CharonY

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.

Well, most of the time you would have some idea how similar they are. If you really have no clue, then I would just try common two common algorithms for each case.

There are certain things on your wish list that are mutually exclusive. Obviously if cure cultures of something exists, they are not unique anymore. Or do you want to isolate a pure culture of something? Well, that requires a huge lot of trial and error. Depending on the bacteria you may well be trying out media and culture conditions for a year or more before you really get something.

For instance. So basically the overall proteome profile (or at least subsets of it). There are a huge numbers of applications and methodologies. But the basis is that it involves monitoring the presence and often the (relative or absolute) abundance of a large set of proteins (i.e. the proteome). Biomarker is a special area, though I could rant all day about the problems.

It depends on what you want to see. Local alignments are superior in detecting local similarities and are generally better suited for sequences that are overall dissimilar but with smaller conserved areas. Global alignments are better at aligning larger stretches of sequences, however. Again, it depends a lot on the type of sequence you got (e.g. overall similarity) and what you want to see.

First part hits the nail on its head. The example (as described) does not appear to be proteomics workflow per se. It addresses the expression of a single protein whereas proteomics is generally referring the whole set of proteins (or rather as much as we can technically get).

Actually it is pretty much established that mitochondria and plastids are of bacterial origin. In addition to the DNA the presence of an additional membrane with bacteria-like lipid components are pretty much strong indicators. The point regarding the DNA is not that it is different from human (how could it?) but rather that the organization and genes are closer to bacterial ones. Thus, they encode (and hence, express) ribosomes that are bacterial in structure. However, the timing is not quite clear. I.e. whether the eukaryotic cell arose first and then internalized the bacteria, or whether the original host was a prokaryote itself.

Think about dynamics. What is more stable in short time frames, the proteome or the genome?

The answers as well as the question mix up two distinct elements. The first is nutrition uptake, e.g. the material required to generate biomass. This is what you would generally understand if you talk about consumption. The ability to rely purely on inorganic substances is called autotrophy. The inorganic source for carbon is, as shown in the first part of the OP, obtained by CO2 fixation. However, CO2 fixation requires energy. And here is the second part, some organisms can also rely on inorganic sources for energy production. The one you have heard most about is most likely photosynthesis (where the light reaction provides energy, whereas the CO2 fixation is light independent). In general most respiration (the mechanism that creates energy) requires reductions equivalents that are shuffled through a membrane system to create a proton gradient, which in turn, is used by an ATP synthetase to create energy (I will leave out fermentation here). Thus you essentially need an electron donor and and acceptor for the respiratory chain to work. If the donor is inorganic, (an example is e.g. oxidation of ammonia to nitrite) then it is referred to as lithotrophic. Note that in this case the inorganic substance is used as an electron donor, but is usually not consumed (i.e. internalized to build biomass) and can also (of course) not serve as a carbon source.

Actually mitochondria and plastids are endosymbionts, and it is not a nested symbiosis (for that the endosymbionts would have to carry other, smaller bacteria themselves). There are a lot of interesting symbiotic relationships around. For instance, Photorhabdus is a bug that is a symbiont to nematodes. The fun bit is that the nematode infects bugs, regurgitates the bacteria, those then kill the host, and both feast on the dead insect. Then, in the next cycle the next generation of nematodes takes Photorhabdus up again and searches for new prey.