CharonY

With regards to MRSA, it is not a disease per se but the short form for methicilin-resistant Staphylococcus aureus. I.e. It is group name for specific S. aureus strains that are highly AB resistant. They may or may not cause diseases. Mostly in immune-compromised persons.

If you use certified weights the only thing you generally have to do is to go into the calibration mode, put the weight on it and then just type in the value. If you want to know whether your measurements are within allowed tolerances there are generally reference handbook from NIST (i.e. for overall guideline) or from the manufacturer.

OK in order to explain that one has to be careful from which viewpoint you start the discussion. As such we cannot e.g. state that the role of TSH is to cause hyperplasia, for example. Its production is altered involved, but only under extreme conditions. So again the baseline is the regulation of T3/T4 via inhibitions of TSH. So normally higher iodine concentration would tend to increase baseline T3/T4 up to the point where the levels of their level would inhibit further production. The Wolf-Chaikoff again is a phenomenon happening under conditions when the regulatory system is overloaded but involves a different regulatory circuit. While the circuit itself affects TSH and T3/4 levels, the mechanisms are independent. In fact, the mechanisms have not been completely elucidated. What is known is that organification of iodide is inhibited at this point it depends on how high the actualy thyroid hormone levels are how TSH is getting affected, how long the inhibition is maintained. Often Wolf-Chaikoff can continue for up to a few days, before the escape mechanism kicks in (basically reduction in iodine uptake due to inhibition of transporters). During this time thyroid hormone levels may become depleted and then TSH rises. If the effect is shorter it may not happen (but usually a short inhibition would not be noticed clinically, anyway). Now finally to the point of vascularity. The link between TSH, and iodide treatment to vascularity are much more vague than the OP indicates. I.e. it is not a straightforwarded regulatory control or link between these items. In fact there are studies indicating that iodide treatment has little to no effect on vascularity on Grave's disease patients, whereas other found them to be beneficial, for example. Likewise (at least to my knowledge) it has not been shown with absolute certainty whether TSH or actually TSH receptor antibodies are responsible for changes in vascularity. Finally you have to remember that in cases when iodide therapy is indicated, parts of the usual regulatory control is messed up (which actually leads to e.g. hyperthyroidism). So again using the example of Grave, here we have a case where T3/4 are high, TSH is low whereas TSH receptor as well as antibodies against these receptors are elevated (the primary cause of the condition). I.e. the assumptions in OP are too simplified to explain occurrences (which are not terribly well understood, unless there is some very current literature that I may have not seen).

If it is not autoclaved or filtered there is a good chance of contamination, even in the fridge. But you would have to sterilize it before use at some point, anyway. If it is sterile storing it in fridge or RT is both OK for a while (but avoid direct sunlight).

I think you got the effect of TSH wrong. As its name (thyroid stimulating hormone) implies, it induces production of thyroid hormones. However the hormones themselves inhibit TSH production and thus limit their own production. Hyperplasia happens if regulation is disrupted.

I think the point he wants to stress is that under the current conditions in many countries that getting killed accidentally is much more likely than killing in self-defense (at least nowadays).

On that note, in which system (i.e. country) is this happening? Since you are in grad school for two years and only have been actively working for 6 months on your thesis I presume it is the UK/US style, which generally involves a committee as swansont mentioned. In that case it would be a good opportunity to talk to other members of the committee to get a more objective view on that matter. There is also a good chance that the data you have collected was presented not in a very concise and convincing manner (which is rather typical if you just start out) and he may have just been confused by it and running out of patience. It would be wise not to tell your advisor to "shut up and listen", though. BTW, is this not more appropriate for the science education section rather than ethics? Unless we want to discuss cases in which advisors try to suppress valid data that disprove their theories, which may or may not be the case here.

The void volume is important in assessing when the unretained i.e. very large molecules pass through. So in certain applications, e.g. for desalting purposes (or group separation in general), your sample should elute at or shortly after the void volume. Checking the void volume is generally to establish that nothing is wrong with the column (e.g. whether channeling occurs) as well as getting a background measurement (e.g. of the solvent itself). In these cases where you want to separate a high MW from a low MW species, the void volume determines how much you can load. In a well packed column this is about 30% if the total column volume. For high resolution separations a lower volume is required as explained by BabcockHall. I.e. it is the other way round, a small volume increases resolution (usually down to 0.5% can be used). On the other hand, assuming equal concentration, a lower volume will get less signal, so if you approach detection limits you will have to increase the concentration or volume (and sacrifice resolution in the latter case).

For enzymes typical some companies to look at include invitrogen, new england biolands, fermentas etc. For DNA I have no clue what you are looking for, as it would be highly dependent on organism. Also, I do not know what PMCR is. Do you mean PCR?

The reason they used yeast and hey infusion is because they were not certain what would be required to generate life, if it happened spontaneously. What was know is that boiling liquids would kill of the organisms, as at that point Pasteur showed that without exposure to air, no "alteration" of the water, as they put it, was seen. The alteration being of course clouding of the liquid due to the formation of microorganisms. Pasteur demonstrated (or rather proposed) in his experiments that particles in the air may have been the carrier of those microorganisms (and he even tried to correlate it by exposing samples to air in different areas which he assumed to be more or less pristine). Pouchet set up to disprove this notion in his experiments. In his case, he used artificial air, as well as heat-inactivated hey. Remember, a that point they did know nothing about the molecular composition of life, Pouchet assumed that living things contained a kind of life force that would spontaneously give rise to new life without parents. And indeed, he found something growing in his experiment despite the fact that there was no exposure to ambient, the main source of microorganism in Pastuer's experiment. Later Pasteur would find that there were sources of contamination in Pouchet's experiments, though.

With 20 kDa G-25 is a good bet (cut-off is around 3-5k, IIRC). G-50 is about 30k, which would not be useful to you application (assuming globular proteins that is). Maximum volume is directly dependent on the pore volume (and other factors such as particle size as it affects sample dispersion and thus peak width).

Is this a homework question? There are quite a number of suitable experiments. The general elements are the modification of the elements of interest (most cases that would be mutagenesis) and monitoring the outcome (for regulatory elements it could be expression studies, for example). For protein-protein interactions there are also many techniques available, depending on what you want to see at the end and what kind of instrumentation you may have available. Considering that this may be related to some kind of course you should probably just look at the techniques being discussed to find the suitable ones/

Well, both are linked to cancer and are known to be mutagenic. Due to the way the respective compounds are taken up and metabolized, some tissues/organs tend to be more affected than others. That said, tobacco consumption has been found to be implicated in buccal cell changes (for review: Proia et al. Cancer Epidemiol Biomarkers Prev. 2006 15(6):1061-77). I am less certain about alcohol, especially as it is converted to acetaldeyde before being genotoxic. From that I would assume that during non-excessive alcohol consumption the effect on buccal cells could be rather low..

Oral tolerance is, to my knowledge, only partly understood. The common part is that both antigens (food and pathogens) are presented to T-lymphocytes, however the way they are presented changes the antigen-specific responses.It has been found that in absence of inflammatory signals, presentation of antigens to T-cells by dendritic cells favors induction of tolerance rather than activation. The precise molecular reasons are (again, to my limited knowledge as it is not my field) not quite clear but IIRC numerous activities in the spleen, and various lymph nodes as well as the lymphoid mucosa were found to be involved. Another route is the presentation of food antigens by enterocytes which, in absence of further stimulating molecules causes the T-cells to be unresponsive to further exposure to the antigen (anergy). I am pretty sure that more up-to-date research should be available, if you look for articles about oral tolerance.

Excellent point. I (obviously) have not thought of that.

You mean there is a fungal infection, or how did you determine that a) there was yeast and b) that the adverse effect was by nutrient competition? The reasoning is likely to be off, indoles do not "produce" yeast. There are plenty of sources very fungi can come from, especially if you do not work under sterile condition. However, if you did your own nutrient solution under non-sterile condition, there is a good chance that you accidentally cultivated fungi in it and then infected the plant with it.

I never mentioned metabolic independence. In fact, interdependence is quite common. The distinguishing factor is that viruses are unable to do any type of metabolic activities on their own.

I do not think that one can reasonably assess that. Many heart attacks are not associated with pain, for example http://www.nhlbi.nih.gov/health/health-topics/topics/heartattack/signs.html

Which metrics did you use to assume that and what are the comparative scales? I.e. do you compare biodiversity say, per area unit or per country (that is, political borders)?

Injecting foreign antibodies will elicit an immune response (that is how secondary antibodies are raised). AFAIK there are trials of using transgenic mice to produce human sequences. I think some of them even went to the trial phase, but I am not up to date on this matter. However, these are supposed to be used for therapeutic purposes and I would be surprised if that would be able to be diverse enough to replace a complete immune response.

Rare relative to what?

It depends quite a bit on the protocol (and kit components). I always made the stains myself and use the MS-compatible staind. One of the first things to go tends to be the sensitizer. If made yourself or the bottle has been opened (but stored appropriatelyI would think that within a few months the components would degrade significantly. Fully closed kits tend to have shelf lives of 1-2 years (though I would check the manual and lot information). 3-4 years may be pushing it (especially if they have been around a while before purchase), but I would simply run a test gel with a dilution series of a reference sample and look how sensitive it still is and whether it is sufficient for applications.

It is also quite a bit dependent on perspective. Scientists from different (sub-)discipline. From a physiological perspective the lack of own metabolic activities is probably the most important distinction (whereas symbionts engage in metabolite exchange, for instance).

Excellent point!

Well, GCMS is more for identifying metabolites, as many of the more interesting compounds tend to be volatile (terpenes, flavenoids and lipids come to mind). But isolating them would be difficult endeavor with that, I agree. It really depends on what you want to do, but for a metabolomic approach I would do an extraction and run it on a GCMS to see whether there is anything of interest to begin with (which can be coupled with pre-fractionation). Especially because a decent GCMS is generally way cheaper than a comparable LCMS.