human biology - What is the molecular basis of hangovers?

First, the hormonal and hemodynamic changes seen in hangover are distinct from those seen in alcohol withdrawal, so the advice to drink more is not good, even if some symptoms are in fact improved. See tables 2/3 in the cited review.

It appears the molecular mechanism of veisalgia (HA, a new word) is not well known.

1. acetaldehyde Part of it may be attributed to acetaldehyde but there is clearly more to it. The liver enzyme alcohol dehydrogenase 1 (ADH1) produces acetaldehyde from ethanol, and aldehyde dehydrogenase 2 (ALDH2) makes acetate from that, so the aldehyde does not exist for a long time, and is rather responsible for short-term illnesses.

2. ADH and diuresis

Hangover severity is proportional to antidiuretic hormone
concentration (46). Alcohol inhibits the effect of antidiuretic
hormone on the kidneys, thereby inducing diuresis that is out of
proportion to the volume of fluid ingested. As blood alcohol
concentration decreases and dehydration persists, the serum level of
antidiuretic hormone increases, maintaining water retention in
dehydrated patients with hangover. In our clinical experience,
hydration attenuates but does not completely relieve hangover
symptoms.

3. cytokines

The constellation of hangover symptoms (nausea, headache, diarrhea)
resembles that seen in conditions related to dysregulated cytokine
pathways (for example, in viral infections and after administration of
interferon-alpha). Alcohol alters cytokine production through a
thromboxane pathway. Levels of thromboxane B2 are elevated during
experimentally induced alcohol hangover (42), and the administration
of tolfenamic acid, a prostaglandin inhibitor, at the time of alcohol
consumption has a small prophylactic effect in reducing hangover
severity (9).

4. further substances

Congeners, the byproducts of individual alcohol preparations (which
are found primarily in brandy, wine, tequila, whiskey, and other dark
liquors), increase the frequency and severity of hangover (24, 39,
40). Clear liquors, such as rum, vodka, and gin, tend to cause
hangover less frequently.

So there are factors that aren't even identified exactly, and these could fit the mixing of drinks observation.

There are several reviews out there, just search for hangover at Google Scholar.

Wiese, Jeffrey G., Michael G. Shlipak, and Warren S. Browner. "The alcohol hangover." Ann Intern Med 132.11 (2000): 897-902. Online at http://dionysus.psych.wisc.edu/lit/topics/Hangover/WieseJ2000a.pdf

virus - What decides whether a lysogenic cycle or a lytic cycle will take place?

It depends on a few factors, such as how many phages infected the cell, whether or not the cell is in good growth conditions, and so on. If the cell is in stress or has low amounts of nutrients, the lysogenic pathway is typically activated.

The underlying mechanism has to do with a protein cascade involving either the cro or cI protein that is encoded by the virus. The cI protein is a repressor, and it will prevent the lytic genes from being transcribed. By default the virus will transcribe the lytic genes, so they must be repressed for lysogeny to occur. Similarly, cro is also a transcriptional repressor. The two proteins work in opposition to each other. cro binds to an operator, oR3, that is involved in repressing cI, which may prevent cI from being expressed and thus preventing it from repressing lytic genes (however the importance of this is debatable because if you replace oR3, the cell can apparently still lyse).

There are numerous other proteins, such as N and Q, that are involved. The N protein has to be transcribed by the polymerase ‘anti-terminating’, or reading through a termination signal. This will happen more frequently when the protein RNase III is present at high concentrations. The N protein is a lytic regulator. Thus, when there are high amounts of RNase III there will be more N expressed which leads to the lytic cycle. RNase III is not a viral protein. It is a host protein and the host expresses more of it when nutrients are abundant. This is how the virus is able to ‘sense’ if nutrients are high enough to enter the lytic cycle.

The whole system is way more complicated but this is it in a nutshell.

http://www.annualreviews.org/doi/full/10.1146/annurev.genet.39.073003.113656

genetics - Precursor miRNA and a mature miRNA

precursor miRNA is ~70mer RNA with a stem loop structure. It is cleaved by dicer to generate one or two mature miRNAs (from one or both the 'arms' of the stem ; called 3p and 5p which are ~22nt long). Refer to this review. (It is an old one and some facts might have changed, but the basics are there.)

Yes, there can be different precursors giving rise to same mature form. There are a few cases like that (check for entries like mir-x-y [where y can be 1,2,3,...], in miRbase).

Usually pre-miRNA is shortlived and is immediately converted to mature form. Therefore, in small RNAseq data, most miRNA reads (more than 90% [at least that's what I get]) come from mature form (pre reads would be longer [after adapter removal] and will contain sequences not retained in mature form). Most algorithms select for the mature reads.

It is difficult to determine which precursor gave rise to a certain mature miRNA, using an RNAseq data. The usual practice is to assign the average read count to each locus. E.g., for a mature form that has 3 precursors, each precursor is assigned 1/3 of the total mature reads. However, in most RNAseq experiments, the objective is to obtain the mature miRNA profile and which precursor gives rise to it becomes immaterial.

zoology - Why does ostrich meat look and taste more like beef than chicken?

There is a very plausible explanation here.

Basically, it explains that meat colour is due to the protein myoglobin (a haem-containing protein related to haemoglobin). There are two types of skeletal muscle: fast-twitch and slow-twitch (Wikipedia). Slow-twitch muscle is red muscle because it contains lots of myoglobin. Fast-twitch muscle is white muscle, containing less myoglobin. The Wikipedia link explains a little more about these muscle types and their functional differences. Evidently the lifestyle of the ostrich dictates that it have more fast-twitch muscle, and so it has red meat. It isn't unique in this: duck and goose are classified as red meat too.

Incidentally the role of myoglobin is to improve the rate of diffusion of oxygen from the haemoglobin in the capillaries through the cytoplasm of the myocytes to the mitochondria. It has also been suggested that it acts as an oxygen storage mechanism in diving mammals which have very high levels of myoglobin in their muscles, but this storage function is unlikely to be important in other mammals, despite what you may read in textbooks.

What are the methods for infering genetic interactions?

BioGRID is an interaction database, and they catalogue interactions by (among other things) the class of experiment that discovered them. See http://wiki.thebiogrid.org/doku.php/experimental_systems#genetic_interactions

Other than that, you should look at recent reviews and publications, but you will easily get lost unless you figure out some important particulars, like:

• What species? Yeast, worm, human, cell line?


• What sort of interaction? Synthetic lethality? Complicated, fancy epistasis?


• How much? Genome-wide? 2-3 genes?

zoology - Do fish break a water molecule to absorb oxygen?

The answer to this, I reckon, is that they don't.

They use molecular oxygen (O₂) dissolved in the water for respiration, where it acts as a terminal electron acceptor, just as we use molecular oxygen in the air for respiration. We can speak of the water as being oxygenated.

Water is split in photosynthesis, where reducing equivalents from water are used to reduce NADP⁺ (giving NADPH).

One of the great discoveries of biology, IMO, is that the oxygen formed in green-plant photosynthesis comes from water, not CO₂.

Tricarboxylic Acid Cycle (Krebs Cycle) Rant

Despite claims to the contrary, most infamously by Racker (1976, pp 28 - 29) and Wieser (1980), but also by Madeira (1988) and Mego (1986) for example, water is not split in the tricarboxylic acid cycle (Krebs Cycle). Banfalvi (1991) also sails pretty close to the wind on this one.

That is, reducing equivalents from water are not passed down the respiratory chain, or in any way used to make ATP, or are in any way a 'source' of free energy. Such claims, IMO, are nonsense.

The definitive answers to the Wieser (1980) paper are given by Atkinson (1981) and Herreros & Garcia-Sancho (1981). Both of these articles are models of clarity, and categorically refute the claims of Wieser (1980). Nevertheless, as shown by the references above, the controversy surfaces periodically.

The only sources of reducing equivalents in the TCA cycle are carbon compounds, and the only electrons passed down the respiratory chain are those 'held' in C-H and C-C bonds (Herreros & Garcia-Sancho, 1981). An ionization is neither an oxidation nor a reduction (see Atkinson, 1981) and neither is a hydration. Adding water to (say) a double bond does not make the compound any more oxidized or reduced. As far as oxygen and electrons are concerned, and to generalize from a biological point of view, what is has it holds - except in photosynthesis.

As you may have guessed, the splitting of the water in the TCA cycle is a pet rant of mine. Thanks for the opportunity of airing my views!

Edit 3

Found this one when searching Google (Brière et al, 2006). In an invited review for the American Journal of Physiology (Cell Physiology) at that!

Finally, TCA cycle should also be considered as a water-splitting process generating oxygen for acetyl-CoA oxidation [they quote Wieser]

So now the TCA cycle is producing oxygen from water. Wonders will never cease!

(end edit)

(end rant)

Edit 2

As rwst and Alan Boyd have drawn attention to, the concentration of dissolved oxygen in water is all important, and varies with (for example) temperature.

In air-saturated buffer at 25^oC the concentration of oxygen (O₂ molecules) is about 0.24 mM (0.24 μmoles/ml, or about 0.474 μg-atoms of oxygen per ml). [Chappell (1964)]. This figure decreases with increasing temperature.

Great question, BTW.

References

(Apologies for the incomplete Atkinson and Herreros & Garcia-Sancho references. I have a photocopy of these papers but have been unable to trace the full source. They are both in the 'Letters to the Editor' section of the February 1981 edition of Trends in Biochemical Sciences. They do not appear to be in Pubmed, or anywhere else on-line. Has anyone ever seen these references quoted, or can provide me with a full source?. I'll update if I find anything)

• Atkinson, D.E. (1981) TCA Cycle Confusion. Trends in Biochemical Sciences (February 1981 edition; full ref to follow)




• Banfalvi,G. (1991) Conversion of Oxidative Energy to Reductive Power in the Citrate Cycle. Biochemical Education, 19, 24 - 26 [see here] (pdf apparently free to all)




• Brière, J.J., Favier, J, Gimenez-Roqueplo, A.P. & Rustin, P (2006) Tricarboxylic acid cycle dysfunction as a cause of human diseases and tumor formation. Am J Physiol Cell Physiol, 291, C1114-20. [Pubmed] [pdf]




• Chappell (1964) The oxidation of citrate, isocitrate and cis-aconitate by isolated mitochondria. Biochem J., 90, 225-237.[pubmed] [pdf]




• Herreros, B. & Garcia-Sancho, J. (1981) TCA Cycle Confusion. Trends in Biochemical Sciences (February 1981 edition; full ref to follow)




• Madeira, V.M.C. (1988) Stoichiometry of Reducing Equivalents and Splitting
  of Water in the Citric Acid Cycle. Biochemical Education 16, 94 - 96 [pdf] (apparently free to all.)




• Mego, J.L. (1986) The Role of Water in Glycolysis Biochemical Education, 14, 130 - 131. (see here)




• Racker, E. (1976) A New Look at Mechanisms in Bioenergetics. Academic Press, New York.




• Wieser (1980) Textbook Errrors: The splitting of water by the tricarboxylic acid cycle. Textbook error or textbook omission? Trends in Biochemical Sciences, 5 (Issue 11), 284. [see here]. [pdf], apparently free to all.

What is a good Microbiology atlas for Bacteriology as online version?

Not sure what you are exactly looking for? If you change the question or comment I can update my answer...

NCBI's taxonomy site has a listing of bacteria. Encyclopedia of life is also great.

Then there's UCSC's microbial genome browser.

Biocyc is great reference for bacterial genes. to get into E coli, which is the model bacterium there's Port Eco featuring 130 E coli genomes.

Am Soc Micro has an excellent E coli/ Salmonella site based on their classic reference - you have to pay for access though.

evolution - Randomness in living systems

In an evolution mutations are often random and lead to differences in phenotype that can be adaptive under certain pressures. A lot of times mutation is a random process, but here are three cases I can think of off of the top of my head where I would say the organism is 'trying' to do it:

HIV is a retrovirus, which means in its viral form its genome is single stranded RNA, which is then converted into double stranded DNA within the host. That conversion is carried out by a virally encoded reverse transcriptase. This enzyme has a much higher error rate when making the RNA into DNA because it cannot proofread like our DNA polymerases. This means that HIV mutates incredibly fast. Many of these mutants are not very fit, but since there is so much selective pressure against staying the same due to attack from the immune system, some mutants will be much more fit if they can avoid that attack. Its a numbers game, and by making lots of random mutants HIV is very good at it.

A related, but different case is found in the diversity generating retroelements of certain bacteriophages. These are double stranded DNA viruses that infect bacteria. The bacteria these viruses infect could mutate to escape the viruses by losing a certain receptor that the virus binds to. It was observed however that the the virus would mutate incredibly quickly to bind to a different receptor, a lot faster than would be expected for a DNA virus. Also, it was found that these viruses contained reverse transcriptases, which is bizarre, since there is no reverse transcription step in a dsDNA viral life-cycle (so we thought). To make a long story short, this virus will transcribe the DNA that codes for its binding proteins into RNA, then use its reverse transcriptase to turn that RNA BACK into DNA, but uses a sophisticated targeting strategy so that it only mutates the region that is used for binding to the bacteria. It will only mutate adenine residues, leaving the C's, T's and G's alone. This is a much more clever system than HIV, because this virus uses site-specific mutations on its binding feet, and doesn't mutate its core proteins, the mutation of which would probably just lead to viruses that couldnt replicate. Here a reference for the interested: http://www.nature.com/nature/journal/v431/n7007/abs/nature02833.html

Just so you dont think this is reserved to viruses, we do this as well with our immune system. In order to recognize antigens in attacking pathogens, our immune cells have two methods for making diverse, random, receptors. First is V(D)J recombination, where the multiple diverse copies of the V, D and J regions of antibodies and receptors are combined at random to make one set. Wiki says theres 3x10^11 possible combinations here. After that, theres also somatic hypermutation during the proliferation of B cells. In this process, the random mutation rate is hugely increased in the region of the B cell receptor gene, specifically for making slightly different versions of the already 'OK' receptor to make it a great receptor.

General theme: raising your mutation rate, either across the board(HIV) or specifically (DGRE and SHM) is a good way to intentionally add randomness for a beneficial purpose (to the extent that you can attribute 'intent' to a viral particle).

What would happen if you slowly crushed a live brain?

It depends on what part of the brain you are "crushing."

When we do brain surgery we often do exactly what you describe. That is, we open the skull and often remove part of the brain. However, in our case usually the part we are removing is diseased or malfunctioning to begin with.

There are areas of the brain that are known as eloquent and those that are considered "not eloquent." This is an overly simplistic but educationally instructive way to classify things. Eloquent brain regions are those regions that when disturbed will cause an obvious and devastating neurological injury. Examples are primary motor/sensory cortex, broca's area, wernicke's area etc. Noneloquent areas are those that can be damaged or resected and the sequelae are less obvious. For example, you can remove quite a bit of frontal lobe before you notice a problem. However, an appropriate and sensitive behavioral test/instrument may still pick up the deficit.

Damage to the brainstem and thalamus is more devastating and even small injury to this area can cause major deficits and changes in the level of consciousness. Injury to different levels of the brainstem produces different level of consciousness. Again, it really depends on the precise location and extent of injury and there is no single answer to your question.

As the brain itself has no pain receptors the patient would not really feel much pain even if you caused major deficits. However, again it depends on the location. You could theoretically irritate thalamic sensory regions and cause chronic pain syndromes but your lesion would have to be pretty precise.

human biology - Ill effects of urea and NH₃ on metabolism

The denaturing effect of Urea is mostly at very high concentrations. (~Molar levels)!

Physiologically, urea, a product of the breakdown of retired amino acids, will build up rather quickly if it weren't secreted in the urine. Looking into this, it doesn't seem as there is a clear understanding of why this causes a disease, though the buildup of a waste product definitely is a unifying concept.

Uremia - kidney failure - causes a build up of urea in the blood as the kidney eliminates urea from the blood into the bladder. The specific effects of Urea on cell metabolism are probably numerous as the symptoms: anorexia and lethargy, and late symptoms can include decreased mental acuity and coma. Other symptoms include fatigue, nausea, vomiting, cold, bone pain, itch, shortness of breath, and seizures.

Being a metabolic waste product, it certainly would interfere with and inhibit any enzyme that produced urea - the Urea cycle in particular. Its clear that uremia is ultimately associated with cell death, oxidative stress, some cell signalling and proliferation.

I'm just googling around here, but I don't think there is any one single answer as to what goes wrong when the cells are exposed to too much urea.

evolution - Why don't flies avoid the motorway?

I also got an answer via email that I think is worth sharing.

Mrs Price:

I'm not answering officially as I’m probably wrong but…

The main point mentioned is that because flies have such a short
lifespan, so they should evolve faster than elephants or other slow
growing species. While this is true, and there are many examples of r
(ruderal) species evolving rapidly* evolution is not a predictable or
sensible process, and there are many other factors that contribute to
evolution other than a short generation time.

One main question to consider is… how many flies are there? And how
much of that population is affected by the road fatalities? Whilst
there are over 23,000 insect species in the UK, your question
specifically concerned flies so… An average fly lives for around 35
days and can lay roughly 750 eggs in her lifetime, so fly numbers are
bloody huge! Although a small proportion of flies may be killed by a
car, the proportion will be so small as to make no impact to the
overall population; therefore the driver for evolution is not strong
enough to have an impact on the species as a whole.

Another reason why motorway deaths may not have a significant impact
on the fly population is due to when the flies breed. Even if
motorways killed 90% of all flies, the fact that many insects breed
hours after hatching from their egg means that the population is still
able to reproduce. Killing something after it has bred is again not a
driver for evolution, it would have to be a very strong force that
kills a high number of individuals before they have chance to breed.

In summary, motorway deaths affect such a small amount of individuals
that it does not have a significant impact upon their populations, I
imagine that many many more of them get killed in spider webs each
day, however the idiots are still flying into those too!

Hope this helps :)

• *The peppered moth changed colour from mottled to black due to the
  population from the industrial revolution and then to white once the
  air pollution had cleared as the ones that stood out had such a high
  predation rate




• *in the last 50 years some fish species have evolved a much smaller
  body size due to the advantage of escaping through a net and being
  able to carry on breeding

evolution - Why does sexual selection evolve beautiful features?

I think I can expand on the answer by @boo2060.

The evolution of female mate choice depends on females achieving higher fitness by choosing certain males over others. At the broadest scale, there are two mechanisms by which this can occur, direct benefits, and indirect benefits.

Direct benefits
These are material things that (surprise) directly benefit the female. This might be the provision of food by the preferred male, access to a good territory or shelter that is under the control of the preferred male, protection by the preferred male, that sort of thing. Females will accordingly favour male traits that advertise potential direct benefits. These might include male size/condition/colouration, or even built structures like those of the bowerbirds. Basically, these traits show that the male knows how to look after himself, and by extension, he knows how to look after her (as males in good condition generally inhabit the best habitats and will offer the best protection and parenting).

Indirect benefits
These don't do much for the female, but they increase the genetic quality (and thus potential fitness) of her offspring. This is a much more complicated area of mate choice, and can be split into a bunch of (non-exclusive) hypotheses (below). And of course, attractive males may well offer both direct and indirect benefits.

Sensory bias: Males may, by chance, possess a trait that holds intrinsic appeal for a female. The best explanation might be that it mimics the colour or shape of a food source (e.g. fruit) that the animal eats, and thus the animal has pre-evolved preference for that colour or shape (e.g. red patches). From that point, males with more of that trait, whatever it is, will tend to be more attractive, for no rational reason. This hypothesis is sound, but is currently lacking good empirical evidence.

Fisherian sexy sons: This can in fact lead on from an initial sensory bias. Females may choose males that they find 'sexy', because their offspring will also be sexy, and thus be successfull in reproduction. This can lead to 'runaway' selection for sexier and sexier sons, at considerable survival cost for males. In this case, natural selection and sexual selection work in opposing directions.

Indicator mechanisms: This is the handicap principle or 'good genes' principle. If a structure is costly to produce or maintain, or increases the risk of predation, and yet the male possessing it is still alive, he must have good genes to have withstood such a handicap. It may also advertise that the male is not infested with parasites. The extravagant plumes of birds may be largely explained by this one, but also sexy sons and sensory bias.

Genetic compatibility: Individuals seek partners that are genetically compatible. A certain proportion of the fitness of the offspring depends on the specific combination of genes (i.e. it's not additive), and individuals that can signal or detect signals in such a way that they can choose compatible partners will have an evolutionary advantage. The best example is scent (e.g. preference for dissimilar MHC immune genes - see the human t-shirt experiment).

These mechanisms are well known in theory, but not always well-supported by evidence (yet). This is probably the best reference.

neuroscience - Least painful way to die

The American Veterinary Medical Association (AVMA) has thought about humane methods of euthanasia quite a bit and has an extensive (102 p. PDF) set of guidelines for the euthanasia of animals. The guidelines are not the same for all animals. Some examples:

Companion animals (e.g., dogs and cats): injected barbiturates are recommended

Laboratory animals (e.g., mice and rats): injected barbiturates are acceptable as are inhaled agents (isoflurane, carbon dioxide).

As for humans, you might look into the physician assisted suicide literature. I think that these generally use a sequence of drugs. As far as natural deaths, kidney failure is supposed to not be very painful.

cell biology - Does endo- and (or) exocytosis require energy? Do they belong to active / passive transport?

Just to extend the answer from @Amory slightly, I think that the terms active and passive transport are best kept for describing transmembrane movement of molecules.

In the case of exocytosis the only transmembrane event is when a secreted protein is first inserted (usually cotranslationally) across the endoplasmic reticulum membrane. I'm not aware of any evidence that this uses more energy than that already expended during polpeptide elongation by the ribosome. At that point the secreted protein is topologically extracytoplasmic, and everything else is achieved by rounds of vesicle formation and fusion of vesicles with target membranes.

The same is true in reverse for endocytosis. Any molecule that is internalised in an endocytic vesicle is still extracytoplasmic unless some process specifically moves it across the membrane of the vesicle, or a downstream organelle such as the endosome. At that point whether the transport process was active or passive would depend upon the properties of the carrier system.

molecular biology - What is the purpose of Y-shaped adapters in Illumina sequencing?

Normally, when you need two unique adapters, say A & B, on either end of unknown insert sequences, cohesive-end ligation is difficult because the insert sequences are "unknown". So you have to do blunt-end adapter ligation, in a reaction containing Unknown Inserts + adapter A + adapter B. This can result in 3 possible versions of insert-ligated product: A-insert-A, B-insert-B and A-insert-B, among which only A-insert-B is the only desired product.

1) Ligation of A-tailed inserts with Y-adapters gives you 100% A-insert-B.

2) Lets now assign a directionality to the insert - say from base 1 to base 400. Following Y-adapter ligation, you will have 2 kinds of insert-ligated products per insert: A-Insert (1-->400)-B and A-Insert(400-->1)-B, both of which are very useful. Each will create a separate clonal cluster and you will get sequence information starting at both base 1 and base 400 of the insert, since in single-read sequencing, the instrument always sequences from Adapter A. However, to know that both these sequences belong to the same insert, one will need to do paired-end sequencing.

human biology - How do people who have lost both of their legs produce red blood cells?

Red blood cells are produced in the red marrow which...

"is found mainly in the flat bones, such as the pelvis, sternum,
cranium, ribs, vertebrae and scapulae, and in the cancellous
("spongy") material at the epiphyseal ends of long bones such as the
femur and humerus." - Wikipedia

So you are partly right; the femur is associated with red blood cell production, or Erythropoiesis to give it it's technical name, but there are other bones within the human body that also do this job. The process of erythropoiesis is stimulated when the kidneys detect low levels of oxygen in the blood stream and stimulate production of the hormone erythropoietin. Further, the role of the tibia and femur in erythropoiesis also decreases with age whereas...

"the vertebrae, sternum, pelvis and ribs, and cranial bones continue
to produce red blood cells throughout life." - again from the wiki page

So I'd suggest it is unlikely that loss of the legs would have a major impact on the production of red blood cells in adults. I imagine that with the loss of legs comes some reduction in functionality of erythropoiesis but also a lower requirement of red blood cell production (less blood capacity = less blood cells needed = less blood cells need to be produced). I can't find any studies which explore the ability or needs of amputees and non-amputees with regards to red blood cell production.

biochemistry - How are the correct tRNAs transported to the ribosome?

The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.

Yup, basically. This is an extremely cool figure showing the process. There are various elongation factors that aid the process, such as EF-Tu, which essentially waits until there is a good codon-anticodon match before hydrolyzing GTP and allowing the tRNA/amino acid to enter the ribosome.

This process can be particularly salient when you look at a concept such as codon-usage bias. Certain tRNAs are more common in the cell, so if a given mRNA uses codons to match those tRNA instead of matching other degenerate but less common anti-codons, translation will occur faster. This is more obvious in organisms such as E. coli where growth is paramount.

human biology - Can a person die instantaneously from internal damage to the brain?

Please consider this only as a starting point (although a lengthy one), and a race against an acute onset of tl:dr ...

A person cannot die instantaneously from internal brain damage (under everyday circumstances). The reason is the non-centralized architecture of the brain and that consciousness is a global phenomenon which underlie the activity of many brain structures.

These brain structures are themselves comprised of a cellular hierarchy, with each cell being self-sufficient for at least a time regime in the order of minutes. As such the brain underlies to some extend the study of networks and robustness thereof. The brain also maintains a scale-free organization . Actual Scale free networks in nature are known to be robust.

Instantaneous in this context means a consciously discernible difference in time, which is on the order of tens of milliseconds (See: Inspection time, mental chronometry).

Also I narrow the medical cause of death down to a intracerebral haemorrhage, systemic shock or hypoxia. I definitely leave out all (rare) CNS-immunological phenomena (e.g. explosive brain death, Immune reconstitution inflammatory syndrome related,... )

But, effects that can mimmick instantaneous brain death are very plausible.

Notably, this question can be answered despite there being no rigorous consensus model of consciousness.

---

Consider the following just as pointers, but not as qualified, thoroughly sourced information, - contrary to a paper or review ( I will gladly include your resources, or turn this post into a community wiki if demand to do so exists):

Consciousness:

The brain weighs only 2% of the human body mass, yet consumes 20% of the total energy at rest. Crucially the brain can deplete oxygen at a great rate, which is proportional to the brain activity in various regions, giving rise to indirect measurements of brain topology and images like these:

"Visualization of a DTI measurement of a human brain"-2006, 
author: Thomas Schultz, DOR: 25/09/2012

Humans have different states of consciousness which show different overall patterns of brain activity. As such the result a scientist would witness through an high-resolution fMRI/PET scanner in a stroking-individual would differ during sleep, sleep/wake transition or various levels of awareness during the days. Stroking and the effects on the brain is studied quite extensively with rats(See: rat, fMRI, stroke).

Moreover the brain activity, fine-anatomy and orchestration of brain utilization differs from individual to individual. In short the brain is what neurologists call "plastic" Neuroplasticity is the change of entire brain structures, and the brain itself from experience and physical stress/trauma (on the brain).

We are biologial enetities which have evolved to be in-sync with the planetary rotation and solar energy influx. As such brain activity changes during the day, in accordance with our circadian rythm or biorhythm, and if it weren't for artificial lightning brain activity would change over the seasons as well.

Connecting all the dots: Describing brain death in a seconds-regime comes down to which areas in an individual brain consume the most oxygen and "shut down" first, and which processes steer brain activity till organic shutdown.

Since Stackexchange has a strong programmatic background, to put it in a somewhat programmatic analogy:

The output of a memory dump and its analytic result depend on the hardware, the software and the state of the application. Unfortunately the software is spread across processors, has multiple threads and applies a genetic algorithm with dynamic recompilation.

Death Definitions:

The notion of instant death is a cultural meme (which one can witness in child's play) and is further propagated in the media. Additionally "death" is a highly political matter...
"Death" has numerous legal definitions (throughout various cultures) medical definitions and biological definitions depending on the context. Legal definitions depends on the culturally dependent legal corpus, medical definitions on the state of (pragmatic) technologies. The medical definition of human death is influenced by the legal definition. The legal definition in turn is influenced by politics.
The biological definition of death depends on the context and a threshold thereof, which in turn describes the level and and of hierarchical systems or one large system comprised out of systems such as organs. An organ is the collection of units in one structural one to serve a common purpose.

Finally to answer more accurately, a person cannot (under everyday circumstances) shutdown brain activity within the time-interval of one reaction time-unit or 'cycle', but may transition between discernible states of global brain-activity. Such states may only be measurable with functional Imaging techniques and classifiable using computer algorithms.

molecular biology - Preparation of normal DNA polymerase

This is a very ambitious project for a DIY-er. To explain why, I'm going to use the example of DNA polymerase I from E. coli.

DNA polymerase I is the most abundant DNA polymerase in the E. coli cell, but nevertheless is still only present at around 300 copies per cell

Ishihama Y et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics. 9:102.

This was the first DNA polymerase that was ever purified, in the laboratory of Arthur Kornberg

(Enzymatic Synthesis of Deoxyribonucleic Acid : I. PREPARATION OF SUBSTRATES AND PARTIAL PURIFICATION OF AN ENZYME FROM ESCHERICHIA COLI Lehman, MJ et al. (1958) J. Biol. Chem. 33:163-170.).

In this paper a method of purification is described that starts with 60 litres of culture. There is also this statement:

"One kilo of E. coli yields less than 10 mg of the purified enzyme."

I'm guessing that you have no experience of protein purification, so I'll just tell you that this is very discouraging: these days, with overexpression, people expect to get mg quantities of their protein from just a few grams of bacterial cells.

This is a clear illustration of why it is pretty much unthinkable for you to set out to purify an enzyme like this using small-scale methods, and explains why techniques of overexpression and the use of affinity tags have revolutionised protein purification.

And it gets worse: even if you did manage to purify some DNA polymerase I from a bacterial source you would find that it is actually not very good at making DNA. This is because as well as extending primers in a 5'>3' direction, it is is very good at degrading DNA in the same direction. In other words as the enzyme moves along a template molecule, copying it, it will degrade any existing DNA that it meets "ahead" of its direction of travel. This is why the most commonly-used form of this enzyme in research is the "Klenow fragment", a fragment of the polymerase that lacks the 5'>3' exonuclease activity. This fragment was originally made by treating DNA polymerase I with the protease subtilisin, but it is now expressed from an engineered polA gene. Klenow fragment polymerase was used in the original PCR experiments (it had to be added afresh at every cycle).

I don't know how much money you have to spend on your projects, but in fact these enzymes can now be bought relatively cheaply. I don't think that you can expect to make them for yourself, without this becoming the actual project.

Finally, if you can get hold of a strain of E. coli with an expression plasmid for Taq polymerase then you really could make your own very easily - I've done this myself (but I no longer have the strain) and the heat stability of the enzyme makes the purification trivial. It would be much easier to use your own Taq with a heated water bath than to try to make DNA polymerase I. But obviously it depends upon what you are trying to do: Taq polymerase may be unsuitable for other reasons.

biochemistry - PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?

The binding of proteins (and cells) to glass (or silicon) surfaces can be prevented by coating the glass with polyethylene glycol (PEG) groups. PEG-silane is a reagent used to create this coating.

PEG-silane (the image shows a methoxy- version) (image taken from here; no connection) will coat glass surfaces because the silane portion (right hand end of the structure shown) will react with -OH groups on the glass surface.

I can't help with the part of the question about time and temperature of incubation, but it seems longer and hotter than protocols I have seen. Perhaps the indium tin oxide (ITO) coating on the slides has something to do with it?

nutrition - Is the amount of phosphoric acid added to colas enough to disrupt the function of the kidney over the long term?

The phosphoric acid in cola will contribute to dietary intake of phosphate. I may be missing something, but, since the transporter functions to reabsorb phosphate that has been filtered out at the glomerulus, excess phosphate will spill over into the urine.

According to Wikipedia the RDA for phosphorus is 700 mg and the tolerable upper intake level is 4000 mg. Coca cola contains 17 mg phosphorus (as phosphate) 100 ml^-1 (which is 340 mg in 2 L)

According to this source,

in the United States, an average person drinks 412 8-ounce drinks — or 3296 ounces — of Coke per year.

This works out at 9 oz per day = 266 ml = 45 mg phosphorus

For comparison (from here):

• white flour contains 595 mg 100 g^-1


• one boiled egg contains 220 mg


• canned salmon contains 240 mg 100 g^-1

endocrinology - Why is epinephrine not part of the somatic nervous system?

You are confusing different functional systems. Epinephrine released by the adrenal medulla circulates in the blood and indeed dilates the blood vessels in skeletal muscle. This ensures that enough oxygen and nutrients are available for the muscles to perform in a fight/flight response.

The somatic nervous system utilises acetylcholine not as a hormone but as a neurotransmitter. It is not released into the blood but only into the tiny (about 10nm wide) gap (synapse) between the nerve cell's axon terminal and the next nerve cell or muscle cell respectively.

This release by the somatic nerve cells causes an electrical potential in the muscle which makes it contract.

In summary:

The somatic nervous system controls the muscles because it stimulates the contraction which makes e.g. your arm move. Epinephrine released into the blood by the adrenal medulla serves to ensure the muscles have the blood supply they need in a stress response (e.g. a dangerous situation).

Along with muscular blood vessel dilation, epinephrine in the blood for example also stimulates the heart to beat faster and stronger, and dampens down mechanisms involved in digestion - essentially it does everything necessary to allow a quick escape or a strong fight.