Monday 28 May 2012

proteins - Two subunits connected by only one disulfide bridge: quaternary structure?

I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides were only connected by one covalent disulfide bridge, would this be considered as quaternary structure, assuming that non-covalent interactions between the subunits are either negligible or even repulsive?



In other words, can a disulfide bridge, on its own, convey quaternary structure?



On a side note, are there any notable examples of this type of interaction?

Saturday 26 May 2012

Last-ditch efforts to maintain thermal homeostasis

I was in the gym's steam-room today and a thought occurred to me: have I truly thwarted all possible mechanisms for maintaining thermal homeostasis?



There's sweating, which is thwarted because the steam-room's atmosphere is as close to 100% humidity as possible, so there's almost no evaporative cooling.



There's convection, which is thwarted because the ambient temperature is above normal body temperature.



And I can't get rid of heat by exhaling, because every lungful of air I inhale is already above normal body temperature.



I think that, eventually, I should go into hyperthermia, but beside the above, are there any other last-ditch attempts to lower core temperature that my body could take?

Thursday 24 May 2012

How can I normalize mRNA samples for sequencing?

Is there an easy, inexpensive, not too labor intensive way to normalise mRNA samples so that even though one loses information of gene expression levels, each of the transcripts in the transcriptome is equally represented in the sample for sequencing? This is to say, one has a uniform distribution of transcripts, so that the lowly-expressed transcripts still have a good chance of being sequenced.



I have seen a few papers mentioning protocols for mRNA normalization, but I can't tell if any of them are practical in real life wet lab situations.

cell biology - What's the distinction between a tetrad and a synaptonemal complex in meiosis?

As far as I can tell there is a distinction.



A tetrad refers to the entire group of four chromatids after they have come together for crossing over in Prophase I (synapses).



A synaptonemal complex as you would expect is formed in synapses. This is a protein-RNA complex that connects the intervening regions of matched chromosomes in some circumstances - it is not required. Mutated yeast that can not form this complex has still been shown to be able to exchange genetic information.



In other words, you can have a tetrad without a synaptonemal complex, but not vice versa.

history - Why does the Hertzsprung–Russell diagram's x-axis go from large temperatures to lower?

The original Hertzsprung-Russell diagrams constructed by Henry Russell and Eijnar Hertzsprung consisted of absolute magnitude on the y-axis and a spectral type or an indicator of spectral type on the x-axis. Below you can see an original HR diagram produced by Russell in 1913.



Original HR diagram



When the diagrams were constructed, it was not at all clear what the sequence of spectral types or spectral type indicators actually meant. It turned out of course that the sequence (in modern day parlance O,B,A,F,G,K,M) actually corresponds to decreasing temperature.



Astronomers have simply stuck with this convention to the present day, there is no particular reason for that. Most HR diagrams are now plotted with temperature (decreasing) along the x-axis, although that is not what the original HR diagram was.

Thursday 17 May 2012

saturn - How long do planetary rings last?

I'm surprised that this question hasn't been asked before (here or on Physics), to the best of my knowledge. It's one that I might have asked when I was a bit younger, and one that I think other people will ask.



Anyway, it's clear that Saturn's rings won't form a moon, and the same is likely to be true for other ring systems. However, I'm guessing that they won't last forever (it's just a guess).



How long do planetary rings in general last? What mechanisms could cause them to dissipate/fall apart/end? I'm guessing the Poynting-Robertson effect could come into play, but I'm not sure.



And for anyone curious, yes, I checked just for the fun of it, and Yahoo Answers had a bunch of really, really bad, unsourced and most likely inaccurate answers (given that there was no consensus), ranging from '3 million years' to '13-18 billion years' to 'forever'.

evolution - How does Artificial Selection work?

You seem to have a few different concepts in there...




But mutations are always completely random and human beings have no control over it.




Aside from the fact that mutations are not completely random (not always, at least), it is not true that humans have no control over them. Imagine you grow plants, and you start to cross those plants that have a larger stalk, allowing them to be more resistent to wind: you are effectively selecting a certain mutation. Surely, you cannot choose which specific sequence you want to mutate, but still you are enriching your population of plants with a specific mutation.
Nowadays of course you can specifically mutate the genome in the lab, but that is a different matter.




Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?




Note that artificial selection has been used to generate the different breeds of dogs, by breeding animals with specific characters.
However, domestication is a different matter. Wolves and dogs are the same species (Canis lupus) and domestication is not strictly dependent on selective breeding. You can domesticate an adult animal without inducing mutations in its DNA. Probably epigenetics plays an important role there, and epigenetic patterns could possibly be transmitted to the offspring.



Of course, then you will use selective breeding to expand the domesticated population, and to select those traits you are interersted into. With artificial selection you are just selecting the mutations you want, the way you generate them is irrelevant to the matter: for instance you can irradiate plants to enhance mutation rate, and consequently the appearance of new favorable traits.

Friday 11 May 2012

dna - Synthetic biology using existing cells

There is this guy, Martin Hanczyc, working on protocells to better understand how the beginning of life occurred. He makes synthetic protocells. They don't have any DNA in them but they are pretty cool and maybe the beginnings to making synthetic cells. Perhaps once science has figured out how cells began and their very minimal needs they can create completely synthetic cells.



http://www.ted.com/talks/martin_hanczyc_the_line_between_life_and_not_life.html



Also, just thinking, what would we consider completely synthetic cells? If we took synthetic protocells and they eventually evolved into a cell with DNA would that still be synthetic?

Thursday 10 May 2012

botany - Do any plants exhibit hormonal changes similar to puberty?

In flowering plants (the angiosperms) there are several developmental transitions in the life of the plant. I won't list the plants, because the list includes pretty much all of them (although the magnitude in the change of developmental pace differs widely between taxa and environments).



First there is seed germination, which is controlled hormonally. Absence of germination is usually imposed by abscisic acid, whilst germination is caused at the appropriate time by gibberellic acid and ethylene (among other things; Holdsworth, Bentsink & Soppe, 2008).



Next, in many herbaceous species there is a transition between a spreading growth stage (e.g. rosette growth) and the flowering stage. The 'growth spurt' here is the differentiation and elongation of the flowering stem, and then subsequently the sudden flowering of buds. The transition is also controlled hormonally, by a variety of hormones including auxin (Zhao, 2010), gibberellic acid, ethylene (Schaller, 2012), and the long anticipated, recently confirmed florigen (Choi, 2012). Ethylene and abscisic acid then play important roles in the next developmental transition when seeds and fruits are produced and dehisced.



Small RNAs are also now being revealed to play a large role in controlling the timing of developmental, but they are upstream of the hormonal changes. In particular some key miRNAs are involved in auxin-based regulation of branching, and in embryogenesis (Nodine & Bartel, 2010), and RNA silencing is involved in the switch from rosette growth to flowering growth (reviewed in Poethig, 2009 and Baurle & Dean 2006).




Monday 7 May 2012

spectra - Are hot stars like O-type stars entirely composed of helium?

The lines that appear in a stars spectrum mainly reflects its temperature not its composition, see here



O-type stars start out with the same sort of composition as other stars, that is they are mainly H and He (approximately 75% and 25% by mass) with traces heavier elements.

Saturday 5 May 2012

telescope - Nebula and galaxies using 70mm scope

Whether you'll be able to see them depends on the levels of light pollution in your area. As TildalWave mentioned, a number nebulae and galaxies are perfectly observable with the naked eye so unless you live somewhere very bright, you should be fine. Under really dark skies, objects like M31 are very easy to find with the naked eye. Where I live, I hardly see it with a bright binocular due to very poor seeing, induced by a large number of shopping centres fond of pointing powerful searchlights at the sky for whatever reason.



As to how much you'll be able to see, you can get a general idea of what you should be able to see in ideal conditions by calculating your telescope's limiting magnitude



In reality, you'll also have to factor in the quality of the optics (mainly transmission), both the telescope and the eyepieces. Of the two you mentioned in your question, you should use the 25 mm one. It will give you a lower magnification, a bigger field of view (better for most bright nebulae and galaxies due to their often significant angular dimensions)



Here's a highly configurable calculator that you can use.



Since you live in the northern hemisphere, objects from the Messier catalogue are great candidates to begin your observations with.