CharonY

Just off the top of my head: depending on size differences between isolated mRNA and the small RNAs: -denaturing PAGE and then reisolation of the right band -chromatography (e.g. LC; nano-LC) if sequence of small RNA known: -make biotinylated oligos with the sequence of the small RNA, couple it to magnetic beads and fish the desired mRNA by magnetic separation follow a cDNA normalization procedure (still needs screening, though) That's basically what I can come up with in the spur of the moment. For better ideas I need a coffee, first. (so what's your plan? )

For long term storage lyophilization and storing it cold is probably the best. It still has decent activity after ~6 months and more. If you want to store it in solution use a alkaline buffer ~pH 8, avoid glass wares, as it readily adheres to it. If it is only for a couple of days I'd store it at 2-4°C, as freeze/thaw cycles rapidly reduces elastase activity (true for all proteins).

I once had a dog who worked doorknobs quite well with his teeth. But then I guess anecdotal evidence shouldn't count. Getting attention? PhDs are overrated anyway. Doorknobs too. Bloody knobby things. No caffeeine left, either.

Most a priori hypotheses that you want to subject to tests are phrased as null hypotheses. So your project my be "the analysis of flight aerodynamic properties of lemurs." In which you test the null hypothesis that lemurs will fly once thrown. Of course you need to define the parameters and then, after experiments you can accept or falsify the null hypothesis.

I have a slightly higher value for the density, but otherwise you are right on track.

The protocol appears to be find. Also, the primers should not be a problem (they are pretty standard). Increasing the annealing temperature will lower the yield (but increase specificity). The following things should be checked: - was the DNA extraction from deer manure successful? Check the DNA quality and quantitiy. -is the DNA pure enough? Contaminations can ruin the PCR esp. if you use 13 µl of template -are the components still OK? Make another PCR with a positive control to check that

The first five minutes after submitting a manuscript.

2-line Ferrihydrite is also blackish (with a slight brownish hue) like magnetite but it's non-magnetic. FeO(OH) (goethite) can range from yellow to reddish brown. After all there are around a dozen iron oxides and hydroxides around each with overlapping colour schemes. Anyhow, prussian blue is a good way to find iron traces. However, if I recall correctly one has to be careful that it does not get oxidised as it might then react with itself. I think the pH had to be controlled or something like that.

Unfortunately you cannot easily build an x-ray diffractometre on your own. I got access to one, but it only works well if the sample is sufficently pure. The question is what species of iron oxide it is. If it is darkish brown you may be in luck and it might be ferryhydrite. This is readily soluble in HCl. However if you got goethite or hematite you either have to incubate it longer or heat it slightly to solubilize bits of it. Alternatively reduce it with hydroxylammoniumchlorid (Fe(II) is soluble) and then make a colorimetric assay. In general, the darker the iron oxide is, the less crystalline it is. However, there are differences between iron(hydr)oxides.

Please post in the homework section. Also try to at least make an effort to describe your problem with understanding. For starters you could point out that RFLP=Restriction fragment length polymorphism. And that that name alone hints at what it actually is.

You have to read up on types of restriction/modification enzymes, the genes encoding them and then check the genotypes of the strains used for transformation.

X-ray diffractometry? ;P Alternatively use a dye specific for iron (e.g. 2,2-diypridyl, ferrozine). You have to reduce it beforehand, though, as the dyes are Fe(II) specific. This includes incubation with a potent reductant in an acidic solution.

Warhammer 40k. Necrons, I guess.

I agree with the internet, but disagree with wikipedia. The references in Wikipedia (at least in my field) are often sub-par and often biased. However, there are search engines (e.g. ISI web of science and Pubmed) which have been quite long around which one usually should use to find papers. In fact, the classical way was to start off with a review and grab the original reports from there. Wikipedia might be sufficient for highschools (but far too convenient, thus disrupting any pedagogical effects) but clearly not on the university level. Well, maybe except the first two semesters or so. My main concern however is that in the lower uni-levels people would stick to wikipedia instead of grabbing a textbook. Good textbook knowledge (rather than original research papers) is in my opinion an essential basis for doing "serious" research work. Without that many simply do not understand the implication of new papers.

The OP refers to methylation, so clearly it meant degradation of DNA after uptake. Also, transformation is usually done with a vector, which is propagated in vivo. However, even those can be unmethylated. As I said before, it depends on the strains.

Depends on the stain being transformed. Read your protocol.

You are a bit confusing things here (and I was a bit unspecific). The theory assumes that most mutations that are fixed (and not every occurring mutationas you might be thinking ) are in fact neutral. The "neutral" thus refers to fixed mutations and not to new mutations. The selectionistic theory states that the fixed mutations are the result of positive selection and therefore have to be benevolent. In other words, the neutral theory assumes that random effects (like e.g. genetic drift) are the major forces in molecular evolution and not natural selection. Also keep in mind that we are talking about molecular evolution and are not yet on the phenotype level of the organism. On that level it is generally agreed that selection plays the major part. If we take a look a new (random) mutation that has not been fixed in the gene pool yet then chances are that they are mostly neutral or deleterious. In general, a single point mutation is usually neutral. Accumulation (in case of high mutation frequencies) usually leads to a decrease in fitness. Advantageous mutations are in all models (known to me) extremely rare. The neutral theory states that these are so rare that they do not play a major role in molecular evolution. So if you make a plot of mutation frequency vs the selection coefficient (in this case as a measure of fitness), you will find that in the neutral theory the frequency is high for neutral and negative selection coefficients, and low to non-existent for positive coefficients. In selectionism you will find a high frequency for negative selection and a low one for both 0 and positive selection coefficients. Meaning that if mutations out of these are getting fixed, they'll have to be advantageous. The only theory that has an equal (low) frequency for negative and positive mutations is the pan-neutralism. Here it is stated that all mutations are neutral. This theory is almost surely refuted, though.

It is not THE but an accepted model and is especially used as a null model (in order to describe non-neutral frequency changes). There are also slight variations of this model that appear to describe some phenomena better than the original proposed on (by Kimura, I think). Almost all theories assume that. The main difference between neutralism and pure selectionism is that the neutral theory assumes that the amount of favourable mutation is too low , whereas selectionism proposes that the amount of favourable mutation is sufficient to explain all molecular evolution. In both cases neutral and deleterious mutations are in the majority, though. It is always determined via the fitness (often expressed via a selection coefficient).

I accidentally clicked theist instead of atheist. I practice lab-vodoun on a regular basis, though

Actually I recall that cat fleas are rather host unspecific. Quite a number of dogs are actually infected by cat fleas. But other than that follow the above given advice. My parents had at times over 13 dogs, most of them strays and by simply washing them with a flea shampoo and then spraying Frontline later on, we got them essentially flea free (or at least below detection limit).

Actually this is not that new. The technique (pyrosequencing) was published last year (or the year before) and actually there is already a thread about it http://www.scienceforums.net/forum/showthread.php?t=27427 The disadvantages of the technique are shortly described there, too. And just fyi the thing is called Genome Sequencer FlX (not flex), also the run takes about 8 hours. The price tag was around 10k $ per kit. Though I am repeating myself: these new sequencers are suitable to sequence human genomes (as a draft already exists) within a week, though the use for novel genomes is still limited. Nonetheless, at the moment the use is still somewhat limited because for the most part we still do not really know what to do with the sequence. This will hopefully change with further genetic analyzes within the next decade(s) or so. For mere assessment of identity other (PCR-based) techniques already exist and are in common use.

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.