CharonY

Nature has its ups and downs. I would consider it mainly a bio journal, though. At least much in it is not rigorous enough for pure bio, but have some sexy stuff (often interdisciplinary) to sell it. I assume due to its format, about any discipline has something to complain about Nature (or, for that matter, Science). Formats of papers (whether it includes a long or short intro, discussion or not, numbering, etc.) are outlined by each journal, so that is usually the first thing to check. However, it is impossible to write a decent paper without knowing the background of the topic (and thus knowing what is the novel aspect of ones own work).

I see your point. In the end, it depends on how the lecture was set up. If I have e.g. discussed the principles of, say, an analytical method in class, I like to evaluate how well students have understood it by giving them a paper that inserts a little twist on the method. What I want to see is whether they understood the principles well enough to explain what the twist does. Or, lacking that, at least figure out that there was a difference and at least try to figure out what it does. Direct and specific questions will be answered, of course. However questions on the level of "I do not understand, gimme all the material so I can understand it" without any specifications are frowned upon. I do not think that most here mean that "you have to do it on your own" equals no assistance whatsoever. However, I see my main role as a guide, not as a spoon feeder.

QFT Many important things have already been mentioned. Regarding undergrad talks: it is rare that a great polished talk is expected. In fact, at the undergrad level talks are often used as a means to gauge the level of understanding as well as ability to fill knowledge gaps of the student. The form and style are also often discussed, but (depending on the prof, of course) rarely the centerpiece of it. Almost all first talks are (from a style viewpoint) bad. And this is OK, and it forms the basis for improvement. Not understanding the material on a basic level is something different, though.

It is not a problem of number, but the ability of the virus to successfully infect a bacterium. If it is resistant throwing a whole lot at them won't do much. Also if the bacterium is confined to a location it is easier to kill it with unspecific disinfection methods.

In cases when you deal with diverse range of expertise another approach could work, if you have enough time. Essentially give the bare minimum needed to understand the concept, then declare that you are going to give more in-depth info for those interested (so that those without expertise are prepared), summarize the gist again, and move to the next topic. By stating easily, going into depth and rising back again one can provide the depth without frustrating the non-experts too much, while satisfying the experts (which, depending on the format of the talk, may actually otherwise interrupt the talk).

Viruses can kill bacteria, but almost inevitably there will be resistant bacteria. It is good for destroying e.g. a monoclonal lab culture (which are all genetically identical). But destroying a wild-type population is very unlikely to happen.

Well let us interpret the curves in more detail. First, in order to differentiate between the two alleles I presume that different primers were used. That alone will result in differences in amplfiication efficency and thus render a direct comparison between orange and blue irrelevant. I.e. you generally can only compare CTs of orange to orange (one set of primers) and blue to blue (the other set) without further normalization. However, one tricky bit is determining the threshold, i.e. where you determine the CT. Note that in your two plots the indicated threshold would result in very close CTs, however in plot 2 the absolute signal in the blue curve is much lower. The shape of the blue curve in plot 2 indicates that the efficiency of the PCR is very low. One key element here is the threshold. It should be: 1) way over the background noise of the initial cycles to ensure detections and 2) be in the exponential part of the amplification curve Looking at plot 2 it appears to me that the threshold is very close to the initial noise (i.e. early amplification cycles where there should be no meaningful signal) and the exponential part is hardly visible. Based on that I would conclude that the threshold has to be higher and no proper CT can be derived from the blue curve. In other words, the curve appears not to be indicative of a proper product. The observed signal could be easily background (again, note the hump at the beginning) or unspecific amplification. Either the sample contained no blue allele, or the PCR simply failed for technical reasons. To be certain I would have to see the actual values, of course. The melting curve could give hints whether unspecific amplification may have occurred. Of course, the PCR could simply be super-inefficient for the blue primer pair, but looking at blue in plot 1 reveals that the curve can look very similar to the orange one (assuming in plot 1 the same sample was used). So based on the curve shape and assuming the PCRs worked fine, my assessment would be sample1: heterocygote, sample 2: homocygote. Note that the CT did not play a role (provided it is not something like cycle 30 or above, depending on the polymerase).

Bottom line, molecular rhythms have (surprise!) inherent variability that can adapt to external stimuli.

You have to understand that these circadian clocks are not precise. One single cycle has individual-to individual variation, as well as day-to-day variation. 24h is just the approximate for the diurnal cycle. The studies that analyzed human behavior found anything between 23-27h cycles, with an average close to 25.

For the first part, genetic memory, i.e. the notion that memories can be transmitted by genes is mostly nonsense (if that is what you mean). Although of course, brain development (i.e. the basis for memory formation) has clearly a genetic basis. For the second part, all cells can be infected by viruses. A virus is essentially a gene that can move between cells. And yes there are examples were viruses got into an organism and stayed there. You may have a slightly wrong view on how they mutate, though. Essentially the mutation occurs by the virus inserting its genes into the host. This is how it replicates and that is how it persist in a host population. Humans are a good example. We have many areas in our genome that were once active viruses (the genomic landscape is an odd place).

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.