CharonY

1) I generally try to keep my samples MS-compatible, so I generally use DTT rather than mercapto for reduction. Generally, I would not expect to have much of it left after the run, though, so it should not interfere too much with immunoassays post-blot. 2) That highly depends on the particular instrumental setup you have.

The website is lousy in terms of information, as it mixes up different aspects and levels of genomic organization quite a bit. In any case, a flat value such as 95 or 99% is not very helpful to draw direct conclusions, especially without a proper context. What has been shown, for instance is that coding regions differ by around 1-1.8% IIRC between chimpanzees and humans. However non-coding regions under much less selective pressure and thus the average over the whole genome (the sequence) amounts to the 95% shown by Britten. Note that despite the mentioned differences in genomic organization, the DNA-sequence is roughly 95%-98% identical (depending whether you analyze only coding regions or not). That being said, I am not quite sure what the OP meant. Genetic differences between bird species can be quite large, depending on how related they are. The same with apes, and other mammals for that matter.

It is a pretty standard technique. I am pretty sure that me and a couple of others on this board can help you out, if you got specific questions. For broad overviews obviously other sources are obviously better. Bioanalytical and molecular technique textbooks, for example (Sambrook is a standard). Also some manufacturers offer surprisingly nice manuals.

Yes, you do. Though it depends on the type of test you are interested and can be rather tricky. For instance, the alternative could be that the phototactic is stronger, weaker (i.e. one-tailed), or either stronger or weaker. However, in case of Fisher's approach an alternative is not even used to formulate the test. Here, the experimental data is tested against the probability that it arose from chance alone, assuming H0 is valid. However, in the ideal case the H0 and H1 are formulated in a way that makes it possible to accept H1 by rejecting H0. Though depending on the experiment there is also the chance that you reject H0 but cannot decide on H1. Also note that you do not accept the H0. You either reject it, or fail to reject it. In the latter case it just means that H0 may be a possibility (but so are others).

Separating Staphylococcus and corynebacteria can be done as described, but is often tricky. Very often you will find contaminants even after serial streaking. Manitol agar is generally already selective, but many corynebacteria (darn them and their hardy cell surface) are very resistant to a wide range of pH and osmotic challenges. Unless you know precisely which strains you have, I am not sure that there is a easy way with selective media.

You can be more specific by framing the null in terms of the parameters being measured. E.g. instead of "effect" you may want to posit that whatever being measured will not be influenced by light intensity (e.g. phototaxis).

Here some primers: U is indeed the activity (short for unit). You need to figure out/decide how much enzyme activity (how many Us in total) you need in your assay. With that known, you got the volume of your enzyme. Next DNA, here you got all the info. How many microliters of your DNA solution correspond to 6 micrograms? Then there is the buffer. 10x refers to 10 times concentrated. What concentration, should be in an assay (hint: it may depend on the enzyme)? With these quantities known you only need to fill up with water to the final 20 microliters. You may also want to check out the websites of restriction enzyme manufacturers, such as Fermentas or NEB.

With groups I meant the composition of people under a given PI (or, in short, the one who provides the money). However, also in biological sciences collaborations (resulting in multiple authorships) are often limited. Often authorship are shared not due to the actual work done, but e.g. by providing resources, such as samples, instrumentation, etc. Exceptions (more than in mathematics) exist, though.

This is incorrect. The rise of oxygenic photosynthesis is placed around 2.5 Gyr ago (studies that place it earlier are heavily contested). AFAIK the latest studies place cyanobacteria around 2.15 Gyr (and eukaryotes around 1.8 Gyr), but I may be remembering it wrong, it is just something I picked up talking with colleagues and I may be remembering the precise numbers wrong. But in any case it would be at best in the late Archean, way later than the first prokaryotes. Also nitrogen fixation has evolved earlier than photosynthesis, especially considering that the nitrogen fixing apparatus is very sensitive against oxygen (something that the early prokaryotes did not have to worry about). What you may have read is from a paper in the 90s (and which is erroneously propagated in many sources) in which it was claimed that records of cyanobacteria are way older. But this has been basically dismissed by now. According to molecular clocking mitochondria evolved earlier. Evolutionary evidence favors the assumption that the rise of the first eukaryote is bound to the endosymbiosis with prokaryotes.

As a rule of thumb in the lower levels (i.e. students and postdocs) the female to male ratio is higher in biology (with over 50% of women in many areas), then drops from chemistry, engineering, physics and mathematics (very roughly). Within individual groups a lot of factors play a role whether one joins a given group, though gender rarely plays a role. I have been working in groups where I have been the only male, though it happened during that time that not many males approached the group and the women just happened to be better. Depending on the PI some try to get a balanced group (to avoid the impression of gender bias), but a good fit is still the most important issue. In addition, it is often that one is approached by a group of students who want to join for undergrad research (and these are then more likely candidates to be accepted for grad research). These groups tend to be all-females or all-males, for some reasons.

Why do you think that an endospore is not a spore? Maybe you are confusing bacterial spores with eukaryotic spores?

As a rule of thumb the error rate scales most strongly with the number of reactions (i.e. length and cycles). The lenght is not an issue here, so keeping the cycle number as low as possible can help. Think of it that way, during any single reaction there is a (mostly) stochastic chance of an error, and then there is the chance that this molecule is used as template (and hence increasing erroneous products within the population). Sequence also has an influence, though unless you have runs (i.e. a stretch of identical bases) it is most likely less of an issue. Of course, using high fidelity polymerases are always preferred. Remember you do not amplify the 25 bp once, but many times and the error rate is a function of the total reactions occurring within the sample.

Excellent. I just did not want to write an answer here, because as it is always better to go through the official lines rather than listening to what someone may tell you on an anonymous board. I am happy that you took care of that. Regarding the coverslip it depends on the precise setup and what you need to do. In some cases lifting the coverslip with a sticky tape may work. I also have very fine tweezers that work fine, however you can also prick yourself with them (though not quite as easily as with needles).

It will depend a bit on the nature of your unspecific products (e.g. are they bigger than expected, or smaller?) and what their source is. Is the colony clonal, for instance (i.e. are the different plasmids in your isolation). As long as the regions are not highly repetitive high AT should not be a problem.

Except that the processes that are possible in the brain (i.e. integration of signals above the cellular level) are not present in bacteria. Sure, there are certain bacteria that create multicellular structures, however the involved signalling cascades allow only for simpler (though overall, still relative complex) information processing as compared to even relative simple neuronal systems. The point is that multicellularism allowed the evolution of novel information processing methods that are not possible with a bunch of individual cells. However, some bacteria are borderline multicellular (in certain developmental stages) and show the first signs of emergent properties. Though certain limitations (e.g. possible length scales) exist that true multicellulars have eventually overcome.

All accidents of this nature have to be put on record. I.e. talk to your labmanager/PI and also the safety manager. Also, I would take a close look at procedures and get rid of sharp implements whenever not necessary. The coverslips can also be lifted by tweezers that can be sterilized, for instance.

It is fairly easy when working with fast growing bacteria, however if you need to incubate plates for weeks or months particles in the air (of which the experimentator is a significant source) are a big problem that cannot be circumvented by spraying disinfectants. But I agree, careful planning and placement of the experiments is extremely helpful. Depends on what you sterilize. Metals (such as inoculation loops can) can be directly heat sterilized directly (i.e. glow them). For glassware burning with ethanol is preferred (though the effect is heat sterilization and not chemical). Finally 70-80% ethanol can also be used for surface sterilization and then burned off. The two ethanol-based techniques have different uses.

Unless immunocompromised (or allowing it to enter bloodstream by some route) dying from it is extremely rare. Though from a safety point of view I am surprised that you actually managed to swallow medium. Needle accidents are more common, though. In Germany a researcher managed to prick herself with a needle that contained Ebola. Was quarantined but apparently did not show signs of infections. I also managed to prick myself once, but with nothing harmful in the syringe.

Indeed. Also in this context it is relevant to mention that the sense of animals vary widely and it is to be expected that their perception will reflect that. An animal that mostly rely on smell, for instance, may pay less interest to visual cues that do not contain olfactory components (to give a simple though example.)

1. There are certain elements that are needed by almost all organisms (think in terms of C and N sources, for instance. As well as of the composition of biomolecules found in all organisms, such as DNA). Certain elements are needed by almost all organisms, but there are (few) specialists that can do without (iron being an example). 2. The question is very open. I would interpret it in terms of additional needs (above the absolute minimum for all organisms) that certain bacteria might have. 3. As already mentioned it is the non-organic contamination that is undesirable, Ultrapure or double distilled water is used for microbiological applications. If you just have complex media (and rather simple lab bacteria) you may get away with simple distilled water. 4. What happens if you use them subsequently? What happens if you inoculate them (with your sample) at the same time? Think about known samples vs. unknown. 5. Agar is not the issue. 6. If you want to culture bacteria in a big batch bottle, would you put agar in? 7. Think about reproducibilty of the count as well as accuracy. 8. How did you do your dilutions?

This is odd. In smaller institutes I worked in usually a faculty member is appointed to be in charge of lab safety, whereas in bigger ones there are sometimes positions dedicated to it. The absence of any such person is most likely against regulations. Also, at least on the grad level and above (i.e. for people working in labs) safety classes are mandatory. The question is where they get them. If the university is so small the chances are that someone in some department may be responsible. But if that is somewhat obscure, the job is not being done well, I assume. Of course it should not be the job of students to identify safety violations in the first place.

Well, IIRC the work with microbial agents follows guidelines from the CDC and NIH, whereas the occupational exposure to bloodborne pathogen standards is based on OSHA rules. The actual oversight is usually conducted by appointed laboratory safety persons in your department and usually there is a committee that oversees the university-wide implementation of the guidelines. So basically for these kind of question you should find out who you appointed bio/labsafety guy is and as him/her.

Actually there is quite a variety for basically all the components described. Gram+ and Gram- cell walls are vastly different, for instance, but even among the groups there are larges structural differences. The one that is probably most conserved is the ribosome complex, the rest has all kind of variations (including number of chromosomes, linear vs circular and so on). I have never heard the term glycol x in this context. What you refer to is most likely exopolysaccharides. As the name implies it is not a polyether.

If you have cultured unknown bacteria from human samples you are required to treat it as potentially pathogenic. If it is from a flu patient even more so. That, in turn, requires a biosafety 2 lab. Including a biosafety bench of the required safety level, for instance. Also blood-borne pathogen training (or equivalent) is normally required. So what you remember and what your advisor told you are bot correct according to current regulations (in the US and most, if not all parts of Europe). Just out of curiosity Is your Prof really from a microbiology background? I find that kind of behavior odd, as in my personal experience microbiologists are more paranoid regarding biosafety than biotechs.

Publishing papers is basically just a means to demonstrate research being done (and to disseminate it, of course). In most cases you pay the journals for publishing it (in case it gets accepted). If you have something patent worthy there are several layer of claims that have to be filed (quite a lengthy and costly process, as DrRocket mentioned). However, assuming that it was in an university setting, there is usually someone around that assists with that because in the end intellectual property belongs to the university. Some do assist in creating a start-up, though.