CharonY

I see. I have not found paper with regards to WGS, but I stand corrected. However, after a quick view over the notes it appears to me that they do not address whether they were able to assemble properly. I do not have time to delve into the lit. right now, but it appears to me that they just blasted sequences against the human database and assigned whether it was a hit or not. Again, more typical for genotyping workflows. Note that WGS is also often used in this context, i.e. do one (or several runs) and then utilize the data for searches without too much of an assembly and let gaps be gaps (I would call that high-throughput genotyping). However, since I am an "omics" guy I specifically refer to it in terms of reconstructing the complete genome (just so that there are no misunderstandings). You could check the associated papers (if any) whether and how well the assembly went, or maybe ask the technical support of these company for that data. If they think they can sell something they are often willing to tell you stuff (short of the actual formulation that is). Huh? Is a horse growing out of my lower back? I should better check... Edit: I was curious and quickly peeked into the Lam et al. paper cited in the notes and there they processed saliva directly. Also note that with next-gens a single run is usually insufficient to get enough coverage to assemble the whole genome.

Genetics, by definition, means that it involves genetic material. Surgery, or any other procedure may affect metabolism or general physiology, but it will leave your genes unaltered.

Maybe I should say that I was thinking in terms of genome sequencing (as you mentioned whole-genome sequencing), however it appears you are more interested in genotyping (e.g. SNP analysis etc.). For the former, having a very intact and clean chromosomal DNA is important to be able to do decent assembly. What I have seen from the respective manufacturers were not information regarding the quality of the genome except PCR and a simple gel. Both of which show that you do not have totally degraded chromosomal DNA but do not give sufficient information regarding the integrity. It is possible that I overlooked that part, but human whole genome sequencings are done rather rarely. But again, if you do not want to assemble the whole genome, which is highly unlikely considering the number of samples you want to run, it is much more feasible. In the end, I have not idea how the mixture is going to interact (with each other and the cells) and I would resign to a testing run. E.g. preserve it for a few months, then run e.g. PFGE or even a shotgun run with a sample and check the results. 23andme are doing microarrays, IIRC, so again different needs as opposed to whole-genome sequencing. And in fact, all commercial labs are just doing genotyping. The postanalysis for whole genome sequencing is still just too time and money-consuming to have a high throughput, especially with the next-gens.

The vials that we use contain 1.8 mg EDTA per ml blood. Note that in commercial tubes EDTA is sprayed to the walls, which facilitates easy mixing. If you just pipette it in, you have to be quick and ensure thorough mixing.

One could even argue that cancer is, in certain contexts, not even a malfunction per se. Early in our development all cells are multiplying with little restraint. Only somewhat later signal gradients are formed that result in a more refined control. It is not clear how these regulatory cascades kick in, and what may make them not kicking in. Cancer cells could revert back to earlier stages, possibly by certain unknown perturbations of their regulatory circuits, that may well be caused internally (i.e. without outside agents such as mutagens). Maybe there is normal physiological change during aging that makes it occur more often, etc. etc. You may live the healthiest life, and keep yourself away from viruses and so one, but the mere fact that you need to breathe, that your cells need to replicate, that tissue needs to be regenerated all has the inherent potential to result in something that we would classify as cancer. From a research perspective my point of view is that we need a more fundamental knowledge of cell physiology and the underlying regulation. Much research nowadays bypasses that (IMO) critical point and just aim at nailing cancer. But then this is where the funds go to.

T7 RNA polymerase is a phage enzyme. They specifically deliver to the cell to synthesize their own proteins. Plasmids rely on their host machinery for transcription. They too, however, provide genes for their own replication. If they do not possess the right promotors, the transcription rate is going to be very low (if transcribed at all).

I would involve you in a long and convoluted discussion about why it is not going to work. Also I would steal your coral.

Some of the holes are part of our normal cellular processes. Plug them, we die. Getting rid of water would be.. hum.. getting rid of your body? I sense an analogy fail here somewhere.

Considering that especially for 454 the DNA quality is a huge issue I would be kind of surprised if it works out. RNAlater was the high-salt formulation I was referring to. In that case one would store the tissue sample in it, but even so at 4° usually it is not more stable than a month. With 454 around 3-5 µg could be enough, so from 1-2 ml saliva, freshly prepared, it may be enough. However, purity and integrity could be an issue. I doubt that you could get enough with sufficient purity and integrity out of it after prolonged storage at RT. In fact, I would actually check whether someone did next-gen sequencing, or at least built and checked libraries using that kit. PCR is a rather weak quality control and I would not trust a standard agarose gel to give me sufficient info on quality.

What we see today in form of NRP does not have in any shape or form similarities to what the article alludes to. They involve multi-step enzymatic pathway that are impossible with today's well-established machinery. Just because a word sounds like what you mean, it does not necessarily mean it. Earliest form is almost inevitably a simple self-replicating machinery. Reading up keywords on wiki and building up a story is a shortcut to the speculations section.

RNA polymerases are not specific to promotors. The strength of binding to certain promotors is mediated by transcription factors (including sigma factors).

Technically we are most likely only discussing a handful of different allele variations. As mentioned, there is nothing like a pure race from which you can derive a fraction of. There are not really shades of something as we are talking only about a tiny percentage in difference. The relationship of their ancestors would provided the strongest impact. Also, "black", for instance denotes a much larger genetic variance than all other common denominators (such as asian, caucasian etc.) taken together.

Urks, sorry to say, but this is a muddled piece of unfounded assumptions and more or less random intuitive leaps. First of all, there are certain peptides that considered secondary metabolites and synthesizsed independent of the ribsomal machinery. They are not related to what is discussed in the article (initial peptide synthesis is arguably of much lower complexity than what we see today). The article deals with the evolution of ribosomes. Thus, using sequence analyses they tried to figure out, which part(s) were first in the facilitation of translation. I.e. they argue that the early machinery could not be pure RNA-complexes but were early on RNA-protein complexes that coevolved and progressively increased protein quality. The result was a dominance of proteins derived from this apparatus and essentially replacing whatever worked before. Thus the authors conclude that an earlier form of peptide synthesis must have existed. Although they did not elaborate that in the article. It should be noted that one of the reasons why a pure RNA world appears attractive is that AFAIK we do not really have good data on self-replicating peptides. I cam across a paper once, but it is pretty much controversial. But then it is not really my field.

From anecdotal conversations the work hours are not too different from the US (In an Uni-clinic the average hours were 60ish in Taiwan and the US). A large difference is the number of patients that they see in that time frame. This has (again, based on anecdotes) at least two reason. One is that the number of patients has an direct effect on their income. Thus they tend to squeeze in as many as possible. A second thing is that traditionally in Taiwan many see doctors for preventive care or minor ailments (especially for those enrolled in NHI) which arguably takes less time. Plus, if they visit a doctor often, he/she becomes more familiar with them and it may (together with the medical database) cut down on overhead time.

Replace fight with bind. Also one part of the name is missing (i.e. the target molecule). It should be clear in the name or from context (e.g. anti-bovine IgG, would be an antibody directed at other IgGs, as in the case of ELISAs).

My guess is that they provide a powerful protease inhibitor to the mix. I am not sure whether there are actually other companies selling competing kits. Others like Qiagen have storage solution for samples (not specific to saliva), but again, the formulation is proprietary. In one case it is a high-salt formulation. We generally process frozen samples (for other biomolecules though) and I am not sure how many labs are using the kit. It sounds nifty for DNA, though. Also, I am not sure that there is no degradation. Not massive maybe, but if all you do is PCR that is still fine (different story if you want whole genome sequencing).

It really depends how clean you can work. Your buffer seems a bit like a mix of everything which to me does not make terribly lot of sense. What you want to get rid of are DNAase activities. Bacteria are less of a problem when a) working clean and b) using a buffer that does not promote growth. My take is that freezing your saliva samples would be your best bet if it is only for a few month. Within the cells the DNA is nicely protected. If you need pure DNA you have to make additional extraction steps (e.g. with phenol) anyway, which nicely kills bacteria and also removes DNAse (and other proteins, of course). Simple Tris-EDTA buffer works well after that. However, without removal of proteins, your DNA is going to degrade within your cell lysate. Just FYI, the low amount of NaCl is not going to pertain to cell lysis, nor is DTT (a reducing agent). Mixtures of detergent are usually not helpful, it is easier to stick to one. EDTA is not a buffer, but functions as chelator. It reduces DNAse activity (by binding necessary divalent ions), but in a cell lysate there is likely too much for it to do enough.

Very good answer(s). Edit: I wanted to vote the post up, but being tired I clicked the wrong button. Sorry about that.

It is very tricky to impossible to "design" antibodies from scratch. It would require the knowledge of the 3D structure of the target and especially of the epitopes under quite a bit of different conditions (the structure of proteins is rather dynamic and highly dependent on its environment). For this reason, even having a crystal structure would not automatically solve the problem. Plus, you got the precise problem on the antibody side, of course. And finally the binding is often not absolutely specific, as ecoli pointed out.

I do not really see any connection to memory. However, the domestication of other animals was most likely utilitarian in nature, depending on the animal it would be symbiotic, though in other cases much less so. The enjoyment of companionship however, is part of our nature. Nature's rule book (if you will) is extremely flexible and much more complex than we can imagine.

That would be very very odd.

You misunderstood something. Mitochondria are almost certainly bacteria. However, molecular evidence shows that early eukaryotes arose from fusion of archaea and bacteria. Not the mitochondrium- the whole eukaryote! There are different hypotheses, but they have in common that presumably an archeaon underwent a symbiotic relationship with a bacterium. Later a fusion of these cells occurred. Depending on whom you ask some may argue that the first result was a eukaryote-like cell with a kind of nucleus and that a second symbiotic event led to the formation of a mitochondrium, whereas others propose that everything went in a single symbiotic event. Quite the contrary, using sex for reproduction is, from an evolutionary point of view rather weird (due to the two-fold cost of reproduction).

As Arete said. Mutualism for starters. Nutrient exchange then may prove beneficial and becomes a conserved trait, whereas other abilities may become lost (as there is no selective pressure to maintain them, for instance). The end result can be an interdependence. Many intestinal bacteria can survive outside of the gut, though they tend to be rather bad as competing with other bacteria.

Just the some minor comments (I also have comments on the content if you are interested): line3 : assess whether... line 5-6: try to split the sentence in two. Abstract 2: line: AuNPs have not been widely line 4: You can probably shorten: the ESR spectra suggested that the probes do not interact with the AuNPs? Abbreviations (as NNO) should be written out once

Nope from the 20k genes any number could be identical to a given ancestor 20 generations ago. They do not get (necessarily) outdiluted over the generations. To make a correct guess (using only genes, although non-coding regions are also critical) you would have to know how many variants of a given allele exist in the relevant pool (consisting of your ancestors). If, for instance, in a given locus an only one allele exists within your family, you would have that allele and, assuming that you do not mate with someone who has a variant, so will your offspring. edit: it could be that you are using genetic ancestor in an unusual way and I may misunderstand you.