CharonY

Ah, OK cross-faculty theses are little bit harder, I suppose. However, most reputations of mean examiners tend to be exaggerated (well, I managed to get some diploma students crying myself).

But if he is a real meanie, well you are the expert in your field. He is not

Actually it is traditional to write up till the last minute.

On the other hand, I found writing my phd thesis (Ok, it is a little while back, but not that long that it is totally blurry), somewhat less tedious than writing the papers.

I mean the thesis only goes to your prof and other usually benevolent reviewers, while the latte actually tend to go to experts and more often than not competition in the same field ;-P

If it's adventagous then those who have evolved thrive and reproduce more. If it is disadventagous then those who have evolved struggle. If it's neutral, it's neutral.

I just wanted to point out that this is not evolution per se. What you describe there is mutation plus natural selection, a mechanism of evolution. Evolution cannot be ascribed to single entities (what you said with "thos who have evolved...") but only to complete populations.

As has been said before, evolution is the change of allele frequency in a population. Therefore the occurance of mutations (be it beneficial or otherwise) does not equal evolution. Only if these new alleles spread through the population do we observe evolution. As such there cannot be individuals in a population that have evolved and other that have not.

Precisely. I suppose this misconception is partly derived from the image of evolutionary trees. They only depict the history of species and not a trend of evolution towards anything.

Furthermore, natural selection alone does not likely lead to speciation. Spatial separation for instance, maybe together with genetic drift (see allopatric speciation) are far more likely to contribute to this.

If for instance the whole population adapts to a given environment there won't be a speciation event as per definitionem no new species arises.

Drats, I missed doomsday.

Others' date='

If I make a phylogetic hierarchy of animals it's suppose to end up as a bush or tree right? The more complex animals of each kind tend to be higher. What's at the bottom? What's at the top? [/quote']

 

I think you are confusing things here. If you build a phylogenetic tree, every now living organsims are at the same level or height.

Do not get confused by split offs in radial trees, they are sometimes bent just to visualize things.

That is, now living protists, bacteria, animals and so on are on one level. Nodes further down the branches indicate common ancestors. What you see in such a tree (depending on how it is built) is for instance when the lineages split (if using e.g. molecular clocks) or the relation of different lineages to each other.

So basically you do not get a tree from simple -> complex.

In addition, a larger amount of genetic information does not equal complexity.

An amoeba for instance has one of the largest genome sizes known to date (order of magnitudes higher).

 

Other than that I do again have to stress (as have several others in various threads) that evolution is neither about direction nor complexity but it merely indicates changes in the allele (basically sequence variations on a given chromosomal locus) frequency in a given population.

Maybe it is higher in China and Japan? I did see somewhere that many Japanese still think their race was created from a Sun god, but I haven't seen any polls.

I suppose you are refering to WWII. As far as I know the belief that the Japanese were some kind of chosen or descendents of some divinity were used to justify slaughters on "lesser races", like e.g. the Chinese.

But actually I cannot find any current polls either.

It does not look like a pure culture, at least.

Well, I dunno, I find cultivating bacteria extremely boring. Especially if you have to deal with slow-growing anaerobes.

And that is just to get to the time-consuming boring actual experiments. Having the data on the hand...hmmmmmm:D

To be a scientist, I think, you have to have a drive for it in the first place. I mean the pay is bad, the workload is high and

as in most other professions a lot of it is probably boring routine work.

Then it is fairly easy to overcome the boring parts (especially if the alternative is having no job that is )

That's very unusual. Such prolonged sleep deprivation should lead to severe health problems. I get around 4h sleep a day (do to a lousy stess-full job) for something more than two years now. And apparently getting some symptoms already (including migraine, slight cardiovascular problems etc.). I should learn to sleep again.

On topic: the longest time frame completely without sleep was around 71-76 hours (thrice) due to a lab-experiment that required constant supervision.

There are gazillions of DNA isolation protocols, depending on the organism (sometimes even lab), though most basics are the same.

I could answer more specific if the complete protocol is given.

Do you use TES to resuspend your cells? In that case it could be use to prevent osmolysis. Alternatively there are certain columns to which DNA binds with a high salt-content buffer for instance...

There are several bacteria that produce thermophillic spores that can survive over 100C but their optimal growth temperatures of the active growing bacteria is usually within the mesophillic range. However species where there optimal log growth is above 45C are quite rare and are not known to be pathgenic.

Spores don't propagate and can't be thermophilic per definitionem. They are thermo tolerant, however

Regarding thermophilic pathogens, thermophilic Campylobacter species comes to my mind there are also some clostridia that have been classified as thermophilic.

Actually I think I read somewhere that annealing of the DNA-templates (that is, forming of hydrogen bonds) is a (the?) rate limiting step in this reaction. At high temperatures these bonds are naturally less stable or easier disrupted.

Of course, a host of protocols exist and depending on your templates it might not be essential at all. With sufficient vector and insert e.g. an 1-2 h incubation on the bench usually works. On the other hand I often do o/n incubations in thermos flasks in the fridge for blunt end ligation. Using the thermos flask the temperature decreases more slowly and supposedly increases efficiency...

How about checking with a microbiologist at the nearest university?

Setup is pretty straightforward. A standard test is to plate the bactaeria on an agar plate and put discs with antibiotics on it. Measure the zone of inhibition. Each discs contains a different AB (or concentration).

Another standard test are MIC-tests (Minimum inhibition concentration). THese are more work. You need liquid medium, each containing rising concentrations of AB. You measure the optical density (OD) to determine which cocentration of a respective AB inhibits growth.

Note that in many countries for safety reasons you are required to kill the bacteria after use, which requires autoclaving.

Well there is actually quite a a bit research regarding introns and their function and it is now more or less known that they do carry information that will not directly transform to proteins (that is, get translated). And it ain't some central "dogma". The only dogma i am aware of is the information flow from DNA to mRNA to protein (although in case of reverse transcrpitase activity the information of mRNA might actually lead back to DNA).

Same goes to so-called "junk" DNA. For quite a few of them ideas begin to develop what they might be fore (and as such the term junk is clearly a misnomer). Especially the research on small RNAs has led to the discovery of new regualtory roles (or in some cases, splicing functions).

Check this for instance http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14550267

One can either add the substances to the (slightly cooled) agar while before pouring it into the petri dish). Alternatively there are antibiotic discs to test them. Or you can put a sterile filter disk on a plate with bacteria and drop around 10µl on it.

For E. colis you might want to ask nearby universities, however you won't (or at least shouldn't) get Streptococci or Salmonella. Both species are usually human pathogenes and may not be cultivated outside specially equipped laboratories!

Edit: forgot to add: most chemicals can be acquired by e.g.Sigma, but you may need an authorization to buy there (depends a bit on local laws).

You could look for a change in a protein as a result of a condition and then make an inference about it.

I suppose you mean a change in protein abundancy? That's theoretically possible but for a true quantification you got to use techniques like radioactive labelling or DIGE, or the usage of heavy nitrogen.

With 2D PAGES as compared to 1D you get a better resolution and therefore you can visulize more proteins.

And in fact there are plenty of papers regarding the proteome of fungi.

I don't think that there are 2d gels only woth ribosomal proteins around though, since one of the strength of this technique is the visualisation of a lot of proteins in one gel. If one could separate the ribosmal proteins from all others (at the moment i'd have no clue how short of His-tagging and purifying them) an 1D PAGE should suffice.

None of these qualify as new species. They are just mutant strains.

It's the stretch of DNA after a start codon that doesn't contain any stop codons. So everything between a start codon and the next stop codon. This may contain one gene only, it maybe contain several genes, such as in operons in bacteria, or it may contain a gene and noncoding material, such is in most of our genes.

Ah I think you are confusing stop codon with terminator here. An operon can contain several ORFs, but not the other way round. A gene ends with its stop codon