CharonY

Sequencing an eukaryote, is still awfully expensive and time consuming (and identification of genes is even worse). After skimming over it I could not see any reference whether the morphological changes are at some point genetic. This is btw. quite interesting. According to the Darwinian theory of evolution (remember, Darwin knew nothing about genes) this would be an example of adaptive evolution. However according to modern synthesis it would not. It would be interesting to breed them with a different diet, though. It would only be lamarckism if the traits are becoming inheritable regardless of diet.

Hrmmms it is not really related to the the question, however the (human) lung only retains a small fraction of the O2. On average your breath contains ~15% O2 (with an average concentration of ~21% O2 in the atmosphere). But what really has an effect on pH is CO2 (which is an acidic oxide).

I am not sure what you mean by "catalyst" in this context. Actually the definition of genetic modification is simply the alteration of genetic material of an organism by means that could not occur naturally through mating and/or recombination. This is a definition as issued by the EU, but afaik it is rather similar in the US. The rules that follow are different, though. To clarify, in your example it is not critical what the end product is, but how it is achieved. I will now simply assume that you are talking about an organism expressing genes (or alleles) a, b and c. Adding d is a genetic modification if you for instance create recombinant DNA and introduce the DNA e.g. via micro-injection. If, however d is introduced by conjugation or other naturally occuring DNA transfer mechanism then it is not a genetic modification. Likewise if you delete d by using mutagenic agents, for instance it s not genetic modification, but if you use a recombinant deletion construct, it is.

Hmm, Pubmed central has been around for some time already (~8 years, with only few journals, though) and I assumed that the rule regarding NIH funded publications was also longer in place. I may be wrong with the latter, though.

Also, although it already has been mentioned, I just want to stress again that evolution and theory of evolution are two distinct things. In addition the current theory of evolution is quite different from the original Darwinian notion. For example Darwin could not be sure how inheritance. The original Darwinian theory evolution included for example Lamarckian inheritance as a possibility. This was only refuted by the Neo-darwinistic theory. This again was surpassed by the modern synthesis which started to develop around the 1930s and 40s. However many basic tenets of the modern synthesis have been found not to be as universal as believed half a century ago and a new modern synthesis, sometimes referred to as postmodern synthesis is starting to form. Note that in all case not evolution as a process is challenged, evidence for this are rock-hard (literally in some cases), however the actual mechanisms are the element of the theories. What has survived from the Darwinian notion is that a populations are inherently variable and that natural selection is acting on it. What has been challenged is the relative importance of natural selection compared to other effects and mechanisms, especially when it comes to speication.

Right, it is short for Biosafety 2 Lab. The details how the setup has to be is likely differ from country to country, though. This includes e.g. restricted access, biosafety benches, available autoclave etc. Anyhow, getting the exact amount for consumables is tricky, if not impossible. The best you can do are rough estimates and then add a chunk more, as usually during the grant review process a big chunk will be slashed off again. Also you cannot know beforehand what will work and what has to be repeated how often. E.g. you may design four primer that looks perfect on paper only to find out that one (or both) pairs do not amplify. What you can do is to identify every component you need, take down the price, and then add 25% or so for replicates. It is going to be an estimate, anyway.

Well you need a medium with agar with it. But two caveats: a number of mouth bacteria are potentially pathogenic. So I would not advise to use media in which they can propagate. I probably would not want to do the experiment with younger kids, actually. Second: unless you brushed teeth just before sampling, the amount will not be significantly different between humans and dogs. Expect in the area of 10^9 bacteria per ml of saliva (so dilutions are necessary to count the colonies). And yes, definitely wrong forum section.

I assume this is just a "training" proposal? Usually you first to have to make sure that basic equipment for handling is present P. falciparum, as well as labspace (e.g. you need at least a BS2 lab). Most project grants do not cover basic equipments. Before I comment on the consumables I would advise you to look at existing protocols for the manipulation and maintenance of Plasmodium cells, though. You need to know this before you can write the grant. Check the malaria journal (it is open access) as well as some of the parasitology journals for this. I recall a paper about the assessment of different deletion protocols for P. falciparum around last year or so in the malaria journal. For standard cloning techniques check out "Molecular cloning" (Sambrook and Russell). There are tons of information in it and I recommend it to everyone. If you got a basic idea of the experiments you want to do, you can start checking out prices. Mutagensis kits are, btw. not essential. What they do is creating a mutated insert. Most of the time you can do it just with the right primers for less money. In order to get an idea how much the kits cost, I'd advise you to browse at least to Promega, Qiagen, Invitrogen, as well as general lab equipment vendors (e.g. VWR and Fisher).

Well, these are two issues. Basically if the data (analysis) is not of sufficient quality one cannot declare an effect as busted. This problem does not go away if you just do something else with the same lack of rigor. Also they usually do not really produce an awful lot of data. Usually there are only two to three data points per experiment. Much of the fun is not in the results but the whacky way they try to approach it. Also the replicates are quite often not really replicates in the strictest sense and so on. Of course there are limitations due to time and cost and it is an entertainment show after all. However, sometimes they do use the word "science" or "scientifically" quite a bit too often for my taste.

Also what they do as replicates are usually not statistically significant. It is often fun, though. Maybe a bit like CSI for the forensic community, only better. Well, Zombie Feynman is quite convincing, though.

Afaik there is almost nothing definite about them. Just to give an example I checked the same journal as the link above (PloS Path.) and found this: Link From the abstract: "Our results definitively ruled out the existence of “nanobacteria” as living organisms and pointed out the paradoxical role of fetuin (an anti-mineralization protein) in the formation of these self-propagating mineral complexes which we propose to call “nanons.” The presence of fetuin within renal calculi was also evidenced, suggesting its role as a hydroxyapatite nucleating factor." Well, OK according to these authors they are definitely not living. I have not checked into this topic seriously, though. I would be interested to look at some samples under the AFM myself, though. The report is quite convincing, btw.

Hello, you may have a problem there. The only methylation system (E. coli has several) that interferes with XbaI is Dam. Unfortunately I belive that DH10b are dam+. So if you isolate DNA out of DH10b chances are that it won't cut. So if you are dependent on that particular restriction site you can either transform a dam- E. coli strain with the vector and then re-isolate it from it. Alternatively you can try to look for an isoschizomer that is not methylation-sensitive. I do not know one out of my head, though.

Actually I have to complicate matters by adding that occasionally paternal transmission of mt DNA in animal, including humans, occurs. For instance: Schwartz M, Vissing J (2002). Paternal inheritance of mitochondrial DNA. N Engl J Med 22: 576–580

Trouble with this is that we would have to distinguish living from non-living a priori. Which is the basic problem I have when it comes to the definition of life. Edit, I missed that one:

In Germany you used to have work on your own on a science project (often a smaller part in an ongoing research effort) for around 6-9 months in the lab to get your degree in the last year in chemistry (and physics and biology). As there were no bachelors degrees that was the only degree (diploma) you can get (and had to get if you wanted to continue to a phd).

Is the calibration consistently off? Possibilities: array is not correctly installed, or it may be somehow damaged. Try reinstalling it again. If it does not work I'd suggest calling the support.

I have to edit my post, as I was referring to the wrong PloS journal. However, quite a number of papers are being rejected even in PloS one due to the same reasons as in other papers. The things, the editor's name gets published, but not necessarily the other referee's he/she has been consulting. Lack of importance (or lack of novelty) is quite a common reason not to publish something for basically all journals.

Depending on the field you might experience that any jobs are in fact not directly involved in research per se. Other job for phDs include product management, sales/support, consulting and so on. In numbers, at least for biologists, the average salary for a postdoc is at around 30000-35000$ annually in academic jobs. This varies depending on field, country and experience, of course. These jobs are usually time limited, though. Faculty jobs are higher (often around 50-90 k, depending on position), but getting one is not easy and it takes quite some time. I think most score full positions when they are around 40ish at the earliest. Chemists and physicists usually have a higher average salary, though. Jobs in the industry (e.g. as technical consultant or similar) often start at around 60000$. ...

That would not pose a problem for anaerobic respiration, though.

You generally use polyclonal antibodies as second ones. These happen to be IgGs

That's rather unlikely. Just by browsing I do not see an awful amount of paper on whales and many of them are using molecular biological techniques. In other words, you only need a couple of cells to do the respective experiments, slaughtering a whole whale is, in the truest sense of the word, "overkill". Also apparently a lot of the meat that is not getting eaten simply lie rotting around: http://www.news.com.au/adelaidenow/story/0,22606,23206289-5006301,00.html Finally you may want to read the following article: Parsons et al 2006, Marine Pollution Bulletin It’s not just poor science – Japan’s “scientific” whaling may be a human health risk too

Yes, that's why it is important to include statistics

So do you mean that you made a run with various concentrations on a single day and then repeated the whole assay on another (i.e. there is not likely a bias towards specific concentrations?). Regarding the analysis, "the error bars are pretty tight" is at best just a qualitative assessment. At the very least do a t-test.

Before you proceed thinking in that direction have you double checked that your results are statistically relevant? Moreover are the results repeatable? Was everything standardized? That is, where the experiments done in one go, or on different days? Where the cells from a single split culture or could they have different histories? Whenever something counterintuitive pops up it makes sense to be really really sure that the effects were not due to handling, different batches of cells etc. Otherwise you are going to lose a bunch of time.

Well, basically it is not uncommon to have concentration dependent effects. It is kind of strange that a high amount has seemingly beneficial effects, though. In general, concentration-dependent effects can be unspecific. E.g. w/o knowing details one can speculate that the redox enzymes decompose and increase the amount of copper in the medium. However, I'd not assume that this would be beneficial (an iron enzyme might make more sense, depending on the cell culture). One question would be how this bacterial proteins is supposed to affect the growth of the cell line in this particular experiment?