CharonY

There may be a little bit of confusion here. Just to clarify, the ct value indicates when a certain amount of product has been produced (using the first derivative of the curve). I.e. it is dependent on the efficiency of the individual PCR reaction. As such there is no absolute cut-off value whatsoever. If your PCR mix is optimal (in terms of purity and perfect ration of primer, target, polymerase, etc), you will have the lowest value, if the situation is suboptimal, it will take more cycles, the curve has a different slope and hence, the ct changes. What it really tells you, however, is that if the CT value is not too high (at very high cycles unspecific signals occur), you got a product. This qualitative analysis is similar to standard PCR and gel-based detection. Using calibration curves you can then use the CT value to assess, semi-quantitatively, the initial target concentration. This is the basic use of qPCR. Note, that you cannot easily cross-compare PCRs with different primers, as all quantitative differences can be due to difference in primer efficiency (i.e. you cannot easily infer abundance based on CT values for different alleles. Now regarding your example, if you got two significant signals, regardless whether in gel or using real-time, it means that two allels are present in your samples. And hence, it is heterozygous. If it was homozygous only one, or the other signal would be apparent (in the same sample, of course).

The conditions are largely dependent on your sequence. Also the T-overhang can cause problems. If you need troubleshooting help, you should post what precisely you are doing and what worked/did not work. Fusion PCR is basically the same as an earlier technique named Gene SOEing published in Biotechniques, btw.

A nice discussion roughly pertaining to this topic. Does college make you smarter?

Slabs are generally used for longer cultivation or storage or when e.g. a certain gas composition is neeed. Petri dishes are easier to handle and usually preferred when possible.

Real-time PCR covers a wide number of application and it works excellent for some, lousy for others. But first of all, no bioanalytical technique is 100% accurate (depending on what is determined as accurate, i.e. accurate detection of a certain molecule is not equivalent to an accurate determination of a state of the organisms). That being said a problem with the use of real-time for quantitative analyses is its semi-quantitative nature, coupled with the exponential signal increase (i.e. small inaccuracies in the method can lead to large differences). That is why controls are often crucial. The use of the target sequence (e.g. synthesized oligos or cloned constructs) can really help in normalization. Depending on what you really need (i.e. quantitative vs qualitative data, throughput etc.) a traditional PCR can lead to more stable and reproducible results.

A talk has a very different format and purpose than an article. Thus, you need a completely different approach to it. There are tons of advice on how to present a scientific talk and even more on how to do a good talk. Much of which is controversial, of course. The most important point is to make clear what the paper is about and why people should care. Not a lengthy introduction but rather why this one is interesting. Essentially, set the tone for the talk early and show what the listeners can expect. Again, show why this article is interesting. Bring in context early. Methods are only necessary if it is unusual or highly relevant to the point. Results should not be shown isolated (as in a typical results section in papers) but clearly and immediately relate to the conclusions i.e. the interesting stuff (remember, during a talk the listeners cannot go back and forth between slides). Actually reading parts of the articles or just summarizing it is a big no-no. People are guaranteed to get bored. Lack of feedback is often a result of it. At the end a short summary is often useful. Presenting your own work is somewhat similar. But you have to focus on why the audience should care (not why you care).

NIH-funded projects are generally freely available via Pubmed central (as are others), and of course there are open access journals. Regarding access via research institutions and unis, it is often a mxied bag. The MPI has great access to about anything (though some more exotic ones are not available), however universities with more limited budgets often struggle. If the uni has no subscription it can cost around 3 euros or so (IIRC) to get a scanned version sent to you. Which is still cheaper than what you would have to pay as an individual.

Well another aspect may be that the competition pressure between scientists is ever increasing. There is an ongoing trend of having more publications and in some cases this will lead to overhasty publications that may be erroneous. Of course, this climate may in some cases may encourage fraud (especially if the choice is between tweaking a "minor" data set or losing your job). However, I would say that outright fraud is still very rare. Publication of crap, on the other hand, is not that rare.

It gives time for the homogenate to settle a bit and allow for more thorough precipitation.

As it is implied in my post, there is not a singular property that makes an allele dominant. It all depends on how the respective allele interacts with the organism. If it confers a trait, regardless of other alleles it is dominant. It can be because of its own activity, as in my example or due to interactions with other genes that other alleles may not be able to do. Or they fulfill certain regulatory roles differently. In other words, for each group of alleles, the mechanism will be different. Or, in other words, dominance is caused by the different mode of interplay of the respective alleles within the organism. If all are similar, no dominance is observed. Asking the purpose of it is akin to asking for the purpose of rain.

Actually all regions of China (as far as I can see) are above average in science and mathematics and only Macao scored worse in the reading scale. However, if all schools, even those in the poor low-industrialized areas are taking into account, the overall score for China would be arguably low. Individual accounts still indicate that at least in mathematics they may be above average US public schools, though (which I find quite astonishing, if true).

I believe there may be some confusion in the use of the word expressed in the context of gene expression, vs phenotype. Dominance has little to do with being expressed or not (i.e. acting on the transcriptional level) per se. However, in some cases it could be. Both alleles can, and often are, expressed similarly. Dominance is a description on the phenotype level. For instance, an organisms has to allele of a certain enyzme. One of the alleles produces an active enzyme, the other a non-functional one (at least non-functional in terms of the specific activity we are looking for). Thus, an organism possessing both allele would be positive in enzyme activity and the the functional allele would be dominant, as it will always confer the activity, regardless of the presence of the other allele.

Strong smears are often due to DNA contamination, or serious degradation. Some smear is expected, though the rRNA bands should be the strongest. The water comes from your lysis buffer and the sample itself. If no phase separation is observed, it is often one of the following : - contamination of sample or reagents with organic solvent. If the chloroform is e.g. contaminated with isoamylalcohol there will be a no phase separation - incomplete mixing of the homogenate: mix again, let rest at RT for a few mins then centrifuge

This is an important aspect of undergrad teaching. It is (or should not) only be about gaining the knowledge in order to be able to contribute to actual research later in grad school and maybe even further on. One basic element is simply to appreciate nature, and figuring out the inner workings and how little we actually know about it. If one does not acknowledge that, actual science can be perceived as incredibly dull.

It may depend on the isolation and (if required) separation method, I would say. However if it would not even survive that one would require serious explanations how it is going to maintain integrity within a cell (where it is processed heavily).However, if it we end up with single nucleotides, it does make things easier to interpret, as we have defined m/zs to search for.

Probably I would use the MALDI. The likelihood of fragmentation is probably a bit lower. Also I suspect quite a bit of salt contamination.It could be a bit tricky to deal with adduct formation.

I would have just used soft ionization of the DNA and see whether there is a mass increase from P to As. If there was a significant exchange at least some should be detectable. Considering the relative ease of that experiment, I am quite confused why they did not try that.

Well, I would not know why they would be called remnants.Also, they are generally considered to be mobile genetic elements (or selfish agents, if you want) that may have arisen very early in history.

Essentially the saliva itself (or most biological matrices for that matter) contain nucleases that can rapidly degrade free DNA. Add microorganisms to the mix and you look at a highly unstable system. However, for some SNP analyses even the degraded DNA may be sufficient (as only very small fragments are required). Unless, however the information of likely candidates or very close relatives is stored somwehere, the identity may be very hard to assess.

Note that I said that teen pregnancies carry increased risk for infant death and did not give any indication of possible causes. This may not be that obvious as bodily changes are still happening between age 12-16, where the largest increase in infant mortality was observed.

Teen pregnancy increase the risk of infant death by something like three, IIRC. So together with Timo's calculation it is clear that it cannot be a major reason for the differences in infant mortality (though it certainly contributes to some extent).

AFAIK it is not possible to filter for a single hit per species. What you can do is to limit your search to a certain groups of species, depending on what you want to see. Alternatively, save the complete output as table and filter it.

Actually the mass does not really play a role in the calculation of electrophoretic mobility (think Smoluchowski). There appears to be a MW-dependence on charge density, that may allow for the differences at lower MW, though. M/Z really only is relevant when e.g. looking at movement of charged particles in vacuum.

1) Are you mixing up gel electrophoresis and Southern hybridization? 2) Free electrophoretic migration is dependent on electrophoretic mobility. For DNA it becomes size independent above a certain length (bit above 20, I think). The major difference, however is the use of a gel. The sieving effect has a dependence on the linear size. Due to this dependence, you can relate the migration back to the DNA length.

Simply put, the genome of an organism is the total of its genetic information. Thus, the genome sequence of humans consists of the sequences of the 46 chromosomes. Heterogeneity can refer to a lot of things, including distribution of genes but also as mentioned the GC content. The latter is often indicative of horizontal gene transfer, or mutations and rearrangements of some sorts. Conserved genomic areas which share a long evolutionary history (i.e. derived from the same ancestor) tend to have similar GC contents.