CharonY

To me, it is more an arms race rather than brickwalling (i.e. dynamic non-equilibrium situation). Especially in hospitals the bacteria appear to be winning, though a rethinking (not only of the use of antibiotics, but of hospital hygiene in general) has started.

As already mentioned, recovering memory is a creative processes. I.e. memories are recreated and not stored as a 1:1 representation. Moreover, on every level, starting at the retina, image information is heavily processed and only very limited, but often focused information actually reaches the brain (neglecting for the moment that eyes are actually part of the brain, too). This is the reason why under highly suggestive conditions (as e.g. hypnosis) suddenly details may pop up (i.e. they were created on the spot and are barely distinguishable from real memories, provided such a distinction really exists).

I should note that afaik there is no expert here on this board currently who would be able to evaluate histological data.

With regard to the dynamic range: the calibration curve is based on the actual output of your measurement system (in this case the OD readout of the photometer). Moreover, for most photometers an OD of over 1 is highly inaccurate and requires dilution before the measurement. PH is certainly a factor. A slurry is not a good thing as particulate matter absorbs or deflects your beam. I.e. for a decent measurement you analyte has to be completely dissolved. With regard to background: I recall that Biorad had a nice summary of a number of things. You may want to check their website. With regards to denaturation: in the Bradford reagent phosphoric acid is actually used to denature the proteins in order to enhance the complex formation. Also to think about it in a practical way (at least for those familiar with protein analyses). Bradford is based on coomassie. Where else is it used and are the proteins still native? What was meant is possibly that without homogenization the denatured proteins (i.e. cooked meat) will simply accumulate as precipitants. Relatively little of it will be found in the supernatant. I am surprised, though. If you really want to figure out the protein content the first step would be to homogenize it and then get rid of interfering substances.

Also known as clear communication.

I would suggest keeping as many as possible. Textbooks are often very helpful to refresh memories, if one stays in academia or similar settings. Being somewhat familiar with a textbook has the added advantage (as to getting new sources) that you can find your way around it pretty fast.

There is no simple statistical measure that determines the significance. Whether any given similarity is purely by chance depends to a lot of factors, including the type of sequence, length, search space, etc. BLAST has such a measure, for instance, however there is no clear cut-off that you could conveniently use. Especially if you only got two random sequences, you cannot assign a probability, as you do not know the population from these sequences where fished out (and hence, how much of it was just chance). The only you can describe is the distance, in this particular case. Also, this is more a computational/mathematical problem that is absolutely not related to DNA or biochemistry per se.

This is precisely the point. I also want to mention that there are different measures being thrown around in this thread. One being the impact factor, which is a measure of the journal, not the individual works, and the number of citations in a given paper.. It is generally accepted that comparisons are only valid (if at all) in a specific field. And finally there are also measures that are based on the publications of a given author (most notably the Hirsch-index). So the goal is to measure quality of a journal, of an individual paper and of an individual author. But yes, the overall problem is how to measure quality in research as a whole, which is a giant can of worms in its own right.

The way Bradford works, denaturation should not influence it by too much. There are a variety of caveats, though. First is the influence of other stuff in your sample. Assuming that you did not include purification step, other compounds that are not proteins may influence the assay. Some may, for instance absorb at 595, whereas other (e.g. high salt levels) may inhibit or promote formation of dye-protein complexes. It is also relevant to note that the efficiency of the dye-complex formation is also dependent on the protein itself. For instance, at the same concentration, BSA generally yields higher ODs than IgG. That being said, there are also some issues with your data. For instance the OD readings are well above the dynamic range of your standard curve or are in the lower range. This is not very helpful for an accurate determination. Overall I would say that the influence of other compounds, especially particulate formation in your sample are playing a bigger role. For proper protein content determination it is generally a prerequisite to have at least one extraction step prior to actual measurement.

It depends on how it is drawn, but in square representations the horizontal length represents the node distance. The vertical line is just there for visual reasons (in other representations it is actually absent).

This is less a genetic, but more a physiological issue. That being said, many bacteria are able to synthesize all the compounds they need, we (humans) and our relatives have lost many of these anabolic pathways.

Burners are a mixed issue, I did both and it really depends on handling. Advantage are of course the heat that kills microbes, but the disadvantage is convection. I found that flames are more useful if you have lengthy work (e.g. Hungate). For quick plate pouring I found it unnecessary with a little bit of practice. Ethanol cleaning is a good idea, unfortunately it does not help terribly much against DNA contamination (e.g. for PCRs).

Hrrms, awfully slow. But OK if you only pour few dishes at a time.

Primary sources of contamination are your body and dust circulation in the lab. There are several methods to pour plates but first you need a clean area with little to no air circulation (e.g. avoid being in an area where people move or where air inlets are). Sterilize your hands, never move parts of your body (i.e. arms and face) over stuff that are supposed to be sterile. Work quickly but move accurately (takes some practice). The longer stuff is open, the higher the contamination risk. Plan all your moves before execution. Usually you autoclave the medium with agar first, and then pour it into dishes. Stack the empty dishes and pour from bottom up (i.e. lift the cover of the lowest dish together with the other dishes on top, pour, replace, lift the next lid, etc.). In my hands this is the fastest way to pour while minimizing exposure. Horiziontal clean benches are good, if you do not work with anything hazardous (as the flow keeps plates clean). Laminar flow hoods are also decent, although they are more designed to protect you. Still the overall airflow is controlled. Zero-flow boxes also work. Do not use the fume hood (unless you really got some nasty stuff in the medium).

OK, I still do not understand the purpose, however the problem here that I see are the distance matrices. The substitutions in an amino acid are related to the changes on the base level (i.e. it is connected to the genetic code). So an amino acid exchange that only requires one base exchange is treated differently than one that takes to, for instance. Since your amino acid string is based on a completely different system the distance estimations will be off. In fact, I think what you have is a simple computational problem that I am not qualified to solve. Since the string has no biological basis, you cannot apply the same theoretical framework. From what I understand the only reason to call it an amino acid sequence is because you use the same 20 letter code. I am going to move this to the computational science section, maybe someone else can look over that.

Check the scale at the bottom and use that to measure distance (and then convert it into substitutions/site).

Yes pairwise is appropriate (though not precisely necessary). I am still not sure regarding how the sequence is supposed to look like and what kind of clusters you want to have (or what you mean with cluster for that matter). For starters I would just go for a tool that e.g. uses an implementation of the Smith-Waterman and take it from there. Again, since I am not quite sure what you really want to have I would just hunt down some tools and play around with it.

If you just want to separate out existing strains, I would go for a mix of well-culturable strains (think E. coli, Bacillus subtilis, etc.) and read up on selective plating. Then choose strains according to the chemicals/plate types you have access to, and select the strains accordingly. Starting from a mixed culture this will give you defined strains in the end. A more inelegant way is dilution plating, but even with established cultures it is often tricky to have a really pure one in the end.

As I said in my earlier reply, there are whole disciplines dedicated to this particular question. It is quite a non-trivial process. And no, it is not explainable outside the framework of evolution in general and social evolution in particular. Note that cellular behavior is the consequence of the working of their regulatory networks. I would avoid terms like instinctive as much as possible, as it may be misleading in many ways.

Short answer, one of the major mechanisms in social evolution appears to be kin selection (read up on that as well as Hamilton's rule to get a rough idea). There are certain elements that are extremely tricky (most notably the threat of cheaters). There is a whole branch of evolutionary biologists that focuses on this particular area. Sex is an extremely bad example as it actually is a case against collaboration. It is associated with the famous two-fold cost as opposed to non-sexual reproduction and models using the increase of allelic variance have not been able to resolve this problem. Other, more molecular oriented explanations appear to be more reasonable, but I am not sure if it has been shown mathematically to be a viable solution.

What you have to take into account is the final concentration in your solution. So you have to take the dilution into account as a result of mixing. Hint1: the final volume is 5 ml.

Yes, but the carbon source can be inorganic. I.e. CO2.

Motility refers to the ability to move around. Note that currently the 6 kingdom (three domain) classification is the most widely accepted classification system based on molecular data.

Ok, do you have two or more sequences and more importantly, what do you want to see?

I think you are underestimating the time and effort you need to do create and characterize pure culture. As a rule of thumb, characterizing one novel species is basically one paper. I know of some PhD students that manger to create roughly 3-4 pure cultures from soil samples, for instance. And they considered themselves lucky (there are attempts from water samples that have been going on for roughly 20 years). It is much more difficult than just a simple dilution plating and picking colonies. Creating pure novel pure cultures is definitely not something that you can do quickly. But if you want just to create a pure colony based on known species, just mix some well-known ones with distinct attributes and try to recreate a pure culture out of it.