CharonY

Technically you cannot get the correct molecular weight by using markers (at least not electrophoretically). The reason is that the electrophoresis separates by size, however the different bases possess different MWs and such at best you can only estimate the MW based on the DNA size. So my question is, do you really want to know the molecular weight, or the length of the DNA? Of course, both correlate, but the measurement of either may differ.

Actually the cut-off of silica columns can be tweaked. Regarding the microchips, what is emphasized just means that the material itself is hydrophilic. All microchip based DNA separation require a hydrophilic surface. This can be a property of the material, or you have to treat the surface (e.g. with oxygen plasma). In any case again, you require something in the channels (e.g. linear acrylamide, a sieving matrix, whatever) to allow for size separation. In other words, you employ similar techniques (with few exceptions as dielectrophoresis) in microchips as in conventional DNA electrophoresis. Advantages are mostly speed and sample consumption.

Ah, I am not a grad student anymore, however at least a part of what you describe is found quite often (at least according to own experience, as well as from mentoring grad students) . Maybe I should add that I am talking as a postdoc working so far in three different institutes (University as well as research institutes) in two different countries (Germany and USA). Just to put it a little bit into perspective on what I am writing here. First of all you are concerned what the PI thinks about you and the lack of communication between you two. The more serious part is lack of communication, however you are also overly concerned regarding your performance (in his eyes). I do not have details, so I cannot easily evaluate it, however in many, if not most groups the contact between PIs and grad students can be rather sporadic. That is, unfortunately, not unusual. However, you must be aware that you are building your own career. Your PI does not have to be a mentor (in fact, these cases are rather rare). If you cannot find any labmates, you will have to teach the stuff yourself or look in another groups for help. During my undergrad and grad times for "administrative" reasons I essentially had the lab for me alone and wrote my own grant proposals. It is slower than simply to do as you are told, but you learn a lot this way. Either way, do not be too concerned what the PI thinks about you, you are not in a popularity contest. You do have to get a grasp on your project, or draft a poject that better suits you, that is still within the scope of what the group does and which can be published. Publication being the main point here. Hardly any PI would deny you working on something publishable. If you think that you are not up to this and need more mentoring you can look for another PI. This again has its risk. People that jump ship are sometimes regarded with caution. Also you may run into precisely the same problems. So if you do change, check the group carefully and talk the both, the potential new PI, as well as your potential labmates. Be aware though, in many groups you will have to claw your way through your phd anyway. In my opinion the best way is to read the papers in the respective field, draft out a proposal that will allow you to publish (in most computational disciplines one should roughly aim for three publications or more during the phd, though there are differences in sub-discipines). Then talk to you PI and try to see how appreciative he is. If he wants to control every aspects of your work, but does not give any suggestions, then it is probably better to leave. If he lets you do the proposed stuff, then you got a chance. If he denies it, but gives a good counter-proposal, think about it. Edit: noticed a lot of typos, but cannot correct them all atm. sorry.

Actually this is not limited to microbiology. In botany cultivars are often used. I am not aware of a similar typification in animals, which makes sense as they were not categorized as excessively as crops or diseases.... Subspecies are sometimes but rarely used in microbiology (afaik, but then I am not a microbiologist). Mostly "strain" is used to designate certain lines. The same goes for (lab-) animals. These are, however, usually clonal lines.

Sorry, this does not make it really clear to me. Size separation are usually done in a matrix of whatever kind to exploit the morphological or weight differences (as DNA of different sizes do not differ in their overall chemical properties). Another method is for instance to exploit dielectric properties of DNA. While it does not require a matrix per se, one has to create areas of different electric potentials. Using e.g. silica columns only allows a very rough separation, that is, everything below a certain cut-off will not be retained within the filter. All of this can be done in an aqueous solution (though a certain amount of ions are needed), without an actual agarose gel.

No argument from me here. I tried to make clear that the call for a revision (however it is called) is not from a single source (like evo-devo) but from a variety of disciplines. Moreover it is less the need to integrate new findings, but to discard some obsolete one, which is more important in my opinion. Of course due to the fragmentation of biology proposals will always have a big influence from the discipline of the respective proponent. Just to get it correct, you mean you fear that there is a "selection-centric" view on evolution? Again, no argument from me here. Integration of molecular data is often rather complicated to translate into population genetics as some features were driven towards persistence within an organisms without actually benefiting the organism as whole, but yes I do agree to this point, too.

Also the density is dependent on the concentration of HCl 1.18 g/ml is at around 37%, around 32% it drops to roughly 1.15 g/ml

So it sounds to me that in Harvard alcohol is cheap and abundant?

Well, actually those classification are taxonomically meaningless, but are used as an ad hoc distinction in a variety of fields, usually focussing on one particular diagnostic or physiolgocal aspect like serovars, pathovars, biovars, etc. They often lose their significance outside the respective fields.

Let us put it into the right context. The only reason why lack of colon bacteria is lethal is due to the fact that harmful bacteria can reside there easily, killing off the organism. This can be even simply a bacterium from another part of the body. However, it will never happen within two hours. Period. A sterile organism in a sterile environment lives (with adjustments of the diet). Oh, I forgot to add, you get inoculated with bacteria while being in the womb.

Actually I would not be disturbed by "simultaneously " either. And Y or V is a pretty dumb distinction. If you monitor it you either see blobs (microscopy) a three-dimensional mess (crystallization, AFM). Hardly except for idealized drawings will you see anything precisely like a Y or V. I would possibly give extra points for mentioning that.

Which build did you download?

Separation according to size or from other molecules?

I have moved this thread to the evolution area. To PhDP, there have been added syntheses since the forties, however some of the basic tenets simply have to be revised, which I think is at least one of the reasons to call for a new nomenclature

Hardly so. Most thermophilic bacteria also require a rather high pressure for stabilization. Also there is quite a large physiological jump between the aerobic bacteria you will find and (anaerobic) thermophilic ones. In other words, the temp changes are too fast, and there is not enough pressure to prevent the the water from boiling. What one can do, however, is to select for heat resistant strains. That is, having some rich media and keep it at 40-50° maybe.

It is virtually impossible to simply sterilize the gut just by intake of antibiotics. In the worst case you would just select for resistant strains. Also you cannot take in a high enough concentration to kill all bacteria and still survive (as ABs are also quite toxic to begin with). In general, residual bacteria are of concern for intestine transplants, for instance. Stable sterile models are usually only established e.g. in mice. However, I recall a rather recent report in which a colon was sterilized and the de novo colonization by bacteria was monitored. I just cannot bloody recall the authors...

Psst, thymine is methylated uracil. The T-arm requires to be highly conserved as it is one of the anchor form to maintain the shape of the tRNA. The modification (in this case methylation) ensure a higher stability. Also, the thymine is not directly involved in the codon pairing, so it does not have a direct effect on the translation per se, but rather has structural functions.

How about genomics and postgenomics (e.g. proteomics, metabolomics or any other omics that might eventually pop up). Biophysics is normally in the firm hand of physicists. Well not in our case cause we barged in and demanded to be heard but still....

Actually I do like the idea. Main problem is that the guy formulating it of course thinks that his/her theory would be the end of all others

One with a lot of function is the Staden package (probably more than you need). I think there is a built for Mac around now (OSX that is).

Wait a tick. What precisely are you doing with them? Seqman is normally used for sequence assemblies. So do you sequence your putative mutated area and use Seqman to assemble it? Or do you actually need a sequence alignment programm? Or in other words, what parts of Seqman do you really need? Sequence editors are around aplenty. I have to check whether there are Mac compatibles, though (I normally run them on a solaris or linux system)

In that case the documentary is clearly faulty. Especially because it has both been shown in humans and mice not to be the case.

AFAIK the indy gene was primarily analysed as a potentially life expanding gene in Drosophila (which has been challenged recently). Given the fact that the transporter itself has been identified not so long ago, I doubt that there are very deep analyses regarding the regulation yet. Much less specific tissue-dependent regulatory networks.

I think there was similar thread somewhere already, but anyway. I would like to discuss it in some more depth when I got more time (maybe around next wee or so). But I would like to state that it is clear that the modern synthesis clearly needs an update. This has been apparent at least the last decade or so. The modern synthesis has never been as concise as, say, the darwinistic theory, simply due to the problem of summarizing all the available, very different type of data into one single theoretical work. As such the modern synthesis grew over time, without a real complete update. In my opinion the real need for a new theory is not the fact that new data is available, as these can be integrated rather easily, but rather because some of basic assumptions of the modern synthesis are now generally regarded as wrong. These include: -that genomes are well ordered libraries of genes (partially true for prokaryotes, not that much for most eukaryotes) - genes have usually have single functions honed by natural selection -Species are finely adjusted to their ecological circumstances due to efficient adaptive adjustment of biochemical functions. (well due to the fact that species concepts are arbitrary, especially within the realm of prokaryotes this does not make any sense anymore) -The durable units of evolution are species, and within them the organisms, organs, cells, and molecules, which are characteristic of the species. (see above) -Given the adaptive nature of each organism and cell, their machinery can be modeled using principles of efficient design. (newer modeling approaches showed that this usually does not work for eukaryotes. Though sometimes it has limited uses in prokaryotes). In any case there has been a rather large discussion to what has to be added into a new synthesis and how it should be called. EES is by no means the only call for an update, though we could use the given paper as a basis and compare it to other similar papers. I do recall that someone here (sorry, forgot who) actually had a nice idea of starting to call it alpha, beta... synthesis.

You may have misunderstood my point. It was talking not about the modification of one or two bases, but those throughout the whole tRNA. You may want read up on Dalluge et al. 1997 (one of the few papers I remmeber on this subject). Journal of Bacteriology (so it should be long free by now). IIRC it dealt with the high abundance of pseudouridine in psychrophiles. However, giving that structural RNAs are single stranded molecules, it is not that much surprising that even single nucleotide modifcations can have profound effects on their local structure. For more info on this you should read up on models for RNA folding (papers from Michael Zuker's group might be a good starting point). More specifically, the modifications in the T-arm contribute to stabilizing the (L-shaped) tertiary structure of the tRNA. However, as always, things are a bit more complicated. As tRNA are the structural element of the genetic code modification not only are involved in maintaining a certain tertiary structure, but are also involved in the actual translation process, most notably in wobble pariring.