of human nutriton.

The answer should cite its sources, crucial for fact checking and good science. Where's the graph and the table from, for example? That said, this answer is top notch and the missing references are small fry. Well answered.


text:
Is this ventricular tachycardia?
I am investigating the public data of this.
Its specification
201 2 360 650000
201.dat 212 200 11 1024 972 -519 0 MLII
201.dat 212 200 11 1024 982 30947 0 V1
# 68 M 1960 2851 x1
# Digoxin, Hydrochlorthiazide, Inderal, KCl
# The PVCs are uniform and late-cycle.  Junctional escape beats occur following
# episodes of ventricular trigeminy.

The data is taken from the interval $[200000, 205000]$ in the following picture with the sample rate 500 Hz.

There seems to be more than Premature Ventricular Contractions (PVC), extrasystoles, so possible ventricular tachycardia.
The same patient has six minutes later this

I think you can see clearer here those PVCs, when the ventricle is starting to contract too early.
Both are very pathological situations.
How can you differentiate between the two?
Are there PVCs in both pictures?

I have looked at this ECG using LightWAVE.
The first part is showing atrial fibrillation or flutter with variable conduction because:

arrhytmia
no P waves or coarse fibrillatory waves
tachycardia at about 95-100 beats/minute
can be seen better in V1

Sample from 00:00:40
The second part is showing premature ventricular contractions with trigeminy because:

different morphology of QRS - ectopic
wide QRS
two normal complexes followed by one ectopic
presence of the compensatory pause after PVC

Sample from 00:09:20
References:

ECG data: PhysioNET MIT-BIH Arrhythmia Database
ECG criteria: LearnTheHeart.com

So the ventricular tachycardia is at about 95-100 beats/minute.

@Masi you can't call it ventricular tachycardia. It appears because of the numerous stimuli generated by atrium. Only a few of these stimuli reach the ventricles because of the atrio-ventricular node. How many - that depends on the subject's age (it lowers the number of stimuli that pass through). At a younger subject atrial fibrillation may cause 150-200 beats/minute or even more.

I am particularly interested in the second part. I completely agree with you about these three findings: different morphology of QRS - ectopic, wide QRS, two normal complexes followed by one ectopic and presence of compensatory pause after PVC. Those two normal QRS complexes seem to different little. Do you see any other else in the second picture? Uneven rhythm, I think. Very low rate tachycardia remnants probably 95-100 beats/second.

@Masi yes they are sometimes different. Are you thinking of ectopic pathways?

Yes, I am thinking ectopic pathways.


text:
mixing beer with spirits, increase alcohol content?
I decided to mix beer with vodka hoping it would make me more drunk due to the alcohol content but then remembered the rest ISNT alcoholic and i cant figure out if mixing beer with vodka or other spirits would increase the alcohol content or not i would really like an answer to this as well as any health risks if there are any, thanks.

Please note that whilst health risk discussion for individual cases are outside of the scope of this site, risks associated with alcohol are well known and available from good sources online: http://www.nhs.uk/livewell/alcohol/Pages/Alcoholhome.aspx

Perhaps it's worth adding for absolute clarity that the proposed mixing will definitely increase the total alcohol consumed e.g. comparing one shot of vodka with the same shot plus a beer - obviously. The linked answer discusses the physiological effect of this mixed drink.


text:
Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA
We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The SCA calculation involves determining independent components (IC) of positional covariation by applying the "Infomax" algorithm to a few top eigenmodes (that have been obtained from the positional correlation matrix). Here, we observed that the output (IC vector weights) seems to depend on the no. of top eigenmodes chosen as input (i.e. on choice of the parameter kmax). If this is indeed the case, then is there some "working rule" to optimally choose kmax (say, based on the number of significant eigenmodes turning up)? Since this isn't made very clear in the tutorials (at least to me), I thought of trying my luck here.
Would really appreciate some guidance/pointers from SCA users. Thanks a lot!

This question is has a very narrow scope. Please post this in its designated google-group or other forum.


text:
Static in limbs
I have noticed that while sitting in the Sukhasan posture(picture below) for a long time, my feet suddenly become all stiff and i am unable to move it. What I deduce from the experience is that it is static, though I fail to understand how it accumulated at my feet.Does anyone have an explanation for this?

It's not clear to me what you mean by "static." Are you describing paresthesia (http://en.wikipedia.org/wiki/Paresthesia)?

I have no idea how "static" comes into this, do you mean static electricity? Why would that be related?
Anyway, what you are probably experiencing is simple numbness caused by your posture applying pressure to a nerve:

In the image above, the right leg is likely to be pressing the the left which can cause paresthesia, more commonly known as "pins and needles". As explained in the NIH's paresthesia information page:

Most people have experienced temporary paresthesia -- a feeling of "pins and needles" -- at some time in their lives when they have sat with legs crossed for too long, or fallen asleep with an arm crooked under their head. It happens when sustained pressure is placed on a nerve. The feeling quickly goes away once the pressure is relieved.

it feels as if my leg is brimming with static electricity but i guess your explanations sums it up...

When I sleep more on one side I get more pain than tingling. But not only that but the pain is close and prolonged as if my muscles have been injured.


text:
Has Colony Collapse Disorder (or its equivalent) been noted in other species?
Colony Collapse Disorder is a well studied phenomenon relating to the decline of bee populations - has this disorder, or its equivalent, been observed in other colony-based species?

not that I know of but this may be worth a look http://www.unep.org/dewa/Portals/67/pdf/Global_Bee_Colony_Disorder_and_Threats_insect_pollinators.pdf

Exactly what are you asking? Do you want examples of large-scale colony abandonments in particular (i.e. abandonment by "healthy" individuals, mainly in insects) or population collapses in colony-living species in general?

both would be interesting; however, the 2nd question more so

bats are having similar problems http://www.nytimes.com/2012/09/25/science/in-tennessee-building-a-bat-cave-to-battle-a-plague.html?_r=0

In some ways tangent to what you are asking, but many cases of classical Allée effects (i.e. a positive relationship between population growth rate and population size, see Allée & Bowen, 1932, Drake & Kramer, 2011) should be relevant, especially after your clarification in the comments.
One famous, early example of species collapse and extinction in a colony living species is the Passenger pigeon. This was an extremely common North American bird, estimated to 3-5 billion individuals, and maybe the most numerous bird species on the planet. It was heavily hunted during the 19th century (mainly by netting), which coupled to deforestation of nesting grounds led to a population crash. One of the main reasons for the rapid collapse was probably that the species was a colony nester and depended on large flocks for courtship/reproductive behaviour. This also meant that conservation measures failed when the critical situation was noticed (although hunting bans/restrictions was also weakly enforced). The few remaining wild individuals failed to breed and artificial breeding attempts also failed. The last individual died in 1914 at Cincinnati Zoological Garden (extinct in the wild from ~1900). For more information on the Passenger pigeon extinction see the wikpedia page and Encyclopedia Smithsonian.

I hope you find this example useful, even though the collapse was initiated from hunting. There are many more examples of Allée effects in colony living species that describe similar effects, but maybe not as strikingly as the Passeger pigeon case. There is a fairly recent book "Allee Effects in Ecology and Conservation" (Courchamp et al, 2008), which might be of interest to you.

here is a paper about community collapse - published today! http://onlinelibrary.wiley.com/doi/10.1111/ele.12236/abstract;jsessionid=8DF00C9033B7929B0825F322FF145C39.f03t01


text:
What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?
The recent news about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but what is it about SNP analysis that makes it so poor as at predicting disposition? Even other SNP companies have similar problems with accuracy and can't agree on disease disposition (Tonellato et al., 2011). Why might they differ from 23andMe's predictions?

There is a quite extensive discussion about 23andme on Biostars. It has lots of links to helpful and interesting sites. http://www.biostars.org/p/87272/

I believe the issue is not the predictive power per se. 23andMe is a service that provides a fairly comprehensive analysis of your SNPs, and prepares a report collating the conclusions of published scientific research regarding your SNPs. I believe the FDA decision is motivated by the fear that some laypersons will see "you have a SNP that Jones and Doe, 2009 have associated with higher risk of a certain kind of cancer in a certain population" and take that to mean "You will get cancer tomorrow! Better start drafting your will!" (despite the information 23andMe provides on the contrary).

The long and short of it is that genetic variation is actually not very predictive in comparison to "environmental" effects such as lifestyle.
Only a quarter of the variation in lifespan between twins is attributable to inherited factors (including genetics and epigenetics) [1] - the rest is environmental, from lifestyle to air quality.
Most genetic variants (such as those measured on the chip used by 23andMe) have a very small impact on outcomes such as "Risk of disease X, Y or Z". Many risk loci have been identified, but without a full understand of what this risk means, the results of the 23andMe analysis can be misleading.
Some few rare genetic variants have a larger impact on diseases (such as early onset diabetes), but this comes under the "monogenic" category of genetic variation, rather than the common variants typically observed in large populations.
Basically, genetic risk scores are, at the moment, only indicative of an individuals risk, and to get the real picture a lot more information is required - for instance smoking is a better predictor of early mortality than any "common" (>=5% frequency in a population) genetic variants, likewise a high fat diet is more indicative of cardiovascular disease.

Skytthe A, Pedersen NL, Kaprio J, et al. Longevity studies in
GenomEUtwin. Twin Res. 2003;6(5):448–454. [PubMed link]


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Difference vector target and genomic target
In Pfu turbo DNA Polymerase AD information sheet (and possibly in many other) different amplification targets are divided in Genomic DNA targets, Vector DNA targets and cDNAs.
What is the difference between the first two?

Genomic DNA is a DNA that has whole set of genetic data of an organism. You usually extract it with a whole DNA extraction kit.
Vector DNA is a vector (usually a plasmid, it can also be artificial chromosome,...the type of vector depends on the species and strategy you are using) that has you desired string of DNA in it (for example a gene you want to insert in to a organism) and you are using it to get your recombinant DNA to the organism.
I hope it helps!

Genomic DNA is usually bigger and more complex than plasmid DNA which is a relatively simple DNA ring of limited size.


text:
Identifying the inheritance pattern
                      GrandParents                  -- 1
                            |
                            |
                -------------------------
                |S                      |D          -- 2
            ---------                ----------
            |S(A)   |D               |S(A)    |S(A) -- 3
            |S      |D                              -- 4

S = Son
D = Daughter
(A) = Affected with a degenerative disease.
The question is how to identify the type of inheritance of the disease - whether
X-based, Autosomal dominant or recessive. Which sex of fourth generation are likely to have the disease? Does it depend on the disease?

This pedigree can not lead to one absolute answer. There should be more information.

And also, Can you present your ideas on this question?

Short answer
As said @Biogirl, "This pedigree can not lead to one absolute answer". We miss information in order to answer this question.
Long answer
Should we make the assumption that the allele causing the disease (A) necessarily come from the lineage you draw or can it come from the partners of the second generation (offspring of GrandParents)?
Then, depending on your answer to this question...
If yes (= if the allele causing (A) comes from the GrandParents):

This genealogy is impossible if the type of inheritance is as simple as you suggested (either recessive or dominant, no epigenetics, no epistasis, no effect of the environment, no protein-mediated disease via the vomb,... even if it can be autosomal, sexual or mitochondrial genes)

If no (= if the allele causing (A) do not come from the GrandParents only)

Everything is possible (from the space of possibilities that you suggested)

some possibilities would be more probable than others (depending especially on the allele frequencies)

We are missing some information, but (by what I recall from my little inheritance genetics knowledge) it looks X-based. I will make up some of the missing information.
Lets say, an "affected X" is H (I wanted to use x, but it will be harder to see), HY will be diseased, XH will be carrier, but not diseased. XX/XH means unclear if carrying.
Grandparents:               XY-------------XH
                                    |
                           -------------------
                           |                  |
Parents&Partners      XH---XY                 XH---XY
                         |                        |
                     ---------               ----------
                     |        |              |         |
F1                  HY       XX/XH          HY         HY
                     |        |
F2                  YX       XX/XH

The F2 son is not carrying (because he is healthy). The F2 daughter could be carrying if her mother was, but even then does not have to. Unless her dad was also carrying it.
Please correct me, if I am totally off.

This would be one possibility. I guess you say that it looks like the disease is X-linked because all sick people are males but we only have three sick people. Among three guys, the probability that all have the same sex is $\frac{1}{4}$! Moreover, for your tree to be likely you would need that the allele causing the disease is present in high frequency in the population (which is rather rare for a X-linked disease)! I think it is better just to say that we don't have enough information to infer an inheritance type.


text:
What is the most genetically simple organism except viruses?
What is the most genetically simple organism (except viruses) on this planet?
By simple I mean the least number of genes.

I did a  google search and got this

I would guess it is a symbiotic bacteria! The mitochondria maybe (if we accept it to be an organism). Here is an article that you will appreciate. If you search for "tiniest genome" on google you will find some stuff

@biogirl So, the smallest organism (except viruses and mits) has 159,662 TACG pairs? No smallest number found so far? Any knowledge about this thing?

In the link I gave you, there is an insect that has only 112k base (112,000 ATCG pairs)

Mycoplasma genitalium

Note that the mitochondrial DNA is 16k base long and contain only 37 genes (Wiki Source). But you might not want to consider it as an organism.

Mycoplasma genitalium is fairly good with 583k base pair Wiki

@Derfder Would you accept to consider the mitochondria (for example) as being an organism?

@Derfder I dunno much about this. So many organisms's dna has not been looked into. So, in the future one may find smaller genomes

Mycoplasma genitalium was one of the first full bacterium genomes sequenced and since its a symbiotic organism that lives on the moist and warm genital skin surface it doesn't need as many genes as many bacteria.  It has a 582 kbp genome sequence with only 521 genes.
But that is so 1995.
The 159 kbp genome of Candidatus carsonella was published in 2006. It is thought to only contain 182 genes.  Its an endosymbiont of some sap eating insects.
But the current record holder, published this year, is Nasuia deltocephalinicola, discovered survey of insect endosymbionts, has only 112 kbp in its genome. Smaller than some viruses.  It's thought to contain 137 protein coding genes with 29 tRNA genes, so its not a lot smaller than Carsonella in terms of gene count.
There's no reason to expect that this is the minimal viable genome by any means.  I'm sure this response will need revision in a year or two.
M. genitalium has become the model system for minimal genome work.  Many of these other bacteria might be difficult to culture, molecular biology lab techniques might have to be developed, so hopping onto newly discovered bacteria isn't always the best idea from a standpoint of producing science.  It does suggest that M gentalium doesn't need all of its genes!  A possible cause for these extra genes might be a more complex immune response in human beings where its found.  It might also be because of the symbiotic requirements of insects is simpler.

Genome of 'Candidatus
Tremblaya princeps' is a bit larger (138931 bp), but contains 116 protein-coding genes: kegg, original paper. It's an insect (P) symbiont and has in turn its own bacterial (S) symbiont.


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What type of mutation causes Progeria?
I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease.
I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains a farnesyl group that is then not able to be removed (in the case of Progeria). The abnormal form (with the farnesyl still attached) of prelamin A is then called progerin, and attaches to the nuclear rim resulting in an abnormally formed cell nucleus, making mitosis impossible.
Is this a structural mutation? What sort of mutation is this?
Thanks in advance.

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is used it results in the deletion of information corresponding to about 50 amino acids internal to the protein and near to the C terminus.
During biogenesis of normal lamin A a C-terminal -CAAX motif is recognised as a signal for isoprenylation, in this case farnesylation. The added lipid group acts as a C-terminal membrane anchor. However this anchor is subsequently removed when the protein is proteolytically cleaved near the C-terminus, removing 15 amino acids including the C-terminal cysteine (by this point the three C-terminal residues have been trimmed away). The cleavage site for this final modification is missing in HGPS lamin A so the farnesyl group cannot be removed. The accumulation of unprocessed lamin A causes the observed defects in the nuclear membrane.
Eriksson et al. (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423: 293-298
Capell et al. (2005) Inhibiting farnesylation of progerin prevents the characteristic nuclear blebbing of Hutchinson-Gilford progeria syndrome. Proc. Natl. Acad. Sci. USA 102: 12879-12884


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Is it possible to use microalgae to produce food and live on it?
I know microalgae have not less protein and starch, grow quickly, require less. So, is it possible to use them for producing food (replace rice and wheat) and live on it?
Currently, I only saw people eat it as an extra-nutrition.

I don't see why microalgae couldn't be a main food source (putting aside the taste factor).
It contains many different lipids, carbohydrates, proteins and other essential nutrients that are digestible and would be beneficial to humans. I do know that microalgae has a very high lipid content (hence why they're often harvested for biofuels), but it can nonetheless provide nutritional value (ie. feed a starving man).
However, not how this is completely different from living solely off of microalgae. This likely wouldn't be possible, as us humans cannot synthesize all nutrients that we need from scratch. These nutrients are deemed essential nutrients. This problem usually arises when your diet is too restricted to certain types of food. So whether it's microalgae or any other type of consumable, you wouldn't be able to live by only eating that thing.
Another related problem is that growing microalgae is more difficult than it would seem, as is once again usually encountered in second-generation biofuel manufacturing. Temperature, light, cell density, nutrients, and much more must be precisely managed to obtain a increasingly growing population of microalgae. The pros and cons of farming microalgae for billion of hungry people would have to be contrasted with other current agricultures, like corn, soy and rice.

do you have any idea whether algae don't provide the essential nutrients?  a lot of animals only eat algae.

as i knew, the germany use Chlorellaceae for food during the World war 2, the problem is can we relied on it for long term use

@shigeta different animals have different metabolisms and different essential nutrients. For example,  most mammals can synthesize Vitamin C from other nutrients. Humans and other primates have to find it in the food they eat, they can't synthesize it.

while the nutritional profile can change there are also many microalgae and you would have to look pretty hard to find a microbe that is missing, say an essential amino acid.  its more of a problem finding an occasional compound that might not be healthy for human consumption , say.  in terms of making food nutritionally competent supplementing with vitamins minerals and fats is really common in food. its not technically prohibitive to add a vitamin...

lots of filter feeders would agree with you if their throats weren't clogged with algae.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Basic definitions for biology terminology
I am currently writing a mathematical biology paper, however it is very hard for me to follow the existing literature due to specialized terms. I have tried googling but most explanations are very technical and filled with more biology jargon. I have absolutely zero biology experience, so if anyone could please give a very very basic, non technical/rigorous, and intuitive explanation of the following terms, that would be great.

Nucleotide
Protein
DNA
Adenine, Thyine, Cytosine, Guanine
RNA
Single Nucleotide Polymorphisms (SNP)
Base: e.g. "1% of the human genome (about 30 million base pairs) will
be treated."
Eukaryotic
Genome
Genome sequence
Whole-genome
Partial-genome
GC content
conservation: e.g. "degree of evolutionary conservation"
conserved region: e.g. "functional elements are more likely to be
found in DNA regions that are the best conserved across species"
conserved sequence
chromosome
binary sequence
non-coding DNA/RNA
non-protein-coding genes/sequence/portion/elements
protein-coding genes/sequence/portion/elements
gene sequencing
gene promoters
purifying selection
positive selection
functional element: e.g. “…classes of functional non-coding elements
remain to be discovered”
non-functional element: e.g. "identify all non-functional elements in
the human genome."

Wow, these are quite a lot of questions. How do you want to write a paper on mathematical biology without at least a basic understanding of biology? My advice would be that you go into the stuff and then ask more specific questions.

There are too many questions that ask for too many explanations, I don't think anybody wants to answer to all that. It is not really possible to give a "very basic without technical term" definitions to most of these words. If you want to write an article in mathematical biology, I am afraid you will have to take some time to learn a bit about biology. Go through some books that will guide in the basic understanding of biology. I know we all would like things to be easy when starting a new field but unfortunately there is no easy answer to your questions. This book for example might help you. It is a classic in first year Bachelor in biology.
If you have some specific questions, you are very welcome to ask them. But this post asks for a whole book!
Here is a small quickly written text that will maybe help you a bit. Note: it might be oversimplified sometimes!
DNA is a big molecule made of (among other things) nucleotides. There are 4 nucleotides (adénine, cytosine, tyrosine (or Uracile on RNA) and guanine often just called ACTG and they can be categorized in two types of molecule depending on their number of cycles) which sequence form the genetic information. DNA, in eukaryotes (which are cells that contains DNA in a nucleus (which is the case of all non-virus, non-bacteria and non-archaebacteria)) is grouped into chromosomes (which are usually represented by a "X" as they more or less appears at the metaphase (a phase during the life cycle of a cell)).
DNA is transcribed into mRNA (a kind of RNA) which is then translated into protein (by rRNA and tRNA). While RNA and DNA are made of nucleotides, the protein is made of amino acids. Three nucleotides (one codon) codes for 1 amino acid.
In the genome there are sequences that code for proteins, sequences that code for RNA, sequences that allows other proteins to bind into in order to influence gene expression, promotors, enhancers… You will have to accept taking some time learning a bit about that stuff I guess.
Sequencing is the (artificial) process of reading a DNA sequence. This can be achieved on a whole genome or on small chosen sequences.
As the nucleotides G binds only with C and A binds only with T (two nucleotides together form a base pair)(there are two strands of DNA linked by the nucelotides), the amount of G equals the amount of C and same for A and T. The GC content gives the proportion of G and C of the total number of nucleotides of a sequence (or a whole genome). Oh by the way, a genome is the totality of the DNA of a given individual.
Positive/purifying selection are cases of natural selection. Natural selection is a process by which the frequencies of alleles (variant of a gene) does not vary randomly. They vary according to the reproductive success (= fitness) they confer to the individuals that bear the allele. Positive selection on an allele means that this allele is selected for. Purifying selection refers to the wildtype allele (most frequent allele) is selected for and all mutations (DNA modifications) that appear are deleterious and therefore counterselected,
A SNP is a genetic variation between individuals in a population (or along populations or species) that involves only one nucleotide.


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How do transplanted stem cells find their way to bone marrow?
Miraculously, transplanted stem cells find their way to the bone marrow missing the stem cells. How do they achieve this?

The transplantation is an equivalent of a process that naturally occurs in human body, homing of the hematopoietic stem cells.
Immature hematopoietic stem cells have the ability to pass the bone marrow barrier, and therefore is able to migrate between bones and other organs within an individual. (e.g. thymus, which is how it can produce T cells.) Williams et al. believe that the process, homing, is a complex interaction and is similar to the migration of leukocytes to inflammatory sites. 1
Peripheral stem cell transplantation makes use of this ability. The donor first will be administered with certain drugs to proliferate stem cells in bone marrow and hereby raising the concretion of hematopoietic stem cells in blood. Those stem cells in blood then will be collected and transfused into the recipient. Eventually those cells will find their way home.

similar to migration of leukocytes to inflammatory sites... so you mean it's somehow like chemotaxis?

@GreekFellows I believe so. In fact, a research I found suggests HSC will respond to some factors.


text:
Organisms as potential Bio-Weapons?
Question:
Given that with genetic engineering we can customize organisms as bio-weapons. Which species have the most worrying potential to be weaponized for mass destruction?
Background:

Biological warfare — is the use of biological toxins or infectious agents such as bacteria, viruses, and
  fungi with intent to kill or incapacitate humans, animals or plants as
  an act of war.

Examples:

E.G. bio-weapon species: Anthrax fungus -  was first tested as a biological warfare agent by Unit 731 of
  the Japanese Kwantung Army in Manchuria during the 1930s; some of this
  testing involved intentional infection of prisoners of war, thousands
  of whom died. Anthrax, designated at the time as Agent N, was also
  investigated by the Allies in the 1940s.
E.G. bio-weapon vector: Anopheles labranchiae (malarial mosquito) - According to Prof Frank Snowden, a history professor at Yale
  University whose book The Conquest of Malaria in Italy draws on
  American archives and the diaries of Italian soldiers, the scheme was
  orchestrated in the autumn of 1943 by Erich Martini, a medical
  entomologist, Nazi Party member and friend of the SS commander
  Heinrich Himmler.

When was anthrax used to assassinate US politicians?

You remember these mysterious letters in the US following 9/11 containing a white powder? This were actually weapon grade anthrax spores.

@AlanBoyd, here's the wiki all about it: http://en.wikipedia.org/wiki/2001_anthrax_attacks, i've updated the question to include some details on this

Which confirms that no politicians were assassinated.

oh my mistake! I meant attempted*

I would say by far the most worrying potential is that of H.sapiens sapiens.

There is both a set "list" of agents, but more importantly, a set of properties that an organism needs to be in order to be truly worrisome.
First, the list:
The CDC classifies agents into one of three categories, Class A, B, or C.
Class A: These are organisms that are hard to control, highly transmissible, and lethal:
Anthrax (Bacillus anthracis)
Botulism (Clostridium botulinum toxin)
Plague (Yersinia pestis)
Smallpox (variola major)
Tularemia (Francisella tularensis)
Viral hemorrhagic fevers (filoviruses [e.g., Ebola, Marburg] and arenaviruses [e.g., Lassa, Machupo])

Class B: These are organisms that are fairly easy to disseminate, make people sick but don't necessarily have high mortality rates, and may be difficult to detect.
Brucellosis (Brucella species)
Epsilon toxin of Clostridium perfringens
Food safety threats (e.g., Salmonella species, Escherichia coli O157:H7, Shigella)
Glanders (Burkholderia mallei)
Melioidosis (Burkholderia pseudomallei)
Psittacosis (Chlamydia psittaci)
Q fever (Coxiella burnetii)
Ricin toxin from Ricinus communis (castor beans)
Staphylococcal enterotoxin B
Typhus fever (Rickettsia prowazekii)
Viral encephalitis (alphaviruses [e.g., Venezuelan equine encephalitis, eastern equine encephalitis, western equine encephalitis])
Water safety threats (e.g., Vibrio cholerae, Cryptosporidium parvum)

And finally, Class C, which are emerging threats that may be dangerous if engineered largely due to their novelty and their potential lethality/transmissability. The CDC uses examples like Nipah virus and hantavirus.
So that's the list of what the CDC thinks is a big deal. You'll note influenza isn't even on there. I'd argue that any given novel influenza strain belongs in Class C, and likely not Class A because, while potentially both transmissible and virulent, a known vaccine exists and simply needs to be formulated.
In terms of properties for an organism, I'd suggest the following, in no particular order (it likely depends on what said organism is meant to do):

Highly virulent: The disease needs to be able to cause human disease, with high rates of both morbidity and mortality.
Highly transmissible: Unless the goal is to cause a "one off" incident, the disease needs to be able to establish a productive chain of human-to-human infections. Humans can't be a dead-end host. Ideally, this needs to be direct human to human transmission, rather than a vector born disease like West Nile.
Stable and amenable to engineering. It needs to be something that's easy to culture and grow in large numbers. This one often gets overlooked somewhat, but despite the fact that its now somewhat commonplace, bioengineering isn't exactly easy.
Not amenable to treatment. The organism needs to not be easily treatable - broad spectrum antibiotics, existing vaccine stock, etc. mean that the normal public health infrastructure can address, or at least mitigate, an attack. For an attack to be truly effective, it needs to swamp existing infrastructure, and one way to do that is to necessitate intensive, unusual care in hospitals and out of the ordinary action on the part of public health officials.

No doubt influenza. The horizontal shift makes it very virulent and only a few mutations allow it to transfer from birds to mammals (as little as two). See here. There was a big push not to publish these as it would be so easy to make recombinantly. However, thanks to quick work, we have determined that our seasonal flu vaccine protects against this variant.

I would put all zoonotic viruses into this. They passed a species barrier, are new to our immune system and there are no vaccines against them. The flu is one example, corona viruses are another (SARS or even newer MERS). With SARS we had a lot of luck that this didn't end in a bigger epidemic.
A good book about these viruses is the book "Outbreak" (hence the title) by David Quammen.

A more abstract idea for a Bioweapon species could be one that targets key organisms required for completing the nitrogen or carbon cycle. This would likely cause the entire biosphere to collapse though.


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Why is there more variation in proteins than genes?
The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular).
How do you account for the presence of more variation among of proteins than there are in genes?
The simple answer would be "there are more proteins than genes", but I'm more interested in why. Is it sufficient to say that during gene expression a single gene codes for multiple proteins (Alternative Splicing) and ribosomes translating mRNA to polypeptide chains (Posttranslational modification)? Could someone expand more on this?

There are several concepts to understand:

Alternative splicing

From one gene, several proteins can be constructed depending on which introns are spliced.

Tissue-specific genetic expression

Genes are differentially expressed (and differentially spliced) depending on the tissue.

Post-transcriptional modifications

Those are modifications that are made directly on the proteins (in opposition with alternative splicing which are modifications made on the RNA)

Structure of the proteins

Proteins may fold (to what we call primary, secondary, tertiary and quaternary structures) differently in different environment.

Therefore there is variance in proteome between cells although there is no variance in genome between cells (except mutations and red blood cells). Moreover, one gene sequence can give rise to many different proteins due to the processes of alternative splicing and PMT.

On a similar note: What is meant by the 'complexity' of the proteome? Why is it described "the proteome has at least two levels of complexity lacking in the genome"?

The word complexity is used with many different meanings. Here is another post that maybe interest you. Or the Wiki article I don't quite know what can be meant with this sentence: "the proteome has at least two [...]". I guess that indeed it is closely related to your question. I would suggest you to post it as another question and give a link to your article and maybe a small summary of the context in which this sentence come from.

This is according to the Wiki page regarding the proteome. Perhaps the following sentences will help: "The proteome has at least two levels of complexity lacking in the genome. While the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins."

aha. Here is the link to the wiki page for others. Ok, so I missed this point in my answer. The proteom is indeed greater than the genome due to alternative splicing and PTM. Let me try to improve my answer (but I am slowly affraid to go into details that I might not know very well..)

@Cloud I think, by saying two levels of complexity , it means that proteins are not mere chains of amino acids they also have to have specific structure and interaction with other molecules.

To comment on the "why" question: I would say that its a relatively simple way to get a high number of proteins with more or less slight differentiations. This can include exons which are only present in special environments or cell types and so on. It saves a lot of energy for keeping all the information about every single transcript (the BNC2 gene for example can produce up to 90.000 different mRNA transcripts coding for up to 2000 different proteins of unknown function, see here) and makes the genome a lot less complex, despite the fact that we now need an also complex regulation.

90 or 90,000 mRNA Transcripts?

@TalhaIrfan If you look at the linked paper, you would see that the number 90.000 is true. I think that this is a theoretical number and less transcripts are made, but it shows the possibilities.


text:
What evidence is there on the medical effects of circumcision?
If this is the wrong place to post this question, then I will delete it and post it were it belongs.
I have heard many conflicting things about circumcision.  I have heard that it reduces the rate of STDs, including AIDS, and cancer in the man and his wife.  On the other hand, I have also heard that circumcising babies can cause psychological harm and increases the rate of urinary tract infections.  Are there any reliable studies on this issue and what do the conclude?
Thank you for any and all answers.

This question has already been answered over at the Skeptics site in great detail.
See Does circumcision reduce HIV risk? and Does circumcision lead to a net increase in quality of life?. The answers are well-sourced and there are answers addressing both sides of the issue.

This is community wiki since it doesn't really add any new information outside of links to another stackexchange site. Feel free to add more links and resources if you wish.

Thank you for the information.  I will go to the skeptics site and read those links.

authors: خالد العيساوي


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Bird identification: Warora, India

These photographs have been taken in Warora, India. Could someone please help identify this bird?

This is a pond heron or paddy bird. The de-facto source for identifying Indian birds is Birds of the Indian Subcontinent by Richard Grimmett, Carol Inskipp and Tim Inskipp. The book is remarkably complete and contains the vast majority of species found in the Indian Subcontinent.


text:
pfu Turbo DNA polymerase AD
What is the duration (Life") of pfu turbo DNA polymerase AD. I am trying o Amplification a 3.3kb fragment and the PCR schedule is 6 hours long. The manufacturers notes just specify that its activity remains 94-99% in 1 hour at 95, nothing more.

I don't know the exact half-life of this special Pfu polymerase, but generally Pfu polymerases are pretty stable. This source gives a half life of 18-25 hours at 95°C, meaning you keep the enzyme at 95°C for the whole time a you still have 50% activity after that time. Since you don't do that, I wouldn't worry too much about the activity. To be safe, you can add an extra long (probably 10-15 minutes) single amplification step before cooling down.


text:
What is the cause of singularity in phase response curve of human sleep and bright light?
I have no background in science as I am a computer programmer, but I am trying to get information on phase response curves, human sleep and exposure to bright light as I am trying to get to grips with a possible diagnosis of delayed sleep phase disorder.

The point marked phase delay is typically where someone would go to sleep and they would typically wake a couple hours after the peak marked phase advance. What is the physiological process that cause the move from delay to advance via the point marked singularity? In other words, why does light cause a delay initially but then cause an advance?


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Is there a PSI-BLAST for nucleotide sequences?
I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs (typically 50-200 nucleotides long and noncoding).
If there is no such resource, what are the main obstacles to this implementation?

why not blastn?

have you tried the HMMER program yet? Theoretically it is very similar to PSI-BLAST in that it is a profile method but bolted with a more rigorous probabilistic framework + it is used to search for remote homologues

if either of my answers have actually "answered" your question please click "accept" (tick) - this both improves the site and is good etiquette

I need a bit more tinkering time

First check if your RNA sequences are described by existing covariance models (CMs) available in Rfam. You can do this using the Infernal package to search the Rfam database of CMs. For those RNA sequences which match an Rfam CM, you can then use that CM to search the sequence databases for additional matches.
For those that do not match an Rfam CM, you will want to build your own models. In order to do this you need to identify homologues for each sequence which you can use to produce an alignment from which a model can be built. In order to do this you will want to use a method which is RNA aware and uses a rigorous search method. For example from the FASTA suite, which has an RNA mode which adjusts the scoring accordingly:

Smith and Waterman for local/local alignment (e.g. SSEARCH)
Needleman–Wunsch for global/global alignment (e.g. GGSEARCH)
Hybrid alignment for global/local alignment (e.g. GLSEARCH)

Your coverage requirements and the nature of the database being searched will determine the most suitable method to use for the sequence similarity search. Combining the best search method with appropriate selection of the database to search, for example the European Nucleotide Archive (ENA) provide a set of non-protein coding sequences (ftp://ftp.ebi.ac.uk/pub/databases/ena/non-coding/) derived from the annotations in EMBL-Bank that could be a good starting point your search. Will improve the sensitivity of your search.
Given the set of homologous sequences you need to produce a multiple sequence alignment (MSA) to generate a model from. To do this you will want to use an RNA aware MSA tool, for example R-COFFEE or Clustal Omega in order to produce an alignment which attempts to take into account the folding of the RNA molecules.
Given the alignment you can create a CM using Infernal or an HMM using HMMER, and use this to search the sequence database (cmsearch or hmmsearch) to find additional homologues in the database.

If you have a non-coding gene sequence (e.g. regulatory sequence) this answer should hold your solution:
Background theory

Firstly you must realize that PSI-BLAST is built for detecting "romote homologues",  (i.e. those that have a very "distant evolutionary relationship" to your query) - from a database of sequences. It is therefore known to be a "sensitive" analysis which can recruit distantly related matches but has a small chance of recruiting some false matches - "rogue homologues".
Secondly PSI-BLAST is known as a "profile method" that is it uses multiple sequences that are cumulatively recruited with each "psi-blast iteration", to build an empirical profile of amino acid residues along the positions of your query. This is in the same family of analyses as "Hidden markov models" (HMMs) in that HMMs use multiple sequences to build an empirical profile that is able to recruit distant homologous, except the "profile" includes probabilistic pathways to all the recruited sequences.

My Answer
I suggest you use a software package called HMMER. Indeed this method shares critical theoretical similarity to PSI-BLAST as well as functionality in your case (searching for remote nucleotide sequence matches in a database vs. a nucleotide query), it also does not assume your sequence is protein-coding - here is the wiki description:

HMMER is a free and commonly used software package for sequence
  analysis written by Sean Eddy.1 Its general usage is to identify
  homologous protein or nucleotide sequences. It does this by comparing
  a profile-HMM to either a single sequence or a database of sequences.

Other possible answers
If you are afraid of using HMMER, then here is a list of all alignment software tools represented in a table that allows you to focus on only those that use nucleotide sequence as input:
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software

Assuming you are using PSI-BLAST to recruit coding homologous nucleotide sequences to your query nucleotide sequence.
Here's a work-around using PSI-BLAST itself:

Translate your nucleotide sequence into amino acid sequence
Run psi-blast to recruit matching homologous protein sequences
Store the names or database IDs (e.g. genbank accession numbers) of the best matching proteins
Acquire nucleotide sequences of your matches by searching the IDs against a nucleotide database

Extra details:

This type of alignment is called a "codon alignment" (as opposed to DNA alignment or protein alignment)
This assumes your DNA protein codes for a protein whose functionality is constrained by evolution
You must remove all introns from your sequence prior to aligning
Your first codon must be a start codon (ATG)
Your last codon must be a stop codon.

Ok, but the problem with this is it assumes conservation based on the coded protein sequence, not the nucleotide sequence. I suppose it will get some of the distant homologs, but:
a) it wouldn't be optimal
b) it might be weirdly biased (if that matters)

Firstly for your peace of mind, this strategy - called "codon alingment" is a standard for your type of situation as long as the sequence is protein coding: http://bit.ly/18odX27. The only situation I can see where this will "go wrong" is if you are using non-coding DNA (e.g. regulatory sequence). Indeed you must remove all introns before running the "codon alignment" as I mentioned above. The starting codon must be 'ATG' (i.e. start codon) and the last codon must code for a "stop codon"

W.r.t the assumption of conservation at protein level: indeed I make that assumption, and this is a valid assumption given that the dna sequence you are using DOES code for a protein and whose functionality is constrained to the protein level (i.e. the protein has a function that benefits the host)

That's exactly the situation I'm facing.  My bacterial small RNA genes of interest are indeed noncoding.

oh dear, I feared that may be the case...! I will see what I can come up with for you

I have posted a new answer dealing with your case of "non-coding" sequence query


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Anti-antibodies for preventing transplant rejection
Transplanted organs from the donor are attacked by antibodies from the recepient. So can't we construct anti-antibodies and destroy specifically those antibodies which are causing the rejections ? (Instead of giving immuno suppressants)
Well, I can think of some problems :

You would have to administer this for life time which is really expensive.
So, what if anti - antiantibodies were made by the body ?

Any other problems you can think of ?

The root of the problem in this case are not the antibodies but the antibody producing cells (APC). They are capable of producing vast amounts of antibody, so I doubt that this approach would be successful. The problem with targeting these APCs is, that you have to know exactly which are the ones which cause the problem, if you want to target them specifically.

yes, the no. of clones our immune system can produce after it decides on one is enormous. Good point !

Do u think anti-antiantibodies could be made by our body ?

@Biogirl: No. Antibodies against human antibodies would be sorted out in the differentiation process. It would be fairly dangerous to have such antibodies, since antibodies mainly differ between each other in the site which recognizes the antigen. The rest is highly conserved. So it would be very likely to direct the anti-antibody against these parts and then hit all antibodies.

Within an organism, antibodies which bind to other antibodies in the body would be eliminated during clonal selection.  They are not made by the body after that period, which is in the first few months of life.
Such antibodies would have to be introduced from the outside.  Many have been designed or engineered for biotech and as therapeutics.

Problems:
Where are the anti-antibodies created? In a mouse or in a human? Well, of course, you can't use humans to create antibodies so we are left with mice. So what's  wrong with that?

Anti-antibodies will be created to the Fc (the constant section of the antibody) region of the antibody because the antibody is foreign and is treated as a foreign antigen.
So, you would have to use chimeric (or humanized) antibodies... I believe they are pretty expensive and takes a long time to make. Let's see that in current time. By now, I am sure you have heard about ZMapp, the drug that treats Ebola. Well, creating that drug is similar to this because they are creating antibodies as well. But I heard that a few doses of this drug takes 3-6 months to make! In this article , it mentions that it takes half a year to make ZMapp!

In conclusion, it's a real challenge, which is why we haven't found drugs that work like how you describe out in the market... But it's nice that you are thinking about this stuff...

Antibodies are already widely used in treatment of organ transplant rejection. However their targets are not donor specific antibodies as you proposed. Current anti-rejection antibody based treatment targets T lymphocytes (Basiliximab/Anti-thymocyte globulin/Anti-lymphocyte globulin/Campath etc.), B lymphocytes/plasma cells (Rituximab/bortezomib etc.). Here is a slightly old review of some of these antibodies (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840233/).


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Histidine - why essential for children?
Why is histidine an essential amino acid for children but not for adults ? What changes in the body occur which lead to the formation of histidine in adults but not in children ? What causes these changes ?
UPDATE : Source : Campbell Biology

Do you have a reference for this fact?

Some sources suggest that histidine is essential for human in all ages.

@Mys_721tx Oh yes. There is controversy regarding this. Some of my textbooks say different things too. Maybe the scientific community hasnt decided on this.

If an amino acid is essential it means that we cannot synthesise it de novo from central metabolites, or from another amino acid. Since histidine isn't related structurally to any other amino acid we can assume that in this case we would require a pathway for de novo biosynthesis.
The biosynthetic pathway enzymes for histidine in yeast (Saccharomyces cerevisiae) are encoded by the genes HIS1 - HIS7. In a BLAST search using yeast His4p against Arabidopsis (plants can make histidine)  there is a significant match to a histidinol dehydrogenase (the penultimate step in the pathway). In a similar search against humans there is no significant hit. Expanding the search to all mammals there is only one significant match, which is to the Tibetan antelope, Pantholops hodgsonii. This puzzled me, but when I searched with the antelope sequence as probe I got lots of perfect matches to bacterial histidinol dehydrogenases, so presumably the antelope sequence is a contaminant.
I also searched for human matches to His1p (encodes ATP phosphoribosyltransferase - the first step in the pathway) and His3p (encodes imidazoleglycerol-phosphate dehydratase - the sixth step in the pathway) and found no significant matches.
I conclude that humans have no capacity for histidine biosynthesis and thus histidine must be essential in the diet.

This has been down-voted today without a comment (17th December 2013). It would be helpful if down-voters would explain why they disagree with a post.

-1 because the lack of a homologous gene does not at all imply histidine biosynthesis is impossible. Just because birds lack homologous wings to insects and insects require wings to fly doesn't mean that birds cannot fly.

There are many articles in health literature debating on the question. Everytime the experimental setup seem to me quite basic and I am affraid that one cannot infer many things from these experimental designs. I guess the ethics is limiting much of the medical experimentation (which is good!). Usually it is just the report of observations of what happen to the global health of a patient when one amino acid is missing in their food. Therefore, these articles does not explain much about the metabolism reasons of these needs (which was your question) but only try to define what are the needs. Moreover statistics seem sometimes a bit fuzzy (or absent) to me.
Anyway here is a review of these results and there is a whole paragraph on the question of histidine. The best is that you read it yourself. To make it short: Histidine doesn't seem to be more important to the children than other amino acid. Moreover there is big storage of histidine in our body suggesting that one that is histidine deprived for a while might use these stored histidines.

The OPs question wasn't about whether or not Histidine was more important than other amino acids, but whether or not Histidine was only essential for children. The article you link indicates that it is essential for both adults and children, even if the experiments are primarily based on macroscopic health effects.


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Mutation in pre-mRNA sequence
Has there any mutations been recorded which cause harmful effects due to change in the part of pre-mRNA responsible for proper m-RNA splicing ?

Do you mean mutations in donor and acceptor splice sites?

Adding to Alans question: Mutation of the pre-mRNA only (due to mistakes during transcription) or mutations in the genomic DNA which are then transcribed into the pre-mRNA and which affect splice acceptor sites?

@chris I mean mutations in the genomic dna. By the way, can we call mistakes during transcription as mutations ?

@Alan Yes, any site in the pre - mRNA involved in this.

see http://biology.stackexchange.com/questions/13908/what-type-of-mutation-causes-progeria

Yes, you can find mutations in the genomic DNA which affect splice acceptor sites. Wikipedia lists the following outcome:

Mutation of a splice site resulting in loss of function of that site.
Results in exposure of a premature stop codon, loss of an exon, or
inclusion of an intron.
Mutation of a splice site reducing specificity. May result in
variation in the splice location, causing insertion or deletion of
amino acids, or most likely, a disruption of the reading frame.
Displacement of a splice site, leading to inclusion or exclusion of
more RNA than expected, resulting in longer or shorter exons.

The article lists two interesting papers:
Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (2011). "Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes". Proc. Natl. Acad. Sci. U.S.A. 108 (27) 11093–11098.
Ward AJ, Cooper TA (2010). "The pathobiology of splicing". J. Pathol. 220 (2) 152–163.
Both papers are open access.


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When might an inhibitor of bacterial transformation be useful?
I am part of a project elucidating some structures that are required for bacterial transformation. We have the opportunity to screen inhibitors of the system to stop it from functioning. I am not a microbiologist and have never worked with transformation, and this research process would be time and resource intensive. I am weighing up the pros and cons, however am struggling with how the inhibitors could be practically applied.
How useful would stopping transformation be? My thoughts so far boil down to:
Could it enhance controls by allowing two separate strains to grow on the same plate without any genetic conference?
Could it be applied to stop contamination of genetic information from otherwise insignificant contaminants?
Are there any other problems that transformation is causing in laboratory experiments?

In the research lab? I thought about it for a while and found no usage. But it could be interesting for clinical applications to prevent bacteria spreading their resistance genes (which are usually organized on extra chromosomal plasmids) and thus preventing multi-resistant bacteria.

I did explore this avenue briefly, but although multi resistance may have started by competence (Yeh, 2002: Association of metronidazole resistance and natural competence in Helicobacter pylori. Antimicrobial agents and chemotherapy), I have found no evidence that transformation occurs in patients. It seems that multi resistant bacteria infects a patient, then grows into an established multi-resistant infection.

So you have bacteria coming from outside which make the problem and they are not spreading this ability? Thats interesting.

Well I'm sure they are causing the problem in the body too, but it hasn't been observed or measured. I don't see how a drug would stop reduce multi-resistant bacterial infections since there is so much transformation of these genes externally.