text:
What alternatives are there to the amyloid hypothesis?
Given the recent failure of the Bapi clinical trial, there is a lot of questions that have arised from he amyloid hypothesis. However, I can't really think of many other mechanisms that don't involved plaque formation via protein aggregation.
What are the other dominant proposed mechanisms for the biochemistry of Alzheimers?
Reference: Alzheimer’s Drug Fails Its First Big Clinical Trial. Unfortunately, the results of the study have yet to be presented at a medical conference but will be in September.

Could you link to the relevant studies for those who are not familiar with them?

Well, I am sorry but I fail to understand how that would refute the amyloid hypothesis... it just tells us that a monoclonal Ab against amyloid is not a good cure for Alzheimer's.

@nico, strongly agree but I also get the idea that many alzheimer's researchers are beginning to back off on the mechanism and looking for alternative pathways to attack.

I am not really in that field, so I cannot really comment. However, I would not expect anyone to really say that amyloid plaques are not an important mark of Alzheimer's. They are possibly not the good target for a cure.

Hi all. See this article in Nature - very interesting.

Alzheimer's disease is a very complex field, and I am going to restrict my answer to two particular areas: the neuritic plaques and the neurofibrillary tangles. This area is also of interest to me, hence the protracted answer.
The two pathological hallmarks of Alzheimer's disease, first described by Alois Alzheimer in about 1906, are the extracellular neuritic plaques and the intracellular neurofibrillary tangles which occur (exclusively) in the brain of humans with this disease.
The Neuritic Plaques (Amyloid Precursor Protein and β-Amyoid)
[References to the information given below may be found in Price & Sisodia (1998) and in Lowery et al. (1991)]
The major component of the extracellular neuritic plaques is a small, appromimately 4 kDa protein known as the β-Amyloid (Aβ),  or A4-protein.

The Aβ, whose tertiary structure is that of a β-pleated sheet, is itself derived by proteolysis (see below) from a much larger protein known as the Amyloid Precursor Protein (APP).
A number of isoforms of Aβ are known which contain between 36 and 43 amino acids, the most common of which are  Aβ40 and Aβ42.
The Amyloid Precursor protein (APP) is a very large protein (≥ 695 amino acids) of unknown function which is a normal component of brain. It is predicted to have a single transmembrane span.
A number of isoforms of this protein are also known, which contain  695, 714, 751 & 770 amino acids.
The AA751 and AA770 isoforms contain a domain (Kunitz domain) homologous to a class of protease inhibitors, strongly suggesting the proteolysis plays a key role in normal function, and perhaps in (abberant?)  Aβ formation.
One of the cleavages which produces the Aβ, that catalyzed by γ-secretase, occurs within the transmembrane-spanning domain of APP.  How the protease has access to its substrate within the lipid bilayer is a major source of interest.

Researchers who believe that neuritic plaques and  Aβ hold the key to Alzheimer's disease are known as baptists. Their counterparts, who believe that the neurofibrillary tangles are key, are known as tauists, for reasons that will become obvious (see also here).
For the past number of years, baptists have been to the forefront. In my view, the tauist story is even more interesting, and must surely be important in any final understanding of Alzheimer's disease.
 Neurofibrillary Tangles, Paired Helical Filaments and Tau Protein
Examination of the neurofibrillary tangles under the electron microscope revealed that they had a twisted ribbon-like structure which was called the paired helical filament (PHF) (Kidd, 1964; Wisniewksi  et al., 1984).
PHFs are practically insoluble and for a long time this impared progress.  However, extraction using the detergent sarkosyl, followed by sequence analysis and immunological investigations, produced a  major surprise:

A component of the paired helical filament is the
  microtubule-associated protein tau (Goedert et al., 1988;
  Wischik et al., 1988), a most unusual and interesting soluble protein
  which had already been purified to homogeneity and extensively characterized by Kirschner & co-workers
  (Weingarten et al., 1975; Cleveland  et al., 1977a, 1977b).

A perusal of pubmed shows that at this stage interest in tau increased dramatically!

It is now accepted that microtubule-acssociated protein tau in a
  hyper-phosphorylated state is the major structural component of the
  paired helical filament (Lee et al., 1991; Kosik & Greenberg, 1994).

Some key properties of tau are the following.

Tau was first isolated as  a series of closely related proteins (isoforms) which co-purify with porcine tubulin during successive cycles of polymerization/depolymerization (Weingarten et al., 1975).  On an SDS gel, one sees (with bovine brain tau) 4 bands quite close together from (say) 58 - 64 kDa.
Interaction with tubulin is the only known 'normal' function of tau.  It promotes the polymerization of tubulin into microtubules under polymerization conditions, for example (Cleveland  et al., 1977a, 1977b).
Tau is encoded by a single gene, located on chromosome 17, and differential mRNA splicing gives rise to the brain isoforms (six in humans and four in cow) [Andreadis et al., 1989; Goedert et al., 1989; Himmler, 1989], and a single high molecular weight tau ('big tau') in peripheral tissues (Goedert et al., 1992).
Tau contains a series of imperfect amino-acid repeats, located in the C-terminus of the protein.  These repeats are thought to be responsible for microtubule binding (see, for example, Lee, 1990).
Although tau occurs in a hyper-phosphorylated state in the PHF, and may be phosphorylated in normal brain, phosphorylation is not necessary for formation of paired-helical filaments (Goedert et al., 1996).
The tau gene may be knocked out without any visible alteration of phenotype! (experiments done in mice) (Harada et al., 1994).
Mutations in the tau gene are not known to cause Alzheimer's disease, but are associated with very rare 'taupathies', such as an inherited dementia called frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17; possibly identical with Pick's disease) [Hutton et al., 1994].
The crystal structure of tau has not been obtained to date.  Current thinking is that the soluble form of tau is mainly a random coil (see von Bergen et al., 2006).

The fact that tau can be knocked  without serious consequence, together with the lack of mutations causing Alzheimer's,  has led to much criticism of the tauist story.
However it still is the major structural component of the paired helical filament (neurofibrillary tangles), and must surely be a key player in the understanding of Alzheimer's disease.

This is not to imply that Aβ and tau are the only shows in town.  As stated above, the field of Alzheimer's disease is very complex
An allele of Apolipoprotein E (ε4 allele) is genetically associated with an increased risk in late-onset Alzheimer's, for example (Corder et al., 1993).
Mutations in the presenilin genes are also associated with the disease (Sherrington et al., 1995).  Presenilins form part of the γ-secretase protease complex involved in Aβ formation (see Takeo et al., 2012).
I do not know enough about these fields to comment any further (although this does not usually stop me).
It should be emphasized, however, that most cases of Alzheimer's disease are sporadic, and only a small subset has a genetic component. It is a disease of the brain, and of aging. There is no known cure, no known cause and no reliable (biochemical) pre-mortem test (although a clinic diagnosis may of course be made).

References

Andreadis, A., Brown, W. M. & Kosik, K. S. (1992) Structure and novel exons of the human tau gene. Biochemistry, 31,  10626-10633.
von Bergen, M, Barghorn, S, Jeganathan, S, Mandelkow, E.M., Mandelkow, E.  (2006) Spectroscopic approaches to the conformation of tau protein in solution and in paired helical filaments.  Neurodegener. Dis. 3, 197-206.
Cleveland, D. W., Hwo, S.-Y. & Kirschner, M. W. (1977a)  Purification of tau, a microtubule associated protein that induces assembly of microtubules from purified tubulin. J. Mol. Biol. 116, 207-225
Cleveland, D. W., Hwo, S.-Y. & Kirschner, M. W. (1977b)  Physical and chemical properties of purified tau factor and the role of tau in microtubule assembly. J. Mol. Biol. 116,  227-247.
Corder, E.H., Saunders, A.M., Strittmatter, W.J., Schmechel, D.E., Gaskell, P.C. Small, G.W. Roses, A.D., Haines, J. L. & Pericak-Vance, M.A. (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 261, 921-923.
Goedert, M., Wischik, C. M., Crowther, R. A., Walker, J. E. & Klug, A. (1988)  Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of alzheimer disease:  Identification as the microtubule associated protein tau. Proc. Natl. Acad. Sci. USA 85, 4051-4055. [pdf]
Goedert, M., Spillantini, M. G., Jakes, R., Rutherford, D. & Crowther, R. A. (1989) Multiple isoforms of human microtubule associated protein tau:  sequences and localization in neurofibrillary tangles of alzheimer's disease  Neuron 3, 519-526.
Goedert, M., Spillantini, M. G. & Crowther, R. A. (1992) Cloning of a big tau microtubule associated protein characteristic of the peripheral nervous system. Proc. Natl. Acad. Sci. USA 89, 1983-1987. [pdf]
Goedert, M., Jakes, R., Spillantini, M. G, Hasegawa, M., Smith, M.J. & Crowther, R. A. (1996) Assembly of microtubule-associated protein tau into Alzheimer-like filaments induced by sulphated glycosaminoglycans. Nature, 83, 550-553.
Harada, A., Oguchi, K., Okabe, S., Kuno, J., Terada, S.,  Ohshima, T., Sato-Yoshitake, R., Takei, Y., Noda, T. & Hirokawa, N. (1994). Altered microtubule organization in small-calibre axons of mice lacking tau protein. Nature 369,  488-491
Himmler, A. (1989)  Structure of the bovine tau gene:  alternatively spliced transcripts generate a protein family. Molec. Cell. Biol.  9,  1389-1396.[pdf]
Hutton, M., Lendon, C. L., Rizzu, P., Baker, M., Froelich, S., et al. (1998) Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17. Nature 393, 702-705.
Kidd, M. (1964) Alzheimer's disease - an electron microscopical study. Brain 87,  307-320.
Kosik, K. S. & Greenberg, S. M. (1994)  Tau protein and alzheimer disease. In Alzheimer Disease.  Terry, R. D., Katzmann, R. & Bick, K. L., eds.  pp 335-344.  Raven k. Press, New York.
Lee, G. (1990) Tau protein:  an update on structure and function. Cell Motil. Cytoskel. 15, 199-203
Lee, V. M.-Y., Balin, B. J., Otvos, L. & Trojanowski, J. Q. (1991) A68:  A major subunit of paired helical filaments and derivatized forms of normal tau. Science 251,  675-678.
Lowery, D.E., Pasternackj, J.M., Gonzalez-DeWhitt, P.A., Zurcher-Neely, H.
Tomich, C-S. C., Altman, R.A., Fairbanks, M. B., Heinrikson, R. L.
Younkin, S. G.  & Greenberg, B. D. (1991) Alzheimer’s Amyloid Precursor Protein Produced by Recombinant Baculovirus Expression. Proteolytic Processing And Protease Inhibitory Properties.  J. Biol. Chem. 266, 19842-19850.  pdf
Price, D. L. & Sisodia, S. S. (1998) Mutant genes in familial alzhiemer's disease and transgenic models. Annu. Rev. Neurosci. 21, 479-505.
Sherrington, R, Rogaev, E.I, Liang, Y, Rogaeva, E.A, Levesque, G, Ikeda, M, Chi, H, Lin, C, Li, G, Holman, K, Tsuda T, Mar, L, Foncin, J.F, Bruni, AC, Montes,  M.P, Sorbi, S, Rainero, I, Pinessi, L, Nee, L, Chumakov, I, Pollen, D, Brookes, A, Sanseau, P, Polinsky, RJ, Wasco, W, Da Silva,  H.A, Haines, J.L, Perkicak-Vance, M.A, Tanzi, RE, Roses, A.D, Fraser, PE, Rommens, J.M, St George-Hyslop, P.H. (1995)  Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature, 375, 754-760.
Takeo, K, Watanabe, N, Tomita, T, Iwatsubo, T.  (2012)  Contribution of the γ-Secretase Subunits to the Formation of Catalytic Pore of Presenilin 1 Protein.  J. Biol. Chem. 287, 25834-25843
Weingarten, M. D., Lockwood, A. H., Hwo, S.-Y. & Kirschner, M. W. (1975)  A protein factor essential for microtubule assembly. Proc. Natl. Acad. Sci. USA 72, 1858-1862. [pdf]
Wischik, C. M., Novak, M., Edwards, P. C., Klug, A., Tichelaar, W. & Crowther, R. A. (1988)  Structural characterization of the core of the paired helical filament of alzheimer disease. Proc. Natl. Acad. Sci. USA,   85, 4884-32768. [pdf]
Wisniewski, H. M., Merz, P. A. & Iqbal, K. (1984) Ultrastructure of paired helical filaments of Alzheimer's neurofibrillary tangle. J. Neuropathol. Exper. Neurol.,  43,  643-656.

Alzheimer is also considered a tauopathy due to abnormal aggregation of the tau protein. There has been succesful research in that direction, recently, which was a bit neglected, presumably because of vested interests in the amyloid hypothesis.
http://en.wikipedia.org/wiki/Tauopathy
However, another alternative to amyloid (and tau) is the hypothesis that Alzheimer is caused or enhanced by Herpes Simplex virus (HSV-1). One landmark paper found HSV DNA in amyloid plaques and another hint is the association of a lysin-poor/arginine-rich diet with Alzheimer risk (the connection being that HSV thrives in Arg-rich tissue). Also, a cohort study found a direct association.
N. Zilka, Z. Kazmerova, S. Jadhav, P. Neradil, A. Madari, D. Obetkova, O. Bugos, M. Novak: Who fans the flames of Alzheimer's disease brains? Misfolded tau on the crossroad of neurodegenerative and inflammatory pathways. In: Journal of neuroinflammation. Vol.9, 2012, p. 47 doi:10.1186/1742-2094-9-47. PMID 22397366. PMC 3334709. (Review).
A. M. Geppert: [Alzheimer's disease and HSV-1 infection]. In: Neurologia i neurochirurgia polska. 40, 1, 2006 Jan-Feb, 57–61. PMID 16463223. (Review).
M. A. Wozniak, A. P. Mee, R. F. Itzhaki: Herpes simplex virus type 1 DNA is located within Alzheimer's disease amyloid plaques. In: The Journal of pathology. 217, 1, Jan 2009, 131–138. doi:10.1002/path.2449. PMID 18973185.
Letenneur, L; Pérès, K, Fleury, H, Garrigue, I, Barberger-Gateau, P, Helmer, C, Orgogozo, JM, Gauthier, S, Dartigues, JF (2008): Seropositivity to herpes simplex virus antibodies and risk of Alzheimer's disease: a population-based cohort study." In: PLoS ONE 3 (11): e3637. doi:10.1371/journal.pone.0003637. PMC 2572852. PMID 18982063.

Whilst there are several competing ideas for the cause of Alzheimer's, it seems to me that the deposition of β-amyloid (Aβ) is key to the understanding of the disease progression. In many of the papers I will go on to cite, they suggest that prevention of Alzheimer's may be the only cure, as neurons (once damaged) cannot be replaced.
During aging there is a progressive increase in the systemic pro-inflammatory state (sometimes called 'inflammaging'). This is also true for the brain (commonly known as neuroinflammation), and is known to contribute to neurodegenerative diseases by promoting the destruction of local tissues (i.e. neurons) [ref].
Under normal circumstances microglia (resident macrophages of the brain) clear any excess protein depositions (plaques), such as Aβ, in much the same way as macrophages respond to carotid plaques (as can occur during cardiovascular disease). With age, the immune system becomes less functional - a process known as immunosenescence - which contributes to the pro-inflammatory state of aging [ref].
As the immune system becomes less functional, the clearance of Aβ deposits is reduced, possibly contributing to the increased plaque deposition [ref.1][ref.2]. There is also discussion on whether it is the decreased effectiveness of the blood-brain barrier that allows peripheral (from the blood) immune cells to infiltrate the central nervous system, possibly kick-starting the degeneration [ref].
There are many more factors than this, but this is certainly one that interests me as I can see that individuals will have different responses and predispositions to plaques formation in the first place (i.e. the ApoE risk allele, exposure to certain pathogens over the lifetime).
I therefore don't think the study rules out the amyloid hypothesis, in that removal Aβ does not restore the lost neurons (did they really expect it to?). What it does show is that the emphasis should be on prevention, not cure, as 'early-warning' signs, such as biomarkers of Aβ deposits, will be the best way to prevent the loss of neurons.


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Expression of an ancestral gene
Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?
Update:
By ancestral gene I mean a gene which was used by an ancestor but than changed slightly through evolution, though it still serves the same purpose. And by the misleading conclusion I mean that using this similarity between the product of the ancestral gene and the modern protein as evidence that the organism is descended from the ancestor.

What context are you working in? What're the misleading conclusions?

Without further information, question is impossible to answer.

specifically, please try to explain what you mean by ancestral gene?

I think that this pretty clear now. The first things that comes to mind is the convergent evolution and hereditary gene transfer.

I still think the question is too vague. Could you make an example with a specific protein and showing what conclusion would be misleading?

Do you mean expressed recombinantly?

Your updated question is still very vague, but I'm going to assume it is basically: "Why would the ancestral version of a gene be mistaken for a more recent version than the modern gene?"
If this is incorrect, please let me know and modify your question to clarify.
The simple answer to that question is that the mutations that occurred after the Ancestral gene resulted in less apparent divergence than the LCA (last common ancestor), which would cause the Ancestral gene to seemingly have more polymorphisms - and the general assumption is that the more polymorphisms (mutations) that a gene has undergone, the more recent it is.
So let's say you have the following DNA sequences:
5' - AAAT - 3' = LCA (Template)
5' - AAAG - 3' = Sample 1 : # Differences = 1 Nucleotide
5' - AACG - 3' = Sample 2 : # Differences = 2 Nucleotides
The general assumption is that the larger the difference from the LCA, the more mutations have occurred over time. So, under the general assumption, Sample 2 is probably the most recent version of the sequence.
However, and this is what I think is the answer to your question, because mutations can occur in any order and at any place in the genome, it is entirely possible for the third (from left) Nucleotide to have followed this mutation path: A -> C -> A
That would make Sample 2 appear to be more recent than it is because it essentially mutated "back" to the LCA version of the gene, despite being a linearly older version than Sample 1. In this way, an Ancestral gene can be mistaken for a more recent evolution of a gene. This is also why genomic data is never as strong as when paired with fossil records or other corroborating data that also aligns with the genomic data's proposed timeline; though the odds of a mistake being made grow exponentially less as more of the genome is compared and analyzed.
With very recent mutations; on the scale of hundreds to thousands of years, it's sometimes necessary to analyze thousands of base pairs to calculate an adequately confident answer.

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What is the Edward O. Wilson fuss about?
I have just read this article on E. O. Wilson and I don't understand what the difference is between what he is arguing and "standard" natural selection.
I read "the extended phenotype" some years ago and from what I vaguely remember that argued that everything about selection comes down to genes: they are the units of what is inherited and drive everything else (and their reach can be quite surprising).  At first glance that seems inconsistent with the article, since it mentions "group selection".  But when you read the details it includes things like

Group selection begins when a colony of creatures develops a behaviour
  that gives it a competitive advantage over other groups. Initially,
  this could be down to a random genetic mutation.

which sounds like it's gene-based too (and examples seem to come from ants and the like which I thought were closely genetically-related across a colony too...).
So what is the fuss about?  And how will it be resolved?
Maybe the difference is easier to explain in terms of some difference between mathematical models?  If so, that's fine (I hope - it might make more sense than jargon in a field I am unfamiliar with ;o).
[Is this too "general public" for this site?  Apologies if so.]

After reading the article, the fuss is about this:
In currently accepted theory Eusociality or "kin selection" explains altruistic behavior (the sacrifice of yourself or resources you control for the betterment of something else besides you) by relating the act to the amount of genetic information passed on.
The relevant equation is Hamilton's rule:
                                                                $rB > C$
C is the cost to the actor (the person giving up resources). B is the number of others involved, and r is the relationship value to the actor in terms of genetic similarity.
So if you and two full-siblings (who each share on-average 50% of your genome) and a bus comes straight at the group, and you have the capability to push them out of the way while dying yourself, kin selection suggests you shouldn't because the genetic cost is equivalent. You eliminate yourself from the gene pool, and save the equivalent of yourself for future generations (2 x 1/2 = 1).
However, if you and three siblings were in the situation, then it's evolutionarily advantageous to be altruistic. You would die (a cost of 1), but you would save the equivalent of 1.5x your genome (3 x 1/2 = 1.5) to pass on to future generations.
Thus, communal and social behaviors like those of ants basically boil down to: Everybody is so closely related that spending resources to help your kin is essentially spending resources to ensure the majority of your genome survives (which is the big point of evolution, after all).
Wilson's argument, what I can glean from the small brief of the study and the article, is that you don't need the relatedness equation to explain altruistic behavior in social situations (basically the row is he's saying the currently accepted theory is wrong). All you need to start with is a genetic mutation somewhere along the line that causes the offspring to stick close to home. Once you have a few generations that don't leave the nest, you start to develop social behavior that results in altruism because you've gone from selfish individuals to a group setting.
The article and Wilson don't give any more insight other than altruism apparently develops spontaneously from the formation of groups. Simply being social is the explanation for why some individuals will give resources to others to ensure the success of the others.
Whether or not Wilson is correct isn't really discussed. He openly admits to needing a lot of research, some of which is being performed.

Hamilton's rule... :)  I feel that the fundamental argument for individual selection is as much ideological as it is scientific.  There are quite a few edge cases which both sides explain away I feel.  To me the big question is how does this explain human social behavior, which is the brass ring, still ungrabbed by biology.

I started reading David Sloan Wilson's work on group selection a decade ago and am surprised that the field still has such a reluctance to move on.

@Abe - The duty of scientists is only to move on if better information is presented. I'm not familiar with D. S. Wilson's work, but the current textbooks feature Hamilton's Rule. If Wilson's work provides a better explanation, it will eventually get accepted. :-)

So what is the fuss about?

The fuss isn’t so much about biology as it is about the circumstances of the argument. in particular, I gather that there are two complaints people have with E. O. Wilson’s (and his collaborators’) arguments:

The Wilsonians pretend that kin selection (inclusive fitness) is just a quaint, outdated theory which is trivially dismantled because its mathematics don’t work, while in reality it represents the view of most people in the of field evolutionary biology, and has for years. Regardless of its actual scientific value, it certainly isn’t outdated – it’s the majority view among experts.
Proponents of kin selection feel that the Wilsonians misrepresent their views by citing and attacking outdated knowledge rather than the state of the art, thus creating a straw man argument. In the same vein, they argue that since Wilsonians obviously don’t know the state of the art, they cannot contribute meaningfully to the debate.

In addition, proponents of kin selection argue that group selection theory simply doesn’t hold up in theory1. I find those arguments highly compelling. At the same time, I’m not an expert and the Wilsonians argue that kin selection is equally flawed so I won’t weigh in on the debate.

1 The article is not written by an expert in the field but it has been endorsed by experts as a lucid explanation of the matter.

How is the fact that group selection does not hold in theory reconcile with observations / experimental tests? Is there another explanation for inherited religious, social, or political groups?

@Abe I’m not an expert but as far as I know none of those actually requires group selection. Many phenomena are simply explainable by kin selection. And while we don’t have comprehensive explanations for large-scale phenomena such as religion etc., you can construct potential explanations without invoking group selection. Indeed, just because there’s interaction within and between groups involved doesn’t mean that evolutionary selection happens on the level of groups, just like genetic selection doesn’t happen on the level of individuals, it happens on the level of alleles.

It is maybe of note that E O Wilson is first and foremost an entomologist and has developed many of his ideas to explain the evolution of ants and bees first.

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Physiological or molecular difference before and after sleep?
I know that the details of the process of sleep aren't entirely known, but have always wondered why I feel rested after sleep.
Biologically, what differences can be directly observed in the human body before and after a good night's sleep?

Can you be any more specific? Sleep affects every single organ and organ system in the body, and everything from hormone levels to cytokine levels change from tissue to tissue based on the amount of sleep you get.
Your question is almost impossible to answer concisely.

Similar: http://biology.stackexchange.com/q/3028/6422


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Can an organism obtaining a part of its genome via horizontal gene transfer be called a "hybrid"?
Wikipedia definition of "hybrid" offers many competing definitions. But most seem to be centered on sexual-reproduction gene transfer.
Is there an official (in a textbook or widely accepted peer reviewed work) definition of a "hybrid"/"hybridization" that would clearly include ANY genetic mixing, most specifically obtaining genes via horizontal gene transfer?
If not, is it specifically because "hybrid" requires sexual reproduction, or merely because it requires a certain minimal amount of inherited genetic material from both sides, and horisontal genetic transfer in practice involves significantly less genetic material being inherited?

Full transparency: the question originated on SFF StackExchange, pertaining to whether Alien chestburster can legitimately be called a "hybrid" from a biology point of view, on the basis of it obtaining a variety of phenotypal features of the host body via horizontal-gene-transfer. It's mostly a definition issue.

As you point out, there isn't a singularly accepted biological defnition of 'hybrid.' The most basic would be a single organism that exhibits traits of two individual organisms, but that will find perfectly acceptable disagreement depending on who you talk to. You, for instance, are human - but a hybrid of your parents' genomes.
So I would personally say that horizontal gene transfer is equivalent to gene inheritance, and that as long as the organism exhibited traits of both 'parent' individuals - then yes, it is a hybrid. Some might include that even if it didn't exhibit traits and merely contained the genes in any inherited genomic data that the hybrid label would be appropriate.

I'm looking for definitions that could be considered "legit". Textbooks, or barring that, widely respected/cited paper; that explicitly defines "hybrid" as inclusive of H.G.T. (or rather not exclusive of it). E.g. where the end result (gene mix) is relevant as opposed to mechanism of mixing.


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Disadvantages of unihemispheric sleep
Is is well known fact that marine mammals and some birds can sleep with one brain hemisphere at a time, since it's essential for their survival.
However, at least in my opinion, such mechanism would give significant advantage to many other species (e.g. to antelops) because it helps avoiding predators.
While answers to this question explain why sleep is necessary, animals with unihemispheric sleep mode does not seem to suffer from any of mentioned drawbacks of non-sleeping (except maybe increased energy consumption).
Are there any particular disadvantages of unihemispheric sleep versus "normal" sleep?
EDIT: I've stumbled upon the following paper:  Rattenborg N., Amlaner C., Lima S.. 2000. Behavioral, neurophysiological and evolutionary perspectives on unihemispheric sleep. Neuroscience & Biobehavioral Reviews 24: 817–842, which discusses several possible reasons for absense of unihemispheric sleep in most mammals, but does not present any evidence to support their hypothesis. The main reason (from authors' point of view, at least) is the need for very loose coupling of both hemispheres to allow them sleep independently, which might negatively affect overall brain effectiveness.

Along these lines, sleep may play a role in integrating the
  functions of different brain regions. Thus, BSWS1 in terrestrial
  mammals may be superior to the BSWS in animals with USWS2
  because it allows integration within and between hemispheres, rather than
  just within a particular hemisphere.
...
Specifically, the reorganization of the central nervous system
  required for USWS may interfere with other adaptive brain functions,
  such as integrating the functions of both hemispheres.
1 Bihemispheric Slow Wave Sleep; 2 Unihemispheric Slow Wave Sleep

They also argue that the unihemispheric sleep might have been present in first mammals, but wasn't giving any advantages on first stages of evolution.
However, this paper was published more that 10 years ago, so there might have been some advances in the field since then.

I would assume that to give your brain the rest it needs you would have to spend double the time sleeping when resting one hemisphere at a time. For humans at lest that would be kind of disastrous.

@UltimateGobblement I agree that it might be bad for humans, but I doubt that most low savannah animals have more complex lifestyle than dolphins, so using one hemisphere most of the time might be enough, and enhanced alertness during night increases chances of survival during attack of nocturnal predators. Giraffes and elefants, e.g., sleep approx. 4 hours a day, so reduced sleep time is likely very beneficial to them.

that would make it easier to work as a night watchmen or some other jobs like working in a toll booth.

I am pretty sure one hemisphere of my brain is asleep when I watch TV...  ;)

Interesting note, seals which can sleep both on water and on land, employ unihemispherical sleep in water but whole brain sleep on land, so this suggests unihemispherical sleep is non-optimal

I thought this was an interesting subject and I had some time to do a little search around today.  I can't find anything better than the review you point out. All I can do is add a few interesting notes since 2001.  Nothing really turns over Rattenborg et al.
Sleep is itself a poorly understood process and most of the theories of the necessity of sleep can teeter precariously with discoveries like this report that baby dolphins and killer whales and their mothers simply don't sleep at all for the first few months of life.
The Rattenborg review is only guessing, but I think its clear that there is a cost to unihemispheric sleep, even if we don't know what it is.  Cetaceans and birds and perhaps reptiles having unihemispheric sleep are all cases where there are perpetual and strong selection forces that maintain the ability in these animals.  Without constant predation experienced by tasty ducks or the vagaries of being an air-breathing underwater mammal, animals quickly lose their ability to sleep with one half their brain, one assumes because the ability to maintain it is particular and easily lost with variation.  Modelling work of the hemispheres in sleep indicates that the connections between the hemispheres are modulated between the two modes of sleep - there may be advantages to such brain structures for instance.
This blog post is a good read though and a bit more recent, though most of the references are from before 2001. Dolphins do use both hemispheres to sleep, but just not very often (about 15% of the time), indicating there is some advantage even for these animals.  Seals may alternate between bi and uni-hemispheric sleep when they are on land and at sea.
If you were wondering if there was something you were missing - I'd say no.  At the time of this writing THIS web page is the sixth hit on a google search for the term 'unihemispheric sleep'....


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Does every mitochondrion in a cell contain the same DNA?
I know that mitochondria of eukaryotes have their own DNA, more similar to that of bacteria than to the rest of the cell's DNA. I also know that a cell can have plenty of mitochondria, and I understand each of them has it's own DNA. Is it the same DNA?
I know that when a human is conceived, the mitochondria of the sperm are destroyed and don't contribute to the new cell. If there were no mutations and the process started with a cell with homogenous mDNA, that would mean that the mDNA not only within one cell but among all of the descendants was the same. But there are mutations because we have different mDNAs. Then shouldn't the mutations cause variety within single cells? It's hard for me to believe that there can even be a single human cell in the world that has homogenous mDNA because, if I understand correctly, an ovum retains many mitochondria during conception, not just one, so at least some of the variety within the ovum should be passed over to the conceived human. But perhaps it's extremely difficult for a cell with variously DNAed mitochondria to survive? Can it be estimated what the percentage of human cells with homogenous or nearly homogenous mDNA is across the world?
I'm asking this because I've heard that the mDNA can be considered another chromosome. I wonder if then every single piece of mitochondrial DNA should be considered another chromosome.
Please note that all I know about biology is what I learned in high school several years ago and the bits I know from Wikipedia and other internet sources. I would like to ask for possibly accessible answers.
EDIT: Reading up on this, I came across the term heteroplasmy. So it does happen that mitochondria of an organism can store different genetic information. But the article seems to suggest that it is an anomaly rather than the normal course of things. That seems strange to me. I understand of course that some mutations have to be harmful, but shouldn't some mutations and some kinds of in-cell variety turn out to be neutral or even advantageous?
I've also just read that a mitochondrion stores more than one copy of its DNA. That seems to allow for variation even within a single mitochondrion.
EDIT 2: I think it's possible that my question is unclear. There seem to be four levels on which mDNA variety can be considered: a species, an organism, a cell, a mitochondrion. I ask the answerers to focus on the third one. I will be happy to learn about the other levels too and I will consider such information on-topic, but my main question is about what happens in a cell.

Why would be mtDNA any different from nuclear DNA in that sense? They are both sensible to mutations.

@nico Yes, of course there are mutations in mitochondrial DNA. Otherwise there would be no mDNA variety across the human population. But nuclear DNA is different from mDNA in that the latter occurs in very many (possibly thousands as I understand) copies within a single cell so there is room for variety within that single cell. That's impossible with nuclear DNA.

sure, but what I wanted to say is that by the same principle you may as well ask "does every nucleus contain the same DNA"? Surely, having thousand of copies increases by 3 orders of magnitude the probability of having mutations, no doubt about that. I am wondering, however, if there are repair mechanisms for mtDNA... I would assume so but I am not sure

@nico That wouldn't be exactly the same kind of question, although certainly related. I'm asking about what happens in a single cell. There is only one nucleus in a single cell so your question has to be about a larger structure like an organism. I will edit the question to make it clear.

oh, OK, I am sorry I read the question too quickly and I misunderstood what you were asking :)

This link seems to have good information that answers most of your questions.
In my mind, there are two types of mitochondria: ones that work and ones that don't. Mitochondria do have DNA but that mDNA is there to encode proteins for their specific functions (e.g. to create ATP). So, although the mDNA may not be uniform for every mitochondrion in your body, it is most likely functional unless you have a mitochondrial disease. If you do have a mitochondrial disease then it suggests that some of your mitochondria are functional and some are not (otherwise you would be inviable).
As discussed in the comments, all DNA undergoes mutations so that even identical mDNA genomes may vary after undergoing some mutations. It's possible that only one genetic line of mitochondria was passed to you from your mom. In this case all the mitochondria in your body would be identical (except for minor mutations). It's also possible that your mom inherited and passed on to you more than one genetic line (as is the case in viable mitochondrial disease).
Mitochondrial repair mechanisms do exist but they differ in various ways from nuclear DNA repair and may be more prone to damage.

Thank you. The first document seems to be concerned only with the mutations that make genes faulty. But surely there must be mutations that are not harmful to the cell or the organism? Is it more difficult for an mDNA mutation to be neutral or advantageous than for nuclear DNA mutations? Is it common for a cell to have several different but (nearly) all perfectly good sets of mDNA in its mitochondria?

You're correct, there are mutations that are not harmful to the mitochondria or cell. 2) Mitochondrial mutation is probably more likely to be harmful than nuclear DNA mutation since it is much less vast. Nuclear DNA is much larger and thus there is less change to mutate something important. 3) I don't know how common it is, but it is possible.


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Why do DNA and RNA have the functions they have?
I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if there is a reason for this choice of directions. According to this article, all other directions are possible. Why do we use DNA for example? RNA is capable of self-replication since it happens in viruses. And why do we use RNA, not DNA, as messenger molecules? Is it just an accident or is it possible to explain why this is the right way of doing it?

One reason is surely that DNA is chemically more stable than RNA.

@nico Thank you, I didn't know that. That seems to explain why RNA is not used to store genetic information. Could you explain why RNA is used instead of DNA for communication? Is RNA easier to build?

On top of my head I cannot think of a reason. I will try to write an answer if I can find something about it.

RNA folds better than DNA.

For a reference of the RNA folding stability see http://biology.stackexchange.com/a/769/389

DNA is more chemically stable than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by with a less chemically stable genome.
RNA is a useful format to transcribe since it has multiple forms and functions (e.g. rRNA, mRNA, tRNA, siRNA, snRNA, miRNA, etc.). RNA can sometimes function like a protein in which it carries out cellular actions without needing to be translated. It has been hypothesized that RNA were the first molecules as precursors to life since they can function for both storage and action. The theory is that RNA was the first molecule but was then able to be translated into proteins (which were more variable/useful) and able to be stored as DNA (which was more stable as a storage medium).

The first sentence of your second paragraph is essentially proof by intimidation: you’re not giving any reason here. Just because RNA can take on multiple forms doesn’t by itself say anything about the suitability of mRNA as an intermediary between DNA and proteins, especially since all the examples you’ve cited are noncoding.

True, I didn't mention any reason that it's a particularly good intermediary to be translated. I'm taking a different angle in answering the question by suggesting that maybe it has more to do with the sequence of origins instead of its usefulness as an intermediary.

Yes, in fact I’m convinced that sequence of origin is the real reason. The similarity with non-coding RNA is notable only insofar as much of the machinery for treating RNA (any RNA) is ancient and very well conserved, and thus the cell requires less innovation by relying on mRNA than it would by having some kind of mDNA.

@KonradRudolph, or RNA structure is simply more stable. see http://biology.stackexchange.com/a/769/389

@bobthejoe While that’s interesting in general (good answer!), here we are talking specifically about mRNA where structure plays no or only a very minor role.

@KonradRudolph, Well... that is a massive assumption that mRNA structure plays little to no role.

@bobthejoe Is it? Most of the mRNA seems to be unstructured, apart from cap, tail and maybe 3ʹ UTR. I admit that I haven’t read anything stating this definitely but I’ve also never read anything to the contrary (and a structure in the coding sequence sounds worth mentioning), and in fact the (electron scanning) photographs I’ve seen of transcription show elongated, unfolded mRNA tails.

I suggest going to the original refernces instead of wikipedia. Look up Gilbert (1986) in Nature for the RNA world.

If you had a complex life form which used only DNA or RNA, it would have no way to tell transcribed mXNA from genomic gXNA. This would cause problems during cellar replication, as you could also replicate your mXNA along with your gXNA. It would also cause problems repairing breaks in your gXNA, as you would run the risk of including mXNA during the repair process.
Therefore it seems advantageous to have a storage system for information which is not currently being translated into protein (i.e., DNA), as compared to just having RNA.
On the other hand a completely DNA organism would need RNA for functional ribosomes anyway. If RNA is being used for ribosomes, using it for mRNA as well to avoid confusion with genomic DNA seems advantageous.
In order to test this hypothesis, you would need to create a completely RNA/DNA based lifeform and investigate its properties. Short of starting life from scratch as RNA based and monitoring its evolution over a few million years, a conclusive proof as to why things are the way they are as opposed to being down to an evolutionary historical accident is difficult to obtain!

There are simpler ways to distinguish mXNA from gXNA. For example, single vs. double stranded, chaperone proteins or the simple absence of an origin of replication in the mXNA messenger.

https://www.quora.com/Why-do-cells-use-both-DNA-and-RNA also mentions that RNA is cheaper to replicate as it is less stable. While I don't know anything about this, I would guess that that is true.


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Does making yogurt from non-pasteurized milk work against possible disease bacteria?
In the past, when there was no pasteurization, could making yogurt from milk lower the chance of getting infected by bovine tuberculosis (or other diseases from infected milk)?
For example, would yogurt cultures reduce the amount of "bad" bacteria or create a less hospitable environment for them?

In short, 'No.'
Yogurt, in and of itself, is the product of milk with specific strains of bacteria that are not particularly unique. Yogurt is just as hospitable to harmful bacteria as beneficial bacteria.
The two mechanisms which spring to my mind that would prevent infection by harmful bacteria in yogurt would be the following:
*The already dominant beneficial bacteria outcompete for the harmful bacteria, effectively limiting the capacity for harmful bacterial growth.
*The already present beneficial bacteria create extracellular products which damage harmful bacteria.
The second, if it happens at all, doesn't happen on a scale that I'm aware of. The first could happen, but I highly doubt it. It seems, to me, that it would be more likely to happen in cheese when most of the easy resources have been consumed, which in yogurt they haven't.
Yogurt, and all products stemming from milk, are inherently safer not because of any bacteria that take up residence, but because the mammary glands inside the animal producing the milk are effective filters for a variety of infections. Milk is a product that is constructed in the mammary glands, and the cells are selective about the output. Keep in mind, however, that it is by no means sterile. There are dozens of virii and diseases which can be imparted by breastmilk, and nursing women must adhere to guidelines concerning exposure to medications and diet. It's also possible for DDT and other compounds to become concentrated in breastmilk, resulting in harm to the child.
http://www.breastfeedingbasics.org/cgi-bin/deliver.cgi/content/Drugs/pre_pass.html
So, yes, while milk in and of itself is safer than other options, it is not risk free. A virus could easily infect the mammal or herd producing the milk for sale to humans, and only exhibit dangerous symptoms after the milk had been sold. This is why it's illegal to sell unpasteurized milk for human consumption in most U.S. states.

You should change that last paragraph from in most states to in most states in the US. Unpasteurized cheese and milk is legal and common in many countries in Europe for instance. I am so glad I live in a country where cheese from unpasteurized milk not only is legal, but it is considered (rightly) a delicacy. By the way, maybe I am misreading what you are writing, but pasteurized milk is NOT sterile either. If you need sterility you need to buy sterile milk, which is a different thing.

There have been studies regarding whether or not the bacterial load in yogurt (which would be the "Live and active cultures" part of yogurt - or the part where Jamie Lee Curtis talks about how you'll go back to pooping on schedule) helps protect the gut against the proliferation of certain pathogenic bacterias like C. difficile when we've otherwise wiped out the gut's natural flora - say with antibiotics.
So far, the results from that have been middling and inconclusive. And honestly, that's the best shot the cultures in yogurt have of showing a good effect.
In the scenario you ask about, you'd be trying to protect against diseases that haven't been handed a competitive advantage in the form of an obliterated gut flora, and have added in the risk of introducing pathogenic bacteria from the milk itself. A staggering proportion of milk-related food-born illness in the U.S. is due to unpasteurized milk. I'd say the chances of that being net-positive as slim, and more importantly I don't think you could slip that study past an IRB - at least in the U.S.
From Nico's question:
http://wwwnc.cdc.gov/eid/article/18/3/pdfs/11-1370.pdf Would be a decent place to start. Dairy is, admittedly, responsible for a small number of food born outbreaks overall - various fruits and vegetables, chicken and beef are still the top causes.
The issue is in how many outbreaks are caused by raw milk given how little of it is consumed in the U.S. The study I link above looks at known dairy outbreaks from 1993-2006. Of the 121 outbreaks, 60% of them were from unpasturized products, with a ~2 to 1 split between milk and cheese. All of them were caused by bacteria (addressing the idea that it might be a viral pathogen that wouldn't have been deactivated anyway).
The problem is though that many states prohibit the sale of raw milk products, and its relatively rare. If you weight the incidence of disease according to consumption patterns, one finds that the incidence per unit of dairy consumed is ~150x greater in non-pasturized products.
So while the overall numbers are not huge (though far from zero, and I've seen people consider lesser things public health emergencies), for such a rare product it's a big deal.
I've seen no suggestion that the patterns in Europe are different. For example (in Finnish) from this year: http://www.vsshp.fi/fi/7273/58327/ from this summer. But only the really massive outbreaks catch major media attention.

speaking of the proportion of food-born illness in the US due to unpaseurized milk, what makes you think it is the cause of that? Bad handling? Otherwise I cannot explain why the same is not true for the great part of Europe, where people eat Roquefort, Fontina, Gruyére, etc etc. Do you have any refs for that?

@nico Added information and some nuance to the answer. It's a "staggering proportion" given the volume of raw milk consumed in this country. I suspect the same is true for the great part of Europe - people eat food that will give them food-born illness all the time. Unless its a massive outbreak in a popular food item, you won't hear about it.

maybe there is some genetic part to it? Could it be that people, say, in France where it is extremely common to consume raw milk products are somehow "adapted" to them? On a side note, Slow Food even has a campaign in favour of raw milk

@nico I very much doubt there's a genetic component - the time scale we're talking about between the divergence from raw milk to widespread pasteurization is quite short. Odds are that people in France simply accept the risk, in the same way people in the U.S. accept the risk of say, medium/medium-rare hamburger.

@nico As to the Slow Food page, while I have some issues with it overall, whether or not raw milk is good 'on the whole' was not the question - the question was whether raw milk yogurt would represent a new positive prevention for disease bacteria. I'd argue that the weight of the evidence for that is still firmly "no".

that is my point. Say people in France "accept the risk" (and, in effect here people love their steak tartare with raw egg on top... :P) then there should be way more sick people when compared to the US.

@nico And you have not established that there are not. I pointed to a raw milk outbreak in Finland less than a month ago. There are others - your perception that they're aren't any doesn't necessarily mesh with reality. But foodborn outbreaks have to be very large to get much press, and raw milk products, even in Europe, aren't big enough to command that kind of attention. Also steak tartare has a very different pathogenic risk profile to hamburger meat ;)


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Is there an advantage to having cellulite
There are many ads nowadays advertising cellulite removal, and it causes me to wonder if there is an advantage to having cellulite or if it is just a result of too much fat unevenly spread?  Is it structurally more efficient at storing energy or providing insulation?

There's no advantage or disadvantage (beyond personal perception of attractiveness).
It's a benign condition that can occur with hormone changes, weight changes, and especially genetic predisposition.
It occurs in most women (up to 90% will have it at some point) and some men, and physicians consider it 'normal.'
http://www.mayoclinic.com/health/cellulite/DS00891


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When should endocytosis inhibitors be used in cell binding assays?
I'm beginning to do some cell-binding assays and I would like for my proteins to not be endocytosed by my mammalian cells. Typical suggestions are for the cells to be kept on ice and that the binding experiment also occurs when the cells are chilled.
However, to be sure it has been suggested that I use endocytosis inhbitors. So my questions are, when are the endocytosis inhibitors necessary? How would I know that endocytosis inhibitors are necessary? Which ones would I actually use?
I recognize that there are both clathrin and non-clathrin mechanisms of internalization. Which mechanism would be more useful to study for an antibody-receptor interaction?

As with so many things, it depends. Also, I'm a bit unclear when you say antibody-receptor interaction, do you mean that you have an antibody that's specific for a receptor, or that you're studying Fc receptors binding to antibodies? (for the following, I assume the former)
For most cell types and most cell surface molecules, simple antibody binding isn't going to induce endocytosis, and keeping the cells on ice is sufficient to prevent most background endocytosis (i'd do the assays in a cold room as well so that even when you take tubes out of the ice bucket they stay cold).
On the other hand, if you're using highly phagocytic cells (like macrophages), and/or you're triggering a receptor through cross-linking or some other mechanism, you might get some endocytosis that affects your results.
The mechanism (clathrin vs non) can also vary, again depending on what's being bound.
You should do some optimization - ie: do the same assay on a set of samples, with or without  inhibition and see if your antibody binding is affected. But be aware that a lot of drugs for inhibiting endocytosis can do other stuff too, so watch out for artifacts. Maybe read this: http://www.ncbi.nlm.nih.gov/pubmed/18369934


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Why is GTP gamma S non hydrolyzable?
GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving Phosphate group. However, this is not the bond that is hydrolyzed (dashed line). What makes it non-hydrolyzable then?
GTP:                    GTPgS:

Indeed a good question. Bet it's got something to do with electronegativity XD

I'm almost certain its got something to do with the amino acid in the P-loop that contacts the gamma phosphate, however without a reference I am not going to post it as an answer yet. I can ask my PI but then its more fun to find it out myself ;)

"more fun to find it out myself" - ~asks on Bio.SE~

Gamma thiophosphate-analogues of nucleotides were first synthesized in the 70s (Goody and Eckstein, J. Am. Chem. Soc., 1971) and have been used to decipher many intracellular pathways.
To understand why GTP-γ-S is not (or very slowly) hydrolysed by GTPases, we can look at the structure of a GTPase-GTP complex.
GTP binds to various sites on GTPases. This is the binding of GTP to Rap2A, as described in (Cherfils et al., EMBO J. 1997).

As you can see four different sites bind to the γ phosphate.
From the paper:

The interaction of Tyr32 with GTP suggests that its general conservation in small G proteins may have structural or functional advantages. Tyr32 is located three amino acids upstream of a threonine (Thr35 in Ras) which is extremely conserved in most G domains. The alpha subunits of heterotrimeric G proteins have a conserved arginine equivalent in sequence to Tyr32, which was shown from crystal structures to interact with the γ-phosphate of GTPγS

In particular, the position of Tyr32 is different, when Rap2A is crystallised with GTP-γ-S. This figure shows the position of the Tyr32 with GDP (A), GTP (B) and GTP-γ-S (C)

Crystals of Rap2A–GTPγS, whose structure we also report at 3Å resolution, are isomorphous to the Rap2A–GTP crystals. Both structures are essentially similar, except that Tyr32 no longer forms a hydrogen bond with the corresponding atom of the γ-thiophosphate, which is probably the sulfur atom. The Tyr32–γ-thiophosphate distance is 7.2 Å. The conformation of switch I and II and their interaction with the nucleotide are otherwise identical. Thus, the Tyr32–γ-phosphate hydrogen bond forms only in the presence of the true ligand, but is probably not essential for the triphosphate conformation of Rap2A nor for proper binding of the nucleotide. In particular, the position of Thr61 compares well between the GTP and GTPγS complexes.

The author conclude that:

Our study shows that the complex with the natural ligand GTP is similar to the complex with GTPγS, and thus justifies most conclusions obtained from previous structures of G proteins with GTP analogues. However, the structure of Rap2A with GTP reveals a novel interaction of Tyr32 with an oxygen of the γ-phosphate of GTP and with the amide group of Gly13. In the GTPγS complex, Tyr32 is shifted away from the corresponding atom. The Rap2A–GTP and Rap2A–GTPγS complexes are otherwise identical, and form isomorphous crystals. Thus, the interaction of Tyr32 with GTPγS is prevented solely by the presence of the gamma-sulfur, but the conformation of switch I and II is similar whether GTP or a GTP analogue is bound. GTPγS probably introduces a different charge distribution on the gamma-(thio)-phosphate and/or modifies the polarizability of the β–γ P–O bonds as compared with GTP


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What are the units of enzyme activity?
I was looking at this graph of turnip peroxidase activity and I saw that they use units of 1/sec for enzyme activity. What does this unit intuitively represent and how is it calculated?

The Wikipedia "Enzyme Assay" page looks pretty good.

This refers to the turnover number (a.k.a kcat or k2) of an enzyme and is usually calculated using Michaelis-Menten kinetics. Jump to the summary at the end if you want a simple answer. If you want a more thorough answer, consider the following chemical equation:

[E] + [S] ⇌ [ES] → [E] + [P]

This says that a certain concentration of enzyme mixed with a certain concentration of substrate will first combine and form a complex depending on the enzyme's affinity for the substrate. Then the enzyme complex will generate a product depending on the enzyme's ability to convert the transition state into product. The k1 constant is the arrow moving from [E] + [S] → [ES] and the k-1 is the arrow moving from [ES] → [E] + [S] (they oppose each other). The k2 constant is the arrow moving from [ES] → [E] + [P].

Vo = [ES]k2

Vo - this is the rate that product is being formed, which can be measured.
[ES] - this is the concentration of enzyme-substrate complexes.
k2 - this is a constant value comparing the two.

This can also be expressed in terms of maximum rate:

Vmax = [E]Tk2

Vmax - Vmax is catalytic rate when [E]T = [ES] (when all of the enzyme present is bound to substrate/saturated).
[E]T - [E]T is the total enzyme concentration. [E]T = [E] + [ES].
k2 - the kcat is the catalytic constant. It is a constant indicating how quickly an enzyme can convert substrates into products. It is easily observed by this equation.

Summary
So k2 is basically an indicator of how efficiently or quickly an enzyme operates. Not all enzymes follow standard Michaelis-Menten kinetics. For example, the allosteric properties of some enzymes cause a non-linear saturation curve. Because of this, the turnover number is commonly referred to. The turnover number's units of s-1 indicate one product molecule per second, so a turnover rate of 3000 means you can create 3000 products in 1 second at Vmax.


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Why isn't there any repulsive force between Na+ and K+ disrupting thier roles in transmembrane voltage/ action potentials
Pretty self explanatory question. I have a basic grasp on the "How" and "Why" of Reversal/Action Potential in and between neurons, but this question lingers.

I’m not sure the question is quite clear: the repulsive force of the ions is necessary for their role (otherwise you wouldn’t get an electrochemical gradient across the membrane).

The electrochemical gradients are estabished from movement and difference of each ion internal and external concentrations - K+intracell/K+extracell -, NOT between differing ions ie not between Na+ and K+.

Actually a fair point.

I agree with rwst's response below, and just wanted to add that it's not the individual ion species that matter, but the fact that there are several ions, each with ion channels of varying permeabilities. Both sides of the membrane are electrically neutral, but the chemical potentials differ due to the channels. More specifically, the resting membrane potential exists because of the higher permeability of the K+ channels.

The carriers of the charge are ions and they get repelled from each other well enough. Other than their charge there is only the size in which they differ (for all practical purposes). This means, as long as we are talking about membrane potential, the actors are just a mix of 1+ ions which don't come near each other. When size matters, for example in an ion channel, we are talking about single particles, so there is no action of a repulsive force between K+ and Na+.
From another angle: The charge is a force that emerges from a sea of particles, regardless if they are all of one kind or mixed K+/Na+. If you talk about a force between K+ and Na+ then you would have to separate all 10^15 or so K+ ions from 10^15 or so Na+ ions which is simply impossible, as they are mixed up.
http://en.wikipedia.org/wiki/Brownian_motion
http://en.wikipedia.org/wiki/Ion
http://en.wikipedia.org/wiki/Ion_channel

Ok, in other words.. the ions are too small and not uniformly purposed/moving to have such any such disruptive effect from hindering the AP process. Thanks for the insight, if I could trouble you for a source you surely would receive the BEST answer and this would be a resolved question.

This is elementary physics/chemistry. I don't need to show that atoms/molecules have no purpose, they undergo Brownian motion except when spatially hindered by a channel molecule. OK, I'll give suitable Wikipedia links.

Please forgive my elementary knowledge :) A good habit to source answers nonetheless, thanks!

Also remember that it is not Na+/K+ ions which go through the ion channels, but the solvated ions which are encased in a highly ordered water solvation sphere around them. The different sized sovlation spheres is what causes the difference in sizes for the ion channels. In a cell, negative ions would screen the positive charges from each other unless they were very close.


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Do mosquitoes need to pump blood out of the host?
Many species of mosquitoes have bloodsucking females.
When they bite a host, do they need to pump? Or does the sheer blood pressure combined with capillary action suffice to make the blood rush into the mosquito's stomach?
If the blood pressure is enough, can the mosquito "explode" or simply die from having too much blood rushing in?

Take a look at Ramasubramanian et al.[1] The authors have some great SEM images of the proboscis and fascicle tip and derive a mathematical model for the "bite" itself.
They mention that there are two types of feeding: pool feeding, where the mosquito creates a hemmorrhage and feeds slowly via capillary action, and capillary feeding, wherein the mosquito taps into a capillary and the feeding process is much faster, as the blood is driven under pressure.
Another source to check, one that the authors above cite, is by Kashin[2]. This only links to the abstract, however.  You'd have to hit the stacks to get the article, I'd imagine.

Edit
This source[3] indicates that:

"The blood is imbibed by action of the cibarial and pharyngeal pump muscles via the food canal formed by the labrum and hypopharynx. Blood then passes into the midgut."

For @Luke, and others:

All images are from Ramasubramanian et al.[1]

Ramasubramanian MK, Barham OM, Swaminathan V. 2008. Mechanics of a mosquito bite with applications to microneedle design. Bioinspiration & Biomimetics, 3: 046001, doi:10.1088/1748-3182/3/4/046001.
Kashin P. 1966. Electronic recording of the mosquito bite. Journal of Insect Physiology, 12(3): 281-286, doi:10.1016/0022-1910(66)90143-0.
Robert V, Brey PT. 1998. Biting physiology of Anopholes affecting Plasmodium transmission. Research and Reviews in Parasitology, 58 (3-4): 203-208.

Nice answer. Any chance you could include the SEM image for those you do not have access to that journal? Sounds worth seeing! Thanks

BTW, it appears that mosquitoes really can drink themselves to death, if you somehow prevent them from knowing they are full (e.g. by crushing their ventral nerve cord): https://entomologytoday.org/2020/03/19/when-a-mosquito-cant-stop-drinking-blood-the-result-isnt-pretty/


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What would need to be discovered to prove there is extraterrestrial life?
Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment. What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA (or its Martian equivalent)?

I think in a more literal rather than biological sense, life that did not originate on Earth

The definition of 'extraterrestrial' is trivial (unless you subscribe to the 'flat earth' theory, or some such nonsense).  The real question here can be boiled down to 'what is life?' - a somewhat tougher question with no clear answer.

Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment.

But not, incidentally, equipment to detect life.

What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA …?

No. In fact, DNA would be lousy evidence of life on Mars, it would almost certainly be a contamination from Earth.
Lacking equipment, I’m not even sure how Curiosity would go about finding traces of DNA but assuming that it did (through some sort of chemical assay), it has no way of telling the origin of said DNA.
And even if the genetic material could be sequenced there are a number of scenarios. It could be very similar to what is found in extremophiles on Earth, in which case we wouldn’t necessarily know the origin (but due to the aforementioned contamination risk, the prior probability of it being Earth life would be very high). If it were completely different, that might be compelling enough to consider it extraterrestrial.
But maybe not: estimates for the number of existing species on Earth vary drastically. One thing is certain, though: we’ve only scratched the surface of prokaryotic life in particular. So if we find something new, that wouldn’t even be very surprising.
More interesting would be an alternative genetic material, neither DNA nor RNA. So far, we haven’t discovered anything like this on Earth (despite earlier hopes) so it would be more likely of extraterrestrial origin. But again, as the refuted study shows, we cannot entirely exclude the possibility of such life being found on Earth either.
All this is just to show that proving microbial life to be extraterrestrial is quite hard. It would be much easier if we were to find non-microbial life on Mars (i.e. something multicellular). However, I don’t know of any serious scientist who seriously entertains this possibility.
But the reason to prefer such a discovery is simple: the bigger the life form, the less likely that we haven’t found it yet on Earth, and the smaller its viable niche. So if we find multicellular life adapted to the surface of Mars there aren’t many places on Earth where it could have originated from, never mind the low chance of having survived the ride aboard the probe.

Answer to your title:
ex•tra•ter•res•tri•al [ek-struh-tuh-res-tree-uhl]
adjective

outside, or originating outside, the limits of the earth

Answer to your post:
There is a whole field of study revolving around these questions called astrobiology. It is assumed that extraterrestrial life forms will have some sort of information storage similar to DNA but that it will probably not be identical. Accessible water is considered the most important indicator for the potentiality of life. Oxygen or some kind of reducing element is also considered to be very important.

In the simplest sense, extraterrestrial life is life found beyond the Earth. Defining what life itself is notoriously difficult - perhaps the best is a system which is subject to Darwinian evolution?
However, the term "extraterrestrial life" does not necessarily imply that said life (if found) originated in situ. For example, if we do find (presumably microbial) life on Mars, I would not be completely surprised if it had a DNA/RNA (or PNA or similar) information system.
The amount of material exchange (due primarily to asteroid impacts) between the Earth and Mars is large - significant quantities of Martian rocks have been found on Earth, and the reverse is presumably also true. Earth's higher escape velocity would reduce the amount of material ejected from the surface, but Mars' thinner atmosphere would facilitate the successful "landing" of any ejected rock without being burned up on re-entry beforehand.
So, Mars may have been seeded by Earth life traveling on rocks ejected by impacts. Whether this life could adapt to extreme cold, saline regolith, ionising radiation, dessication etc. is another matter although extremophiles on Earth are seen to (individually) have some of these qualities (psychrophiles, halophiles, "radiophiles", etc. Deinococcus radiodurans actually does quite well in all these areas.
Alternatively, Earth life may  have been seeded by Mars rocks traveling the other way. If Mars was warm and wet in the past as some advocate, this idea may not be so crazy.
Look for "panspermia" and "lithopanspermia" for more information.


text:
Could silicon oil block Na+ ion channels in the membrane of an axon and prevent Na+ influx?
Could silicon oil block Na+ ion channels in the membrane of an axon and prevent Na+ influx?
I have been wondering if Na+ influx could have been a diluting factor in anterograde fills.  If so, could coating the axon with silicon oil prevent this?

Why not directly using a Na+ channel blocker then?

No, silicon oil couldn't block an ion channel. Oil is a nonpolar substance, just like the membrane lipids, so if you can get your oil to that cell, it will mix with the lipids within the membrane. The ion channel, which sits in the membrane, too, is rather closed to the membrane interior and opens to the inside and outside of the cell which, contrarily, is a polar solution of soluble molecules in water. So, to block one of the openings you better have a polar molecule that is water-soluble.
http://en.wikipedia.org/wiki/Ion_channel
http://en.wikipedia.org/wiki/Polarity_%28chemistry%29

Ah, I think I see thank you. I wanted to figure out a less toxic way of blocking the Na+ pumps than say... TTX.

Things behave unexpectedly when you're at molecular size. Unfortunately, there are precious few videos with animations that could give a feel for it. Now, there is the next question.


text:
Do dogs have something different about their physiology that allows them to pant without hyperventilating?
I was wondering this as I considered how effective panting would be for humans as a means of cooling.

This article quotes a professor of respiratory physiology that says "dogs are built to pant just right. The mechanics of their lungs and chest set a precise rate for panting that minimizes the amount of work while maximizing cooling power." They also don't breathe fully when panting, so they can still cool themselves without increasing gas exchange. This is different than humans, who will hyperventilate to get rid of carbon dioxide (or you can intentionally hyperventilate and cause respiratory alkalosis).

What about panting with breaths that are only slightly more than the amount of dead space?

Not knowing the physiology or the literature, I can say based on personal observations that dogs, even when extremely hot or exhausted, mix in a routine of deep inhales and exhales to their panting.  Perhaps this prevents unwanted side effects of their cooling mechanisms.

Our physiology is quite different. I guess their larger surface-area tongue is one obvious difference, and the fact that they have limited sweat glands. I actually thought they had none, but this article states that they have them on their feet.
Another fun fact there is that they don't just use panting -- they can apparently  constrict/dilate vessels in their face and ears..


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Why do cockroaches flip over when they die?
This question has always mystified me since young. For beetles, I can reason that they flip over because they have a higher centre of gravity causing them to be in unstable equilibrium when they tuck in their legs when they are about to die. For cockroaches with a lower profile, I would expect them to stay upright. But why do they flip over? Is it more comfortable for them to die this way or is there a scientific explanation for this?

Edit:
As noted in some of the comments below, this is a general observation based on cockroaches being killed by insecticide. I haven't got the chance to observe (or notice) cockroaches that die in other ways and therefore do not want to limit the scope of my question to just insecticide poisoning.

Do they flip over? I’ve always considered that to be just a comic representation. Maybe it’s just easier to spot dead cockroaches which have flipped over, since the others aren’t easily distinguishable from live ones? …

@KonradRudolph, image for your reference.

That's a picture of some cockroaches on their backs. There's no way for the viewer to know whether they died that way, or (as it seems) were arranged that way.

@RichardSmith: I am pretty positive that when you put some roach poison you will then find them on their back.

I agree, I was just pointing out the the picture doesn't demonstrate anything. The reason, if I remember rightly, is that most cockroach control agents are neurotoxins which cause the legs to spasm, so they get flipped onto their backs.

Yesterday I found ~200 dead chinese stink bugs on my hallway carpet(I assume they crowded the light and someone sprayed them with insecticide) and spent some time cleaning that up, having an opportunity to observe A LOT of dead bugs. A lot of them were indeed on their backs, which puzzled me. It might be of interest to clarify your question with the cause of death. Is it natural death of "old age" or due to poison bait /insecticides?

@AlexStone, please refer to my clarification under "Edit". I am not fortunate enough to observe cockroaches dying a natural death. If someone has made that observation to prove or disprove, feel free to answer below :)

Flying insects land on their back when they fall since it's heavier. Stands to reason whether that applies to cockroaches.

It is a result from the insecticide you are using.  From this excerpt from the 10th Edition of the Mallis Handbook on Pest Control:

Neurotoxic insecticides cause tremors and muscle spasms, flipping the cockroach on its back. A healthy cockroach can easily right itself, but without muscle coordination, the cockroach dies on its back. Cockroaches exposed to slow-acting insecticides that target respiration (energy production) also can die “face-down,” as they run out of energy without experiencing muscle spasms.

Here's also a website from UMass describing it in more detail:

Most of these insecticides are organophosphate nerve poisons.  The nerve poison often inhibits cholinesterase, an enzyme that breaks down acetyl choline (ACh), a neurotransmitter.  With extra ACh in the nervous system, the cockroach has muscular spasms which often result in the cockroach flipping on its back.  Without muscular coordination the cockroach cannot right itself and eventually dies in its upside down-position.

And an entomology professor even answered this for Maxim:

Most insecticides are poisons that target a bug’s nervous system. When you spray a roach, those neurotoxins cause tremors and muscle spasms, which flip
  it onto its back, and without muscle coordination, that’s the position it dies in

Thanks. This answer is really useful. I guess the rapid leg kicking caused by muscular spasms is powerful enough to lift the cockroach on one side and flip it over.


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What would cause proteins to get stuck in the stacking layer of a SDS-Page gel
Typically when proteins aggregate, they will get stuck at the top of the well. However, we're seeing some protein aggregate in the stacking layer even when we're treating the loading volume with DTT.
One peculiar attribute of this experiment is that we're trying to carry out a Cu(I) catalyzed Azide-Alkyne Click rxn. Without the Cu(I), the proteins run normally. However, after Click rxn, we do see some of our expected clicked product, one of our proteins is disappearing into the top band. Hypothesis is that either the copper(I) is changing the migration or oxidative damage from the Cu(I)-> Cu(II) transition is altering the protein.
Returning to the original question, what would cause a protein to stop at the stacking layer vs. at the combs?
[edit]
According to my labmate who was having this problem, the protein was crosslinking with itself to create fairly sizeable polymers. We also saw ladders of the protein with ascending size. Spinning the clicked reaction removed the issue but also resulted at a lost of the protein. It sounds like he wasn't treating with a sufficient amount of DTT to break up the mixture.
This unfortunately still doesn't differentiate between proteins stuck at the combs vs stuck at the stacking layer.

@TomD, we're using pre-casted bis-tris 10% gels. It seems to be stuck at that border.

Sounds like the copper cross linking the protein or creating aggregates that the SDS  buffer can't break up.  add EDTA to your loading buffer before you cook it?

At the interface of the stack gel and resolving gel is a pH change and a change in gel density.  If you feel certain that your protein is not crosslinking so much that it can not enter the gel than I would think about the pH of the sample and the effect of Cu ions on the stacking effect of the stacingk gel.  Is your sample the normal blue color (indication of pH) when you load it (compared to other samples you load)?  Are you overloading the gel?  I have seen overloading cause the effect you describe because the proteins get concentrated to a very high degree before entering the resolving gel.  Could the Cu ions be affecting stacking itself?
Read http://en.wikipedia.org/wiki/SDS-PAGE.  Specifically the section on buffer systems.  You might want to try a different buffer system.
Finally, you could try an acetone precipitation to try to remove the Cu ions and other chemical and see if that helps.

Most of the other proteins are running through the gel as normal. The non-Cu lanes doesn't exhibit this technical issue. Alternatively, I can try prerunning the gel to get a consistent pH environment.


text:
Predators faking to be not hungry?
I believe that there are predator/prey combinations where the prey can easily spot that the predator is not hungry and will not try to flee from it. I’m thinking, for example, of gazelles who will happily graze in sight of sleeping lions. (Please correct me if this is already wrong.)
It seems to be sensible (in an evolutionary sense) for the predator to not put unnecessary stress on the prey. First question: Are there predator who actively signal that they are not hungry, e.g. by a certain sound?
And my second question: Is there such a combination where the predator will, in times of severe hunger, pretend not to be hungry in order to more easily catch a prey?

It seems to be sensible (in an evolutionary sense) for the predator to not put unnecessary stress on the prey. What leads you to believe that?  I don't know one way or the other, but what is the evidence in that direction?

I suppose that the reason why gazelles could graze in sight of sleeping lions is because the prey are aware of the predator's presence. That's why gazelles do not came close enough to be catched. Also lions quickly learn that there is no point to chase a prey if it already notice the threat. I'll make it an answer when I find adequate references.

@jonsca: Naive thinking maybe, but isn't it in the interest of the predator that the prey population thrives?

I would suggest that the behaviour of the gazelles you are citing is perhaps over simplified. There will likely be temporal and spatial dynamics in their behaviour... Prey will probably spend more time concentrating on observation when they know there are predators around. There will also be likely peak times during which hunting occurs (in savannah systems it tends to be dawn and dusk) and prey would be more cautious at these times.
It seems to me that the prey would not be judging the hunger of the predators but instead they learn the consistent patterns in the level of risk associated with being near predators. This could be genetic in its cause. If there is a gene (or genes) which determine when a prey individual is most likely to be out in the open grazing then the higher probability of predation at certain times would reduce the frequency of the genes which cause that choice.
There could also be fluctuations over time as the predators learn that the prey have become less cautious, which then causes predators to take advantage of unsuspecting prey, which you might be interpreting as the "faking" behaviour... it is not a deliberate fake, more taking advantage of the risk taking behaviour of the prey (as time passes without attack they will become more brazen). To the best of my knowledge there are no examples of the deliberate fake but predator prey dynamics are not my specialism.
Overall, I think you are asking a question based on learning and information use of repetitive patterns in behaviour of predators by prey, and have interpreted these behaviours in an over complex way (see Occams Razor).


text:
Determining if a Protein Model Contains a Backbone Clash
I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be accepted for publication.
What is the best (reproducible) method to determine if a particular protein model contains a backbone clash?

The way to check for steric clashing between any two atoms, backbone or otherwise, is to compute their Euclidean distance. If a and b represent two atoms (with a_x being the X coordinate of atom a and so forth), you can calculate their Euclidean distance as follows.

d(a, b) = sqrt( (a_x - b_x)^2 + (a_y - b_y)^2 + (a_z - b_z)^2) )

So essentially the idea would be to calculate the pairwise distance between each of the backbone atoms. For any pair of atoms, there is steric clashing if the distance between them falls below a certain threshold. If I remember correctly, this threshold is the sum of the van der Waals radii of the two atoms.

I am assuming that the variables a and b represent atomic radii of the two respective atoms. So a_x is the atomic radii of a * the x co-ordinate? Wont this equation return an error if I try to square root a -ve number? To determine a steric clash I add the radii of atoms a and b and if this value is greater than the value from the equation I have a clash?

Yes, a and b are 3-dimensional vectors each containing the X, Y, and Z coordinates of the two atoms. However, the value inside the sqrt() will always be non-negative since each of the three differences is squared, so getting an undefined value shouldn't be a problem. I have updated the answer.


text:
Are there verbs for "undergo mitosis" and "undergo meiosis"?
From my experience on SE sites, I believe this is the right site to ask this question under "terminology".
I've been trying to find out whether English has one-word verbs for "undergo mitosis" and "undergo meiosis". I haven't been able to find confirmation on Google, but my linguistic imagination is limited, and I may have failed to google the right things.
Could you tell me if there are such verbs in common use in biology? I mean, if such verbs exist, can I find them in modern biology books or papers?

How about "divide" or even "multiply" (if you include the entire cell cycle)? Those are generic terms, but the process is called cell division. And minor pet peeve of mine: "Google" isn't a verb...

What's wrong with "to undergo mitosis"?

@nico Nothing is wrong with that. I just wanted to know if there's a shorter way of saying this.

I'm voting to close this question as off-topic because it is about linguistics rather than biology. There is no real problem. If you are writing a paper you would write "undergoes mitosis".

I'm actually not sure myself. If I were to use something, I would go with "Mitos'd" and "Meios'd".
However, you may not win over many fans, depending on the audience. If it's with students or maybe a professor, you could get away with shortening the processes. If it's in any formal setting, be as precise and descriptive as possible. It's not a lot of trouble to be more accurate and add "underwent" to the sentence.

I agree - I do not recall seeing a verb for these actions, so in a paper or report use the actual terminology. But during discussions I'm sure people will get your meaning if you shorten the terms to "mitose" or "mitosed", or something.

Mitosis as a process does not have a verb form. However, as a process, there is an adjective; you could describe cells that undergo mitosis as mitotic.

Wiktionary suggests mitose: https://en.wiktionary.org/wiki/mitose.

The question asks “In common use in biology”, specifying books and papers. Wiktionary does not address that.

Was just researching your exact same question.  Self-replicate is the closest I could find or think of... but it's a very general verb, not even biology specific.
e.g. Please don't self-replicate, I'm already having trouble with just one of you -- said the programmer to his memory gobbling AI program.
https://en.wikipedia.org/wiki/Self-replication

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text:
E. coli values for [enzymes], [metabolites] and kinetic rates
In my attempt to create a metabolic model of E. coli, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is E. coli model iJO1366 (more here). What I have not yet found is a comprehensive list of kinetic rate constants associated with these reactions. I also require a data source of concentrations of these enzymes and metabolites at steady state in E. coli. Where can I find information on concentrations and rate constants?

why do you want to compile this?  Flux analysis is looking pretty useful and does not require all this data.

I found SABIO: http://sabio.h-its.org/

I would advise you to use the SMBL for iAF1260 E. Coli with a COBRA toolbox on MATLAB. It has all the constants you are looking for optimized for the steady state and have been extensively tested for simulation of single and multiple genes deletion / mutation. Even if you want to stick with your model you will be able to copy the constants from there.
However depending on what you are doing you might not be satisfied by the whole models, since the they are computationally too complicated to simulate and optimize and lead to computationally unstable results, especially when you try to simulate colony collaborative mechanisms.

Do you have any literature to support your claim of computational instability?

This is my personal experience. When you use the COBRA toolbox, you use an external module for linear optimization to get your "objective" function. When I computed the base model from iAF1260 E.Coli, it worked well, just as a system of two bacteria living together. But as soon as you started to perform single or double gene deletion analysis, your objective function maximum started to behave erratically. You could make it bit better with it by using a different external linear optimization module, but still no analysis was possible.

This work was based on this paper and I had an impression that the authors run into pretty much the same limitations: only qualitative analysis is provided with the computational model, whereas they could have gone quantitative with this model and had quantitative experimental results.


text:
Is it possible for a parasitic wasp to alter the behaviour of its host after emerging from it?
I know that parasitic wasp larvae can live for a long time inside their live host (eg. caterpillar), but I always thought that they kill the host when they eventually get out of it. But I've seen a film, where it's shown that not only can a caterpillar survive the emergence of a wasp larva, but also the parasites infect the host with some kind of virus that changes the behaviour of the caterpillar to protect the wasp’s pupa. Is it possible and common among parasitic wasps? What species of wasps and viruses cause such effect?

Are you asking about parasites (i.e not lethal to host) or parasitoids (i.e. host killing) insects? In the question, the distinction seems to be muddled.

Another example is the wasp species Dinocampus coccinellae, which lays its eggs inside certain species of ladybug/ladybird - most notably the "twelve-spotted lady beetle" (Coleomegilla maculata). It also infects the "seven spot" ladybird.
(I'll stick with "ladybird" instead of "ladybug" for the remainder of this post.)
This is actually very similar to the Glyptapanteles example in the most-upvoted answer so far. (Though I would like to point out that OP's video in fact does not in fact show Glyptapanteles, but the extremely similar Cotesia glomerata.) In this case, though, only one egg is laid inside the host, and the wasp larva is nothing like as small relative to its host as the Cotesia and Glyptapanteles larvae were.
The wasp larva, after emerging from its ladybird host, spins a cocoon underneath the ladybird, between its legs, and pupates. Unlike Cotesia, this wasp larva needs to use its own silk and spin its own cocoon. The hard-shelled ladybird is trapped on top of the wasp pupa, rather like an armoured shelter. While mostly immobile, if potential predators/hyperparasites come close, the ladybird will thrash out at them with its limbs. I'm not sure if this is to attack them directly, or to deter them from coming close, or both.
Since no other larvae are left behind in the host, Dinocampus coccinellae must be using some other means to influence its behaviour after emergence. A virus, the "D. coccinellae paralysis virus", is injected by the adult wasp at the time the egg is oviposited. As well as suppressing the ladybird's immune system, it infects the ladybird's brain and may explain one or both of:

The ladybird's general immobility after the larva emerges
The ladybird's thrashing out at potential predators that may attack the larva.

The virus replicates rapidly but for unknown reasons doesn't spread to the beetle's brain until just before the larva emerges from her belly. At first the virus seems to build up harmlessly in brain cells, but as soon as the larva breaks out, these cells burst open, unleashing destruction all around them.
The researchers suggest that the beetle's own immune system may be responsible for this damage. They discovered that crucial immune genes are suppressed while the larva lives within the ladybug, but then reactivate after the larva emerges. The researchers speculate that the beetle's revived immune system discovers and attacks DCPV-infected cells. The self-inflicted brain damage could temporarily paralyze the beetle just when the newly vulnerable wasp larva needs protection.

Also:

DcPV is stored in the oviduct of parasitoid females, replicates in parasitoid larvae and is transmitted to the host during larval development.

If I understand correctly, this virus is not one of the so-called "polydnaviruses" injected by other species of parasitic wasp.
For some reason, the wasp prefers to parasitize female ladybird hosts, although I think it will still use male hosts in a minority of cases.
Sources:

Dheilly Nolwenn M. et al. (2015). Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation. Proc. R. Soc. B vol 282 issue 1803:
http://doi.org/10.1098/rspb.2014.2773
Maure F et al. (2011). The cost of a bodyguard. Biology Letters volume 7 issue 6: http://doi.org/10.1098/rsbl.2011.0415
Davis D.S., Stewart S.L., Manica A. and Majerus M.E.N. (2006). Adaptive preferential selection of female coccinellid hosts by the parasitoid wasp Dinocampus coccinellae (Hymenoptera: Braconidae). Eur. J. Entomol., 103(1), 41-45. doi: 10.14411/eje.2006.006.

See also:

https://www.naturespot.org.uk/species/dinocampus-coccinellae
https://www.discovermagazine.com/planet-earth/biological-warfare-parasitic-wasp-uses-a-virus-to-control-its-host
https://www.sciencemag.org/news/2015/02/wasp-virus-turns-ladybugs-zombie-babysitters

Great job (+1). (I have the same suggestions for improvement that I made on your other answer and did a little tidying up of the formatting for your sources.)

The species of wasp in the video you link to is Cotesia glomerata. Furthermore, there is at least one other species, Glyptapanteles, which parasitizes other caterpillar species in the same way and induces the same behaviour in its host.
I'm not sure which virus it is.
http://www.newscientist.com/article/dn14053-zombie-caterpillars-controlled-by-voodoo-wasps.html?feedId=online-news_rss20
Is it possible? Of course, you have an example! Though, there is a small caveat. Some of the offspring sacrifice themselves to induce the behavioral change after the rest of the brood has emerged.
Is it common among parasitic wasps? No. While injecting offspring into host species is a common theme for parasitic wasps, and while there are a handful which somehow induce behavioral changes in the host animals - continuing the manipulation after leaving the host animal is extremely rare among parasites in general.

Thanks! It's even more fascinating, because of altruistic motive (unless polyembryony was common among Glyptapanteles so that all larvae in one host will be genetically the same). I ask if such change in behaviour is possible, because I don't completely trust the information in popular science sources. I would accept your answer, but first I'd like to wait, maybe someone will find anything about that mysterious virus.

In the study by Whitfield 1990 (1) I found the information that the parasitic wasp from family Ichneumonidae have interesting symbiotic viruses called polydnaviruses. This virus stay as provirus in the wasps genome and is transmitted vertically between subsequent generations of parasitoid. It does not harm the wasp and it is transmitted to the wasps hosts (usually caterpillar). The virus does not replicate in the caterpillar, but alter it's physiology: supress immune response and metamorphosis and increases the amount of nutrients in caterpillars hemolymph.
Still, I have not found any references about this kind of virus altering the behaviour of the caterpillar after the emergence of wasps larvae.
[1] Whitfield, J. B. (1990). Parasitoids, Polydnaviruses and Endosymbiosis. Parasitology Today, 6(12), 381-384. (free PDF)

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


text:
Under what circumstances will a human neuron divide?
I read somewhere that a mature neuron loses its ability to divide, except for very specific situations. I was unable to find the description of those situations. What are they?
(I'm sorry I'm not saying where I read that, but I simply can't find it.)

I was under the impression that neurons do not divide - will have a look around later, but will be interested to see other answers too!

Mature, differentiated neurons do not divide (undergo mitosis), but apparently there is a small population of self-renewing neural stem cells in adults that can produce new neurons. Neurogenesis predominantly occurs in the subventricular and subgranular zones of the brain.
Peripheral nerves can regenerate along its axon as long as the endoneurial tube and the Schwann cells are intact. Here's a picture of a neuron regenerating.

As was pointed out by @jello differentiated neurons do not divide, instead new neurons are recruited into existing networks from undifferentiated cells. This process is called neurogenesis. A high level summary of adult neurogenesis:

Neural progenitor cells differentiate into new neurons that have zero (or very few) synaptic connections, but are sensitive to the local chemistry.
(Optional) Sometimes (such as in adult neurogenesis in the olfactory bulb) these immature neurons-to-be are produced far away from where they are needed and follow standard pathways to migrate to the correct brain region
The immature neuron extends dendrites towards upstream neurons and starts to develop an axon
The immature neuron extends axon towards downstream neurons, and
The neuron matures and becomes indistinguishable from the network it joined.

For more information, consider the question: How are newly created neurons recruited into existing networks?