CharonY

So much for short. Anyway just to continue the thread: The easiest explanation for the discrepancy is that the majority of mutations are not beneficial. The earlier increase of fitness is possibly due to rapid adaptation to the new medium, but after that the continuing mutations will be (near) neutral. The initial beneficial burst would then be overshadowed by the continuing accumulation of neutral mutations. However the authors found several aspects that would contradict this scenario. First, if the majority were neutral mutations, one would expect a higher frequency of synonymous mutations (i.e. mutations that do not translate into a different amino acid). In fact, the authors found that all mutations in coding regions were in fact non-synonymous. Second, if the spread was due to random drift then one would expect different mutations in the different cultivations. However, in 11 independent cell lines a high proportion of similarities were found. Third, if drift was a major factor (as opposed to selection) then many occuring mutations are unlikely to be fixed in the population. However, mutations were found to be persisting through time (they froze sample throughout the generations to be able to track changes). And finally they generated strains artificially with the same mutations and found that at least8 loci actually did confer fintess advantages (and were therefore not neutral).

Actually I do not think that is what is meant. Beside the fact that such short primers are usually not very useful and that the ends will be different. Just from memory XhoI recognizes CTCGAG but generates sticky ends, i.e. 5'C TCGAG3' and 3' GAGCT C 5' respectively (as mentioned above). However, EcoR1 recognizes GAATTC and cuts between G and A (again sticky ends): 5'G AATTC3' and 3'CTAA G5'. The space indicate cuts. What you normally do is that you know the sequence beforehand, then you digest the DNA virtually using the above information and see what fragments are expected. In addition it yields a little bit of sequence information, but this is most of the time obsolete. If the fragments in question are cloned into a vector for sequencing purposes (using the double digest), then the primer will normally be generated based on the flanking sequences of the plasmid, rather than starting off with the restriction site. The reason is that longer primers ensure a higher fidelity of the product and the fact that polymerases work better with a certain minimum length (routinely 18-20 are used). In the end I do not really understand the question in the OP. It sounds to me that the purpose is a restriction analysis of a vector but why would primer be necessary? In order to sequence a whole vector, depending on its overall size it would be fragmented (which can be done with restriction enzymes) and subcloned into sequencing vectors. One can also do thinks (albeit with lower efficiency) like primer walking. But I do not really believe that that is what is meant.

Essentially yes. "Motifs", however are used in again a different context, so it may not be optimal to use this term to describe it. The secondary structure tends to refer to the structure of local segments. It can also describe the totality of said structures (e.g. proteins x has so and so many alpha helices) but it does not refer to the complete interaction within, or between polypeptides and proteins. Thus one would not normally use primary, secondary etc. structure to classify protein (e.g. protein x is a quarternary protein), as this does not really make sense, but one could state that the quarternary structure of collagen consists of three chains twisted into a helix. The secondary structure of collagen consists of a triple helix (ignoring the fact that several peptides are involved). An easier way to think of secondary structure is to refer to it as the spatial arrangement of the peptide backbone while disregarding side chain interactions. Normally a quarternary structure would be dependent on the side-chain interaction. The case for collagen is somewhat complicated due to the unusual triple helix which just does not require that (though they add to the stabilization of the fiber).

Well the formal definition of quarternary structure only refers to the interplay of polypeptides but does not include any necessary complexity. It is easier to see it if thinking hierarchically. The triple helix is a secondary structure. It is a local structure. The whole complex however, would be described as a quarternary structure. It does not matter that the whole protein complex is merely consisting of helices.

Proline is special due to two reasons, first it lacks an amide hydrogen therefore the backbone hydrogen bonds for the carbonyl groups at positions (i−3) and (i−4) is missing. Secondly the proline ring destabilizes the backbone by increasing the helix rise in one turn (to avoid the carbonyl group at position (i−4)). Both elements destabilize the alpha helix. This is actually important for certain functions, especially of transmembrane proteins.

It does not refers to stages of a protein but to the different complexities of its structure. Every proteins has a primary structure, which is the pure amino acid sequence. If the amino acids would not interact, that would be the end of it. But essentially due to hydrogen bonds they form up secondary structures like helices or beta sheets. A long protein can have many of those. The secondary structure essentially refers to these local conformations. But there are other forces, including ionic or hydrophobic interactions and disulfide bonds that can further determine the structure of the protein. This is then referred to as the tertiary structure. The proteins does not got through stages but these are just different levels of complexities to describe the protein. As the amino acids alone will normally interacti with each other, native proteins will all have a tertiary structure (and implicitly also a secondary and primary) unless you denature the protein (i.e. break up all interactions either) which causes the protein to lose its tertiary and secondary structure. The quarternary structure refers to protein complexes in which several proteins or polypeptides interact to form a superstructure. A single polypeptide can have any amount of helices. It only depends on the composition of it. Yes, it consists of serveral polypeptides interacting with each other.

The critical point is when it injects its saliva. That is when the transmission of bacteria or viruses occurs. Moreover, if you injure it or squeeze it during removal it may actually continue or secrete more, that is why it is recommended to remove it carefully. In addition to Lyme disease caused by Borrelia burgdorferi (which is quite an interesting bug for several reasons) they may also transmit a number of other bacteria and viruses that cause encephalopathies. That being said depending on region the ticks are more or less likely to transmit diseases. That is something you may want to look up. Also if there is no reddening of the bite, it is possible that he did not hit any blood vessels, further decreasing the likelihood of any infection. If you develop a rash or any other persistent symptoms you should seek medical attention and mention the tick bite. However they can take quite a while to develop. And finally,

This is off-topic, but why would you think so? Per definitionem most of us will be average (well, depending on the distribution, as well as the kind of average, given variance etc.). If everyone tries to be exceptional, well that would just shift the average, no? Reminds me a bit of something a student wrote on an evaluation (not mine): "This lecturer makes it really hard to get an average of A"...

The charge of DNA is primarily due to the phosphate groups in the sugar backbone. But first for the definitions. What does melting of DNA mean (or using your words, what should dissociate?). And what is the bond that holds it together?

I am not familiar with psychology databases (with the exception of those that are also present in pubmed). With regards to keywords it is usually helpful to look if there is a specific term describing what you need. As I am not familiar with the subject I would start with "feedback intervention" get a couple of reviews and try to work backwards from there.

In vertebrates it is TAP/NXF1. The homologue with the same function in yeast is Mex67p.

Some shops want to minimize the risk of selling alcohol to minors. Many (especially chains) therefore have implemented the rule that if the buyer looks younger than 35-40 (varies from shop to shop) the driver's license has to be shown. But of course other info including zip code are also often picked up. I have no idea at why you would assume that the government has a hand in it, as this info is mostly used for marketing purposes (or sold for the same reason). If the the government (e.g. police) wanted to know what you are buying they usually just get your credit card info (which probably is also somehow sold by the credit card company). In fact it is more likely that the private sector is toying around with your private information as they have more direct interest in it.

Just a short note: I messed up on a point The wait time is of course [math]\omega[/math]. That is what you get when posting in a rush. Geez.

First of all, most health related issues due to dampness are afaik more due to fungi (i.e. mold) rather than bacteria. Most that are pathogenic are not that competitive outside the body. Also the counts themselves are not helpful by itself if there is no quantitative reference to what is expected. That being said, starting with the bottom, Rhizobium is a root nodule bacterium that forms symbioses with legumes. It is absolutely harmless. Corynebacterium these are ubiquitous bacteria, often associated with soil samples, but also commonly found on the body. Most are harmless, but there are a few pathogenic strains. However the mere presence is usually not cause to alarm as they are expected to be there. Bacilllus same as with corynebacteria. Chances are that they are harmless. Staphylococcus are also found in soil and on your body. Most are harmless and are expected to be presence in a house. Micrococcus species are also found in skin and afaik there are no reports strains pathogenic for healthy humans. Kocuria kristinae (finally something on the species level) are also known to be part of the skin flora (they were initially classified as Micrococus and similar to those only cases where the immune system was already compromised infections were reported. Do not take this as a medical advice, as I am not qualified to give any, however the list of bacteria is not uncommon to be found in a house. Most of them are part of the normal skin flora and are the likely source. Also many are found in soil, which provides an additional way of getting them in. Unless the titers are unnaturally high they are not by themselves a matter of concern. It should also be noted that most of the pathogenic species are less competitive than their soil living counterparts so that if they are found on some surface it is more likely to have the non-pathogenic ones than the others.

Ok continuing the post: So keep in mind that the authors took a look at fitness increase and mutation rate (=genomic changes). One question is what the expected relationship between those two is. To summarize what I said in the earlier post the time until a beneficial mutation escapes extinction is [math]\omega[/math] [math]\approx[/math] 1/(2SN[math]\nu[/math]) And the time for the beneficial mutation to spread to 50% of the population (and assuming a Poisson distribution of offspring) is [math]\tau[/math] [math]\approx[/math] log2(0.5N)/S With S being the selection coefficient (high values indicate higher selective advantage), N being population size and [math]\nu[/math] the rate of beneficial mutations. The important bit is only to keep the relation of the parameters in mind. So assume the following scenarios: 1) no effect on the selective advantage or beneficial mutation rate due to substitutions of beneficial mutations. In this case both, the rate of genomic changes as well a increase in fitness should remain constant. 2) assume that the number of beneficial mutation sites is finite. The more beneficial mutations it already has, the less likely it is, to gain a new one. Hence [math]\nu[/math] declines over time. Thus, the wait time [math]\tau[/math] becomes longer and both, the fitness increase, as well as the genomic change rate will decelerate over time. 3) assume that the selective advantages decline as more beneficial mutations arise. I.e. the first mutations gives a large boost in selective advantages, but the second one only adds a little bit more to it, etc. With a decline of S both [math]\omega[/math] and [math]\tau[/math] increase. And the effect would be a deceleration of fitness increase and genomic change rate. Note that in all scenarios fitness increase as well as genomic change rates either decline or remain constant, without the need of changing the mechanisms that lead to mutation. In scenario 2, for instance the deceleration is merely due to the constraints on targets that may mutate (i.e. due to the limited beneficial sites). Now take a look at the abstract again. . Here they state that the fitness increase decelerated, whereas the genomic change rate was constant. This does not fit any of the simple models stated above. How do the authors explain this? Stay tuned for more after a short break.

Yeah nomenclature is quite a bit messed up with regards to amoeaba. Essentially it is a catch-all name for anything that does not appear to have a rigid structure. Naegleria for instance are (as pointed out) called amoeba, but they belong to a completely different phylum (Percolozoa, I think). But my knowledge is pretty dated and I may find myself wrong in a number of details.

Read up on gluconeogenesis.

Yes mutation rates vary, but adaptive mutation is not a point in the paper there was no selective pressure involved. In fact the increase in mutation rate is based on a frame shift mutation in the mutT gene. This gene is known to be involved in base transversions. Also it was only a minor element of the whole article and I am a bit surprised that SA highlighted it as much. The original article is this here, btw. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. Nature. 2009 Oct 18 In which Lenski and Kim are the corresponding authors. Take a look at the abstract: The authors investigated two elements. The rate of genomic changes (=observable mutations) as well as the relative fitness increase of the new strains compared to the original parent strain. What is important to keep in mind that even a mutation that gives a selective advantage may be lost due to stochastic events (drift). The larger the selective advantage the larger the chance that the mutation persists. Thus, in order for a mutation to spread through a population it first takes time for it to escape extinction. This time is inversely proportionate to the selective advantage it confers and the mutation rate with which this particular mutation occurs. And then the mutant spreads by selection. The required time for t to become the majority is again dependent on the selective advantage it confers. --------Just running out of time, if interest exists I will continue when I get a break sometime----------------------- Just btw. increasing mutation rate is for most multicellular organisms a bad idea. Think cancer. Asexually reproducing organisms can do it, as even if a lot of sister cells die, almost complete copies of their gene sets will survive (in those that adapt). This strategy obviously does not work with other organisms as well...

Could you point out the context in which they used it? I do not have the article with me right now. But it is likely that you are on the right track.

Weird, I could have sworn that we had a thread about it already, but I cannot find it. The key paper is this here, btw. Proc Natl Acad Sci U S A. 2008 June 10; 105(23): 7899–7906. Published online 2008 June 4. doi: 10.1073/pnas.0803151105. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli Zachary D. Blount, Christina Z. Borland, and Richard E. Lenski

Dictyostelium is a slime mold. It also belongs to the amoebozoa. The ones that are more commonly called amoeba (e.g. the Enatamoeba and Amoeba) belong to the Tubulinea, whereas slime molds belong to the Mycetozoa. The latter are the ones that form macrocysts, which represents a form of sexual reproduction (as indicated by GDG). I am pretty sure this has not been shown in the non-social amoeba.

You forgot the most important one. Personal protection. S. aureus are biosafety level 2. Before thinking of handling them get a formal training. At minimum a biosafety hood is required (certified for BSL2 and up, which most are). All work that may create aerosols (including pipetting) or involves handling of cultures in significant amounts have to be conducted under the hood. In addition appropriate personal protection gear has to be worn. Finally the details of cultivation depend on volume and type (e.g. batch cultures, plate cultures, etc.). There is quite an assortment of techniques that are regularly used. Depending on the hood, burners may be inappropriate, for instance (as they may interfere with the laminar stream and hence reduce the protection).

The transfer between pro- and eukaryotes often depends on type four secretion systems. The actual transfer is somewhat different between eu- and prokaryotes, though. The transfer of the ti-plasmid between bacteria, for instance relies on different mechanisms than the transfer to the plant host cell. As such I would assign different names to the underlying mechanisms. Though I think around 2000 there was a high-ranking paper that described the acquisition of plasmid DNA from bacteria by a hamster cell. I believe the author ( I cannot recall the name right now) also referred to this mechanism as conjugation, although the actual transfer was not observable. As I originally came from the prokaryotic side may definition may be a bit more stringent. It is an interesting topic, though and I would be happy if anyone would like to discuss anything in that regard

Conjugation relies on a specific machinery in either pro- or eukaryotes. They are unable to conjugate with each other. Horizontal gene transfer between the kingdoms is dependent on other mechanisms. However, is there anything specific that you want to understand or discuss?

It is cooling to 38° C here. Yey. Bleh.