text:
How does skin healing work?
I stacked my bike and split my head right open.  About three weeks later the scab falls off and the skin is sealed over, like magic!  How does it all work?  How does the brain know that part of the body is injured and needs repair, or does the brain know at all?  What kind of signals between brain/cells/body are involved.
Sorry it's probably a basic question for a biologist, but I come from a different field and have always wondered about this amazing process.  It's also a very hard topic to google about, because most results are about spiritual healing, crystals, prayer and a lot of pseudoscience rubbish.

There's a WP page at http://en.wikipedia.org/wiki/Wound_healing , and I'm pretty sure that your brain has nothing to do with it.

Healing in the body is normally independent of the brain. Following an injury, a process of inflammation attracts lots of cells to the site of the injury (including platelets, white blood cells, clotting factors). There's also vasoconstriction (tightening of your blood vessels) to reduce blood loss from the injury site. Your skin cells continue to divide rapidly until new skin replaces the damaged one which later falls off. This is a highly simplified version of the process but hope it makes sense. So in summary, healing takes place by cell division (also known as mitosis).

Amongst other things, contact inhibition is also important to stop the cells from over-proliferating.

Hm, do you think that is also possible explanation of the kind of placebo case with soldiers whose injuries healed more slowly if was stressed? How brain tightens the blood vessels?

aha, http://www.dana.org/Publications/ReportDetails.aspx?id=44313 says something quite different


text:
Why does strenous exercise cause vision of "lights"?
I had a hard climb a week ago. I got so tired then any time I closed my eyes I saw these lights inside my head. I see these lights almost every time that I run fast or some thing like that. What are they and where do they come from?

Here is a picture I drew using Photoshop ;)

I sometimes see similar “lights”, too. Although of somewhat different shapes.

interesting that you see hexagonal shapes. Hexagons often appear in 2D sensory processing due to its relation to sphere packing.

I have exactly the same, and have had for at least the last 40 years with no apparent ill effects.  They are in the middle of my foveal region and flash fast, maybe 30 Hz.  I get them during exercise but more noticeable immediately afterwards, until my heart rate slows.

I also get "seeing stars" but that's completely different.  For me seeing stars when I stand up suddenly involves multiple (10ish) tiny, bright white points of light randomly distributed across my entire visual field, that move rapidly (maybe 10% of the visual field) in semi-straight lines, for about 1-2 seconds, then suddenly stop, one by one, with a few persisting longer than the others.  It's a totally different visual phenomenon than the "centre flasher" the questioner describes.

This is a common phenomena which most of us come across. Seeing flashes of light, stars and other shapes in the eyes occur when the body goes through stressful activities. For example while you are climbing the blood flow will be more to other prominent parts like hands and lower waist so brain and eyes will get less supply of blood as well as nutrients. Hence those flashes or stars are visible to us. This phenomena is called "Phosphene" and a phosphene is a phenomenon characterized by the experience of seeing light without light actually entering the eye.
Wikipedia/Phosphene gives an explanation for occurrence of Phosphenes:

Phosphene is "seeing stars", from a sneeze, laughter, a heavy and deep cough, blowing of the nose, a blow on the head or low blood pressure (such as on standing up too quickly or prior to fainting). It is possible these involve some mechanical stimulation of the retina, but they may also involve mechanical and metabolic (such as from low oxygenation or lack of glucose) stimulation of neurons of the visual cortex or of other parts of the visual system.

So seeing flashes of light can be due to:

Blood shifting.
Low blood sugar(causes weakness).
Head trauma.
Headache.

So to summarize this thing, we should have enough nutrients, water supply to the body whenever we come across stressful activities. Phosphenes are temporary stuff which do not harm eyes.

One question, I also experience this pattern in my eye all the time I do workout. But in my case the pattern is always the same, meaning the "stars" are always at the same place, having always the same shape. Are those also phosphenes or are they normally 'random' in shape or position?

It could be posterior detachment of the vitreous humor. Stress on the optic nerve caused by motion of the vitreous humor inside the eye can lead to the sensation of lights. And since the nerve is circular, you see a pattern of circular light. Normally its not serious, and many people experience it as age progresses. If you are not hydrating well during your climbing that might also be aggravating it. To be safe you should have an eye doc check you out though since there is slight risk it could lead to retinal detachment.

This is very much like calling out "Zebra!" when you hear hoof beats (unless you happen to live on the grasslands of eastern and southern Africa. In that case, it's more like calling out "Caribou!"

@anongoodnurse I'm also a climber, a runner, experience dehydration and on occasion experience the same light sensations when I press my eyelids tight suddenly or turn my head suddenly left to right at night. And this is what my doctor diagnosed. So what are you suggesting might be the issue otherwise besides grassland animals?

What your doctor said doesn't carry much weight with me. They and I are of differing opinions. I don't think I could be any clearer expressing my opinion. If every time someone who exerted themselves saw lights it turned out to be a pulling on the retina, opthalmologists would be more common than dirt.

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text:
What is the difference between SOLiD, 454, and Illumina next-gen sequencing?
I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in terms of sample/library preparation and chemistry. How difficult is it for a protein veteran but next-gen newbie to get high-quality useful reads? I'm mainly going to be looking at antibody diversity, but consider this in general terms for any next-gen project.
I understand the basic theory of fluorescent chain-termination sequencing, but it's been a number of years since I last did it, and my career is now taking me back into the DNA realm.

I think this question is a bit broad and perhaps you should read through the manuals / data sheets for the respective products.

I'll narrow it a bit.

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one.
Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further takes part in downstream light-producing reactions. The amount of light is proportional to the incorporated number of nucleotides. The DNA is fragmented and adapters are ligated at both ends. The fragments are mixed with agarose beads, which carry adapters complementary to the library adapters, and thus each bead is associated with a unique DNA fragment. The beads and DNA fragments are isolated in individual micelles, where emulsion PCR takes place and million copies of the single fragments are amplified  onto the surface of each bead. Each bead is placed in a well of picotiter plate (PTP), as the wells have dimensions such that only one bead can fit per well. Enzymes are added to the beads and pure nucleotide solutions are added with an immediate imaging step. On one side of the array a CCD (charge-optic device) camera records the light emitted from each bead. The first four nucleotides (TCGA) are the same as the start of the adapter, which allows for the emitted light to be calibrated according to the type of nucleotide added. The major disadvantage of this method is the misinterpretation of homopolymers (consecutive nucleotides, e.g. AAA or CCC). Such areas are prone to insertions or deletions, as the length of the stretch can be inferred only by the intensity of the light emitted. On the other hand, substitution errors are very unlikely. The 454 FLX instrument generates ~400 000 reads per instrument-run, as the reads are 200-400bp. The greatest advantage of this platform is the read length, which is the longest of all second generation technologies. Although sequencing on 454 platform is more expensive than sequencing on Illumina platform (40USD per Mega base versus 2USD per Mega base), it could still be the best choice for de novo assembly or metagenomics applications. (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
Illumina is the most frequently used one. The DNA to be sequenced is fragmented into about 200 base strands. Adapters are ligated onto the ends of the fragments and one of these adapters is hybridized on a flow cell. Illumina essentially utilizes a unique "bridged" amplification reaction that occurs on the surface of the flow cell. Localized PCR reaction is performed, and each of the hybridized pieces of DNA will get locally amplified to generate clusters which will have the exact same molecule. Subsequently, the DNA sequence is determined by adding a primer on one of the ends of the molecule. A mixture of modified nucleotides is added. Each one of them carries a base-specific fluorescent label attached to it. Also, each one has the 3' OH group blocked which ensures the incorporation of one nucleotide at a time.  The flow cell is placed under a microscope and when light is shined on its fluorescence, the emission light shows which base was incorporated on each one of those clusters. The Illumina read length is approximately 35 bases, but over billion reads are generated at a time. The major error type is substitution, rather than deletion or insertion (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
The SOLiD platform utilizes the use of DNA fragmented library, which is flanked by ligated adapters. The fragments are attached to small paramagnetic beads and emulsion PCR is performed to amplify the fragments. In contrast to the other sequencing platforms, sequencing by synthesis is performed by utilizing DNA ligase, rather than polymerase. Each cycle of sequencing involves the ligation of a degenerate population of fluorescently labeled universal octamer primers. A specific position of the octamer (e.g., base 5) carries a fluorescent label. After ligation, images are acquired in four channels, followed by cleavage of the octamer between positions 5 and 6, removing the fluorescent label. After several rounds of octamer ligation, which enable sequencing of every 5th base (e.g., bases 5, 10, 15, and 20), the extended primer is denatured. Different primers can be used to examine the previous or next positions (e.g., base 3 or 6).  The platform can use primers which carry two adjacent correlated with label bases. This approach involves the examination of the bases twice in a cycle, which decreases the error rates. SOLiD read lengths are 25-35 bp, and each sequencing run yields 2–4 Gb of DNA sequence data (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).
References:

Mardis, E., Next generation DNA sequencing methods. Ann. Rev. Genomics Hum. Genet, 9: 387-402 (2008). DOI 10.1146/annurev.genom.9.081307.164359
Shendure, J. and Ji, H., Next-generation DNA sequencing. Nat. Biotechnol., 26: 1135-1145 (2008). DOI 10.1038/nbt1486

Do you have links to the papers and figures you cited? This kind of looks like it was cut and pasted from somewhere...

@MattDMo Yeah, it was pasted from an essay/review which I wrote for next generation sequencing. I will add  the references.

@MattDMo Thanks for your edit (I'm sure a second person will approve it soon), but if you're adding links, consider adding a DOI link as well, that way if PubMed changes their IDs or something, people can still find it.

@jonsca I use this link format according to the recommendations by PubMed. As far as I know, PMIDs are immutable. Also, this link format provides an abstract, and sometimes several choices for retrieving the full text - PubMed Central, journal homepage, Springer and its equivalents, etc.
Has there been any discussion on meta about which link format is best? If not, I can start one...

@MattDMo Definitely feel free to leave the PubMed link.  I was saying add the DOI link as well.  The DOI is a permanent identifier that follows the publication around nearly forever.  The link is http://dx.doi.org/<identifier here>.  If you'd like to start a Meta question about it, feel free.  I'm not trying to pick on anyone here, I just figure if you're already taking your valuable time to edit in the PMID, it's just one step further to get the DOI.

@jonsca Got it. Links have been added for your pleasure :)

@MattDMo One too many "feel free"s, I hope you felt free :) Thanks for doing so!  I may start a Meta question about it anyway, as I think it's great prevention against link rot.

It's not easy to write down a comprehensive answer to your question, I would suggest you read this paper Field guide to next-generation DNA sequencers, which provide very good comparison of the NGS platforms

Can you summarize that paper?

It's also not open-access, so I can't read it...

Which is why a summary would be nice...

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text:
Do cold blooded animals generate any heat?
In explaining energy and work to an 8 year-old I said that all conversion of energy generates heat as a by-product.  For example, cars generate heat in their engines and running generates heat in our bodies.  Then the 8 year-old said, except for cold-blooded animals.
So my question is, do cold-blooded animals generate any heat in their conversion of stored energy (food, fat, etc) into motion?  If they generate heat, why are they cold-blooded?

An easy way to convince the 8 year old is to catch a lizard sunning itself. I assure you it will be warm to the touch.

They do generate heat. They just do not SPEND energy specifically on heating their bodies by raising their metabolisms. This is a form of energy conservation. The metabolic rate they need to live is not nearly enough to heat their bodies.
An example of spending energy to heat the body is seen in humans  shivering. Here muscle is activated not for its usual purpose, but to function as a furnace. "Warm-blooded" and "cold-blooded" is somewhat a misnomer. The correct way to think of it is...
Endotherm or ectotherm. Does the heat primarily come from within (endo) or from the surroundings (ecto). Endothermic animals include mammals. Most of their body heat is generated by their own metabolisms. Ectothermic animals include reptiles and insects. They absorb most of their body heat from the surroundings. This is not the same as saying they let their body temperature fluctuate with their surroundings, some avoid this by moving around to accomodate themselves.
Homeotherm or poikilotherm. Homeotherms want to maintain homeostasis for their body temperatures. They don't want it to change. Poikilotherms do not exhibit this behaviour, instead their body temperatures vary greatly with the environment.
We can have endotherm poikilotherms, such as squirrels, who let their body temperature drop while hibernating. Endotherm homeotherms, such as humans, where temperature is constant by means of complex thermoregulation. Ectotherm homeotherms, such as snakes (moving into shadow or into the sun to regulate temperature), and ectotherm poikilotherms, such as maggots.

Are birds endotherm homeotherms even though they are technically considered reptiles?

I'm fairly certain that you were right in your initial hunch that heat is almost always a byproduct of metabolism (which is never 100% efficient). The difference between endothermic ('warm-blooded') and ectothermic ('cold-blooded') organisms is just where the primary source of body temperature regulation comes from (either from metabolic reactions in endotherms or from the environment in ectotherms).

In other words, warm blooded animals have physiology to actively maintain their body at a certain temperature whilst cold blooded animals don't bother, just matching their environments temperature and using behavioural strategies to avoid dangerous temperatures.

As the others have said, animals and insects (and even plants) generate heat through metabolism and can regulate their temperature this way.
Just wanted to add a third point that mammals have developed brown fat, fat tissue which is dark with extra mitochondria which burn energy to generate heat.  These are rich with uncoupling protein (a particular uncoupling protein called thermogenin) which passes protons through the mitochondrial membrane to generate heat rather than generate ATP.
Most of the heat generated by mammals is not from brown adipose tissue, but it is a particular adaptation to generate heat that endotherms have evolved.  The brain alone is responsible for 16% of the heat generated by human bodies.


text:
How do circulating androgens contribute to higher rates of hirsuteness in some women?
I was reading up on ethnic groups in which the women are naturally more hirsute (such as South Asian women) in the context of evolving standards of beauty. I came across this statement on a forum:

Hirsutism is much more common in South Asian women (particularly North Indians such as Punjabi Sikhs) asymptomatically because they tend to have higher levels of circulating androgens than your typical [North or Western European ethnic group]. This is also true of Eastern European women to an extent.

Per Wikipedia, I learned:

Circulating levels of androgens can influence human behavior because some neurons are sensitive to steroid hormones. Androgen levels have been implicated in the regulation of human aggression and libido. Indeed, androgens are capable of altering the structure of the brain in several species, including mice, rats, and primates, producing sex differences.

So: do circulating androgens trigger higher testosterone production in some women? Is this what yields higher instances of "hirsutism" among certain populations? How are some women more prone to this than others? (That is, per the forum post, why are South Asian women more likely to have this than Western European women?)

I'm something of an armchair biologist, so please edit this to use better/more standard terminology as needed. I don't mind at all!

Testosterone IS an androgen, so I'm not really sure what you are asking.

@AlanBoyd Ah! See, that's the piece that I'm missing. I guess then, I'm asking: why do some women have more testosterone than others? And does this directly relate to how "hirsute" she is?

This review may be of interest:
Sharma D, Shanker V, Tegta G, Gupta M, Verma GK. Clinico-investigative profile of patients of hirsutism in a tertiary level institution. Int J Trichol [serial online] 2012 [cited 2013 Feb 9];4:69-74. Available from: http://www.ijtrichology.com/text.asp?2012/4/2/69/96904
As for the genetic causes of hirsutism, researchers thought the number of CAG repeats in the androgen receptor gene might play a role, but there was no evidence to that effect, as of 2000.  I couldn't find any newer papers, but here you go: http://jcem.endojournals.org/content/85/4/1735.
This paper was cited by the previous review, but Sharma et al didn't read more than the title, because they cited Calvo et al as evidence for the role of CAG repeats in hirsutism.
tl;dr: read Sharma et al, and look up the references.


text:
Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?
Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?
Wikipedia says

The actual role of bacteria in the low-temperature formation of
  dolomite remains to be demonstrated. The specific mechanism of
  dolomitization, involving sulfate-reducing bacteria, has not yet been
  demonstrated.

I wonder if someone has any updates on this. The reference given in the Wikipedia article is from 2000, from a source titled suspiciously "Journal of Conference Abstracts". Now it's 2013 and maybe someone else has found out something new.

The appropriate answer seems to be that bacteria help somewhat sometimes, maybe.
The evidence for this appears to be mixed, and appears to have been historically controversial.
One old-ish paper claims that bacteria (and more importantly, Archaea) are necessary at least under some conditions. Another somewhat later paper including some of the same authors claims to have found conditions for abiotic dolomite synthesis in the laboratory.
It appears that in terms of mechanisms, the relevant process may involve the proper state of magnesium ions, to which apparently microbes contribute via extracellular polysaccharides:

Literature values for carboxyl group density are not available for all bacteria involved in dolomite formation, however Braissant et al. (2007) demonstrated disordered dolomite phases forming in the presence of the EPS of sulfate reducing bacteria with a carboxyl group density of ~10-3 moles g-1, similar to our values. We suggest that these carboxyl groups promote desolvation of the Mg ion, known to be a kinetic inhibitor in dolomite precipitation (Wright and Wacey, 2004), but are needed in a high density for nucleation to commence.

However, what process exactly is generating geological dolomites appears to be still a matter of debate, and also here, with some suggestive evidence in favor of microbes affecting that process.

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text:
Manipulating Gut flora in vivo
I am tasked with designing an in vivo experiment in humans that requires manipulating the gut flora in one sample group to gauge its effect. Please suggest ways of doing this besides administering antibiotics.
I am of the view that antibiotics may have unintended consequences and may be unethical; explain any opposing view.

I think it would be helpful if you explained more about what you want to compare, and/or the rationale for experimentation. What do you want to gauge its effect on? Before/after antibiotics is probably the simplest and certainly statistically the most powerful approach.

i'm sure that changes of diet would also substantially change the gut flora mixture.  this has been shown already, but i don't have the reference at hand...

I can't think of any way to start with an intestinal "blank slate", so to speak, except with antibiotics.
Perhaps it's possible to at least partially homogenize/standardize a sample group's biota with probiotics?
If it's ethics you're worried about, perhaps draw experimental subjects from a pool already being treated with antibiotics (although this, I suppose, introduces it's own biases?).

Thank you Atticus29, this has re-assured me that antibiotics is the way to go..

I'm no expert, but I read this, and I found it very intresting:

In its study, Henry Ford treated patients between May 2010 and June
  2012 with a therapy called intestinal microbiota transplantation
  (IMT), using donated stool from a healthy family member.

Here are the results:

“More than 90 percent of the patients in our study were cured of their
  C.diff infection,” says Dr. Ramesh. “This treatment is a viable option
  for patients who are not responding to conventional treatment and who
  want to avoid surgery."

http://www.henryford.com/body.cfm?id=46335&action=detail&ref=1757

Thanks. I knew that was an option, but not viable for my study. Reason is: I want to gauge low level microbiome against normal. In essence, I need reduced gut flora and not different flora..+1 though. Just realised I cant't upVote..:)


text:
What is Chronic immobilization stress (CIS)?
I am trying to self study BNDF a little bit when I found this article:

Abstract Stress impacts multiple systems within the CNS, including the
  hippocampus. A key molecular mediator in hippocampal functions,
  including learning and memory, is brain-derived neurotrophic factor
  (BDNF). BDNF mRNA is reported to be decreased following chronic (every
  day) immobilization stress (CIS) in the rat, however the effect on
  protein is unknown. Utilizing a mouse model of CIS, the hypothesis
  that total hippocampal BDNF protein, in addition to BDNF mRNA, would
  be decreased was tested. The effects of intermittent (alternating day)
  immobilization and cold stress on hippocampal BDNF protein levels was
  also examined.
In this study it was demonstrated that CIS results in a small (8 per
  cent decrease relative to non-stressed controls), but significant (p =
  0.0013) decrease in the exon coding for mature BDNF (exon VI). In addition, there was a significant (34 per cent, p = 0.005) decrease in
  the mRNA coding for exon I in the stressed animals. Contrary to
  expectations, however, CIS resulted in a significant (116 per cent, p
  = 0.0087) increase in hippocampal BDNF protein levels. Furthermore, both intermittent immobilization and chronic cold stress both
  increased BDNF protein levels. Chronic stress, therefore,
  differentially regulates BDNF mRNA and protein levels in the
  hippocampus. Copyright © 2004 John Wiley & Sons, Ltd.

I'm really curious what they mean with CIS: Chronic immobilization stress.
I can't find anything on the internet that actually explains what this is.

There are >1200 articles tagged "chronic immobilization stress" on pubmed.
From Hennebelle et al. (2012):

Half of the 6-month old male rats from each dietary group were subjected to a validated chronic stress procedure (Buyntsky and Mostosky, 2009) based on a restraint stress procedure adapted from Veena et al, [32]. Rats were placed in wire mesh restrainers for 6 h a day (fom 10 am to 16 pm) for 21 days (5 days a week) over a period of 4 weeks. Unstressed rats were handled weekly. The unstressed and stressed animals were housed in different rooms.

Hennebelle, H., et al. 2012. Influence of Omega-3 Fatty Acid Status on the Way Rats Adapt to Chronic Restraint Stress. PLoSOne 7: e42142.

So Chronic Immmobilization Stress means they don't allow (the rats in most cases) to move freely ?

Yes for certain period of time.


text:
What kind of bird species is this?
Every now and then I got a glimpse of this bird which I'm pretty sure is not native to Northern Germany where I live. There are at least three of these birds around but I usually only see something quick and green somewhere in the trees. I finally managed to get some decent pictures so I'm hoping someone can tell me what kind of bird this is. I'm curious what biological niche this bird is likely to fill and which native species it might compete with.

Almost definitely (I'm not a regular birder) European Green Woodpecker (latin name: Picus viridis) and it is native to your area according to its species distribution map.

"Green woodpeckers are the largest and most colourful woodpeckers
  native to Britain. They are easily recognised by their laughing
  ‘yaffle’ call, which they use to demarcate their territory. They also
  drum on trees, though the sound is not as resonant as that made by the
  other two British species (the greater and lesser spotted
  woodpeckers). Green woodpeckers survive on a diet of insects and have
  a particular fondness for ants. They return day after day to their
  favourite ant hill to feed." - BBC nature

I confirm rg255's answer: it is a Picus viridis.
Additionally we can see it is a young male (immature).
Young because the spots; picture of an adult here and young here.
Male because the red spot under the cheeks, the females get this part only black.


text:
How do Opioids Stimulate a Histamine Release?
Histamine is a neurotransmitter that also has peripheral functions such as the regulation of gastric acid secretions, allergic responses, etc. I know that opioids stimulate a release of histamine but I want to know how?
What exactly I would like answered is:

Which of the opioid receptors are involved in the histamine release that opioids stimulate and to what extent are they?
How does the activation of the opioid receptors in question lead to a release of histamine?
Are there any ways of suppressing the histamine release stimulated by opioids without compromising the analgesia they elicit?

I would like an answer, not just links. However I would like you to cite journal articles, although a formal reference list is not required so long as I can easily find the link to the abstract/full article.

This might get you started: consider the references in http://www.acnp.org/g4/GN401000037/CH037.html, especially in the section "modulation of histamine synthesis and release in vivo".  This is not my area of expertise, so I will leave it to someone else to explain things.


text:
Which classes of drugs (filed by their pharmacology) induce a release of β-endorphin?
Which classes of drugs (filed by their binding sites) induce a release of β-endorphin? I know of agonists of the nAChRs and 5-HT1A and ethanol. Are there any others?
Please cite journal articles with links to the respective articles


text:
Question about equilibrium potential formula
My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$
Where does the 62 mV come from? How was this value derived? I understand that it's the equilibrium voltage of $\ce{Na+}$.

The System intracellular/membrane/extracellular space is well described by the model of a Concentration cell (see more on Wikipedia). The equation you mentioned is also called the Nernst equation.
$$
E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)= \frac{k_\mathrm{B} T}{z \mathrm{e}} \biggl(\ln\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)
$$
where $k_\mathrm{B}$ is the Boltzmann constant, $T$ temperature (310 K), $\mathrm{e}$ elementary charge and $z$ the number of elementary charges per ion (1 in the case of Na+)
Thus the $62 mV$ come from $\frac{k_\mathrm{B} T}{\mathrm{e}}   ln(10)$
As you can see, as the temperature increases, entropic effects gain strength and thus more ions move against the electric field, raising the membrane potential.
So your 62 mV are not only empirical but also based on a well defined physical model.
And the equilibrium voltage of Na+ is the same because at physiological conditons the intracellular concentration is ten times smaller than the extracellular. Thus $\log\frac{[ion]_{outside}}{[ion]_{inside}}$ equals to $log(10)$ which is $1$.
The total membrane reversal potential is well described by the Goldman Equation.

Nice answer. I like the relation to entropy, as it really does help you get the bigger picture in the long run. :-)

That quasi-travesty is the Nernst equation in $\log_{10}$ for a positive monovalent ion at physiological temperatures (37 degrees celsius), but they've hidden all that from you. Shame on them.
The canonical form of the Nernst equation, for an ion $S$ is
$$
E_{S} = \frac{RT}{z_{S}F}\ln{\frac{[S]_{out}}{[S]_{in}}}
$$
where $R$ is the gas constant, $T$ is temperature expressed in Kelvin, $F$ is Faraday's constant, and $z_S$ is the charge of ion $S$. This is the actually useful form of the equation that can be used for any ion for any temperature.
The Nernst equation is a limiting case of the Goldman-Hodgkin-Katz equation for a single ion. The Nernst equation is useful for directly determining the equilibrium potential of a single ionic species. The GHK equation is used for determining the reversal potential of a membrane or channel in multi-ion cases.
Note that the terms "reversal potential" and "equilibrium potential" are not synonymous, except in the case of a single ion system. The reversal potential is where the direction of current switches. An equilibrium is when net ion flux is zero (although, in a living cell, it is more appropriate to call even this situation a steady state). If membrane were only permeable to one ion, the reversal potential will be at the equilibrium potential (given by Nernst) for that single ion. However, when there are several permeant ions, usually none of the ions will be in equilibrium at the reversal potential--that is, all the ions will have a measurable flux across the membrane even though the sum of those fluxes (weighted by permeabilities) is zero at the reversal potential.

Converting natural log to log base 10, you can use the identity $\log_b{a} = \frac{\log_{10}{a}}{\log_{10}{b}}$, which gives
$$
E_{S} = \frac{1}{\log_{10}{e}} \cdot \frac{RT}{z_{S}F}\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$
In the case of sodium ions (Na+) at 37 degrees (physiological temperature), $T$ is 310 and $z_S$ is +1. Substituting in these values, we have
$$
E_{S} = 2.303 \cdot \frac{(8.3145) (310)}{(+1) (96485) }\log_{10}{\frac{[S]_{out}}{[S]_{in}}} \\
E_{S} = 61.5 \text{ mV} \cdot\log_{10}{\frac{[S]_{out}}{[S]_{in}}}
$$

YAK uses a less common form of the Nernst equation in membrane physiology which uses the Boltzmann constant directly and deals with elementary charges instead of moles ($R = N_A k_B$). It is a wonderful exercise to derive the Nernst equation from the Boltzmann equation,
$$
\frac{p_2}{p_1} = \exp{(-\frac{u_2 - u_1}{k_BT})}
$$
where $p_i$ is the probability of a particle being in state $i$, and $u_i$ is the energy of state $i$. All it takes is some rearranging and keeping careful track of the units.

In my experience it is indeed more common in bio to talk about the nernst equation rather than Goldman.

probably because it is the Nernst not the Goldman eq. Thanks @Armatus ! I corrected it abvove.


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Excretion of small kangaroos while in the pouch
How is the excretion of small kangaroos done when they are in the pouch of their mother, fastened onto her teat? My question is what happens with the products; do they accumulate in the pouch?

Wow! What an interesting question!
I did a bit of searching around, and here's what I found. It looks like the baby kangaroos, or joeys, do in fact produce excrement while in their mothers pouch. The mother kangaroo uses her tongue to clean her joey and her pouch.
I found this information in a couple of differently places by doing a google search for "biology of marsupial reproduction pouch excrement."
One of the first sources I found was a New York Times article titled "Marsupail Maintenance." You can find this article at this link:
http://www.nytimes.com/2012/08/14/science/how-do-female-kangaroos-keep-their-pouches-clean.html?_r=0
The article was published in a reputable news paper, and used an interview with a curator of mammals from the Bronx Zoo as a source.
Another resource I found when researching this topic was an Australian wildlife sanctuary. This wildlife sanctuary has information web pages online to help visitors learn more about the animals that live in the sanctuary. You can find their entry on Eastern Grey Kangaroos at this link:
http://billabongsanctuary.com.au/native-animals/mammals/eastern-grey-kangaroo/
This web pages gives a pretty detailed overview of the Eastern Grey Kangaroo. The information on joeys and pouch cleaning can be found in the section called "Raising the Young."
I hope this fully answered your question!

i'm glad i'm not a marsupial

@shigeta: Koala's feed their faeces to their young so in Australia it goes both ways.

my desire not to be a marsupial remains one way...  :)


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What is the biochemical reason for mental fatigue?
Is it known exactly why the brain needs sleep? What's dropping low / going high when we experience mental fatigue? I can see why low glucose could result in mental fatigue, are other reasons known?

Because the brain cell highly sensitive to glucose when its level decrease the we feel fatigue

This is not the biochemistry, but the brain regions involved are described in this article about an fMRI study: http://www.sciencedaily.com/releases/2012/12/121210101630.htm
EDIT:
From what I can tell, mental fatigue is attributed to low oxygenation levels.  Here's a study that examines the effect of creatine in preventing mental fatigue: http://jtoomim.org/brain-training/watanabe2001-creatine-reduces-mentalfatigue.pdf

I know that these pieces of information don't directly answer your question, but they're related (and the best I could find).


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Why did animals evolve genders?
The majority of animals have two genders, and both are needed in reproduction. It seems like it would be more advantageous for creatures to be hermaphrodites, since they could mate with any member of their species instead of needing to find a partner of the opposite gender. Why did animals evolve to have genders instead of being hermaphrodites?

The title is a bit misleading. Hermaphrodites still have genders, if you consider the reproduction system. The title looks more like that you ask for a reason for meiotic reproduction, as opposed to mitosis, which is an interesting question, too.

Even yeast have a gender or mating type, called as A type or α type


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What is the mechanism behind ventilatory acclimatization?
In my respiratory physiology lectures, my professor explained that hypoxia-induced hyperventilation occurs in 2 stages when people try to acclimate at high altitudes. My question is about the long-term 2nd stage, listed as #2 below:

there's an immediate increase in alveolar ventilation triggered by peripheral chemoreceptors, but this only leads to a small increase, and also decreases levels of $p_{CO_2}$.
over 8 hrs, there's a slow rise and 2 mechanisms are involved:
a) bicarbonate ion ($\ce{HCO_3^-}$) in cerebrospinal fluid is shuttled out and chemoreceptors increase their sensitivity to $p_{O_2}$
b) kidneys excrete more $\ce{HCO_3^-}$ to normalize blood pH

I get that the $\ce{HCO_3^-}$ and $\ce{H^+}$ comes from $\ce{H_2CO_3}$ being broken down through carbonic anhydrase. But she never mentioned where the $\ce{HCO_3^-}$ is shuttled to or which chemoreceptors are increasing their sensitivity to $p_{O_2}$ (I assume peripheral since it's mentioning sensitivity to $\ce{O_2}$). She then says that because of this $\ce{H^+}$ and $\ce{CO_2}$ levels increase, stimulating central chemoreceptors to increase ventilation to help decrease the acidity/$\ce{CO_2}$ levels. I don't understand how $\ce{H^+}$ and $\ce{CO_2}$ levels are even rising because I don't know where the $\ce{HCO_3^-}$ is even going and what it's role is. This professor is terrible at explaining things, and I'm just so confused at this point! Any sort of direction would be so helpful! Thanks!

not a complete answer, just a comment: $CO_2 + H_2O$ <--> $H_2CO_3$. This is going on all the time (e.g. in a soda bottle) without the need for an enzyme.

Some links might help you: http://fblt.cz/en/skripta/vii-vylucovaci-soustava-a-acidobazicka-rovnovaha/7-acidobazicka-rovnovaha/ http://www.ccmtutorials.com/renal/Acid%20Base%20Balance%20in%20Critical%20Care%20Medicine-NELIGAN.pdf http://mcat-review.org/excretory-system.php

@Michael Kunh Carbonic anhydrase is used in the human body to tip the balance of the reaction  $H_2CO_3\rightleftharpoons H^++HCO_3^-$ to the right side, and is an important player in acidobasic homeostasis.
To answer the question:
$HCO_3^-$ is excreted through the kidneys. This represents the metabolic compensation to respiratory alkalosis that appears in altitude.
To summarize:

ascension leaves us in with a lower partial pressure of oxygen. This will stimulate the peripheral chemoreceptors of the carotid bodies and aortic arch to increase ventilation (hypoxic ventilatory response). In consequence, an acute respiratory alkalosis develops.
renal adaptation begins after more or less 8 hours, and reestablishes homeostasis after 24-48h. To do that, the kidney will excrete $HCO_3^-$, which will tend to acidify blood (metabolic acidosis to counterbalance respiratory alcalosis). To accelerate this phase, one could take some acetazolamide, a diuretic drug that causes $HCO_3^-$ excretion.

Please note that enzymes do not tip the balance of any reaction in a direction. They specifically speed up reactions that are already thermodynamically favourable.

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


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A question regarding evolution
I'm not a biologist so bear with me. I know that the DNA molecule carries extremely large amounts of information. If the process of evolution is driven by completely random process .I think about it as the complex interactions between environment and random genetic mutations that leads to natural selection.
I've two questions:
What's the probability of evolution of intelligent human beings within this scenario? I've heard that the probability of spontaneous generation of a good protein molecule should be nil in our universe: is this correct ?

This question has a few problems at the moment, the two questions are pretty much creationist strawman arguments, which are not on-topic here. The probability of intelligent life evolving is not really answerable in my opinion, but the question about the evolution of a "good" protein (needs a better definition) would be okay.

good protein molecule = one that has biochemical activity, which is often one that has regular structure.  some good work on the density of well structured protein sequences in sequence space has been done, but I don't have them myself.

While some don't like  Richard Dawkins, he did bother to write a book about the probability of life and how evolution has the ability to make improbable things reality.  As such, I think this question is legitimate and often asked.  If we can't explain fundamental biology to the public who needs such an explanation we are really limiting what the site should be used for in a detrimental way I feel.

I think it could be improved as a question - for example, actually having a question in the title.

The human genome is 3Mb in length.That is about 6M bits of information. You can buy a 32Mb microSD. So the human genome does carry as much information as you might think.

If the process of evolution is driven by completely random process...

It's not.  The evolution of "better" protein (and other) molecules happens because of selection, a very non-random process.  The repeated selection of better molecules, and then of the variants of the better molecules, repeated many times, will lead to "good" molecules (in the sense that they work better for their producers).

Exactly how genetic material changes from one generation to the next is a very complex subject. But essentially you are right. The change in genes from one generation to the next is not only mutations though. It is also mixing of the genes carried by the male and the genes carried by the female. The selection process is also very complex, and sexual selection is, for some species, a large part of it as well.
As for the probability of intelligent life emerging... Obviously, it's happened. The probability is at best extremely difficult to even provide an estimate of. How do you define a "good" protein molecule :-)?

Since we only have one planet that we know of with life, it's a bit difficult to make good estimates on the probability of various events in the history of life.  To make a good estimate, you'd want to have thousands of planets very similar to earth to compare.  Since we don't have access to that kind of data, one proxy which you can look at is how long did it take for some event to happen in earth's history.  In a vacuum you'd expect things that took longer to happen to be rarer.  From this point of view, it seems likely that the development of multi-cellular life from simpler life forms is a low probability event because it took 3 billion years of simpler life forms before it happened.
Another way to get information on probabilities is to look at widely separated branches of the tree of life.  Since wings evolved separately in birds, bats, insects, and pterosaurs, the probability of wings evolving in a planet with a similar atmosphere and multicellular animals is likely pretty high.  Similarly, you can argue that the development of human level intelligence is relatively low probability because it has only developed once in the history of the planet in one lineage that very nearly died out.  Dinosaurs never developed human level intelligence, nor did rodents, or mollusks, or arthropods.  On the other hand, it seems that a lower level of intelligence at say the dog level is relatively high probability (since it has evolved separately in mollusks, birds, mammals, etc.).


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How do bats distinguish between day and night?
How do bats distinguish between day and night? Do they hunt at night - if yes, how they know that?
Are they afraid of sunlight?

Worth noting: Bats can see as well with their eyes as most other mammals. They know it's night because it's dark out.

Bats distinguish day and night the same way that other animals do, with an internal circadian clock and by environmental cues (dawn and dusk).
Most bats (over 1000 different species total) are nocturnal, meaning that they are out of their roost and foraging at night. This includes that vast majority of bats, which also echolocate. Some bats, notably pteropodid "Flying foxes" are diurnal, meaning they are active during the day and sleep at night, like humans. These bats are typically fruit-eating. There are, of course, exceptions, but these general patterns hold.
Bat Conservation International has good educational information about bats.

Mammals have what are called intrinsically photosensitive retinal ganglion cells (ipRGCs) (Wikipedia), including bats (ref). These cells are responsible for modulating mammals circadian rhythms (differently for diurnal and nocturnal species). These cells are interesting because retinal ganglion cells are not normally photosensitive, but receive high acuity images from rods and cones. Interestingly, people with cone-rod retinal dystrophy (including those with complete blindness) still have their circadian rhythms set by ipRGCs in the retina, because these cells are spared. This was unfortunately demonstrated by a doctor that removed the eyes of someone who was blind, which resulted in the patient being unable to have a regular sleep cycle (citation needed).
Hence, even though bats (may?) have poor eyesight, ipRGCs in their retina still set their circadian rhythms. I don't believe they are afraid of the sunlight per se, but the sunlight makes them sleepy. They typically use echolocation at night.


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Range of feasible coefficients in an unlimited growth model
If you are given an unlimited growth model in the form:
$\frac {dP(t)}{dt} = k P(t)$
Obviously the population growth would never be unlimited, but let's presume for the moment that we are introducing a species into an environment where there is the possibility for unlimited growth, at least on for a given time -- i.e. invasive species.
$k$ is some rate of growth of the population at time $t$, denoted by $P(t)$
What are some feasible values of $k$? In other words, if a number is way above or way below $k$, where would I know that the research I am reading is preposterously off-base?
I am sure it is different for different types of animals, including mammals, birds, bacteria, etc.

The feasible value for K depends on the growth rate and is variable. The good thing with using mathematical models is that you can provide a range of values for a parameter and observe the effect on the system.
You can get an idea of the feasible values based on literature evidence. You first decide what that invading species might be.

A solid limit: k must be greater than zero. Unless you're talking about some cannibalistic species or something that isn't suited to the model at all.
As long as the species is productive in the new environment: k is greater than 1. The population is probably growing or again you probably won't be using an exponential growth model.
As mentioned before you would need to know the species for more information. But if you look at generation times and litter sizes:

Some bacterial generation times (from here) range from 10 to
2000 minutes (33 hours). So that is $k=2$ per generation time. Per
day you're looking at a lower bound of 2 per day and an upper bound
of $k=2^{14}=10^{43}$ per day.
Mice are something like 12 week generation time and a litter of 10
giving something like $k=10^{10}$ per year.
Elephants are one young every 25 years. So $k=16$ per century or so.

Of course this is all based on gross assumptions. But you're looking for guidelines for a unrealistic model so hopefully they'll do.

Why k greater than 1?

If k is between 0 and 1, the population is dying out. Of course that is possible but the question seemed to be asking about growing populations, not dying populations.

"If k is between 0 and 1, the population is dying out." Certainly not, if k is between 0 and 1, the population grows exponentially. Likewise, k being negative does not mean cannibalism, only some death rate greater than the birth rate.

Hm. Yes you're right. I'll point out that this answer is 2 years old and I haven't thought about it since. I suggest you edit my answer or add your own as I've got it wrong.


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What are gram negative and positive bacteria?
I've just finished a course of double antibiotics for Helicobacter pylori in my stomach.  I looked up H. pylori and found that it was a gram-negative bacterium.  I looked up gram-negative and didn't understand the definition.  I assume that if there are gram-negative bacteria then there are also gram-positive ones.  Can someone explain the terms gram-negative and gram-positive in basic, layman's terms?
Thanks,
Sachin

Just to make @yamad's answer more layman friendly, essentially Gram-positive bacteria have thicker cell walls than Gram-negative bacteria.

Why is this distinction important anyway?

It is simply one of the major ways that bacteria are categorised. The cell wall will affect what drugs can kill them for example.

@yamad is right on - Gram stain is a major way of categorizing bacteria. Its worth mentioning what the Gram stain color means.
While not failproof, the Gram stain test reflects a major division of the sorts of cells bacteria, helping to type the bacteria of interest
Gram stain reacts with the peptidogycan to create the purple color.  The peptidoglycan is a mesh of carbohydrate (sugar) chains with short peptides attached to them that gives the bacterial wall mechanical strength against osmotic changes in the environment (e.g. large concentrations changes in sugars or salts) and mechanical stresses such as shearing from current.

Gram Negative bacteria have two lipid membranes with peptidoglycan sandwiched in between them while Gram positive bacteria have a single lipid membrane with the peptidoglycan mesh surrounding the membrane, forming an outer coat to the bacteria.  There is typically 5-10 times more peptidoglycan by weight in Gram Positive bacteria.  As such these two distinct categories of Bacteria is often the first determination used to characterize a bacterium.  Again while not without some error, Gram stains reflect a significant cell physiological division in bacteria.

The Gram stain is one of a large number of techniques used to characterize bacteria. In particular, a bacterial species is usually either Gram-positive (purple when stained) or Gram-negative (pink when stained). In Gram-postive bacteria, the cell wall is thicker and has much more peptidoglycan compared to Gram-negative bacteria. The chemicals in the stain react with these molecules in the cell wall and result in the purple color. All of this information is well covered in the Wikipedia article on the subject.


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Molecular cause of cramps, spasms and strengthening in muscles? (incl. intro to muscle contraction)
When motor neurons are stimulated to trigger an action potential, this potential propagates down the spine, eventually reaching a neuromuscular junction, causing the release of acetylcholine (ACh).
ACh binds to nicotinic ACh receptors (nAChR) on the muscle fibers, leading to an action potential. The nAChR is a non-selective, ligand-gated ion channel, permeable to sodium-, potassium- and calcium ions. This means sodium ions will flow in, leading to depolarization, but potassium will flow out, working towards hyperpolarization.
If enough of these channels are opened, the post-synaptic membrane potential will be drawn towards $E_{Na}$ enough to reach a threshold, so that voltage-gated sodium channels open on the post-synaptic membrane, causing a post-synaptic action potential.
This action potential travels down inward extrusions of the plasma membrane, called transverse (T) tubules. Is the membrane continuous along these tubules, or does the tubule just end somewhere inside the muscle fiber? Anyway, the action potential comes in contact with the muscle fiber version of an endoplasmic reticulum: The sarcoplasmic reticulum (SR).
Upon contact with the action potential, the calcium ion channels in the SR open, causing calcium ions to flow into the cytosol. Here they bind to troponin complexes on the tropomyosin protein - a regulatory protein, that twists around the thin filaments of the muscle fiber. In short, when calcium ions bind to troponin, it reveals binding sites for myosin on the thin filaments, letting the muscle contraction cycle of the myosin heads proceed, and the muscle contracts!
When the stimulus goes away, calcium ions are transported back into the SR, and myosin has nowhere to bind, thus the cycle is halted, and the muscle relaxes.
When the muscle is twitching... is this neurological of nature, or is it related to a molecular cause in the muscle itself?
When the muscle is cramping... I'm almost certain this arises in the muscle. What causes it? A malfunction with regard to the calcium ions?
Lastly, and on a slightly different subject, what are the microlesions in the muscles that occur during strength training, and what is the overcompensation that happens? The basis of this might not be entirely on the molecular level I feel.

This might be easier to answer as separate questions rather than one question with lots of subparts.

I think a lot of your questions try to split the hair; is this happening at the chemical or the histological level and I do get what you're asking, but you should know that the distinction is often not worth making. Pretty much whenever a neuron's involved, the interesting biology is multi-scale.

Is the membrane continuous along these tubules, or does the tubule just end somewhere inside the muscle fiber?

The membranes are continuous.

When the muscle is twitching... is this neurological of nature, or is it related to a molecular cause in the muscle itself?

Most things you'd call a muscle twitch are at the whole-muscle-group scale, involving the coordinated contraction of many individual motor units, so it's basically neurological.

When the muscle is cramping... I'm almost certain this arises in the muscle. What causes it? A malfunction with regard to the calcium ions?

A muscle cramp is a colloquialism for a couple of things that are quite different from each other. Overall, as with the previous question, if someone's experiencing a muscle cramp that means it's a fairly macroscopic phenomenon and it likely involves a whole group of muscle filaments, so it's neurological. Most spasms and cramps are neurologically mediated.
The connections with electrolyte balances (cramps from low sodium, potassium, magnesium, or calcium) also hint at the neurological basis because neurons act on each other (and on muscles) by forming or dissipating ion gradients. You may know that low dietary calcium can lead to muscle cramps; if this was relevant to the calcium release within the myocyte (from the sarcoplasmic reticulum) then the calcium-starved muscles wouldn't be expected to chronically contract (which requires calcium) but to chronically relax.
That being said, there's a lot of room for feedback mechanisms. So, let's say a person experiences a muscle tear; the tear is small enough that it doesn't compromise the function of the entire muscle group. In this case it's adaptive for the local damage to 'signal' to the rest of the muscle group to initiate spasm so as to stabilize the damaged structures as they're repaired. In this scenario the local damage would 'inform' a neurological (and/or endocrine) response that actually effects the spasm.

Lastly, and on a slightly different subject, what are the microlesions in the muscles that occur during strength training, and what is the overcompensation that happens?

Last time I was updated on this (not my bag), there were some large questions remaining. The tricks used by growing muscle to establish large, regular arrays of contractile machinery, that is organized over many spatial orders of magnitude, are poorly understood. There are structures that monitor the overall organization and that detect any large deformations. Regarding overcompensation, let's play through a generic scenario. A muscle cell is loaded too much and becomes physically damaged. It has to stop taking orders (stop responding to contraction/relaxation signals) and to initiate repairs. The overcompensation results because muscle cell's not really capable of knowing how large it was before the damage, so the safe amount of repairs to do is extra. Probably there are epigenetic processes that let a muscle cell 'count' the number of times its been greatly damaged and to scale-up the response appropriately.
If you just consider two likely sources of damage -- mechanical strain and lactic acidosis -- you can see that there are widely different mechanisms that would be required to detect the damage and to initiate repairs.


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Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?
I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with plate reader. I don't remember having any problem up until today.
I used 20 mM phosphate buffer instead of water to dilute them today and measured the absorbances at 280 nm repeatedly three times and the absorbance for one of the solutions went up from 0.043 to 0.068 (absorbance of 20 mM phosphate buffer is 0.030 at 280 nM with same volume); I stopped measuring after third one but it would probably go higher as I measured until I hit a plateau.
I measured absorbances of two proteins and only one of them went up that much, other one went up from 0.071 to 0.088; if this were to be concentration dependent I would expect the second solution go even higher but it didn't happen.
I know there may be differences in UV absorbances if protein is folded or unfolded; would it be that dramatic? What is the reason for that increase? I will be grateful for an explanation and a practical solution to the problem.
NOTE: I increased the total volume to 200 uL by simply adding 100 uL of 20 mM phosphate buffer into all wells and the signal increase slowed down a lot; there is still some increase though with 0.001-0.003 increments in each measurement.

Could it be a slow precipitation?

I don't have any precipitation in stock solutions and I think it wouldn't precipitate after I dilute them.

Is the stock solution in phosphate buffer or water? Depending on the protein, just changing buffers can induce folding changes and aggregation.

It is in phosphate buffer in stock solution.

It looks like your protein concentrations are right on the limit of detection of the spectrophotometer, and changing the diluent buffer changed their concentrations. The samples may not have been thoroughly mixed after dilution and before measurement, so the varying measurements may simply be the solution coming to equilibrium. Temperature can also affect absorbance, so you should verify that your samples have equilibrated before drawing any conclusions. If the absorbance of your phosphate buffer is 0.03, I'd try to keep the sample absorbances above 0.075 or higher to avoid getting too close to the limit of detection. Also, make sure your buffer isn't too old or contaminated with something which could be affecting its absorbance characteristics.
I would suggest taking one or two protein samples and doing a dilution series (1:1, 1:5, 1:10, 1:20) in a large-ish volume (say 400 ul each, if you can spare it), vortex briefly to mix well, then measure triplicates of each dilution on your reader, along with appropriate blanks (buffer only). You will see differences between each measurement, but it should be quite small, depending on the accuracy and precision of your instrument.
Measured values will not be exactly the same from measurement to measurement, and it would take a lot more than three repetitions to determine if there was an actual drift trend occurring. Measure your sample plate every 5 minutes for an hour and plot the values (don't just eyeball them) to see if the machine may need to be serviced.

These are really great suggestions but most of the time I don't have much protein. I tried using higher volumes but I don't get much absorbance; they are very close to background absorbance. If I use too much protein I both waste my samples and a huge meniscus forms which prevents me from determining the pathlength. I always pipette them very well to make sure they are well mixed too. But your suggestion for measuring for an hour and plotting a graph is a good idea, maybe UV lamp is too old. Thank you!

Could be protein unfolding or changes in conformation. Absorbance at 280 nm is mainly due to the tryptophan residues, and can change substantially as these residues move from a more hydrophobic (buried inside the protein) to a more hydrophilic (exposed to the solvent) environment. Your protein may be reacting to the new buffer.

According to the OP's comments the protein is being diluted into the same buffer (I think).

The way I understood it, OP swtiched from water to phosphate buffer for this particular experiment, and is getting the result for one particular protein sample in that buffer.

This article explains the effect of protein unfolding on amino acid absorbance with clarity detail: http://www.life.illinois.edu/biochem/455/Lab%20exercises/Photometry/spectrophotometry.pdf

I diluted the protein with the same buffer I it was in. Sorry for the confusion. Thank you for the paper.


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Simple diffusion of lipid-soluble molecules through phospholipid bilayer -- does anything get "stuck" in transit?
It's a pretty elementary concept, and when I first learned of it I don't think I had the foundations to even think of such a question, but I found myself the other day thinking about the amphipathic nature of the phospholipids in the plasma membrane and why it might be that lipid-soluble molecules don't stay in between the layers (of the bilayer).
I know that simple diffusion is a response to a concentration gradient, but consider a case where equilibrium is being restored and lipid-soluble molecules are diffusing from whatever extracellular matrix through the membrane and into the cytosol. Towards the end of this process, when equilibrium is nearly restored and the last few molecules are making their way into the cell, the rate of diffusion for these last couple molecules will be slower than those that diffused when the concentration difference was greater. Since the polar heads on the outside and inside of the bilayer are hydrophilic but the inner part, where the fatty acid tails are, is hydrophobic, what drives a molecule to leave the cozy, accepting, lipophilic environment of the middle (of the bilayer) to cross through the cytosolic-side rejecting polar heads and enter the cytosol?
I understand that initially these molecules were moving into the cell in response to a difference in intracellular vs extracellular concentration, but I'm asking whether we would ever see a case where the gradient is nearly zero and a molecule in transit simply decides to reside in between the layers instead of crossing all the way into the cell; as if moving through the cytosolic polar head side is not worth the effort to reduce a nearly-zero gradient to zero.
Please ask me if I can clarify my question in any way -- I'm finding it difficult to phrase. I asked my professor (who has her doctorate in toxicology & pharmacology) and she understood what I was asking but didn't have an answer.

I'd say it's certainly possible, but I doubt it would be for very long. I cannot think of a single concentration gradient that's at equilibrium for every long with respect to cells. They are always quickly restored to some imbalance, so as soon as the cell starts to restore the imbalance, the molecule/atom would be urged to choose a side.

I think, given Alan's answer the question you might be asking is something like
'do compounds become concentrated in the lipid bilayer', as opposed to achieving high concentration inside the cell after diffusing through the membrane as he describes.
This could certainly happen (if that's what you're thinking), but usually won't for I think two reasons.
The first is that any molecule that would not soluble in the interior of the cell is going to have a correspondingly small not going to be found in the blood or lymph, tissue, ocean or other milieu the cell is living in, which will be mostly water.
You might well ask whether there are cases where the compounds in question might be available in low concentrations around the cell and over time accumulate in the lipid bilayer. This slow concentration model probably happens, but there is a compensating mechanism - the lipid bilayer is taken into vescicles and degraded, to be replaced by newly synthesized such that membrane components renew themselves.  This process includes the cell engulfing by endocytosis and specifically turning over membrane proteins.
The turnover rate for most cells is on the order of days, some of the best numbers for this are behind a paywall, but a reference to synaptic membrane turnover shows some components turn over varying between 6 and 24 days.  Different components such as cholesterol, phosphatidylcholine and phosphatidylethanolamine have differing rates of turnover.
So between these two effects, the concentration of 'permeant molecules' would be low for most cases.

is "permanent molecules" a typo -  permeable molecules?

its at term they used on wikipedia - it seems like a conventional term for the standing concentration in the membrane..

Just checked - is it "permeant"?

Thank you -- I wasn't thinking about turnover and synthesis of new membrane lipids, and this is exactly what I needed. I thought for sure that at least theoretically a molecule could remain in between the bilayers, but I agree that the amount of this occurrence is relatively insignificant.

I interpret your question to refer to the movement of a lipid-soluble molecule that is therefore able to diffuse into cells down a concentration gradient. I think that you are asking whether as the gradient collapses, some of these molecules would "stay in the bilayer".
You are thinking about the diffusion process in the wrong way. There will always be a pool of these molecules in the bilayer, and these will be continually exchanging with molecules in the two aqueous phases on either side of the membrane. The net flux which results in diffusion in any particular direction will be the  movement that results from these equilibria. Diffusion isn't a directed process in the way you define your question.

My diagram shows on the left the progress towards equilibrium and on the right the situation where it has been reached. Note that at equilibrium, because it is lipid soluble, the molecule is at a higher concentration (larger typeface) than it is in either aqueous phase. And - importantly, molecules will still be moving into and out of the bilayer at both faces.
Added later:
A classic example of a lipid soluble molecule able to diffuse in this way is oxygen. According to this paper, at physiological temperatures, and at equilibrium, the concentration of oxygen in a bilayer will be approximately 3x that in the surrounding fluids.


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Does an allergic reaction kill body cells?
I have wondered what actually happens in an allergic reaction that causes the symptoms such as pain, rash etc.
Is it possible that the human body actually kills its own cells in the process?

I would imagine that the complement system may trigger cell death.

@bobthejoe Do you have any paper or article regarding this topic?

Actually, the body often kills its own cells, look up apoptosis.

Is it possible that the human body actually kills its own cells in the
  process?

Yes it is. It is happens not only as a result of allergic reactions (see comment of @terdon). But in case of allergy our body have 3 methods for killing own cells.

Cytotoxic, antibody-dependent (Type 2 hypersensitivity) The antibodies produced by the immune response bind to antigens on the patient's own cell surfaces.These cells are recognized by macrophages or dendritic cells, which act as antigen-presenting cells. This causes a B cell response, wherein antibodies are produced against the foreign antigen.
Immune complex (Type 3 hypersensitivity) Occurs when antigen-antibody complexes that are not adequately cleared by innate immune cells accumulate, giving rise to an inflammatory response and attraction of leukocytes
Cell-mediated immune memory response (Type 4 hypersensitivity) is an immune response that does not involve antibodies, but rather involves the activation of phagocytes, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen.

See Wiki about types and diseases and about Hypersensitivity

Thanks a lot for the detailed answer, but in the wiki it says that only Type I Sensitivity is an allergy. So are your answers still relevant?

If you ask about Type 1 hypersensitivity - my answer is "No. Type 1 hypersensitivity didn't kill own body's cells directly". But if we talk about an allergic reaction that causes the symptoms such as pain, rash etc my answer still relevant

So basically you are saying that a Type 1 hypersensitivity could possibly trigger Type 2, 3 or 4 hypersensitivity? If so, how?


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What is the advantage of circular genomes for bacteria and linear genomes for other organisms?
Bacterial are a great group of organisms. They have circular genomes and never went toward linear genomes while other organisms show the opposite strategy and don't have circular genomes (disregarding their cytoplasmic genome). Why they have followed these different strategies?

The bacterium Borrelia burgdorferi has a linear chromosome as well as a number of linear and circular plasmids. http://pbil.univ-lyon1.fr/members/lobry/articles/MolMicrobiol_1999_32_437.pdf

Interesting. Why it has not circular chromosome?

I checked mentioned article to see how bacteria terminate replication and what do with its telomeres; its what I saw: >The
mechanisms for termination of replication and resolution
of the telomeres remain important unanswered questions

@AlanBoyd related to the discussion below regarding replication speed, it is interesting to note that B. burgdorferi has a very slow doubling time of 12-18 hours.

You can package linear genomes much more efficiently than circular genomes, and bacteria simply don't require the information density to be prosperous.
To be a bit more specific, it's the torque strain put on the double-helix while it's being wound that makes the difference. Linear genomes can be wound around Histones, and these Histones can be further formed into more complex and dense patterns so that the DNA of a linear genome is condensed to a mere fraction of the size it was before. The high density allows cell division to occur much, much easier than it would otherwise happen in Eukaryotic cells.
Circular genomes cannot get rid of the torque stresses like linear genomes can. To attempt a similar packaging scheme as Eukaryotic cells would result in the DNA breaking apart at some point before you reached a high level of information density.
I'll look through my BioChem books again to find a reference later on, but hopefully you should have a solid idea of "why" from the above. For now you can do a little thought experiment: Think of all the ways you can wind a single piece of string or thread around things to make it as dense as possible. Then think of all the ways you can try to achieve the same density with a rubber band without breaking it. The string should win out in both the ease at which you can manipulate it, and the level of density you can achieve.

While I agree with your answer, the question remains why don't the bacteria have linear genomes also, since it is very easy to create linear genomes. My guess is that a circular genome might be easier to replicate faster, since eukaryotes typically have longer cell cycles. Anyone else have ideas about that?

@Bitwise why easy?You need all sorts of helper proteins, helicases, histones etc.

@Bitwise - Speed is definitely part of it. It takes time to condense all of a linear genome into Chromatin. A circular genome isn't necessarily easier to replicate (the proteins involved operate at about the same speeds if I remember correctly), but when your species depends upon a very, very fast generation time then a genome that you don't have to pack is a huge advantage.

I don't know if it is a significant factor, but maintaining the linear DNA takes some effort in terms of making sure the telomeres stay intact for cells that divide often. A circular DNA can completely avoid that complexity.

@MadScientist good point, I hadn't thought about that. Still, if you take a eukaryote like a yeast, it seems to manage with telomeres and with having a relatively short cell cycle time (~twice that of E coli). So I am still not sure that speed or not having telomeres are a sufficient advantage.

@MCM this might be a bit off topic, but I wonder if a linear genome really requires condensation into chromatin. If it was the same DNA content as the circular uncondensed genome why would it need to be packed? are there examples of species with linear genomes that are not packed into chromatin (bacteria/archea)?

@Bitwise - I'm sure there are examples of linear chromosomes in Bacteria/Archea. I don't think there's an explicit need for it to be condensed, but its ability to be condensed is very useful to the cell. B/A don't sexually reproduce, may not have a nucleus smaller than the cell to stuff all the DNA in, and may not need to shut down large swathes of genes they are forced to keep around (like women do with many genes on X-chromosomes). So I'd say not necessary, but very useful.


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How to wash the column during protein purification with GST tag?
I have been working with GST tagged proteins for the last 4 years and after loading the cell lysate into the column I was washing it with 20-30 column volumes of PBS and sometimes my proteins were eluted very pure sometimes with a lot of impurities.
A few times I tried washing with NaCl gradient (0-400 mM) but later decided not to do that because it may denature the protein and some of my proteins may not refold.
What do you suggest for washing step?
Note: I don't have any UV detector to see the washouts/flowthroughs/elutions.

Use your plate reader to see the elution peak by collecting 100 ul or so as you are washing and eluting. You can also set up a Bradford-type colorimetric assay in a disposable microplate and add aliquots as you're washing and eluting to check for the presence of protein.

Bradford idea is really good actually, I will try that in my next purification. Thank you!

You're quite welcome. I did that before we got a little Biorad FPLC with a UV flow cell. If your lab does lots of purifications you might want to check it out - they're fairly inexpensive (as I recall) and you can just set the program up and walk away until it's done.

The standard when purifying GST with Glutathione agarose beads is to use STE buffer (10 mM Tris-HCl (pH 7-7.5), 150 mM NaCl and 1 mM EDTA) for washes and we have had no problem with this in our lab!


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What Conditions must Drugs satisfy for them to be Deliverable via the Transdermal route?
What Conditions must Drugs satisfy for them to be Deliverable via the Transdermal route? I assume a high $\log{P}$ (lipophilicity) would be one, are there any others?

Whether a drug can be delivered transdermally?  I think that carriers can be formulated to carry a small molecule through the skin into circulation, so I don't even know about lipophilicity. I believe if you spend enough money, you can overcome many of these problems.  I think that pharmacology might be just as important.
I think the first condition of a transdermal administration is that the drug cannot be effectively administered orally.  This is the most cost effective route go get a pharma compound into the body. It requires no devices, no fancy coatings or vaporizors.
Reasons that a pill (or its less popular cousins the suppository and sublingual tablet) cannot be used as the delivery system for a drug include effect of pH and other degradation of the compound in the GI tract, absorption rate from the GI tract and other factors such as effect of food in the system, other drugs which might interact in the system.
Another advantage of absorption through the GI tract is that this is the physiological system which is meant to be ingested and introduced into the body - its relatively fault tolerant, even if less of the drug actually reaches the blood stream.  There's more, but that's not a bad outline.
After pills and the like, the second choice is intravenous administration, which puts 100% of the drug into the circulatory system.   This has its own disadvantages, requires a clinical setting and the needle and breaking of the skin are not ideal in many cases.
If the drug needs continuous and non clinical administration there are many other means of drug delivery, including transdermal administration.  Differentiating these methods often includes making sure the drug is available specifically to the part of the body that needs it.  E.g. topical administration; putting on a medicated cream for a skin condition or use of an inhaler which delivers the drug directly to the lung for an asthmatic condition.
Transdermal administration has its own specific advantages; continuous distribution of the compound over long periods of time.  Disadvantages include: poor ADME properties for biologicals like antibodies and other proteins, low delivery concentrations where you need a large amount added (epinephrine, and maybe antibiotics come to mind).
Examples of successful transdermal delivery are testosterone gels and the nicotine patch.  Both of which apply continuous controlled low dosage that is important there.
There are three typical routes of drug absorption in transdermal delivery.  The drugs can diffuse through the membranes of dead cells of the stratum corneum, which works if the drugs are lipophilic enough.  They can diffuse around these cells, through the intercellular spaces, which can work for more polar drugs although this path is not usually as efficient.  The most extreme means are patches which contain tiny needles that can deliver straight through the protective layer of the skin.  With enough economic investment probably any sort of compound could be introduced through a patch.
Most of this is just cribbing off the notes from this lecture on coursera: Fundamentals of Pharmacology.  Its probably outlined on any pharmacology text.

What about fentanyl? Fentanyl can be delivered orally yet it is also available in transdermal patches. Nicotine is water soluble but it is also lipophilic which is how it manages to cross the BBB so easily.

I tried to address this in edits.  I don't claim to cover all transdermal delivery, just trying to answer the question at the fairly general level it was being asked.  I would have to do some digging re: fentenyl.  I might have time tonight.


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Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?
I have been reading with fascination about the several molecular- and cellular-scale mechanisms and structural changes that underlie what we refer to as long-term plasticity. For instance, [1], [2], [3].
In particular, there seem to be at least: synaptic scaling, synaptic pruning, synaptogenesis, spinogenesis, neurogenesis.
My questions:

How do each of the above mechanisms/ events affect the classical extracellular single/ multi-unit spikes, postsynaptic potentials (LFPs), and local electric fields? Does a mechanistic forward model exist, which specifies the biophysical transformation from synapse-level changes to spikes and LFPs? Are there spike simulators out there that model these properties?
Using such a forward model, can we solve a statistical inverse problem to infer anything at all about these LTP/LTD-induced small-scale structural and functional changes?
For instance, one metric of analysis could be: post-spike-time filters (self-terms and cross-terms) inferred using statistical point-process models. Another could be the shape of the action potential itself, which is typically used only for spike sorting, and then discarded.
Has something along these lines been done? Or is it infeasible? If so, why?
Finally, If anyone could give a brief overview of the gamut of synapse-scale physiological/ imaging techniques used to characterize these mechanisms, I would be very grateful!

this is a pretty broad question. I can answer parts of it, but it would be insufficient overall. If you can break the question down to smaller chunks, you may get better responses.

Thanks Memming. I need to do some more reading and thinking to break down the question. Will do. Feel free to share some thoughts in the mean time.

Just adding a little bit here. Estimating changes in connectivity based on STDP is hard
http://klab.smpp.northwestern.edu/wiki/images/2/2b/Stevenson_Inferring_Plasticity_2011.pdf
but yes - these questions are enough to keep a big field busy for a long time.

Thanks!
I was thinking along the following lines.
(1) Write down the cable equations for neurons within a network, given: anatomical layout of the network, spatial distribution of dendrites, spines, synapses, and synaptic strengths (forward model).
(2) Acquire joint microscopy + electrophysiology dataset.
(3) Invert the forward model with synaptic strengths as free parameters.
(4) Track these inferred parameters over time or compare them between conditions.

Yes, that could be a strategy. I like your idea. But, you'll need to record from pairs of connected cells intracellularly which is not impossible, but limits long stable recordings. I guess imaging techniques may be able to get over this limit.


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How selfish is Dictyostelium slug formation?
Dictyostelium is a slime mold which is well known for having a single cell free living phase and other some conditions (e.g. when food is scarce) for forming communal piles of cells called 'slugs' which migrate as a proto animal.  Eventually the slug can turn into a fruiting body with a stem and a nodule of spore forming cells at the top.  The spores can then be carried off by the air and seed dicty further away.
Apart from being amazed at the seeming ability to form amoebic, animal, plant and seed like forms, there must be a lot decision making happening at the formation of the stalk and fruiting node at the top.
So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile?  Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?  Links to references after 2007 or so would be appreciated unless it's all been decided.
By analogy its always been pretty altruistic of 99% of our bodies to let our gonads reproduce, but we are (approximately) homogeneous genetically.  In the wild is slug formation heterogeneous?  How does genetic diversity influence slug and fruiting body formation?

Yes we're homogeneous genetically and each (well OK, most at any rate) of our individual cells reproduces, just not sexually. I am not sure altruism enters into it for bona fide multicellular organisms. Perhaps we could say the same of dicty? Do the stalk cells also replicate in order to grow the stalk?

That is the theory, but in practice, I think its stickier than that - there is some heterogeneity in the cells of the body.  I doubt there would be any mysterious force that would cause a conflict in the organism if the germline contained a code for some significant genome changes in some of the organs of the developed body.  If there were an advantage to it, it would persist....

Joan Strassman's work is probably the route to go for this.
The short of your answer is that several things mediate who ends up where in the slug:

Cheaters are limited from exploiting other
  clones by high relatedness, kin discrimination, pleiotropy, noble
  resistance, and lottery-like role assignment.

Here's the most relevant paper:
Strassmann, J. E., & Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108(Supplement 2), 10855-10862. [pdf]

thanks @Atticus29 Let me take a look and see if this is clear..

The answer appears to be 'not very selfish' as over 90% of slugs found in the wild were all closely related.  Is that right?

The answer to your original question, "So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile? Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?"
is that the assignment to the spore part is by lottery. It is very altruistic (in the sense that individuals die in the stalk). As you point out, it seems pretty common for individuals to be very closely related (although chimerism seems possible).

well its not really altruistic if they are all closely related.  I think the fraction of others are being selfish, but that ratio they find is usually similar to the amount of selfishness allowed in such systems in the simple simulations I know.  you have got your checkmark sir.


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Does this patient have HHV6 or HCMV after transplant surgery?
I have been given mock results from a PCR test on blood samples taken from kidney recipient patients and their donors. The PCR reaction can detect single copies of viral DNA. I have been asked to determine whether 5 patients have been infected with either human herpesvirus 6 (HHV6) or human cytomegalovirus (HCMV) following kidney transplants. I have results for patients pre-transplantation and 1/3 weeks post-transplantation.
The results are as follows:
Donors:

Donor for patient A = HCMV+
Donor for patient B = HCMV+ & HHV6+
Donor for patient C = Neg for both viruses
Donor for patient D = HHV6+
Donor for patient E = HCMV+ & HHV6+

Recipients:

Patient A = HCMV+ before and 1 & 3 weeks post-transplant
Patient B = Neg for both viruses before, then HHV6+ at week 1 & HCMV+ at week 3 following transplantation but negative for HHV6.
Patient C = HHV6+ before and 1 & 3 weeks post-transplant.
Patient D = HCMV+ before and HCMV+ & HHV6+ 1 & 3 weeks  post-transplant
Patient E = HHV6+ before and HCMV+ & HHV6+ 1 & 3 weeks  post-transplant

Answers: I am guessing that Patient A was re-infected by donor A. Patient B was neg for both viruses, developed HHV6  week 1 but this test was neg week 3 & instead positive for HCMV – these viruses do not disappear, you either have it or don’t so assuming there is no contamination error then what virus did he develop post-transplant?? Patient C was HHV6+ prior to transplant but donor is neg for both, so what virus did he develop following transplant? I can see that Patient D was infected with HHV6 from donor post-transplant. Patient E was infected with HCMV from donor post-transplant.
I am struggling to determine what virus Patient A, B and C was infected with following transplant. Can anyone help? I know almost 100% of us are infected with both viruses but do not cause disease in healthy people, that both latent and active viruses show positive when in blood and that both viruses can re-activate under certain conditions such as via infected organ transplants and immunosuppression.

I get the feeling that there's something we should probably know from your textbook or notes that you have not included. As-is, here's my best shot:

It is impossible to determine if Patient A was infected by the transplant since the virus they had before the transplant is the same virus carried by the transplant itself. Without running further tests to separate the two lineages you can't tell. It's likely, though.
While HHV6 has been known to precede HCMV in certain cases the conditions don't seem to apply here. My best guess, which is something I'm pretty loathe to say, is that if you're positive the tests are accurate then it's possible that Patient B's immune system alternately suppressed each virus below detectable levels. Since Patient B is receiving donor tissue with both viruses, and transplant patients are put on immunosuppressants following surgery, it could simply be that at first the immune system was capable of dealing with HCMV for the first week, but not HHV6. Then as it adapted to HHV6, HCMV evolved to evade so it showed up on the assays. That is entirely speculative, though. Another explanation might be that the viral titers of HCMV were too low to detect at Week 1, but it had reproduced enough to show up at Week 3 while the immune system dealt with HHV6. There's a lot of information that's missing on how the virii behave, the characteristics of the immunosuppressants given to the patient, and so on.
Patient C was clearly infected with nothing. They already had HHV6, and that's what showed up post-op.
Patient D was infected with HHV6. They had HCMV before, and both after.
Patient E was infected with HCMV, although like Patient A they could have been infected with a different strain of HHV6 as well, but the tests probably aren't specific enough to determine viral lineages for the before and after strains.


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Trigger allergic reaction in non-allergic people?
Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people? I have wondered if this is possible, since allergies are basically just a form hypersensitivity - so could this be triggered somehow?

Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people?

No.
At least, not that I've ever heard of. Allergic reactions, as you point out, are an overactive immune system response to an allergen (anything that causes the reaction). What determines who is allergic to what is a mix of genetic and environmental factors, and because an allergic reaction is categorized as an error on the immune system's behalf, inducing an allergic reaction is essentially finding a way to force the immune system to make a very, very specific error.
What can (and does) happen is the development of new allergies. Almost all allergies are acquired after birth, and repeated exposure to substances can lead to the appearance of new allergies - one case that stuck out in my head was a woman developing an allergy to a copper IUD that she tolerated well when it was first put in place.
I am not aware of any ability to predict what substances will cause the development of a new allergy. Both the unpredictability and inability to induce allergies comes down to how the immune system reacts to antigens (foreign substances). The machinations of the immune system's response to an allergen or antigen is fairly complicated, and at any point in the chain of events the potential for an overreaction is there. That's probably another question, though, and a much longer answer.


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How do Benzodiazepines induce Rewarding (Euphoric) effects?
Benzodiazepines are a class of drugs that serve as positive allosteric modulators of the GABAA receptor by binding to their own "site" on the aforementioned receptor. By doing this they produce euphoria and a wide range of effects characteristic of Central Nervous System (CNS) depression (e.g. anxiolysis, sedation, amnesia, mental confusion, muscle relaxant effects).
I know that an interaction with the mesolimbic dopamine ("reward") pathway would have to come in somewhere but where? I also know that GABAergic neurons downregulate activity in the mesolimbic dopamine pathway and that this is how opioids and cannabinoids induce euphoria -- they inhibit the release of GABA from presynaptic neurons in the mesolimbic dopamine pathway. I just find that this would be confusing in the case of benzodiazepines since they increase GABA activity, presumably also in the mesolimbic dopamine pathway thus producing dysphoria and not euphoria.
I just would like to know how they manage to induce euphoria in full (what they do to increase activity in the mesolimbic dopamine pathway that thus leads to euphoria)
Please cite journal articles to substantiate your claims.

Thanks for the edit. Could you be a bit more specific about what you need to know? You seem to be giving the answer in the question.

I think it'll be clear now.

Euphoria is linked  to opioid receptors and (more recently) with the endocannabinoid system. The dopamine pathway you talk about is linked to addiction.

Okay, I read the question wrong.
Benzodiazepines do not bind to GABAA receptors universally. Thus the presumption that it inhibits the mesolimbic dopamine pathway may be wrong. They may not interact directly with said pathway at all.
Many subtypes for the GABAA receptor exist. The receptor consists of 5 subunits. The following subunits are known to exist: α1-6, β1-3 and γ1-3. The most common combination has two α, two β and one γ. You find ones with distinct compositions at distinct locations in the brain. All have two bindingsites for GABA, but only a subset has an additional binding site for benzodiazepines.
The benzodiazepine binding site is at the interface of an α and a γ subunit, so receptors without this structure will show no affinity for benzodiazepines. Additionally the α subunit must contain a histidine residue, which is only true for α1, α2, α3 and α5. That is paraphrased from wikipedia, where you can find the sources as well.
I still think you need to consider the idea that benzodiazepines may not interact directly with the dopaminergic reward pathway, like opiates and cocaine does. I attribute the euphoria to be an indirect effect, resulting from the muscle relaxation (which will feel like you had a good massage), and the calmness of the mind.


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In the diffraction pattern of a protein crystal what exactly determines the intensities of the spots?
What I have read is that the contents of the unit cell affect the intensities, but how? I am also unclear on why you need to know the symmetry of the unit cell, what is that used for?
I understand segments of this topic (x-ray crystallography) but I am having trouble piecing all the segments together to make a complete picture. I've been spending hours every day on this on this, any help would be really appreciated!

Two questions here:
1) What does the symmetry of the crystal mean?
The symmetry of the unit cell is the symmetry of the crystal.  Its really useful thing to know about the crystal in practice.  You can always pretend that any crystal is space group P1 - with no internal symmetry.  This implies half of the diffraction data is needed to get a complete set.  Why half? The Laue symmetry of typical X-ray diffraction shows that the diffraction should be centrosymmetric  I(hkl) = I(-h,-k,-l).
If you do this and the crystal has more symmetry than that you are collecting too many data.  Here I take the example of a 2-fold axis.  Along that axis the space group shows that the symmetry of the crystal should be 4 fold along the x axis (x axis is chosen by convention):
I(hkl) = I(-h,-k,-l) (as above) and I(hkl) = I(h,-k,-l)
This fact means we actually can collect less data and know the crystal diffraction pattern easily.  In practice we collect from more than just the unique data, but the more diffraction data we take it also means that we can assume equivalence and have taken more  measurements, giving us better experimental accuracy for the same effort. It also means that when we build a molecular model for structure in the crystal we have a simpler model - one only creates a model for the unique assymmetric unit of the crystal unit cell. Fewer atoms in the structure, fewer degrees of freedom and less error in our resulting model.
There's more... screw axes 2(1), 3(1) and non primitive lattices create systematic absences which helps us collect more accurate data and do refinement more easily in the same vein...  but maybe this gives you an idea...
2) how does the unit cell contents reflect the diffraction intensities
X-ray scattering from crystals is the result of the photon causing an elastic scatter from atomic, inner shell electrons - Bragg scattering.  By considering the crystal as a series of slits in 3 dimensions, it can be shown that the average positions of atoms in the crystal reinforce each other to give the reciprocal lattice that is diffraction data in 3D.

In the picture above from Wikipedia you can see a beautiful protein crystal diffraction pattern.  The rings of spots are a spherical section from a 3D orthorhombic lattice of spots.
Rather than digress into the reason the diffraction appears this way, back to your question: what causes the intensities to vary from spot to spot and crystal to crystal.  The crystal lattice contains atoms which are in the same position in every unit cell which are creating the diffraction by Bragg scattering.  As such, it is the positions, relative electrons in orbit that dictate the diffraction intensities measured.
The models built to model diffraction typically translate a set of atomic positions to the structure factors (square roots of the diffraction intensities), but this is an approximation that works pretty well - the full model is not atomic positions, but an electron density function in space.
There are other sorts of scattering methods, more that could be said about all these subjects, but I hope that gives you some help with your specific questions. If you want clarifications in this, I can edit the answer from comments...