CharonY

You can convert not too complicated formated pdfs to mobi with calibre, btw.

Well, reproducible RNA extraction is often somewhat tricky (hence all the normalization steps). I have not used cartilage, by my feel is that the reproducibility of initial lysis is the major factor here. The low cell to crap (i.e. ECM) ratio makes it hard to have precisely the cell amount, as well as inhibit complete homogenization.

Well, unless you got a contamination the results indicate that there has been mannitol fermentation. I am not sure how you streaked them out (looks a bit weird). However, you are right in assuming that the color change indicates fermentation somewhere in there. Well, technically it indicates acid production...

Technically, it is possible. This is especially true, if you know someone to introduce you to a given group, or if you directly know the PI. If you are an unknown quantity it is still feasible, however you are likely to have more chances if you got some own money (e.g. a postdoc grant). It is less likely to get a position in a different field that requires working on a running grant with looming deadlines, unless you can demonstrate that your acquired abilities can be transferred to that particular topic. Note that depending on what your goal is it may not be wise to change fields too much (I am not familiar with either discipline and your invovlement in them, so I cannot evaluate how far a stretch it would be). You want to be able to establish yourself in a particular field, if your goal is an academic career, for instance.

I would actually focus less on the study topics upon entering grad school and network more (or rather train myself in networking). Also I would have though harder about the requirements and necessities to get a science job. If I wanted a industrial job, a focused internships or equivalent may have been an option.

I only read quickly over the post and may have missed some finer points, but I see no real problems here. One legitimate concern is that of what you want to do, assuming you have a PhD. There are basically two major aspects to it. 1) Research in academia: the only positions that are not on soft-money (i.e. grants) are tenure position. While you will be leading a group, your direct involvement in actual wet-bench research (if that is your goal) will be relatively small. Also, the competition is fierce (e.g. only 20% of all PhDs in academia are likely to get tenure). I suppose the link you provided will provide information on it. 2) I am far less familiar in industrial research, but from what I heard of colleagues they are not too many positions doing wet-bench research. The PhDs there are mostly in sales or have organizational duties (e.g. preparing paperwork for pre- and clinical studies). Alternatives: If you want to engage in research (and again, we are talking wet-lab here) setting yourself up as a technician may be a possibility. Microbiology and molecular biology would be more fitting in the biotechnological area, whereas in areas of drug development pharmacy or similar is preferred. Also, pharmacists with PhD are often preferred by drug development/production companies are preferred over bio PhD. Regarding financing, if you are accepted into a graduate program you can usually get financed by TAing or working on a funded projected. Of course, there are no clear-cut rules and each individual path will look slightly different, but there are some common guidelines that one may want to look into.

The NIH has set up a database for that. It is called research portfolio reporting tool (report) or something like that. Should not be too hard to find with a google search.

Actually that is not gluconeogenesis, but glycogenolysis (sounds similar). Gluconeogenesis refers to the formation of glucose by basically inverting the reactions of glycolysis with three bypasses of essentially irreversible reactions. Other than that, yes glycolysis is glucose to pyruvate. Glycogenolysis is from glycogen to glucose-1-P. With a mutase it is converted to glu-6-p and can enter glycolysis from there.

Interesting, care to point out the inconsistencies? Also note: GIGO.

Actually this sounds like a plausible question that a non-specialist would ask during an exam to bring something up. It is rather uncommon that all the members of a committee are specialist in what you are doing. That being said, I would advise against personal attacks. People may or may not be who they claim. Refute their arguments, if necessary, but personal attacks serve no purpose.

Was the medium prepared anaerobically and is a redox indicator included? The amount of cells is suspicious for only two days of pure anaerobic growth. Unless the starting titer was very high (which would not be ideal for these kind of tests). Also, was sufficient agar in there?

That is partially wrong and partially inaccurate. All organisms have certain limits to their pH tolerance. Not all algae (which are plants) are low pH tolerant, not all bacteria (such as cyanobacteria) are pH sensitive. What is true is that the physiology of both organisms are so different that one would not expect large similarity in their physiology. Bacteria as well as plant cells have cell walls, which are chemically and structurally very different. The presence of either does not automatically confer pH resistance, though. This is down to other mechanisms but may (in bacteria) also rely on modifications of the outer cell surface.

Well depends on the resolution and type of the gel as well as size of the protein. If you are in a very well resolved range it could be possible to see a shift.

Basically all permeabilization and fixation methods put stress on cells. The composition of the solution and the resilience of the cells varies somewhat, though.

Well, detection of viruses is normally either PCR or antibody based. I.e. antibodies that the immune system raises against the virus. Direct detection of the virus protein in body fluids while technically possible tends to give relative weak signals. Based on that one could of course change the binding regions of the primers, although they are of course designed to match conserved areas, which, in turn, are generally necessary (and therefore conserved). The major problem is that luckily there is no easy way to rationally improve virulence based on structure (yet).

Well, since scientists don't make money with their publications, it is a non-issue. Quite the opposite, really. The more exposure, the better. The journals may complain, though. However, there are always open-access journals or you can just link the article (which would be a bit limiting).

It is more of a taxonomical convention. For instance, names above the genus level are usually not italicized. Same for genes (non-capital, italics) protein (capital, non-italic). Edit, this is only the case for prokaryotic gene symbols. For eukaryotic gene labels it is customary to have it italicized but the first or sometimes all letter are upper case (for the WT).

On the other hand, explaining an interesting paper in a simple way is a good training. The question is then whether there would be any interest. Or whether a blog would be a better medium, for instance.

I agree with ajb. Considering that it takes time I think it would be very tricky. However, if it works out, it would be very interesting, too.

I don't know the quote but it can be interpreted easily. I would argue that biology is far more complex than most of astrophysics, for which a lot of number of explanatory models exist. Not knowing them, expresses ignorance (the knowledge is there, but you may be unaware of it). Biological knowledge is very much fragmented with enormous gaps, due to its complexity. There are no good mathematical models for most of it. Most biologist know a lot about not knowing something. Edit: did not see the second page. Bleh.

Right, I forgot about typewriters. Good thing they phased out during my undergrad times (well before thesis writing times, luckily).

IIRC the duet vectors are routinely used for multiple co-expression, so as long as you use a host strain that is compatible to both plasmids, you shold be fine. Novagen also sold at least one of those. Novablue or something like that. Other strains include B834 and/or Bl21 derivatives, I think. But better check that out, as my recollection is a bit hazy on that.

Just to add, underlining is generally only used if written by hand.

It is important to understand that there are at least two different variables. One the total elements within a population. This constitutes the complete genetic variability, i.e. all variations of all genes, for example. The second is their respective occurrence (frequency) within a population. Mutation, for instance, may add a new variant of a gene into the pool, thus enhancing the overall variance of the gene pool, when it appears. However the overall composition of the pool will hardly change as at the time of the mutation only one individual carries it. With no natural selection acting on it, the likelihood is very high that the mutation vanishes within a few generations. If it there is high selective pressure to keep this novel allele, it can spread, thus increasing its frequency. The overall gene pool composition (i.e. frequency of each allele) will then significantly alter over time.

You have to be careful to differentiate between mechanisms that increase variability in the gene pool and those that change the composition. Roughly speaking natural selection and drift belong to the latter, mutations and recombinations to the former.