CharonY

I would assume that this is true for almost any field. During undergrad one almost exclusively learns from text books for the next exam. There is hardly any hands-on experience (a few weeks practical courses do not count). Depending on the course one usually starts getting a feeling for the topic during the master/diploma thesis. Even then most are still struggling with getting into serious lab/science work.

If your question is why you only sequence one strand, I cannot answer that (I'd always take both to reduce errors). Regarding the sequencing direction: You essentially got two possibities 3'->5' or 5'->3'. Now think about how Sanger sequencing works. (In the end it is only a question where you put the primer, though).

Well, most commercial sequencing services are massively cheaper than academic ones. However, to date few are offering 454 sequencing. In my old workplace they bought a 454 to sequence a vast number of genomes, which are related to known ones. The price tag here is, of course nothing a traditional sequencing service can compete with.

Actually some antioxidants as selenium and mangenese are essential cofactors of proteins involved in oxidative stress response (I'd rather say that proteins are involved to prevent oxidative stress rather than being antioxidants, the latter might be misleading). This includes for instance superoxide-dismutases (in case of manganese) and glutathione peroxidases (withe a selenium center). Manganese does also counter oxidative stress all by its own, though one would need concentrations that are toxic to many organisms. To complicate things, we got elements that are both causing oxidative stress, and are also involved in preventing it. For instance, iron can cause massive oxidative stress in presence of hydrogen peroxide (a common sideproduct of oxygen respiration) by formation of oxygen radicals by the Fenton reaction. However, some organisms actually use iron as a cofactor in superoxide-dismutase that are involved in detoxification.

A260/230 does not necessarily mean polysaccharide contamination. Other contaminants absorbing at 230 include for instance guanidine thiocyanate and phenol. Also insufficient resuspension of RNA has an effect on this value. For a simple cDNA it might be not that much of an issue, contamination might effect enzyme activity and are therefore really detrimental for quantitative assays (e.g. QPCR, Microarrays). Otherwise a normal cleanup is recommended. Either use columns or precipitate the RNA and wash with ethanol.

I wouldn't disregard lab experience as simply as that. By actual doing the stuff you do learn much more than you would just by reading the text books. Also, for the interpretation of many papers it is necessary to be familiar with the techniques used in the studies. Just knowing the protocols is often not enough as the pitfalls of certain especially newer techniques are hardly documented anywhere.

Yes I do. It has its advantages as employed in the 454 system. Main advantage is the the huge amount of reads per run (~ 20 megabases), and the resulting low cost per base. Main disadvantages compared to the Sanger method are the short reads (> 100 bp), though a next generation model should be able to double the current system. The latter limits the utilization of 454 for sequencing of complete novel genomes a bit. Most of the time you need a scaffold (already sequenced organism, or a library) to reconstruct the genome. Other sequencers exit that can sequence ~ 1Gbase per run (Solexa) with even shorter reads (~20bp), for specialized applications (clearly not genome sequencig). Currently a variation of the Sanger sequencer (with immobilized polymerases) is under development, combining long reads with a large number of parallel reads. Unfortunately I probably cannot afford that one.

Actually from what how I understand it, it is slightly similar to the German system. Essentially everyone is obligated to have some kind of health insurance. These come in two flavors, the private health insurers and the statutory health insurers. The latter have to take everyone in and those that cannot afford it are subsidized by the state. The private one usually offer more (e.g. you can get single bed rooms in hospitals or get to choose the senior physician over juniors. It is a rather expensive system, especially if unemployment is high, as all unemployed have to be taken in by the statutory insurers. However, if you income is at the lower end you will get all necessary treatments fairly fast. If resources are limited privately insured patients will get (unofficially) treated faster, though.

Uhmm.. quod erat demonstrandum?

99.9% of these numbers are pulled from thin air.

Introns are also have regulatory effects and supposed to stabilize essential domains. For higher eukaryotes the costs for additional DNA elements in form of introns is arguably not that high (when compared to the overall metabolite content of a given organism). This is not true for very small single-cell organisms (all prokaryotes for example). In these there is a selective pressure towards compact genomes (as here DNA replication can be one of the limiting factors of growth rates.

From what I know Freud is more of historical interest for modern psychology. He gave essential inputs in his time, but psychology/psychoanalysis moved on from there. Some of the most basics tenets have still a (limited) validity though. Much that he developed from that is considered too crude or inaccurate nowadays. Also I am not aware that he proposed any religious dualities at all. Are you thinking of the superego/ego/it trinity? This was more a model than anything else.

I assume it is one of the kits which utilizes biotin-(strept)avidin-conjugates for visualization of the DNA. I usually just use cy-labeled oligos for PCR (easier, more direct and non-radioactive, saves paper work). EtBr staining is a good idea, though. I was just thinking, the OMP does not happen to bind to biotin, does it?

Drinking cold drinks will also close the pores on your skin thus inhibiting transpiration.

I need a bit clarification first. You have a purified OMP for the shift with the biotinylated DNA and you use (strept)avidin conjugate for Chemiluminescence? 1st question: is the OMP known to have a specific DNA binding site (I am a bit unfamiliar with that concept as I usually only do shifts with TFs). And the following happened: 1) you increase OMP concentration, but not DNA -> intensity reduction 2) you add unlabeled but specific DNA (constant protein concentration)-> no intensity change 3) you add unspecific unlabeled DNA (control) with constant protein conc -> no intensity change Did I follow you so far? 2nd question: do you only observe a single band in all EMSAs? My quick'n dirty interpretation: If I assume that no technical errors occured (e.g. during chemiluminescence detection) then it is no sufficient proof for DNA-protein interaction. First, of course, because no shift happened (d'oh). Second, because the control (adding specific unlabelled DNA) did not result in an intensity shift (displacement from regulator). The strangest part is possibly the reduction of intensity by adding the protein. It is possible, that the protein in fact binds the DNA, however for some reasons the DNA-protein complex did not migrate into the gel. In that case an increase of prot would deplete the DNA, whereas increase of DNA wouldn't change much as you'd only see unbound DNA in the gel in the first place.

Well, I have no intention of buying these books, so I can only comment it from the summaries. They are disturbing, of course as they try to put politics and religion into natural science and some of their proponents are even scientists themselves (though thankfully rather seldom biologists). On the other hand, since when was science fully free of politics? Grants position etc. are not always purely based on scientific achievements. There is never too much coffee.

Well it depends how sterile the surrounding is and how the air movements are. If you want to store them you can put your petri dishes in a larger jar that can be sealed, sterilize them within the jar and then seal it after sterilization. For short term you can sterilize the dish in an oven then let it stand in it until agar is done.

Simply put, most complex traits including those often rather imprecise defined ones as "personality" are in part genetically defined (e.g. sensitivity of certain receptors to their cognate hormones) but are also shaped by the environment. Just as a thought, maybe a person is susceptible to certain stress hormones resulting in stronger aggressive behaviour under stress. However, same person learns to avoid stress situations (or not to perceive certain events as stress, or lives in an environement with less stressors...) and thus given personality trait is not exhibited.

Well, to sterilize glass wares you got two options. Sterilize them in a steam cooker (I am not sure how much pressure a normal steam cooker can build up. It is possible that they do not sterilize completely), or you can just bake them at at least 180°C for ~12 hours. Usually agar and dishes are sterilized independently, and then you pour the agar under sterile condition into the dishes.

Ah, well too late to answer then. But if memory serves in denatured gels the speed is roughly equal (would make sense if both are linear ss, of course). However in PAGE (as opposed to agarose) 22bp can be resolved. You can clean-up DNAseI treated RNA with columns w/o phenol extraction, btw.

- structure of micro-organisms very complex -culturing micro-organisms sometimes a huge pain in the lower back -life processes of micro-organisms essentially all that are feasible

In theory yes, however the field created within the oven is quite inhomogenous. Very small particles (as bacteria) can quite easily be missed.

fats store more energy than polysaccarides (or rather the metabolization of these are more efficient than sugar oxidation).

Yeah it is not precisely my field of expertise but when I read the first paper (Takahashi and Yamanaka) I was pretty excited. My first thought, however was that hopefully it wouldn't be a fraud case (as Hwang). But now that more papers are popping up also from another group (and due to the ease of actually creating them), the hopes are high. Of course these cells are not as stable as embryonic ones, due to the fiddling in their transcription machinery, but an important thing nonetheless. Bloody hell, this stuff fascinated me so much that I actually sound like a salesman.

Hmm maybe I understand a bit better what you mean now (but then, maybe not ;P) I assume that may main problem with your reasoning and my focus in forces vs. structure is this from your OP: These sentences consists of a number of different assumptions that, at least to me do not sum up. Therefore I will try to ignore what I assume to be inconsistencies and try harder to get what you mean (yeh, I am probably thick-headed). Anyway, what I do not understand yet is what you mean with geometry? Do you mean structure? And do you mean identifying given structures in nature or about creating them, as e.g. in nanotechlogical applications? Or are you more interested mathematical modeling of said structures? Anyway, I still got to read the pdf first, when I got more time. Will get back to you then.