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How to identify active protein in a complex mixture?
I am trying to figure out how to identify which protein in a complex mixture is producing a certain effect.
There is an assay for the effect, so anything (a fraction of the mixture) can be tested on microplate.   The part of the mixture producing the effect is pretty definitely a protein (or has a protein component).
Unfortunately, the mixture is serum... which contains >10,000 proteins and peptides, some in tiny amounts and some in huge amounts.
There is not enough information to go the other way, ie guess what is producing the effect and test that by itself (or remove it from serum and test the depleted serum as a confirmation).
There is also no possibility to use affinity (use a receptor as bait, etc) because many components of serum stick to the cells in the assay (or, practically to any cells).
I need a way to narrow this down from "serum" to one specific protein (or a handful), but how?

Liquid Chromatography may help

Perhaps you can clarify a little more? Are you investigating a protein endogenous to serum (e.g., bovine or horse serum), or are you collecting cell medium which contains secretory proteins plus the obfuscating serum content?

@leonardo: It is endogenous to serum (maybe only sometimes).  Samples are from animals not cell culture.  Thanks...

This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation.
Salting out
The solubility of proteins is affected by the ionic strength of the buffer. If the ionic strength is raised above a critical value (which is a characteristic of an individual protein) the protein  will precpitate, usually without being denatured. By doing a series of such precipitations at increasing ionic strengths a protein mixture can be fractionated according to this property. The salt used is ammonium sulphate, because of its very high solubility. You can find more details at this Wikipedia page (ammonium sulphate precipitation).
Ion exchange chromatography
Proteins have different intrinsic charges, and the net charge on a protein will vary with pH. This property is exploited in ion-exchange chromatography. In this technique the protein mixture interacts with a solid matrix carrying fixed charges. Under the correct conditions your protein plus others will bind to the matrix, while lots of other proteins won't. That's already a purification step, but you can then treat the matrix with buffers of increasing ionic strength. Weakly-bound proteins will be eluted from the matrix first, and as the ionic strength of the elution buffer increases proteins will elute in order of strength of interaction. By performing this procedure with the matrix in the form of a chromatography column and collecting eluate fractions you can achieve another step in the purification of your protein.
Size exclusion chromatography (gel filtration)
This technique is used to fractionate a mixture of molecules according to size. In this case the solid matrix that is used is charaterised by pores of a specific size. Proteins that are too large to enter the pores will pass through quickly;  small proteins will spend a lot of time moving in and out of the pores and so will pass through slowly; and proteins of intermediate size will spend some time in the pores. Essentially the average time spent passing through the matrix will depend upon size. Read more here.
These are just three of the possible fractionation procedures - others, including  hydrophobic interaction chromatography are described here). The key point to grasp is that using any one of these techniques will give you your protein in a fraction which also contains other proteins, but if you apply them sequentially you will progressively remove contaminants because each approach is based on a different physical property of proteins, and your target will have a unique combination of these properties.
At each step you will be assaying fractions to locate the protein of interest, and also running fractions on  SDS-PAGE to get a feeling for the number of proteins left. If you have an assay that lends itself to measuring some kind of unit of activity (as you would with an enzyme), then by also measuring the protein content of the active fraction you can express the purity as a specific activity (units of activity per mg protein). At each step in your purification this specific activity should increase because you recover most of the activity, but discard a lot of the proteins that were present in the previous material. The increase in specific activity can be used to assign
a purification factor to each step. A useful purification step will give a reasonable yield in combination with sigificant purification.
Finally, what order to do these steps in? I've listed them in a logical order - salt precipitation is a low-tech method that can give a quick first step and which has the advantage that it concentrates the target protein (since the precipitate is redissolved in fresh buffer). Size-exclusion chromatography doesn't deal well with large amounts of protein so is best left until later. However, protein purification is a craft, and an expert will use the available techniques according to the exact nature of the project.
UPDATE
From the tone of your original question I had inferred that you were a beginner, but from your comments, apparently not, since you are thinking in terms of mass spec as an endpoint.  A starting concentration of pg/mL is quite a challenge, and clearly you are never going to have enough material to see your molecule on standard gels.
Here are a couple of thoughts on aspects of your problem.
It seems that  in trying to purify minor components of serum a good starting point is to deplete the serum of its major proteins. This is a link to an imunodepletion product, and here is a related product from Biorad (no connection with either company and no recommendation implied).
I also found these papers which may be of interest. (Incidentally I think you'll find that each of the techniques I described is still used, perhaps just with modern instrumentation.)
Li,J et al. (2012) Purification, identification and profiling of serum amyloid A proteins  from sera of advanced-stage cancer patients. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 889: 3-9
Fertin, M et al. (2011) Strategy for purification and mass spectrometry identification of SELDI peaks corresponding to low-abundance plasma and serum proteins. JOURNAL OF PROTEOMICS 74: 420-430
Finally, a quick look at the Wikipedia page on plasma reveals that brain natriuretic peptide seems to be present at the levels that you are considering  perhaps you should look for papers describing its purification.
Other than that I think you have to hope that a proteomics expert will come by and give you an expert answer.

Alan, Thank you, excellent answer.  Could you possibly direct me to a paper where someone else tackled a similar problem using modern techniques?  (in serum samples)

Alan, Part of what makes this one tough is that the level of what I'm looking for is probably pg/ml (by analogy with other proteins likely to be similar), whereas the total protein content of serum is ~70mg/ml.  It seems I need a total purification factor of tens or hundreds of thousands, before it is even possible to try to identify this using mass spec.

Answer extended somewhat in response to your comments.


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Assumptions of Hamilton's rule
Which elements of the following list are  assumptions of the Hamilton's rule?

Population structure (non-panmictic population)
Additivity

= Fitness of the heterozygote equals the mean of the fitnesses of both homozygotes

No epistasis or pleiotropy
Stable population size
Inifinite population size
Sexual reproduction
Selection on diploids or selection on haploids
Recombination (cross-over)
Mendelian segregation
Iteroparous population
smooth fitness landscape
mutation rate is high enough

Are there assumptions of Hamilton's rule that are not listed above?

A paper detailing the controversies about the assumptions of kin selection can be found here: http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02236.x/pdf

Unfortunately, the answer depends completely on how stringent you are with "Hamilton's rule". If you just mean the equation $r \geq c/b$ then it is important to look at modern usages. In modern usage, all three of the terms $r$, $c$, and $b$ can be arbitrarily complicated. My favorite examples include when $r$ takes into account spatial structure saying that an agent near you is more "related" than a genetically identical agent far from you. Assumptions like that are a must, if you want to look at things that much of modern research is concerned with.
For this "most general" interpretation of Hamilton's rule, only one property is required and this property does not appear on your list: linearity. Note that this is not the same thing as the additivity you describe. Linearity means that your equations for small changes in proportions are linear in fitness: i.e. $\dot{p} = pf(E)$ where $E$ is some description of the environment, and $f$ is a linear function of the variables of interest (I used a continuous or large-population limit here, but similar things hold true for distributions over discrete populations).
Note, that in the above general and super-vague use of Hamilton's rule, the rule itself is not a biological observation but a simple fact of linear algebra. Of course, if you want to get linearity out as a consequence of some biological assumption, then the most common way to do this is by assuming weak selection.
If you put restrictions on what kind of features of the population, interaction, and environment structure $r$, $c$, and $b$ are allowed to incorporate then this will result in biological theories which will be mathematically true under only some of the assumptions you list. The subset of required assumptions will depend on what specific restrictions you place on $r$, $b$, and $c$.
There are no standard assumptions accepted on these parameters, so (unsurprisingly) I can't answer your question further without more specification on your part.

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Why use DNA polymerase in making cDNA?
RT is capable of synthesizing a complementary dna strand ( as in HIV life cycle.) Then why is
DNA pol used when cDNA (synthesizing the second strand of it ) has to be synthesized from mRNA ( For eg.to construct a cDNA library) ?

where did you read that DNA pol is used ?

@WYSIWYG I read that in Campbell.

Reverse transcriptase, as the name suggests, uses an RNA template to create a DNA transcript (i.e., complement). Once the DNA complement has been made, DNA polymerase is used because it uses a DNA template to produce a DNA complementary strand.
In your specific example, HIV contains a positive-stranded, RNA genome. The HIV RT can use either RNA or DNA templates to produce DNA complements, and this is how the single-stranded RNA genome is transcribed into double-stranded DNA, before integration.
To my knowledge, the RT enzymes sold commercially (for applications like RT-PCR) are typically a mix of an RT enzyme and a DNA polymerase, isolated from other retroviruses, such as murine leukemia virus. An important consideration for lab application is the production of cDNA that truly represents the RNA template of interest. Since RT enzymes typically lack a 3'->5' exonuclease activity, they are unable to "proof-read" the complement strand as it is being produced. In contrast, there are very efficient proof-reading DNA polymerase, and this is why a DNA polymerase (with high proof-reading ability) is used after first-strand synthesis by RT.

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Interpreting graph of mitosis and meiosis

Note : Consider the y axis as 1,2,3,4(not 2,3,4) and x axis as time. Roman numerals should be considered from I-X ( some are not correct here )
Which stages show mitosis?
My answer : III-V
Which stages show meiosis?
My answer : VII-X
Am I right ?

I think there is no problem in your arguments. The part IV-V can also be considered a part of interphase (G1 phase), and not mitosis, though it is still ambiguous in the diagram.

@SatwikPasani Could you post this as an answer?

I believe III → IV is mitosis and VII → X would be meiosis. As Jam explained in comments below, the stationary points of the graph (II → III or VI → VII ) do not count as part of either process.

DNA is replicated during interphase, not mitosis. So I → II cannot be part of mitosis.

Ah I see where I went wrong. Would II to IV and VI to X be correct?

I think III → IV and VII → X would be the right answer. The gap between II → III is referred to as a separate phase outside of mitosis (G2, which is part of interphase). It might seem redundant since it looks like nothing's actually happening on the graph between II → III or VI → VII (and I can see why you'd suggest starting there) but there are other cellular processes that happen during these gap phases :)

Penny has dropped, thank you that is very helpful! :)

Np - If you edit your answer, I can upvote it. The site won't let me change my previous vote until the answer is edited.

From your question I can conclude that if you consider only chromosome number changes (excluding DNA and Chromatid number changes, which would dramatically change the graphical interpretation):
• I to II would represent anaphase (note chromosome doubled in a single cell)
•II to III would represent karyokinesis
•III to IV would be cytokinesis ( note the chromosome number returns to its initial for the given cell taken into consideration)
•IV to V would be a complex of interphase , prophase and metaphase
• V to VI can be again anaphase
• I have interpreted that from VI to VII there has been a chromatid doubling but the number of chromosome remains same
•Steps VII to X are clearly the steps of meiosis
So to conclude steps I to VI are mitosis and VII to X are meiosis

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How does promoter sequence affect initiation?
I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear"
I'm wondering if anyone can suggest sources for more information, or perhaps has seen recent research papers highlighting the properties that cause such variation between strong promoters and the weakest?
I've tried researching but the older research is descriptive rather than mechanistic and the search terms involved are quite ubiquitous so it's hard to actually find more on this specific point.

I agree that it is hard to search for papers but from graduate level classes this is some of the additional insight I have gained. Sequence context of promoters is important. Specific DNA sequences (motifs) can act as binding sites for specific transcription factors and combinations of these transcription factors help recruit RNA pol II to the promoter. These combinations of proteins are spatially and temporally regulated and will help decide if gene that is next to promoter will be activated. A luciferase reporter assay is often used to determine the strength of a promoter.
An example is as follows: A strong promoter might have certain histone marks that would recruit proteins to remodel the chromatin to be more accessible exposing binding sites of transcription factors that help recruit RNA Pol II. A weaker promoter might have less transcription factor binding sites or less chromatin accessibility and thus it is harder for RNA Pol II to be recruited. There are also some kinetics aspects you must keep in mind.

Echoing what was already mentioned: the DNA sequence directly affects the ability to bind sigma factors (http://en.wikipedia.org/wiki/Sigma_factor). Sequence --> bonding --> how often sigmas bind and for how long they bind --> initiation of transcription


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Orientations of codon and anticodon
So 5'-AUG-3' is the start codon on an mRNA transcript
Does that mean that the tRNA anticodon is 5'-CAU-3'?
Here, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify which end is 5' and which end is 3', but I'm guessing it's 3'-UAC-5'. I thought nucleotides are supposed to be written 5' to 3', and that's a norm, but apparently it isn't the case here? Am I missing something?

That page you linked to is, shall we say, unconventional, in its depiction of the code. I'm not surprised that you were confused.

The tRNA anticodons are both complementary and anti-parallel. That means for $5'-\text{AUG}-3'$, the tRNA anticodon would be $3'-\text{UAC}-5'$.

The image has the mRNA oriented with the $5'$ end on the right end. It shows both, complementarity and anti-parallel configuration. The reference you cite might have cited the anticodons $3'\rightarrow 5'$ and mRNA codons $5'\rightarrow 3'$. In general, we usually cite the codes from $5'\rightarrow 3'$ but it doesn't matter until it is explicitly specified or unambiguous.

Pasan did you draw this tRNA? May I know what tool you used ?http://tex.stackexchange.com/questions/164206/draw-a-trna-diagram?noredirect=1#comment377038_164206

@Mariya I wish. But this is one picture I found online. But if I had to draw, I would have preferred Corel Draw.


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Transduction with P1 lysate prepared from strain that is proC::Tn10
If I do a transduction with a P1 lysate prepared from a strain that is pro*C*::Tn10 and the recipient is wild type, will all my recombinants  be ProC- and Tet resistant since the Tn10 is in the proC gene?

Slightly confused by this  - what are you going to plate on after the transduction step?


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Recombination frequency, linked genes, and independent assortment
Gene R is genetically linked to gene T with a recombination frequency of 0.3. Gene T and gene X assort independently from each other. Your colleague tells you that gene T and gene X reside on the same chromosome. How is this possible?
So I know that R and T are on the same chromosome. T and X assort independently, so they should be on different chromosome. And then due to recombination, X gene crosses over so that it's also on the same chromosome as T and R? Can someone please help me?

remember that chromosomes can be quite large - especially if T and X are on opposite sides of the centromere, if they are far enough apart from each other they will appear to assort completely independently from one another.

I don't understand. If two loci segregate independently, it means that the recombination frequency equals 0.5, isn't it? In which condition they might or not be on the sea chromosome. But as soon as the recombination frequency is lower than 0.5, then the don't segregate independently and therefore, they are necessarily on the same chromosome (except if there is a segregation distorter). Let me know if I'm wrong

homework? If so, use the tag.

The comments pretty much answer the main concern here. But just to sum up:-

"....T and X assort independently, so they should be on different
  chromosome...."

Not necessarily. They can be on the same chromosome at such a distance that there is usually atleast one chiasma formation between them, and will undergo independent assortment, i.e.  segregation of one gene among the gametes will be independent of the other. They will pretty much act and segregate like mendelian factors. Specifically, if the recombination frequency is 0.5 (50cM or map units' distance on the chromosome), they will assort independently.

"....And then due to recombination, X gene crosses over so that it's also
  on the same chromosome as T and R...."

This part is a little bit unclear. I assume (correct me if I am wrong) is that you are assuming X,T,R to be alleles, which can be present on only one chromatid and hence recombination might change their distribution and positions relative to one another. But as the question states, they are genes (or specifically gene loci) which are present on both chromatids and their relative position is fixed. The recombination frequencies refer to the recombination of different alleles at this locus.


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Can sugar alcohols, and glycerol in particular, cause intoxication?
I'm mostly curious about glycerol, which I use as a sweetener. I've been told that it can cause intoxication, because it is an alcohol. Is this true?
If so, are there any good sugar alcohols which can be used safely without intoxication (or nasty side effects)?

Well, I was intrigued by this, and my intuitive response was that it would never be toxic at reasonable doses, but I was wrong.
A quick Google search led me to this paper:

Andresen, H. et al. (2009) Severe glycerol intoxication after Menière's disease diagnostic--case report and overview of kinetic data. Clin. Toxicol. 47: 312 - 6

Apparently in the Klockhoff test for Menière's disease the patient is given an oral glycerol dose of 1.2 - 1.5 g/kg (50% in water) then observed over a period of 4-5 h. The other details of the test don't concern us here. In this case report a patient suffering neurological symptoms was found to have previously undergone a Klockhoff test at another hospital, and it was estimated that he must have received a dose of 3.88 –3.95 g/kg.
Here are two sections from the paper's introduction (references removed).

Glycerol is well known as a nontoxic substance (LD50 > 25 g/kg in the rat). Possible side effects of the Klockhoff test include headache and nausea. During treatment of brain edema, additional adverse effects such as diarrhea and vomiting were reported, symptoms comparable to those reported for intensive osmolar diuretics. The GESTIS database ranks glycerol in general as a substance with very low toxicity. However, severe symptoms after oral ingestion of glycerol have been reported to occur. Doses exceeding 0.7 g/kg BW have been regarded as potentially toxic for adults. After doses of up to 1.4 g/kg BW, only mild symptoms such as headache, nausea, and diuresis appear. Reportedly, these symptoms are also associated with glycerol treatment of brain edema. In individual cases, an oral dose of 100 g of glycerol has been reported to cause drowsiness, cyanosis, renal pain, and bloody diarrhea.
Martindale Reference Desk reports headache, thirst, nausea, and hyperglycemia as adverse effects. Glycerol may also produce cardiac arrhythmia and hyperosmolar nonketonic coma. These effects are mainly based on its dehydrating properties. Hemolysis has been reported to exclusively occur after intravenous infusion. In fact, most of the major toxic effects of glycerol, such as hemolysis, hemoglobinuria, and renal failure, seem to strictly correlate with serum concentration of glycerol and the route of administration.

It appears then that any toxic effects of glycerol are not due to its alcohol nature per se but rather because it can become elevated in the blood leading to osmotic effects. The authors estimated that 10 h after administraion of the glycerol the concentration in the patient's serum was approximately 39 mM, compared to a physiological basal level in the range 0.05–0.3 mmol/L. The patient's serum level fell to the basal level over a period of 30 hours.
Just to put this in some perspective, in the UK the legal alcohol limit for drivers is 80 mg/100 mL which corresponds to 17.4 mmol/L.
I think that recommending sugar alcohols would fall under the heading of medical advice (not that I have any such recommendations).


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Telomeres in cloning experiments
In whole animal cloning ( eg. Dolly ) the nucleus is taken from a somatic cell. So isn't shortening of telomeres a problem ?

Yes, it is. Dolly died of cancer in early years. Length of the telomeres depends on the donor tissue: "In Dolly's study, the animal produced from fetal tissue appeared to have telomere lengths non-distinguishable from normal controls, while the other two, including Dolly, which originated from adult cells, were found to have shorter telomeres." (Xu & Yang, 2003) This statement doesn't mean that embryonic cells are the only cells able to maintain telomere length.
This also doesn't mean, that offspring of animals cloned from nuclei with shorter telomeres, inherits this shortedness: Miyashita et al, 2011
The Xu & Yang, 2003 review is pretty old, you can find newer articles on the topic.

After cloning, the recipient cell is converted into embryonic stem cell. When it is a stem cell, it can produce enzyme telomerase itself which a naturally occurring enzyme that maintains telomeres and prevents them from shortening during cell division in cells. So i think there are no problem on shortening of telomeres.

@Duc Could you give a source for this ?

@biogirl yes, you can search about telomerase activity in embryonic stem cell, and you will see a lot of source document : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2360127/ . "Thus, telomerase activity and telomere maintenance are associated with the immortality of cancer cells, germ-line cells, and embryonic stem (ES) cells."


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What happens between making a DNA library and screening by nucleic acid hybridization?
I understand how a plasmid library is made and how each clone is put on the nitrocellulose membrane and nucleic acid hybridization is done. What I don't understand is how each clone is "identified" and separately put on the membrane?

The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform E. coli, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in the terms that you use.
I don't know if anyone really does things like this any more, but originally each plate would be transferred to nitrocellulose, for probing, and to a fresh plate for archiving. This way, any colony identified as positive after nucleic acid hybridisation could be picked from the archive plate for further characterisation.
This screening can be done on large format Petri dishes to reduce the number of plates needed. I know of one lab which in the 1980s used to screen λ libraries after plating out for plaques on cafeteria trays. That was the heroic era of molecular biology.


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How much does the Hayflick limit/telomere length vary across taxa and within humans?
Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the Hayflick limit numbers 40-50 thrown out repeatedly for humans (probably relating to the WI-38 tissue line), but how universal is this really? I Know there are particularly long lived species, but has research been done to correlate this with telomeric length, or do they simply have slower cell division?
I suppose it is worth mentioning that a Hayflick limit of 40 rounds of division is massively different from 50, since each round of division conceivably could double the number of cells...

Many studies, including those of Hayflick himself, have found a strong correlation between a species' Hayflick limit and its maximum lifespan. For example, Galapagos tortoises, which can live over a century, have a Hayflick limit of 90-125, and mice, which live only a few years, have a Hayflick limit of 14-28.
However, the mechanism connecting the maximum number of cell divisions and maximum lifespan is not entirely clear. Cell division is associated much more with growth and development than with the maintenance of mature tissues. Cells that have stopped dividing can be perfectly functional for decades. Cells that don't stop dividing are called "cancer". So, while the correlation is strong, the reason for the correlation remains something of a mystery.
Rose, Michael R. 2005. The Long Tomorrow: How Advances in Evolutionary Biology Can Help us Postpone Aging. Oxford University Press, New York. pp 20-23


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Independence of Light independent reaction in photosynthesis?
Inspired by a question asked to me by a classmate, I have the following question about Light-independent (dark phase) reactions in photosynthesis:-

Let us suppose an algae sample was exposed to light for a considerable
  time so that maximum( if there is a limit) NADPH concentration was
  achieved. Now if the sample is placed in dark and radioactive
  ¹⁴CO₂ bubbled, will the cell be radiolabelled after some time of
  bubbling continuously?

I guess the answer depends on the active life of ATP and NADPH , the products of light reaction. If they are considerably stable, such that they are in sufficient concentration for executing Calvin cycle although their production (apart from respiratory ATP production) has ceased due to absence of light. If they are, then the ATP and NADPH produced during the initial exposure period will carry out carbon fixation with radioactive carbon and hence radio labelled sugars will be recoverable from the sample. If not, they will quickly degenerate (by hydrolysis, utilization or likewise) and they will be unable to carry out fixation after some fixed time after stopping the light.
What, under normal conditions, should be the time after which the light-reaction products are no longer capable of fixing CO₂ by Calvin cycle? And, ultimately, will the presence of radioactivity in sugars for the scenario above depend on the species of plant?
[I am ignoring all radioactivity due to dissolution of ¹⁴CO₂ in cytoplasm]

It turns out that the so-called light independent reactions are not light-independent at all: there are several regulatory mechanisms in place to prevent the turning of the Calvin Cycle when there is no light energy available to produce ATP/NADPH. The hypothetical situation you described in your question demonstrates the necessity of such regulation. The cell cannot allow levels of ATP and NADPH to drop too low because those two factors are required for everything. So if you let the Calvin Cycle run when there is no means of fueling it (ultimately) from light energy, then the Calvin Cycle will run until ATP/NADPH is too low to sustain it further, at which point the cell dies. So several key enzymes in the Calvin cycle are activated indirectly by light.
One of the most well-studied regulatory mechanisms is the ferrodoxin/thioredoxin regulatory system. The enzyme Ferredoxin-Thioredoxin reductase takes electrons from ferredoxin (which is reduced by light energy via the photosystems) and transfers it to thioredoxin, a disulfide-based redox protein. Then thioredoxin reduces several key enzymes in the Calvin Cycle, which activates them (through conformational changes induced by disulfide bonds). The upshot is that when light is around to facilitate reduction, the metabolic enzymes of the Calvin cycle can work, but in the dark the cell oxidizes and these enzymes are turned off, switching off the Calvin cycle and arresting CO$_2$ fixation.
An orthogonal direction of light regulation of the "light-independent" reactions is RuBisCO Activase, which is required to modify the RuBisCO active site to be active. This requires ATP hydrolysis, which amplifies the sensitivity of the Calvin Cycle to ATP availability.
The takeaway is the light-independent reactions may not directly require light as an input, but they are regulated by light availability. I tried to look up how much time in the dark would be required to shift the redox balance such that the Calvin Cycle enzymes would be inactivated, but I couldn't find that data. People in the literature, however, seem to believe it would be quick (1).
There is some description of this at Wikipedia. If you want to look further, Bob Buchanan at Berkeley made a lot of seminal advances in this area; a review of his you might want to check out is (2).
(1): Ruelland E, Miginiac-Maslow M. (1999). Trends in Plant Science. 4(4): 136-141
(2): Buchanan BB. (1980). Annual Review of Plant Physiology. 31:341-374.

+1 for the comprehensive answer:) On an imaginative side note, had these regulatory mechanisms been absent, what then would have been the time delay before the light reaction products at saturation would go below the minimum concentration required to execute Calvin cycle (just an order of magnitude, i.e. seconds? minutes? hours?)? Would ATP & NADPH utilisation be the only way of their depletion or would their natural decomposition (hydrolysis) also play a part?

@Satwik I am not sure but I think before they would naturally dgrade, ATP and NADPH utilisation would limit them


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How do I compare the variance of a distribution of species in one area versus another?
It's possible that this question is better suited for stack overflow, but I think the ecologists on this site might be better equipped to answer it.
I'm trying to study two geographically-isolated populations of the same species. Inspecting the distributions, I see that both are bimodal (there's some seasonality to their occurrence), but the peaks in one population are much higher and much narrower (i.e., the variance of the local peaks is smaller).
What sort of statistical test would be appropriate to determine whether these differences are significant?

There's now way that I could ever answer this, but it seems a little cryptic. What is the parameter that is being measured in these distributions?

Number of individuals caught in a trap on the y-axis, julian day on the x.

While I am sure someone on this site could help you, this is really better suited to [stats.se] since the fact that you are looking at biological data is completely irrelevant to the actual question. I suggest you flag your post for moderator attention and ask them to migrate it.

I think that the question is useful here as well - this type of problems are common in ecology and there also exists a number of relatively ecology-specific software for studying this. @terdon

@fileunderwater I agree which is why I did not vote to close. I just think the OP is likelier to get an answer on the stats site. There are more users and all of them are stats people. Here we have both fewer users and a smaller percentage of statsheads.

@terdon I agree that some aspects are probably better answered there. Maybe a split Q, with one part focusing of the statistical/test aspects and one on the biological process that is being modelled would be a good idea.

Question now cross-posted: http://stats.stackexchange.com/questions/76962/how-to-test-whether-the-variance-of-two-distributions-is-different-if-the-distri

These are just some preliminary ideas...
I think you should look at the seasonal distributions separately, since the bimodal distribution is the outcome of two fairly separate processes. The two distributions might also be controlled by different mechanisms, so that e.g. winter distributions might be more sensitive to yearly climate. If you want to look at population differences and reasons for these I think it is therefore more useful to study seasonal distributions separately. An exploratory analysis could be to compare distribution percentiles (north/south and east/west coordinates) to look at range edges, or to use a fixed number of edge observations to establish borders. The weighted centre-point of population distributions can be used to look for differences in overall position. If you have grid occurences, percentage overlap between species/populations could maybe also be useful.
If you haven't already, you look also look at Maxent, which is a widely used software for modelling species distributions and habitats. Look at Elith et al. (2011) for an overview. If you want to look at changes over time (even if this doesn't seem to be your main point) you should also check out dynamic occupancy models that use occurrence records to model species distribution while taking detectability into account, e.g. MacKenzie et al. (2009).
As for a simple test for differences in variance (basically a test of homoscedasticity), there is Levine's test, which is used to compare variances of distributions between groups. Bartlett's test is an alternative, but Levene's test is supposed to be more robust to non-normality. In R the Levene's and Bartlett's tests are found in library(car). However, these are only suitable for unimodal distributions so, again, you should look at seasons independently.


text:
DNA and gene activation
As far as the genetic content of each cell is concerned I have read to my satisfaction that all cells of a person's body except the red blood cells (with no nucleus and so no genetic message) and the gametes ( with just half the genetic copy or 23 of the 46 chromosomes) have the same DNA copy and so all the 60,000-80,000 estimated genes. The only difference is that which genes are active and which are dormant. For example the gene for insulin would be present in all cells but would be active and functional only in the cells of pancreas assigned the function of insulin production.
My question is:-

What is the factor or process or molecule or information that
  tells a cell or helps it to activate the genes necessary for its own
  growth and more importantly its designated function?

this assumption is not really correct - its now well understood that epigenetic factors including rearrangement of the chromosomes in the nucleus will affect the expression of genes in different cell lines.  I guess you could say that the genome is not different in this case, though it behaves quite differently, but even then, in some cell lines the telomeres shorten when the cells divide, so even the sequence is not uniform in all cells in the human body.

As i understand, you mean why all cell have the same gene, but they can know what they do. It's because gene like a computer programming language. They are programmed to be converted from stem cell into different type of cells in different environment. There must be a series reaction that cause the environment different for cells itself know what they need to do. And i think this question related to how to convert stem cell into different type of cell. Scientist using different environment to do it.

By the way, lymphocytes do not have all the genes as they undergo recombination for creating antibodies.

Humans have about 20000 genes. But see also this http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898077/:

Your question refers to differential gene expression and methods of Eukaryotic gene regulation. This is a very broad question for there are a lot of methods to control gene expression. They can function as transcription control, mRNA processing control, translational control, post-translational control and so on in eukaryotes. In prokaryotes, the methods include the operon model etc, which is much simpler than eukaryotes and multicellualr organisms but still quite complicated when studied in its entirety. Here and Here are few places where you can study differential gene expression. As an introductory text,  chapter 19 of Life:The science of Biology by Purves, Sadava, Orions and Heller(the link is to a supplementary-material site and not to the book itself), Otherwise, to elucidate all mechanisms here would become too long and in any case uncomprehensive.


text:
(Web)app to search metabolic/signalling pathways
I'm looking for an application where you can find pathways by selecting a chemical occurring in it.
So, for example,
selecting 6-phosphogluconolactone brings up the pentose phosphate pathway or any other where it occurs as an intermediate or product.
Same could be possible for endocrine or any other signalling. The target organism is human.
Is there anything like this in existence?

KEGG  http://www.genome.jp/kegg/kegg2.html
GLAMM http://glamm.lbl.gov/
I had to truncate to gluconolactone to make the search work in both cases.

Thanks, the first seems better though less fancy.

Many would agree with you; KEGG may be the best established pathway database of all.

KEGG has also a very nice API, if you plan some automatable tasks.


text:
Does evolution by selection require that individuals consciously change behaviour in an effort to suit their genes?
Imagine an animal that is incapable of digesting a particular kind of food. Now suppose the mutations for digesting that food were to suddenly appear within the population. There still has to be a corresponding change in the animal's behavior, correct?
I mean, I don't go around thinking, "Gee, how could I get the best out of my genes to get ahead of my competition?" There seems to be a need for changing behaviour to get the benefit of the new mutations, which for me allows room for divine providence (e.g. A God) to guide evolution at the level of animal behavior at least.
Am I missing something? Does evolution by selection not require device providence etc?

The fact that there is not, and there cannot be a scientific proof of God makes any (pseudo)scientific argument referring to God a moot point. If you want to explain something using science then you must stay in the framework of the scientific method. Putting God into the equation is a deus ex machina (pun intended) just doesn't work. You can of course explain evolution by means of divine intervention, but you cannot call that science.

@Nico: I am aware of this. I was primarily interested in the philosophical underpinnings of the naturalistic worldview -- i.e. why certain scientists dismiss God from their personal worldview based on the science. (I initially wanted to post this in philosophy but I wanted a good answer to my question from the biology).

OK, sorry I did not understand that was the sense of your question. In that case, may I point you to this excerpt from Carl Sagan's beautiful book "The Demon-Hunted World"?

Going off of your example: I get hypoglycemic if I dont eat well. So if I sat around eating Legos all day I would become ill from lack of nutrients. It would not take long for me to realize I shouldnt be eating Legos. I dont need God to tell me this. The idea of God subconsciously altering someones behavior to "maximize" genes is ridiculous. Why then, does God not prevent two recessive carriers of a disease from mating? What it comes down to is this: Saying "couldnt God do X" is not proof or evidence, so no scientist is going to take it seriously.

I would also like to point out that as a scientist and a devout atheist, it is not science that convinces me that god does not exist but faith. I can no more prove there is no god than you can prove there is one (or more). Scientifically speaking, the absence of a god is the most reasonable hypothesis given observable data, but that does not make it true. That I feel there is no god is an act of faith no different than yours when you feel there is one. Science can only deal with the demonstrable, faith is beyond its purview.

@terdon - we'll try to ignore that the basis of science is the faith that the universe is reasonable and orderly :)

@MattDMo that is not faith, it is an assumption on which our later conclusions are based. Assumptions in logic or science are the equivalents of theorems in math, they are not arguable, they are premises. In any logical edifice, the premises are taken as given and the logic is built on them. You need to accept certain things as premises in order to construct your logic. In a philosophical discussion, I am willing to accept that my perceived reality is likely not real. I cannot accept that premise for a scientific argument or for my day-to-day life though, because that way lies madness.

Why is it that at least 7 people have voted on answers but only I have voted on the question? Whether we agree with their worldview or not, the OP has asked a perfectly valid question in a non-confrontational manner and deserves an upvote. We should not refrain from upvoting valid questions just because we have a philosophical disagreement with the OP.

@terdon - I dont think it was a good question. For starters the title is "Why is there such an argument about evolution" but thats not what he is asking at all. Indeed, what he is asking is clear as mud. He first asks about how / if (?) genes can influence behavior. Not a bad biology question, but then he asks about why scientists ignore this, which is a wrong assumption, and not so much a biology question but a philosophical question about scientists. And he ends by asking if he is confused. Four questions if you count the title, none of them related. Im guessing thats why it got 0 upvotes.

@vonMises I was not suggesting that the question should be upvoted, I was asking people to vote, one way or another. We tend to only vote one answers here and it's a shame. Anyway, the basic question is quite clear, "why do scientists ignore the possibility of a guiding hand in evolution". Yes, it is based on many wrong assumptions but it is clear.

I edited the title as the previous one was really not helpful. Feel free to roll back if you don't like the edit

Understanding Evolution by UC Berkley is a very short and very introductory course on evolutionary biology that you might want to have a look at.

@Remi.b — Although the poster may be a troll, your change of title to something that is neither what he intended or, indeed, a title, is unacceptable. I have changed it again (even though it invalidates the argument of my own answer). I would say a better way of dealing with this is to vote to close it as opinion-based. Arguing on the basis of opinions or belief in the divine is clearly unsuited for a scientific forum of this type. I appreciate people not wanting to be accused of avoiding an argument, but do you argue with Jehovah's witnesses and the like that knock on your door?

The theory of evolution via selection does not require any kind of divine intervention. It proposes that mutations randomly occur within the DNA, this causes changes in the phenotype (e.g. allowing digestion of a common food source), these changes can be good or bad (beneficial or deleterious). As a result, those with "good" mutations achieve more reproductions (the fitness of those mutant allele carriers is higher) and those mutations spread through the population. You can not direct the evolution of your DNA because mutation is random, even if we artificially induce mutations, we can not direct what the mutation does to the phenotype (though we can sometimes induce specific mutations known to have certain phenotypic effects). Selection favours some phenotypes over others but can only work with the mutations it is presented with - it can not direct the evolution of animals with wheels if mutations that allow wheels to form do not occur.
From this sequence you can see the evolution of a phenotype is best explained in a most parsimonious way without the inclusion of divine intervention. It is the principles of Occam's Razor. Calling divine intervention in to this theory would add further, and unwarranted, complication to the model and we would then have to find strong evidence for the existence of a divine being, something which is still yet to happen in the eyes of most evolutionary biologists. Strong evidence has been found which suits the theory without divine intervention (including unnecessary and untestable components to a theory goes against the basic principles of science).
Selection itself, though largely involved in evolution, is not necessary for traits to evolve. The neutral theory proposed by Motoo Kimura and developed in the last few decades suggests that traits can evolve with out selection, via genetic drift. This means traits develop in populations purely due to random sampling of neutral (or near neutral) random alleles. The relative importance of Selectionist vs Neutralist theories remains hotly debated within evolutionary biology.

Explaining your imaginary scenario with a current theory of evolution: A new digestive enzyme
The scene: There is a population of 100 deer. 50 males and 50 females. There is a potential for variance in mating success and that mating success is defined solely by the strength of the male.
Selection affects a trait: Males that digest their food better grow bigger and stronger. Thus selection favours males that get the most out of their food. If the ability to digest is completely genetically determined by a single locus (for simplification lets say it is) and there is only one allelic variant (one version of the gene) in our first generation then mating success will be equal among the males.
A mutant arises: In the next generation a single male carries a mutation in that locus. It is a mutated version of the gene which makes a key digestive enzyme work more efficiently.
Selection acts: This male is 10% larger and stronger than other males, and therefore sires more offspring in the next generation than any other male. These next generation offspring (technically half if it was a single mutation in a diploid organism - the other half have the ancestral haplotype) have the mutant allele. Then those males with the mutant allele also get more of the matings and so on and so on.
The allele is then spreading through the population. It will continue until all members of the population have the same allele (fixation) or will start over if a new allele arises which is even better. That's all evolution is, no divine beings necessary.
What if the allele was neutral? If the gene for a digestive enzyme existed but was not necessary in an organisms diet it would not know it could go out and use that food source. It may not even be able to. For example, a single fruitfly carries a mutation which has no cost and allows it to digest lactose. It is unlikely to be able to utilize that allele, because dairy products are not part of it's diet and not available in the wild. The allele would only drift in the population, eventually being lost (most likely as it starts at low frequency) or becoming fixed in the population. You can see a genetic drift simulation I wrote in R here. You can set f=1 and then play around with population size, number of generations, and replicates to get a feel for this process.
Note it is worth considering the effects of pleiotropy (if an allele has a good effect on one trait but a negative effect on another - including traits in different environments) and linkage (if the good allele is close to some deleterious mutations in the DNA it will struggle to spread until it is separated by recombination).

I think you might improve your answer by telling a bit about what might happen to newly arisen mutation that would be beneficial if the genetic background was different. What is the fate of this mutation allowing to create a new enzyme to digest a food when individuals behave (let's assume the variance in behavior are 100% genetically coded). You might as well give a word about pleiotropy.

The OP was asking what happen if the beneficial effect of the mutation (new enzyme allowing to digest a new food) is hidden because it is genetically coded that deer (to follow your example) don't eat the food it can now digest. In such a case, the mutation (new enzyme) is not beneficial and does not spread (or only by genetic drift).

It doesn't mean that you need a god for evolution to occur, it just mean that a mutation that allow better lactose (milk) digestion has a different effect on the reproductive capabilities of a mammal than of an insect. The effect of a mutation depends on the environment and the genetic background in which this mutation appears.

@Remi.b that's is covered by the neutralist side of things - "..traits develop in populations purely due to random sampling of neutral (or near neutral) random alleles"

I felt that the OP might wanted a explanation of what might happen to the mutation he was talking about. I wanted to be specific to the OP's example where you provided very good general description. +1 good answer mixing basic process of evolution, philosophy of science and Kimura's neutral theory.

@Remi.b I get you now, added in a bit.

@GriffinEvo

if we artificially induce mutations, we can not direct what the mutation does to the phenotype.

I don't think you meant that. Yes we can direct what the mutation does to the phenotype - we routinely do it in organims we can genetically manipulate (bacteria, yeast, mice etc.) and of course only in cases where we understand the
relationship between genotype and phenotype.
Better way of putting it would be that in most cases in natural populations we cannot predict consequences of a given mutation, as there are many factors in nature that can influence the fate of that mutation.

@yotiao by "we routinely do it in organisms we can genetically manipulate" do you mean we can cause a specific mutation to occur?

@GriffinEvo Yes. We can introduce a specific mutation (substitution, insertion or deletion of a single base pair up to large chunks of DNA) into a specific position in the genome. In many cases, we know a good deal how if affects the phenotype. In other cases, we have no idea but this is exactly the reason it's done.

@yotiao but this is using an induced mutation to produce an effect on the phenotype, for which the specific mutation has previously been observed to cause the intended phenotype - it's subtly different to what I said. Without a priori knowledge of how a mutation affects a phenotype, we can not know what effect a mutation will have on the phenotype,  we must first observe it to understand it's effect (though I'm sure predictive models can or will be built that can simulate the effect of specific mutations).

@GriffinEvo Yes, you're right for the majority of mutations (some obvious ones excluding, like stop mutations in housekeeping genes). We must have an idea of a genetic basis of a certain phenotype to be able to speculate about effects of potential mutations underlying the phenotype. But the ability of induction of mutation in a defined genomic position allows us to verify/narrow down these speculations in a really clean and clear experimental way.

AlleleA1 is a great population genetic software that really gives you a good idea how the frequency of alleles is affected by various factors. You don't have to know R to run it, but you need a Mac (a double bonus :-)

@yotiao the point I am making is that it is not possible to know it without any prior knowledge of the mutation's effect - I can't say "I want to start digesting cellulose better so I'll change my 5,694,237th nucleotide from an A to a C" unless I have tested that beforehand or have explicit information telling me such a change will give that result.

@rg255 already did a good job answering the main thrust of your question, I will address this part: "There seems to be a huge amount of room for divine providence to guide evolution at the level of animal behavior, at least. Why then do scientists with a philosophical materialist outlook gloss over this?"
Of course there is "room", there is room in the theory of evolution to posit that small, green, tasty but mean little pixies come and push the new food down the creature's gullets, thus teaching them to use new food sources. There is room to posit that invisible, intelligent lichen from Alpha Centauri are actually using brain waves to guide the evolutionary choices of species in a global scale.
While there is clearly room to posit these theories, there is absolutely no evidence for them. The scientific community is not "glossing over" anything, it is just ignoring various (infinite in fact) theories for which we have absolutely no evidence in favor of those for which we have. This is a classic fallacy that was very nicely put to sleep by Russell's teapot argument:

Many orthodox people speak as though it were the business of sceptics to disprove received dogmas rather than of dogmatists to
  prove them. This is, of course, a mistake. If I were to suggest that
  between the Earth and Mars there is a china teapot revolving about the
  sun in an elliptical orbit, nobody would be able to disprove my
  assertion provided I were careful to add that the teapot is too small
  to be revealed even by our most powerful telescopes. But if I were to
  go on to say that, since my assertion cannot be disproved, it is
  intolerable presumption on the part of human reason to doubt it, I
  should rightly be thought to be talking nonsense. If, however, the
  existence of such a teapot were affirmed in ancient books, taught as
  the sacred truth every Sunday, and instilled into the minds of
  children at school, hesitation to believe in its existence would
  become a mark of eccentricity and entitle the doubter to the
  attentions of the psychiatrist in an enlightened age or of the
  Inquisitor in an earlier time.

If you feel that the world you observe is best explained by assuming the existence of an omniscient god who guides the evolutionary process, then that is your right. However, the fact that you believe this to be true does not make it so any more than my believing it to be false disproves it. We are not glossing anything over when we don't take that belief seriously, no more than when we don't take Russell's teapot seriously. The Christian faith, like many others, is built on the assumption that a god exists, it will never attempt to prove or disprove that assumption because such proof would be sacrilege, the entire edifice is built on faith not evidence. If we do not share that belief, why should we attempt to fit our observations into the ideological scaffold provided by someone else's belief system?
If you feel that one theory explains what you observe better than another, the onus is on you to prove it so. That is in fact the beauty of science, it is what sets it apart from most other areas of human endeavor: we change our minds when presented with compelling evidence to do so. Indeed, the history of science is littered with discarded theories. If you can come up with any decent evidence to support a theory, then that theory will (eventually) be taken seriously. Until you do, asking others to consider it based solely on the fact that you believe it to be true is hubris to say the least.

This is a complicated topic. Basically, we differ on what can be known. Knowledge of God more properly falls into "personal knowledge", like knowledge of a particular person. You're quite right to demand a certain level of "proof"(proof, i.e. 100% certainty, only exists in mathematics), and for that I'd recommend Vishal Mangalwadi's "The Book that Made Your World". But to go from mere propositions about God to a personal understanding takes faith.

@Joebevo exactly, and as such does not fall within the purview of science. That's why nothing is being glossed over, faith is not something that can be approached by the scientific method of observable and repeatable experimentation. Therefore, any theories that base their conclusions on arguments of faith are not relevant to scientific debate. Science only deals with testable, disprovable theories and the existence of a guiding hand in evolution is neither.

But you can of course argue against the existence of god on the basis that in many religions there are beliefs in acts of god(s) or features of god(s) that are in opposition to scientific knowledge (walking on water, wine from water etc.). By asserting a level of probability on things that people say god does you can indirectly assert the likelihood of god existing in the first place. So because nothing god does / what god is is physically possible as far as science can tell, very likely there is no god at all.

@yotiao well, not really, no. If you start with the premise that god(s) exist, by definition they are above and beyond the laws of physics. Therefore, you expect them to be able to do things that are impossible, otherwise they would not be gods. Deities are not expected to conform to the laws of Nature, they wrote them.

Heh, this is way OT so we should not go much longer, but I then ask: what is your argument for the premise (god(s) exist) in the first place?

@yotiao absolutely none, it is not a premise that I hold to be true. However, if you do accept that god(s) exist, then it is to be expected that they don't conform to the laws of physics. If you believe in a creator(s), then you believe that they also created the laws of nature and, therefore, would expect them to be immune to those laws and cannot use these same laws to argue that they don't exist.

@terdon Yes, in this case this is simply out of realm of science.

I think it pertinent to answer the question posed in the original title, although I will make passing reference to the specific argument the poster makes.
“Why is there such an argument about evolution?” This is because evolution is an example of a scientific question which one party approaches from a philosophical standpoint that asserts a particular answer, and so they will never be convinced by scientific arguments that ignore this philosophical position.
Note, that I am not saying that the arguments from those of a particular philosophical standpoint are necessarily wrong, only that its exponents will continue to argue (or try to engage people in argument) when the vast majority of scientists have come to regard the question as settled in favour of the counter-view — indeed when that view underpins their daily work.
There are other historical examples of this. Most well known is the Roman Catholic Church's refusal to accept Galileo’s espousal of the Copernican view of the Solar System — even to look through his telescope to see the evidence. (I think they have thrown in the towel on that one now.) On the political left you have the promotion of Lysenkoism by the Soviets.
I would suggest that philosophical attitudes colour contemporary arguments. I suspect many ‘progressives’ would never accept scientific evidence that indicated one ethnic group were less intelligent than another. And it would be naïve to think the stage at which one regards a life as having been formed is independent of any religious or feminist views one may hold. There now. I’ve lost the friends I made in the previous paragraph.
Finally, your example of an individual acquiring the ability to digest a different food illustrates my point. You are so convinced that you are right that you have never taken the trouble to find out what the arguments for evolution actually are. It is only under circumstances that an acquired trait provides a competitive advantage that it will be selected for. Think multi-drug-resistant bacteria. You’ll find much more sophisticated arguments on the various ‘scientific creationist’ sites on the Internet, but you would be advised to save your breath, because nobody is listening. As I said, la guerre est finie.


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What are the advantages and disadvantages of being ambidextrous?
Most of us have one dominant hand. We find it nigh on impossible to do very delicate or dextrous activities with our other-hand. This seems like an apparent weakness, and a rather odd one when you first think about it.
Cursory internet searches revealed unexpected findings. One website said it has mostly negative effects on the brain. However I don't trust the source at all.
I'd be interested to know about the "story" about the good and bad of ambidextrous physiology. Particularly, I am interested in the neuroscience of ambidextrous people.

It would also be interesting to know whether our ancestors used both the hands and using just one hand is  recently evolved

@biogirl great comment needs more attention from everyone

@agha rehan abbas Thanks ! Thinking about something from evolution point of view always helps.

@biogirl It's a contentious issue, but chimps do indeed display handed-ness for tasks like termite fishing.

One side effect of being ambidextrous is that I also find it very easy to read mirror writing. This may seem like an advantage but in practice it can cause difficulties. I frequently find myself pushing glass doors when I should be pulling because I have inadvertently read the instructions through the glass on the opposite side of the door and my brain has not registered that it is the wrong way round.

I think that the advantages of using both hands with equal ease is quite evident whether it be sports, at your work or while you are doing your household chores.

An obvious advantage is using both hands to write or draw with both at the same time.
I would be focusing on the disadvantages that may be faced.

1) Ambidextrous people are more prone to suffer from Synaesthesia
  (reference)
2) They are likely to possess (not necessarily) the LRRTM1 gene which
  is linked with Schizophrenia (reference).
3) They score lesser in intelligence testing (reference).
4) Mixed handed children are more likely to suffer from ADHD
  (reference).
5) Mixed handedness is associated with greater age-related decline
  (reference)
6) They are easier to anger and influence emotionally (reference).

There are quite a few studies that have pointed out that it may not be all that good a condition but Leonardo da Vinci who was probably the most diversely talented man who ever lived is said to have been ambidextrous. He apparently could draw with one hand and write with the other at the same time, so I would have to say that the positives of the condition are extremely good (reference).
edit:
This probably qualifies as a second question :-D but I just saw a thought by biogirl in the comments section on "whether our ancestors used both the hands and using just one hand is recently evolved" and she has a point there. From a study publlished in 1977 I quote.

The predominance of the right hand over the left was also reported
  among Egyptian art forms 3,500 to 4,500 years old, where the ratio of
  left- to right-handers was 9:111 and 5:100, respectively. However,
  going further back using the "Draw-a-Man Test," found that ancient
  paleolithic man, from 1,750,000 to 8,000 years B.C., was probably
  either more ambidextrous or that there was a greater proportion of
  left-handers than there are now. (reference)

Also from a study titled "Evolutionary Back Grounds of Human Left Handedness", the authors concluded that

For most manual tasks, especially those tasks involved in competitive
  activities, increasing performance by the specialization of one hand
  is certainly adaptive. Aggressive interactions are responsible for
  fundamental selection pressures acting during primate and human
  evolution. The higher prevalence of right-handedness might well be due
  to a previously existing cerebral bias. But the specialization of one
  forelimb leading to right or left-handedness is better viewed as the
  result of natural selection. (reference)


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Can two denatured DNA strands reassociate?
What matter if I increase the temperature to 95°C. So double-strand DNA denatured into two ssDNA, and then I decrease the temperature to room temperature. Are they able to reassociate after denaturation?

I've edited this to remove the use of the word recombine which has a special meaning when talking about DNA. I assume that you meant reassociate.

In PCR there is always some strand reassociation. This is why the primers are added in excess, to make it much more likely that a DNA strand anneals to a primer than back to its anti-sense strand.

Yes, heating the DNA above 94°C for some length of time will melt, or denature, dsDNA into two ssDNA strands. Upon cooling, the complementary strands will come back to anneal. The degree and completeness of annealing, or association, is dependent on a number of factors including the rate of cooling and structural properties of the DNA itself (%GC content, secondary structure). I would not expect that the majority of ssDNA strands will completely anneal to a single, complementary dsDNA strand. What is more likely is that the DNA mix will look more like spaghetti with one strand partly annealed to two other strands. When performing PCR, the primers are designed to be specific, and added in excess, so that you bias the odds of annealing to favour a primer:ssDNA association. If this weren't the case, we could not possibly have efficient PCR amplification.

Because the DNA is too big, from hundred to thousand bp, it's not ~20bp in length like an oligo primer. In PCR the primer always have length ~20bp and i don't know if a bigger primer like template DNA itself can associate to the template strand.

Right, length is also a factor. The smaller the DNA length, the more likely for reassociation to dsDNA, but the probability drops as length increases.


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Interdependency between organsims on our planet and its relation to ecosystem?
I am not a biologist but I just wonder if all species are interdependent. I mean if the tiger becomes extinct does it affect the ecosystem? If the mosquito or mouse become extinct does it affect the environment and us?
I am asking because this question was raised by one of my friends when I was in favor of protecting tigers, lions but I had no answer to "tiger extinction will not affect humans".
So, is it true that the extinction of any species will affect all other species?

The problem is not really that we don't understand some stuff (lthough this is certainly true) but that an ecosystem, or the biosphere is a highly complex network of interactions. This network is continuously displaying some chaotic (determinist but not foreseeable) behavior. In such a system it becomes very hard or practically impossible to predict what the impact of a change (even a minor one) might be. To illustrate, one could say that killing half of the world's lions might cause the population of rabbits in Norway (!) to increase but killing two thirds might cause the same population of rabbits to decrease. Note: Stuart Kauffman wrote some articles where he argues that life is a system which is always balancing between chaotic dynamic and non-chaotic dynamic. Today, many conservation biologists use the tools of graph theory (network analysis) in order to get a better understanding of how things are influenced by a minor change.
But defending an endangered species like the pandas or elephants is certainly much more a matter of ethics than of human security faced with environmental shifts. I would guess (a reference on how the world's money is spent on conservation action would be interesting) that an important part of the money  spent on programs for the defense of endangered species are for ethical reasons, just because these species are big, clever, sing well or display nice colors.
There are many false reasons in ecology (in the political sense of the word) where people act for their ethics rather than to defend humans from environmental change. (I don't mean that ethics is stupid, or that only defending the environment for the benefit of the human species should be considered). You may already have heard "the amazonian forest is the lung of our planet" suggesting that this forest produces lots of $O_2$. This is completely wrong! Cutting down this forest would not change much in terms of either $O_2$ or $CO_2$ levels (except if the wood is burned!).
So to summarize I would say:

We spend quite a lot of money defending species for ethical reasons rather than to protect humans from environmental shifts.
Changing a little thing might affect the world-wide biosphere in a way that is practically impossible to predict.

Could you elaborate on your point about the amazon? While it is probably true that little of the world's oxygen comes from the Amazon, your sentence seems to be equating O2 to CO2.

@terdon I have no reference for the following! The amazon forest is an ecosystem that reached its climax, meaning that trees are not growing more that what they're dying. Or in other words, trees don't fix more CO2 than what they free up to the atmosphere. So yes, $V_{CO2}=V_{O2}$ in the amazon. Therefore, in terms of CO2 there is no cost of cutting down this forest (except for the fuel to be consumed for the work and except if the wood got burnt). And globally speaking, indeed most of the oxygen is produced of several species of plankton.

I know, my point is that your phrasing is confusing: "Cutting forest != decrease in $O_2$, therefore no difference in $CO_2$ production. I have edited to show what I mean.

Remi.b's answer is spot on - predicting the effects of losing a given species is nigh on impossible. However, I do think that there are some general trends that can give us some intuition, and make the campaign to protect certain species more than just an ethical issue.
Biodiversity (i.e. having a wide range of different organisms (and genetically diverse organisms)) has a number of potential benefits (for references see the work of David Tilman, among others):

Improved resilience to catastrophic events.
Improved temporal stability of populations within an ecosystem (which kind of dovetails with (1))
Improved ecosystem productivity (this has mostly been studied in terms of the amount of biomass grown by plants in an ecosystem, but may generalize to other kinds of ecosystem functioning)

Ecosystem services are effects that various ecosystems have on the world that makes it more hospitable to humans. While some may be, as Remi.b suggested, overhyped, some are very real, such as bioremediation (the removal of compounds toxic to humans from the air and water), the continued presence of pollinators and nutrient-rich soil in which to grow crops, and carbon sequestration. Given that the continuation of these ecosystem services is necessary for our long-term survival as a species, it is in our interest to ensure that ecosystems remain intact to provide them. Increasing resilience and temporal stability of ecosystems reduces the chance that we will lose ecosystems and the services they provide. Increasing the productivity of an ecosystem in many cases increases the extent to which it can perform that service (this is most obvious in the case of carbon sequestration). (NOTE: I'm phrasing this all in terms of human survival because I think that's the most clear cut argument. I think there are other arguments, but they're murkier)
Of course, this raises the question of how much of an impact the loss of a single species (such as a tiger) is likely to have on the benefits associated with biodiversity. There are a few hypotheses here, but in any specific case the impacts will be fairly dependent on the role of the extinct species in the ecosystem. The loss of some species (keystone species) will have a disproportionate impact on the rest of the environment. While it is hard to predict which species will turn out to be keystone species until it is too late, apex predators (like tigers) are more likely than average to be keystone species, or to have an important but not disproportionate role in the ecosystem. This makes sense, because such predators are fairly often the only species at their trophic level in an ecosystem, and having more trophic levels dramatically increases the biodiversity possible in an ecosystem.
Even if there isn't reason to think that a certain species is relatively important to an environment, there can sometimes be benefit in trying to save it via what's called "the umbrella effect." This boils down to the idea that saving one species generally involves saving the rest of the ecosystem that it lives in. So sometimes, from a funding perspective, it makes the most sense to choose the most charismatic species from a given ecosystem and attempt to get public investment in saving that species. An attempt to save this species can then result in preserving a great deal of biodiversity in the rest of the ecosystem.
So, ultimately, no, we cannot know how important a given organism is to an ecosystem or to human well-being. But we can make some fairly well-informed guesses.

+1 Indeed the notion of resilience is important to add to this discussion. The danger does not only come from in unpredictable ways which is what my answer suggested.


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Bacterial cell lysis buffer used in proteomics procedures
What kinds of detergent-free bacterial lysis buffers exist? The proteins we're extracting will be later analyzed by LC-MS/MS, and we're looking for a lysis buffer that won't interfere with this downstream analysis.

I'm a HUGE fan of FASP (filter-aided sample preparation) which is an in-solution preparation/digestion. It is very fast, allows you to not worry about a protein precipitation step, and gets rid of all MS incompatible substances with the wash steps (so doesn't matter what lysis buffer you use). It requires very few, inexpensive materials (a pack of 100 centrifuge filter units is less than 250 USD from VWR) and has great recovery. This is the link to the Nature Methods paper that the linked protocol is based on (the linked protocol is an updated, faster version of the Nature Methods one).

There are a few techniques available for this.
Some recommend a urea-based technique, others recommend a chloroform. Do you have more information about your specific needs?
A Chloroform-Assisted Protein Isolation Method Followed by Capillary NanoLC-MS Identify Estrogen-Regulated Proteins from MCF7 Cells

why not use a french press?   put a few thousand PSI on the sample and the cells just pop open.  The lysis buffer contains no detergents:
Lysis buffer:
50 mM Tris-HCl pH 7.5
50-200 mM NaCl*
1 mM MgCl2
5 mM DTT
1 mM PMSF

the salt concentration is variable and you could probably do without the DTT too if thats a problem ...

As pstew mentioned, SDS based lysis followed by FASP is a very good way. However, FASP can lead to sample losses. I would use it only if you have large culture of bacterial cells.
If you want totally detergent free method then, lyse cells in 8 M guanidinium hydrochloride buffered to pH 7.5-8.2 using 50 mM Tris buffer or 50 mM freshly prepared ammonium bicarbonate. If your cell pellet is approximately 20 uL then add 60 uL 8 M GuHCL buffered solution so that final conc of GuHCL is ~ 6M, heat to 65 degrees C and shake for 30 minutes or so. Spin down to remove any insoluble debris. Measure protein concentraion, if you want to, using BCA assay. Then, reduce with 10 mM DTT for 30 minutes at 56 C, alkylate with 25 mM iodoacetamide at room temperature and in dark (for this step it is crucial that the pH of your sample is around 8.0 otherwise iodoacetamide will cause side reactions). Dilute at least 8 times and digest overnight with Trypsin.


text:
Assay for Beta-galactosidase activity in single cell microscopy
I'd like to be able to measure the activity of $\beta$-galactosidase in living cells with simple optical (maybe fluorescence) microscopy. Ideally I'd like to do a minimum of genetic engineering, and use this assay with strains I already have (that have a WT lactose system), i.e. a fluorescent lactose-mimic would be ideal. Additionally, it would be nice if the lifetime of the fluorescent byproduct of $\beta$-gal activity was short, so I could detect a decrease in $\beta$-gal activity as well as an increase. Does such a fluorescent analog exist? I'm hoping to look at the switch from lactose to glucose utilization under the microscope, so I want lactose-using cells to light up and glucose-using cells to be dark, or vice versa. It does not have to be fully quantitative--a qualitative sense is fine.

Here is a link to on the Invitrogen/Life Technologies webpage detailing various probes to detect the activity of glycosidases, including $\beta$-galactosidase. These include DDAOG as mentioned by @Alan Boyd, as well as Fluorescein Digalactoside, Resorufin Galactoside, and  Methylumbelliferyl Galactoside, among others. NB, this is an Invitrogen/Life Technologies website, so all the reagents they mention are ones sold by the company; there may be others not mentioned here. Of these, DDAOG is very stable, which would allow for measuring the initiation of $\beta$-gal activity, but might not work to measure decreases in $\beta$-gal activity (without bleaching the dye). Resorufin Galactoside is sensitive and stable at physiological pH, allowing measurement over a long period of time. Fluorescein Digalactoside is the most sensitive assay, but since it requires the removal of 2 galactose moieties for full fluorescence it's activation time may be slow.
For my particular usage (limited access to near-red frequencies), I think that Resorufin Galactoside or Fluorescein Digalactoside might be the best choices. However, given the cost of these probes, I might be better off just finding some lab with a strain with gfp under the lac promoter in the chromosome and asking them for a sample!

I found this paper.

Zhang GJ et al. (2009) In vivo optical imaging of LacZ expression using lacZ transgenic mice. Assay Drug Dev Technol.7:391-9. doi: 10.1089/adt.2009.0195.
Abstract
beta-Galactosidase (beta-gal) (encoded by the lacZ gene) has been widely used as a transgene reporter enzyme. The ability to image lacZ expression in living transgenic animals would further extend the use of this reporter. It has been reported that 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one)-beta-d-galactopyranoside (DDAOG), a conjugate of beta-galactose and 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one), is not only a chromogenic lacZ substrate but that the cleavage product has far-red fluorescence properties detectable by in vivo imaging. In an attempt to noninvasively image lacZ expression in vivo, we applied fluorescence imaging to a G protein-coupled receptor (GPR56), knockout (KO) mouse model, in which the lacZ gene is introduced in the GPR56 locus. Compared to wild-type (WT) mice, GPR56KO/LacZ mice showed three- to fourfold higher fluorescence intensity in the head area 5 min after tail-vein injection of DDAOG. beta-Gal staining in sections of whole brain showed strong lacZ expression in homozygotes, but not in WT mice, consistent with lacZ activity detected by in vivo imaging. The kidneys were also visualized with fluorescence imaging both in vivo and ex vivo, consistent with beta-gal staining findings. Our results demonstrate that fluorescence imaging can be used for in vivo real-time detection of lacZ activity by fluorescence imaging in lacZ transgenic mice. Thus, this technology can potentially be used to noninvasively image changes of certain endogenous molecules and/or molecular pathways in transgenic animals.

The work in the paper is cited in a more recent paper which reports beta-gal-based chemiluminescent imaging in mice.
It's unclear if any of this would be successful at a single bacterial cell level.

I posted this as an answer because it was too long for a comment. In general, your experimental approach is feasible, however, the devil is in the details.
Firstly, your biggest challenge will be to gain access to suitable optics. Imaging individual eukaryotic cells is relatively easy with any diffraction-limited optical microscope, because their scale is usually 10-20 $\mu$m. Bacteria are a much smaller cell size, and they (mostly) cannot be imaged using diffraction-limited techniques on a single cell level. To image a single cell requires super-resolution optics/techniques.
Secondly, it sounds like you're doing diauxic shift curves. It may not be necessary to image at a single cell level, and you may be able to get away with making good measurements of cells in aggregate using any camera-equipped microscope, or even an optical plate reader since you mentioned $\beta$-gal.
@Alan Boyd pointed out a chemiluminescent substrate for $\beta$-gal which could work well if you have access to an optical imager that can give you readouts of photon counts/second. This would give you readings of average enzymatic activity (which you can correlate to expression level).
Also, you describe having cells be bright/dark depending on the utilized substrate and that would be harder to achieve. There are many ways I envision to do this, but they all take some amount of genetic manipulation. Perhaps the easiest thing to do might be to make an expression plasmid that places LacZ under control of an IPTG-inducible promoter. These plasmids are very common and would give you an easy entry to image lactose usage.

Thanks for your answer. It turns out that imaging single bacteria doesn't require that much extra work; my lab does it with a 60x oil immersion objective and not much else. Though you're right, using a less powerful objective and looking at aggregate cells will probably be sufficient. I also am required to use microscopy because I am testing a microfluidic device which continuously supplies fresh media to cells; I'm trying to visualize how quickly these nutrients diffuse through the device.

That's true about imaging at 60x, but it requires cells to be well separated for individual detection, and that's not usually the case with bacteria, especially when actively growing. That said, the resolution requirements were a big ambiguous. :) If you're using a microfuidic device, the sugar gets washed in with the bulk flow, so wouldn't that occur on a much faster time scale than the uptake and metabolism in bacteria?

If you dilute your sample before microscopy, it's pretty easy to spot individual bacteria. Even when the OD has been ~0.1, I have been able to see individual bacteria with no problem. The microfludic device washes nutrients over an agar pad; they diffuse through the pad to the bacteria. I don't know how quickly this happens. I'm also looking for the time to diffuse from device to bacteria, and for how the nutrients spread through the agar (on the focal plane with bacteria) over time. Regardless of the details of my exp., I'm looking for probes of beta-gal activity, like the one Alan mentioned.


text:
Time spent in phases of cell cycle
I am looking for references to papers containing the time intervals spent in different phases of the cell cycle (ej., G0, G1, S, G2, M for eukaryotes) for different cells. In particular, I am interested in E. coli and CHO (Chinese Hamster Ovary cells), but any reference to studies of this kind for any typical cell will be useful.
I'll accept an answer containing a representative sample of references to the literature on this subject. Preferably recent papers (since 2010).
If you can provide the times spent in each phase but don't have references at hand, that will also be useful.

This is the data for a few cell types:

Cell type   Total      G1      S      G2      M      Ref
----------------------------------------------------------
Neuro2a        9       2       5      1.5    0.5     [1]
Hela         16.2     7.7     7.2     0.8    0.5     [2]
A549          18       7      7.5     2.5     1      [3]
MCF7         21.3      9      9.3      2      1      [4]
CHO           15       6      6.8     1.2    0.65    [5]

The timescale is in hours.

References:

De Laat et al. 1980
Kumei et al. 1989
Orfanoudakis et al. 1989
Taylor et al. 1983
Harada and Morris 1981

+1 Thanks. This is useful, but I am looking for recent papers mostly. If you provide some more recent references (from 2010, preferably reviews), I'll accept this answer. Also, do you have any data on CHO or NS0? And what are the units of time in this table (hours, days)?

its not a popular thing for researchers to reproduce old results... not sure you will find more recent ones.

@shigeta so you're saying that these measurements have not been significantly improved/corrected in 20 years?

Not definitively, but its quite possible.  I'm sure we could measure melting points and osmolarity better now, but I can't recall seeing someone spending their time to do it.  Science famously doesn't even try to reproduce some of their most important cancer research.  I wouldn't fault WYSIWYG if they can't be found.


text:
what are hyperbranched amplicons in DNA sequencing?
I am reading an article about single-cell sequencing:
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html
And came across the concept of "hyperbranched amplicons". I googled for it but don't get much luck. The best I could find is it mentioned in another single-cell sequencing method here:
http://en.wikipedia.org/wiki/Multiple_displacement_amplification
Can someone give me a definition for it?


text:
Mesosome - does it exist?
This wikipedia page says that mesosomes are artifacts produced by chemical fixing techniques. Most of my textbooks still show a mesosome and describes it as having functions like - respiration, helping in DNA replication, etc.
Has the idea that it is an artifact been widely accepted by the scientific community ?

when are the textbooks from?

@GriffinEvo I read that, in 1970s this was recognized as an artifact but all my textbooks are written well after 1970 and also if u google mesosomes u will get most of the results showing the "old" answer.

I've always wondered about mesosomes. They were controversial 35 years ago when I was working in a related field. I decided to check the current status of the term.
I checked for research activity in this area using a Web of Science search "mesosome" in Title: this gave just 54 hits. I list the most recent here (unless otherwise indicated, these are single hits per year).
2010; 2008; 2004 (human cell mesosome??); 1994; 1988 (geology); 1983; 1982 (2); 1980
So it doesn't seem to be a very active area of research. The 2008 and 2010 papers are from the same group. The earlier paper is:

Li, X et al. (2008) Mesosome formation is accompanied by hydrogen peroxide accumulation in bacteria during the rifampicin effect. MOLECULAR AND CELLULAR BIOCHEMISTRY 311: 241-247   DOI: 10.1007/s11010-007-9690-4
Abstract: Ultrastructural alteration and hydrogen peroxide localization were examined in Xanthomonas campestris pv. phaseoli during rifampicin effect using transmission electron microscopy. Bacterial cells were treated with rifampicin and then were examined by electron microscopy to observe the changes of ultrastructure or hydrogen peroxide accumulation in living cells that took place before lysis. Intriguingly, rifampicin treatment led to presence of an additional location of hydrogen peroxide accumulation within the cells. There was an association between the frequency and size of the additional location of hydrogen peroxide accumulation and the concentration of rifampicin. Furthermore, an additional ultrastructure, mesosomes, was also present in cells during rifampicin effect. The frequency and size of mesosome increased with the increasing concentration of rifampicin. Result of multiple linear regression showed that the size of mesosome plays as a key factor in the quantity of excess hydrogen peroxide accumulation in cells during rifampicin effect. Linear correlation was confirmed between quantity of excess hydrogen peroxide accumulation and the size of mesosome in cells during rifampicin effect. This finding intensely indicated that mesosomes are just the additional location of hydrogen peroxide accumulation in cells under cellular injury caused by rifampicin treatment. The mesosome formation is always accompanied by excess hydrogen peroxide accumulation in X. campestris pv. phaseoli during rifampicin effect.

This paper has been cited 7 times. One of those citations is from:

Saier, MH. & Bogdanov, V. (2013)  Membranous Organelles in Bacteria. JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY 23: 5-12   DOI: 10.1159/000346496

Free full text here.
The language used in this review seems to support the existence of mesosomes as some sort of intermediate in the formation of intracellular membranes in prokaryotes. This review is a polemic in favour of the idea that prokaryotes do indeed contain intracellular membrane-bounded compartments. It has no abstract, but the first paragraph gives a flavour of its stance:

The traditional view of life on Earth divides the living world into two major groups, prokaryotes and eukaryotes. These two groups were originally suggested to differ in very basic respects. While eukaryotes had complex cell structures including a cytoskeleton and intracellular membrane-bounded organelles, prokaryotes were believed to lack them. In fact, numerous textbooks and current sources still note this distinction and hold it to be true. For example, in Campbell’s Biology [Campbell, 1993, p. 515] it is stated without equivocation: ‘Prokaryotic cells lack membrane-enclosed organelles.’ In ‘Functional Anatomy of Prokaryotic and Eukaryotic Cells’ [Tortora et al., 2009, chapt. 4] it is similarly claimed that ‘Prokaryotes lack membrane-enclosed organelles, specialized structures that carry on various activities’. In the current Wikipedia, under ‘Prokaryote’ the following statement can be found: ‘The prokaryotes are a group of organisms whose cells lack a cell nucleus (karyon) or any other membrane-bounded organelles’. In the same online compendium under ‘Organelle’, one can read: ‘whilst prokaryotes do not possess organelles per se, some do contain protein-based microcompartments’. Proteinceous microcompartments will be the subject of a forthcoming Journal of Molecular Microbiology and Biotechnology written symposium, but this one will show that these generalizations, suggesting a lack of subcellular compartmentalization in prokaryotes, are blatantly in error [Murat et al., 2010a].