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What causes humans to be sleepy?
Is there a hormone or group of hormones that regulates when we feel sleepy late at night, or in the morning?  Or is sleepiness caused by some other non-hormonal mechanism?  (e.g. pure psychological, or neuronal.)

The release of the hormone melatonin is responsible for the feeling of sleepiness. It is released by the pineal gland and production starts when the light fades, as it's production is inhibited by light stimulation of the retina, the onset of the production is called dim-light melatonin onset. Artificial supplementation can increase sleep quality and regularity related to some sleep disorders and is often administered as pills or patches.
Adenosine is an inhibitory neuromodulator, ie it inhibits neural activity. Neural activity can be either excitatory or inhibitory and adenosine more strongly inhibits the excitatory neural activity. Thus, increased adenosine levels should decrease excitatory effect of nervous stimuli and make you feel more relaxed & sleepy.
Other hormones & neural pathways may be involved (serotonin and the serotonergic neural pathways for example) as well as other stimuli like other people's behaviours (yawning, stretching etc.).
This page and the wiki entry on melatonin have much more information.
From sleepfoundation:

Melatonin is a natural hormone made by your body's pineal gland - a
  pea-sized gland located just above the middle of the brain. During the
  day the pineal is inactive. When the sun goes down and darkness
  occurs, the pineal is "turned on" and begins to actively produce
  melatonin, which is released into the blood. Usually, this occurs
  around 9 p.m. As a result, melatonin levels in the blood rise sharply
  and you begin to feel less alert. Sleep becomes more inviting.
  Melatonin levels in the blood stay elevated for about 12 hours - all
  through the night - before the light of a new day when they fall back
  to low daytime levels by about 9 a.m. Daytime levels of melatonin are
  barely detectable.

Thanks rg255.  Unfortunately the link "This page" in the last sentence is inaccessible.  Also,  during my own research today I found something on "adenosine" influencing sleepiness but found the article hard to understand.  Do you know what triggers adensine build up, which apparently causes sleepiness?

@chris did the first link work? ("release of the hormone...") if so, that is the same page

No the first one didn't either.  Even just vaxa.com gives the error "403 - Forbidden: Access is denied."

@Chris edited to include quote from Växa site and effects/action of adenosine

What about sleepiness during day time? How is that brought about?


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How high is the energy yield of photovoltaics compared to photosynthesis?
I'm not an expert in plant physiology. I was wondering if, per square centimeter, leaves are converting more or less energy than photovoltaic systems. Can this be estimated? How?

In areas where our technology is advanced, you often get us doing better than nature because natural selection only does 'as good as necessary so as not to be outcompeted' whereas our technology can actually do 'as good as practically possible' :)

Your question could use some clarification. As stated, the premise is wrong because neither leaves nor PV cells produce energy. They can capture or store energy, they can also reflect or absorb and release energy. What pools or fluxes of energy are you interested in comparing? a common comparison is "quantum efficiency", but it is not clear if this is the comparison that you are looking for.

Does energy used to evaporate water count? Or the energy required to physically transport water from the soil to the air? PV cells don't evaporate or transport water. These are not accounted for in standard measures of quantum efficiency.

@David. Thanks, fixed the point: of course energy can not be produced/created. My curiosity indulges in the application: could we ever use plants for domestic energy requirements?. It seems photovoltaic are much better, do you agree?

I don't think either could meet domestic energy requirements alone, at least not in the near future. Your question could be improved with better definitions; it still says "converting", without saying to what. See, for example, quantum efficiency and quantum yield.

According to wikipedia, plants typically convert around 5% of the energy of the sunlight that hit the leaves into energy usable by the plant.  Sugarcane seems to be the best, it converts up to 8% of the energy into actual biomass.
The best solar panels on the market, according to the Independent, convert 21% of energy from sunlight into usable electricity.  Experimental prototypes do much better, and there are some that get over 40%.  Wikipedia has a nice graph of the most efficient solar cell prototypes.

By the way, the Forbes article is only the best poly-crystalline, not the best PV in general. Poly is typically less efficient than mono. There are mono panels on the market that are better than 16%

Good point!  Replaced that with another link and a bigger number.

Photovoltaics made from organic sources, like Graphene, (OPVs) have the potential for efficiencies exceeding 24% in a stacked structure. A theoretical max efficiency has not been  proposed, but it is expected to be less than silicon. The main benefit of OPVs is the rock-bottom price and the ability to make very tiny panels.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Can mutation rate be selected for?
Can the mutability of DNA be selected for in a population? I don’t mean selection for the phenotype that is the result of a mutation. Rather, can the rate of mutations in a population be increased by natural selection?

You might be interested in this question and answer.

The short answer is yes. There is quite a bit of work, theory and empirical on the evolution of mutation rate. To nicely answer, one would need to make a good review, probably inspired by some existing review. Such answer would take some time but I think is worth it.

You may like this reference. It clearly makes the case for the selection of an "ideal" mutation rate in the HIV virus.

The answer is yes and your nice question was answered several decades ago by Luria and Delbruck. Take few minutes to read their experiment that gives them the Nobel prize:
https://en.wikipedia.org/wiki/Luria%E2%80%93Delbr%C3%BCck_experiment

I think the OP is not asking about wether the trait "mutation rate" is affected by selection on the mutation rate and not whether mutations appear as a response to a selection pressure for a given trait. I understood the question as you did at first (and got four downvotes in a few hours!) and ended up deleting my answer.

Well partially I think that can be answered by their experiment. This because in their experiment they show that bacteria have already all the possible mutations that can be "selected" in a particular environment. The selection of a mutation can happen randomly or as evolutionary biologist think it is selected by "natural selection". But what is natural selection? Are there specific mechanisms that can explain natural selection? I think this is still an open question nowadays. Please tell me what you think am open for this discussion :)

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Does the formation of water inside the mitochondrial matrix help contribute to the proton gradient during the electron transport chain?

Does the synthesis of water in the final step of the electron transport chain significantly increase the electrochemical gradient across the matrix? I understand that pumping protons out of the matrix clearly increases the positive charge in the intermembrane space, but the chemical reaction in Complex IV O2 + 4H+ + 4e− → 2H2O also reduces the protons in the matrix by binding them in water.
Since ATP synthase relies entirely on the electrochemical proton gradient, it seems like this might be worth mentioning, yet I haven't seen this explicitly explored in any textbooks. If there is any literature about this topic, I would love to see it.

Your description of it is largely correct, but the electron transport chain does not simply "dump" charged oxygen ions in the mitochondrial matrix. Instead, cytochrome C oxidase (complex IV) binds the O$_2$ molecule to one of its heme groups, and the reduction O$_2$ + 4 H$^+$ + 4 e$^-$ $\rightarrow$ 2 H$_2$O occurs at the heme group before water is released. Some more details on the enzyme is found here and here (or in any biochemistry book).
In theory you're right that producing water in the mitochondrial matrix would dilute the H$^+$ concentration there a little (along with the concentration of everything else). But this dilution is negligible: the mitochondrial matrix has pH $\approx$ 7.8, which is the same as a H$^+$ concentration of about 15 x 10$^{-9}$M, while the concentration of water (yes, there is such a thing ;) is 55 M. So adding a water molecule has virtually no effect compared to removing a proton.

Thanks for the explanation. Although I still have the same question - does the removal of the protons (H+) inside the matrix in the the final reduction step (O2 + 4 H + 4 e− → 2 H2O) increase the electrochemical gradient? Protons are not only being pumped out of the matrix, but they are being bound up - 2 per water molecule. Then in addition to being bound up, they're also diluted. I could've been a little more eloquent before.

Ah, I see. Yes, in this sense respiration does affect pH I think, although it is counterbalanced by H+ production in metabolic pathways. But I think the H+ concentration in the intermembrane space (cristae) is much more important for the concentration gradient, since this space is much smaller, adding a protein there has a larger effect than removing a proton in the mitochondrial matrix.

The missing science to the question is the failure to realize that water inside a cell is bound to hydrophilic proteins which form an exclusion zone.  This EZ is well described in the literature by Pollack.  The EZ carries a strong net negative charge and it excludes protons.  This has also been confirmed by numerous researchers across the world.  The exclusion zone has specific physical properties that make it a different form of matter from bulk water that biologist normally are familiar with.  This is why Cayetano's question is excellent and why the answer he has been given is incomplete.  Any addition to the charge dramatically affects the charge across the membranes in mitochondria because they are only 4-6 microns thick.  The biophysics and mathematics of cell membrane electrochemistry prove that small charge differences are magnified on membranes of this thickness. The charge across this inner mitochondrial membrane is massive. It has been shown that this change across this membrane causes a pH gradient as well as an electrical charge of about 150 millivolts across the inner mitochondrial membrane. This may sound like a small amount of charge, but consider how charge is calculated and then scaled by math: the inner membrane is only 4-5 nanometers thick, so the voltage across this membrane is about 30 million volts per meter! Dr. Nick Lane from the UK has done this work and it is published in his book called "The Vital Question"  You can google his name for all the cites you want.  For comparison, that is equivalent to the energy in a bolt of lightening.  It is an electrical gradient that drives electrons from food to reduce oxygen from our lungs.I would also direct the readers to Dr. Martin Chaplin's work on water which takes Pollack's work to the quantum level.  EZ water is a capacitor for light energies from the sun.  All redox reactions in the body are tied at some level to the photoelectric effect, water chemistry, and the electromagnetic force. I will remind everyone reading this that the EMF only deals with charge particles.  Electrons and protons are those particles and both are found in mitochondria in massive quantities.  All foods are broken down into electrons to enter ECT.
Glutathione production in cells links the photoelectric effect in foods.   When we are oxidized,  we use up our stores of cysteine and glutathione.   Excessive inflammation (High proton content), from any cause, does not allows cells to replenish its levels and it does not allow us to separate water into its positive and negative charges and create large exclusion zones in mitochondria.  This limits energy production in a cell while slowly degrading cell signaling.  We see this in % heteroplasmy increases as laid out by Dr. Doug Wallace's seminal work on mitochondria.
References:

Gerald Pollack "The Fourth Phase of Water." 2013
Dr. Jodi Nunnari, Professor and Chair of Molecular and Cellular
Biology at the University of California, Davis was one of Wallace's
post doc's: Her work in size and shape links water thermodynamics to
mitochondrial energy production, see this article.
Dr. Doug Wallace: Head of mitochondrial medicine at the Children
    Hospital of Philadelphia.
     - youtube.com/watch?v=KwbIR2yUziw
     - youtube.com/watch?v=ahlDLjf8c90
Dr. Nick Lane You can google his publications which are large or
just read his books "Oxygen", "Power Sex and Suicide", "The Vital
Question".
ER-mitochondria contacts couple mtDNA synthesis with mitochondrial
division in human cells
Genetics: Mitochondrial DNA in evolution and disease
Scientists Learn How Mitochondrial DNA Replication is
Controlled
Here is Martin Chaplin website: He is a PHD researcher from the
UK.

Welcome to BiologySE - Thanks for your contribution. As with all of the answers we appreciate citable references, such that others can follow your answer and read further. Please see the help page on "How to write a good answer" for more information - Thanks!


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fast metabolism and law of conservation of energy
Usually if person take more calories with food than he spends, he is gaining weight.
But if he has fast metabolism, his weight stays the same.
Where these calories go? Maybe food is not completely digesting?
PS. How it related to Basal metabolic rate?

"fast metabolism" usually refers to the daily energy expenditure, also known as the metabolic rate (https://en.wikipedia.org/wiki/Basal_metabolic_rate)  Incomplete uptake of nutrients ("not completely digesting") is distinct from metabolic rate. So it sound like your question is whether metabolic rate or nutrient uptake is the key factor?

@Roland, I just want to understand how this metabolism works, why people can stay slim. So you saying that they waste more energy, so they have low energy conversion efficiency?

No, I'm not saying that (and I don't know what you mean by "conversion efficiency"). I'm trying to figure out more precisely what you're asking. If a person has a high caloric intake and does not gain weight, then obviously there is either high energy expenditure ("fast metabolism"), or there is incomplete uptake of nutrients, or both. This varies between individuals. Are you asking for population data / studies on metabolic rate, or on digestion, or ... ?

@Roland, I'm interested in fast metabolism mechanics, how it's actually works in simple terms. About Energy conversion efficiency: https://en.wikipedia.org/wiki/Energy_conversion_efficiency

probably relation with Basal metabolic rate

One known mechanism is how efficient your mitochondria are, or more precisely how leaking your mitochondria membranes are. https://dl.sciencesocieties.org/publications/jas/abstracts/87/14_suppl/0870064

@John, tried to read, but difficult to understand

It is alright, most of mechanisms are still poorly understood but one that is is the the membrane that the ATP pump sits in, it varies in how effective a barrier to protons it is. brown fats cells have mitochondria that leak like a sieve so they they just pump protons endlessly and make very little ATP but in the process make a lot of heat. That's an extreme case but there is some variation in normal mitochondria as well making the more or less efficient at producing a proton gradient to run ATP pumps. How much of an impact this has is still under investigation.

@John, so it's losing some energy by heat? maybe you can write something like this as an answer?


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Single Nucleotide Polymorphisms and diseases
I am writing a report on how Single Nucleotide Polymorphisms occurring in each of these regions:

Transcription factor (TF) binding sites
Epigentic signals
Splicing variants
MicroRNA binding sites
Coding regions

can cause diseases.   Related literature suggestion from you or just informations that you know would be grateful

SNPs in all these regions will modify the DNA sequence. Effects will depend on where exactly the SNP is. I'll summarize the conditions in which effects can be maximum

Transcription Factors (TFs) binding sites: SNP in the nucleotide positions that bind to the recognition amino acids in the TF
Epigentic signals: C->X [x: A,G,T] SNPs can disrupt DNA methylation hotspots
Splicing variants: SNPs at splice donor/acceptor sites can cause intron retention
microRNA binding sites: SNP in seed region can abolish miRNA targeting
Coding regions: certain SNPs can create premature stop codons for e.g. CAG (Gln) -> UAG (stop)

there is a lot of work on SNPs. If you search in pubmed for all these categories, you'll get many research articles as well as reviews.

SNP in the nucleotide positions that bind to the recognition amino acids in the TF.. What consequence does it have? H can it cause disease?

I meant what is the mechanism by which regulatory region SNPs causes diseases?

@Zizo here is an actual example where a SNP in a regulatory region leads to disease: http://www.ncbi.nlm.nih.gov/pubmed/16728641

Thanks @Bitwise, if you could kindly also give me examples for Epigenetic singlas, Splicing variants, MicroRNA binding sites and Coding regions or just some of them it would be awesome

@Zizo Google it - it is easy to find.


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In vitro enzyme production
I need to express a protein in vitro but I don't know where to start.  I will likely do a  T7 transcription protocol but for translation I am not sure what to do.  Are there any good kits?

there are in-vitro protein synthesis kits.. but you may try expressing the enzyme in bacteria and purify..

There are kits: Google "in vitro expression" and you will find that all of the major companies do one. I have no experience with any of them.

Don't take me wrong, but if you don't know where to start, kits are probably the worst starting point. It is not by mixing unknown solution A with proprietary buffer B that you will understand in vitro enzyme production. Once you master and troubleshoot the technique, using kits as pipetting shortcuts is fine.

@GianpaoloR what is your recommendation to use besides kits?  Should I use T7 RNA polymerase to create mRNA from my gene of interest, purify the mRNA, and then use a lysate for translation?

yes, rabbit reticulocyte, wheat germs or Hela extracts. There are detailed steps on Current Protocols.

New England Biolabs, which has an excellent reputation for well-tested, well-documented, and robust products, has a line of protein expression and purification products that I'd definitely take a look at. I've used the pMAL system for expression of fusion proteins in E. coli, and the PURExpress system looks just like what you're looking for. I have a personal (but not financial) connection with them, and I can vouch for their quality and technical support.
Pierce/Thermo is generally a good place to look when dealing with protein stuff. I've had good results with lots of their stuff, but I haven't done in vitro expression in ages, so I can't remember what I used. (BTW, I have no connection with them, I just tend to like their products.)
As Alan Boyd mentioned, lots of companies like Life Technologies, Promega, Qiagen, and Sigma have in vitro expression kits. Which one you pick will ultimately be influenced by what exactly you need your protein to do, the desired scale of expression, the type of tag(s) you want to put on it, what equipment and expertise you have in your lab, and how much time and money you want to invest.


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Ligase Chain Reaction: Determining the annealing temperature for gene synthesis
Using the tool Gene2Oligo I have a set of DNA oligonucleotides to synthesize a gene using ligase chain reaction (LCR).  The average melting temperature is 72 degrees Celsius.  I am going to use a the thermostable Taq ligase enzyme for the LCR reaction but I am unsure of the annealing temperature to use.  Should I use the standard recommendation as in PCR of 5 degrees less than the melting temperature or should I use another tool?  Taq ligase has a cutoff in activity at 65C so that is the highest I can use.


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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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What is the average volume of the hippocampus?
I'm trying to find any information on sizes of the hippocampus?
Ideally in the average adult male & female brain

The average values of right hippocampus were recorded as follows weight 4.11572 gm, length 6.996 cm, width 1.998,volume 13.978 and surface area11.839 cubic centimetre while left hippocampus mean values were weight 3.96458gms,length 6.995, width 1.998,volume 13.976 and surface area 11.713cc. B. Narasinga Rao, K.R.S. Prasad Rao, R. Ramana Rao. 2012. Morphometric study of hippocampus in adult human brains. Int J Basic Appl Med Sci 2: 139-143.
Men and women had identical volumes of amygdala and hippocampus, as well as dorsal prefrontal cortex Ruben C. Gur, Faith Gunning-Dixon, Warren B. Bilker, Raquel E. Gur. 2002. Sex Differences in Temporo-limbic and Frontal Brain Volumes of Healthy Adults. Cerebral Cortex 12: 998-1003
Hippocampal volume change with age: Hippocampal volume diminished by 20% from 3,584 ± 136 mm3 at age 36 to 2,870 ± 220 mm3 at age of 85, corresponding to a volume loss of about 14.6 mm3/year (Schuff N., et al. 1999. Age-related metabolite changes and volume loss in the hippocampus by magnetic resonance spectroscopy and imaging. Neurobiol Aging 20: 279–285).


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Is fluoride toxic, and how worried should I be about it?
A recent flurry of "fluoride is bad!" posts are appearing on my social network news feeds.  Usually I can simply ignore them after a brief look, but this one, stemming from a recent article in The Lancet, isn't easy enough for me to understand and apply or ignore.
The posts link to a March, 2014 article, Neurobehavioural effects of developmental toxicity, from The Lancet Neurology, Volume 13, Issue 3, which has the summary (emphasis added):

Neurodevelopmental disabilities, including autism, attention-deficit hyperactivity disorder, dyslexia, and other cognitive impairments, affect millions of children worldwide, and some diagnoses seem to be increasing in frequency. Industrial chemicals that injure the developing brain are among the known causes for this rise in prevalence. In 2006, we did a systematic review and identified five industrial chemicals as developmental neurotoxicants: lead, methylmercury, polychlorinated biphenyls, arsenic, and toluene. Since 2006, epidemiological studies have documented six additional developmental neurotoxicants—manganese, fluoride, chlorpyrifos, dichlorodiphenyltrichloroethane, tetrachloroethylene, and the polybrominated diphenyl ethers. We postulate that even more neurotoxicants remain undiscovered. To control the pandemic of developmental neurotoxicity, we propose a global prevention strategy. Untested chemicals should not be presumed to be safe to brain development, and chemicals in existing use and all new chemicals must therefore be tested for developmental neurotoxicity. To coordinate these efforts and to accelerate translation of science into prevention, we propose the urgent formation of a new international clearinghouse.

I don't have full access to the article, so I can't refer to the epidemiological study it says shows fluoride to be a developmental neurotoxicant.

What is a developmental neurotoxicant?
How strong is the research that claims fluoride is a developmental neurotoxicant?
What relationship, if any, does this report or research have with typical fluoride compounds used in US water treatment at the levels typically present in US water (sodium fluoride, fluorosilicic acid, or sodium fluorosilicate at 0.7 mg/L)?

The PDF of the paper can be found here. I'll have a look at it later and write an answer about it.

The paper references the following paper regarding the fluoride meta-analysis: Choi AL, Sun G, Zhang Y, Grandjean P. Developmental ﬂ uoride
neurotoxicity: a systematic review and meta-analysis.
Environ Health Perspect 2012; 120: 1362–68. This appears to be available here: http://ehp.niehs.nih.gov/1104912/ Thanks for reviewing this!

I don't really understand your third question.

@Chris I should probably rewrite that.  Just because fluoride may be considered toxic doesn't mean that any or all of the compounds used deliver effective levels of fluoride to the brain, so I'm asking if this information about fluoride toxicity applies to fluoride as it is currently used in our water systems.

Well, that is the question. The Choi paper does its meta-analysis on research which has been conducted on water fluorine levels. So this is not unimportant.

I don't care about additional reputation. If my answer doesn't fit your question, there is no need to accept it. You can also add some points which are not covered and I will probably try to answer them. I only remove obsolete comments.

First of all: Yes, fluoride is toxic, but the toxicity depends largely on the form (soluble vs. unsoluble, which fluoride salt etc.) occurs. It also depends on the environment since insoluble salts which are subjected to strong acids can release fluorine ions.
The certain toxic dose for adults is 32-64mg/kg body weight, a 75kg adult needs to take up between 2,4 and 4,8 grams of fluoride ions (for sodium fluoride this would be between 5,3 and 10,6 gr of the salt). For children this is about 5mg/kg body weight.
For the water the added dose of fluorine is much lower, somewhere between 0,7 and 1.2 mg/l. Other sources of fluroride are food (especially sea food) and also black tea.
The toxicity of fluoride is mediated by different ways: First it forms an insoluble salt with calcium in the cells, effectively causing hypocalcemia. Calcium is an important second messenger in different signal transduction pathways as well as highly important for the functioning of nerve cells (which also explains why it is neurotoxic in the development of nerve and brain cells). It also causes the inhibition of a number of different enzymes as enolase (disturbs the glycolysis) but also phosphatases and katalase. For all of this have a look into the Wikipedia if you want to know more details.
About the paper: It is a review of published research articles which sums up the situation in this field. The paper mentions fluoride only twice: Once on the abstract and once in a table about newly identified developmental neurotoxins (table 2 to be precise). It references only one meta-analysis on this topic.
The cited meta-analysis ("Developmental fluoride neurotoxicity: a systematic review and meta-analysis") which did a statistical meta-analysis of published papers and their data. They find a significant relation between the fluoride content of the drinking water and the IQ of the children.
However this is not undisputed (to say it mildly), since while a finding can be statistically significant, it doesn't necessarily mean that there is clinical importance. The other important point which @Doctor Whom mentioned is that a correlation doesn't imply a causation. So even if there seems to be a correlation between two things, they are not necessarily connected (see the famous example of storchs and birth rates).
This paper ("Developmental fluoride neurotoxicity: clinical importance versus statistical significance.") is published as a comment on the original paper and claims exactly this. They say the the mean difference in IQ is about 7 points, which is not of clinical importance. Another paper critizes the relatively low quality of the original papers used for the study ("Fluoride and children's IQ.").
They also mention a low consensus about what is a high concentration of fluoride in the drinking water and also show the very wide variation of the fluoride concentration in the original studies. The highest concentrations mentioned are around 10mg/l which is about 10x the concentration used for adding fluoride to the water. Even if we take in account that children are more sensitive to fluoride and also need lower fluoride concentrations to cuse some developmental damages (below the fatal concentration) this would still add up to quite absurd amounts of water they have to drink.
Regarding your questions:

A developmental neurotoxin is a substance which interferes with developing neurons or nerve cells. It either inhibits their growth completely or at least impairs the cells.
Given on the articles I found (and cited above) I would say that fluoride is a developmental neurotoxin. Nevertheless it seems to me that it is not very strong in this context as the current studies are contradictory. Thinking about the amounts of fluoride present in water (even if the concentration is much higher than recommended) makes me doubt if this is really the causative agent.

Well written, Chris.  I would recommend the addition of two points.  One, to the "significance" discussion, the point that correlation does not infer causality.  That study had a strong likelihood for bias, as there are MANY regional factors beyond yes/no fluoridated water that could influence this marginal difference in IQ results.  Secondly, to the final point (#2), I would comment on the issue of dose.

Good points, thank you for mentioning. I added them.

7 IQ points is rather significant - 10 points is supposed to be one standard deviation.  Do you mean that the IQ difference was not statistically significant?

The original authors say that 7 IQ points difference is statistical significant. We are less than 1 sigma away from the mean here.


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Why is there a difference in the rotation of the tail fin in fish compared to marine mammals?
I've been thinking about this one, but I can't seem to find what causes this difference.
All fishes that I've seen have their tail fin positioned vertical:

But all the marine mammals I know have their tail positioned horizontal:

Why is there this difference? Is it because it's mammals compared to fish? Or could fish as well have horizontal tail fins?

While fish tend to move from side to side (lateral undulation) for which a vertical tail makes sense, the land ancestors of marine mammals had their limbs under them and so their spines were already adapted to up and down movement (dorsoventral undulation). When these animals moved to marine environments, they continued up and down movement in their swimming, for which a horizontal tail makes sense.
(The wikipedia article on fins gives some more detail, and links to this webpage on Berkeley.edu. A paper by Thewissen et al. suggests that for cetaceans, dorsoventral undulation as a swimming strategy came first, and the horizontal tail evolved later.

More detail:
In a third example beyond fishes and marine mammals, the icthyosaurs and other aquatic reptiles developed vertical tails, even though like marine mammals they evolved from four-footed land animals. This may be because the legs/spines/gaits of land reptiles differ from those of land mammals, so that the earliest icthyosaurs swam with lateral undulation, as reflected in their spinal modifications.
This blog post by Brian Switek gives a really superb run-down on the issue, with figures and citations. I'll quote this part which deals with the dorsoventral undulation theory:

...mammals and their relatives were carrying their legs underneath their bodies and not out to the sides since the late Permian, and so the motion of their spine adapted to move in an up-and-down motion rather than side-to-side like many living reptiles and amphibians. Thus Pakicetus[the pre-cetacean land mammal] would not have evolved a tail for side-to-side motion like icthyosaurs or sharks because they would have had to entirely change the way their spinal column was set up first.

Switek goes on to to talk about exceptions in some marine mammals:

At this point some of you might raise the point that living pinnipeds like seals and sea lions move in a side-to-side motion underwater. That may be true on a superficial level, but pinnipeds primarily use their modified limbs (hindlimbs in seals and forelimbs in sea lions) to move through the water; they aren’t relying on propulsion from a large fluke or caudal fin providing most of the propulsion with the front fins/limbs providing lift and allowing for change in direction. This diversity of strategies in living marine mammals suggests differing situations encountered by differing ancestors with their own suites of characteristics, but in the case of whales it seems that their ancestors were best fitted to move by undulating their spinal column and using their limbs to provide some extra propulsion/direction.

Cetaceans (i.e., marine mammals) evolved from certain ancient land based mammals, thus the tail is essentially convergent evolution of the tail function.

I've thought about this many times but enjoyed theorizing on possibilities vs researching evolutionary theory.  I like these thoughts above- def agree to certain extent- but it seems to me that:
    If almost all "fishes" utilize side to side motion/morphology, it seems that this is certainly more efficient, and would be adopted, over many millions of yrs...at least in some examples...by marine mammals; HOWEVER, there's one difference and physiological necessity that I believe actually may make the horizontal fluke/tail advantageous. This would make the vertebrae idea just a shaping mechanism in such evolution- instead of a restricting agent.
In order to breath -in order to do so efficiently- surfacing is necessary, thus vertical thrust is of the utmost importance.  Esp, since other air-breathing marine species (evolved from land animals...) that have NOT evolved a solid fluke (whether by lack of evolutionary time, or prior morphological diffferences...) in most cases have a more flexible propulsion system to achieve efficiency via improved or altered maneuverability.
Certain pinnipeds- as discussed in article above- have less solid structures, thus improved flexibility/mobility and in my mind- going hand-in-hand with creating sufficient breathing efficiency.  Then, in non-mammal instances, penguins are a solid example- as the use of "forelimb" (wings) create both the flexibility/mobility to achieve said necessities, but also... effectively acting quite similarly (in the vertical thrust department) to the horizontal fluke----in the process of surfacing to breath, porpoise, or reach land.

It would be great if you could add some references to your response!

However icthyosaurs, which are air breathing, fusiform reptiles have vertical flukes like fish. So... while your theory of air breathing sounds making horizon trust an advantage sounds convincing on paper. it may not be true.


text:
How fast will cells lyse under hypotonic conditions?
Routinely, lysis of cells with hypotonic solutions is carried out along with some physical (douncing) or enzymatic (lysozyme) method to break open the cells. If one were not to do any of these and just resuspend cells in water, how long would it take to lyse the cells? I was discussing with a lab mate who claimed it would take hours while in my understanding, salt equilibrium should not take very long (maybe on the order of minutes?) and hence, lysis should be done within 20-30 minutes.

this is more of an anecdotal answer but I put sheep blood cells in pure water in a lab that I use in my organismal bio course and they lyse almost instantly.  I have not timed it but I would say less than a minute.

In the case of red blood cells, hemolysis in pure water occurs at just over 1 minute, 30 seconds, according to this paper. (Osmotic Properties of the Erythrocyte, M.H. Jacobs and Arthur K. Parpart, The Biological Bulletin, 1932)


text:
Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?
We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 fold lesser (ie ~100nM) whereas the EC50 in an enzymatic assay using vesicles in ~1-2nM. Would it be reasonable to say that the "real" affinity is ~1nM than 100s of nM based on the biochemical assay?
Alternately, is there a documented system where a huge discrepancy exists between measurements from direct binding and biochemical assays?

You can certainly get massive differences between EC50 and affinity. This is especially true for cell-based assays and membrane protein systems.
The reason why is because the appropriate time scales to achieve binding equilibrium (hrs for nM affinity, days for picomolar, feptomolar affinity according to back of the envelope calculations) may be and likely will be different from the appropriate time scales of activation, endocytosis, degradation, etc. Furthermore, you can have avidity effects that would not be apparent in a dilute membrane assay compared to a cell's surface. It could very much be that the dominant terms in mass transport change depending on the geometry and antigen density and while I'm not entirely sure bout vesicles vs. emulsions it is true for cancer models. Theoretical analysis of antibody targeting of tumor spheroids: importance of dosage for penetration, and affinity for retention.

Case study number I: hGH:hGHR interactions have been extensively studied and high affinity hGH have been produced. However, none of the variants showed improved EC50. It turns out that the binding was primarily influenced by the off-rates which were so slow, that affecting those values did little to the kinetics of the system. Growth Hormone Binding Affinity for Its Receptor Surpasses the Requirements for Cellular Activity
Case study number II: CEA-antibodies have been affinity matured to have pM activity compared to the wild-type nM affinity. However, the antibody had minimal effect on tumor uptake. As CEA gets endocytosed on the order of 30 minutes, all of the antibody was simply getting endocytosed rather than acting as an inhibitor. Directed evolution of an anti-carcinoembryonic antigen scFv with a 4-day monovalent dissociation half-time at 37°C.
(edit)
I realized that this answer is more applicable to IC50s vs. the EC50 experiments described above. However, many of the points remains. The Km between a substrate and its enzyme is a thermodynamic property where as the EC50 also has dynamic factors that may influence its measurement.
I would also add that simply adjusting the pH 2 units may result in a 2 orders of magnitude change in activity.
(edit2)
A further point to make about enzymatic assays is that from an observation of Michaelis-Menten kinetics, the KM of the reaction isn't the KD of the enzyme but alternatively the effective binding constant.
Recall that:

If there is a non-trivial kcat comparable to the dissociation rate kr, the enzyme will have an effective half maximal concentration that is significantly higher than the Kd. There are multiple ways how your assay can result in the discrepancies that you're seeing. The first would your strategy in measuring your EC50. If one is an enzymatic readout and the other is a binding readout, you would naturally have very different results.  Alternatively, the enzyme in the detergent system may be catalytically more active than the vesicle system resulting in a higher effective KM. Again, the pH thing.
Finally, there is always that awkward moment when you realized that you might accidentally have measured a titration curve rather than a binding curve.

bobthejoe: I like the detail in your answer, especially the hGH example is very surprising. However, my question pertains to comparing affinities and EC50 measurements, both being derived from in vitro assays with purified proteins. I would think the avidity argument might hold, especially when the same system were compared in a vesicular environment versus detergent solution.

bobthejoe, just thought I'd say this: You've laid out really well why interpreting Km is not always trivial. Exactly why I chose to focus on EC50 (with the trivial(?) assumption that substrate far exceeds enzyme concentration). I'm going to accept your answer, given the richness of detail that you've laid out!

In what follows I am going to attempt to answer your question using a specific example of  (competitive) reversible activation, and I hope to show what a misleading parameter EC50 can be.  (Rate law derivation is an area of interest, hence the long-winded answer).
It can of course give information, but IMO it needs to be used with extreme care.
I am restricting my comments to the case where A is a reversible activator and where  [A] >> eo and [S] >> eo.  (All constants are defined below).
In short, I am not treating irreversible activation, and I am not treating the case where A is considered a tight-binding activator (so that [A] ≈ eo). In other words, I am making the steady-state approximation (Briggs & Haldane, 1925)
Consider the following simple mechanism for activation in a single-substrate enzyme:
A Mechanism for Competitive, Reversible Activation

The substrate (S) cannot bind to the free enzyme (E) unless the activator (A) is present.  That is, only the activator can bind (reversibly) to E, and the substrate binds (reversibly) to the EA complex.  Reaction occurs within the EAS complex (giving EAP). Dissociation of product (P) from EAP gives EA.
The (steady-state) initial-rate law for the above mechanism is the following:

As stated, all constants are defined below and follow the usual definitions in enzyme kinetics.  I'll mention just one here: KA is the dissociation constant for the activator, and has units of concentration.
I derived these equations using a computerized version of the King & Altman method (King & Altman, 1956), but it is not difficult to do. It was pure laziness that prevented a 'first principles' derivation. Rate law derivation is treated in depth in most books on enzyme kinetics and good accounts may be found in Segel (1975) and Cornish-Bowden (2004).
One can now make the following points

There is no activity without A (as one would expect).
When [A]  >>  KA, the rate law becomes identical with the Michaelis-Menten equation (as one would expect).
The equation is similar to the case of competitive inhibition, but (note subtle change) with (1 + KA / [A]) substituted for (1 + [I] / Ki)
One can consider this mechanism an example of competitive activation

Defining

νiexc     =     the initial velocity when A is in vast excess [ie setting [A] equal to ∞ in eqn (1) ].
EC50    =     the concentration of A that gives νi equal to νiexc / 2 (half-maximal activation)

allows the following two equations to be derived:

Setting the left-hand side of the above equal to 2, and solving for [A], gives the following all-important equation

One can now draw the following conclusions

When [S] = KSm

In words, when the substrate is present at a concentration equal to the Michaelis constant the value of EC50 is half the value of KA!.
When [S] >> KSm

When [S] = 10 x KSm, for example, EC50 is one-tenth the value of KA, and when  [S] = 100 x KSm the figure is one-hundreth.
When [S] << KSm

Thus, for a competitive activator, it is only when [S] << KSm
that EC50 gives a reasonable estimate of KA.
The substrate concentration in a 'normal' enzyme assay will probably be equal to or greater than the Michaelis constant (in order to 'see' activity), and thus EC50 will be an underestimate of KA.
If the substrate is present at a 'saturating' concentration (say 10 x KSm) then one is in real trouble.
However, this is not the only consideration.  As well as being substrate-concentration dependent, the manner in which EC50 depends on [substrate] depends on mechanism.
As briefly discussed below, the competitive activation case is analogous to that of competitive inhibition. However for uncompetitive inhibition the Ki (inhibition constant) is only equal to IC50 (the concentration of inhibitor giving half-maximal inhibition) at high substrate concentration! (see Naqui, 1982). By analogy, one can conclude that the same is true of uncompetitive activation.
It is very difficult to see how EC50 can be of any practical use, except perhaps when the mechanism of activation is known.  At the very least, conclusions drawn from EC50 data should otherwise not be considered definitive.
In addition, I have discussed the only the case of a single-substrate reaction.  Two-substrate reactions have the potential for even greater complexity.

Illustrative Example (Competitive Activation)
Let's take an example, and check some conclusions:

kfcat   =   1000 s-1
eo   =   1
KSm    =   10 µM
KA      =   50 µM

It may be calculated that:

When [S] equals  10 µM (ie when [S] is equal to KSm) and when [A] is 'saturating' (for the sake of argument set equal to ∞) the velocity is 500 µM s-1 [from eqn (1) ].
From eqn (2), the concentration of A required to achieve half this value (half maximal activation) is 25 µM (EC50 equals 25 µM)
This value can be directly calculated from eqn (3)
When [S] equals  100 µM (ie [S] equals 10 x KSm) and when [A] is 'saturating' the velocity is now 909 µM s-1 [from eqn (1) ].
From eqn (2), the concentration of A required to achieve half this value  is now only ~4.5 µM
This value can be directly calculated from eqn (3) [EC50 equals (50 / 11) µM]
When [S] equals  1 µM (ie [S] equal to one-tenth the Michaelis constant) and when [A] is 'saturating' the velocity is now only ~91 µM s-1 [from eqn (1) ].
From eqn (2), the concentration of A required to achieve half this value is ~45.5 µM (now almost equal to KA)
This value can be directly calculated from eqn (3) [EC50 equals (500 / 11) µM]

Reversible Inhibition & IC50.  A Brief Comment
There is nothing much new in any of the above. In the field of enzyme inhibition, the inadequecies of IC50 (the concentration of inhibitor giving 50% inhibition) and the relationship to the Inhibition constant are well-known  [see, for example,  Chou (1974), Segel (1975), Naqui (1982) & Tsou (1987)], but (it seems to me) often ignored.
The paper of Naqui gives a very succinct analysis of the situation and the pdf is freely available to all.
Reversible inhibitors may be divided into four classes, depending on the pattern of inhibition: competitive, uncompetitive, non-competitive and 'mixed' (see Naqui, 1982, and references therein).
In all cases except non-competitive inhibition, Ki ≠ IC50, and IC50 is substrate- dependent.
(Non-competitive inhibition is the 'fluky' one where it just so happens that the catalytic constant and the specificity constant (kfcat / KSm) are changed to the same extent or, to put it another way, the slope and intercept of a Lineweaver-Burk plot (it just so happens) are changed to the same extent)
For an uncompetitive inhibitor (as stated) the IC50 only equals Ki at high substrate concentration (see Naqui, 1982).
Like the case of competitive activation, IC50  equals Ki for a competitive inhibitor only at low susbstrate concentrations (see Naqui, 1982).
'Mixed' inhibition is even more complex, and the inhibition constant may be greater than or less than IC50 depending on experimental conditons (see Naqui, 1982).
Great question, BTW.

Addendum
As I have derived the full form of the rate law (as opposed to the initial-rate law), it is probably worth posting it. The initial-rate law is obtained from this equation by setting [P] equal to zero.

Kinetic Constants defined in terms of Rate Contants
Rate constants are numbered (as subscripts) from species, to species, with numbering as in diagram.
Thus the rate constant k1,2 is that from E (species 1) to EA (species 2).

Catalytic Constants

Michaelis Constants

Specificity Constants

Activation (Dissociation Constant)

Kinetic Constant Definition

ν     velocity
νi   the initial velocity
KSm    the Michaelis Constant for S
KPm    the Michaelis Constant for P
kfcat   the catalytic constant (in the forward direction)
krcat   the catalytic constant (in the reverse direction)
Vmax    the maximum velocity, equal to kfcat eo
eo   the total enzyme concentration

KA      the dissociation constant for (activator), equal to k2,1 / k1,2, with units of concentration (Molarity, say) [rate constants are numbered from species, to species, numbering as in diagram].
νiexc    the initial velocity when A is in excess ([A] = ∞).
EC50   the concencentration of A that gives νi equal to νiexc / 2 (half-maximal activation)
[A]     The initial concentration of activator.
[S]     The initial concentration of substrate.

The rate law and the diagrams were obtained using Mathematica.  For Matematica at SE see here

References

Briggs, G. E. & Haldane, J. B. S. (1925). A note on the kinetics of enzyme action.  Biochem. J. 19, 338 - 339.[pdf]
Chou, T.C. (1974) Relationships between inhibition constants and fractional inhibition in enzyme-catalyzed reactions with different numbers of reactants, different reaction mechanisms, and different types and mechanisms of inhibition. Mol. Pharmacol., 10, 235-247 [pubmed]
Cornish-Bowden, A. (2004). Fundamentals of Enzyme Kinetics. 3rd edn. Portland Press Ltd, London.
King, E. L. & Altman, C. (1956). A schematic method of deriving the rate laws for enzyme-catalyzed reactions.  J. Phys. Chem. 60, 1375 - 1378. [ACS site]
Naqui, A. (1982). What does I50 mean? (1983)  Biochem. J.  215,  429-430 [pdf]
Segel, I. H. (1975). Enzyme Kinetics.  Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. John Wiley & Sons, Inc., New York.
Tsou, C. L. (1987) The screening of enzyme-targeted drugs.  Bioessays, 6, 237-238. [pubmed]


text:
The effects of dust particles
When sun rays shoot through my house from a window, sometimes if the lighting is correct, it will reveal a huge amount of floating particles and dust.
Are these particles dangerous to humans if you live with them constantly?

You asked the single most difficult questions ever, so be proud of yourself! I've spent some time in the lab with a post doctorate trying to answer that particular question. It all is based on something called the hygiene hypothesis: the belief that as we are getting cleaner we are seeing less and less bacteria and so our immune system isn't working as it should so we get allergies. There's lot to this theory with regards to the different white blood cells in our body (specifically Th1, Th2 if you've ever heard of them). Of course there are reverse hypotheses, because we avoid eating stuff like peanuts, but minute amounts is found in dust, dust exposure (which also contains bacteria) makes us think peanuts are harmful so that's why we have allergies.
Realistically a bit of dust to the most of us isn't harmful but if it contains things like dust mite poop which many people are allergic to, cat skin (another seriously common allergy) or is leaking from a place with mould... you should be okay :)

It's not just a bit of dust though... there is so much everywhere when the sun reveals it. It looks unhealthy....

I wonder if there's an optical component to this as well. If I cross my eyes the right way, I can see dust particles in bright light too...

Our basic defenses such as nasal hairs and mucus help in trapping the dust particles and other Suspended Particulate Matters (such as smoke etc).
However, if there is too much of dust inhalation then, as you suspect, it will be harmful. This can be seen in quarry workers who inhale a lot of dust- which causes silicosis.
Dust also instigates asthma.
You would feel much more comfortable in a dust free greenery but the mild dust which you would notice in your house wont be very hazardous in usual circumstances.


text:
Why do ion concentrations change with different secretion rates in pancreatic juice?
Why is it that when secretory rate increases in the pancreas the concentration of chloride ions decreases, and the concentration of bicarbonate increases in the production of isotonic NaCl secretion?
The modification that goes on in the duct of the acinus is dependent on flow. If the flow is faster, then less ions can be reabsorbed from the primary secretion. In the pancreas, chloride ions are removed, so surely their concentration should go up as the flow increases?
Bicarbonate on the other hand is added to the primary secretion in the duct. So shouldn't its concentration in the secretion stay the same or even increase as flow increases?

This is an approximation of the graph given in our lecture notes; from Boron & Boulpaep, Medical Physiology, 1st Ed, p919 - Sorry for the bad quality reconstruction

" In the pancreas, chloride ions are removed, so surely their concentration should go down as the flow increases?"   According to the logic of your question I think this should be "should go up".

An interesting question!
I am attaching the picture from Boron & Boulpaep, Medical Physiology, 2nd Ed, p921 here to clarify the details left out in the hand drawn picture.

The flow of the digestive pancreatic enzymes increase mainly during food consumption. This is brought about by a number of redundant systems. The fasting secretion of pancreatic enzymes depends on the MMC (migrating motor complex).

Bicarbonate ions are exchanged with chlorine ions in the apical membrane of the acinar cells through a Chloride Bicarbonate Exchanger. This process is driven by:

Secretin - most important humoral factor - Increases secretion
ACh through muscarinic receptors - Increases secretion
GRP (Gastrin Releasing Peptide) - Increases secretion
Substance P - Decreases secretion

Mechanism of action of secretin seems to be through activation of cAMP. However even small amounts of secretin which do not raise the cAMP levels measurably can stimulate bicarbonate secretion. This suggests secretin response may be by

Unmeasurably small amount of increase in cAMP
Raise in cAMP levels in localised compartments
Activation of alternative second messenger pathways

In case of GRP the second messenger is not known.
The answer to your question is that when secretin is secreted, the Bicarbonate-Chloride transporter is accelerated to achieve the result displayed. This mainly happens when food enters the small intestine so as to neutralize the acid permitting the digestive enzymes to function at the optimal pH.
The Chloride-Bicarobonate Transporter is an exchange transporter which explains why there is a sharp fall in the chloride levels.

Taken from the same text book quoted above


text:
Does malaria have a reservoir host?
Can warm blooded vertebrates other than humans act as reservoir hosts for malaria parasites? I'm mainly interested in Plasmodium vivax and possible reservoir hosts in the wider area of Europe/ Eurasia.

There are a few species of monkeys which can be infected the question here is if there are reservoirs or not. As far as I know humans are the main host for these microoragnisms.

Thanks for your response @Chris, I wasn't entirely sure. I shall drop that line of inquiry!

There are 5 species of Malaria the can infect humans, and Chimpanzees and gorillas have also been found with 5 species, including vivax and falciparum.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089193/
The parasite can go dormant in the liver for days to years, causing no symptoms and remaining undetectable in blood tests. They form what are called hypnozoites (the name derives from "sleeping organisms"), a small form that nestles inside an individual liver cell. The hypnozoites allow the parasite to survive in more temperate zones, where mosquitoes bite only part of the year.
Cows are known to carry falciparum protozoa, which has at least four reservoir species. (cows, chimps, gorillas, humans) Human with sickle cells also act as a reservoir in a different way, perhaps more or less invisible or innocuous, i haven't studied recent research, and sickle cell may also have some effect in cows and chimps and gorillas.

From Wikipedia Plasmodium spp. have a huge range of hosts, including: human, primates, mammals, reptiles and birds.
Four important points to note:

The Plasmodium genus contains about 200 species.
Further important to note is that P. falciparum, P. vivax, P. ovale, and P. malariae are responsible for almost all of human malaria infections, and the distribution of Plasmodium species varies between different animals.
Humans are not in fact the definitive host of Plasmodium species. Vertebrate hosts simply serve as a site for the parasite to replicate asexually, and the sexual replication occurs in the mosquitoes.
To act as a reservoir, the host needs to suffer a long term infection. P. vivax is one species noted for its ability to form a dormant stage in the liver, and cause relapses.

So I think it would certainly be possible for there to be other vertebrate hosts (warm blooded or not) aiding in the spread of malaria to humans, but I think it's unlikely to be occurring at an epidemiologically significant rate. I think if that did happen, we would already know about it, given the considerable study that has been done on malaria.


text:
Is it possible for two brown-eyed parents to have blue-eyed child?
Here's the (real) story: A young man has stunning blue eyes. On his mother's side are lots of instances of blue eyes, but on his father's side is no history of blue eyes. Both parents have brown eyes.
When he was born, with these bright blue eyes, it was considered a "miracle". As an adult, he still has these potent blue eyes.
How is this possible?
I obviously understand the popular science behind dominant and recessive genes. The mother could be Bb, but if the father was BB, it doesn't seem possible that he could have blue eyes... but I've read more on eye colour recently, and it appears to be a lot more complicated than I initially thought.
For example, this article goes into some detail explaining How Blue Eyed Parents Can Have Brown Eyed Children, but I've not seen anything that talks about it being the other way around: Could a BB parent have a bb child?
If so, how? And what is the rough probability of such a thing?

Possible, yes but probable, no. (I assume that the history of the parental family as you mention is important)
Let us first consider HERC2 (H=brown, h=blue) and OCA2 (O=brown, o=blue) as per the names mentioned in the reference you cite, to be completely unlinked, such that they are independently assorted. Since the father's lineage has no history of the recessive phenotype(blue), and the genes segregate independently (our assumption), we can conclude that the father is homozygous for the dominant allele in both the genes(HHOO). In this scenario, it is very unlikely to get blue eyed children, but is still possible in the following two ways:-

The father's lineage does have a recessive gene (which probably entered his family gene pool due to non-consanguineous mates carrying a heterozygous phenotype in either of the gene pair HERC2 or OCA2), and has evaded expression by pure chance or because the recessive gene carrier entered into the family very close to the father,i.e. probably just one or two generations above the father(so that not enough generations have passed to allow the homozygous recessive trait to develop). In each of these cases, one or both the gene loci in the father might be heterozygous(HhOO or HHOo or HhOo) and coupled with the mother's heterozygous genotype(a good guess considering the history of many recessive phenotypes), might produce a blue-eyed child due to homozygosity in any one of the gene.
There is a mutation in the germinal cells of the father which creates a non-functional mutant allele and thus can give a blue-eyed child with a heterozygous mother.
But in either case, considering independent assortment, the chances are very bleak.

But if we also take into account the linkage of the two genes, then the probability rises significantly. Now there is a good chance that the father's lineage might contain a heterozygous (or homozygous recessive) allele pair on a single chromosome, which due to their tight linkage, might pass on without any recombinations and therefore might evade phenotypic expression more efficiently(although, since a dominant allele in both the genes is required for the dominant phenotype, the extra evasion efficiency due to linkage is less). As given at the end of your reference, suppose there is one chromosome in the parental ancestry that carries both the recessive genes. If they are linked, the chances of brown eyed parents to have blue eyed children decreases (and the chance of being heterozygous also decreases) thus making it more likely that the father's lineage could have a recessive allele in spite of there being no significant expression in his family history. Therefore, more tightly they are linked, greater is the probability that the father is heterozygous. Linkage does not significantly lessen the possibility for the father to have a blue-eyed child since the mother does contain a recessive linked- phenotypic pair in all probability. (Actually, the probability is also based on which combinations are linked, but the possibility of there being a heterozygous allele remains positive with most combinations).This again gives some chance for brown eyed parents with the history you mention, to have a blue eyed child.
In any case, there is a chance but the probabilities depend a lot on the linkage, the linked combinations, and the actual genotypes of the parents but there is always a possibility.
ADDITION
Just to add a bit of information, the kind of recessive epistasis we described here, where the homozygous recessive (at the hypostatic,HERC2, loci) phenotype resembles the phenotype for the recessive condition at the modifier pair (OAC1), is only a part of the story. Actually, certain polygenic influences further complicate the situation by introducing a variety of phenotypes.

Nice answer, +1. Could you tone down the bold and italics please? It's really hard to read.

@terdon Sure. On reading the answer after all the boldifying and the italicizing, I could see what your concern was! I have already toned down quite a bit, however, feel free to reformat my answer according to your aesthetic understanding as I am not much of a formatter.

its worth mentioning that many babies are born with blue eyes, even those of african descent - it can take several months for pigment to start up.

@shigeta That's good to know, but in this (real life) case, he's now in his 30s with the same stunning blue eyes.

It's also worth mentioning that the example suggested is incorrect. Human eye color is multigenic (i.e. MORE than 2 genes, probably more like 7) with more than one possible allele per gene. Epistasis can certainly occur, and combinations can happen which give rise to very uncommon colors, such as yellow. A simple one or two gene model will suggest brown eyes can't have blue eyed kids, and that is incorrect. This also ignores the frequent occurrence of mosaicism at the tissue level, which can yield kids with two different eye colors, or irises with two colors within them, which neither parent might have shown.

Can you please add some references?


text:
What is the impact of prolonged electromagnetic exposure on human health?
What are the health effects of being exposed to a very strong electromagnetic field caused by  two resonating superconductive coils (not static magnets) for a period of years?

Your question would be a good fit for [skeptics.SE][http://skeptics.stackexchange.com]. There, you can provide a claim and they will tell you if there is some scientific support for this claim. And there are already many questions asked on the subject. If you can't find your answer, I'd suggest you to re-ask your question on skeptics.SE

Actually the applications of magnetism to organic systems is new to Science.  Duke Univ in NC is currently experimenting with humans sticking their heads into large electromagnetic coils while electrodes are attached to the outside of the skull. A small amount of research has been done with magnetism and plant physiology (my interest), but in the main very little published research is available on the topic.  I might direct you to use Scholar.Google to find more technical articles rather than just using Google itself.


text:
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).

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.).

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


text:
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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Is it true that oxygen has a diffusion rate in air 10,000 times greater than in water?
According to the Wikipedia page on the design of gills, oxygen has a diffusion rate in air 10,000 times greater than in water. Is that true?
The WP entry refers to: M.B.V. Roberts, Michael Reiss, Grace Monger (2000). Advanced Biology. London, UK: Nelson. pp. 164–165.

There's no clear biological scope in this question, although a good answer has already been posted.

I've slightly rewritten the question to make it clear that the OP was coming at this from a biological perspective. (The OP had already linked to the page on gills and cited the Advanced Biology textbook.)

Yes, according to calculations presented here and here the conclusion is that:

The O2 diffusion coefficient in saturated air (15% oxygen) is 5,700 to 10,800 times greater than in water (60°C and 20°C respectively).

And here is a paper using this difference to investigate the transfer of O2 through the tracheal system of a click beetle.


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Why are human children more likely to get lice (nits) than adults?
By my own experience, lice seems to be prevalent in the hair of human children, but not in adults.
My question is Why are human children more likely to get lice than adults?
Assumptions:

Can be referred to lice/louse/nits

I would say it is a simple psychologic phenomenon: Kids come in much closer contact than adults usually do. So there is much more chance for spreading lice.

i think its only because there is more human to human contact - heads touching, hugs and full contact jostling in a school (and locker rooms) than at an office or other typical adult days.  I simply touch fewer people than my 5 year old...

Thanks guys - add that as a full answer - and if no one has a better explanation, then I'll mark it as answered.

"Children are most likely to get lice because of the close physical contact they have with playmates in school and day care centers." - http://healthvermont.gov/prevent/lice/headlice.aspx

Additionally, adults get aware of the lice earlier and will then (hopefully) avoid close contact with others until it is cured.

I will second Amory's comment.

Children generally don't care about their hair as much as adults do. So unless parents insist, they don't care for their hair as much (reference). Kids generally get lice because they are in close contact with each other during play-dates, slumber parties, and sports activities. They are also prone to exchange hair brushes and other personal items more often than adults (reference).
An interesting difference I came across between articles is that one article says that its

theoretically possible to get infested if your hair makes contact with
  items such as hats, combs, or brushes (reference).

Another article insists that

You’re extremely unlikely to get head lice by sharing hats, combs or
  pillows – a louse’s lifespan is very short once it’s removed from your
  head (reference).

Between the two, I believe that it is extremely likely that lice would spread if you use a infected hairbrush immediately after it was used by someone harboring the parasite since the time span is short.

Can't lice larva lie dormant in a comb or jacket as a means of transmission?

@aitchnyu Yes, but they can only stay alive upto 48 hours from the body

Lice prefer clean hair, so in addition to closer contact among children, adults seem to use more hair product (gel, hair spray, etc.) than children in preparation for their day. Lice have difficulty moving through hair strands that are stuck together with product, so this may also contribute to the prevalence in children.

It would be great if you could provide references for your response.


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Biological advantage of electric synapses
Electric synapses are synapses that do not process information but simply foward one action potential from one neuron to the next. There are no neurotransmitters, no inhibitory and exitatory postsynaptic potentials that would cause different responses in the post-synapse.
So, I'm wondering: What are the biological advantages over just one long axon? My research has only told me the advantages over "normal" synapses (speed), but I couldn't find any advantage over just using one longer neuron which, I suppose, would be even faster.

I can't answer this but just to consider: firstly, this may be a way to overcome the limit of length of an individual cell before intracellular transport of proteins and organelles becomes impracticable. Aside from this, the difference between one long neuron and two connected ones is that they are separated by a membrane and can have different interiors. This means different internal cell states e.g. signalling molecules, ion concentrations,...

Having just read this article (http://www.ncbi.nlm.nih.gov/books/NBK11164/) there are several advantages/functional reasons that seem apparent and important in having electrical synapses with gap junctions compared to just a very long neuron.
a) signals in electrical synapse can be bidirectional.
b) electrical synapse synchronize electrical activity among populations of neurons.
c) The large pores in gap junctions allows passage of ATP and other important intracellular metabolites, such as second messengers between neurons.
I'm sure there are plenty of other reasons but these should provide a better picture in terms of the functional significance of having electric synapses.
Hope this helps!

Also. If there is one long neuron then the nucleus will have difficulty coping up with the maintenance of the cell

The advantage I have heard of is synchronization, as can be found in the Wikipedia article on electrical synapses:

The relative speed of electrical synapses also allows for many neurons
  to fire synchronously.

Synchronization in turn has many advantages and is supposed to play roles in different contexts, e.g. in binding.

Synchronisation through electrical synapses, which is covered by the previous answer, is much faster and stereotyped compared to gamma synchronization hypothesized to underlie feature binding.

Ah, I did oversee b). Should I delete my answer or just the hint on binding?

@vkehayas: You mean the maximal firing rate of neurons (1000Hz) compared to the 40Hz of gamma oscillations?

Correct. That said, gap junctions may not be responsible for the characteristic frequency of the oscillation, but they could increase the level of synchrony in the population (https://ac.els-cdn.com/S0896627304000431/1-s2.0-S0896627304000431-main.pdf?_tid=de9b03ec-af4d-11e7-add4-00000aab0f6c&acdnat=1507813644_721ef4edc7c1752e1634aa21b6f2eaa2), so there is a point to be made there.

This reassures me, i.e. I am not on a totally misleading track. (General increasing the general level of synchrony is something.) This is what I found today: Neuronal synchrony measures (http://www.scholarpedia.org/article/Neuronal_synchrony_measures)


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What is a simple protocol for staining cells in suspension?
I am an engineering student studying how electric fields affect cells, specifically the phenomena of electroporation in living cells.
I know that electroporation is widely used for introducing genes into cells, but running a full transfection experiment is not so feasible in the lab I am working in.
My question is:
If I want to demonstrate the principle of electroporation, i.e. that cells open up and intake substances from the environment, by using some kind of a dye which i can later visualize, what could be a good model for this type of experiment? Specifically - what dye, what cells could be used for this?

Are we talking about mammalian cells or bacteria?

That's probably part of his question ;)

You will get a lot of false-positives using the following method, and a real transfection of a fluorescent protein is always the way to go, because then you will prove that the transfection was really successful.
That said, you could try to use DAPI, followed by fluorescence microscopy or flow cytometry. DAPI is a very bright stain for DNA and cannot pass an intact cell membrane. If the cell membrane is disrupted, e. g. by necrosis, DAPI will enter the cell. I have never seen anyone trying to prove electroporation this way, but it will be worth a try. It could be that the time is too short for DAPI to enter the cell, so you'd need to tweak your setup.
I'd try the following: Prepare a cell solution with DAPI (something like 5 µM concentration should do). Split the solution into two electroporation cuvettes, perform the electroporation with one cuvette, leave the second one untouched as a control. After the electroporation, analyse the samples MOMENTARILY (means: within a few minutes) using a flow cytometer (if possible).
As for the cells, you could use anything. I suggest eukaryotic cells because they are more easy to visualize than bacteria. However, you would need a laminar flow hood for aseptic handling of cells. In theory you could also use bacteria, which are more easy to handle, but I'm not experienced with immunofluorescence in bacteria.


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Difference between Bioscience and Lifescience
Are bioscience and lifescience the same things? I am a little bit confused about it. If not, then what is the difference between the two?

they're pretty much the same thing in my mind - bio means "life" and biology is the study of life.

I agree with everyone. Also, you originally tagged this question bioinformatics - that is not the same.

I agree with the comments and largely see them as the same thing, and many dictionaries would probably agree with this. However, in practical use (from my experience) Life science is used somewhat more broadly (everything from ecology and agricultural science to genomics and biochemisty), while Bioscience is more often applied to "whiter" lab-based biology and more technical applications (biotechnology, genetics, etc.). Personally, I would feel comfortable to label my research as life science but a bit more uneasy with bioscience. However, the terms are so vague that I wouldn't pass judgement on the content of research just based on these labels.

Whiter? What do you mean by whiter?

Lab coat (white) vs. field clothes (green), not caucasian ;).

hah. I've only seen one person wearing a lab coat lately, and it was an undergrad. No one here does field work, either. :P

@dd3 Wearing a lab coat in a lab is a sensible, if minimal, way of protecting your clothes and body against chemicals, radioactivity and biological agents. Not wearing one is neither clever, professional, nor, in some countries, legal. Certainly in my University students are not allowed into teaching laboratories without one. The same probably applies to research laboratories under British Health and Safety regulations. Your comment does you no credit.


text:
Resources for finding all drugs of a certain class
I may be embarking on a project involving a fairly extensive healthcare records data set, looking for the use of a particular type of drug (for example, "Proton Pump Inhibitors"). But these drugs are usually listed by their trade or generic names - is there a well maintained resource for looking up what drugs are members of a certain class (if class is indeed the right word)?

The WHO has their own methodology, the Anatomical Therapeutic Chemical (ATC, thank you commenter) classification system, for organizing such data (its impetus is comparing results between studies).
Also, if you have $900 sitting around, you can get a subscription for the United States Pharmacopeia.  I'm not sure if that can be spread across multiple subscriptions for an organization like the Red Book David mentions.

@DavidP.Hochman I think all of the WHO's data are public, but I don't know where it is published.


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What is the reason behind choosing the reporter gene when experimenting on your gene of interest?
I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you may insert the gene for fluorescence next to your gene of interest so you know if it is transcribed or not by whether the organism's cells are fluorescent and to what degree they are fluorescing at.
I have noticed in some experiments that have multiple versions that in one case they use the fluorescent gene and in the next a different gene (for example lactose). Both portions of the experiment use almost the exact same steps so why would they not choose the same reporter gene?

Already good answers here. Btw, I'm keeping a blog about reporter genes if you are interested.

Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different filters on your microscope for the various fluorophores. For morphological assessments, perhaps a LacZ gene or alkaline phosphatase may be better suited, since the detection of these enzymes is compatible with standard histological techniques and you get usually much better contrast than with fluorescence. For quantification purposes, you would use probably firefly luciferase or CAT, since there are very good quantitative assays for these enzymes.
The decision will also depend on the degree of experience of the lab with each detection technique and even in the availability of the constructs. If a reporter is already made by the lab next door and if it fits your needs, you'll just use it, instead of creating your own, even if the reporter gene would not have been your first choice.

Reporter genes have become an invaluable tool in studies of gene expression.A gene consists of two functional parts: One is a DNA-sequence that gives the information about the protein that is produced (coding region). The other part is a specific DNA-sequence linked to the coding region; it regulates the transcription of the gene (promoter). The promoter is either activating or suppressing the expression of the gene.
The purpose of the reporter gene assay is to measure the regulatory potential of an unknown DNA-sequence.So it is quite helpful,it;s kind of reverse engeneering the function and then let know what exactly it does.

This answer addresses what a reporter gene is, but it seems like the OP already knows that. The OP is actually asking why you would use a particular reporter gene in a particular context. If you have additional insight about this question that has not already been included in the two posts above, please revise your answer.


text:
What medical and commercial proteins are made using genetically modified animals?
Recombinant technologies in micro-organisms being used to produce commercial and medically useful proteins like insulin are fairly common.
However some proteins are still produced commercially in genetically modified animals. Why are animals a better choice than microorganisms, and which are the most common proteins produced this way?

Transgenic animals are not used for commercial activities as of now.

The rationale for the choice of higher organisms as the producing source is based on costs and biological activity.

Biological activity. In their active forms, various proteins have
post-translational modifications (i.e. glycosylation) which are
difficult to reproduce in bacteria. Alan's answer is already
exhaustive.
Costs. Mammalian cell lines are easier to generate and maintain but
suffer from genetic and epigenetic instability (the transgene can be
lost or inactivated). Contrarywise, transgenic animals require more
investment but once established that the transgene is present in the
germline and breed through, the protein can be produced in larger
quantities with ~1/10 of the costs required to setup a
GMP-bioreactor. This is particularly appealing for small
pharmaceutical niches, i.e. drugs targeting rare diseases: if the
market is small, farming few goats can be more profitable than
building and maintaining sterile bioreactors. Downstream purification
facilities are however required for both cellular and animal farms.
That's why animal models that produce high levels of the therapeutic
protein in secreted matrices (i.e. milk, egg white) are preferred:
this facilitates bulk storage of unpurified protein prior to
purification.
A good and recent review comparing models and strategies is from Wang
et al., Expression Systems and Species Used for Transgenic Animal
Bioreactors (doi:10.1155/2013/580463).

To stay updated on recombinant proteins from transgenic farms entering the market, the official reference would probably be the FDA section on Biologics. Two companies actively working on transgenic farms are GTC Biotherapeutics and Synageva.

GTC Biotherapeutics produces human antithrombin alfa (ATryn) in the milk of transgenic goats, for use in patients with hereditary antithrombin deficiency (HD). Quoting the ATryn executive report:

Antithrombin III (recombinant) is a highly purified, well
  characterized recombinant glycoprotein consisting of432 amino acids, 3
  disulphide bridges between cysteine residues and 4-N linked
  glycosylation sites, identical to human plasma-derived antithrombin.
  Recombinant human antithrombin is produced in the milk of transgenic
  goats. For expression of rhAT, the DNA construct contained a goat beta
  casein promoter with the cDNA coding region for human antithrombin
  (hAT). The DNA construct was microinjected into fertilized one-cell
  goat embryos, which were transFerred to female recipients. Kids born
  from the recipients were tested for presence of the transgene and
  expression of the human protein. A founder transgenic goat was
  selected from which subsequent offspring were generated by natural
  breeding to give rise to a production herd of hAT transgenic goats,
  which are milked to provide the source material for downstream
  purification.

Synageva produces Sebelipase alfa (SBC-102) in the egg white of transgenic hens, for use as an enzyme replacement for Lysosomal Acid
Lipase (LAL) Deficiency. I think they are in clinical phase 2/3 (not
yet on the market). According to their 2012 Annual Report:

Our proprietary vectors allow incorporation of the gene of interest
  into the genome of normal cells of an avian (Gallus) with selective
  expression of the resulting protein in the oviduct tissues and
  secretion into EW. The importance of this cellular environment for
  therapeutic protein expression is highlighted by the tight consistency
  of post-translational modification, including glycosylation, seen in
  proteins manufactured using our platform compared to cell culture
  produced material. Furthermore, our expression system yields
  consistent expression levels and quality of protein within production
  lines and through multiple generations.

ATryn is a human antithrombin produced in the milk of transgenic goats by GTC Biotherapeutics. It has FDA approval and I believe that it is available for prescription in the USA.
Added later, after the emphasis of the question changed somewhat.
Proteins produced in a mammalian system are more likely to have post-translational modifications that are much closer to those found on the human protein. Antithrombin, for example, has four disulphide bonds and four glycosylation sites. Although it is reasonable to assume that the disulphide bonds would be correctly formed in a eukaryotic microorganism, the same isn't true of the glycosylation: microbial glycans differ from mammalian glycans, and these differences could affect the stability of the protein in the mammalian bloodstream, or the response of the mammalian immune system to the protein. Mammalian cells in culture could be used but are, of course, quite fastidious. So the holy grail of recombinant protein production has always been to get the protein secreted into an animal's milk, allowing the use of very cheap feedstocks and the easy harvest of the protein over a period of years, notwithstanding @shigeta's remarks.

might well be right that this is the only current case.  Transgenic animals are really expensive compared to transgenic bacteria - its very expensive to make a transgenic goat and the ability to produce the transgenic product often doesn't breed through - making you start all over again from scratch when the goats die.


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BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:

It looks like it's saying that the match starts at 10835 and ends at a smaller index (10714).
I tried clicking the link to view the full sequence, and I couldn't find the highlighted portion anywhere (not at 10835 or at 10776).
My question is: Where (in NR_046235.1) can I find the highlighted sequence?
And what does it mean to say that the Sbjct starts at 10835 and ends at a lower index?
I can post my query if necessary.
Thanks.

Just to help you with the answers below - there are lots of online tools which allow you to generate the reverse complement of a sequence if you have difficulty  'seeing' this, e.g. http://www.bioinformatics.org/sms/rev_comp.html

@Alan No need for that, a simple console command does the same for you: (tr ACGT TGCA | rev) <<< 'GATTACA'

I like @KonradRudolph 's one-liner better as a direct solution, but also note that many programming languages have libraries for everyday sequence-processing tasks.

Just to flesh out Daniel Standage's answer a bit, remember that a genome is double stranded with one strand being complementary to the other. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for.
BLAST and similar algorithms take this into account and will compare your query sequence to both strands. If your query hits the target sequence on the - strand, BLAST will give a a result like what you have obtained, where the start of the HSP is lower than the end. This is because RNA translation (though not DNA transcription) goes in a 5' to 3' direction, on both strands. We therefore "read" genes in that direction. The coordinates are always with respect to the + strand since we always consider DNA in a 5' to 3' direction, this means that its start position will appear to be after its end position. This is better explained using an image:

In the image above, the blue line represents your BLAST hit. It stretches from position 10 to position 40 (with respect to the + strand). However, since it is on the minus strand, BLAST will show it starting at position 40 and ending at position 10.

Note that the query sequence you have provided matches the minus strand of your target sequence. That means not only that the target sequence will be reversed (as you have noted), but it will also be complemented as well. So in the GenBank record, you should not look for the sequence CCGACCGA... starting at position 10835, you should look for the sequence ...TCGGTCGG ending at 10835.
ccgaccga...    minus strand
||||||||
bbɔʇbbɔʇ...    forward strand

The sequence in the GenBank record contains spaces, so that complicates finding your sequence using the browser's "Find" function, but if you use the position indices at the beginning and end of each line of sequence, you will be able to find the reverse complement of the matched sequence reported in the BLAST results.

Thank you for this explanation! I accepted the answer by @terdon because it was slightly more beginner-friendly.