text:
Why do not I have spot in my SDS-PAGE?
I do a 2-dimensional electrophoresis for a human tissue. My steps were as below:

Whole protein extraction from 4 samples
Protein concentration

Save samples in -20 Frizzier for 3 days

IPG rehydration with 450 micrograms of protein for 18 hour
Isoelectric focusing by Ettan IPGphor3 system (GE Healthcare)
Save IPGs in -20 frizzier for 3 days
SDS PAGE with GE healthcare system on 25 cm Acrylamide/bisacrylamide gels (12%) and ladder input

At the beginning of the SDS PAGE, we had to stop the running several times because of leakage from the upper buffer to the down buffer. Finally, blocking all seams, we successfully ran the SDS PAGE for about 1.5 hours after sitting IPGs on 12% gels.
Problem: Unfortunately after overnight staining by CBB R250 we found no protein spot; however, some smears appeared in the gels.
I want to know why I did not have protein spots in my gels.

You'd need to provide quite a bit more information for us to work out where the problem is - the first thing would be to find out whether your protein samples are degraded or not and the way to do that is to look to see if they migrate in a conventional SDS-PAGE 1-D system.

As I mentioned, The ladder was also smeared in gel. Today, I performed an SDS-PAGE on my protein sample solved in the rehydration buffer. During the SDS-PAGE, I found that the samples moved backward into the upper buffer instead of into the gel. The electrodes were connected correctly. I do not have any idea about this phenomenon.

@mojtabazare IMHO, I would start with the current setup as is and use a common protein of known charge to confirm it was not a machine problem. If the machine is correct, it is likely something with the protein, buffer, or gel.

@Young Jun Lee, The machine works correctly. I want to know which fault made my bad result?!

@mojtabazare I think then, bob1's hypothesis regarding protein sample degradation might be worth considering.

@mojtabazare You didn't mention the ladder was smeared - you mentioned "some smears on gels" but nothing else about smearing that I can see. -20 might not be cold enough to store these proteins. What buffer?, what concentration of protease inhibitors? What were the samples from, incl. which tissue? How did you extract (sonication, homogenization)? All are relevant. You need a lot more details edited into the question to be able to answer.


text:
How can I avoid digesting protein-bound DNA?
I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion.
When digesting protein-bound DNA, is all of the unbound DNA digested? Is there a way to maximize the amount of unbound DNA that is digested?

Well, it depends if you just want to sequence your protein bound fragments.
If that is the case, I suppose you could go for a FAIRE-seq.
Basically, you perform several iterative phenol/chlo extractions, thus separating the bound and unbound fragments.
Then you sequence the unbound fragments that are present in the aqueous phase, and after the mapping, you can deduce the regions that were actually bound to proteins.
I don't know if it is possible to treat your bound fragments (that you isolate after a phenol/chlo extraction in the organic phase) with proteinase K, then perform another phenol/chlo extraction to purify your formerly bound fragments and sequence them.
Could be worth trying.

Are you interested in transcription factor binding (and similar), or in histone modifications?
If you are looking at investigating something with a short binding motif that occurs redundantly across the genome, ChIP-exo works: http://www.cell.com/abstract/S0092-8674(11)01351-1
This technique involves digesting one strand of the DNA up until the bound protein-DNA complex via exonuclease, while leaving enough of a tag on the other end to uniquely identify it's location within the genome. I have no first-hand experience with it, and it's yet to be independently replicated, but it looks fantastic. I don't recall whether they investigated the extent to which off-target DNA was digested by the exonuclease, but theoretically I expect a significant portion would have been eaten up.
If you are interested in ChIP of histone modifications, you can use micrococcal nuclease (MNase) for your sample prep instead of sonication. Again, I have no first-hand experience, but I understand that this enzyme can be used to digest DNA until it reaches the nucleosomal core particle, and there are published ChIP-seq experiments employing this strategy. The MNase would be expected to digest unbound DNA fragments.

This is a difficult experiment.  It's usually done by digesting the DNA under conditions where the binding protein is solidly attached.  DNAse is added, and then after some time, the DNAse is degraded with heat or the addition of an inhibitor.
What you get depends on the length of the DNA protected by the protein and the tenacity by which the protein binds itself to the DNA.

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text:
How can I produce milligram quantities of an isotope-labeled DNA oligomer?
I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs.
I'm also only interested in the single-stranded DNA, so a method that produces double-stranded DNA without any way to easily separate the strands would also not be useful.
What methods are there to produce labelled DNA that fulfill these requirements?

You can also design a plasmid that has your 35mers and raise the bacteria with isotopic carbon and nitrogen C13 acetate and N15 ammonium sulfate will work with E coli in a minimal medium.
this is not cheap, but the cheapest available sources of the isotopes can be used.

That doesn't give me single-stranded DNA. It's also very inefficient as I only use 1/200 of the plasmid DNA (30bp single-strand of a 3kb plasmid), so a Megaprep with 2.5 mg yield would still only give me 0.0125 mg of my DNA. I can't reasonably make 100 Megapreps to isolate 1mg of my sample.

I found a couple of methods using M13 phage growing on E coli:

Reddy P, McKenney K. Improved method for the production of M13 phage and single-stranded DNA for DNA sequencing. Biotechniques. 1996 May;20(5):854-6, 858, 860.
I Jupin and B Gronenborn. Abundant, easy and reproducible production of single-stranded DNA from phagemids using helper phage-infected competent cells.Nucleic Acids Res. 1995 February 11; 23(3): 535–536.

You could easily adapt these protocols to grow on 13C, 15N-containing medium. Then you could use a restriction enzyme able to cut ss DNA and purify your fragment through a PA gel. Clontech's gigaprep kit (up to 50 mg of DNA) will cost you $546 (in the US, before any quote).
Disclaimer: I've never done any of this!

The cheapest way to make that large quantity of DNA without the need of the whole oligomer being label would be to produce 34 nucleotides by chemical synthesis. The 35 nucleotide can be labeled and ligated to the remaining strands. This should reduce the costs of producing the oligomer since the most expensive stage, the labeling is limited to just the final nucleotide.

I need all of the nucleotides labeled, only the last one is not enough unfortunately.

I realized that the other suggested ideas are pretty effect. I would culture the plasmids with non-labeled bacteria and using a cesium gradient, you should be able to separate half-labeled DNA from unlabeled and fully labeled DNA. After a restriction digest, you should be able to isolate single stranded DNA by density centrifugation.

What about PCR using labeled nucleotides? Might have to run several reactions to get miligram quantities you need, but 35 nucleotides seems really really small for growth in bacteria, and purification would be extremely difficult. But 35 bases might even be too small for PCR, hardly bigger than your primers.
If you do need to grow in e coli, it might make sense to create a plasmid with multiple repeats of the 35 base sequence separated by the same restriction site. You can grow e coli in c13 n15 media, but it's expensive and you have "train" the cells over several generations because the heavier isotopes create differences in chemical kinetics that make the labeled nutrients hard for enzymes to use, but I've seen people do this for making proteins for NMR.
I bet you need this labeled DNA for NMR, don't you?
Have you considered phosphate NMR? No need to label it, P-31 is already NMR active.
If it must be C13 N15, I highly recommend having it synthesized, it will be expensive, but that 35 base length and the requirement for single strandedness are ideal for chemical synthesis.

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text:
How long does antibiotic-dosed LB maintain good selection?
Various people in our lab will prepare a liter or so of LB, add kanamycin to 25-37 mg/L for selection, and store it at 4 °C for minipreps or other small cultures (where dosing straight LB with a 1000X stock is troublesome).  Some think using it after more than a week is dubious, but we routinely use kan plates that are 1-2 months old with no ill effect.
How long can LB with antibiotic such as kanamycin, chloramphenicol, or ampicillin be stored at 4 °C and maintain selection?

This Bitesize Bio article is very informative on this issue.  The 1970 study they cite found negligible reduction in the the efficacy of non-beta-lactam antibiotics (kanamycin, chloramphenicol) over spans of 4 weeks or 60 days.  Ampicillin loses about 10% activity at 4 weeks.
In my lab, we only take care not to use LB/Amp plates that are older then 4 weeks, for LB/Km, we store them at 4 °C for more then a month, sealed in a plastic bag.

As far as I know, that is fine.  Thats the temperature that Amp is regularly stored at.  I always do a negative control anyways to ensure that my antibiotics are still lethal.  Just don't stick it in the microwave to make plates

Ampicillin degrades by hydrolysis (albeit very slowly if not catalyzed), difficult when in dry, much easier when in solution.

"That's the temperature that Amp is regularly stored at" - and in fact, Amp does lose activity (a few % per month?) as a consequence.

I don't know about solutions, but we keep LB-Amp/Carb/Gm plates in 4°C for two-three weeks at a time, and the antibiotics seem to work.


text:
How do I change bond colors to something besides a different hue in Coot?
I can modify the colors of carbons in Coot under Edit, Bond Colours..., but that only gives me different hues.  Is there a way to change the color to something less-saturated (or perhaps slightly transparent) so I can identify the "active" molecule I'm working on versus a template?
The menus seem no help, I'm wondering if there's some scripting magic that can do this.

@Rory, they're not buttons

You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:
.
.... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html

procedure: hilight_binding_site (imol, centre_residue_spec,
  hilight_colour, radius): hilight-colour is specified in degrees (round
  the colour wheel - starting at yellow (e.g. 230 is purple))

It looks from this like you only get to choose Hue (color_map_rotation) and not Saturation or Lightness, even with the script interface.
However, text can be full RGB

3.28.3 (set-font-colour red green blue)
where:
red is an inexact number green is an inexact number blue is an inexact
  number


text:
How do you turn a minimal CIF description into a complete one?
I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition.  This page provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.
Maddeningly, I see in my project job history a couple "dictionary" jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):

When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF ("mmCIF") file, nothing happens.
Also under the sketcher, I can severely abuse the "Load Monomer from Library" and it looks like I get the right thing:

However, when setting up the above, it throws "Error: can't read "monomer_lib(code,n..." warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.

If there are other solutions, I'd be interested as well.  I've used PRODRG to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.

Not quite as ideal as I had hoped, but it works:

Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere.  Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return

If it complains it's not found, the CCP4 bin directory may not be in your PATH environment variable.  You can get around this by specifing the full path to the program, e.g.: c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe (may vary with version)

Say "Y" or "A" at the _DOC: prompt for some more files, "N" if you don't care (I generally don't)
At the --> prompts, specify:

the input file, e.g.: file_l: ABC.cif
the monomer: mon: ABC
output file name: file_o: ABC_out

Leave a prompt blank and hit return to start processing.

If it runs successfully it might look something like this:
C:\Users\Nick>libcheck

  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/

  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: libcheck.bat
 _DOC:n

 #
 #      Keywords:
 #
 #FILE_L:   < >  - additional library, " " means without this file
 #MON:      < >  - give info about this monomer
 ... (shortened) ...
 #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
 #                 (only with NODIST = N)

 #---  type "keyword   parameters" and/or ---
 #---  press key "CR" to run program      ---
 -->file_l: ABC.cif
 -->mon: ABC
 -->file_o: ABC_out
 -->
 MON   : ABC
 -------------
 Output file   :ABC_comp
 Input user lib:ABC.cif
 _chem_comp.name "DRUG INTERMEDIATE"

          17          55
 "DRUG INTERMEDIATE"

 -------------
 Keywords:
 HFLAG : Y
 COOR  : N
 LCOOR : Y
 SRCH  : 0
 REF   : Y
 NODIST: Y
 ERROR ==> In the loop containing the item_chem_comp.three_letter_code
 ERROR ==> The number of expected items and the number existing items do not match
 ERROR ==> The number of expected items is    7
  NUMBER OF MONOMERS IN THE LIBRARY          :     1
                with complete description    :     0
  NUMBER OF MODIFICATIONS                    :     0
  NUMBER OF LINKS                            :     0
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  I am reading library. Please wait.
      - monomer"s description
  WARNING : monomer:ABC      - has the minimal description.
  now monomer:ABC      - has complete description.
  I will check it.
 * CIFile  : ABC_out_ABC.cif
 * PDBfile : ABC_out_ABC.pdb
 * Plotfile: ABC_out_ABC.ps
  I am writing new description to
  file: ABC_out.lib

C:\Users\Nick>

It yields the following output files:

(file_o): looks like a CIF file with lots of whitespace and records stripped out
(file_o).lib: the desired, complete definition file
(file_o)_(mon).cif: an even more minimal CIF file with only XYZ coords
(file_o)_(mon).pdb: a PDB file
(file_o)_(mon).ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes.  Can convert it to the easier-to-use PDF format using this http://www.ps2pdf.com/convert.htm, or other tools.


text:
Glomerular Filtration Rate
In practice, when you have vasoconstriction of the glomerular capillaries and subsequently an increase in blood pressure, glomerular filtration rate increases. However, this seems counterintuitive to Bernoulli's principle.
During vasoconstriction, because the radii of the capillaries are getting smaller, we should expect an increase in flow rate and blood velocity. According to Bernoulli's principle, the outward hydrostatic pressure should drop.
How does this lead to an increase in filtration rate?

The previous answer isn't quite correct, because, well, blood flow is complicated and the body has autoregulatory mechanisms. As Alex mentioned, vasoconstriction doesn't occur in capillaries because they lack a muscle layer. It does occur in the small arterioles before and after the glomerulus (the afferent and efferent arterioles, respectively).
Bernoulli's principle mainly applies to larger arteries and arterioles, and not capillaries. Capillaries are so tiny that the red blood cell is a significant portion of the diameter, so the assumption of no viscosity is no longer valid. See this discussion for an explanation.
To address your question, here's a basic picture of the glomerulus, from Gray's Anatomy.

The afferent arteriole is in red, and the efferent arteriole in blue. The glomerular filtration rate (GFR) depends on the pressure difference between the two, which affects the hydrostatic pressure at the glomerulus. Also, note that vasodilation has the opposite effect of vasoconstriction on GFR.  (For a nice image and explanation, look at Figure 6 here) So:

Constriction of the afferent arteriole decreases the blood flow into the glomerulus and thus the glomerular hydrostatic pressure, which leads to a decrease in GFR.
In contrast, constriction of the efferent arteriole decreases blood flow out of the glomerulus, and this increases the glomerular hydrostatic pressure and leads to an increase in GFR.

Both the afferent and efferent arterioles are regulated through hormones (and drugs that inhibit the hormones). Prostaglandins dilate the afferent arterioles, and NSAIDs inhibit this action. Angiotensin II preferentially constricts the efferent arteriole, and this action is restricted by an ACE inhibitor. (Source: First Aid for the USMLE Step 1)

It's worth noting that the afferent arterioles are significantly larger than the efferent arterioles, which creates the high-pressure environment required for filtration in the first place.

To my knowledge, capillaries in general and the renal capillaries in glomeruli in particular do not have muscle cells to constrict. The latters have only a basal layer with podocytes lying directly on it (link to the open textbook).
Therefore, the vasoconstriction takes place only in arterioles before the glomeruli, and this vasoconstriction leads to the increased hydrostatic pressure which propagates to the glomerular cappilaries. The blood flow rate and velocity do not change, therefore the increased hydrostatic pressure works against the constant pressure of Bowman's capsule and osmotic pressure of the colloid medium, leading to the increased net filtration pressure (NFP). Filtration rate and filtration pressure are directly connected, so that the rate increases either.
For more details, please, refer to the textbook I provided the link to above.


text:
Why doesn't a substance like loperamide promote analgesia?
Loperamide is frequently used to slow gastrointestinal motility.  It is available over the counter (in the US, I don't know about elsewhere) without any regulations whatsoever, yet it's derived from an opiate.  Knowing that the opiates slow the intestinal motility, it makes sense that it shares the same side effect.
What doesn't make sense to me is why it doesn't share the same primary effect of analgesia?  Clearly it binds to opiate receptors in the gut, but are they the same subtype as those in the CNS?  Or is it that the structure of the drug is such that hardly any crosses the blood brain barrier?


text:
(Rough) Model for DNA evolution in E. coli genes
I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone.
Here is what I understand:

Sequences corresponding to genes have both exons and introns, but in bacteria the proportion of introns is low.
Because I'm talking about genes, sequence changes are not very neutral but subject to selection.

I have checked a few papers linked in Wikipedia about this subject, but I notice that they are tuned for entire sequences, and many of them almost predate the genomic era.
What are some current, canonical sources in this area?

There is nothing like introns in E.coli because there is no splicing in bacteria. What is unclear for me, are you asking about mutations/indels? Then please say so.

Bacterial DNA evolution is like other evolution in the sense that the mutation rates are probably random and biased somewhat by the physical and chemical structure of DNA as well as the presence and activity of DNA repair enzymes.  The mutation protocols for preparing mutant libraries from UV or chemical mutagens are a good place to start I would think - like this reference. Most of this stuff is oriented towards protocols used in the lab, not in the wild.  Like how much UV does E coli get in your gut?  Not much.  Still it does happen and is a typical baseline factor in evolution.
Bacteria also mediate their own adaptation via phage transfer as well as direct lateral gene transfer, chromosomal rearrangement.  The dynamics of this evolution is just as interesting I think as site mutation as the bacteria can use its repair mechanisms and even actively upregulate some adaptation itself, responding to environmental changes.  The fundamental differences between bacterial evolution and say evolution of animals and plants come from the fact that life is relatively cheap - a single well adapted survivor can repopulate very quickly and so that even radical genetic diversity has a benefit even if some of the population dies off every generation from being a bad adaptive experiment.  (BTW animals do this too, but in the short lived haploid gamete phase, not so much as diploid animals).
Well anyway back to bacteria.  Eric Alm's lab at MIT started with his work with operon evolution.  Genes grouped together on a single mRNA leap from one cluster to another across evolution, allowing for coordination of biochemical processes in the cell.  Lately they have been looking more intensely at the evolution of bacterial species, and how the selective environment influences bacterial adaptation.
Its hard to be more specific since I'm not completely clear on your focus and needs here, but this is what I know.

That helps a lot, I just added some papers from the people at MIC to my reading list. My core question was this: what are the differences between DNA stretches under selective pressure and DNA stretches which is garbage... I suspect that because there is not that much garbage in bacterial genomes, I might very well not care that much.

a better question definitely.  Its very hard to tell the difference unfortunately.  Anyone who has actually tried to find a transcription factor binding site knows that in many cases, while the DNA sequence varies substantially and still functions, its pretty hard to tell whether its noise, spacer, or totally functionally important.  I wish I knew the answer.. I'd probably be typing from my office across the hall from Eric Alm...seriously though, that deserves an entire new question.  cant' cram that into a comment.


text:
What is the "lifecycle" of an average eschar and what types of cells are involved in each stage?
(after some deliberation in the comments, I've decided to make the question more general)
An eschar or "dry scab" often forms at a site of injury over a large cut or sore.
It seems as though the healing scab portion binds more strongly to the other scab cells than to those of the surrounding healthy tissue initially, as evidenced by the ability to remove the scab en masse without disturbing the edges of the actual wound (in surgical debridement or when the area is "picked" at).  Then, the eschar bonds then bonds more strongly with the edges of the wounds (so it's more difficult to remove), and then finally, the underlying newly formed skin seems to push it off completely.
Does this accurately describe the "lifecycle" of a common dry scab, or are there other well defined stages in the process?  What types of cells (platelets in the beginning?  epithelials at the end?) are involved with each stage of the process?

What makes you think that it starts binding more strongly?

I thought that scabs were essentially just a protective layer of dried-out and tightly bound platelets (etc) that eventually came-away when the tissue underneath had properly formed/healed, rather than forming the new tissue themselves. Not my field though!

@KonradRudolph Empirical evidence, no, I'm kidding, but just that there seems to come a point between when the healing begins and when it "comes away" (as LukeTheDuke put it) that it adheres to the wound edges more strongly than to itself, otherwise it would just fall off right away.

@LukeTheDuke Yes, not mine either, so I'm struggling with digging out the terminology a bit.

Terminology aside, I don't think there is a distinct point where the scab starts to bind to the wound - this is likely to be an inherent process started when with the initial clotting of the blood. As the clot thickens and binds, the scab will become harder to remove. As the skin underneath heals, the scab is gradually 'excised'(?!). This is purely speculation!

@KonradRudolph Rather than ask an open-ended question about the entire process, I thought that this got more to the heart of my question.  However, if you (or @Luke) have a more general answer, I would certainly take it.

@LukeTheDuke Sounds reasonable, but if you can dig up a source, you should definitely take a shot at answering it.

@jonsca Ah, I misunderstood you, I though you meant that it formed the new tissue, rather than falling off.

@Luke I've made the question a bit more general now

@KonradRudolph I've made the question a bit more general now

Response to cutaneous tissue damage occurs is several distinct but overlapping phases. First an scab is formed as the blood is 'allowed' to clot. A matrix is formed as the platelets adhere to one another, which contracts and 'dries' (forces out the serum) to form a scab. This process clearly happens prior to tissue regeneration/formation to reduce further blood loss.
Fibrinogen
In response to damage to blood vessels a signaling cascade is initated that results in the massive production of fibrin, which is deposited at the site of wounding and subsequently forms blood clots by activating platelets and stabilising the matrix by cross-linking (see PDB's protein of the month 2006).
So this is why clots do not appear to be attached to the surrounding tissue; the fibrin causes the blood to form a matrix that is very tightly bound to itself. Only after clot formation does the tissue remodeling occur, and it is during this stage that the scab will 'bind' more stongly to the surrounding tissue.
The Cell Types and Processes of Wound Healing
This figure (from (Li, 2007)) shows the various stages that occur and cells that are involved in acute wound healing  (wounds such as burns and cuts that heal "in a timely fashion");

Wow, that was perfect. Another great answer.

First, eschar ("es-CAR") is NOT a scab.  They are entirely different, both physically and biochemically.  A scab is made up mostly of blood products and fibrin, and sits on top of the wound or skin.  Eschar is the skin itself (or other tissue), which has died and as a result turns black (or brown).
Scabs will detach from the underlying skin fairly easily, and fairly quickly as the skin heals under it.  Skin eschar heals from the edges inward, and usually takes months to heal, as opposed to weeks for scabs.  It is very hard, leathery, and acts as a natural bandage.  It used to be the "norm" to remove it, with the idea that the skin would grow back faster if it was not "in the way"; however, today that is less common, unless there is an infection at the site that must be treated.  It is considered a "normal" part of the healing process.  (summary of a large number of articles I looked up trying to get answers for myself; facelift patient who had two very rare "hematomas", and as a result developed bilateral necrosis.)

Welcome. Can you add sources to your answer to allow others to background read on your answer?

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text:
How does an inhibitory synapse communicate to the cell body of a neuron?
I picture a neuron as having multiple trees of dendrites attached to the cell body with a single axon leaving the cell body.  I believe the cell body near the axon root makes the decision to fire or not fire an action potential.

If the neuron has both excitatory and inhibitory synapses in the dendrite trees, how do these communicate to the cell body?
Does something like an action potential get transmitted down the dendritic trees to the cell body?
What is the difference between the excitatory and inhibitory signals that are transmitted?

From your comment to nico's good answer, it seems that your question is really about how synaptic potentials propagate through dendrites.
Canonically, synaptic potentials travel passively along membranes and is described by cable theory. The cable equation describes how the voltage will change over time and space along a cable. The theory was originally developed for signal decay in trans-Atlantic telegraph cables, but the principle holds for a voltage-independent length of membrane like a dendrite.
A key point is that the potential change "seen" by the cell body is different from the potential change seen locally at the site of the synapse itself. In fact, the voltage decays exponentially with increasing distance from the synapse. The extent of the signal decay is governed by the axial resistance (influenced by dendritic diameter), the membrane resistance, and membrane capacitance, and the branching pattern. A common neuron modeling environment called NEURON is basically a fancy solver for the cable equation.
You'll note that a consequence of this signal decay is that synaptic location matters a lot. Given an identical synaptic potential, a very distal synapse will have much less of an effect on the soma than a more proximal dendrite. Sometimes, the synaptic strengths are scaled to compensate for this location issue (a distal synapse will have a much larger local potential change). Many inhibitory synapses capitalize on this location dependence and are located close to the soma to act as shunts for all signals coming from the dendritic tree. When activated, an inhibitory synapse will decrease the local membrane resistance thereby decreasing cell excitability.
Finally, I'll note that although we often talk about dendrites as being passive conductors, dendrites are actually quite active and have many voltage-dependent channels. The voltage-dependent phenomena in the dendrite complicates the use of pure cable theory to understand the dynamics of synaptic potentials. However, cable theory is still the essential foundation upon which our growing understanding of the active dendrite is built.

An inhibitory synapse works just like an excitatory one!
When a presynaptic neuron fires it will release a neurotransmitter at its terminal(s). This neurotransmitter can be excitatory or inhibitory, the main excitatory one in the central nervous system being glutamate and the main inhibitory one GABA.*
GABA and Glu are far from being the only neurotransmitters in the brain, they're just a classic example, so we'll stick with them. When the neurotransmitter is released it binds to receptors on the postsynaptic neuron (provided, of course, that the postsynaptic neuron expresses these receptors).
Various GABA and Glu receptors exist, both ionotropic (i.e. channel-receptors that let ions flow through the membrane upon binding of the ligand) and metabotropic (i.e. receptors which activate an intracellular pathway that does not per se start the flow of ions, but that can induce it or prevent it indirectly).
For simplicity we'll stick to ionotropic receptors.
Glu binds to three types of ionotropic receptors: AMPA, NMDA and kainate receptors. These have different kinetics/properties, but the bottom line is that they let cations (positively charged ions, such as Na+ and Ca++) into the cell. When this happens a postsynaptic depolarization happens, which is named EPSP (excitatory post-synaptic potential).
So, if the resting membrane potential was, say, -57mV, it will become, for instance -52mV.
This means that, if the threshold potential for firing an action potential were -43mV the cell, which first needed a 14mV depolarization to fire now will need a 9mV depolarization.
If subsequent EPSP sum they can depolarize the cell sufficiently to reach threshold and let the cell fire.
This image from Wikipedia is quite self-explicatory: in this case 3 synaptic events generated 3 EPSPs that summed, making the cell depolarize enough to reach threshold potential, and generate an action potential, that will then propagate to the cell body.

GABA, on the other hand, binds to the GABA-A receptor, which is a chloride channel. In most cases, upon binding of GABA, GABA-A lets Cl- in the cell, effectively hypopolarizing it and generating an IPSP (inhibitory post-synaptic potential). The situation is the same (but opposite) to Glu, this time, though, the potential becomes more negative.
EPSP and IPSP can and do happen at the same time: as they can vary in frequency and intensity depending on the firing frequency and firing pattern of the presynaptic neuron, a pretty much continuous range of voltages can be achieved in the postsynaptic neuron.
Other controls over this process come from metabotropic receptors that can, for instance [de]phosphorylate (add or remove a phosphate group) ion channels modulating their permeability to ions or from the different kinetics of the different channels (for instance certain channels stay open for longer or open in a delayed manner etc), allowing for fine-tuning of the system.

*I am making a gross generalization here. A neurotransmitter is not excitatory or inhibitory per se, it depends on the context. For instance excitatory GABA synapses do exist.

I had read about EPSPs and IPSPs before and I now see that the main difference is the sign of the delta voltage change - thanks. My question still remains about how these travel down to the cell body down the dendrite tree.  These are not action potentials and I thought action potentials were required for signals to travel unchanged over any distance. Do these EPSPs and IPSPs travel unchanged down the dendrite tree to the cell body to get "summed"? The membrane potential near the synapse changes but how does that change travel down the dendrite?  The dendrite is not an electrical conductor.

I think the answer provided by @yamad answers your concern very well

I wish I could "accept" both your answer and yamad's answer ;-).  Thanks again for a great answer...

A small linguistic side-note: the term "stimulatory synapse" is not used in neuroscience. A search in Google scholar gave me 183 results and they were almost all, if not all, from immunology studies. Perhaps @Nico you meant "excitatory"? I replaced the occurrences in this answer and my edits got accepted, but they were now reverted back.

@vkehayas I reverted the edit, since I have definitely heard "stimulatory synapse" and "excitatory synapse" used in an exchangeable manner. To be fair, I did not check Google Scholar, but if you feel strongly about that please change it back and I will not revert it.


text:
Do drugs always degrade after they have passed their expiration date?
I have been wondering for some time whether several drugs really have an expiration date.
Let's narrow the scope and think about only "common" drugs, e.g NSAIDs, antibiotics etc.
For example, would antibiotics in the pills get deactivated or decomposed?

Question sounds appropriate. I suggest reading http://www.quora.com/Drugs-and-Pharmaceuticals/What-does-it-mean-for-a-medicine-to-have-an-expiration-date

Could you clarify whether you're interested in antibiotics, activated carbon or about expiration dates in general?

@bobthejoe: thanks that link really helped, but I guess it would be good to have something similar written here as an answer just to gather more knowledge on this site.

It really does depend on the drug in question

@RoryM: ok then, you're suggesting that the question is too wide and can't be answered exhaustively. Then I'll reduce the scope.

@zeller I consolidated all of the updates down and reworked the title with what I think is your intent, if this is not the case, feel free to roll it back.

Drugs do not have to degrade after their expiration date and passing the expiration date has more than one possible meaning.
First of all chemical compounds vary in their susceptibility to breakdown over time.  If they are kept away from oxygen, high temperatures (or kept in very low temperatures), and they are of a robust chemical nature, they might be stored for much longer than their expiration date and remain just as strong.
Over time, pharma compounds will chemically break down and lose their potency.  In many cases, you will find that they simply don't do anything when you take them.  This link cites a study that many drugs can retain their potency 15 years after they are made.
There are important exceptions.  Two examples are tetracycline and acetaminophen (tylenol) whose breakdown products can increase the tendency for these drugs to induce liver damage.


text:
What evidence gives clues to the physiological basis for conversion disorder?
Conversion disorder has a set of DSM diagnosis criteria, which, among other things, includes ruling out all neurological disease.
However, as the media has shown us (and one could argue a biased portrayal), many of these young people in Le Roy, NY who were diagnosed with conversion disorder have exhibited tics and starts that are highly reminiscent of Tourette's Syndrome, which is thought to have some basis in pathology of the basal ganglia (and perhaps the thalamus and frontal cortex).
Granted, the issue is being looked into as having an environmental cause, so I can understand how the diagnosis may be reshaped, but I'm more curious about the initial diagnosis of "mass hysteria".
If this syndrome causes real physical symptoms and yet is "psychogenic", through what physiological means is the disease acting?  Why would ruling out a neurological basis be a valid criterion?

It's usually important to rule out other medical conditions when considering many psychiatric diagnoses due to similarities in symptoms between them. There are many examples but I'm not sure if it's appropriate to note them here as a lot of symptoms have to be considered in a clinical context and might be mistaken as medical advice. It's also important to note that concurrent medical and psychiatric conditions frequently occur with individuals diagnosed with conversion disorder.(2).
Conversion disorder was previously combined with somatisation disorder and was known as hysteria.(2). Conversion disorder is a diagnosis of exclusion where the symptoms are not a result of:

neurological or other medical condition;
the effect of a substance; or
cultural behavior or experience.(1).

The key is that these are not intentionally or medically driven symptoms but rather physical manifestations of psychological needs ("unconscious manifestations of emotional conflict"(3)). Psychoanalytic theory suggests that "conversion disorder is caused by repression of unconscious intrapsychic conflict and conversion of anxiety into a physical symptom"(2).
In terms of physiological basis of conversion disorder, it's been suggested that an imbalance in metabolism between the dominant and non-dominant brain hemispheres; and impaired communication between the two may be an issue.(2). There are some other points you can also read at MedScape.

Ferri. Ferri's Clinical Advisor. 2012. Mosby.
Sadock. Kaplan & Sadock's Synopsis of Psychiatry. 10th ed. 2007. Wolters Kluwer.
Jacobson. Psychiatric Secrets. 2nd ed. 2001. Hanley and Belfus.


text:
Which aspects of renal physiology are standing in the way of an artificial (mechanical) kidney?
Scientists have been able to create artificial organs with varying degrees of success.  The mechanical heart (in its various forms, e.g. ventricular assist) is able to sustain life for some period of time.
Efforts to grow whole organs in the lab will probably ultimately lead to a more pragmatic solution.  What aspects of the renal physiology are standing in the way of an implantable mechanical kidney (fashioned more so from tubules and membranes than simply being a shrunken down dialysis machine)?

@J.M. No, I had not previously.  I had looked into this about 10 years ago, but it looks like the field has come pretty far.  (I'll pull papers, but) Do they actually have a deliverable?

@J.M. It's definitely a huge step forward.


text:
How does the eugeroic modafinil work?
How does the drug, modafinil (Provigil), exert its eugeroic (wakefulness-promoting) effects? I've read that it works by increasing dopamine and histamine concentrations in the CNS and by serving as a partial agonist at the dopamine D2 receptor. Perhaps by interfering with the function of orexin?

The exact mechanism is not known:

Modafinil has wake-promoting actions similar to sympathomimetic agents like amphetamine and methylphenidate, although the pharmacologic profile is not identical to that of sympathomimetic amines. [...] Modafinil-induced wakefulness can be attenuated by the α1-adrenergic receptor antagonist prazosin; however, Modafinil is inactive in other in vitro assay systems known to be responsive to α-adrenergic agonists, such as the rat vas deferens preparation. [...] Modafinil is not a direct- or indirect-acting dopamine receptor agonist. However, in vitro, Modafinil binds to the dopamine transporter and inhibits dopamine reuptake. This activity has been associated in vivo with increased extracellular dopamine levels in some brain regions of animals [1].

A 2010 study has concluded that:

Recent evidence suggests that modafinil may block the dopamine transporter (DAT) and that the dopamine D1 receptor (D1R) may contribute to modafinil effects [2].

Another one confirms modafinil's dopaminergic activity:

These findings indicate that modafinil has a long duration of action, with alerting properties arising predominantly from dopaminergic activity [3].

It seems to be dependent on catecholaminergic signaling:

It binds competitively to the cell-membrane dopamine (DA) transporter and is dependent on catecholaminergic (dopaminergic and adrenergic) signaling for its wake-promoting effects. [...] Modafinil is an exceptionally weak, but apparently very selective, DA transporter inhibitor. [...] The conformational constraints on the interaction of modafinil with the DA transporter - and probably, as a consequence, its effects on trace amine receptor signaling in the catecholaminergic cell - are unique among catecholaminergic agents [4].

References:

Drugs.com. Modafinil. Clinical Pharmacology. Available from http://www.drugs.com/pro/modafinil.html (accessed 29.07.2014)
Young JW, Geyer MA. Action of modafinil--increased motivation via the dopamine transporter inhibition and D1 receptors? Biol. Psychiatry. 2010 Apr 15;67(8):784-7. doi: 10.1016/j.biopsych.2009.12.015. PubMed PMID: 20132929.
Turner C, Belyavin A, Nicholson A. Duration of activity and mode of action of modafinil: Studies on sleep and wakefulness in humans. J. Psychopharmacol. (Oxford). 2013 Dec 3;28(7):643-654. doi: 10.1177/0269881113508173. PubMed PMID: 24306135.
Wisor J. Modafinil as a catecholaminergic agent: empirical evidence and unanswered questions. Front Neurol. 2013 Oct 7;4:139. doi: 10.3389/fneur.2013.00139. PubMed PMID: 24109471.

Thanks for the great Answer and Solving 1 year old question!!!


text:
Sparking during electroporation of plasmid DNA into bacterial cells
During electroporation of bacterial cells (I work with Mycobacterium tuberculosis, but I think this applies to E. coli as well), sometimes I get sparking. I've read this is due to salts present, either in the DNA sample or the bacteria.
I use the Qiagen plasmid prep kit, which includes EB (Elution Buffer). This contains Tris-Cl. Could this be contributing to the sparking? Can you explain how this works? Does eluting with water instead of EB reduce chances of sparking?

What media are the bacteria in during electroporation?

Hi notalily, what parameters were you using for MTb electroporation?

In my experience the elution buffer does not matter (both for E.coli and Mycobacteria). I have heard this before from co-workers, but it usually is based on superstition or anecdotal evidence. I have compared water/EB elution and never saw a difference in sparking (in fact, I usually get slightly more colonies with EB).
When I get arcing (sparks), it's usually because I did not wash enough, have bubbles or have to many bacteria. Arcing is a collapse of resistance.

Sparking occurs from having too many salts or possible not enough solution. After fine tuning my electroporation for very high amounts of DNA (16+ ug), what I've found to help are:

Make sure you are using the proper amount of liquid solution to transform. Too little will end up sparking
Clean up your DNA. I wash with twice the recommend amount of buffer PE, but I don't great evidence of how much the 2nd PE wash helps
Elute your DNA clean up with water
Drop dialyze your DNA. This is probably the most important step to prevent arcing


text:
What controls the feeling of discomfort/comfort before and after sleep?
I'm interested in which biological systems or hormones are involved in the following phenomenon:
Before sleep it may be difficult to find a comfortable position, and muscular aches and pains are more evident.
After 8 hours of sleep, many more positions are comfortable, and muscle aches/tension are non-existent. Some time after awakening, the feeling disappears.
What causes the difference in feeling between prior to falling asleep and after? Are there some hormones involved? Is it caused by some form of thought/feeling inhibition (e.g., part of a brain "falls asleep")?
If I remember correctly, after long running muscles accumulate some compound that is a result of metabolizing energy without enough oxygen, which causes muscles to ache. Could a similar process be involved?

The compound you're thinking about is lactic acid. When oxygen is low, pyruvate is reduced to lactic acid to regenerate NAD+. It might have something to do with the aching related to sleep, but I'm not sure.

Any chance you're referring to Willis Ekbom Disease?


text:
Is there a circadian component to hunger?
I'm wondering what produces the feeling of hunger in humans. Checking Wikipedia revealed that leptin and ghrelin are two hormones involved. I've also read that the digestive system produces its own melatonin.
Because melatonin is related to circadian rhythm and the biological clock,Is melatonin involved in feeling hungry? Is there a circadian pattern to the levels of leptin and ghrelin in humans?

Many hormones aside of melatonin show circadian rhythms. I doubt melatonin is directly involved in this, but I would bet cortisol is for instance.

This question demands an answer that is tissue specific. Leptin is produced by skeletal muscle as well as adipose. Production of a hormone or signaling molecule may be under circadian control in one tissue but not another. In addition, a complete answer will talk about aging as circadian rhythms in peripheral tissues break down with aging.

I found additional information on the subject. Apparently Serotonin is also involved in feeling hunger and the motivation to eat. It also follows a diurnal/circadian pattern as described below:
Serotonin as as Gauge of food availability (appetite)

The expression of 5-HT2C receptors in the hippocampus follows a diurnal rhythm,[13] just as the serotonin release in the ventromedial
  nucleus, which is characterised by a peak at morning when the
  motivation to eat is strongest.[14]


text:
How are melatonin levels measured in humans?
I'm wondering how it is possible to measure diurnal variations of melatonin levels in humans. I keep reading that there should be a large difference in amplitude between melatonin levels measured at night and in the middle of the day.
Have there been any studies of melatonin levels in humans where I can take a look at the methods they used for this kind of testing and/or see sample results?

On the analytics of melatonin I have here a german language text by the RKI with references. Translated quote:

Assay of melatonin is done by serum or sputum using RIA or ELISA.
  Alternatively, to infer the nightly amount of melatonin secretion it
  is possible to look for the melatonin catabolic metabolite 6-hydroxy
  melatonin sulfate (6-OHMS) in urine.[1,2] ... standardized
  conditions of sample taking are a must to get good results.[3,4]

Ref.:

P. Levallois, M. Dumont et al: Effects of electric and magnetic fields from high-power lines on female urinary excretion of 6-sulfatoxymelatonin. In: American journal of epidemiology. 154, 7, October 2001, 601–609. PMID 11581093
D. H. Pfluger, C. E. Minder: Effects of exposure to 16.7 Hz magnetic fields on urinary 6-hydroxymelatonin sulfate excretion of Swiss railway workers. In: Journal of pineal research. 21, 2, September 1996, 91–100. PMID 8912234
E. Gilad, N. Zisapel: High-affinity binding of melatonin to hemoglobin. In: Biochemical and molecular medicine. 56, 2, December 1995, 115–120. PMID 8825074
D. K. Lahiri, D. Davis et al: Factors that influence radioimmunoassay of human plasma melatonin: a modified column procedure to eliminate interference. In: Biochemical medicine and metabolic biology. 49, 1, February 1993, 36–50. PMID 8439449


text:
Drosophila reference genome
Does anyone know the details about which line they are using to sequence as the Drosophila melanogaster reference genome?

Did you check the genome publication

As far as I know they just used a generic D. melanogaster lab strain.

does this help? http://www.fruitfly.org/annot/release3.html#strain

That was surprisingly buried.
I found this in a paper describing genome build 3 - See "Materials and Methods".  I imagine that this is consistent through to the current build.  In any case it should get you started.
"Sequencing templates were made from P1, BAC and WGS DNA libraries using the D. melanogaster strain yellow (y1); cinnabar (cn1) brown (bw1) speck (sp1)."


text:
What impacts on metabolism are likely from the 6x increase in water consumption by Americans at restaurants since the 1950s?
CDC data show that American water consumption in restaurant meals is 600% of what it was in the 1950s while meal calorie density has decreased (kcal/oz). What impacts is this likely to have on the metabolism of Americans?
My question is based on this infographic:

What a terrible infographic! 1) It shows water, but what they mean is soda. 2) It strongly emphasize the 56% decrease of kcal/oz, but what is relevant is the 50% increase in total calories. 3) it does not seem to count drinks in calories (not really clear, though). Sodas are very highly caloric drinks and should be accounted for (and that is why mentioning water rather than soda is really misleading)

@nico What about the source CDC infographic http://makinghealtheasier.org/newabnormal does its point about an increase in meal size make sense?  What about the source data used for that infographic?

Another problem with the infographic is that they use the image of a cup which implies the magnitude of the variable is related to the area of the cup. It says '6x more water' and shows the second cup being around 50x the size of the first. The same criticism goes for the CDC infographic site. They really need to employ some people who know about data vis and information design!

As mentioned by nico in his comment, this infographic is very misleading in that it presents quite uninteresting data in a way as if it was a sensation.
It claims the average meal drink has been soda which has increased by 6 times in size. Then it claims most of the volume is water. This is of course true. But while a substance solved in water barely increases its volume, it can still make a difference - soda and water are completely different things and the important statistic to look at here is not the amount of water drunk, but rather the fact that it is soda. Where I live, soda usually contains around 27g of sugar per 240ml (8oz) which is 9% of the GDA. So according to this data, people consume half their energy needs of that day with the drink they get in their restaurant meal.
The other statistic is about calories per ounce of the food. What sense does a statistic about that make? The only relevance of the calorie density of food would be the effect on how well it is digested, and for that only a calorie number isn't really helpful. The relative ratios of fibre, carbohydrates and fats would be much more useful in that case. The only interesting statistic here is that meals have almost doubled in size. The fact that the volume of meals has increased much more hints that there is a higher portion of less calorific foods, such as salads.
Impact on metabolism? Hard to say, this is a statistic about what people eat at restaurants, which is not really something that you expect to reflect their refular diet. It doesn't tell you anything about their general lifestyle, which would be the relevant statistic for effects on metabolism. If you only look at restaurant meals, those could look really unhealthy but on the larger scale, people balance it out in their every day diet and general lifestyle. If you had an additional statistic that shows that people actually eat a significiant amount of meals at restaurants, and they're the kind of meals described by the infographic you gave, that would have some implications.


text:
What is the biological basis for a human's ability to think clearly and be aware while "fighting/competing"?
I'm interested in learning more about the biological systems or hormones or parts of the brain that affect short term (<15 minutes) ability to concentrate attention on the task and be aware of the situation.
I'm particularly interested in humans who are engaged in an activity that can be perceived as threatening: martial arts, competitive video games, sports and other activities which may be considered "fight or flight", but a scenario in which the person has chosen to stay and fight.
To clarify the question further: What is involved in the ability to make decisions based on the competitive situation itself, instead of responding with pre-learned techniques and tactics? In one case, a person may be aware of what his/her opponents are doing, while in other cases the same person may "rush in blindly" and attempt to execute techniques that were learned and worked before, but will not work in the current situation.
What influences this choice of responding versus acting on prior knowledge?

My answer to http://biology.stackexchange.com/questions/2931/does-stress-physically-age-our-body/2947 contains the processes that lead to high blood pressure. This pressure is a main factor why your brain has all substances it needs in fight & flight situations.

Actually, the opinion that I've encountered more often is that when faced with a real fight or flight situation, a person will respond with a pre-learned behaviour.

the last two paragraph read like a question that would find a better home at cogsci.SE.

This is true, it's well established that when people are under high stress, they are more likely to respond with learned behavior. The ability to act intelligently under pressure is probably mostly a result of gaining expertise in a particular domain so that you can recognize what's going on in a situation and figure out an appropriate response without having to engage in careful, explicit reasoning or do things you're not familiar with.

thinking and decision making under stress or pressure is significantly reduced.  its sometimes called the 'fight or flight' condition.
This is a pretty well established phenomenon.  Here's a great radiolab segment on stress response.  Psychologist John Gottman notes how our ability to have a conversation where we can even listen to what someone else has to say is practically nil when we are emotionally saturated (frustrated or upset that is).  Even a mildly stressful conversation with your own spouse can shut down most rational processes.  Gottman can predict couples who overcome this problem which is highly corellated with divorce btw - but most of these couples remove stress in conversations rather than learn to work under pressure as it were.
Jonah Lehrer wrote about how tests to rank quarterbacks in their ability to respond on the gridiron are basically non correlated.  I know there have been criticisms of Lehrer, but this is a good piece and well grounded.  The point is that its hard to tell a-priori whether someone will perform under stress and given different sorts of stress.
In the japanese space program they would screen candidates by making them do highly repetitive tasks like folding 1000 origami cranes.  NASA was just doing interviews with panels of psychologists.  That wasn't infallible.
Such a test would be valuable for fighter pilots, astronauts, maybe presidents too! but it doesn't seem to really exist at this point.
In the end you can winnow out those who break into a sweat in the interview, but to know who is going to really take the beach, I think that the only real answer is to see if they make it through a 'live fire' (or whatever) experience.
Or as Clint Eastwood summed it up: "A man's got to know his limitations."
(apologies to the ladies there - you can know your limitations too).

Very good answer! I especially appreciate the reference about how rational processes can be suppressed. If one relies on rationality in dealing with such situations, one may be surprised.

thanks @AlexStone - also good reading the day before US elections... ;)

I recalled a while ago that I saw a presentation on the concept of "Flow".
Here's an overview by the author :Mihaly Csikszentmihalyi: Flow, the secret to happiness
The kind of difference in cognitive capacity while engaged in such events can be described as flow. I'm still not certain as to what is causing the difference in the cognitive ability at these times, even in the same person.


text:
Conversion rate of topical Retinol to Retinoic Acid (Tretinoin)?
I'm wondering if someone out there has more information than me. Retinoids have well known metabolic pathways in vivo, and it's usually something like: Retinyl Palmitate --> Retinol --> Retinaldehyde (Retinal) --> Retinoic Acid (Tretinoin) which is the biologically active form of the Retinoids.
Retinoids are used in cosmetics all the time, and while Retinol is available OTC, Retinoic Acid (Tretinoin - a.k.a. "Retin-A" by brand) is available by prescription only since it is a 'stronger' version of Retinol. It's not difficult to find 1% Retinol creams or higher, but Retinoic Acid treatments top out at 0.1%.
However, I can't help but wonder 'why'? One study I was able to dig up was here: Retinoic Acid Biosynthesis and Metabolism PDF. The table on page 5 shows Physiological Concentrations - starting at 50 microM for Retinol and ending at "<50nM?" suggesting an ultimate conversion rate of a little less than 10% which would make the 1% Retinol treatments roughly equivalent to a 0.1% Retinoic Acid treatment (and a 2% Retinol treatment to a 0.2% Retinoic Acid treatment - double what's available by prescription).
Do other studies/other evidence support the rate of conversion of Retinol to Retinoic Acid to be roughly 10% or suggest than a 1% Retinol topical treatment is equivalent to a 0.1% Retinoic Acid topical treatment? Or are there some other interfering factors that reduce the utilization of Retinol to Retinoic Acid that I'm missing?

My guess is that the effect you describe is due to compartmentalisation: both retinol and retinoate are practically lipophils and so will localize in membranes and other lipid "pools", while both human retinal dehydrogenase enzymes are cytosolic. Probably the only occasion they have to get at their substrate is when it's bound to RBP. This however introduces another factor complicating the simple model.


text:
Can I estimate leaf temperature from air temperature? What other information would be required?
Physiological measurements such as respiration rate and assimilation rate depend on temperature.
Most papers report tissue temperature (e.g. leaf temperature for leaf measurements), although some report air temperature.
My goal is to compare measurements in the literature.  I use leaf temperature at time of measurement to adjust the rates to a common temperature. Currently, I assume that if leaf temperature is not available, it is the same as air temperature. (This is often assumed in papers where the leaf temperature was not measured).
Is there a way to estimate the difference between air temperature and leaf temperature? I can get fairly good estimates of other physiological traits (e.g. leaf thickness, albedo, stomatal conductance) as well as climate data (e.g. humidity, soil moisture content).
My model is:

$T_{leaf} = T_a + X + \epsilon$

And I currently assume X = 0 in my calculations
Is there a better way to estimate X?
Under what conditions would X < 0? X > 0?

I am not a plant physiologist but it seems very odd to me that people are just assuming that Tleaf = Ta without proving it. Surely there must be some old reference somewhere...

@nico perhaps because the error of measurement is >= than the error introduced by this assumption (e.g. if the delta-T is ~1-2C the error might be on the order of 10%). If there is a reference, I haven't seen it cited, and this assumption is made ~ 10% of the time - usually in older papers before thermocouples on the leaf surface at the time of measurement were integrated into standard equipment.

surely, but at some point someone must have started to use thermocouples on leaves... and didn't they check the relation of their leaf measures to Ta? I understand that you cannot generalize that to all plants/conditions, but at least knowing whether the initial assumption is correct would be good. Unfortunately, as I said, I cannot help you with that, my test subject do not have the same temperature as the ambient (and if they have something has gone terribly wrong... :D)

Leaf temperature is a function of air temp, water vapor pressure deficit, net radiation, stomatal conductance, and boundary layer conductance, among other things. Most of these change significantly within the course of a day (or more often), and consequently, so will the offset between leaf and air temp. There are some energy balance models that would be appropriate for estimating this offset (which I'll dig up if I get a chance).

One way to do this is to use the "humid operative temperature" equation, or something similar. A variant of this equation, specifically for estimating leaf temperature, is derived using a leaf energy balance equation in chapter 14.1 of the Environmental Biophysics book (cited below).
I'll let you look up the actual equation since I'm not sure how to do math symbols here. But, in addition to air temperature, you will need to know a few pieces of information:

Vapor pressure deficit - calculated from humidity and temperature.
Incoming radiation - Measured, or you could model this using time of day, latitude, etc.
Emissivity of your leaves - you can probably look this up for your species or a similar one.
Windspeed
Characteristic dimension of leaves - measure, or look up a value for your species (Use this with windspeed to calculate boundary layer heat conductance).
Leaf vapor conductance - a combination of stomatal and boundary layer conductance to water vapor. You must know something about where the stomata are on your leaf (both sides or one side), but you can often look this value up for a given species.
A few other constants that are easy to look up.

That's about it - its a somewhat hairy calculation, but if you have standard weather data and a little knowledge of the plants you are estimating the leaf temperature of, it should be manageable.
This equation and other relevant info are in this book:

Campbell, G.S. and Norman, J.M. An Introduction to Environmental Biophysics. Springer Science, 1998


text:
How does the brain's energy consumption depend on mental activity?
What is the impact of mental activity on the energy consumption of the human brain?
I am most interested in intellectually demanding tasks (e.g., chess matches, solving a puzzle, taking a difficult exam) versus tasks with a similar posture but less demanding (e.g., reading a newspaper, watching TV).
I heard that energy consumption stays remarkably constant regardless of the mental activity (and energy consumption can be explained by elevated heart rate due to stress). However, it seems to contradict techniques such as fMRI, where the change in metabolism is measured (unless the relative change is really small).

The energy consumption doesn't vary that much between resting and performing tasks, as discussed in a review by Marcus Raichle and Mark A. Mintun:

In the average adult human, the brain represents approximately 2% of
the total body weight but approximately 20% of the energy consumed
(Clark & Sokoloff 1999), 10 times that predicted by its weight alone.
Relative to this high rate of ongoing or “basal” metabolism (usually
measured while resting quietly awake with eyes closed), the amount
dedicated to task-evoked regional imaging signals is remarkably small.
The regional increases in absolute blood flow associated with imaging
signals as measured with PET are rarely more than 5%–10% of the
resting blood flow of the brain. These are modest modulations in
ongoing circulatory activity that rarely affect the overall rate of
brain blood flow during even the most arousing perceptual and vigorous
motor activity (Fox et al. 1987, Friston et al. 1990, Lennox 1931,
Madsen et al. 1995, Roland et al. 1987, Sokoloff et al. 1955).
[...]
From knowledge of these relationships, one can estimate that if blood flow and glucose utilization increase by 10%, but oxygen consumption does not, the local energy consumption increase owing to a typical task-related response could be as little as 1%. It becomes clear, then, that the brain continuously expends a considerable amount of energy even in the absence of a particular task (i.e., when a subject is awake and at rest).

Techniques like fMRI measure relatively small differences, their existence does not contradict the claim that the energy consumption of the brain doesn't change a lot between the resting state and performing an activity.

1. Raichle ME, Mintun MA. BRAIN WORK AND BRAIN IMAGING. Annual Review of Neuroscience 2006 Jul;29(1):449-476.

well there seems to be evidence that there is a lower and upper limit of energy concumption for doing cognitive CONSCIOUS/AWARE tasks my linked papers contain http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855379/bin/ukmss-29376-f0001.jpg So we have some evidence that energy consumption can not raise on and on, as we loose awareness then. It looks more like we need a distinct frame of energetic activity to allow consciousness at all. That fMRI is a pretty inaccurate method mainly useful for visualizing neuronal correlates is no big news.

I found Does Thinking Really Hard Burn More Calories? - Scientific American going in the same way - "Unlike physical exercise, mental workouts probably do not demand significantly more energy than usual. Believing we have drained our brains, however, may be enough to induce weariness".

What I wanna know, since the brain's energy consumption is a) constant and b) high for an organ its size, is: How can we INCREASE its energy consumption and get thin without needing to work out ?!

I answered on the facts of this question already on skeptics.SE, here and here. You should read both papers very carefully, I highlighted the most important facts but this is a very tricky question, esp. when it comes to defining what mental activitiy is. The papers also give an explanation of how fMRI signal is linked to NEURONAL activity, as far as I remember there is no strong direct link.
You assume in your question that a mathematician solving a differential equation needs higher mental activity than a child reading a book. Is this legitimate? It seems intuitive but also very subjective. In the paper they mention that for the highest and lowest energy consumption we lose consciousness. I will not draw conclusions from this. However, you are talking about conscious mental activities so this may answer your question. To me it means more that the understanding of the human brain in neurobiololgy is on the level of the Rutherford Atomic Model in Physics at the beginning of the 20th century. We have not really got a clue how information is processed and how it's constrained by physical laws and principles of entropy and energy. By reading the 2 papers it looks more like the human brain is not raising energy consumption as a computer would (the computer analogy pretty much fails when compared to the human brain). Most of the energy is used for unconscious processes in "standby mode".
As in physics, extreme cases such as savants and the mentally disabled are probably the best starting point to exclude possible models of human brain and physical boundary conditions as we cannot approach the questions of human brain in a reductionistic way. How can savants like Kim Peek process such huge amounts of information AND save it. He is able to scan books pages just once and know them by heart thereafter. His brain does not, however, consume more energy than an average human brain. So mental activity is probably not a very good term, quantity, or even really suited to be scientifically used. Does neuronal activity mean mental activity (in the sense of your definition?) Reading the papers, the problem is the separation of mental and neuronal activities. At first you have to know what are the basic brain functions and processes that are consuming most of the energy. However the brain is not built in modular way like a computer (most energy is used here for constantly refreshing RAM). So there is not really a objective way to analyse and separate this modular energy consumption, if it even is modular.
In my opinion, most models about information processing in human brain are intuitive guessing (again Rutherford). We need much more detailed experiments and data (Blue Brain Project). fMRi is like analysing a atom with a magnifying glass. Also, the more prosperous approach from a biophysical perspective is probably not the level of "mental activity" but the hard-based amount of information processed by human brains and linked energy consumption (Kim Peek). But therefore we need a model of how this information is saved in human brain. Do normal humans save the same information as Kim Peek scanning a page or are we just unable to recall it consciouscly? When solving a differential equation, how much energy do you consume when recalling facts and is that experience not similar to reading a book? How much is mental logical tasks and is there really a difference at all?
I will stop here, hope you gained some insight that the question is of course important but too early to be definitively answered. I think we will learn a lot more from projects like Blue Brain as we have from fMRI experiments.

Thanks, though I am far from making analogy with computer, especially when it comes to the information processed. Actually, the energy usage (at least - in principle) can be measured by heat generation, even if nothing is known about the process. "You assume in your question that a mathematician solving a differential equation needs higher mental activity than a child reading a book. Is this legitimated?" - hard to say; better to compare a mathematician during a few hour competition vs control.

@PiotrMigdal so what answer are you looking for? Any correlation between "mental activity" and energy, although you do not really define what the difference between neuronal and mental activitiy is? I'm a bit confused now. Measuring generated heat is far more inaccurate than oxygen consumption by fMRI. Even more unknown factors. Also in these papers they actually did compare cognitive tasks vs. resting brain afair. I'm not sure where I should point you to. Maybe you should ask first on cognisci.SE wether reading a book and solving a puzzle is really of very different kind. I tried to point

to some neurobiological facts. But lets wait for other answers it's for sure a tricky question, but imho currently too much terminological flaws for a clearcut answer.

@WernerSchmitt you may want to participate in this meta discussion =)

This sounds wishy-washy. In fact, we do have a pretty solid understanding of “how information is processed and how it's constrained by physical laws and principles of entropy and energy.” We might lack the computational power to build good predictive models but the physical, chemical and molecular biological basis is well understood. The whole “we don’t understand the brain” discussion is really a red herring. We do. It’s just that the brain models a very complex network with certain emergent properties, remodelling of which is extremely expensive.

@Konrad: If you don't now about the emergent properties then you don't understand the brain in a meaningful sense. More importantly if you don't think that predictive models are the standard for what it means to know something in science, than what's your standard?

@Christian I disagree. Most of classical science is simple enough to be grasped by us but this is a paradigm of the past. Models of biological systems, be it the brain, a single cell, an ecosystem or sociology, are simply too complex to be looked at in total, down to the smallest detail. You have to zoom in and out. As long as we have understanding on a given level and know how the levels interconnect, we understand the system. If you demand that we can look at all levels at once then I predict that modern science will fail. In all the examples listed.

@KonradRudolph Yes, modern science is a failure. Drug discovery is still mostly a matter of bruteforcering componends through huge screening libraries and then hoping that a few componends that hit go through clinical trials. Nearly all drugs fail. The number that succeeds is statistically insignificant (p<0.05). We don't even make process at getting better but discovery of new drugs. As each year goes by  exponentially more expensive to discover new drugs through Eroom's law. Then we don't even really know how those drugs that do work, work.

@Christian Note I talked about the principle. If you don’t think science can ever understand these subjects, why do you study bioinformatics, then? Drug discovery is a completely different thing: we simply don’t have any good models here (but note that this is changing – will change).

@Konrad: (1) When I choose to study bioinformatics I had a bit more faith in it. I don't think the the molecular biology field produces the return it promises. My personal bets are on QS/Health2.0. (2) I'm not saying that science will never understand the subject. I'm agnostic about whether it will. If you however want to claim that you understand something in a scientific sense than you got to make predictions with your model. Redefining success is silly.

This answer relates closely to the classic myth

We only us 10% of our brain power

As with many truisms it holds a grain of truth.  Large areas of the brain are specialized for tasks like the visual and motor cortices.  Other areas are known to be responsible for spatial memory (hippocampus) and emotional learning (amygdala).  Higher order functions like you're describing are classically assigned to the prefrontal cortex, but that means little.
Because there is some level of functional specificity throughout the brain, the fMRI studies you mention generally look at many places in the brain (nearly) simultaneously.  They then compare relative activation in different areas under different conditions, and are clever about how they frame their experiments to determine which areas are associated with which responses.
The most common method of measuring activity is through the BOLD response, which measures haemoglobin's oxygenation state as a proxy for the amount of blood flowing into the area under the presumption that there is high metabolic demand there.  For the purposes of this discussion, this is fairly useful since glucose delivery should be a reasonable proxy for metabolic demand even if it has limitations when it comes to predicting neural activity.
So which areas are metabolically more active while doing a cognitive activity?  In this study they test exactly that.  Their basic finding is that chess does increase mental activity in certain areas of the brain, particularly the parietal and occipital lobes in real game conditions, and that the activation was relatively bilteral between the left and right hemispheres.  I just glanced through it, but it looks like the authors were surprised that the activation was less pre-frontal and more visuospatial.
I believe this supports the logical conclusion: thinking takes energy.  But your brain is used for many things, so the change in activation is best understood in a relative sense.  Watching TV also takes energy, preferentially in the visual cortex.  As does playing ultimate frisbee, in the motor cortex.
References:

Logothetis, Nikos K., 2008. What we can do and what we cannot do with fMRI, Nature 453, 869-878
Atherton M, Zhuang J, Bart WM, Hu X, He S, 2003. A functional MRI study of high-level cognition. I. The game of chess, Cognitive Brain Research 16.

authors: СМ13-11М Кузин


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By what mechanism does penicillin resistance usually develop in Streptococcus pneumoniae?
There are three mechanisms:

prevention of the interaction between antibiotic and the target PBP;
modification of the binding of the antibiotic to the PBP;
hydrolysis of the antibiotic by a beta-lactamase.

Medical Microbiology, 6e, p. 200, Murray

PBP: penicillin-binding protein
It may be the case that the most common mechanism is not known.
It is just one of these three depending on the situation.
What is the most common mechanism by which penicillin resistance develops in S. pneumoniae?

I think your guess is quite spot-on. According to this scientific article I found online, They did a whole genome sequencing on penicillin-resistant Streptococcus pneumoniae and their conclusion was

....is mediated by a mosaic of genes encoding altered
  penicillin-binding proteins (PBPs). Nonetheless, S. pneumoniae has
  also developed non-PBP mechanisms implicated in penicillin resistance.

In clinical medical laboratory point of view, S. pneumoniae's AST is done with oxacillin instead of Penicillin because OXA gives better cut-off between Susceptible, Intermediate and Resistance. You may see a big zone of inhibition when you used PEN disk but that doesn't mean the isolate is susceptible to PEN. This may suggests that "hydrolysis of the antibiotic by a beta-lactamase" is less likely to be the main mechanism?

Very good answer!

Maybe you are asking where these genes came from and how they became so common?
It turns out that antibiotics are very common - many free living plants and microorganisms make antibiotics.  Penicillin, the first beta lactam antibiotic found is synthesized by a fairly common mold, they kill bacteria by inhibiting the synthesis of the cell wall.
All three of these classes of defense have evolved over the hundreds of millions of years of evolution since antibiotics like penicillin started showing up (probably more like billions of years).  They have all probably been with us for quite a long time.
Beta-lactamases, which enzymatically neutralized the beta lactam ring of penicillins and related compounds seem to have evolved three times and its not hard to imagine why the genes have stuck around for so long.
dd-transpeptidase, the 'penicillin binding protein' is actually an enzyme that helps to synthesize the peptidoglycan of the cell wall.  It can also mutate such that it tends not to bind penicillin so well, creating a second sort of penicillin resistant bacterium.
Other genes such as ABC drug transporters can kick out strange molecules before they can cause any damage.
These and all other sorts of mutants and genes that convey resistance, once created through selection are around in the huge bacterial gene pool.  Bacteria can pick them up through lateral gene transfer, plasmids (sex), phages and by taking in DNA from the environment.  Most of these genes and traits were sitting around for millions of years, but the increased use of antibiotics has increased the selection pressure to retain these traits in many more bacteria.  That's really where bacterial antibiotic resistance comes from.


text:
Cell proliferation limit and senescence of embryonic stem cells and fibroblasts
I am trying to understand the importance of proliferation limits and cell senescence. In particular, I would like to compare the proliferation limit of Embryonic Stem cells (ES) and fibroblasts (which would be trans-differentiated) and describe how this difference plays a role when thinking about engineering organs, for example a heart transplant.
How do ES cells and fibroblasts compare with regards to the Hayflick limit?

You are right but this is  Not a homework question.

You may want to change the wording a bit, then as compare the proliferation limit and describe how makes it sound like it came from an assignment, it will probably get more attention :) I will delete my other comment then.

Telomeres (caps on the ends of chromosomes that are gradually shortened during each cell division) determine the maximum number of times a cell can divide, known as the 'Hayflick limit'. Cells that are able to express telomerase, an enzyme capable of extending the telomeres, can divide indefinitely.
There are various types of stem cell in a body which replenish the 'pool' of cells in the tissue once they reach the end of their useful lifespan. Each stem cell expresses telomerase to lengthen the telomeres after a round of cell division. The inhibition of telomerase in somatic (normal) cells is a major 'challenge' for cancerous cells - in order to achieve uninhibited proliferation, they must express telomerase. Thus, there are many molecular similarities between stem cells and cancerous cells (well, with regards to telomerase, anyway!) [ref].
Fibroblasts are somatic cells - they are the 'normal' cells that make up the vast majority of organsisms. The only cells not known as somatic are gametes/germ cells and stem cells. They thus do not express telomerase, and have a replicative lifespan, also known as a Hayflick limit.
With regard to your question about engineering organs, there are many resident stem cells in tissues (and thus organs) that 'top-up' the somatic cells when required. As organisms age, this pool of stem cells becomes depleted [ref]. Artificially engineering an organ such as the heart (I assume this is what you mean) would be inherently difficult, as many vascular cells are not replaced, but can last a whole lifetime - this is also true for many neuronal cells. So replicative lifespan is not necessarily related to lifespan!


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Why can't a human regenerate limbs like some other species?
When a person's arm is amputated, the arm will no longer be able to grow back. However, in salamanders, the arm actually grows back.
In comparison to a human, what is really happening to the cells in the wounded area in salamander ?

Certain parts of the human will regenerate, though (liver for instance)

well it is not as fast as the salamander .. lets say an arm why wouldn't it regenerate ?

Our limbs do regenerate - but only up to a certain point. If you cut off up to about 0.5cm from the tip of your finger, it will completely regenerate. (No, DO NOT try this just because I said so.)

After salamanders (or certain other amphibians) lose a limb, the epidermis migrates to cover the wound, forming a structure known as the apical epidermal cap. The underlying "stump" then generates a de-differentiated mass of cells from normal tissue. In most cases, these cells will express genes that are vital to the proper formation of limbs, such as HOX genes. This "lump" of cells at the stump of the wound are typically referred to as a blastema. Basically, the blastema continues to grow and regenerate the limb in a way similar to fetal growth. Though mammals (including humans) also have some regenerative capabilities, they are much more limited. In addition, many regenerated limbs will also be mildly deformed (square fingernails). In axolotl salamanders, it was found that certain retrotransposons, such as the LINE-1 element, were prevented from "jumping" around in the developing blastema during limb regeneration. The two active proteins PL1 and PL2 were responsible for inhibiting the activity of LINE-1 and other such retrotransposons. Active retrotransposons can potentially rearrange the genes in germ cells can be detrimental to the mechanisms that allow the blastema to replicate and differentiate, so the PL2 and PL1 proteins play a vital role in their regenerative capabilities. When the PL2 and PL1 proteins were "switched off" in certain axolotl salamanders, their regeneration was much less efficient. Since mammals lack the PL1 and PL2 proteins and have a different LINE-1 retrotransposon, they have reduced regenerative capabilities.
Sources:
Wei Zhu, Dwight Kuo, Jason Nathanson, Akira Satoh, Gerald M. Pao, Gene W. Yeo, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Development, Growth & Differentiation, 2012; 54 (7)
Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology, 2012; 370 (1)
Odelberg SJ (August 2004). "Unraveling the Molecular Basis for Regenerative Cellular Plasticity". PLoS Biology 2 (8)

For salamanders, when they lose a limb, they have cells called fibroblasts that migrate to the wounded area. These cells are not differentiated and are able to be differentiated to whatever is necessary for regeneration. That sort of cellular differentiation for repair doesn't happen for us humans, yet. Give synthetic biology about 20 more years. :D

Sorry, but this answers only begs for the question: how are salamander fibroblasts different from human fibroblasts? By the way fibroblasts are differentiated cells.


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How can GMO contaminate biologic plants?
Let consider two use cases :

I am the only farmer within a 200km radius. I first grow GMO plants. A few cycles later I decide to grow bio plants, so I uproot all of the GMO plants and plant fresh new bio plants.
I am surrounded with GMO plantations and I decide to grow bio plants.

In both cases, can we consider the plantation as bio or was it contaminated and how?

First let me say this: I am no gardener. Every plant that enters my home or yard dies a slow death of neglect. I do have some experience trying to remove weeds from other non-weeds, and there is a practical aspect of "uproot every GMO plant" that I think may be impossible, but this is speculation. Let's get into a literature review.
A frequently cited paper is Dröge, M., Pühler, A. & Selbitschka, W. Horizontal gene transfer as a biosafety issue: A natural phenomenon of public concern. Journal of Biotechnology 64, 75–90 (1998). Table 3 contains the most relevant information about horizontal gene transfer between plants.
In situation number 1, consider that the rhizosphere (the area of soil around the root of a plant) is constantly populated with bacteria. These bacteria are shown to sometimes transfer genetic material to and from the plant, through the roots. Unless you somehow sterilize the soil after uprooting your previous crop, consider everything you plant in that field possibly contaminated.
Situation 2 is less clear, but Monsanto does sue farmers found to be using their seeds without a contract, and many farmers say this is because of cross-pollination. I think you should assume that your field will soon be contaminated.

Unless you somehow sterilize the soil after uprooting your previous crop, which is not very smart if you want to grow something else afterwards!


text:
Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology
Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?
I have tried the following:

Batch tool for GSFS: PROBLEM: It says that my input yeast genes are not human genes (which probably means that the tool will work only with Human genes).
http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php : PROBLEM: provides score for every gene pair input. I have ~3600 genes. Impossible to do it for eveyr pair.
DAVID batch viewer gives a 1xN matrix (functional similarity score of one gene to a set of N genes, when I want all possible pairs of similarities which will give an NxN matrix)
GO funsimmat- I am unable to get this to work, so I'm not sure if it will give me the desied results.
GO FastSemSim- same as 4.

I think that you could try a similar approach to GSFS:

use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene)
use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..)
divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order frequencies

Now, you could use DAVID or similar (try wconsensus: it's old, basic but very custom) to compare similar sequence and obtain your scores.


text:
Where can I find a transcriptome of a normal uveal melanocyte?
I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?

I can't find any transcriptome data, but I did find miRNAome data from GEO at NCBI and Array Express at EMBL.


text:
How do archaea relate to eukaryotes and bacteria?
I've read that they all share some genes, internal structure, and behaviour with each other, but with different degrees of overlap depending of what the function is. E.g., archaea have some eukaryotic and some bacterial function, and eukaryotes have bacterial function in the form of mitochondria and plastids.
However I'm finding the nitty-gritty of all this rather confusing. Could anyone please explain some of the detail for me as I can't seem to make any sense of this from reading Wikipedia, etc.

Heheh!  Wish I could upvote your username, "Luke".  :)

The relationship between the three is so overly complicated because of horizontal gene transfer, i.e. cells sharing parts of their genome with others instead of the normal passing-down to the next generation. This works between eukaryotes, archaea and bacteria and causes the mixing of the three.
An overview (originally proposed by Woese et al):

Bacteria are simplest considering cellular organisation. They have no nucleus or other internal membranes and no cytoskeleton. Their DNA is generally "junk-free"* (i.e. no introns), not bound by histones ("organising" proteins) and the organisation of regulatory sequences is relatively straightforward, typically with one 'operator' sequence before a gene.
Eukaryotes are complex cells in comparison. They have a nucleus and are full of internal membranes (ER, golgi, vesicles,...). Their complex cytoskeleton allows them to grow very large in comparison. Their DNA is usually full of more or less "junk"*, organised into tight bundles by histones and they tend to have a ridiculous amount of regulatory sequences way before, just at the start and even inside genes. Very importantly, they possess endosymbionts as you mentioned - mitochondria or plasmids, derived probably from some protobacterium.
Archaea at first appear to be a mixture between the two. A nice way to sum it up (though not very accurate) is "eukaryote in a bacterium's clothing". Their cells look a lot like prokaryotes because they are similar size, have no nucleus, endomembranes or cytoskeleton. However, some archaeas' DNA is bound by histones and they use similar machinery as eukaryotes for DNA replication, transcription and translation.

One possible explanation for this (theory by Margulis & Schwartz as explained by my tutor) is: From the last universal common ancestor, first prokaryotes and archaea diverged. After this branching, the differences in genetic machinery evolved. Archaea then branched, producing a protoeukaryote line which went on to endosymbiosis with some protobacteria. That would explain the similarities I outlined above: similar cell structure between archaea and prokaryotes but similar genetic machinery between archaea and eukaryotes.
It gets a bit more complicated though, because archaea and bacteria can exchange genetic material, and eukaryotes incorporated a lot of their endosymbionts' DNA in their own genome, so you end up with all of them having a huge mix of genes from the others.
Edit: Genetic machinery refers to the enzymes used for DNA replication and transcription (DNA and RNA polymerase and the transcription initiation factors) and translation (ribosomes and several other translation factors involved). For example: Prokaryotes only have one type of RNA polymerase which uses sigma factor to bind the initiaion site. Eukaryotes and archaea both have three types of RNA polymerase which use TATA-binding protein for initiation. Or: In Prokaryotes, the translation start codon codes for formyl-methionine while in eukaryotes and archaea it codes for "normal" methionine. (Source)
*) Unrelated to your question, but in my own defence: I am aware that the usage of the word "junk" is somewhat unaccepted nowadays, because it supposes that there is "useful" and "unuseful" genetic material. Also, some of what was thought to be junk has been identified to have regulatory function etc. However, it's also a fact that a lot has been identified to have no function to the cell whatsoever, most of it parasitic DNA which is dead or still happily replicating away (LINEs and SINEs). That is, "junk" to the cell.

Thank you for your reply, very interesting and certainly explains a lot! Could you please clarify a little further what you mean by genetic machinery though, and what are differences?

Made an edit :)

“just a theory” … aaaargh! Otherwise very nice summary, the only thing it’s missing is references. If I find time later today I’ll dredge them up, I have them somewhere …

Here's ref :) I could only find it on amazon though.

Isn't this the Margulis & Schwartz paper?

The link is the book my tutor gave as reference but that paper could have the same content.

Indeed the situation is a bit complicated and not totally well understood.  Archaea and bacteria are superficially very similar, they're both small, have circular chromosomes, and not a lot of internal complexity.  However, there are some very important differences, most notably they have very different cell membranes.
The origin of the eukaryotic cell is a very difficult subject, as it evolved over 2 billion years ago in organisms that don't fossilize well and there are no living descendants of intermediate forms.  (E.g. every known Eukaryote is descended from a eukaryote that already had mitochondria.)  My understanding is that the leading theory is that the eukaryotic cell was formed by endosymbiosis between an archaeon and two bacteria.  In that model the nucleus is descended from a methanogenic archaeon, the cell membrane is descended from a myxobacteria, and the mitochondria is descended from a proteobacteria.  But this is not fully understood, and there are several competing theories on the details.
One place to start reading about this (beyond wikipedia) is a nice article by Carl Zimmer in Science.


text:
How Do Large Ocean Viruses Form Their Own Organelles?
Several large viruses (Arslan 2011) form their own organelles within the amoebae they invade.
How do these organelles form?

Reference:
Arslan, D., Legendre, M., Seltzer, V., Abergel, C., Claverie, J-M. (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. PNAS 108(42): 17486-17491 [DOI]

The organelle form in the same way they would if they were coded for by the host's genome, except in this case the virus uses its own genome to specify the type of organelle.
The article you link to indicates this.  The "systems" in the quote are in part the organelle that it needs

A study of the giant virus’s DNA shows it to have over a thousand genes, the biochemical instructions it uses to build the systems it requires to replicate once inside its host.