text:
Why is there a difference in the rotation of the tail fin in fish compared to marine mammals?
I've been thinking about this one, but I can't seem to find what causes this difference.
All fishes that I've seen have their tail fin positioned vertical:

But all the marine mammals I know have their tail positioned horizontal:

Why is there this difference? Is it because it's mammals compared to fish? Or could fish as well have horizontal tail fins?

While fish tend to move from side to side (lateral undulation) for which a vertical tail makes sense, the land ancestors of marine mammals had their limbs under them and so their spines were already adapted to up and down movement (dorsoventral undulation). When these animals moved to marine environments, they continued up and down movement in their swimming, for which a horizontal tail makes sense.
(The wikipedia article on fins gives some more detail, and links to this webpage on Berkeley.edu. A paper by Thewissen et al. suggests that for cetaceans, dorsoventral undulation as a swimming strategy came first, and the horizontal tail evolved later.

More detail:
In a third example beyond fishes and marine mammals, the icthyosaurs and other aquatic reptiles developed vertical tails, even though like marine mammals they evolved from four-footed land animals. This may be because the legs/spines/gaits of land reptiles differ from those of land mammals, so that the earliest icthyosaurs swam with lateral undulation, as reflected in their spinal modifications.
This blog post by Brian Switek gives a really superb run-down on the issue, with figures and citations. I'll quote this part which deals with the dorsoventral undulation theory:

...mammals and their relatives were carrying their legs underneath their bodies and not out to the sides since the late Permian, and so the motion of their spine adapted to move in an up-and-down motion rather than side-to-side like many living reptiles and amphibians. Thus Pakicetus[the pre-cetacean land mammal] would not have evolved a tail for side-to-side motion like icthyosaurs or sharks because they would have had to entirely change the way their spinal column was set up first.

Switek goes on to to talk about exceptions in some marine mammals:

At this point some of you might raise the point that living pinnipeds like seals and sea lions move in a side-to-side motion underwater. That may be true on a superficial level, but pinnipeds primarily use their modified limbs (hindlimbs in seals and forelimbs in sea lions) to move through the water; they aren’t relying on propulsion from a large fluke or caudal fin providing most of the propulsion with the front fins/limbs providing lift and allowing for change in direction. This diversity of strategies in living marine mammals suggests differing situations encountered by differing ancestors with their own suites of characteristics, but in the case of whales it seems that their ancestors were best fitted to move by undulating their spinal column and using their limbs to provide some extra propulsion/direction.

Cetaceans (i.e., marine mammals) evolved from certain ancient land based mammals, thus the tail is essentially convergent evolution of the tail function.

I've thought about this many times but enjoyed theorizing on possibilities vs researching evolutionary theory.  I like these thoughts above- def agree to certain extent- but it seems to me that:
    If almost all "fishes" utilize side to side motion/morphology, it seems that this is certainly more efficient, and would be adopted, over many millions of yrs...at least in some examples...by marine mammals; HOWEVER, there's one difference and physiological necessity that I believe actually may make the horizontal fluke/tail advantageous. This would make the vertebrae idea just a shaping mechanism in such evolution- instead of a restricting agent.
In order to breath -in order to do so efficiently- surfacing is necessary, thus vertical thrust is of the utmost importance.  Esp, since other air-breathing marine species (evolved from land animals...) that have NOT evolved a solid fluke (whether by lack of evolutionary time, or prior morphological diffferences...) in most cases have a more flexible propulsion system to achieve efficiency via improved or altered maneuverability.
Certain pinnipeds- as discussed in article above- have less solid structures, thus improved flexibility/mobility and in my mind- going hand-in-hand with creating sufficient breathing efficiency.  Then, in non-mammal instances, penguins are a solid example- as the use of "forelimb" (wings) create both the flexibility/mobility to achieve said necessities, but also... effectively acting quite similarly (in the vertical thrust department) to the horizontal fluke----in the process of surfacing to breath, porpoise, or reach land.

It would be great if you could add some references to your response!

However icthyosaurs, which are air breathing, fusiform reptiles have vertical flukes like fish. So... while your theory of air breathing sounds making horizon trust an advantage sounds convincing on paper. it may not be true.


text:
Why does the T7 RNA Polymerase require a reducing environment ie. DTT
Every bloody protocol suggests adding in DTT when doing in vitro RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein we care about is the T7 polymerase, why is this necessary.

You're right. I just looked up a couple of protocols (an example from Promega ) and it has a final concentration of 10 mM DTT. They don't explain why, however it must be important for it to be included.

A quick search on T7 cysteines gave some clues:

Bacteriophage T7-induced DNA polymerase is composed of a 1: 1
  complex of phage-induced gene 5 protein  and Escherichia coli
  thioredoxin. Preparation of active  subunits in the absence of
  sulfhydryl  reagents  indicates  the reduced form of thioredoxin  is
  sufficient for formation of  the  active holoenzyme. The oxidized
  form of  thioredoxin, thioredoxin modified  at  one  active  site
  sulfhydryl by iodoacetate or methyl iodide, or thioredoxin modified
  at both  active  site  sulfhydryls  by N-ethylmaleimide,  are  all
  inactive,  being  defective  in  complex formation with  gene 5
  protein.

Adler and Modrich, J Biol Chem 258:6956 (1983)
There's a more recent paper (Aguirre et al, Inorganic Chemistry 48:4425 (2009)) that mentions the "the enzyme critical sulfhydryl cysteine groups", but unfortunately I only have access to the abstract.
Update: It seems to be an old finding, rather than a rationale concerning the cytoplasmic redox state. According to Chamberlin and Ring, JBC 248:2235 (1973),

General Requirements-The general requirements for T7 RNA
  synthesis directed by T7 DNA polymerase are shown in Table
  I. As expected for a template directed polymerase, RNA
  synthesis shows an absolute requirement for DNA, the 4
  ribonucleoside triphosphates and Mg++.

(no surprises there ;)

The activity of the
  enzyme is reduced significantly if a sulfhydryl reducing
  agent such as b-mercapto-ethanol is omitted from  the
  reaction. The addition of 10^-5 M p-hydroxymercuribenzoate to
  the assay system in the absence of b-mercaptoethanol
  abolished all activity, indicating that the enzyme contains a
  sulfhydryl group necessary for activity.

However, if you see the table I, the remaining activity after removing bme is still 74%
There seems to be 7 exposed cysteines (Mukherjee et al, Cell 110:81 (2002)), but I could not find any paper discussing their roles.

Here's a copy of the paper. Enjoy.
http://cl.ly/101U380b3r261i0w0v1d

How strange. I'm looking at the crystal structure (1QLN) and there aren't a lot of cysteines near the active site. Will have to take a look at those papers.

@jp89 Thanks for the copy of the paper. I'm not sure though if this is allowed here, since it is breaking copyrights. Anyhow, for now I believe it is still fair use. Regarding to the question, I'd follow citations 59-62 from there (last paragraph on page 2/first on page 3). Cheers.

Bacteriophage polymerase is active within the cell, which has a reducing environment.  Most protocols of intracell proteins include DTT or glutathione for this reason.   Disulfides are mostly for secreted proteins.

@Aleadam Yeah, that is the sad case. I honestly don't understand the concept of copyrighting human knowledge.

@jp89 it is slowly improving, with the PLoS effort, and NIH manuscript requirements, but there is still a long way to go

I always assumed it was because DTT is useful in inactivating ribonucleases (by reducing their disulfides) which are notoriously stable and pervasive. It would be pretty unfortunate to get your RNA synthesized only to have it immediately be destroyed by a contaminating RNase.

Welcome to Biology.SE! This may be correct, but answers are much more likely to receive a favorable response if they are based on research rather than speculation. Consequently you should include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— Please also take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
Why do people say that trans fatty acids are bad for your health?
I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible.
But I also learned from biochemistry that they are digestible. What is the reason for this, or is it true at all?

I'll try to get to a formal response later. In the meantime, fatty acids are not bad or unhealthy for humans if taken in moderation. We need fat and cholesterol in our diets, but too much raises the risk of poorer health. Some fatty acids are more beneficial than others.

Trans fatty acids are digestible, but they cause an increase in LDL and a decrease in HDL, which is the leading mechanism for atherosclerosis. So, they increase the risk of a cardiac infarct.
LDL means Low Density Lipoprotein, it's one of the 5 major lipoprotein groups. Lipoproteins carries the fatty acids and cholesterol which were absorbed from intestines (because lipids are hydrophobic and cannot be carried within the blood directly like glucose or proteins.)
So, LDL mainly carries cholesterol and fatty acids from intestines to tissues. (fatty acids and cholesterol are essential for cells.) But in excess levels, they tend to accumulate in vessel walls, which also starts and inflammatory response and makes the situation worse. (mainly includes macrophages and T cells) This is the main mechanism for atherosclerosis.
In the other hand, HDLs serve as a reverse cholesterol transport system, which carries the cholesterol back, mostly to the liver (for bile secretion) or steroidogenic organs such as adrenals, ovary, and testes by direct and indirect pathways. So a high HDL reduces the atherosclerotic process.

Thanks, nice response, but could you give me some resources on why transFAs raise the LDL level more than any other fatty acids? If they don't than this is just an argument against consuming excessive amounts of fat.

No, it's not an argument just against consuming excessive amounts of fat. Trans fatty acids increase LDL more than cis unsaturated fatty acids, even equal to saturated fatty acids. http://www.ajcn.org/content/59/4/861.full.pdf+html You can check the discussion section.

Thanks, I'll read it more in depth on the weekend. Anyway, I'm still a bit skeptic about the topic. Do  you (or anybody) have some texts on the physiological background of the phenomenon?

When you say they are digestible, do you mean that the GI tract can cut off the glycerol and make trans-fatty acids, or do you mean that cells can process trans-fatty acid into other molecules? I thought the problem was lack of enzymes that can handle the trans double bond.

Studies have been done in which saturated fats and cis-unsaturated fats in the diet were replaced with trans-fatty acids. In all cases there were increases in LDL cholesterol, blood triglycerides and Lp(a) lipoprotien, and decreases in HDL cholesterol and particle size of LDl cholesterol. All of these changes result in an increase in the risk of cardiovascular disease. Beyond that the incidence of CHD in prospective studies looking at trans fatty acid consumption has been greater than what would be predicted from the changes in blood lipid profiles. Over the past decades it has become clear that trans fatty acids increase the risk of CHD more than do saturated fats. In addition, they have been shown to increase systemic inflammation and decrease endothelial cell function. The FDA suggests that consumption of trans fats should be kept at 2 gms/ day or lower.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
What is the advantage of using starter cultures for growing bacteria?
Many DNA isolation and protein expression protocols contain instructions to use a starter culture of E. coli that is then used to inoculate the main culture.
What are the advantages of using starter cultures compared to just let the bacteria grow in the same medium for a longer time? When should one use starter cultures and when can one safely skip that first culture?

Larry's answer is correct. The other advantage with respect to DNA isolation is that it's very easy to grow up a 5 mL miniprep (ie, overnight) so that the next day you can triage your bacterial colonies (eg, check if they harbor a subcloned DNA fragment in a plasmid). Once you run your diagnostics, then it's very easy to take a small sample of your colony to innoculate a larger growth and carry on for downstream purposes. You could go directly from picking a colony from a plate to grow up 500 mL of your bacteria, but it would be rather wasteful if you aren't certain it is useful.

Growth can be quite slow for some species under certain conditions when the concentration of cells is too low. Log-phase growth is powerful, and so one would like to keep cells in this state for the experiment at hand. Different genes are expressed then compared to a stationary phase.
In addition, you'd like your culture to out-compete a contaminant if there is one. That is more easily accomplished with a starter culture, which is then used to inoculate a larger culture for scale-up. Inoculating directing into the large-sized flask may allow your bacteria to enter a stationary phase, thus giving an opportunity for other species to out-compete your bacteria.

I'm not sure if I'm reading into this incorrectly, but does E. coli (or monocultures in general) function commensally?  e.g., if I inoculate 5 mL or 1 L with the same number of cells, will the 5 mL produce more cells (not density) faster?

If a culture is too dilute, it can have a reduced doubling time.

I agree that a starter culture would out-comete a contaminant (especially if there is no antibiotic in the media).
Another advantage of inoculating with starter culture is that your results concerning plasmid preps or preparing competent cells will be easily reproducible. By inoculating with a colony, the starter number of cells is different each time you do that, so you might not know how long your cells have to grow to reach a certain OD (e.g. for preparing competent cells) or you have to measure the OD before you isolate DNA to be sure that your yields are comparable with your previous ones.


text:
Do immature fruits perform photosynthesis?
Most immature fruits are green: peppers, pine cones, plums, lots of them. I want to know if the green is from chlorophyll in the cells. Do the fruit cells perform photosynthesis? When you cover a green stem or leaf, it will turn pale and stretch. That is because the stems have little need for chlorophyll in the dark, which is why they are pale. They stretch because the auxins in the stems are not destroyed by the photons, and the stems stretch out and topple over. If a green fruit is covered, will it turn pale and stretch like that?

The green pigment is indeed chlorophyll, and the fruits do perform photosynthesis.   It's not just "fruiting" plants that do this either.  Some shading experiments i saw estimated that  up to 30% of the sugars assimilated into the barley ears (basically the grain) can come from photosynthesis occurring in those organs.

it would be great if you could provide specific references rather than "some shading experiments" that would be helpful. I am also curious about how such a shading experiment is conducted, what measurements are used to estimate the "30%", and what assumptions are made.


text:
For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?
Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be performed.
I've seen anything from precipitating at room-temperature and centrifugating immediately without any delay to precipitating at -20 °C over night in various protocols.
Is there any published data about the influence of duration and temperature on the yield of the nucleic acid precipitation?

I think the folklore is influenced by how much nucleic acid you are working with. As @Daniel Standage suggests, some conditions wouldn't be influenced by anything.

I always did mine at -80 C, but I never compared the results to other protocols (I don't fix what's not broken). But, I was curious about the same thing, so I looked around. I found one paper discussing this: Paithankar and Prasad, Nuc Acids Res 19(6):1346 (1991)
It shows that at low concentrations, EtOH at RT actually outperforms the precipitations at both 4 C and  dry ice/ethanol bath. That difference is quite big at 100ng/ml DNA and lost when there is more than 10 ug/ml DNA. For typical extractions, based on this data, I'd do it at RT.
On the other hand, Hilario and Mackay say in their book that:

for genomic DNA isolation, different DNA precipitation temperatures
  and incubation times have little effect on recovery rates. One can
  directly centrifuge after adding ethanol without the -20 C incubation,
  and, it -20 C ethanol is not available, room temperature ethanol can
  be used.

They do not, however, provide any citation for that statement.

As a first year molecular biology student, I did a class project on this very question:  trying to see if buffer temperature had an effect on yield during DNA precipitation. This is a far cry from peer reviewed research, but my finding was that there was no significant effect for a wide range of temperatures.


text:
Alternatives to TBE buffer for denaturing polyacrylamide gel electrophoresis of DNA and RNA?
I just stumbled upon an article promoting 10 mM sodium borate as an alternative to the well-known TAE and TBE buffers for agarose gel electrophoresis of DNA (Brody & Kern, 2004). They claim that sodium borate outperforms TBE and TAE at high-voltage conditions due to the significantly lower heat development.
I'm currently using TBE buffer and gels with 7M urea for my denaturing PAA gels, and I'm wondering if there are similar alternative conditions for those denaturing PAA gels of nucleic acids?
I couldn't find anything on using sodium borate for denaturing PAA gels, so I'm wondering if it should work the same as for the agarose gels or if it just isn't a good buffer for that kind of gel.

Brody, J. R. & Kern, S. E. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36, 214–216 (2004).

Not related to your question but what voltage are you running your gels? It seems as if your having all sorts of issues with over-heating.

250V (results in ~30-35mA), I'm having no significant overheating problems, but if I could just run the gels faster at higher voltages it might be useful.

@bobthejoe PAGE and PAA gel electrophoresis are the same thing, if you mean a discontinuous gel like SDS-PAGE for proteins that doesn't exist for nucleic acids as far as I know.

For what it's worth, I use TAE with agarose and never exceed 90 V (~20 mA). Resolution is always better at lower temperature conditions, in this case, meaning lower voltages.

@leonardo, I've always heard that its the other way. CE  is run at a high temperature to improve resolution. This is worth a question...

This is a good question. I'll look around for a reference later, but I'm fairly certain that as long as the current has not exceeded a certain threshold (such that the gel and buffer heat up to the point of causing the gel to contract or distort) resolution is function of migration distance.

I've used Lithium Borate with an agarose gel and high voltages (>200). Didn't turn out as well as advertised the few times I tried it though - worse than TAE.  If I had to try it again I would definitely lower the voltage.

sure.. try it once... and run any marker, along with running the same marker with TBE if possible, if you can to check for possibilities...

As you don't have sufficient reputation to post comments everywhere yet, I have converted this for you as it is more a comment than an answer to the question.

Someone appears to have used sodium borate for denaturing acrylamide gels, with no issues: http://www.protocol-online.org/biology-forums/posts/17703.html (no detail on the exact conditions, though).

A neighbouring lab uses the sodium borate buffer for genotyping in agarose gels. They can run the gels at 10% higher voltages than what I push my TAE buffer at (95V; 20 mA max). Is there a particular reason to use denaturing poly-acrylamide or to run them super fast?

You can try SB (sodium boric acid), LA (lithum acetate) or LB (lithium boric acid) buffers. Thex generate must less heat then TAE or TBE buffers and can be run on much higher voltages and are much cheaper than TAE or TBE. Also they do not interfere with standard applications such as band excision and they last longer.
For more info try this sites:
http://www.fasterbettermedia.com/products.html
http://ddgehelp.blogspot.com/2008/01/alternative-electrophoresis-buffer-to.html


text:
Brain + ethanol experiment suggestions needed
I need to demonstrate the effects of ethanol on a human brain (or other brain with developed telencephalon) in vitro; ideally the effects on vigilance and/or memory.
Could you please suggest such an experiment?
What method would you suggest to demonstrate the effects of ethanol on NMDA receptors or membrane penetration by ethanol?
Edit in respose to the first comment by @MadScientist:
The point is to empirically demonstrate how ethanol affects the cognitive performance of brain (specifically vigilance and memory) and explain the biochemical nature of such an effect on an observable real example (not using computer simulations). It is aimed at mature layman audience.
The experiment has to be in vitro due to ethical and environmental limitations (well, I am not permitted to intoxicate mature students nor animals).
Demonstrating the effect of ethanol in the role of an NMDAR antagonist would be satisfactory as the chain of implications would be illustrated on a theoretical basis.
I have access to standard laboratory equipment on a university level, but the simpler it is, the better. As to the material, the same is true while a fresh brain slice will hopefully be available as well.

In vivo experiments are much easier to perform for this topic ;-). You'll have to specify what exactly you want to achieve, there's a huge difference between "effect on the brain" and "effect on the NMDS receptor". You'll also have to give us a rough idea on what kind of equipment and material you have access to.

@MadScientist I have edited my question to give additional details.

Can you patch? Do calcium imaging maybe?

@nico I have not done it before. Could you perhaps suggest an exact methodology, please?

@Harrold Cavendish: if you haven't done it before, forget about patching, it would be very technically challenging. I will try to write an answer later today, now I'm late for work!!! :D

@HarroldCavendish: Can you explain more about what this experiment is for? Are you trying to do a PSA about the dangers of alcohol? What sort of experimental background do you have?

The main problem with what you are asking is that you want to show effects on vigilance and memory in vitro. That is just not possible: if you want vigilance and memory you need a live animal, there is no way around it.
Next point: you have an audience of non scientists, so you can lose them very quickly if you start speaking about NMDA, LTP or similar things without a clear explanation, so start with that: get a nice review (Pubmed is a good start, as always), and give a simple theoretical explanation of one of the mechanisms involved. It is then important to clearly explain the experiment you will perform, and what you are expecting to see in case there is an effect.
Unfortunately the best way to see effects on NMDA receptors would be electrophysiology. This is not trivial and, if you have never done it, I would not suggest going that way. However, if you have access to an electrophysiology setup you will most likely have access to someone who uses it, and that could make the experiment for you.
I am not an expert on this topic, but a quick research on Pubmed seems to indicate that alcohol can, for instance, reduce LTP in hippocampal neuron.
Maybe what you could do is having someone patch hippocampal neurons and show how an LTP protocol is used. You don't necessary have to show them the whole thing (I doubt anyone in a right state of mind would bare to stay until the whole experiment is performed in control condition first, and alcohol later...).
Also, the results of these experiments are often non obvious to analyse, so you should have some data prepared and analysed earlier and quickly show how analysis is performed, before showing the final results.
Calcium imaging experiments could also be used and would probably give results that are easier to understand for a laymen audience.
See for instance Fig. 1 or Fig. 5 of this paper (just the first one I found, there surely are other):
Ethanol alters calcium signaling in axonal growth cones.

+100 for noting the requirement of a live animal and how non-trivial the proposed experiments are


text:
Species with reproduction barriers that can both reproduce with a third species
To start with, I do not have a sound knowledge in biology or any formal education in the area.
I was told that one of the definition of a species is a reproductive barrier, which means that if two animals can't reproduce, they are of different species. The barrier can be either the inability of the sperm to fertilize an egg, or a physical trait that inhibits reproduction, e.g. a cricket species that has a different mating song than another species or two species of flies, one that mates on yellow flowers, and the other on red flowers.
But what happens when, while two species can't reproduce, but there is a "chain" of "intermediate" sexual partners that can produce reproductive connection step by step. Like 6 degrees to Kavin Bacon, but with animal sex.
I'll try to explain with an example:
A Great Dane and a Miniature Pinscher dogs can't mate due to obvious size differences. But The Pincher can mate with a German Pincher (a slightly bigger breed of Pincher), which can mate with a Doberman Pincher. And the Doberman can mate with a German Shepard which can mate with a Great Dane.
I've also heard that such things happen with birds and crickets, where there is an original species, from which evolved several other, and while the original species (which still exists) can mate with all the new species. Some new species can't mate with some, or all of the other new species.
How are such species are defined, and at what point dogs stop being dogs anymore?

All dogs belong to the Canis lupus familiaris species (which is a subspecies of Canis lupus, that is gray wolf). Great Dane and Miniature Pinscher are not two separate species, but rather two different breeds. A better example would be horse and donkey, different species that can mate to give a mule.

How come they are not of different species if they can't reproduce, while crickets that develop a different mating song are different species?

Are you sure a Great Dane cannot reproduce with a Miniature Pinscher (e.g. through in vitro fertilization)? Anywat, crickets are not domesticated so they don't have breeds! Have a look at this: http://en.wikipedia.org/wiki/Species_Problem

What I was explained is that a physiological barrier that prevents mating only physically (such as a different mating song or different flowers upon which to mate), but still allows artificial insemination also counts as a reproductive barrier.

The stated problem reveals that the bar has been set rather low for macro-evolution: http://en.wikipedia.org/wiki/Macroevolution

There is also interesting phenomena of ring species - the boundaries of species are sometimes really hard to define.

As an aside, I'm fairly sure that a Miniature Pinscher can mate with a Great Dane and produce viable offspring. While I haven't seen that particular crossbreed myself, a friend of mine used to have a dog who was half Siberian Husky and half Papillon. (And before you ask, yes, the Husky was the mother. The moral of the story being either "love conquers all" or "make sure to keep female dogs in heat away from all males if you don't want puppies", depending on how you look at it.)

Ps. See also this question on Yahoo! Answers: Can you crossbreed a Chihuahua with a Great Dane?

As many have pointed out, Canis familiaris is one species.  A more interesting consideration might be wolf-dog hybrids, which are fertile, unlike mules: http://en.wikipedia.org/wiki/Canid_hybrid

You may want to have a look to Ring species and to this post.

How are such species are defined, and at what point dogs stop being
  dogs anymore?

This is a bit like the is-Pluto-a-planet-discussion. A group of scientists have to come together and hold a big conference.
You have a few principles that you want to adhere to and then it's big groups of people making decisions.

Please cite a source and/or big conference and name a few principles.

@JoeHobbit : If you want to pretend that decisions like this are purely made by following a few principles go ahead and write your own answer. I don't think that there's much peer reviewed sociology literature about biology taxonomy but if it exists I would doubt that the result would be that the biological taxonomists follow straightforward principles.

There are many definitions of a species, which may or may not include the concept of reproductive barrier. The Biological Species Concept (BSC) is quite popular and involves a reproductive barrier, but other concepts such as the Phylogenetic Species Concept do not include a reproductive barrier.

Disagreements and confusion also happen over just what the best
  criteria are for identifying new species. In 1942 the famous biologist
  Ernst Mayr wrote that because biologists have different ways of
  identifying species, they actually have different species
  concepts. Mayr proceeded to list five different species concepts, and
  since then many more have been added. The question of which species
  concept is best has occupied many printed pages and many hours of
  discussion.
Some debates are philosophical in nature. One common disagreement is
  over whether a species is defined by the characteristics that
  biologists use to identify the species, or whether a species is an
  evolving entity in nature. Every named species has been formally
  described as a type of organism with particular defining
  characteristics. These defining traits are used to identify which
  species organisms belong to. But for many species, all of the
  individuals that fit the defining criteria also make up a single
  evolving unit. These two different ways of thinking about species, as
  a category and as an evolving population, are quite different from
  each other. Wikipedia Species Problem

The Biological Species Concept does have it's problems:

It is also true that there are many cases where members of different
  species will hybridize and produce fertile offspring when they are
  under confined conditions, such as in zoos. One fairly extreme example
  is that lions and tigers will hybridize in captivity, and at least
  some of the offspring have been reported to be fertile. (see also
  Lions and Tigers)
Mayr's response to cases like these is that the reproductive barriers
  that are important for species are the ones that occur in the wild.
  But even so it is also the case that there are many cases of different
  species that are known to hybridize and produce fertile offspring in
  nature. Wikipedia Species Problem

The Phylogenetic Species Concept also has its problems:

it permits successive species to be defined even if they have evolved
  in an unbroken line of descent, with continuity of sexual fertility.
  However, because slight differences can be found among virtually any
  group of organisms, the concept tends to encourage extreme division of
  species into ever-smaller groups. Phylogenetic Species Concept

When does a dog stop being a dog? Technically all dogs are in the same species: See the definition of Dog, which is a subspecies of the species, Canis lupus, or Grey Wolf. The line between dog and wolf is poorly-defined as there may be hybrid wolf-dogs, since they are both from the same species. Up one level is the family Canidae, which includes wolves, foxes, jackals, and coyote species.

The Biological Species Concept is largely useful in looking at the process of evolution. Since speciation isn't typically (though this isn't always true either!) an instantaneous process, it is useful to observe it in action. The BSC is the best way of approaching this (at least for sexually reproducing organisms).
Back to your original question. It might be useful for you to search "ring species" as this is what you are talking about. The most famous example is the Ensantina salamander complex. They are essentially several species/one species depending on your perspective. It is more-or-less a spatial version of the hypothetical dog analogy, but it is also a natural phenomenon that occurs in many other species....


text:
Somatosensory System
I have a test in my upcoming Neuroscience class, one of the items on the study guide is:
Identify 2 means by which a maintained, constant stimulus produces only a transient excitation of the Pacinian corpuscle (phasic receptor). How does adaptation occur?

I would consider physical filtering properties of the corpuscle sheath as well as adaptation of the neuron or downstream targets.


text:
Effects of beer on muscle recovery after exercise
I noticed it several times that when I drink beer (even one bottle) after some heavy workout, the next day my muscles are more stiff than other times, and not the same way... Is it because that lactate and NADH levels are raised both due to the anaerobic training and alcohol metabolism?

So acute effects rather than chronic?

Yes, acute effects.

Noticed twice the same effect with two glasses of wine drunk the day before the workout

What does "and not the same way" mean?

Can't describe it properly but maybe less sharp and less localized, also there is no intense pain when the muscles are moved after some period of rest. I'm talking about my thighs anyway (and cycling).

There are a few studies around related to this. One particular study(1) suggests that:

Neural drive is decreased following eccentric exercise leading to a reduction in muscle force. Alcohol may further reduce the already depressed neural drive.
Alcohol also has been shown to affect the innate immune system by altering the activity of a number of inflammatory proteins. A lot of these play "important roles in the damage and repair processes occurring after eccentric exercise". Alterations in these proteins may affect muscle recovery post-exercise.(2).

The second point is maybe what's relevant to the question at hand? They say more research is required though.
Edit (expanded discussion per comment below). The study itself was carried out using 8 (+/-1) standard drinks immediately following a workout. The article(1) itself doesn't hypothesise the point made earlier regarding inflammatory proteins, it rather points to earlier research(2), to suggest this may be the case.
Whether a dose-dependant relationship exists, or the magnitude of it with regards to the alteration in inflammatory proteins is not discussed (except in the context of chronic versus acute alcohol use). Just that the possible effect on inflammatory proteins exists which may affect muscle recovery post-exercise.

Barnes, et al. Acute alcohol consumption aggravates the decline in muscle performance following strenuous eccentric exercise. Journal of Science and Medicine in Sport. 2010. 1:189-93.

Edit
2. Szabo. Consequences of alcohol consumption on host defence. Alcohol Alcohol. 1999. 1999:830–841.

The reference is not relevant - the title says "acute" but the question refers to "even just one beer"

Yeah David, acute as in immediate effects as opposed to chronic or long term effects.

Sorry, I meant to write this in the above comment. Acute in this context - http://www.medterms.com/script/main/art.asp?articlekey=2133


text:
How do fibers control muscles?
My professor says

Nervus troclearis IV somatomotor fibers supply musculus obliquus superior.

and similarly for nervus oculomotorius III

Nervus oculomotorius postganglionic fibers supply musculus ciliaris, m. sphincter pupillae.

I understand the verb "supply" as "stimulate" or "allow signal pass from the tract to the muscle that contracts or flexes". However, fibers must have some other functions too. So the verb supply seems to be a general term for these functions.
How do fibers control the muscle?

I'm of the opinion that this question is either too localised or even off-topic in its present form.  Perhaps consider rewording it to sound less like a use of english question - "what is the link between these nerves and muscles" or similar?

I guess that was partly my fault from my edit.

@DanielStandage I wouldn't say that :)  Anyway it's in better shape now, I've reversed my down-vote.

I still think it needs more explanation. Are you looking for the answer to how action potentials are carried along motor neurons or how neuromuscular junctions work or both of the above?

@Kevin so the thing includes the two things. I know about the first one that myelin is used in some cases as a resistant. I know about the last one that there are transmitter substances like acetylcholine that is released from the end of the axon to the extracellular space that activates the action potential in some other cells by attaching to receptors of other cells. So there is a synapse going on between neurons. - Those things should apparently apply to the above examples. However, not sure how m. ciliaris is in connection with m. sphincter pupillae. Fibers activating muscles in sequence?

Read "supply" as "carry action potentials to." When the action potential reaches the junction with the muscle (i.e., the neuromuscular junction), neurotransmitters are released into synapse. A similar membrane depolarization occurs on the muscle cell, ultimately leading to contraction.
Nerves visible to the naked eye are actually bundles of individual axons (hundreds, thousands, or tens of thousands of axons). Nerves have the appearance of branching because the individual axons that travel to muscle fibers don't all go to one muscle.
For example the oculomotor nerve branches:

So what you see as the oculomotor nerve is really a collection of neurons. Some of these carry action potentials to the ciliary muscle and some to the sphincter pupillae. These are the parasympathetic components. There is a completely separate set of neurons (but still contained in the same nerve) that carry signals to the extraocular muscles.
This is really basic material that your professor should have explained to you.

Can you distinct the parasympathetic components of the nervus oculomotorius from a picture by eye?

They would be indistinguishable to the naked eye. You could only tell the divisions by where the (very tiny) branches go to.


text:
How does Iota-Carrageenan achieve an antiviral effect?
"Cold Defence" nasal sprays are recommended to be taken either preventatively or in the early stages of a cold.  The active ingredient in these sprays is Carrageenan.  After some research, the active compound is Iota-Carrageenan (ι-Carrageenan).
This study by Eccles et al[1] shows that this drug is clinically effective.  The study was only designed to test efficacy rather than to explain the mechanism, however. A fleeting mention is provided in the discussion section:

The above results suggest that the treatment with Iota-Carrageenan reduces the viral replication. Consequently fewer cells are infected, the immune reaction against the viruses is less pronounced and fewer symptoms occur.

How does ι-Carrageenan produce an anti-viral effect?

Eccles R, Meier C, Jawad M, Weinmüllner R, Grassauer A, Prieschl-Grassauer E. 2010. Efficacy and safety of an antiviral Iota-Carrageenan nasal spray: a randomized, double-blind, placebo-controlled exploratory study in volunteers with early symptoms of the common cold. Respiratory Research, 11:108, doi:10.1186/1465-9921-11-108.

Through two different pathways, one relying on a non-specific (innate) response, and another through a reactive oxygen species, the level of NF-kB(**) is amplified, as such a response would have happened as a result of the presence of the virus anyway.

In thousands of experiments, carrageenans have been used to
  induce inﬂammation, since inﬂammation is a predictable effect of
  exposure to carrageenan in animal and cell-based models. For the
  most part, these experiments were designed to test the effectiveness of anti-inﬂammatory agents or to study the mediators of inflammation
The innate immune pathway is mediated by toll-like
  receptor (TLR)-4 and B-cell leukemia lymphoma (BCL)10, leading
  to increased Interleukin (IL)-8 secretion by both canonical and noncanonical pathways of NF-kB activation. The ROS-mediated
  pathway of inﬂammation does not involve TLR4-BCL10, but
  requires Hsp27 and IkB-kinase (IKK)b, leading to increased phosphorylation of IkBa, and thereby enabling the nuclear translocation
  of NF-kB.

From the intro to:

Yang B, Bhattacharyya S, Linhardt R, Tobacman J. (2012) Exposure to common food additive carrageenan leads to reduced sulfatase activity and increase in sulfated glycosaminoglycans in human epithelial cells.  Biochemie, Mar 5,epub ahead of print, doi

(As an aside, the direct conclusions of this study are that these changes in GAGs may further influence transcription and play a role in determining cell fate, and perhaps may influence cell/cell interactions)

(**)NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) is a protein complex that controls the transcription of DNA. NF-κB is found in almost all animal cell types and is involved in cellular responses to stimuli such as stress, cytokines, free radicals, ultraviolet irradiation, oxidized LDL, and bacterial or viral antigens  wiki

In the publication by Leibbrandt et al.[1], it could be shown that the iota-carrageenan directly binds to viruses and thereby prevents the attachment to cells. This is a critical step in the viral life-cycle and therefore replication is reduced. Iota carrageenan rather acts unspecifically and besides influenza also other viruses such as human Rhinoviruses are inhibited[2]. Similarly, a direct binding to viruses has been shown for iota-carrageenan and papillomaviruses[3].
In contrast to lambda carrageenan that is widely used as proinflammatory compound in animal experiments, iota carrageenan lacks this activity and therefore a pharmacological / immunological mode of action can be excluded. In addition carrageenans have a high molecular weight which makes it very unlikely that it acts systemically.

Leibbrandt A, Meier C, König-Schuster M, Weinmüllner R, Kalthoff D, Pflugfelder B, Graf P, Frank-Gehrke B, Beer M, Fazekas T, Unger H, Prieschl-Grassauer E, Grassauer A. 2010. Iota-Carrageenan Is a Potent Inhibitor of Influenza A Virus Infection. PLoS ONE, 5(12): e14320 doi:10.1371/journal.pone.0014320.
Grassauer A, Weinmuellner R, Meier C, Pretsch A, Prieschl-Grassauer E, Unger H. 2008. Iota-Carrageenan is a potent inhibitor of rhinovirus infection. Virology Journal, 5:107, doi:10.1186/1743-422X-5-107.
Buck CB, Thompson CD, Roberts JN, Müller M, Lowy DR, Schiller JT. 2006. Carrageenan Is a Potent Inhibitor of Papillomavirus Infection. PLoS Pathogens, 2(7): e69, doi:10.1371/journal.ppat.0020069.


text:
Robotic surgery for treating cancer?
We can localise cancer cells in the body. We can manufacture materials thin and hard enough to penetrate the body without harming it. So what stops us from creating an automated surgery where the patient lies down for some time whilst a machine locates cancerous cells and, using micro tubes, kills them one by one?

Actually we aren't that good at localizing cancer cells.
There need to be around 100,000 cancer cells at a single location for the cancer to be visible on fMRI.
If you want to treat a cancer via chemotherapy it's good to be able to see the cancer. It allows you to see whether the drug you are giving works.
When dealing with a metastasized cancer where you don't think you know every location in which cancer is hiding it therefore often makes sense to avoid to take out everything you can see via surgery.

This is true. With other methodologies using cells that were first "engineered" in vitro, and then implanted, we can detect down to maybe 10,000 cells in a primary tumour, but metastases are harder to see because they tend to to be more diffuse.

I'm assuming you are not talking about a single solid tumor, but rather one where the tumor is loose and is distributed throughout the tissue, or has metastasized
I guess the answer is you could, but it would be one amazing machine.  This robot would have to examine each individual cell and destroy it based on what you could sense about the surface properties.  Identifying cancer cells on the basis of the proteins and glycosyl (carbohydrate) molecules on the cell surface is not embodied in a reliable way in a touch sensor.  Cancer can manifest lots of such patterns and it could quite easily be that if you looked at healthy cells, they look very similar.  Cancer cells don't have an obvious sign they are always holding out saying 'im cancer'...
Then there is the structure of tumors. For instance glioma is one of the most difficult brain cancers you can have.  The glioma cells push out axons - they can be quite long.  Its hard to imagine a robot that could find that in a brain without tearing up all the neural connections.  In prostate cancers - one of the most common cancers in men, the cells are embedded in the tissue surrounded by necessary and healthy cells.
This is why chemicals and nano  structures are the most commonly pursued means of combating cancer; they can enter into cells that are embedded in solid organs.  Differentiating the cancer cells from other sorts of cells in vivo is a pretty hard problem - some antibodies are given as a possible help there, but they are not reliable.
This blog post is a pretty up to date summary of where we are
http://www.sciencebasedmedicine.org/index.php/personalized-medicine-vs-evolution/

May I ask you if there's some way to make cell cancers identifialy? For example, a virus inserting radioactive DNA on cell cancers only? Or anything like that?

@Dokkat : If you would have a virus that could insert DNA in all cancer cells and not in non-cancer cells you could simply let the DNA produce proteins that kill the cells. We don't have such a virus.

@Christian: there are, however, (far from perfect) approaches to that, such as receptor-mediated or pH-mediated targeting of nanoparticles for drug delivery.

@Dokkat radioactively tagged antibodies specific to cancer cells have been used in the past

@nico: It still doesn't make sense to tag cells with such methods and then locate the cells and punch mirco/nano tubes with a robot into them.

@Christian: no, but you can release a drug specifically on those cells.

This is a multibillion dollar question.  jury is still out. I doubt there is a specific 'i'm cancerous' label on the surface of all these cells.

We can manufacture materials thin and hard enough to penetrate the body without harming it.

It’s not a question of materials. After all, we have the materials to build flying cars – so why are there no flying cars? The problem is reliably locating, recognising and selectively killing tumour cells.

using micro tubes, kills them one by one?

“one by one” … for billions of cells? Even ignoring all the other technical problems already alluded to in other answers, this is simply a problem of insurmountable scale. In order to do this efficiently we’d need in the order of millions tiny robots.
Either way, creating appropriate robots isn’t something we can do today, and even if we can someday do it, it will be easier (and much, much cheaper) to just bio-engineer a bacterium which detects and kills tumour cells. While neither nanobots nor bio-engineered cancer killers are reality today, the bio-engineering approach is much easier, and much closer to realisation than the nanobot approach.


text:
Neutralizing TCA washes
Trichloroacetic Acid (TCA) is commonly used for protein precipitation but the wash waste needs to be neutralized prior to disposal. What exactly is required to effectively neutralize TCA waste? Do I just add caustic?

You might want to add a bit here to establish the biological relevance, as it is now this is a pure chemistry question.

How can I migrate this question?

I've been fortunate to find a protocol hidden away in my lab archives.

The acid waste can be accumulated for 10 days before it needs to be neutralized. The waste should be kept in a carboy in a fume hood.
50 mL 50% w/v Sodium Bicarbonate slurry should be added per liter of TCA waste. During neutralization fumes will be generated which may include chlorine gas.
When the pH reaches 6-8, dispose the waste into the sewer.

I know what the structure of TCA is, which is exactly why I'm asking you how you think Cl2 will be generated?

From the MSDS for TCA, it states to neutralize with sodium bicarbonate so as to prevent Cl2 gas formation (like with neutralization with HCl).

Why did this get 2 downvotes? Is it incorrect? Why is it accepted instead of the other, much higher scoring answer?

I accepted it since I was the one who asked the question and wrote the answer. It was downvoted since someone decided that it was "unsafe" despite the fact that this is actually the EH&S determined protocol. There needs to be better comment history on SE.

-1. Unless a proper citation is given, I see no reason why trichloroacetic acid would produce chlorine gas in the absence of an oxidising agent.

A neutralization reaction occurs between Brönsted acids and bases to form a salt.
In this case, you have to add a Brönsted base to neutralize your acid. If the final pH is important, you should work out the exact quantity of base to add. Otherwise, just use litmus paper to check the pH of your solution, and add base until it's neutral.
EDIT
In view of the other answer proposed, I want to stress the following:
Do NOT dispose of your solution in the sink/sewer. Leave it in its plastic bin until a lab technician takes it to the furnace.
If the base you use is sodium bicarbonate (NaHCO3), there will be bubbling, caused by the decomposition of carbonic acid (H2CO3) into water (H2O) and carbon dioxide (CO2). You've successfully neutralized the TCA once there's no bubbling upon addition of NaHCO3.
It is indeed best to proceed slowly while adding your base.


text:
protocol for pulldown of DNA breakpoints?
Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:
 Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.
I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.

Perhaps ChIP can be adapted for this purpose? I don't know how you would identify single-stranded breaks.

The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.
I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:
you could detect them with a tiling array.  - that's an micro array which has an oligomer every 40 bp or so of the genome.  The array could be used in a CHP experiment that detects the same proteins as in this paper.
Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right.  This sounds noisy though.
On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep.  if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply.
any of these sound like a good bit of work :)

The answer is yes, not only meiotic, but any DNA double-strand breaks will be detected as long as they are processed by homologous recombination. This method (SSDS) is based on the detection of resected ssDNA ends at DSBs. The only difference for the mitotic breaks will be that you cannot use anti-DMC1 for ChIP. Instead, you should use either anti-Rad51 or anti-RPA in ChIP.


text:
How straightforward is in vitro compartmentalization?
in vitro compartmentalization (IVC) is one of those technologies that everyone knows about, talks about, but never actual does due to the rather technical difficulties in setting the system up. I was wonder if anyone not named Tawfik, Griffiths or someone who did a post-doc with them have been successful in making IVC work? Details in how stable emulsions and a homogeneous mixture of cell-free components in the droplet are made would be wonderful.

one of those technologies that everyone knows about. Everyone but me! Nice link, always good to learn something new.

You might want to look up synthesis techniques  artificial cells, like artificial red blood cells.  A resource that has led me to believe this stuff isn't impossible to set up is at www.artcell.mcgill.ca

@ThomasIngalls, while certainly neat, the dimensions of artificial cells are completely different from the dimensions of IVC which prevents the concepts learned in this body of work from being translated to smaller emulsions. This will still be interesting reading material.

Thanks for pointing that out, it'll save me some reading, too.  Sequencing technologies like 454, SOLiD, IonTorrent use emulsion PCR on a large scale.  The SOLiD system even has an sample prep machine that automates the creation of these emulsions.  I think these emulsions end up a bit smaller, but they're at least in the right ballpark.

@ThomasIngalls i think you should expand into an answer, eh?

It is actually surprisingly easy and reproducible to make emulsions with defined components. We do it routinely in our lab:
http://www.sciencemag.org/content/332/6026/209.full - CBT protocols
http://www.sciencemag.org/content/336/6079/341.full - CST protocols

Thanks! Since it has been awhile since I've asked this question, I now get the impression that certain reactions like transcription and smPCR work well. When concentrations and size become more important or translation is important things go south.


text:
How does population stability evolve?
The number of individuals constituting a population is called population size.  Over time population size does not remain constant, it fluctuates to different extent over generations because of several internal and external factors.  Populations with violent fluctuation in population size are called unstable and are more prone to extinction as they hit lower population sizes frequently.  And once a population in extinct, it is gone for ever.  Thus it would be interesting to investigate how population stability evolves.

Could the word 'evolve' be confusing the issue here?

I think Rory is correct, evolve here is likely implying too much.

Maybe changing it to develop would be a good idea?

I guess you meant the population size stability.
It is considered that the biosystems will increase their capacity of adaptation when evolving in very fluctuating environments. I believe the population stability is embedded in the adaptability of individuals.
There is a measurement about it, evolvability, when the environment changes, the faster the population adapted to the new environment, the higher evolvability it has. This means that if the population has higher evolvability then the population may be more stable to environmental variation.
Even so, there might be plenty of underlying mechanisms to enable a certain population stability. I recently read a paper about two mechanism: phenotypic switching and sensing machinery, which are common in bacteria and fungi. Please refer to Edo Kussell and Stanislas Leibler's science paper (2005).
As the organism increase its complexity, biosystems invented many more tools to make the individual survival from disasters. Such as human's intelligence. Well it would be an endless issue.

You should consider linking to papers that you mention in answers to help save time for readers :)

I think you are hinting at the right answer with "population stability is embedded in teh adaptability of individuals." Population size fluctuations seem to be easily explained by the underlying differential equations that describe the interplay between internal and external factors that affect the population (eg, birth, death, disease, migration, predation). Within a given environment, there must be an ideal population size range, whereby anything larger imposes too much drain on resources or stress to individuals, and anything lesser leaves room for expansion.


text:
RNA or ribosome, which one moves during translation?
During translation ribosomes decode the genetic information present in the mRNA and protein synthesis takes place.  During this process which of those two does move, the ribosome or the mRNA?

center of mass says - depends on the size of the RNA.  Also at least with prokaryotes, there are multiple ribosomes per RNA, which probably means less movement as they are probably not synchronous movements.

Shigeta, I think you are right about what you are saying but can you please be more specific about the answer...

@Shigeta. I love the argument but conservation of momentum may not hold in these low-reynolds number systems.

With respect to movement, it really is a question of your frame of reference. The rough ER has a number of fixed ribsomes for which concomitant protein translation and translocation occurs. In this case, the mRNA is certainly extruded from the ribosome. With respect to polyribosomes and free-floating cytoplasmic ribosomes, there is no proof that either the mRNA nor the ribosomes have any tethering, therefore we may assume the whole complex moves with respect to some fixed external point.

@shigeta low Reynold's numbers say F = ma --> F = bv: there is no mass in the equations of motion inside a cell. It's probably misleading to talk about the center of mass at all.

@Shep point taken.  Reynolds numbers assume a fluid which is not really true at that size, but its also true that the ribosomes are even less likely to move too much on timescales of the reaction as the water would interfere.

Its the ribosome that moves.....see the book, 'The Cell, a molecular approach" by G.M. Cooper

http://www.jbc.org/content/269/48/30713.full.pdf

Here's an example in which the ribosome is fixed:
During co-translational translocation, the ribosome is essentially anchored onto the ER membrane through the Sec61 complex. It certainly cannot move along the mRNA. The mRNA is fed through the ribosome and the nascent peptide traverses into the ER lumen.

this is the eukaryotic case, the bacterial case is more like the other descriptions, though i'd bet in that case the viscosity of the cytosol makes it so that the ribosome not move very much at all during translation.

The ribosome moves relative to the mRNA by, in effect, pulling itself along it.  If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses.
(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)
As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton.  Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.
Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand.  That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.
Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it.  And I really have no idea how negligible the interactions with the tRNAs and so on are.  It's a mess, but my guess would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).

Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a gedankenexperiment. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls.  Then get in, grab the rope with your arms and legs and try pulling yourself along it.  While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)

Your swimming pool experiment is right on. I'm not so sure about the talk of "center of mass" though. A low Reynolds numbers, it's far more important to consider the linear drag coefficient than the mass of anything involved. To imagine the inside of a cell, you need to forget newton's laws: objects in motion will stop moving unless acted on by an outside force (at low Reynolds numbers).

You may well be right. As I noted in the parenthetical remark, I based my crude back-of-the-envelope calculations on the relative masses because that was something I could get some data on.  If my guessumption about the drag coefficients being roughly similar is way off, then so may be my conclusion as well.

Movement is relative. The real events happening in translation are the conformational changes of ribosome makes itself continuous reading the base sequentially. Please refer the biochemistry textbook or cell biology textbook.
Indeed, if the ribosome is anchored, you may say the mRNA is moving.

Well, thanks for your response but bit of a problem here.  Certainly movement is relative and depends on perspective or reference frame.  What I meant by movement here is relative to more stationary structures, for example cytoskeletons, which one of the two moves.  precise answer in not clear from the first response.  And I did already consult the text books and obviously didn't find the answer either!

Regarding the second response, ribosomes are certainly not 'anchored' to any part of the mRNA, cos had that be the case, how do other parts get translated then?

@balaka: it does not say ribosomes are anchored to mRNA, just that they are anchored.

True, but with which substratum it is anchored is also not mentioned.  mRNA was just one plausible candidate for me for their obvious proximity.

@balaka: not really a plausible candidate because, as you said, it moves! I'm not an expert on the matter but I would not be surprised if they were anchored to cytoskeleton proteins.

The mRNA moves during translation. It is essentially threaded through the ribosome. This has been known ever since polyribosomes were discovered; see paper here. Polyribosomes are a cluster of ribosomes that read a series of mRNA molecules. Often, the ribosomes in a polyribosome will be translating the same mRNA.

Of course it all depends on your reference system. If an observer were on the mRNA then he would see the ribosome moving :)

If you think of the cell as a universal 3D space, the relevant reference point would be a fixed coordinate in this space outside of the mRNA and the ribosome. Why would a cell biologist use either the ribosome or the mRNA as the reference point!? If you adopt your attitude, there would be no motivation to identify motile features. Does the Earth revolve around the Sun, or the Sun around the Earth? By your reasoning it doesn't matter, after all it's just relative.

I think any anyone who has seen relativity understands Nico's point. As for the paper, Warner et al. fix the ribosomes onto the surface. It's an artificial surface that forces the mRNA to be threaded through the polyribosomes. One can't make a conclusion from this study.

We have established that frame of reference dictates which part, if any, moves relative to the observer. My question to you @balaka is, does it matter?

The fact that ribosomes can collide with each other on the polysome during the translation process shows clearly that the ribosome is moving along on the mRNA.

Welcome to SE Biology. We are looking for comprehensive answers supported by evidence on this site. It is not enough to state something is a “fact”, you need to document it with reference(s). So please provide evidence that ribosomes collide with each other. You may well be right, be I am not aware of this and can assure you that 99% of list members will be in a similar position.


text:
What is the difference between copy number changes with and without allelic imbalance?
I require some clarification on copy number aberrations (structural gain and loss in chromosomes). From what I understand, gain/loss per se can be divided into two types.
Consider two alleles, A and B at the same locus on homologous chromosomes.

Allelic Balance: in one type of structural gain/loss, there is no resulting allelic imbalance; examples:

AB ==> AABB (duplication),
AB => -- (loss).

Allelic Imbalance: in the other type of structural gain/loss, there is resulting allelic imbalance; examples:

AB ==> AAB (duplication of A),
AB => -B (deletion LOH),
AB ==> BB (copy-neutral LOH).

First, is what I have described above correct?
Second, if it is correct, what is the biology underpinning these copy number aberration types? Are the mechanisms responsible for bringing about allelically-imbalanced CN change distinct from the mechanisms for bringing about allelically-balanced CN change? What are these mechanisms?
NB. I'm confining this to just copy number-related allelic imbalance.

Allelic imbalance is a pretty broad phenomenon difference in the expression of two alleles.  As such you have listed would probably cause allelic imbalance, but it could be the result of methylation or even differences in RNA sequences between the alleles which say interfere with post translational splicing say.
In the case of copy number variations, if a copy number region (which is often a higly repetitive sequence in the genome and not a gene duplication) might interfere or not interfere with gene regulation. In cancer cells large segments of the genome may be copied or cut out though, so in that case the mechanism you put forth may be important.

Regulatory effects on gene expression are obviously a v important consideration for AI. However, I suppose I'm confining myself to copy number. For e.g., for AI CN changes, the predominant mechanism may be NHEJ, whereas for allelically-balanced CN changes, the driving mechanism may be mitotic defects???


text:
What is the fastest way to build an alanine scanning library?
For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using E.coli cell-free protein synthesis. I already have the template gene which was originally built using PCR assembly. Now, what's the best way to build a scanning library?

do you mean, how do i decide which amino acids to include in the alanine scan or how do i create the library of alanine mutants?

@shigeta, definitely more "how".

http://www.genscript.com/alanine_scanning.html  genscript has some pages to help you reason through the design.  Myself I'm not sure, but it looks like it takes quite a lot of oligos to say the least...

Are you still interested in the answer of this question?

@GerganaVandova, not really but it might be of interest to the broader community.

The fastest will change as time passes and better technologies are developed.
I think the fastest method existing at the moment is Shotgun Mutagenesis (provided by Integral Molecular Inc).
This does not employ any new method of doing that. They just provide a set of plasmids, that has all the possible mutations. The set itself is generated by automated DNA synthesis.
So if you don't have a DNA synthesizer with you then simply order the kit from the company.


text:
Phagemid display
If I'm using a bacteriophage for phage display and I'm trying to avoid avidity effects by using a helper phage what would be the best way to maintain a large library size while keeping everything monomeric? I'm asking in terms of maintaining an appropriate infection ratio and or phage tricks and tools to maintain the that stoichiometry.

If you don't end up getting an answer here, I would recommend reposting on researchgate

I found article in Nature:
A helper phage to improve single-chain antibody presentation in phage display

Experimental protocol
Standard cloning procedures, determination of colony-forming units and
plaque-forming units, and immunoblot after PAGE were carried out
according to Sambrook et al.
Construction of the packaging cell line.
DH5alpha/pIII
[M13KO7DeltapIII]. The M13 pIII gene fused to promoter P/A1/04/03
(ref. 17) was inserted into the multiple cloning site of the
lambdaattP plasmid pLDR9 (ref. 18). The origin of replication and the
kanamycin resistance gene were cut out and the remaining
lambdaattP-pIII nonreplicative DNA was religated. Escherichia coli
DH5alpha containing plasmid pLDR8 (ref. 18) were transformed with the
lambdaattP-pIII nonreplicative DNA and plated on agar plates
containing 25 mug/ml ampicillin. After incubation overnight at 42°C,
the colonies obtained were replica-plated and ampicillin-resistant
clones were identified, named E. coli DH5alpha/pIII. They were
subsequently transformed with M13KO7DeltapIII, resulting in the
packaging cell line E. coli DH5alpha/pIII [M13KO7DeltapIII].
Production of phage.
To obtain M13KO7DeltapIII helper phage,
M13KO7DeltapIII DNA was electrotransfected into E. coli K802
containing pNDI (ref. 15). To obtain hyperphage, M13KO7DeltapIII DNA
was electrotransfected into E. coli DH5alpha/pIII. Phage were produced
by cultivation in the presence of 0.5 mM
isopropyl-beta-D-thiogalactoside (IPTG) at 30°C for 24 h with shaking
at 200 r.p.m. Escherichia coli Top10F' or E. coli Xl1blue carrying the
pSEXphOx(Yol) phagemid or a scFv library in pSEX81, respectively, were
infected with a helper phage preparation at a OD600 of 0.1 at a
multiplicity of infection of 20 as described.
Phage quantification by ELISA.
Dilution series of phage were coated in
100 mM NaHCO3, pH 8.6 in MaxiSorb ELISA plates (Life Technologies,
Karsruhe, Germany) for 16 h at 4°C. Blocking was done with 2% skim
milk powder in PBS (137 mM NaCl, 3 mM KCl, 8 mM Na2HPO4, 1 mM KH2PO4,
pH 7.3) for 2 h at room temperature. Phage were detected with the
monoclonal mouse antibody B62-FE2 (Progen, Heidelberg, Germany)
specifically binding an epitope on the pVIII major coat protein of the
M13 phage. M13KO7 phage of known colony-forming units were used for
standardization.
Immunoblot.
Approximately 1010 phage were applied per lane on a 10%
polyacrylamide gel. Blocking was done with 2% skim milk powder in PBS
for 2 h at room temperature. Immunostaining was done with the mouse
mAb anti-g3p (MoBiTec, Göttingen, Germany) recognizing the pIII coat
protein of M13KO7, visualized with 3,3', 5,5'-tetramethylbenzidene
(TMB) substrate (Promega, Madison, WI).
Antigen-binding phage ELISA.
Dilution series of BSA-phOx antigen in
100 mM NaHCO3, pH 8.6, were coated in MaxiSorb ELISA plates (Life
Technologies) for 16 h at 4°C. After blocking of unspecific binding
with 2% skim milk powder in PBS for 2 h at room temperature, 2 times
109 single-chain phage diluted in 2% skim milk powder in PBS were
applied to each well for 1 h at room temperature. After washing six
times with 400 mul PBS per well, the bound phage were detected with
mAb B62-FE2 as described above.
Panning.
A human scFv fragment library in pSEX81 with a calculated
maximal complexity of 2 times 107 was generated from peripheral
lymphocyte preparations as described21. Tetanus toxin obtained from
Virotech (Rüsselsheim, Germany) was coated to six ELISA wells (Life
Technologies) at a concentration of 0.1 mug/ml in 100 mM NaHCO3, pH
8.6, for 16 h at 4°C. The wells were blocked with 2% skim milk in PBS for 2 h at room temperature, after which 1011 phage of the library
were applied to each well and incubated at 4°C overnight. After five
washes with PBS/0.1% Tween and five with PBS, bound phage were eluted
with 1 mug/ml trypsin (Life Technologies) in PBS for 15 min at room
temperature. Eluted phage were used for the infection of 20 ml of E.
coli XL1blue at a OD600 of 0.4. Infected bacteria were grown on
Luria–Bertani agar plates containing glucose and ampicillin, scratched
from the plates, and used for the production of antibody phage for the
next round of panning as previously described.

Looks great Devashish Das. I'll wait until I'm sure of not getting a better answer, but I think that paper pretty much covered it.

I appreciate that.

Wow! Thanks for answering such an old question. I'm not entirely sure if this solves the avidity issues though.

@bobthejoe: Thanks!! Can you add a little bit what I am missing in this?


text:
How is the blood volume of a living organism measured without killing it?
How is the blood-volume of an organism measured without killing it?
Note:The blood-volume of an organism is defined as the total volume of blood present inside that organism.

I guess it is possible with plethysmography. If someone confirms this I'll look for a detailed answer.

Could this be done with radioisotopes? I'd imagine a set of scans from different angles could give a reasonable estimate of blood volume.

Polynomial, can you please illustrate a bit more?

@Polynomial, This seems to be it. http://tech.snmjournals.org/content/35/2/55.full

Yeah, that's kind of what I was thinking about. My method was a little less refined and involved a lot of "glowing area measurement", but it's essentially the same principle.

Polynomial gives a good hint. By adding in a known tracer of known amount that should only circulate in the blood stream, the concentration of the tracer when completely distributed will give the volume of distribution.

If the tracer only stays in the bloodstream (and that's a fairly large IF), then the VD will be equal to the VBlood. However, as many pharmacologists know, interactions with proteins and cells can skew that number. The blood volume is also reduced by the volume of the blood cells. However, using Andrei's method of dilution, one can merely swap the cell counts with the tracer concentration.

How it is done according to my bioengineering textbook is injection of a water-soluble tracer into the heart or aorta, then 'listening' for the tracer somewhere else in the bloodstream. If you inject into the atrium and listen at the aorta, you can get cardiac output as well. It takes a minute or so, and gets a measure of the amount of fluid circulating, not counting blood that's trapped or basically not circulating(veins from leg muscles while sleeping, compartment syndrome, etc) while counting fluid that freely exchanges with the blood. Not technically accurate, but gives extra information.

The same book described measuring cardiac output using ice cold saline injected directly into the atrium as a tracer, and it was written quite some time ago(70s iirc). On the whole I trust it as far as I can throw it.

It is easy.
Method A, simple, is based on "counting the fish in the pond" method.

Make rough estimate of amount of blood in the organism.
Choose a component of blood that is replenished slowly [from liver or marrow etc]. That takes time to replenish. Red blood cells are probably OK. Some easily measurable and slowly replenished component of blood. Let's call this component of blood G.
Take small blood sample and measure level of G, denote result G1.
Drain N ml of blood, ands refill same amount back with infusion of normal saline.
N can be taken as 10% of estimate of amount of blood.
Take small blood sample, measure level of G, denote result G2.

G2 will be smaller than than G1.
Now from G1, G2, and N it is easy to calculate organism's amount of blood.
You can derive exact formula yourself.

How long would you wait between samples given that you would presumably have to wait for "G" to diffuse throughout the entire blood stream?

@Rory M: I would suspect diffusion in the blood stream to be almost negiglible. If I remember correctly it takes ~1 min for a complete recirculation of blood in a human, and for smaller animals it would be even less than that.

@Rory M: I'd expect minutes. Pharmacokinetics manual shall have answer to this. Wrt drugs administered intravenously, manual shall have the answer (speaking of humans of course).

Your model isn't very accurate since it depends on making a "rough estimate" of the amount of blood before making any measurements. That's a huge bias that can't be overcome later. I also think your suggestion of removing 10% of the estimated blood volume isn't commendable. What happens in a case where you over-estimated the blood volume? Your model works, but only for an estimation. I think you should provide the equation for any readers who aren't very mathy.

@CHM, I believe that N doesn't need to any particular value. The dilution series will allow one to back-calculate what x% N consist of.

You can use ultrasonography (echography) to measure blood flow.
From the blood flow measurements and vessel dimensions you can then determine blood volume!
If you want a full explanation on how blood flow is measured by Doppler ultrasonography, make sure you ask the question to the right people. They'll help you with the technicalities.

I didn't downvote your answer, I'm not really in much of a position to judge it, but it does seem to be unnecessarily complicated.


text:
Can species back-evolve?
One of the tenets of Darwin's theory is the survival of the fittest, ie adaptation of features that allow a species to adapt better to its surrounding environment. I am wondering that given the right conditions, is there a possibility of a more "complex" species, say humans, back-evolving into a less "complex" species, say a dog? Is there anything in Darwin's theory or some experimental proof that excludes such a possibility?
EDIT (4/19/12): Thanks for all the responses! I definitely agree with the fact that we are no more complex than dogs or Drosophila, hence the quotes surrounding complex in the question. I learnt a lot from the answers and don't think there is any one answer that is the best, but read together, they drive home the point. Thanks all!

Since no answer mentions this explicitly, and since it is a very common misunderstanding: humans are not more complex than dogs evolutionarily. The word isn’t even well-defined in this context and no biologist has yet come up with a good enough definition.

@Konrad, I have a feeling that humans, with their speech, math, physics, and understanding of molecular biology, are more sophisticated than dogs and cats. Humans and their associated technologies evolved and developed together, you cannot take technologies away from human development. It is a subtle nuance that part of those human sophistications lies outside of its biology. But it is sophistication nonthe less; and I have to repeat, you cannot take technologies away from human nature, it is part of us. Sophistication way above level of other mammals is present: can other mammals get QM ?

@Andrei I agree with your (implicit) points about cognition and, what Popper has termed, “world 3”. However, this is strictly outside of the scope of biological evolution (even though it’s a consequence). The “aim” of evolution is simply: to reproduce. This is the only measure of evolutionary fitness that counts. And by this measure, humans are usually not better, and sometimes worse, off than other species.

Complexity is a lure. Evolution isn't defined by complexity, but by adaptation to one's environment, as you mentioned.
Evolution is an ongoing, non-deterministic process. There's not one definite evolutionary "path" that brings a unicellular to a modern human being. Nor is there a predictable evolutionary path that brings a dog into becoming a human. You also have to acknowledge that, because evolution is ongoing, the dog of yesterday is not the dog of tomorrow. That applies to all the living.
Is it possible that given the right amount of time and the ideal environment the modern human could evolve into the modern dog?
Yes, it is possible.
Is it probable? No.
The chances are that if humanity were to find itself in such an exotic environment - to which dogs are 100% adapted, but humans 0%, which just shows how unprobable such an environment is - it would become extinct before it has a chance to adapt, much like a lot of other species have done.

Good answer CHM.  It would be a little like running across the field, and then, needing to go back again, stepping in exactly the same footsteps you had taken when coming across the first time.

Good response, but I think it needs to be emphasized that a human evolving into a dog is more than improbable, it is virtually impossible. @shigeta Or hiking a dozen times around the globe, and then retracing each step exactly.

There are several strains of mutant cells from humans, mice and various other species that have found themselves a niche as single-celled organisms living in lab dishes, and seem to be thriving there.  The well known HeLa human cell line, in particular, appears to have adapted to this new existence well enough to have acquired a reputation as a "weed" that easily contaminates other cell cultures.
Nor is the phenomenon confined to artificial human-created habitats, either — some species of animals, including dogs, hamsters and Tasmanian devils, are susceptible to infection by transmissible cancers, which are essentially unicellular pathogens deriving from mutant cells of the host (or a related) species.

Interesting, but how does this answer the author's question :/ ?

Well, he asked "is there a possibility of a more "complex" species, say humans, back-evolving into a less "complex" species".  I provided some examples where one could say that has, in effect, happened.

So HeLa (and company) cells are considered a species on their own, no longer human?

By some people, yes.  But even if not, it's hard to argue about the transmissible cancers: the canine transmissible venereal tumor, for example, is certainly a living organism, and it's certainly not a dog.

The genome of a HeLa cells is no longer quite human. The cell line has tetra- anuploid. ie the cell line has double its genome twice then lost chromosomes. And over nearly 50 years the cell line has also adapted (by means unknown) to grow on glass and plastic. Something that normal cells do not like to do. So yes... you could argue that HeLa isn't quite human anymore. And HeLa continues to evolve and mutate in its unnatural environment. Who know what HeLa will look like in another 100 years.

Abundant example exist to this when it comes to organs. There are plenty of examples when organs that in the past served some function -- because they evolved to serve this function -- later degenerated or disappeared because environment changed. Examples: vision of species that came to live underground, wings/ability to fly of non-flying birds (penguins, ostriches etc), legs of snakes, some organs of sea mammals.
We know what adaptations mammal species develop to life in the sea. However, these mammals do not turn to cold-blooded fish with scales and gills. They take different evoluionary path for adaptation to sea life. In particular, they remain warm blooded, milk-feeding, and  retain lungs. I do not think it is possible that lungs back-evolve into gils, but it is interesting question which mechanisms a mammal like dolphin would evolve if it needed to live all the time under the surface of the sea. It would be matter of inventiveness of mutations in the face of new (old :-) conditions not the issue of back-evolution.
I do not think it was ever shown that genome has mechanism in which instead of mutations, "old" genetic trails (like gils) would be used. I think such mechanism does not exist, and in this sense, the answer to your question is "no".
However, if chain of mutations exist that brings a species back to s atate resembling "old" state, this path might be taken. (degeneration of ograns). In this sense, the answer is "yes".

It should not have been "survival of the fittest" but rather "survival by the most persistant."  Traits evolved by natural selection are not required to be optimal or even adaptive.
In response to your question, consider the case of the evolution of thermal reaction norms.  These mathematical representations quantify an organism's performance across a range of environmental temperatures.  Across the diversity of life, you'll find that some organisms have evolved narrow thermal tolerance windows while others have evolved broad thermal tolerance windows.  These specialist vs generalist strategies have benefits and constraints that depend on environmental and ecosystem stability.
So I think a way of answering your question would be to consider the evolution of thermal reaction norms.  Are there derived taxa that have switched between specialist vs generalist thermal preferences compared to their sister clades?  I'm sure the answer is yes -- but perhaps check out the papers by Kingsolver (Duke) for a more thorough answer!
Also, consider this:  As humans, we are just as much evolved as a fruit fly or a paramecium.  Since the generation time is much less for fruit flies and paramecia, you might even say they are more evolved than we are.

It's always helpful to directly link to papers you mention :)

Just to clarify, as one might read your question as if humans had evolved from dogs - humans and dogs have a common ancestor, one is not a direct descendant of the other.
In terms of evolution running backwards, it has actually been experimentally tested in microorganisms, where you can check the phenotype (characteristics) of an organism over hundreds and thousands of generations. One example that comes to mind is Joe Thornton's research where he reconstructed a gene for an ancient protein and compared it to the more modern versions. They found out that the key mutations that modified the protein sequence could not be simply changed back to obtain the more ancient form, because in the meantime many neutral mutations had accumulated in that protein and while they did not change the protein sequence, they interacted with the protein-changing mutations and prevented the de-evolution of the protein.
The paper I have in mind (there are many more on this) is: Bridgham, Jamie T, Eric A Ortlund, and Joseph W Thornton. 2009. “An Epistatic Ratchet Constrains the Direction of Glucocorticoid Receptor Evolution.” Nature 461 (7263) (September 24): 515–519. doi:10.1038/nature08249.
On the other hand, in a sort of more esoteric example (as it is not directly de-evolution), blind cavefish have multiple mutations (and sometimes in multiple genes) that cumulatively result in loss of vision. Let's then say you have population of the fish that have sight-losing mutations in gene A and another population with mutations in gene B. Both populations are blind, but if you could cross the fish from the two populations, the eye-loss mutations in genes A and B would be substituted by 'correct' versions from the other population and thus both fish would be able to see again. While not de-evolution in itself, it shows that for relatively simple changes that were not influenced by other changes in the genome, you can rewind the clock and get the long-lost phenotypes, even like the sight.
See here: Borowsky, Richard. 2008. “Restoring Sight in Blind Cavefish.” Current Biology : CB 18 (1) (January 8): R23–4. doi:10.1016/j.cub.2007.11.023. (this is a description of the research, not the actual paper; but it links to it).
Both these examples are super-cool (IMHO), and in my collection of all-time favorite evolutionary stories. But practically speaking, what you're asking for (from humans and dogs to their most common ancestor) is not possible. Too many variables (both genetic and environmental and stochastic) to control. The papers are behind the paywall, but if you want them, send me an email.

@myself The above blind fish example assumes that the mutations in genes A and B are recessive (only one correct copy of the gene is necessary for correct function)


text:
Were dinosaurs 'hot-blooded' or 'cold-blooded'?
Were dinosaurs hot-blooded or cold-blooded? NOTE: The popular term 'hot-blooded' means having an internally maintained average body temperature, which is generally more than that of the surroundings, despite the variation of the temperature outside.  And obviously 'cold-blooded' is the opposite of 'hot-blooded'.

This is a question I have often heard and there is no one certain answer to it. There are several scientific hypothesis about the methabolism of dinosaurs, but none of them has been ever proved or completely disproved.
Arts of methabolism
First of all, the term "cold-blooded" and "hot-blooded" are not scientific. In biology the organisms are classified according to how constant their body temperature is:

homeothermic (from greek "hom(e)o" = equal, same) -- organisms, who manage to maintain constant body temperature.
poikilothermic (from greek "poikilos" = changing, changeable) - ogranisms, whose body temperature fluctuates over time. It is implied here, that  the body temperature follows the fluctuation of the environment temperature, even though this is strictly not correct (see below)

There is another orthogonal classification, which takes into account the metabolic properties of the organisms:

endothermic organisms actively produce heat in their bodies, whereas
exotermic organisms mostly rely upon external heat sources.

What do we know about dinosaurs' methabolism?
Unfortunately there is no one living dinosaur, so we can only reason about their methabolism basing upon the fossils (and possible DNA from moskitos trapped into ambers).
One of the most cited works here is the "Dinosaur Fossils Predict Body Temperatures" (link to the free full text), where the authors write:

Perhaps the greatest mystery surrounding dinosaurs concerns whether
  they were endotherms, ectotherms, or some unique intermediate form.
  Here we present a model that yields estimates of dinosaur body
  temperature based on ontogenetic growth trajectories obtained from
  fossil bones. The model predicts that dinosaur body temperatures
  increased with body mass from approximately 25 °C at 12 kg to
  approximately 41 °C at 13,000 kg. The model also successfully predicts
  observed increases in body temperature with body mass for extant
  crocodiles. These results provide direct evidence that dinosaurs were
  reptiles that exhibited inertial homeothermy.

And exactly here we need the terminology I presented above to understand the findings:

Dinosarier were endothermic -- they were able to actively produce heat in their bodies.
The produced heat can only be taken away through their body surface. Due to the fact that the body surface increases quadratically (n2) with the size, whereas the weight grows cubically (n3), the bigger dinosaurs were the higher temperature their bodies reached. That could be one of the growth limiting factors and explains why especially big species preferred to live in water.
Even though the dinosaries were homeothermic, we don't know anything about their thermoregulation. Modern reptilia do not have the thermoregulation mechanisms that would keep the body temperature constant. Dinosariers, however, due to increased heat production might have less fluctuations in their body temperature, than smaller reptilia. This is termed as "inertial homeothermy" here.


text:
How are the various classes of E coli genes determined?
Looking at some more detailed codon usage tables, genes may be further clustered into three gene classes: Metabolic genes, highly expressed genes during exponential growth, and horizontal gene transfer. Looking at the original paper by Medique et al., they clustered the genes based on the CAI and then by a variant of k-means determined 3 classes. Note that this is different from a class II gene which is determined by the types of RNA polymerase used.
How did they end up determining what the three classes are? It seems as if they made this generalization without any proteome data. Would the same genes be classified using a protein expression data during exponential growth and stationary growth?

I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 possible codons. A factorial cluster analysis (the categorical, multi-variate equivalent of principle component analysis) was run on these vectors, condensing 61 dimensions down to 2 dimensions. Now that the data complexity has been reduced to 2D, it is more manageable for a k-means algorithm to partition the data. In the end, the genes were clustered into 3 orthogonal groups (classes I, II and III, with 502, 191 and 89 CDS, respectively).
Only after the authors clustered the gene set were they able to go back and look at the canonical definitions of each gene. It so happened, fortuitously, that each class of the genes had a strong bias for subsets of cellular function (eg, metabolism, protein biosynthesis, transport). They did not use proteome data, but they were able to define the role for a large number of these genes based on the body of literature at the time.

Thanks for the analysis. I'm curious how this dataset matches up with the Highly Expressed Genes Database which uses validated genes. http://genomes.urv.cat/HEG-DB/

I was thinking how this would compare with what is deposited in the NCBI database as of today. This paper is from 1991 so I think it pre-dates many of these larger scale databases. It would be interesting to see how it compares to the HEG database you indicated.


text:
Why do plants' leaves become enlarged in low light areas?
Why do almost all plants in shade have a smaller stem structure and larger leaf than that same species grown in a well lit, sunny area?

I have no idea of the biological mechanisms behind what I'm about to propose. Consider this a hypothesis.
If the purpose of the leave is to collect sunlight for photosynthesis, then the behavior you mention is predictable. I order of trying to maintain a healthy flux of light in dim conditions, the plant adapts by increasing the area of its leaves. Once back in a well-lit environment, the need for larger leaves fades and new leaves are thus smaller, but still catch as much light. Of course, there must be limits to the extent of leaf area variation that one plant can handle.
As for the stem structure, I can only guess it's because plants spend more energy on leaf building than stem maintenance when under such stresses.

Also, plants that adapted to a "shady" ecological niche are competing less for access to direct sunlight, and therefore have less need to invest in height or the larger stem this requires.

The main factors that affect leaf shape are water and light needs. The plant needs a certain area of leaf to provide enough energy to live, so smaller leaves means more leaves(grasses), as opposed to one enormous leaf like a lilypad.
Generally, as light intensity increases water needs increase along with it. A thicker stem with a smaller leaf can support enough water flux to keep a grass blade hydrated in full sun, whereas a big tropical plant in high humidity has low water needs and can therefore use a thin stem to support a big leaf.
I would hypothesize that self-regulatory systems that affect leaf development as a function of available water and sunlight needs are responsible for the effect.