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Burns' "To a mouse" - what species of mouse?
What's the most likely mouse species Robert Burns is referring to in his poem "To a Mouse, on Turning Her Up in Her Nest with the Plough".
Burns farmed near Ayr, which is on the Firth of Clyde in Scotland. So the mouse of his poem would have to live in that area in the late 18th century. The creature obviously was living in an open field in December in a nest made of "leaves an' stibble [stubble]". From the poem's title it appears like the nest was constructed underground. "Sleekit" refers to sleek coated as in shiny fur. A clue to the mouse's diet is given by "A daimen icker in a thrave", ie grain. According to Wikipedia: "Scotland has no population of the Edible or Hazel Dormouse, or of the Yellow-necked Mouse, and the Harvest Mouse's range is limited to the southern part of the country."
The poem is here: http://en.wikipedia.org/wiki/To_a_Mouse

Have you looked at the poem for more information about the mouse's habitat and behaviour?

I've tried to give a bit more information in my original question. Does that help?

Very much, thanks! Deleting my previous comments. Off topic but which word actually refers to grain?

"Daimen means rare or occasional, icker is one ear of corn, a thrave is a measure of cut grain". Taken from http://www.robertburns.plus.com/mouse.htm.

It could be Wood Mouse(Apodemus sylvaticus).

Courtesy : redbubble.com


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Which kit provides the highest yield and purity of extracted DNA from FFPE tissue samples?
I'm looking to extract DNA for sequencing from FFPE (Formalin fixed paraffin-embedded) tissue samples. I'd like to use a commercial kit that provides a high yield of good quality DNA.

source: Stack Exchange

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sort: votes


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Fibrinous inflammation, exudate and scarring in monotonous movements and ageing
I have palpated many hard organs during my work and studies.
I have seen many young and old people who have hard organs, like very hard shoulder - very common.
I have interviewed some of them, some points

only one type of weight lifting
no running
no stretching
no stretching before training
no stretching after training
not age dependent only - very old can be healthy
dynamical movement dependent

There are two mechanisms of fibrinous inflammation

trigger the release of fibrinogen
trigger release of fibrinogen-to-fibrin reaction

which both result in the production fibrin in the interstitium:

The area may also be mixed with serous so two variations of fibrinous inflammation

serofibrinous
fibrinous.

I am interested in the mechanism that leads to this hard tissue throughout the organ.
This raised to me an idea about Fibrinous inflammation in the shoulder.
Robbins say that if the exudate cannot be sucked out, it leads to scarring.
I think this is what is making the organ feel hard.
What is the pathogenesis in such monotonous movements without stretching?

I would now say that the hardening is just local acute venous congestion if in the short term.
Without stretching after practice, it just takes more days to recover.
So lymphatic drainage is the one which helps the muscle get its needs and nutrients.
If this happens during years, it is difficult to say what is the causal factor.
It depends on many factors.
One key factor is how well the lymphatic circulation can recover the body back.
So genomics of the patient comes in the picture.
Many other factors too like anatomical structure of chest.
Then, depending on these factors and other pathological processes may happen many processes like

accumulation of fibrinoid
accumulation of calcium deposits
shorter diffuse distances
smaller total area of cells

which are some adaptation processes to the ageing (also of prolonged monotonous weight lifting).
They can lead to

acute lymphangitis (reddening of the skin)
Chronic lymphangitis
Chronic Granulomatous Lymphadenitis (fibrosis happening between muscles and connection points - not in all cases granulomatous - rare only)
lymphadenopathy (very, very late - after many years)

during ageing (adaptation).
Better question would probably be: what are processes happening during ageing?
And then cover pathologies of ageing separately and also the physiological processes on the weight lifting separately.

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Why can't my body deal with cold-sores
I am not a biologist, but I have always wondered why my body hasn't learnt to deal with the HSV-1 virus. I understand it reamins dormant for a while and things like stress or the common cold can trigger it. I get cold sores about twice to even four times a year and I have had them since being quite young.
Why hasn't my immune system learnt to recognise it and eliminate it?

HSV-1 has evolved mechanisms to thwart the immune system's surveillance.  A number of genes in the viruses genetic material code for proteins that can disrupt the process by which a cell alerts the immune system that it has a foreign virus within in it.
For technical readers, the reasons are described in the links above in detail.
For the non-biologist....
PART ONE  As you note in the question, HSV-1 can remain dormant in an infected cells for a long time.  In general, there is nothing for the immune system to respond to at this time.  So the infection persists in a dormant state.  Whats more, when it spreads, it can spread between cells, without entering the bloodstream.
PART TWO If the virus re-activates. In order for cells of the immune system to recognize and destroy a cell infected with a virus, the infected cell first chops up bits of the virus that are inside the cell and transfers these pieces (called antigens) to the outside of the cell so they may be presented  to immune system cells. At the same time, the infected cell attracts and activates immune system cells using 'distress' molecules.    However, HSV carries genes that make proteins that can thwart the presentation of antigens by a cell as well inhibiting the distress molecules that help activate an immune response.
PART THREE  What about antibodies ?  During the body's response to an HSV infection, antibodies can be produced and persist.  In many infectious diseases, antibodies can be protective as they mop-up any circulating virus and may prevent re-infection.  However, since HSV is already present inside cells, antibodies may have little effect in the reducing the amount of virus-infected cells in the body and may not prevent flare-ups.
Paradoxically, some of the symptoms of HSV flare-ups are due to the immune system's response!  (looking for a good reference)
The good news is that drug options to treat HSV have improved.


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Does yeast grow on LB agar plates?
I would like to grow E coli cells on cellophane on top of LB plate, and then grow yeast cells on the same LB plate. Does (or how well) yeast grow on LB plates? Is there a composition media that can be good for both E. coli and yeast? Has anyone done this experiment?

not sure if LB is a good medium but yeast does contaminate bacterial plates often. Fungi also grow easily. May not be the most optimal medium but nonetheless fungi seem to be quite robust.

Not well, they need  dextrose. Use YBT:
20 g Casein Peptone Tpe-M
10 g Yeast Extract
20 g Dextrose
17 g Agar
q.s. to 975 mls in di-water.
pH to 6.2 w 5M NaOH
q.s. to 1L with di-water.
Autoclave for 45 min at 121C
Aseptically dispense in Petri dishes.
Store at 4C for up to 12 weeks.
If you want to grow Co-culture do so in LB supplemented with 20g/L Dex.


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E coli cotransformation efficiency
What is the E coli transformation efficiency for 2 plasmids? Are any studies that have looked at the correlation between number of plasmids transformed and transformation efficiency? Is there a commercial E coli strain that is better at co-transformation?
For example, electroporation with single plasmid yields around 1 × 10^10 cfu/μg. I would like to know what is the limit for co-transformation and whether it can be or has been improved.

Nothing to back this up with so just a comment: my understanding is that the cells which are competent take up a lot of DNA, so cotransformation is easy to achieve as long as you can select for both plasmids (if they have replication/segregation features from the same incompatibility group they will segregate rapidly). I once did a Tn5 mutagenesis experiment which required propagating the plasmid in a Tn5 strain, preparing plasmid, transforming a recipient at high DNA input and selecting for kanamycin resistance. Many transformants contained more than one plasmid but they resolved easily.

The efficiency is pretty low. You have to be able to select for both plasmids individually (for example plasmid 1 with ampicillin and plasmid 2 with choramphenicol or other possible antibiotics) otherwise the cells will rapidly loose one of the plasmids. Usually the shorter and less "energy expensive" stays, if it maintains the selection marker.

I've always understood for this process to be incredibly low. When you consider how much DNA is added and how many competent cells there are, if you have even 1% transformation efficiency, you'll always get lawns. Since we don't, that gives a rough estimate of the process.

I also make the previous comments into a nice answer.

There is no problem to transform bacteria with more than one plasmid. The usual methods (either chemical competent cells or electroporation) are working fine, although electroporation might give you better results, as the cells take up more DNA. On the downside you have to make sure that your cells are prepared nicely, otherwise the electroporation cell will produce a short circuit (of course chemically competent cells can be problematic, too).
What you will definitely need are two (or more) different selection markers. The easiest will probably be different antibiotics (something I used in the lab and which works nicely) or other like genes which provide essential substances for the cells. As long as the selection pressure on the cells is held up, both plasmids will stay in the cells, when you take away one of them, the corresponding plasmid will get lost within a few days.
Regarding the efficiency of co-transformations I haven't found any papers. There is however, some data available on factors which influence the effiency of single transformations and I don't see, why these shouldn't be applied for co-transformations as well.
First, there is the size of the plasmid. The bigger the plasmid is, the lower gets the transformation efficiency. The figure from Inoue, 1990 is pretty clear in this point:

So for this reason I would use plasmids as small as possible.
Second, the density at which the growing bacterial culture which is used to prepare the competent cells is harvested has a big influence on the transformation efficiency. Tang and colleagues (1994) found out that growing the cells to a higher density than the classical OD$_{600}$ of 0.6 (which for example Inoue recommends in it paper cited above) is not a very good choice in terms of transformation efficiency. They found an OD$_{600}$ of about 0.94 working much better, see the corresponding figure:

And finally the amount of competing DNA is a big factor. Hanahan, 1983 found out that the transformation efficiency gets lower, the more competing DNA is present:

So I would try to use as little of each DNA to work against this effect.

Thanks, Chris, but I was more wondering how high with efficiency (number of clones per ug DNA) you can get with co-transformation. For example for single electroporation the efficiency is around 1 × 10^10 cfu/μg so I would like to know what is the limit and whether it can be improved for co-transformation.

I haven't found any papers looking on this for co-transfections, but some data for single transfections. We can do some interpolation from them, I will expand my answer.


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Is half-a-tablet of X a substitute for a tablet of X/2?
This may be anecdotal.
At the pharmacy earlier, the prescription called for a drug with X mg of the target chemical. The pharmacy however only had stock of a higher potency of the same brand.
E.g. A prescription may call for 25mg of a particular chemical, whereas the pharmacy could only service a request for 50mg of that chemical in the same brand.
According to the pharmacist, and the medic - a proportional fraction of higher potency drug of the same brand may be substituted for the lower potency. Thus in the example above, half-a-tablet of 50mg may serve in lieu of a single tablet of 25mg.
For a given brand

Is half-a-tablet of X a substitute for a full tablet of X/2?
Does the corollary scale upwards too?

Disclaimer: all of this is not to be considered medical advice but rather a general explanation. You should talk with your physician and/or pharmacist on a case by case basis when determining whether to take a drug and how to dose it.

We should consider that most pharmaceutical forms are made up from two main components: the active ingredient(s) and the excipients.
The active pharmaceutical ingredient is:

the substance in a pharmaceutical drug or a pesticide that is biologically active.

That is, the part of the drug that actually "does the job". Note that the dosage on the package refer to this, not the weight of the pill! For instance 500mg aspirin will contain 500mg of the active principle (acetylsalicylic acid) but the pill itself will weight more than 500mg.
An excipient is:

an inactive substance formulated alongside the active ingredient ("API") of a medication, for the purpose of bulking-up formulations that contain potent active ingredients (thus often referred to as "bulking agents," "fillers," or "diluents").

This does not normally have biological effects, but allows you, for instance, to have a pill that is of sufficient size to be easy to take in your hand.
When you split a pill in half you are assuming that each half contains the same amount of active ingredient.
This is regulated by the Pharmacopoeia*. In particular when looking at the monograph for tablets we can read (bold is mine):

Tablets are solid dosage forms usually obtained by single or multiple compression of powders or granules. In certain cases tablets may be obtained by moulding or extrusion techniques. They are uncoated or coated.
Tablets are normally right circular solid cylinders, the end surfaces of which are flat or convex and the edges of which may be bevelled. They may have lines or break-marks (scoring), symbols or other markings.
If the break-mark(s) is/are intended to facilitate breaking the tablet for ease of swallowing a dose consisting of one or more whole tablets, the scoring is not critical. However, if the break-mark(s) is/are intended to permit accurate subdivision of the tablet in order to provide doses of less than one tablet, the scoring is critical. Tablets containing active ingredients having a narrow therapeutic window should generally not be presented with break-marks for subdivision. Non-functional break-marks should be avoided.

The point about the therapeutic window shows why splitting pills may be dangerous. The therapeutic window is the range of concentration of a drug which treats disease whilst staying within the safety range.
If this window is narrow, minimal changes in the dose can cause the treatment to be ineffective -if there is too few of the active ingredient- or toxic -if there is too much.
The Pharmacopoeia also lists several tests to be done on tablets. In particular, in the presence of break-marks, the manufacturer should

ensure the effectiveness of break-marks with respect to the uniformity of mass or content, as appropriate, of the subdivided parts so that the patient receives the intended dose.
A suitable test to assess the uniformity of mass during development is as follows:
Take 30 tablets at random. Break each tablet by hand and take one part for the test and reject the other part(s). Weigh each of the 30 parts thus obtained and calculate the average mass. No individual mass is outside the limits of 75% to 125% and not more than one individual mass is outside the limits of 85% to 115% of the average mass.

I will not go into further details, but there are, for instance, other tests to be done to ensure uniformity of mass and content from tablet to tablet, as well as their physical stability (i.e.: they don't have to fall apart in the box).
Note that the packaging should generally include instructions about whether it is safe to split the tablet and how to store (and how long) unused pieces.
This is for splitting tablets. The opposite situation may also arise. Are 2x2mg tablets equivalent to 1x4mg one (speaking of weigth of the active compound in the tablet, not the weight of the tablet itself)? The same reasonings as above apply, however, because tablets should be uniform and no breaking is involved, this is generally safer than the previous case.
All of this applied to a single dose of a drug. Now I would just add a word about repeated doses. I cannot stress this enough: always refer to your physician about drug dosing. Taking a pill in the morning and one in the evening is NOT the same thing as taking two in the morning and none in the evening or taking four halves during the day. Self-dosing is dangerous and should never be done.
Taking half the dose may result in sub-optimal concentration of the drug (so it won't work as expected). Taking twice the dose may result in a toxic peak concentration, which is obviously not something that you want.

* note that there are multiple Pharmacopoeias, and the exact directives may vary. For simplicity I will refer to the International Pharmacopoeia, 4th Edition, 3rd supplement, published by the World Health Organization, and available online. There are others, such as the European Pharmacopoeia (apparently not freely available?) or the Japanese Pharmacopoeia, but I guess that goes beyond the scope of this answer.

This website gives a nice overview, including how the FDA approve drugs that they expect will be spit and some practical issues of pill cutting.
Yes, half a tablet of (2x dose) is, absent other issues, equivalent to one intact tablet of (1x) dose.  The main exceptions are practical ones.. where the tablet cannot easily be cut; where the dosing is so specific that slight variations of dose (uneven tablet fragments) matter, or where the dose is in a capsule or has some special coating so that cleavage might alter the release of drug into the body.
Yes, dosing scales upwards.  Two pills give twice the total dose of one pill.
All prescriptions are dispensed with specific dosing regimens (i.e how much you take and when you take them) to ensure the drug reaches effective concentrations in the body. You should not try to 'boost' the drugs effectiveness by taking more drug, or taking drug more frequently than your physician has prescribed.  As noted in the weblink above, it can be tricky to keep track of dosing and timing if your pill bottle contains whole and cut pills.  (i.e what does "take one pill every NN hours" mean ?).
This is NOT MEDICAL ADVICE . Always consult your physician and/or pharmacist for your particular case.


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Concerning Apoptosis
What if cellular growth and repair is 'forced' to occur repeatedly in a region where it wouldn't normally happen , if the biological area was 'healthier'. Could this more aggressive cellular growth and repair cause any apoptosis mechanisms to shut down permanently?

One long standing hypothesis of cancer formation is that it originates in a 'wound that never heals'.  I was about to add that there is little hard evidence for wounding as a significant cause of cancers but Google found this fascinating report on Marjolin's Ulcers
 which I had never heard of.   Whether it was the wound or a comorbid virus or something else.....
You may also want to search the current thinking of how a chemically inert 'irritant' - an asbestos fibre - can cause mesothelioma.

The definition of a tumor is a population of cells that:

Divides out-of-control

2.. Does not exhibit apoptosis
3.. Does not differentiate
Additionally the two-hit hypothesis states that at least two genes need to be involved.
There are many genes,  predominantly involved in the regulation of the cell cycle, that when their function is disrupted the cell exhibit uncontrolled replication. Attenuated expression or constitutive activation of the genes does not necessarily affect apoptosis. However, and to give you the quick answer – it depends on the gene involved. Some genes are involved both physiologies. Check out the protein AKT.


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What is the biological reason that some viruses cause sore joints (eg flu)?
Frequently I have experienced sore joints during a bad bout of influenza. I understand that during time of sickness, white blood cells are deployed in the blood stream. I also believe that white blood cells originate or relate to bone marrow. I'm wondering if there is a relationship between each of these
My question is: What is the biological reason that some viruses cause sore joints (eg flu)?

Almost certainly what is causing the joint pain isn't the virus, but rather its the body's response to the infection.   Cells that are infected with viruses can release proteins called interferons. Interferons can act on surrounding cells and cause them to become less susceptible to viral infection.  Other cells, including your immune cells respond to a virus by releasing other proteins into the blood called cytokines.  Cytokines activate other immune cells and can stimulate the body to generate a fever and 'lock up' molecules of iron so they are not available to invading bacteria.
Some cytokines act on the bone marrow and cause the pool of 'reserve' neutrophils (a type of white blood cell) to move into the bloodstream.  Other cytokines shut down the lymphatic vessels, causing lymph nodes to swell up.   And other molecules such as histamine and prostaglandins are released and also play a role.
SO what you are feeling when you get ill from a virus (or a bacteria or parasite) is the effect of this 'soup' of cytokines, interferons and other 'mediators'.  You may have some combination of fever, muscle/joint pain, runny nose, malaise, fatigue etc.
In the US you'll see TV adverts for drugs used to treat Rheumatoid Arthritis.  These drugs include synthetic proteins that bind to a cytokine called TNF-alpha and  block its role in inflammation.


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Missing 4 $\ce{H_2O}$ (per glucose) in Cellular Respiration... Where can they be?
I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $\ce{H_2O}$ molecules. Generally, cellular respiration is written thus :
$\ce{C_6H_{12}O_6 + 6O_2 + 6H_2O -> 6CO_2 + 12H_2O}$
Yet studying the reaction on a molecular level, I realized that the water molecules just don't add up to be six! (on the left side) What I obtained from my textbook and Wikipedia is that (per 1 glucose molecule)

(Glycolysis) (in the reaction that 2-Phosphoglycerate(2PG) forms Phosphoenolpyruvate(PEP)) 2 molecules of $\ce{H_2O}$ are out of the reaction
(TCA cycle) (in the reaction that combines Oxaloacetate and Acetyl-CoA to form Citrate) 2 molecules of $\ce{H_2O}$ are into the reaction
(TCA cycle) (in the reaction that Citrate form Cis-Aconitate) 2 molecules of $\ce{H_2O}$ are out of the reaction
(TCA cycle) (in the reaction that Cis-Aconitate form D-Isocitrate) 2 molecules of $\ce{H_2O}$ are into the reaction
(TCA cycle) (in the reaction from Fumarate to Malate) 2 molecules of $\ce{H_2O}$ are into the reaction

These sums up to a net of (only) 2 molecules of $\ce{H_2O}$ into the process of glycolysis and TCA cycle... additional 6 molecules of $\ce{H_2O}$ comes from oxidative phosphorylation. Then, where can the remaining 4 molecules of $\ce{H_2O}$ possibly be?

Can you point to a source that uses the equation in that form? Everywhere that I have looked has no water on the LHS and 6 water on the RHS, and that is the equation that I'm familiar with. Incidentally in your accounting you missed the loss of 1 water at the aldolase step I believe.

My (possibly) outdated school textbook states the equation like what I wrote before... but I don't think it's trustworthy.(It's weird in many ways) I think the equation with only 6 water molecules is correct. So,(may I ask) is there a water molecule used in the aldolase step? two of them?

@AlanBoyd, I don't think H2O is involved in the aldolase reaction. Aldolase is a lyase, not a hydrolase; see  http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/1/2/13.html

First thing to make clear is that net $6 \, \ce{H_2O}$ go out of the reaction.($12 \,\ce{H_2O}-6\,\ce{H_2O}$)
Let me tell you my calculation, you should then be able to figure out what went wrong.
For the Left hand Side, $6\,\ce{H_2O}$ are accounted here :

$2\,\ce{H_2O}$ go in conversion of 2-Phosphoglycertae to phosphoenolpyruvate.
$2\,\ce{H_2O}$ in TCA from conversion of Oxoloacetate to Citrat by combining with Acetyl CoA.(One for each Acetyl CoA molecule)
The aconitase -cis-aconitase-isocitrate water molecules cancel out. Equal no go in and out.
$2\,\ce{H_2O}$ in TCA from conversion of fumarate to Malate.

For the right hnd side, if we calculate the no. of NADH formed = 10 and assume that each participates in respiratory chain, we have $10\,\ce{H_2O}$ from there. The other $2$ will be from the $2$ FADH produced.
So we have 6 on the LHS and 12 on the RHS. Hope this makes sense !

I'm afraid that per a NADH or a FADH2, these yield only 2 electrons, reducing only 1/2 water molecule. So, only 6H2O produced at the respiratory chain

@ChanheeJeong, No, 2 electrons reduce 1/2 O2 molecule, so forms 1 H2O. So this answer is correct I think.


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Changing time and rpm of centifuge
Inspired by this question, I want to ask a question about centrifugation.
Suppose a protocol says : 10 min at 2500 rpm . Can we instead centifuge for 5 min at 5000 rpm or 20 min at 1250 rpm ?

No, it isn't that simple, because centrifugal force varies with the square of the rotor speed. Have a look at the Wikipedia page for clearing factor.
Those equations are usually used to determine what you need to do if you are going to use a different rotor, but they can also be used to solve your question.
Because you are looking at a situation where the same particles are being centrifuged, the sedimentation coefficient s is the same in both centrifuge runs. Also all of the factors relating to the rotor properties are the same (rmax etc.). So, if you have a set of conditions that work, t1 and RPM1, and you want to choose new conditions t2 and RPM2, you can use the equation:
RPM2 = SQRT(t1/t2) x RPM1
For the example you mention t1 = 10 min and RPM1 = 2500 rpm. If you change the time to 5 min:
RPM2 = SQRT(10/5) x 2500 = 3536 rpm
Because the centrifugal force varies with the square of the rotor speed you don't need to double the speed if you halve the time.

So what if it was RCF instead of RPM in the question, i.e.,10 min at 2500 x g? Thank you.


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Function of heparin and dextran sulfate for removing proteins
From this article :

The reaction was terminated and the histones, and most nonhistones,
  were removed by adding the nuclease-treated chromosomes to a solution
  containing dextran sulfate (2 mg/ml) (Pharmacia), heparin (0.2 mg/ml)
  (Sigma), 10 mM Tris (pH 9.0), 10 mM EDTA, 0.1% Nonidet P40, and 1 mM
  phenylmethylsulfonyl fluoride (PMSF) at a ratio of 1 volume of
  chromosomes to 3 volumes of solution.

What is the function of  dextran sulfate and heparin in removing the proteins ?

See here.
Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.)
Immobilised heparin is sometimes used as an affinity matrix for purification of DNA-binding proteins like transcription factors.


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Cells created using differently aligned proteins
I remember reading that scientist were making cells (I assume bacteria), that used differently oriented proteins to create a whole new class of life. Because apparently right and left aligned proteins don't interact in same way, cells made in such manner would behave similarly but couldn't be interacted with differently aligned bacteria/virus.
However I can't find any proof this story was true? I could be wrong about details. Is there a similar mechanism that would allow a whole case of twin (contain DNA, and most molecules that regular cells posses) cells that couldn't interact with existing bacteria?

That seems extremely far fetched to do with current technology... in any case, natural aminoacids are called L-aminoacids and their "mirror counterparts" are the D-aminoacids. Maybe that can help with your search?

I can see an "easy" experiment involving generation of auxotrophic d-amino acids for any given gene. You can now make certain bacterial stop codons code for non-canonical amino acids. Of course for an entire genome...now that would be something.

The problem with this is something called the structure-function relationship. The function of a protein or enzyme is completely dependent on its structure. For example, take a look at this representation of the active site of chymotrypsin:

The side chains of D102, H57, and S195 all need to be in a perfect conformation in order for the enzyme to function properly, with the hydrogen bonds being essential. If any one of those amino acids was in the D-form, the enzyme would lose its activity completely. Having every single amino acid in the D-form wouldn't help either, as the entire protein's structure (and hence its function) would be altered.

This assumes lots of things. There may be instances in which the active site is a bit "loose" to allow for multiple substrates and in which a D-aminoacid would not harm too much. Plus if everything, including the substrate, was D-form I bet there would be a high chance of it working. There are examples of antibiotics becoming more specific or selective when one aminoacid is changed from L to D (e.g. this and this)

@nico - a few D-amino acids here and there may not affect structure/function too much, I agree. But I really can't imagine that a fully D organism could exist. I didn't get into this in my answer, but I doubt that all tRNAs could bind the D isoforms of their respective payloads. Secondary and tertiary structures often depend on H-bonding, and a change in chirality could destroy those bonds, leading to incorrect folding.

I don't see why. If everything in nature was specular, well, it could in theory work very well! I think we simply do not have any proof in favour or against to say more...

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text:
How can a recessive allele propagate until they manifest?
Suppose a specific gene has two possible alleles. In a given population all members have only the dominant one. By a mutation on member receives the first recessive allele of that population. Is it possible that one day the descendants of this population have this allele manifested? I think it's very unlikely that this allele survive until another similar mutation occurs and they get manifested in the phenotype.

The short answer is: Because of genetic drift. If a mutation does not influence the fitness in heterozygote individuals, then its frequency varies only through genetic drift while it reaches some high enough frequency. If by chance, the frequency of this new allele achieve a high enough level so that the homozygous for this allele given by $x^2$ where $x$ is the frequency of the new allele is high enough to have considerable effect, then the selection coefficient $s$ between the recess if homozygote and the two other genotypes matters.
Hope that helps you. Don't hesitate to ask further more accurate question if you need more details. Or let us know if this does not answer your question.


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Can inhibition of lymphocytes migration be a direct cause of chronic inflammation?
Here is the original slide:

I am thinking about the "cord factor" sentence in a more general case.
Assume you inhibit Leucocytes migration.
How does this lead to accumulation of macrophages in the site of infection?

Can you edit your question to be more specific, and not use "Leu" as an abbreviation ?  (Leu has other meanings).   Leukocytes come in many types - lymphocytes, macrophages and neutrophils, for example.  The effects of inhibiting their migration may vary.  What specifically do you want to know?
I'm not sure if your example with Cord Factor is a suitable basis for your question...According to this cord factor is generally pro-inflammatory and acts by preventing fusion between vesicles that may contain M.tuberculosis and lysosomes.

Can you provide a link to the original document that includes your sentence ?  That might help us.

I edited your question both to add your image of the slide and to remove your "quote", which was not at all what the slide said. Also, it should be clarified here that cord factor comes from M. tuberculosis.

The only reference I can find re cord factor inhibiting leukocyte migration is this one  . It cites reference 33 as a basis for that statement and I don't see any such finding there. Skimming the abstracts of references 32 and 34 also don't seem to suggest such a finding, either. So I think the premise of the question may be in error.  If you can find a reference for such activity, then I think we can look at any such specific activity.   Basically, I think that part of the slide is wrong.

The mechanism is likely very straightforward. Activated macrophages already in the area are releasing pro-inflammatory cytokines like TNFα, IL-1β, IL-6, IL-12, MIP-2, etc. These are not only important for granuloma formation, but they also recruit other immune cells to the area. However, since cord factor has this anti-migratory effect, once the cells get there they can't leave. This is important because activated macrophages are key antigen-presenting cells (once they kill and break down the antigen, in this case Mycobacteria), and they need to move to the spleen to assist in the upregulation of the adaptive immune response. By preventing this, mycobacteria can evade part of the immune system - part of the reason why TB is so hard to clear once acquired.


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Significance of lipids in biological membranes...?
Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as there are also number of water insoluble polysaccharides like cellulose. These hydrophobic and water insoluble materials can also be used to build membranes but why not? Why lipids are only choice?

Membranes are built from a specific class of lipids, namely phospholipids, whose key property is that they are amphiphilic and so can self-organise to form bilayers. Not all amphiphiles do this, some prefer to adopt a micellar organisation. A bilayer composed of phospholipids produces the ideal combination of a hydrophobic barrier with a hydrophilic surface.
Although there are clearly amino acids with hydrophobic side chains, it is difficult to conceive of a proteinaceous barrier that would reproduce the properties of a phospholipid bilayer since it would not have a continuous hydrophobic phase.
Cellulose may be insoluble, but is full of polar groups so again would not create a hydrophobic barrier - I'm sure that ions can diffuse through a cellulose structure for example.
added later
@WYSIWYG raises an excellent point in the comments. Archeal membranes are composed of a different class of amphiphile in which the hydrocarbon tails (branched; derived from isoprenoids) are attached to glycerol by an ether linkage. It's instructive to note that the overall design principles are retained however, suggesting that the self-organising properties of these molecules was the key to the "invention" of biological membranes.

an addition.. archaeal membranes are not made of phospholipids but isoprenoids..


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Advantages of pain sensation?
The hazards of congenital insensitivity to pain (CIP) are well-known.
This question is about the obverse: what selective advantage, if any, does the normal sensation of pain confer? I'm thinking of severe pain such as that associated with back injury, burns, and some intestinal problems in which the pain seems to serve no function other than to incapacitate.
A related question is whether there is a spectrum of sensitivity to pain, ranging from CIP to heightened sensitivity, what the distribution looks like, and whether this is a genetically plastic trait (like color perception)? If the distribution were sensitive to selective pressure then naively I would guess it serves our needs well, but we spend a lot of our collective time trying to dial it back, hence my question.

Yes a range of pain exists. This can be seen probably in your friends who all probably have a completely different threshold for pain. When doctors ask patients to rate their pain it's usually to establish a baseline so after treatment we can see if there's a decrease. The different thresholds have so many factors from general health to receptors to brain activity to emotional state. You name it! Often just focussing on a pain makes it more painful.
It's definitely an unpleasant sensation pain but it's our way of our body saying "hey, you need to pay attention". Usually the response required is rest or to identify what might be there causing the pain. For example pain means we will withdraw very quickly from a hot surface. Doesn't even require the brain as it is a reflex arc which minimises the time we spend burning that part of our body. And as it continues to hurt we use the arm less letting it recover and protecting it from infection by doing so.
As these hazards of being cut, burnt, bit, knocked, fractured are very common there is a survival advantage to be the individual that is alerted to these hazards and take the necessary actions. Particularly in children where pain is necessary as it makes the baby know it needs to eat (or the mother) or that something isn't a good idea (putting hands on something hot).
However as you say there are times when the pain itself is more crippling than anything else and in that situation we have a problem. Childbirth, backache and in cancer or in tension headaches are just some examples. As being able to feel pain is pretty much required for a long life, the disadvantage of having pains like the above is less and doesn't outweigh the benefits. Pain is always going to be necessary. They also usually don't interfere with reproduction and so genes are passed on.

+1 but we could imagine a world in which a much higher threshold (lower sensitivity) was an advantage. You agree that there is a a range--do we know anything about the distribution? Has it been quantized? Does it change in response to selective pressures?

Don't think of the whole world's threshold changing, think smaller. Boxers and fighters are likely a population which represent those with a higher threshold as a selective pressure exists. I've seen a distribution curve somewhere, I don't know where though.

In terms of inflammation, the purpose of pain is to force the organism to rest the area that is inflamed. Thus promoting healing. In terms of chronic pain, this is the same thing. However I think that if the pain will not cease regardless of protection of the affected area, and say if the underlying cause of the pain is ultimately fatal, then the pain is subordinate. The phenotype is already being selected out.
I think the concept shows a lot of parallel to the underlying concept of hypersensitivity (allergy).
Remember that over generations as all different things that can cause and prevent pain in our bodies are evolving, So too is the pain mechanism itself evolving.


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Stomach Virus : How does it affect the bacteria of the intestines?
When you have a stomach virus and it causes extreme bowel movements to the point of almost pure stomach acid, does this kill off the bacteria in our intestinal tracks?

No, since the pH and the conditions are different in the different compartments (stomach, small intestine, colon) of the bowel.
See this figure (taken from this website) for the differences:

There are not that much bacteria in the stomach, so even even nothing else than acidic stuff comes out, the bacteria are not affected. And even when you have a severe diarrhea, there are still enough bacteria left to keep it colonized.

authors: Андрей Калиниченко


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Substitute 25mM dNTPs mix with 10mM dNTPs
I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, can I substitute 25mM dNTP mix with 10mM mix?
TECHNICAL DETAILS

$dATP: C_{10}H_{13}N_5O_{12}P_3Na_3 - MW=557.2$
$dCTP: C_9H_{13}N_3O_{13}P_3Na_3 - MW=533.1$
$dGTP: C_{10}H_{13}N_5O_{13}P_3Na_3-MW=573.2$
$dTTP: C_{10}H_{14}N_2O_{14}P_3Na_3-MW=548.1$

Would it be 50μL of 10mM dNTPs to substitute the 20μL of 25mM dNTPs?

Yes, you can do this. As long as the final mix has the proper concentrations of everything, its fine. Just make sure you compensate the by adding 30 uL (the extra volume) less of water to the master mix.


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How do ants spontaneously grow wings?
On hot summer nights we get flocks of ants that have grown wings (from what I know to migrate nests).
It appears the wings are not permanent, but are grown for a temporary purpose.
From what I know these events are triggered by climatic conditions (warm evenings).
In other species, wings seem like a really big deal and are grown from birth - wheras ants seem to just grow them 'on the spur of the moment'.
My question is How do ants spontaneously grow wings? Are they a spare layer of skin that is normally discarded and only comes into action when necessary?

See the Wikipedia entry for nuptual flight.
The ants that you see most often are (wingless) female workers. The winged ants that you see are male drones whose only role is to fly with young queens for mating. The drones follow a different developmental pathway, emerge from the pupa as winged ants, and then wait in the nest until conditions are right for the big event.


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building intelligent structure with random evolution requires series of non useful steps
In order to build an intelligent design such as a bridge or a mechanical watch, you need a series of non useful steps.
As far as I understand, in random evolution theory, the "intelligence" involved is the process of natural selection.
The problem with this is that natural selection requires that each step be advantageous right away. If I want to build a bridge, I need many steps which would be disadvantageous until the final product which would be advantageous. This would be like trying to write a computer program where each line of code must be advantageous to the program. An intelligent design just cannot be done like this.
How does modern biology deal with this problem? To say it all happened at once, is not possible since the probabilities against this are simply outside the capabilities of a random system. Furthermore even if by some freak monumental event it happened, it would need to happen again many times since there is a huge diversity of intelligent designs in life forms such as lungs in birds vs gills in fish, or sexless reproduction in bacteria versus male/female reproduction in animals (which are fundamentally different).
(Also, as side question has there been ANY experiment demonstrating that such a thing is even possible? I mean for example, to have a computer simulation of random self-replicating molecules, then having an intelligent human being picking out the best version and eliminating the others, then repeating, etc. until you have an intelligent design.)

The key idea you're missing is that evolution is not random. Read up on "selective pressure".

@MattDMo it is random in the sense that there is no intelligence involved. my question is that you cannot build an intelligent design like a mechanical clock without a series of non-advantageous steps. try writing a computer program where each line of code is advantageous to the program. it just doesn't work like that.

Unfortunately, evolution is not like writing a computer program, which has a very strict syntax, type checking, etc. Please read through the comments and answers to this recent question for a more in-depth discussion. This response in particular addresses the computer analogy. "Advantageous" is a tricky word. There are plenty of instances of DNA changes ("mutations" if you like) that may be negative in the short run, but prove protective otherwise. Sickle-cell anemia is one of those.

@user813801 There are already a great number of  answers online to debunk these standard naive intelligence design flaws. Have you had a look at them? It would probably be more helpful to you if you address your potential misunderstanding to these explanations rather than re-asking a question that has already been answered thousands of times.

You probably want to follow an introductory course to evolutionary biology such as the free online course by UC Berkeley Understanding Evolution.

What you say is true, but the answer as to how modern evolutionary theory understand this considers other ideas about living things which seem to allow so called 'neutral traits'.
Neutral traits being those phenotypes which seem to have no particular relationship to fitness. Toungue rolling is an often mentioned example.  Some folks argue that there is only adaptive changes and phenotype, others like Gould and Lewontin argue that some traits can be the result of pleiotropy.
So first of all this sort of discussion can tell us that the question is argued both ways in a convincing enough way that it is not resolved in biology - some argue quite confidently that all traits are selected for and things like flagellar motors and upright ambulation and eyeballs evolve because of and experiencing constant evolutionary pressure.  Others argue that these genes that produce these things are doing something else useful while they are becoming these later more useful traits.
The common twist here is plieotropy.  That the genes that are producing the phenotype one is observing is also participating in one or more other biological traits that may is being positively selected for.
A more interesting example of how this works is the domesticated silver fox experiment. Foxes which have had domestication bred into them (just to show that it can be done by selection) lose their red color and their ears are softer and fuzzier.  Nobody tried to select for these traits, but they come associated with each fox that is domesticated.  Are these traits plieotropic or only very tightly linked?  So far they have not been exhibited separately.  In any case I think its fair to say that the experiment didn't care about the color of the fox - only its meekness towards people.  These traits come along for the ride.
So it might be with any other desirable genetic trait.  If a gene becomes closer to producing a lung from a gill, if that gene is sticking around it must be because there is positive selection for that trait, even if the lung like gill is not particularly useful for that fish.
Sorry but I actually disagree that it is obvious that non-useful steps must be had for any such complicated trait.  If that were true then you would have a point, but not every biologist would give that to you.
It might be a bit surprising that such discussions are and continue to be matters of faith in science, but I hope you don't dismiss it because of this either.  All sciences do assume some things that make their view of the world make more sense.  But there are also other components of these theories which are consistently observed and understood that demand them... until they don't.
I don't give really any credence whatsoever when someone says 'this is a widely accepted theory by the scientific community'.  This in itself is not a scientific statement, but more the hope that someone else has one somewhere.  But a refutation must also take under consideration what is being refuted.

is there any evidence whatsoever that it is possible to build an intelligent design with this method such as a computer simulation as i wrote in the question. thanks

traits which arise spontaneously without natural selection cannot explain this, since that would be even worse since then there is no pseudo-intelligence involved. could also be that the foxes change spontaenously as part of their genetic code to adapt to the environment.

there is a lively conversation going on right here. http://biology.stackexchange.com/questions/16106/how-does-the-creative-process-of-biological-evolution-work/16108#16108   In my opinion none of this rules out intelligent design - but on the other hand I don't think one can prove there is a Maker by looking at evolution either.  that's been consistent with my life experience too...  :)

"This would be like trying to write a computer program where each line
  of code must be advantageous to the program. An intelligent design
  just cannot be done like this."

On the contrary, this is precisely how most successful programs are developed nowadays: using incremental test-driven design. You start off with a blank program and a test (typically "does it compile") which the blank program fails but which it can be made to pass by a trivial amendment (such as adding a function called "main"). With that success under your belt you move on to another test - e.g. "does it produce output", which might be satisfied by the addition of a "print 'dddagcahx'" statement.
Suppose we've decided that the purpose of our shiny new program is to take a year and tell us whether or not it is a leap year. Then our next four tests, expressed in the sort of language commonly used for such tests, might be

    Assert.That(Year.IsLeap(1996), Is.True);
    Assert.That(Year.IsLeap(1997), Is.False);
    Assert.That(Year.IsLeap(1900), Is.False);
    Assert.That(Year.IsLeap(2400), Is.True);

Now it might seem that the next step would involve a "big bang" conversion of our "print random nonsense" program into a fully fledged leap year calculator,  but in fact we can pass two of the new tests simply by always outputting "True" (or alternatively always outputting "False") regardless of what input we are given. So we change "print 'dddagcahx'" to "print 'True'" (or print "False") and already we're passing four out of six tests. Even a stopped clock is right twice a day.
And so on. Even the largest program can be developed incrementally in this manner. Every small addition to the program is "advantageous" in that it enables the program to pass tests which it previously failed.
It used to be that programs were not developed in this way. Back in the 80's, say, the prevailing philosophy was "Big Design Up Front". Not a line of code would be written until after months or even years of meticulous design had taken place. The big problem was that this typically didn't work. Millions would be spent on software projects which then had to be scrapped because of design flaws which only became apparent during implementation - or, worse, only when the program was in the hands of customers. This could have been averted if there had been a partially-functioning system at every stage of the development process.
So the message of software development is that an intelligent design CAN be done like this, i.e. incrementally and "where each line of code must be advantageous to the program"; and it is the alternative "it all happens at once" approach which is problematic for reasons which you yourself have pointed out.
(See e.g. exercism.io for an excellent hands-on introduction to test-driven development.)


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Do chickens always lay eggs?
http://de.wikipedia.org/wiki/Hühnerei says it takes up to 24 h for a chicken to produce an egg.
Is that dependent on the chickens nutrition, i.e., if it does not get enough food or the wrong kind, meaning it can survive on the food but it does not have everything to produce an egg?
Do we have data on this?

In short; yes. It depends on the breed (not all lay up to 1 egg/day), the age of the bird and on nutrition. High yielding breeds of chicken are e.g. dependent on supplements of calcium to be able to produce new shells rapidly (e.g. in the form of ground-up shells). Some information on the nutrient requirements of chicken can be found at Feeding the Laying Hen. Egg production will also fluctuate over the year, and will generally decrease e.g. during molting, since energy and nutrients are then diverted to the production of feathers (see info at e.g. The Poultry site).

Ok. That means they always lay eggs, it can take just a little longer sometimes depending on resources available to the chicken. I guess it might stop at some point, when they are really starved.

They will stop laying entirely if severely malnourished, but may also stop completely during molting.

every 24 hours they can lay an egg new young chickens that are for the first time laying eggs could possibly  but there is no breed that lays two eggs a day. and note it might be about a year for some to start so don't think if there not producing eggs there is something wrong, my chickens didn't lay eggs (note i have Plymouth Rock chickens) and they didn't lay until they were about a year. they may stop for molting or stop every here and there randomly and this is important to them laying eggs they need lots of calcium.

rockinboy3303 please use standard grammar while writing As and Qs. In Eng language sentences start with capital letters.


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Cloning a gene of an organism with an nonsequenced genome
What would be the best protocol to clone a gene about 5kb in size? The genome is not sequenced, but the gene itself very similar to orthologous genes of organisms with known sequences.

Do you want to clone the gene ( genomic DNA) or a copy of the mRNA (cDNA)?  (I imagine it's the latter.)

It's a hypothetical problem. If the gene is eukaryotic then the only possible course of action is to use mature mRNA (without introns) and reverse transcriptase to get cDNA, which can then be inserted into a vector. If the gene is of a prokaryotic organism, the only problem would be finding an adequate restriction enzyme?

How do you know that the gene itself is orthologous? This means that the cDNA sequence is available. So there should be no issue with designing primer for amplifying the cDNA (just that you may not be able to find out other possible targets)

I assume that we are talking about eukaryotic genomes which are split into introns and exons. Depending on what you want to do with your cloned gene, you need different strategies. The method is based on the assumption that the gene sequence has only very little differences to the known sequences of other organisms.
If you want to express your gene from a vector, you need to find the right processed mRNA which is then processed into cDNA and then cloned. Here two strategies are possible: If you have a gene, which is strongly expressed, you can design a primer primer (based on the orthologous sequences) which is anchored in the poly-A tail and has a gene specific seuqence next to it. With this it should be possible to amplify your gene specifically and isolate it. If the gene is not strongly expressed (the resulting amount of cDNA would be very small, since there is no amplification involved), I would opt for making cDNA from total mRNA (use anchored polyA primers) and then amplify the sequence from the cDNA pool with two primers (again based on the orthologous sequences) to amplify the gene sequence. I would go for TA-cloning here, since you do not know, which restriction enzyme recognition sites are present on your gene.
When you need the complete sequence containing introns and exons, there are two possible strategies. First you can use primers to amplify the gene and subsequently clone it. Then it is possible (and this is probably what I would do) to use a set of primers which bind to the end of the gene (and also the reverse strand) to amplify the sequences at the end and then sequence these PCR products. This gives you the exact sequences at the 5' and 3' end of the gene and allows you to include possible regulatory sites, since you then can design exactly matching primers for this region. Again, I would go for TA cloning.
And finally you could start by sequencing the whole region based on homologous sequence primers first and then with primers designed on the newly analyzed sequences. This is the most exact way, but is also costly and takes some time (since you need to make new primers after each round of sequencing until you are done).


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Nervous system: Pain and Pleasure?
If you have a constant pain in your body, why does a greater pain or pleasure make you not feel the original pain?

This question is way too generic as it stands. I suggest asking about a specific situation as an example.

I'm not sure if why is referring to the biological basis or the reasoning for why it is beneficial but I've briefly summarised both. If you'd like more detail just accept and ask again clarifying your exact interest in this broad question.
Pain is taken up through the spinothalamic pathway but at may opportunities it may be blocked. It may be blocked by other ascending pathways or by descending pathways. There are a number of structures involved in this including endorphins and Interneurones which are part of the gate control theory of pain. Basically ascending sensory information is blocked when other sensory information is more acute or more pertinent. This is important for survival e.g. when feeling a lion it is important not to feel pain. That same endorphin pathway is highjacked by drugs such as morphine.


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Nervous system : Nerve signals
If the electrical signals from all the various organs throughout the body eventually connect to the nerves in the spinal column traveling up to the brain, how does the brain differentiate the different signals.  Is the nerve in the spinal column like an electrical conduit with many wires inside?

Yes is the simple answer. A nerve will go up to a specific part of the brain which the brain knows corresponds to a certain region of the body. It isn't perfect though e.g. pain in the diaphragm confuses the brain which doesn't recognise that pain must be coming from there so instead tells the body there is shoulder pain, however this is useful in medicine. Another infamous example is pain from heart disease (angina) which causes pain in the jaw and arm. Perhaps even more interestingly, if a nerve is cut and then grows back linking to the wrong nerve it may lead to the completely wrong part of the body being identified when touched. Also if the brain itself is stimulated in these corresponding areas, a person will feel he or she is indeed being touched in a certain part of the body.

Would you have any references for the wrong innervation?

authors: حسين الاعرجي


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Nervous System : Signal Translation
If a device were created to monitor the nervous  signals from the heart, including stable heartbeats, rapid heartbeats, etc., and this device were capable of transmitting the "stable heartbeat" to the heart, would this have any adverse or advantagious effects for medical science?

Measuring the electrical signals (=nerve signals) from the heart is frequently done in medicine, it is called electrocardiography. It looks like this (from the same article):

Influencing the heartbear can also be done and is done by pacemakers. Depending on the patients necessities the can permanently stimulate the heart or do this only, when certain criteria are met which makes an intervention necessary to prevent cardiac arrest. Wrong stimulation can in fact kill people, since they go into cardiac arrest when the stimulation of the heart is not correct. This is why pacemaker patients have to stay away from strong magnetic fields which make their pacemakers fail and leave them without proper stimulation.
This technique of influencing the heart from outside is used by defibrillators, which use an electric shock to influence the heart beat. It is used for treating cardiac dysrhythmias, ventricular fibrillation and pulseless ventricular tachycardia, which all lead to death if left untreated. A special form are automated external defibrillators, which measure the an electrocardiogram and then decide by the form of it, if an electric shock is needed.

maybe add something about AEDs which can perform ECGs and advise on shocks or perform automatically ?

Good point, I have extended the answer.


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Nervous System : Organ or Gland Failure
If an organ was to start failing, not total failure, such as the thyroid gland, is it possible that the fault may not lie in the failure of the organ but in the nerve signals coming from the brain?

I'm in an inquisitive mood today.  Sorry. :)

In many hormonrs, the hypothalamus produces a hormone which acts on the pituitary gland which subsequently acts on an end organ. Taking your example of the thyroid gland let's take a look at it.
The hypothalamus produces TRH which acts on the anterior pituitary causing it to release TSH which in turn stimulates the thyroid gland to make thyroid hormones T3 and T4.
Abnormal levels of thyroid hormone may be caused by problems in any one of the three stages. Problems on the end organ are termed primary, in the pituitary gland are termed secondary and in the hypothalamus tertiary.
For simplicity let's look at abnormally high levels of thyroid hormones called hyperthyroidism. In a patient with a primary or thyroid gland problem we expect high levels of thyroid hormones but low levels of TSH. The pituitary gland is trying its best to tell the thyroid gland, "No more!" but it won't listen. In secondary or pituitary disease, the pituitary gland is the bully pushing the thyroid gland to make lots of thyroid hormone by over production of TSH. Usually there are other hormone disturbances too in this case as the pituitary gland has a range of hormones it secretes. Also the swollen pituitary gland puts pressure on the nerves carrying vision leading to visual loss (specifically in the temporal fields). In this case the hypothalamus will be secreting low levels of TRH (which isn't routinely measured) trying to get the pituitary gland to stop acting out. The rarest situation is when the hypothalamus has the problem where every hormone is increased. However again this will be causes by something or the other detectable usually on imaging.
So the short answer is yes, but there will be other features. Primary or end organ dysfunction is most common and will cause characteristic findings in blood tests and examination (e.g. swollen thyroid gland) but secondary and tertiary disease can be figured out when other features are found in association.

Hypothalamic/pituitary control of glands is still endocrine. Do you know of a nervous control of an endocrine gland ? (I know examples nervous control of exocrine glands but not endocrine glands; perhaps because nervous control is fast and shortlived whereas endocrine control is longlasting but slow)

Yes. All the above is the actions of the anterior pituitary gland. The posterior pituitary comprises of axons projecting from the hypothalamus which release vesicles full of hormones from neurones themselves. Then the adrenaline release system could qualify. Apart from hormones being slow they also have more widespread effects then nervous control. Perhaps that's why oxytocin and ADH are controlled in this way?

@WYSIWYG Adrenal Medulla?

@AndroidPenguin.. yeah i forgot the pituitary..

@RoryM.. yes i was thinking about adrenaline.. Confirms that nervous control is for quick responses

Pancreatic islets also have vagal innervations, though arguably the nervous control is not the primary control mechanism, the PNS/SNS certainly can exert extensive control over them.


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Real time PCR normalization algorithm
When performing normalization of real time PCR results, I found two ways of doing it:

In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.
On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.

The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve.
Which is correct?

For those who are not satisfied with $2^{\Delta(\Delta Ct)}$ and want to incorporate different efficiencies of the target and normalizer PCR reactions, would this formula work to calculate arbitrary values for relative expression:
$$\frac{\mbox{Efficiency}{target}^{-(Ct{\text{target}})}}{\mbox{Efficiency}{normalizer}^{-(Ct{\text{normalizer}})}}$$
I have compared the results with that of the RTPCR instrument's own software using calibrators from a pool of tested samples, and they fit almost perfectly. But is the equation valid in a theoretical sense?

First step is the calculation of efficiency, denoted by lets say $E_{gene}$. See this post for calculation of primer efficiency.
So the fold change for that gene will be calculated by $E_{gene}^{-\Delta Ct_{gene}}$
Where:
$\Delta Ct  = Ct^{treated} -Ct^{control}$
But these Ct values are not normalized. For normalization, you take some reference gene which need not be a housekeeping gene. Reference gene should chosen such that it is not affected by the treatment. In some cases usual housekeeping genes can also get affected for e.g. in treatments affecting cell cycle or differentiation. In such cases you should use a spike-in (an artificial RNA bearing low resemblance with any known gene).
You can either normalize the fold change (Case A) or find fold change of the normalized expression (Case B).
Means the same mathematically.
Case A:
$E_{gene}^{-\Delta Ct_{gene}} / E_{ref}^{-\Delta Ct_{ref}}$
Case B:
$\large\frac{[E_{gene}^{-Ct^{treated}_{gene}}]/[E_{ref}^{-Ct^{treated}_{ref}}]} {[E_{gene}^{-Ct^{control}_{gene}}]/[E_{ref}^{-Ct^{control}_{ref}}]}$
You can rearrange the numerator and denominator to get Case A from Case B. I'm not sure how you are ending up getting different values. Recheck once. It may be because of numerical approximation errors.
Case A looks much neater; so it is best to calculate that way :)

sorry for the trouble but mistook on the query, my point 1 is edited

Answer still holds :)
Case B is what your lab people follow (point 1) and Case A is the point 2 of your question

Note: you cannot club the fractions in the numerator together to obtain the $point\ 1$ sort of form because the bases are not same ($E_{gene} \ vs \ \ E_{ref}$). It can only be done if the efficiencies are the same.

This topic could probably have it's own StackExchange, there is so much info and trial and error done with rtPCR. Here's my 2 cents:
Your adjusted calculation does not normalize your data, it just subtracts the 'background' or control. For expression studies this is not good enough. Normalizing data for gene expression must involve setting it to a scale of another gene whose expression should be not only present but consistent between your treated and untreated samples. House keeping genes (you are probably using GAPDH) make good candidates for this because their expression rarely changes. If you don't normalize than you don't know if your your expression is actually changing, or if it's simply due to a larger input of mRNA. However it must be shown that the housekeeping gene's expression is also not changing, this is usually accomplished using a different sample set. Take if from me, I've done a lot of this and this step is one of the most important in your experiment. Any reviewer who knows what he's doing will reject a paper using rtPCR without the proper statistics.
I have had a lot of success using Applied Biosystems StepOne software to provide you with accurate Ct values. Generating the variable is complication, use software to do it right every time:
http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042380.pdf
What method/system are you using?

There have been several instances in which GAPDH is not suitable as a reference gene.

SYB GReen and roche, about normalizing no clue really


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Does DNA influence death (e.g. by cell aging)
I know that we age because of errors in the cell replication process and these errors eventually leads to death.
If we exclude environmental factors, are there any other factors that can cause these errors? Is there for instance some kind of "programming" in our DNA of our death?

Perhaps the best type of study to examine the role of genes (DNA) in human aging are twin studies.  They have either: the same DNA (monozygotic, one egg, "identical" twins (MZ) ) or similar DNA (dizygotic twins, two eggs (DZ) ) and are perhaps exposed the same, or different environments.   I won't repeat the information in the link, above, but studies of this type guide that our DNA is not an absolute roadmap of our future.
DNA damage can be caused by exposure to excessive radiation, viruses, chemicals and just 'random events'.  Cells and tissues can also be damaged by oxidative damage - literally oxygen and related molecules that are produced within the body and can react with components of cells (e.g DNA, proteins and the lipid cell membrane).   The accumulation of these oxidized products in and around the cell disrupts tissue function and leads to many of the symptoms of aging, a process called sensescence.
We obviously cannot avoid having oxygen around us.  In the same way, our cells need the sugar glucose as a source of energy. Glucose can spontaneously react with proteins and lipids to form advanced glycation endproducts (AGEs).
 AGEs are pro-inflammatory.  In diabetes, where blood glucose levels may remain at higher than normal for extended periods, the formation of AGEs can lead to nerve and kidney damage.   The chemical reaction that is occurring is the same as when you toast a piece of bread or fry a steak.  So paradoxically, two of the ingredients essential for life - oxygen and glucose - are slowly but surely disrupting our body's function over the course of decades.   Although the body can replace some of these damaged proteins, they accumulate over time, as evidenced by the increasing lack of elasticity of older skin as collagen proteins are cross-linked.
Regular exercise, good diet and friendships all add to mental and physical health, quality of life and longevity.  So, to live a long time, don't stress, have ONE slice of cake and make new friends who will exercise with you.

Obviously, it is conceivable that DNA could be so damaged that the organism dies. Trivially, blasting cells with radiation will cause rampant DNA damage, which will trigger p53 and lead to the cells suiciding (apoptosis), this is a "deliberate" (so to speak) mechanism to manage cancer risk.
In practice, the reason DNA damage leads to death is usually not because the information is corrupted and important functions are abrogated, but because the mutations lead to cancer, and the cancer leads to death.
However, most people don't die of cancer. A lot do, especially in developed countries, but most often people die because of infection or heart failure. Other major causes include neurodegenerative disease (neurons dying) and diabetes.
If you are asking whether in some part of the DNA, there is a bit saying Maximum_Age = 85 (by analogy to programming constants), I don't think anything of the sort has been found. The body naturally has finite lifespan because things break, this is extended up to a point because the body also has mechanisms to repair some kinds of damage.
Why not repair all kinds of damage? Why are the repair processes imperfect, and cannot maintain the organism indefinitely? Good questions, without good answers known to science.

It is important for organisms to be renewed. These organisms have less wear and tear, they are modified through evolution to better fit the current environment, they are more likely to have healthy offspring that they can look after. It must also be considered that genetically we must be optimal in anyway that confers our continued survival as a species. So we should remain alive only for as long as it benefits the species (i.e. raising our young) and die once we are less help and more burden.
So with all that in mind, why do errors or mutations occur? Well we need optimal amount of mutations that allow us to constantly evolve to adapt to the newest environment. If we don't evolve, we die. Keeping our DNA mutation free is too costly anyway for it to confer a survival benefit of the species (rather than the individual). It would require far too many error checking pathways which themselves would be in need of being checked. So yes our cells have programming to allow mutations (by not having completely successful countering techniques) as it is beneficial.
Our cells themselves can only replicate so many times due to the length of telomeres. These are little bits of DNA at the end which after each cycle shorten (as we can't replicate DNA at the end efficiently). After a certain amount of replications a cell is destined to die. An enzyme exists, telomerase, which resets this by lengthening the telomeres. However over expression of this enzyme leads to cancer. Again, it is important for us to mutate in order to evolve but too much is harmful. The same argument applying that it is too costly to be perfect and not mutate.
Logic dictates that if humans survived for much longer, over population would impact on our own survival.

This is the answer that is the most adressing my question. I see that DNA controls cell replication, but allows in its own code mutation. But in the end the bad replication of the edges of the DNA is more an efficiency that something "coded to make us die".


text:
Role of Melatonin in Circadian Rhythm
Melatonin regulates the wake-sleep cycle by causing drowsiness and lowering body temperature, but which specific chemical pathways lead to this drowsiness?

This is a quite complicated question, as melatonin has quite a range of effects on the cells. First, melatonin binds to three different melatonin receptors, which are found in a wide variety of tissues or organs including brain and retina, cardiovascular system, liver and gallbladder, intestine, kidney, immune cells, adipocytes, prostate and breast epithelial cells, ovary/granulosa cells, myometrium, and skin.
Two of the receptors a G-protein coupled receptors (GPCR), the MT1 and MT2 receptors. The third is a quinone reductase called QR2.
For more details, see this papers:

Melatonin receptors in humans: biological role and clinical
relevance.
Melatonin receptors and their regulation: biochemical and structural
mechanisms.

The role of melatonin is pretty broad, see the figure (from this article:"Melatonin: Nature's most versatile biological signal?")

The receptors transport the outside chemical signal (the melatonin) to the inside and activate (or repress) a number of different signal transduction pathways. See the figure below (taken from Qiagen):

This includes MAP-Kinase pathways, proteinkinase C, IP3, adenyl cyclase and so on. This is quite complicated and I recommend reading some of the following articles if you are interested in a deeper insight. Finally these signals are transmitted into the nucleus and result in a changed gene regulation/expression.

Melatonin receptors, heterodimerization, signal transduction and
binding sites: what's new?
Physiological effects of melatonin: role of melatonin receptors and
signal transduction pathways.

The second picture is beautiful !

From wikipedia article on melatonin receptors (with some modifications) :

In mammals, melatonin receptors, which are G protein coupled receptors, are found in the brain and some
  peripheral organs. However, there is considerable variation in the
  density and location of MT receptor expression between species.
MT1
In humans, The MT1 subtype is expressed in the pars tuberalis of the
  pituitary gland and the suprachiasmatic nuclei of the
  hypothalamus....This is indicative of its role in circadian and
  reproductive function.
MT2
The MT2 subtype is expressed in the retina. MT2 receptor mRNA has not
  been detected by in situ hybridization in the rat suprachiasmatic
  nucleo or pars tubealis. This receptor may have a role in light
  dependent functions.

I know this does not tell about the pathway but I suggest you try searching some of the papers cited at the end of the wikipedia article.

Oh, I completely missed this topic. It is interesting and I will have a look into thi later this evening.


text:
People say the cardiac cycle depends on blood pressure? How so?
I know what the cardiac cycle is. There are two phases diastole and systole. One is the relaxed, and the other is the contracted form of the heart. The diastole is where blood is pumped to the ventricles and systole is when blood goes to the aorta, and lungs. But what is the connection to blood pressure?

In the title, by heart pressure do you mean blood pressure ?

yes, blood pressure

"People say..." - What people? Who? https://en.wikipedia.org/wiki/Weasel_word

There are two levels to take your question at.  The first is simpler but I'm not sure if it is what you are looking for:
If you imagine the heart and all the blood vessels in your body as a closed plumbing system with no leaks (not entirely accurate) then when the heart contracts and squeezes the blood from the ventricles the total surface area the blood is pushing against has decreased - there is more blood in a smaller space.  This means that the pressure on the arteries from the blood has to increase when the heart contracts - in systole blood pressure is much higher than in diastole.
The second level is a little more in depth:
Cardiac output (a measure of how much blood is being pumped around the body to the organs where it is needed) is defined as the product of stroke volume and heart rate.
$$CO = SV \times HR$$

Heart rate is the number of times the heart beats per unit time
Stroke volume is the amount of blood that is pumped out of the heart in one beat. It is this that is related to blood pressure.

The relation of stroke volume to blood pressure is defined by Starling's Law.  This states that the more blood that is in the heart, the more its walls are stretched.  The more the walls are stretched, the harder the heart contracts in response.  This increases blood pressure as again more blood is displaced from the heart.


text:
In what ways can mechanisms of apoptosis be damaged?
How many ways can an Apoptosis mechanism be made disfunctional or irreparably damaged? If a cell has damaged Apoptosis mechanisms and it divides will its daughter cells have such damage?

Most of us have had the apoptotic process in our B-lymphocytes disrupted when we had infectious mononucleosis, caused by the EBV virus.  The EBV virus (pardon the virus-virus) encodes proteins, including one that mimics a host cell protein, Bcl-2, which plays an important role in apoptosis.  The set of virus 'decoy' proteins  forces the infected cell to survive and be a host to produce new virus, whereas the cell's normal response would be to apoptose.
Wart viruses such as HPV may have similar mechanisms.
So in summary, excessive growth or transformation to an immortal cell typically requires activation of mechanisms that promote cell growth and the inibition of mechanisms that promote cell death.  "Transforming viruses' often have mechanisms to affect both cell growth and cell death.
This answer isn't to the question 'how many ways can [the] apoptosis mechanism [..] be damaged ', but answers 'what's a common way that apoptosis pathways can be disrupted'.... large DNA transforming viruses.

Could a transfoming virus exist that could turn on apoptosis mechanisms? You could say all cells have self-destuction mechanisms(if I'm correct) , could a cancer cell with its excessive growth still have one type of 'self-destuction'mechanism 'left-over', or could daughter cancer cells have a self-destruct ability that is presently inactive?

@user128932. Could..possibly, although it would seem to be at odds with promoting growth.  Yes, there are at least 2 other cell death pathways that could act if apoptosis is disrupted, but they may share common pathways and may also be disrupted.  Will be cell type dependant.  Daughter cells would have the same phenotype as the parent cell if they: share the same mutations (see AndroidPenguin answer), share epigenetic modifications that alter apoptotic gene expression or the virus genome (and proteins) persists.

Do stem cells have apoptosis mechanisms? Could a stem cell having a 'self-destruction' mechanism repair the cell-death pathways in a cancer cell?

@user128932  I suggest you ask that as a separate question.

Lot's of ways. Apoptosis is complex, but falls under two pathways ending up at caspase 3. Anywhere in the pathway may there be a problem but also in things that trigger the pathway. For example in cancer there is loss of tumour suppressors which ensure a damaged cell undergoes apoptosis or prevents replication and oncogenes which allow controlled replication. Damage to these genes allows a cell to divide in the absence of signals to divide and also forget to check that it's DNA isn't damaged before replicating. This is then passed on to the daughter cancer cells. As each check is removed the cell permits more and more mutations meaning more and more likelihood for the next mutation to occur. Cancer is caused literally by one cell having defects and every daughter cell also possess the defects. Those that have defects which accidentally kill the cell are selected out.


text:
Brainbow fluorescence labeling technique
I have this picture describing the Brainbow system here:

The paper I am reading says it uses Cre-lox recombination to express a certain color. If the cell in question was expressing a yellow fluorescence then what would the construct in that cell look like in terms of the picture given? Would it just be a single line with the UAS, EGFP, and mKO2 in that order or would it be two lines, wone with the UAS and EGFP and on with the UAS and mKO2?

I would suggest to also read the original Brainbow paper by Livet and colleagues, which goes in details in the genetics of the system and its variations. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system - Livet et al., Nature 2007

Yellow would need the expression of red and green so that would mean the excision of the blue fluorophore. It would be one line with egfp and the other line with mKO2--- the order doesn't matter-- these represent chromosomes.

In the line expressing green wouldn't you have to excise the blue and red regions as well in stead of just the blue? Similarly for the line expressing red wouldn't you have to excise the green and blue regions? And also what about the STOP cassette?


text:
Additive genetic variance with $n$ alleles
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:
$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$
, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by
$$\sigma_D^2 = x^2(1-x)^2(2\cdot W_{12} - W_{11} - W_{22})^2$$
$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$
, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.
Question
The above definition makes sense for one bi-allelic locus.

How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for a locus that have $n$ alleles?

Here is a related question

this might be a useful resource for you @Remi.b - I'll read the Falconer and Mackay book tomorrow at work too http://nitro.biosci.arizona.edu/zbook/NewVolume_2/newvol2.html

really like this question, spent some time at the whiteboard today trying to work it out! made good progress!

Chapter 4 of lynch and Walsh seems to deal with this - from around table 4.2

@GriffinEvo At which page is it? I could find table 4.1 at page 11 and table 4.3 at page 22! table 4.2 is probably in between :D

In my copy it is page ~77, I think you should see equation 4.23a and some of the preceeding section on "average excess" - this is Lynch and Walsh Genetics and analysis of quantitative traits. I'm away for the next couple of days but will be trying to write this in an R code with data to test it out next week - perhaps we should move to the chat room to discuss more!

Well, the total genetic variance is just, by the definition of the variance,
$$
\sigma^2 =\sum_{i,j} f_i f_j (w_{ij}-\bar{w})^2
$$
(using $f_i$ and $w_{ij}$ for frequency and fitness, respectively), and
$$\bar{w} = \sum_{i,j} f_i f_j w_{ij}$$ is just the average fitness.
You can calculate the additive genetic variance for different loci by simply assuming that there is no dominance effect, i.e. the alleles are independent. If it helps, think of it as a quantitative trait in a haploid organism. Thus,
$$
\sigma^2_A =\sum_{i,j} f_i f_j (w_iw_j-\bar{w}')^2 = \sum_i f_i(w_i-\bar{w}')^2.
$$
with
$$
f_i=\sum_jf_{ij};  w_i=\sum_j f_{ij}w_{ij}; \bar{w}' = \sum_i f_i w_i;
$$

Thanks a lot for your answer. Could you please help me to develop the formula for $\sigma_A^2$ for a diploid population?

this should be true for a diploid population. The additive genetic variance is defined as the variance in a population where there are no interaction effects between genotypes, so $w_{ij}$ can be written as $w_iw_j$

I'm sorry I might be a bit slow to understand :)… Can you please show the development to find back $\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$ from your equations? Thank you.


text:
Additive genetic variance with $n$ loci
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:
$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$
, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by
$$\sigma_D^2 = x^2(1-x)^2(2 \cdot W_{12} - W_{11} - W_{22})^2$$
$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$
, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.
Question
The above definition makes sense for one bi-allelic locus only.

How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for $n$ bi-allelic loci? Is it:

$$\sigma^2 = \sum_{i=1}^n \sigma_i^2$$ $$\sigma_A^2= \sum_{i=1}^n \sigma_{Ai}^2$$ $$\sigma_D^2  = \sum_{i=1}^n \sigma_{Di}^2$$
Here is a related question

Not in general -- there can be linkage disequilibrium among the loci. For instance, say that there are two di-allelic loci, $A/a$ and $B/b$, and that the frequencies of the $A$ and $B$ alleles are both $1/2$ and that they have the same effect on the trait, with no dominance. If all haplotypes in the population are either $Ab$ or $aB$ (with no $AB$ or $ab$ haplotypes), then the genetic variance at each locus is high, but the total genetic variance for the trait is 0!

Thanks for your answer. Yes that totally makes sense. So the formula would be
$$\sum_{i=1}^{n} \left( \sigma_i \frac{\sum_{j=1}^{n} 1-\text{cor}(i,j)}{n} \right)$$
, where $\text{cor}(i,j)$ is the correlation between the two loci... or something like that…?


text:
Dominance/recessivity of new mutations
What is the distribution/probability density function (PDF) of recessivity/dominance of new mutations?

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution.
Here is a related question

Please provide a basic schematic/equation for a possible underlying model to narrow the question down.

I don't really expect insights some theoretical models but from empirical data. I would not refuse some links or answer that predict this PDF from Fisher's or Wrights models of dominance though.

it is not easy to ascertain if a mutation will be dominant or recessive without the knowledge about the concerned gene and its structure-function relationship.

I don't believe you can produce a general function for this. It will depend on the exact gene and organism you are considering.
From a molecular point of view, the vast majority of recessive mutations result from a change producing either a non-functional protein product or a truncated product that is cleaned up by the cell. We can reasonably assume that most modifications significant enough to produce a phenotype will be of this class since there are more mutational sites which can produce a non-functioning product than can produce a product of changed function but the exact ratio of one to the other is not going to be equal across different genes and organisms.
Note as well that the whole notion of recessive and dominant traits is probably an over-simplification and, in fact, there are subtle differences between homozygotes and heterozygotes in many, perhaps most, cases so I'm not sure how useful an estimate would be even if you had one.


text:
Effect on fitness of mutations
What is the distribution/probability density function (PDF) of impacts on fitness of new mutations?

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: "If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$" are also welcome.
When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.
Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.
Here is a related question
Here is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.

the PDF should be a conditional one.

also your question is quite broad and needs rational modeling for a reasonably accurate answer.

@WYSIWYG The PDF should be conditional on what? On the species. Yes obviously. But any information would be welcome. I re-edited my question to make clear what I understand by mutation. I don't feel my question is too broad. Please let me know if you can think of a way of how I could narrow down my question.

you can narrow down by perhaps assuming a hypothetical statistical model

To a good first approximation $\overline{\Delta f} = 0$. Where $\overline{\Delta f}$ is the mean change in fitness down to any point or indel mutation. The reasons for this are as follows:

In the genome of higher organisms, most of the genome is non-functional ("junk") so most mutations will not have any effect regardless of the change made.
A substantial proportion of in-frame point mutations will be synonymous mutations that result in the same amino acid being coded for (actually this can have an effect on protein expression but I don't believe anyone has - yet - shown a fitness difference?)
Even where a mutation does alter an amino acid many amino acid changes have no measurable effect on the protein produced. Especially where the new amino acid has similar properties to the one it has replaced.
Even when a mutation does alter the protein function, or render the product non-functional, in many cases this will not impact fitness since fitness is conditional on the environment in which it is measured and not all genes impact all environments.

So the distribution, whatever it is, will have a large spike at 0. Probably this spike is several orders of magnitude higher than the next highest value. Further, we can be reasonably certain that $\overline{\Delta f} < 0$ since there are more possible ways to break a Gene through a point or indel mutation than there are to improve it. If this is the case, so that there is a large excess of mutations with a negative effect on fitness, we can conclude that the distribution of mutational changes in fitness will be non-normal (negative skew and spike at zero), and that the normal distribution will be a poor approximation.

I like your reasoning, but dont understand what you mean with the last sentence.

Reminds me of Pareto optimization. But effect of each mutation on a gene still has to be sampled.

@fileunderwater: If it's left skewed and has a central spike at an exact value it therefore will be poorly approximated by any take on the normal distribution.

@JackAidley Gotcha. Suggested clarification.

Take a look at this paper. This talks of a concept similar to Jack Aidley's approach.

[This is purely speculative]
Assumptions:

impact on fitness is measured by survival chance
impact is because of protein coding genes

Probability of a mutation at position $i$
$P(m=i\ |\ g)$
where $g$ is the genome with its annotations.
Probability that activity of some protein changes by X-fold given mutation at $i^{th}$  position(s) in the genome:
$\sum\limits_{i}\sum\limits_{gene} P(a_{gene}= X\ |\ m=i)$
sum over all genes that occupy that locus.
Probability that on a given selection pressure $S$ and protein activity change $X$, the individual survives the selection.
$\sum\limits_{i}\sum\limits_{gene}P(1\ |\ a_{gene}=X,S)$
I am not an expert at Bayesian modeling. But I guess this is one way to go about obtaining the PDF. Each step has to be expanded and combined to get an equation for PDF.
I am not sure if this is of any help at all.

Thanks a lot for your answer. While it is probably interesting I have to confess that I don't understand everything. I don't really understand why defining a locus as a long enough sequence so that it occupies several genes. I don't think it really addresses the question. If $S$ is the random variable of effect that a mutation has, I am asking about the distribution of $S$: $P(S=s)$. Or as you stated, that might under some assumptions, correspond to $P(a_{gene} = x | m=i)$ but there is no need to sum over all mutations in the genome. I am not asking about the effect of the sum of all mutations

I don't think a purely theoretical model might give much insights (or only a model considering the complex network of protein interactions) but I could be wrong.

By several genes I meant splice variants that occupy the same genomic locus. Only by considering all the positions in the genome will we be able to obtain a PDF. And in this case the effect of a mutation is denoted by the random variable $X$, whereas $S$ is the exerted selection pressure.
I totally agree that a purely theoretical model wont give much insights. In this case the prior probabilities have to be calculated from experimental observations. But with a model we can make better predictions.


text:
Property of E.coli harboring F element
From Genetics by Ursula Goodenough

E.coli harboring an F element are endowed with a number of phenotypic
  traits :
1.They are sensitive to infection by ssRNA phages and certain ssDNA phages.
2.They resist the growth of female specific phages as T3 and T7.

What is the molecular mechanism behind this sensitivity and resistance ?

Some bacteriophages adsorb on the pili. So the individuals carrying the F-element will be susceptible to these.
F-plasmid encoded membrane protein PifA is responsible for the T7 resistance [See here]. The exact mechanism is not known

If you see the list of references in the textbook chapter you will be able to trace the reference for a certain quoted fact


text:
How do Gram + bacteria use a proton gradient for F-type ATPase?
Does anyone know of any papers showing how Gram positive Fermiculates or Actinobacteria use  a H+ gradient for an F-type ATPase, It seems impossible since there is no outer LPS membrane to maintain the protons in a periplasmic space. Is the use of ATPase for production of ATP exclusively a Gram negative thing?
I found this question "Production of ATP in Lactobacilli" but no answers:
https://biology.stackexchange.com/questions/14669/production-of-atp-in-lactobacilli

Don't have an answer, but it seems to me that given that the Gram negative outer membrane is stuffed full of porins, there is no barrier to proton loss in this case either.

@AlanBoyd Are porins permeable to hydronium ions as well as water?

found this on wiki: This cation is often used to represent the nature of the proton in aqueous solution, where the proton is highly solvated (bound to a solvent). The reality is far more complicated, as a proton is bound to several molecules of water, such that other descriptions such as H5O2+, H7O3+ and H9O4+ are increasingly accurate descriptions of the environment of a proton in water

Protons are pumped out of the bacterial cell by the electron tansport chain. This creates a protonmotive force with two components, one due to the difference in proton concentration, the other due to the membrane potential that is created. In bacteria and mitochondria it is the membrane potential component that provides most of the driving force to pull protons back in through the ATP synthase. Thus the fate of the protons outside the cell doesn't matter too much. Even if you were to buffer the exterior absolutely, the fact that charge had moved out would drive ATP synthesis.

"the fact that charge had moved out would drive ATP synthesis."
this is only true if the protons are going down a concentration gradient, if they work against the gradient ATP is being used not synthesized...

unless there is chlorophyl involved (ex. chlorophyl G in Heliobacteria) and then there's some oxidoredux work dunno by which electron carrier...

but what if a bunch of fermiculates are in a small space and the fluid isn't buffered, it could work as a community...

In response to your first comment, protons would move up a proton concentration gradient if the membrane potential was favourable, until the chemical and electrical potentials were balanced.

do you know of a good review article on electric gradients causing a substance to move against a chemical gradient in a biological context?