CharonY

A major source of RNA degradation is also of biological origin- RNAses are everywhere. Moreover, RNAses are much more stable than DNAses. The mentioned fast degradation of RNA within a few minutes is almost certainly caused by minute RNAse contamination.

The use of thymine instead of uracil has less to do with molecule stability (in terms of degradation) but is most likely a mechanism to reduce mutations. Deamination of cytosine form uracil. Its presence in the DNA would therefore complicate the repair of this kind of mutation.

Let's make it apnea dive basket weaving and I am in.

That is generally called molecular biology.

The 260/280 ratio is based on the absorbance of the sample measured at the indicated wavelength. On OD of 2 is rather odd unless you factored dilutions in. Most photometers are unreliable with values near 1.

Eh, visual images are recreation based on excitation patterns in your retina due to absorbed photons.

To the topic, for most pictures I do not see that they novel techniques are used. Just nice samples.

They are also able to solve longer logic riddles (e.g. pulling up a short stick dangling from a rope to get to a longer stick that allows then finally to retrieve food) without active training. Also they communicate dangers and teach their kids to stay away from certain individuals. Since the kids react to the person without actually having interacted with them before it is the basis for the formation of culture (in the sense of transmitting information across generations).I think we had a thread about it (specifically the worm and the stone experiment) in the news section. I personally liked the part when one of the crows decided not to participate because he got sick after eating a worm.

I would be surprised if you could gain significant weight on a rice diet.

Short on time just a few quick answers (with lots of typos, I presume):

1) depends on what is known about the RNA and the genome. If sequences are known, a simple sequence search on the genome may be sufficient. Based on that (or even without the knowledge) a number of PCR strategies can be employed to amplify the desired gene.

2)I also have a bit of a hard time to understand that sentence. To me it reads that microarrays (MA) could be used to assess how much each genes pertains to the total pool of expressed transcriptome (i.e. total mRNA-pool). This would be incorrect as whole-genome microarrays have problems normalizing across the whole array to allow cross-comparison between genes. One can essentially only accurate compare the expression of a single gene under different conditions, but not compare one gene with a different one (though there are now special methods available for that)

3) In a standard MA experiment you the whole genome spotted on the microarray unlabelled. They serve as the template for the cDNA probes to hybridize. Then you generally isolate the mRNA from cells grown under two different conditions, or healthy and diseased cells, reverse transcribe (to gain cDNA) and label them with different dyes. Both are then mixed and hybridized against the chip. So on a given target gene on the array, both cDNAs of the respective gene from healthy with dye1 and diseased with dye 2 are allowed to hybridize. A scanner than scans the chip with the specific wavelengths for each dye. The resulting intensity of dye1 in comparison to dye2 on any given gene on the MA thus allows you to assess the relative expression strength from condition 1 (e.g. healthy) to condition 2 (e.g. diseased). Now, the labeling efficiency may be different from dye 1 to dye 2 or the scanner may have a bias. Therefore swapping the dyes (in this case label healthy with dye 2 and diseased with dye 1) can help to normalize potential biases.

Note that the fluorescence levels are measured not the colors per se. They are only measured using different excitation wavelengths and filters.

4) In fluorescent measurements you often have weak background signals that vary from experiment to experiment. You have to account for them. There are a lot of different strategies, the simplest just subtracting the background from the overall intensity value in the vicinity of the spot (as the background may also vary across the chip). If you don't do that, the signals may appear higher or lower due to the background, rather than the true fluorescence signals from your probes.

5) There are a lot of different nomralization strategies for microarrays. I think you may be confusing different medians here, but there are too many schemes to detail them all here. In short, intensity values are not homogenous within a chip therefore often a normalization e.g. according the way they are printed are used, but the differences between MA batches is often higher (another normalization is needed here). The log2 transformation is to make the values easier to calculate. For instance, an increase by two-fold would be, without log transformation, 2, whereas a two-fold reduction would be 0.5. With log 2 transformation the values would be 1 and -1 which creates a nice symmetry.

6) The only difference is how the targets are prepared. The printing is not the differentiating factor. I am sure you are missing some context here, though.

Do you need the theoretical proteome (i.e. derived from the genome sequence) or expression data? For the latter I am not sure whether 20 have been published (I doubt it). Even with complete genomes I am not 100% sure, though JGI for instance has been churning out a lot of bacterial sequences. You should take a look at the ncbi servers.

I assume you mean calcium competent cells (there are different types). The basic protocol is the same for basically all strains, though there are modifications. Most of the time they appear to be more rooted in lab culture rather than real-life increase in efficiency.

I do not know the precise protocol off the top of my head, but I am pretty sure you can find it quickly via a simple search. For more details I would advise reading Sambrook's Molecular cloning.

The basic premise is always growing the cells to the log-late log phase, harvest, keep cool. Then wash with CaCl2 solution containing glycerol, pellet cells again, and resuspend in reduced volume, and quickly freeze them.

Isolating a pure culture from environmental samples is extremely labor-intensive. If I were you I would try to order it from a type culture collection.

I tried to link Mendeley with Endnote but had serious problems. Also when trying to use it to reference papers it sometimes garbled up the author order. Though the newest iteration may have improved.

Actually not education guarantees a job (not even a lousy paying one). It only gives you skill that can make you more competitive. In the end, education is only a part of the equation. A phD opens up certain job opportunities (and closes off some others), for instance.

However, one still needs a strong career development plan, which does not come with the education package.

It is based on phylogeny. I.e. their relation and common history (and where the diverge). An simple (but somewhat inaccurate) analogy would to declare someone as your cousin because you share a common history (e.g. one of your parent is the brother/sister of one your cousin's parents. It is not based on the fact that both of you may have uncle Willi's nose, for instance (though you may actually have it).

Which "he" did you mean?

The one carrying a gun, I presume.

Well with regards to essential amino acids, humans have lost the ability to synthesize roughly half of all amino acids. Also note that some essential amino acids can be synthesized but not in sufficient amounts (and have to be part of the diet).

None of them produce anything. Both are involved in gas exchange, though the main function in plants is the delivery of oxygen and CO2 transport probably does not play much of a role. The reason is that leghemoglobin is necessary to deliver oxygen to symbiotic bacteria. However, the bacteria are there to fix nitrogen and they can only do it at low oxygen concentrations. So the leghemoglobin has a very strong binding constant (higher than hemoglobin) in order to ensure an extremely low amount of free oxygen, but still ensure delivery to the bacteria.

Other than that the functional groups are essentially the same, but the overall protein structure is different (both on the sequence and somewhat on the structure level). Both belong to the same protein family, though.

Compare in terms of what? Functional groups are similar, though there are significant sequence differences.

You would want to know what you want to get rid off, also the parameters of the water should be taken into consideration.

Human flora is a bit tricky as we carry a lot of opportunistic pathogens around. At low titers they are harmless, but cultivating them into high amounts may pose a problem. Using rich media as LB you are more likely to grow fungi rather than bacteria, most of the time. Getting pure cultures of anything is a completely different beast.

If one wants to do an identification, it is probably far easier to amplify 16s and sequence it (which does not require much of an enrichment).

According to this unemployment rate differences between women and men can be explained by the different jobs they hold. Also I am wondering whether stay-at-home moms are counted as unemployed (I should check out the methodology). More to the point, according to the last statistics I have seen women are still underrepresented in top jobs and receive lower salaries in similar jobs.

If I wanted to get controversial, I could say that asians are starting to pull ahead of whites in the American educational system. That, however, may be due to a few things: higher population of asians, more community-based learning styles, and historically a higher emphasis on education. Combine this with free money for education, it would appear that many Asian-Americans are obtaining a particular fitness for success in America.

I would disagree with several points. It is true that there is a high emphasis on education in Asian communities, often paired with strong work ethics. However, increasing number should not be an issue, Asians are still a relatively small proportion of the overall population. Also I do not think that most Asians are elgible for free tuition. In fact, most Asians in universities I have encountered are foreigners. IIRC something ike 50% of all postdocs and 25% of faculty in the US are non-Americans, with Indians and Chinese being among the top groups (numerically).

That being said, I would agree that in most cases affirmative action based on social backgroung rather than ethnicity makes more sense. In many cases they are at least somewhat coupled as in many cases individuals above a certain income (or parent's income) are not eligible for certain stipends. There is, however, another aspect to it. How is the selection process? Ideally one would say that it goes to the most talented from a pool of low-income students. However, as several studies have shown in different countries the very same essay can be graded differently depending on the student's name. That is, if they sounded foreign or, in case of the USA had names associated with the black population, they earned lower scores. Personally I would prefer a socially based, double-blinded selection.

Yeah, I am. I don't think accusatory rhetoric that isn't substantiated by evidence is good for the discourse. My two bits, anyway.

 

 

 

 

This is incorrect. The United Nations supported the Iraq effort after it started:

 

http://en.wikipedia....Resolution_1483

 

 

And this effort enabled a number of other countries to get involved in humanitarian *and* security actions:

http://en.wikipedia....Mission_in_Iraq

 

Both of those resolutions passed in 2003.

Right. in that case Germany could have gotten involved, if they wanted to. Though It would be a tough act after their their resistance to enter the war in the first place (and the resulting falling out with the US). More to the OP, however, at the time of the discussion there was not mandate to invade Iraq. Legally at that point the chancellor could not have provided troops, even if he wanted to. Note that he also supported ongoing inspections by the UN.

I concur. Biology and medicine are often a lot easier to justify under the "what good is that?" heading.

Though I have to add that bio is in decline, whereas biomed is taken over by medical sciences, biochemistry, engineering, bioinformatics and, yes, biophysics (though the latter is rather small addition). To me it appears that classical biology and genetics is in a rapid decline. More engineers are funded for the assessment of health effects of pollutants, for instance, than biologists.

The reason is the same, though. Understanding biological principles does not quickly lead to applications (something that the NIH is strongly interested in).

Also the German constitution generally does not allow Germany to enter an attack war, unless it is under an UN mandate. Since this was not the case, the German government would not have a heap of legal troubles sending troops in (with the possible exception of medics). Theoretically they could have been allowed to conduct peacekeeping missions afterward, but the government could then be made complicit to an illegal war.

The main point, however, is that without an UN mandate it would have been almost impossible for Schroeder to assent to sending troops in.

BibTeX is quite nice, Zotero (a firefox plugin) is free and very useful. Generally I found that indexing all read papers makes little sense as the library becomes so big that after a short while it is often faster to search for certain papers online again. I do have harddisks with several gigs of papers, though.