CharonY

I think you will have to think about how a AFM force profile looks like a bit more. Assumeing you have the polymerase attached to the cantilever. You come close to the DNA, the interaction force changes the amplitude. So far so great. Now at this point you make a leap in assumptions. How do you measure movement on the DNA? How it is tethered and which force change do you assume for each base (hint there are several, depending on how you fix the system)? Even if one is heavily diluted you cannot assume that the diluted one will take precisely 1000th the time of the undiluted one. It would be an estimate with an unacceptable failure rate. Bottom line is that you have problems untangling the involved forces AND you will not be able to distinguish between the bases. Regarding dyes, just check Science for an article last year, they actually sequenced a viral genome just based on fluorescence measurement. Why should it be difficult to have each nucleotide differently labelled? They do it routinely for years even for Sanger sequencing (using one channel capillaries). Also you may want to solve the Michaelis-Menten kinetics (probably assuming three dimensional freedom for this issue) to see how much time difference you would actually expect on average for the given reaction (and think whether there is a way to statistically derive the right base from it at all. Finally, take into account that if the wrong bases are vastly overrepresented, it increases the chance of polymerase errors and stalls. In large reaction it is less of an issue as you will have enough polymerases not doing it, but if you let a reaction continue to go one while monitoring (with whatever means) a single molecule you will run into deep trouble.

Again, what force difference do you expect to measure with the AFM? The strongest force is the attachment of the polymerase to the ssDNA. Then what? Where do you expect to see steps and how do they translate to amplitude changes? More importantly, how do you expect to differentiate between bases? Dilutions do not play a factor as at any given time you only measure the interaction of one molecule. Also, why do you think that monitoring the direct polymerization would be any slower? It is the rate limiting step after all. You do not need different cycles but different dyes.

First, Sanger does not cut anything. You measure when the polymerase stalls. There are other approaches out there, including using the AFM, but most without good results. Mind you, they use intact DNA. Measuring an active process with AFM is hardly practical. Also which forces would you think would change by the insertion of different bases from the viewpoint of the polymerase? The actual interactions happens with the second strand, does it not? The polymerase mostly senses the back of the nucleotides. Incidentally this is also one of the problems with sequencing with nanopores. In other words, the elements that you propose (speed of polymerase) are hard to measure and almost impossible with the required accuracy. Monitoring the insertion of nucleotides whether directly or indirectly is much more accurate. You may be interested in a paper in Science a year or so back where they sequenced a viral genome with fluorescence microscopy. Finally the speed is increased dramatically in the next gen systems due to massive parallelization so getting the required coverage is somewhat less of an issue (though assembly still is).

It should not be only about money but you also have to be realistic about getting a job. Interest is good and fine, but if you want an academic career, for instance, you should know that the competition for jobs is extremely fierce. Worse, in fact, than industrial positions. The reason is fairly simple, there is an overabundance of PhDs in academia in comparison to positions, which have pretty much stagnated in the last decades. It is necessary to establish what line of business we are talking about (i.e. science vs. non-science jobs).

Of course there are more. They require quite some even for energy conservation. Once fertilized they have to grow rapidly. The energy has to come from somewhere. Searching for it is quite easy. Just look for oocyte and maybe electron microscopy and pick out the oldest article you can find. Nowadays you hardly see basic cell descriptions in papers anymore as they have become common knowledge. The alternative is to open a nice cell biology or cytology book.

I am not sure what precisely you propose. Both Sanger and pyrosequencing utilize polymerases and identify bases by subsequently adding or leaving the respective base out of the reaction. The detection of these reactions is far more accurate and direct.

Cane sugar is not much better than high fructose corn syrup. It is essentially sucrose, a di-saccharid of glucose and fructose. The bioavailability of the fructose content may be slightly lower as it has to be cleaved and I am not sure how efficient it happens for a given intake. At least rat studies indicated that while sucrose had similar effects, a slightly higher concentration was needed (IIRC). Also the FDA does not give safety limits for normal nutrients (afaik) especially as it can easily be disputed where they are.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2224648/pdf/327.pdf Take a look at the drawing there (fig.1) the bottom is part of the oocyte. You can quite clearly see inclusion bodies including mitchondria there.

Well, I'd like to see them try. I am almost sure that the companies will cry government interference and somehow shoot it down. At the same time they will start commercials with titles like: "Drink soda for freedom".

Hmm good point. Have not thought of that.

Come one, it is the same with everything else. The dosage is the important bit. It is a bit of a no-brainer that a high-fructose diet is not good for you. The problem is that high-fructose corn syrup (at least in the US) is an almost ubiquitous in rather high concentrations. The main issue is most likely sodas, sweets and possibly some of the ready-made food. Finally, fruit juice (depending on fruit and whether it is 100% pure) also contains more fructose per volume as the original fruit (obviously). Drinking too much juice (e.g. as sole source of liquid) is also considered somewhat unhealthy (though probably less so than with sodas).

Oooohkay. /me drops iNow's brain back into the vat. Though it would be a good incentive for the male students.

Not all archaea are extremophiles. You can find them in soil aquifers, in guts, etc. They possibly not quite numerically dominant, but they often live in consortia with bacteria. Also the text is probably out of date as I remember that people have found Rubisco (which is the central enzyme of CO2 fixation) in archaea. Also, on another note, archaebacterium has essentially been dropped as a name. They are called archaea now.

Huh? Of course the ovum has mitochondria. That is why mitochondrial DNA is almost exclusively inherited by the mother.

Theoretically it is possible. Ideally there should be some overlap, though. Mind you, the job chances do not necessarily improve by that. Fact is that getting a job is all about fit, of which your background is only one factor. If you are concerned about jobs, start searching for one right now. PhDs in other fields will not by default improve your chances.

With the exception of dried food, of course

Excuse me, but stating that genetics is controllable and scalable science is fairly inaccurate. Specifically due to all that we know today we start to appreciate how little we know. I would argue that modeling weather is easier in comparison to trying to model the genetics of a cell (quite specifically because it is not scalable) despite the fact that we got much much more detailed data on cells than on climate. We have, for instance much more predictive models for climate change than working models on cellular activity. The few of the latter we got are often more of a qualitative nature and really limited in scope.

The point is that during the postdoc you have to work towards a faculty position (if that is where you want to end up) and take the necessary steps instead of "just" doing what is in your postdoc work contract. Even if you are extremely productive, unless you get regular papers in Nature and Science, the paper output will not secure you a job. It is more essential to show sufficient productivity and then leverage it to network like a champ. In the end, a position will never present itself, but you will have to mold yourself into the fit for the desired faculty position. What I am trying to say is that due to the fierce competition in academia, your plans have to be laid out very carefully, going from postdoc to postdoc without leveraging each position towards the goal has the inherent danger of ending up in the postdoc loop. And I have seen enough people losing there, or on the next step (i.e. tenure denied).

That is what I meant. While you often need postdocing, you do not go from there to a permanent position but need to become the equivalent of a PI, either as reader or lecturer (I think the US-equivalent would be assistant or associate profs). And from there (which is a major transition) you can start building a career towards a permanent position. Unless in the UK the reader or lecturer position are already tenured, which I kind of doubt. Also note that as a rule of thumb that depending on the field there is an optimumt time for postdocing (often around 2x2 years) after which your value gradually declines. Also fro industrial positions time in academia reduces your chances. One should keep in mind that postdocing is not a goal in the career, or even a milestone, but rather a waiting loop before one can get a real position. It is crucial not to remain in the loop for too long.

Nope (at least not much). But it is there for after the lysis.

I agree with your last statement. But from personal experience I would disagree with the one before a little bit. I overstated the the ease with which it is possible, though. I should rather rephrase it that it is possible, just not on a regular basis, unless the field is very very narrow. I.e. you do not have more than a dozen or so qualified reviewers. I also have to add that in the cases where I was approached by the reviewers and thus got my guesses confirmed, the reviews were all positive, of course. It rarely happens that someone admits of shooting down someone's paper. It also depends if the PI is actually doing the review or whether he is passing it on to his postdocs. The latter should actually not happen, but sometimes it does. But again, it depends on the field and how well you know the opinions of certain groups within the fields. If the review includes very specific viewpoints one can deduce it fairly well at times. Edit: K, so Cap'n and me bow to Mokele's wisdom at the same time. All hail the lizard.

Wait a tick, aren't you in the UK? AFAIK there you also have to become PI as opposed to being postdoc before you can even begin to dream of a permanent position. Too long of postdocing is, in most systems, a career killer. Also, of course, this only applies to a career in academia. One should not postdoc (in academia) if one wants to have a career outside. Quoted for truth:

What Cap'n says is mostly true, once you know other experts on your field you will recognize their style. However the basic idea is that as an referee you can give points without fear of repercussions. Another aspect is that there is a lot of academic infighting. Essentially you have to see that everyone in a given field is a potential competitor as well as potential evaluator for a given grant. Also, like it or not, junior scientists are always at a big disadvantage. Now, if you are a junior scientist reviewing a senior bigshot and realize that the paper is crap you are in a bind what to do. Shoot it down, but fearing that it will have repercussions on your career? I am not saying that there will be any, but the fear that something might happen, especially in an uncertain career as academia, one tends not to take chances. Academic science is not a magical fairy land where human nature suddenly dissipates. Couple it with the high-risk career it entails and you can easily see why it is unrealistic to assume that science will be conducted in its purest form. Humans tend to get in the way.

So, you suggest burning the children, too?

Nope that is something entirely different. The OP was talking about nano-sized actual drugs. Also I am pretty sure that homeopaths would not use words like "polypeptide" or use nano as a measure of size.