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Life without DNA?
I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional double-helix DNA as we know it? Have any serious alternatives been theorized?

I don't quite know if viruses and prions can be treated as "alive"...

What is considered alive? This is a good question. I think it is safe to define something as alive when it is (1) capable of sustaining and replicating itself and (2) able to interact with its environment.

Irregardless if viruses and prions are "alive", those that we know cannot survive in a word without RNA/DNA.

I agree with @Poshpaws it is great question

To follow up what mbq said, there have been a number of "origin of life" studies which suggest that RNA was a precursor to DNA,  the so-called "RNA world" (1). Since RNA can carry out both roles which DNA and proteins perform today. Further speculations suggest things like a Peptide-Nucleic Acids "PNA"  may have preceded RNA and so on.
Catalytic molecules and genetic molecules are generally required to have different features. For example, catalytic molecules should be able to fold and have many building blocks (for catalytic action), whereas genetic molecules should not fold (for template synthesis) and have few building blocks (for high copy fidelity). This puts a lot of demands on one molecule. Also, catalytic biopolymers can (potentially) catalyse their own destruction.
RNA seems to be able to balance these demands, but then the difficulty is in making RNA prebiotically - so far his has not been achieved. This has lead to interest in "metabolism first" models where early life has no genetic biopolymer and somehow gives rise to genetic inheritance. However, so far this seems to have been little explored and largely unsuccessful (2).
edit
I just saw this popular article in New Scientist which also discusses TNA (Threose nucleic acid) and gives some background reading for PNA, GNA (Glycol nucleic acid) and ANA (amyloid nucleic acid).

(1) Gilbert, W., 1986, Nature, 319, 618 "Origin of life: The RNA world"
(2) Copley et al., 2007, Bioorg Chem, 35, 430 "The origin of the RNA world: co-evolution of genes and metabolism."

There actually was a study where they were able to create (using theoretical early Earth conditions) two of the four RNAs. Though I always have a tough time finding the video interview for it I did find this. http://www.wired.com/2009/05/ribonucleotides/

There has been a recent report on Science, which had much return in the general press, in which a bacteria was identified that could live in an environment where arsenic was subsituted to phosphorus (one of the components of DNA, forming the backbone of the double helyx).
This is the original paper:
A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
and the commentary appeared on Nature
Arsenic-eating microbe may redefine chemistry of life
There is, however, much critique on the methodology used in the paper, and on whether arsenic would really be incorporated in DNA instead of phosphorus.
Science published several of these critiques in an Editor's Note
And here you will find the Response of the Authors
Other than that... well if you consider virus as life-forms, there's plenty that do not have double stranded DNA, but have instead single strand DNA or single strand RNA or double strand RNA.

"on whether arsenic would really be incorporated in DNA instead of phosphorus." - I'm quite skeptical, too. The difference in (atomic, covalent) radii is rather big, among other things. The difference in bond enthalpies with oxygen (phosphate versus arsenate) seems substantial, too, as would be expected (the larger the atom, the weaker the bonds).

I am also sceptical - but fascinating if correct !

I don't want to get too deep into the controversy over this study, but from reading the paper myself and talking to others, the weight of current opinion is certainly against the arsenic result.

yamad, is the prevailing scepticism possible to summarize for those of us curious about the result?

@KatieBanks, this is not my field so those interested should read the 8 critiques. One main criticism, though, is that their As+/P- medium has sufficient trace phosphorus to support the growth they attribute to arsenic incorporation. The authors argue that their As-/P- control, which shows no growth at all, indicates that it isn't just trace P supporting growth. This is a good point, but this still doesn't really require an interpretation that As is incorporated into the DNA. Their other data has also been criticized for insufficient purity in their samples/preps.

this was debunked: http://news.nationalgeographic.com/news/2012/07/120709-arsenic-space-nasa-science-felisa-wolfe-simon/

@woliveirajr the original papers can be found here: GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism and Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells. However, I wouldn't go as far as saying they "debunked" the study, just gave better explanation for their results (i.e. applied the scientific method).

Also: http://www.ncbi.nlm.nih.gov/pubmed/22798070

It depends whether you call prions a life form, but prions do not make (direct) use of DNA to propagate themselves. They force other proteins into a misfolded protein state.
Again, the question remains whether prions should be considered "alive".

The question of them being alive is moot; prions are ultimately dependent on DNA for their propagation as the host must generate additional substrate for them to turn over.

That is the reason I put "direct" between parentheses. Strictly speaking, prions do not make use of DNA to propagate. However, as you indicate, there is definitely room for debate.

Prions can't however change any protein into a misfolded state... they are a misfolded state of the PrP protein, which is normally synthetised by the organism, and for which a gene exists.

Luckily they can't. However, keeping the question above in mind, I don't think that this is of any relevance.

There are serious speculations that the origins of life were using RNAs both as enzymes and genetic information carrier.
Later this informative RNAs evolved into a more stable and less reactive DNAs, enzymatic role was delegated to proteins and RNA only remained into most crucial parts of expression chain (mRNA and rybosome) and some regulation mechanisms.

This recent Cell paper mentions a ribozyme (RNA enzyme) that ligates two oligonucleotides into itself. Given a sufficient source of input oligonucleotides and the correct conditions, it can catalyse its own replication and undergo Darwinian evolution, and can be thought of as a rudimentary form of RNA-based life.
The authors hypothesise that ligase-based RNA replicators could have been the first RNA replicators, which were later replaced by the now-standard polymerisation:

A somewhat different approach relies on RNA enzymes with RNA-templated
  RNA ligase activity to join oligonucleotide substrates to form
  complementary RNA products. It has been proposed that the first
  replicating, evolving systems on Earth operated by this mechanism and
  only later came to depend upon residue-by-residue polymerization

It should be noted that RNA ribozyme polymerases already exist, but many of them require proteins in addition to the RNA structure.


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How do the brain and nerves create electrical pulses?
The information between the brain and peripheral nerves is sent via electrical pulses or signals, How then does a non-metallic human cell manage to conduct an electrical
signal?

In order to attract the experts, we should probably avoid wide and basic questions this early in the beta.

This question has brought up a discussion on meta.

I would argue that if someone is so "expert" as to be driven away by a question like this, then good-riddance. Sure, you want to stay on topic, but come-on! This was a terrific question, and a REALLY informative and well thought out answer. A little less technical than the ideal? possibly, but closing it is an overreaction.

@Dr.Dredel please see the discussion on meta and comment there

This is quite a big question! I'll try to outline the basic view.
First, let's review how neurons signal between each other. The canonical way for a neuron to send a signal to a downstream neuron is by generating an action potential, the "electrical impulse" you have heard of. This action potential causes the release of neurotransmitter at a point where the two cells are very close to each other called a synapse. The downstream postsynaptic cell receives the neurotransmitter signal and converts it into a small electrical signal. If enough of these small electrical signals happen in a short time, they sum together and are likely to initiate an action potential in the second cell and the cycle repeats all along the circuit.
How is the electrical signal generated? The basics of how this works was worked out most famously by Hodgkin and Huxley in 1952. The short story is that the plasma membrane is selectively permeable to ions. Let's build the concept from the ground up.
The toolbox

Imagine a sphere of plasma membrane that represents a simple neuron. For starters, we assume that this membrane is bare lipid with no membrane-associated proteins. Because of the hydrophobicity of the bilayer, charged particles cannot diffuse through the membrane.
The cell is bathed, inside and outside, in a solution containing many ions (charged atoms), including sodium (Na+), potassium (K+), chloride (Cl-), and calcium (Ca2+). As we noted above, these ions cannot go through the membrane without "help".
Now we add an ion pump protein into the membrane which will pump sodium ions out and potassium ions in. This particular pump, the Na-K ATPase, creates an excess of sodium ions outside the cell and an excess of potassium ions inside.
Now we add a potassium ion channel to the membrane. This protein creates a pore in the membrane that only allows potassium ions through. This particular protein's pore is always open. Now things start getting exciting...
What do the potassium ions do now that they can go through the membrane? Ions will move based on the forces created by their electrochemical gradients. The pump created a chemical gradient by putting excess K+ inside, so the K+ ions start to flow out through the ion channels. But K+ ions are positively charged, so when they flow out, positive charge starts building up outside and negative charge builds up inside. This electrical gradient opposes the chemical gradient, tending to pull the K+ ions into the cell while the chemical gradients pulls K+ ions out. The influx and efflux reach an equilibrium at the Nernst potential, where the electrical and chemical forces equal out. For physiological concentrations of K+ ions, the K+ equilibrium potential is about -80mV or -90mV. This means that K+ ions will flow until the outside of the cell is 80-90mV more positive than the inside of the cell. We started at 0mV, so K+ ions mostly flow out.
We now have a membrane potential, a difference in electrical potential between the inside and the outside of the cell at about -80mV (usually closer to -70mV or -60mV in "real life"). In particular, this membrane potential is the resting potential that exists when the cell is not active. We can simplify for now and think of the resting potential as being set by a resting permeability of the membrane to potassium ions, but not to sodium ions. We call this membrane polarized, and thus depolarization is when the membrane potential becomes more positive, and hyperpolarization is when the membrane potential becomes more negative.
Now, we add to the membrane a voltage-gated sodium channel, an ion channel that passes only sodium ions but is usually closed. The voltage-gating means that this ion channel is sensitive to the membrane potential. At the resting potential, the pore is closed and the membrane is still impermeable to sodium ions. When the membrane potential becomes slightly more positive, the channels opens and sodium ions can flow. This channel is also inactivating, so that when it opens it only opens for a short period of time, letting in a limited amount of sodium.
What way will sodium flow when we open this channel? Because of the negative resting potential (-70mV) and the excess of sodium ions outside due to the pump, both the electrical and chemical gradient will drive sodium ions into the cell. The sodium equilibrium potential is usually around +60mV.
To complete the machinery for generating an action potential, we also add a voltage-gated potassium channel to the membrane. It works just like the voltage-gated sodium channel that is also closed at rest and opens when the membrane potential becomes more positive. This channel opens a bit more slowly than the sodium channel does, but it does not inactivate.

Generating an action potential
Ok, so how do these parts come together to create an electrical impulse?

The cell sits at its resting membrane potential, with all of its voltage-gated channels closed. It receives a signal from an upstream cell that causes a slight depolarization. The action potential will initiate when the membrane potential hits the threshold potential.
At the threshold potential, the voltage-gated sodium channels open letting sodium ions flow into the cell. The sodium flux pulls the membrane from the resting potential (-70mV) towards the sodium equilibrium potential (+60mV). These values are far apart, so the driving force is large and the membrane depolarizes rapidly. This is the action potential upstroke.
The depolarization also activates the (slightly slower) voltage-gated potassium channels. The potassium ions flow out and drive the depolarized membrane (about +20mV at the action potential peak) back towards the potassium equilibrium potential (-80mV). At the same time, the sodium channels are inactivating so that sodium is no longer depolarizing the membrane. The repolarization rate is usually slower than the depolarization rate. This is the action potential downstroke.
The whole process of the action potential depolarization/repolarization cycle takes about 2-3 milliseconds in an "average" neuron. Once the cell reaches resting potentials again, the membrane is basically reset. The voltage-gated channels are turned off. The ion pump moves the potassium ions that flowed out and the sodium ions that flowed in. That patch of membrane is ready to fire another action potential!

As a final note, I'll mention that the voltage-gated sodium channel provides a mechanism for the action potential to propagate down the axon. The action potential is initiated in one location of the cell, and creates a depolarization. This depolarization causes the voltage-gated sodium channels in neighbouring regions of the membrane to open and generate an action potential cycle of their own. This is how an action potential travel down axons (and sometimes dendrites too).

Neat summary to a broad question! Which differences are you referring to with the resting potential being "usually closer to -70mV or -60mV in 'real life'"? Also, doesn't it vary between cells?

In the answer above, I simplify and say that the resting membrane potential is the potassium equilibrium potential. This is generally not the case, with most resting potentials sitting somewhat more positive indicating the involvement of more ions/channels than just potassium. Yes, resting potentials do vary between cells. I take -70mV or -60mV as my "rule of thumb" resting potential because it generally holds for many primary excitatory neurons such as hippocampal and cortical pyramidal neurons.

That's very interesting, but I'm really wondering when you write "we add" what does it mean? Is there some helping cells giving needed ions to the neurons? Is it somehow transmitted throw the way the neural signal goes (during the impulses)? Or are the nutritions just released into the cerebrospinal fluid like a hormones?

@Probably I'm building a simplified model of a neuron in the answer. When I say "we add" I mean "add this to your mental model of the parts of the system".

Yes, I understand, thanks, I was just asking more into depth. Luckily, I've asked this question already and got this good answer here: http://biology.stackexchange.com/questions/37317/how-do-neurons-receive-the-ions-needed-for-creating-electrical-pulses

So, let us introduce some keywords.
The "electrical pulse" that "is sent from between brain and nerves" is called an Action Potential (AP). This is then propagated along a nerve fiber until the target organ.
Basically, a neuronal cell has a body and several long extended structures that "sprout" from the cell body. Dendrites receive signals from other cells and they convey signals towards the cell body by creating small electrical currents. The axon is a single "sprout" that is usually much thinner and longer than the dendrites and it conveys action potentials from the near the cell body to target cells and organs. Some axons can be as long as 80-90 cm (imagine!)! At the place where axon leaves the nerve cell body there is a small protrusion called the axon hillock.
The AP originates at a special part of the axon called the axon initial segment (AIS). The initial segment is the first part of the axon as it leaves the cell body and sits immediately after the axon hillock.
The electrical pulse is the short electrical discharge, that can be seen as a sudden movement of many charged particles from one place to another. In our cells we have ions of Na+ (sodium), K+ (potassium) and Cl- (chloride) (and in some cases also Ca2+) that constitute these charged particles.
There are two types of driving forces for these particles: besides the potential gradient, e.g. the difference in the total charge in two different places there is also another force called concentration gradient, e.g. the difference in concentration at two different places. These force can point into opposite directions, and thus by exploiting one force (let's say concentration gradient) we can influence another one.
What we need here again is a so-called semi-permeable membrane, this is just a barrier for ions, but only for specific ones. We need this because our main ions -- Na+ and K+ -- are both positively charged. Therefore the cell membrane acts as a semi-permeable membrane, letting K+ into the cells and Ca2+ ions outwards but not the opposite. Therefore we have two concentration gradients: Na+ (outside is the peak) and K+ (inside is the peak).
In order to start the pulse we need to initiate a massive ionic drift from one place to another. This is done by the cell, and the first event here is the drastic change (increase) of the permeability for Na+ ions. Na+ ions massively enter the cell and their charges, moved into the cell, form the upstroke of the action potential.
The protective mechanism of the cell immediately start working against the Na+ invasion and open the reserve shunts -- the K+ channels. K+ leaves the cell, taking away some charge and this is revealed as the decay of the action potential. But potassium channels are generally slower, that is why the decay of the pulse is more steady, not as sharp as the upstroke.
You might be wondering now: what triggers the rapid change of membrane permeability then? There are several factors here that may contribute into this process.

Potential change of the membrane. Sodium and potassium channels are voltage-sensitive, meaning if you manage to change the resting potential of the membrane, formed due to concentration gradients and normally being about -90..-80 mV (millivolts) up to about -40 mV it will trigger the sodium channels. This is how the impulse propagates -- having originated at one place it just decreases the resting potential of the adjacent membrane area, sodium enters the cell there and the AP travels along the nerve. The AIS is the site of AP initiation because this part of the cell has a very high density of voltage-gated sodium channels.
Chemical agents, called neurotransmitters, can be detected by receptors on the cell membrane. Some of these receptors are ion channels themselves and open directly when neurotransmitter is bound. Other receptors act through intracellular signals to open ion channels. This is how the signal appears at the sites of nerve cell contacts -- neurotransmitters, like acetylcholine or adrenaline, just act here as triggers for membrane permeability.

Nice overview, but I wanted to mention a few clarifications. Do you mean axon hillock instead of axonic hill? Also, it is in the axon initial segment (slightly further along the axon than the hillock) that AP initiation actually takes place. Dendrites are shorter but usually larger in diameter than axons. I would use the word neurotransmitters instead of mediators.

@yamad: You are absolutely right! Just feel free to edit my post. I am not a native speaker and haven't written anything about biology for quite some time, so my vocabulary can be rusty and imprecise. Thank you for your corrections!

No problem! You speak/write English better than most native English speakers. Just made some substantial edits to try to make things clearer. Hope it helps.

Thank you for your warm words! I usually go over through my posts next day to polish them up, I will integrate your remarks soon.

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How do fairy rings propagate?
It was somewhat new to me that mushrooms usually aren't individual organisms, but are merely the visible bodies of a bunch of fungi living in the soil. I know that mushrooms emit spores to reproduce, but what has been bizarre to me is how fairy rings form. Why do the fruiting bodies arrange themselves in a more or less circular shape, as opposed to the random scattering one would expect from wind-borne spores?

Furthermore, our normal ideas about what an organism is, and where its boundaries lie, are difficult to apply to these fungi.

When a fungal spore germinates in a suitable location, the growing mycelium will spread underground in all directions. In the ideal situation, the result is that the mycelium will become circular. Over time, the center of the mycelium will die out whereas the newly formed mycelium (underground) will develop the familiar mushrooms above ground and this will result in a fairy ring.

In addition, the mycelia (the underground mass of hyphae which constitutes the bulk of the fungus) expand outwards because they decompose organic matter in soil as they go, leaving very little organic matter in the soil in the interior of the ring. My Campbell & Reece textbook tells me that they can expand outwards at about 30 cm/yr. (1)
(1) Campbell, N.A., Reece, J.B. et al., Biology, 8th edition, Pearson, 2008

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How is Taq polymerase produced?
I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for polymerase production spliced in them, but I am wondering about the "native" variant. I imagine that Thermus aquaticus is rather difficult to culture in a medium; is it thus true that the archaeans have to be extracted from the springs they came from for producing "native" polymerase?

There are protocols on how to culture *T. aquaticus*, but I don't see any on how to get any decent expression of Taq pol.  Maybe it expresses extremely well anyways?  It still seems asinine that companies charge a mere ~10% price premium on the native vs. recombinant protein; probably why a startup that is sharing our building is able to carve themselves out a market.

@Nick: 1969?! Wow, the protocol hasn't ever been modified since then?

It certainly has been, that's just an example demonstrating it's ability to be artificially cultured.  Biotech companies that produce native Taq probably have all sorts of tricks and optimizations that they'd never share.

@Nick T: why would you use native Taq anyways? Recombinant ones are modified to perform better, so why pay more?

@nico I don't know, clearly someone wants them or they wouldn't be offered.  I've only done a couple PCR reactions, and only with Phusion (Pyrococcus derived; "50X" fidelity)

About why you would want a native enzyme: the answer is on this site. Essentially, you want to use the native enzyme when you don't want any E. coli genome DNA contaminants in the reaction mix.

For recombinant Taq polymerase, industrial-scale production produces liters of highly concentrated enzyme in a single run.  It comes in such small, dilute quantities when sold that only a few preps a year would be necessary to satisfy research lab demand.
I don't know the Thermus aquaticus protocol, but considering the achievements in yield for E. coli, and the minimal price difference between the two enzymes, I'd imagine that yields are similar there.  That would say to me that nobody's farming hot springs for T. aquaticus.


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How does cerebrospinal fluid circulate in the central nervous system?
Cerebrospinal fluid (CSF) is produced in the choroid plexus of the lateral ventricles and in the 4th ventricle of the brain.  CSF then circulates through the ventricles of the brain and the subarachnoid space of the meninges.  CSF is returned to the venous system via the arachnoid granulations connecting the subrachnoid space with the superior sagittal sinus at the superior portion of the neurocranium.

What circulates the CSF such that it can return to the venous system against gravity?
In other words, why does CSF not all just pool in the caudal cistern?

There are several points here.
Arachnoid granulations are not the only "sinks" for CSF.
Even though it is true that most of the CSF is eliminated from ventricular system and subarachnoid space through these granulations, there are also suggestions that there are also other potential mechanism of shunting CSF into the venous system:

Cranial nerves leaving CNS go through dura mater and these holes are not sealed, so it is suggested that some CSF can just go along the nerves and then accumulate in the lymphatic nodes in submucus.
Dura mater is mostly perforated at the area of lamina cribrosa, that basically separates the nasal holes and our brain. Leaking through multiple small holes here CSF is accumulated into the lymphatic submucusal nodes, found in abundance here. This way is considered to be primary CSF drainage way in newborns who don't have a well developed granularities in (sub)arachnoid space.
Spinal nerves, especially in the upper part of the spinal cord, also leave unsealed holes and the presence of lymphatic nodes adjacent to the places where these nerves leave the verterbral column also make them a potential place for CSF drainage.

Arachnoid granularitis do not only drain, they are capable of active CSF uptake.
CFS is not just "circulating" here going from the place of its origin in lateral ventricles to venous system. The granularities are here to actively resorb this fluid, meaning that they effectively take it up forming vacuoles and then excrete it to the venous system. Constant uptake leads to the pressure gradient (see also below!) that acts as a driving force for CSF.
Venous system has generally low pressure, thus sucking the CSF up to drainage points.
Speaking about drainage we also should consider the fact that the venous system has a pressure lower than the atmospheric pressure and much lower than pressure in any middle-sized arterial vessels. This is reached by having elastic walls and by transmitting the negative pressure from the mediastinum during the inhale, when the diaphragm and the thorax expand. This negative pressure propagates mostly to the connected vessels, including sinus system. Due to the elastic wall other parts of venous system can accommodate this negative pressure constrict their lumen, but not the sinus system which has a hard external framework formed by dura mater and bones. That is here we can measure the lowest pressure and this is the pressure that sucks CSF in into the venous system.
I hope that answers your question.

Does this mean that a purpose of yawning is to get the CSF flowing?

Perhaps you should add some references.

It is something of a misnomer to speak of CSF “circulation,” particularly in the spinal canal, as there is no continuous loop circulation of CSF as there is in the cardiovascular system.

For quite some time, it has been known that CSF movement results from the formation of new CSF and motion of cilia on the surface of the choroid plexus and ependyma lining the ventricles. - Fluids and Barriers of the CNS

The "circulation" of the CSF, as already mentioned, is something of a misnomer. CSF is not known to "circulate" in the manner of blood. It does get agitated by pressure differentials, and it is 'circulated' in terms of being reabsorbed and replaced every 6-7 hours. Other than that, no circulation occurs.
Blood circulation is not generated only by the heart. Pressure differentials throughout the body affect the circulation of blood as well. One that is easily demonstrated (first documented in 1733) is the effect of intrathoracic (chest) pressure on circulation. The blood pressure of healthy people falls during spontaneous inspiration. When someone takes a deep breath, the blood return to the heart via the vena cava decreases, and pressure is exerted on the right atrium. Both cause decreased filling, which will drop blood pressure. Although this is best demonstrated with a blood pressure cuff, it can be demonstrated without. An unrecommended method is exemplified in a childhood game of passing out. A Valsalva maneuver (deep breath and glottal closure) decreases blood flow to the heart. Squeezing the chest further decreases return, resulting in fainting.
The same pressure differentials agitate the CSF. Additionally, smaller movements were seen with pressure differentials caused by the beating of the heart.

By employing this respiration-induced spin labeling bSSFP cine method, we were able to visualize CSF movement induced by respiratory excursions. CSF moved cephalad (16.4 ± 7.7 mm) during deep inhalation and caudad (11.6 ± 3.0 mm) during deep exhalation in the prepontine cisternal area. Small but rapid cephalad (3.0 ± 0.4 mm) and caudad (3.0 ± 0.5 mm) movement was observed in the same region during breath holding and is thought to reflect cardiac pulsations.

This image from Wikipedia shows "circulation" that normally occurs with heartbeat.

There are other factors that cause movement of CSF, but they are intermittent and variable.
Influence of respiration on cerebrospinal fluid movement using magnetic resonance spin labeling, Yamada et. al., Fluids and Barriers of the CNS 2013, 10:36
MRI showing pulsation of CSF

CSF is actively pumped in an ebb and flow manner by the pressure with our respiratory mechanism transmitted through the pelvic diaphram onto the sacral bone that pulls on the spinal dural membranes attached at S2. Think about it: the pelvic and thoracic diaphragm are linked in a respiratory phasic contraction (confirmed with MRI). The pulling on the sacral end of the dural membranes via the pelvic floor muscle will squeeze the CSF up the spinal canal into the brain with inspiration. This is a much stronger force than any ciliary or cardic induced influence of CSF flow. Recent MRI studies have confirmed this as well.

Circulation of cerebrospinal fluid (CSF) through the ventricular system is driven by motile cilia on ependymal cells of the brain.
Hagenlocher C1, Walentek P, M Ller C, Thumberger T, Feistel K.Ciliogenesis and cerebrospinal fluid flow in the developing Xenopus brain are regulated by foxj1.Cilia. 2013 Sep 24;2(1):12. doi: 10.1186/2046-2530-2-12.

We were talking about humans and not frogs.


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What histological stain can I use for beta-keratin?
I'm trying to find a histochemical stain for beta-keratin, the type found in Reptilia which is organized in beta-sheets. It's different than alpha-keratin which is found in mammalian skin, hair, nails, etc., and is formed of alpha-helices.
Simple searches have produced results specific to mammals and alpha-keratin. Are there any good stains for beta-keratin?

After a quick search, it seems that many people working on beta keratin use specific antibodies. Yet it appears that you could use toluidine blue, but I'm not sure about the specificity regarding alpha/beta keratin.

Not sure if this is what you are looking for, but I did some searching around for histochemicals and reptilia.  I did come across a paper by L Alibardi, Dipartimento di Biologia evoluzionistica e sperimentale, University of Bologna, Bologna, Italy.  Now, that exact application doesn't seem to answer your question, it did open up a web page that contained numerous papers on reptilia and their beta-keratin structure and investigations into that (citations of the original paper, as well as papers by the same author).  I didn't see any that specifically spoke to the exact stain used, but then this is a little outside my area of expertise.  Perhaps this link will give you an avenue to pursue?
Wish I could help more.


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Examples of animals that co-opt toxins?
It is known that there are animals that acquire toxins through their diet or through their surroundings. The examples I know of include butterflies stocking up on alkaloids/glycosides while in the caterpillar stage (monarchs snacking on milkweed come to mind), fish acquiring ciguatoxin or tetrodotoxin from marine bacteria, and arrow poison frogs and pitohuis acquiring batrachotoxin and other nasties from the insects they eat. Are there any other nice examples of animals like these?

When you say co-opt, do you mean they use the toxin to their advantage? Or are you simply asking for examples of animals that can absorb/eat toxins and break them down?

So far as I can tell, all the examples I gave use the toxin they've acquired thusly for defensive purposes. Experienced birds stay away from the monarch butterfly, Japanese chefs have to be exceedingly careful in preparing fugu, and an arrow poison frog in the wild is pretty but deadly. So yes, the first one.

Glaucus atlanticus consumes and reuses the nematocysts of jellyfish siphonophores. Perhaps not quite what you were looking for, as the animal doesn't simply concentrate the toxin, but actually co-opts entire stinging cells.
Further to your mention of dinoflagellate toxins being concentrated by fish, I seem to recall reading something about some toxins being modified in vivo into more toxic derivatives, but cannot find any mention of it.

Hmm, I seem to recall that marine Vibrio species are the ones that produce tetrodotoxin and ciguatoxin; the only dinoflagellate toxins I'm familiar with are saxitoxin and azaspiracid, and I don't think I've encountered dinoflagellate feeders that use these toxins defensively themselves. But +1 for the nudibranch example. :)

@J.M. - Ciguatoxin is produced by G. toxicus. Didn't know about the vibrio toxins though, interesting. There are some other dinoflagellate toxins as well involved in shellfish poisoning, where the shellfish are tolerant of toxin concentrations that would be quite hazardous to people.

I'm familiar with "red tide", but are there mollusks that actually use dinoflagellate toxins for defensive purposes?


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What conditions should I use for Gel Red staining?
What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often indistinguishable. We have tried both pre- and post-staining, together with varying concentrations of Gel Red.
Any advice about how to fix this problem?

Are you sure it's the staining, and not the gels themselves that are the problem?

What wavelength and filter set are you using for visualizing your gels?

I have had success with 1.5% agarose gels in TBE pre-stained with gelred.  I use a 10,000x stock solution of gelred sold by http://biotium.com.  I visualize the gel on an old fotodyne UV transilluminator.
After melting agarose in the appropriate volume of TBE in a microwave, I let it cool to about 50 C (I can touch the flask with the back of my hand without snatching it away) and then add the appropriate volume of stock gelred.
For a 30 mL 1.5% agarose gel:

mix 0.45g agarose + 30 mL 1x TBE
microwave until agarose solution boils and clarifies
let cool to around 50 C
add 3 uL gelred
swirl the mixture
cast the gel (don't forget comb)

This typically works for me.  I run the gel in a 1x TBE buffer at around 120 volts.

i've also had the best resolution with pre-stained gels.  Even so, its better to take long time exposures of the gels on UV sometimes.  Hi Mac!

I don't think you should need to vary the concentration of the GelRed.  Mine came with instructions for the exact concentration and how to dilute.  Optionally salt can be added, which I did, and it has worked for me.
I have only done this with Post-staining.  1-2.5% agarose with TAE.  Used a 10,000x solution from Phenix research. The gelred stock and working solution needs to kept in the dark.  I am assuming you have a transilluminator and (optional) filters to visual though. GelRed has similar excitation and emission [wavelength] properties as EtBr, so a standard transilluminator and filter should work without any changes.  It will not be visible with the naked eye.
That being said there are a ton of things that can go wrong in casting the gel, eletrophoresis, staining, and visualization.  If bands are visible but just blurry I was suspect there is more of a problem with either the gel creation or eletrophoresis though. Make sure agarose is completely clear and cooled down a little before pouring. Otherwise voltage is one of the main things I have noticed that can have significant affects on how sharp or blurry bands appear.  You might try different % gels and different voltages.  There are formulas that can help you estimate the best value for each of those.


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Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?
While investigating the rise of adult lactose tolerance, I came across the news that China has been encouraging its citizens to drink more milk, even though most of the Asian population lacks the SNP (single-nucleotide polymorphism) which conveys lactase persistence.
Is it still possible for an adult without lactase persistence to build-up a tolerance for lactose over time? If so, what's the mechanism?

Have you seen this? Looking around, it seems that you can get some of your intestinal microflora to break down the lactose for you...

@shigeta SNP is a single nucleotide polymorphism (i.e., an allele that differs from another by just one base pair). Many important genetic polymorphisms are SNPs, but not all. I don't know if persistent lactose tolerance is caused by a SNP, or even by a single gene.

It seems that yes, it is possible to increase the tolerance for lactose over time, and it has to do with the adaptation of microbiota.
A simplistic explanation comes in the following article:
 Hertzler SR, Savaiano DA. 1996. Colonic adaptation to daily lactose feeding in lactose maldigesters reduces lactose intolerance. The American journal of clinical nutrition 64: 232–6.
In which the authors claim the following:

"Colonic adaptation appears to reduce the symptomatic response to lactose via several mechanisms. (...)
(...) increased β-galactosidase activity after regular lactose ingestion indicates that colonic bacteria are able to ferment lactose more rapidly. (...)
(...) This metabolic shift is thought to result from the proliferation of lactose-fermenting, non-hydrogen producing organisms such as Bifidobacteria."

This article makes reference to another one which supposedly explains the microbiota adaptation:
Hill Mi. Bacterial adaptation to lactase deficiency. In: Delmont J, ed. 1983. Milk intolerances and rejection. New York: Karger: 22–6.
But unfortunately I could not find the full text. I hope you are luckier than me.

The second 'article' is actually a chapter in a book, which is why you couldn't find the full text :)

Here are my thoughts on the topic.
Dairy good is not only milk, but also the following milk products: sour milk products (like yougurt, kefir, katik, buttermilk, etc.), cheese, etc. These products can contain less lactose than in the milk solids (due to fermentation during processing). It is also common for some of these products to contain living lactase-active bacteria, that can digest lactose.
Regular intake of these products can lead to certain changes in our small intestine microflora, so that the lacking lactase activity is substituted by the bacteria and thereby the tolerance grows. Maybe this is the intend of the Chinese government? Maybe they encourage the intake of sour milk products and not solid milk?
It is known, for example, that children with congenital/primary enzymatic deficiency develop the tolerance at the age of 6-10 years so that no special diet is needed anymore. This is true at least for such common enzymatic deficiencies like phenylketonuria and coeliacia.
In Russia, where I got my medical degree, it is common to use bacteria in the treatment of many types of primary intolerance combining this treatment with dietary support.


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How do cockroaches resist the effects of ionizing radiation?
Cockroaches are very hardy insects. It is known that, among other things, they are able to withstand bursts of ionizing radiation that would kill a human being.
The explanations of this observed resistance I've seen include cell division not being that fast in cockroaches, and the relative simplicity of these insects compared to other organisms. I know that microbes are able to resist radiation by having "tough" DNA (more G-C base pairs) and ready repair systems. Do cockroaches also have mechanisms like these, or is it really as simple as them being, well, "simple"?

Most insects have similar resistance to cockroaches... IMO it is more that humans are weak than insects are strong.

@mbq Strong and weak are pretty subjective words. I could just as validly state my opinion that insects are biologically simpler creatures whose genome can withstand a larger amount of mutation and still be fully functional/viable arthropods, but I've no evidence to back it up.

@Lisa In relation to some median resistance not so much. Also note that this is a comment and I have made a disclaimer that this is my speculation.

Some references on exactly how much radiation cockroaches can withstand in this article.

Off the top of head as a medical professional I can imagine the following mechanisms (everything is just speculative reasoning):

Insects don't have blood. Instead, they have hemolymph whose primary role is not oxygen transport (they have an additional tracheal system for this purpose), but rather that of nutrients. Thus they don't need (and don't have) an intense proliferation of blood cell precusors -- these (bone marrow, spleen) are the most susceptible to radiation in a human and animal body.
Insects have a rather primitive immune system that is mostly humoral[a]  and much less cellular[b] compared to the immune system of animals and humans. This eliminates the next common weak place in the body: lymphatic nodes, thymus, again spleen and bone marrow etc.
Insects have generally a much primitive and in many cases also rather decentralized nervous system: the ganglia are organized in a sort of a cord and even though the capital ganglia are usually larger, these dominance is not as prominent as in case of CNS and PNS in animals and humans. Therefore this system is much more tolerant to losses.

1.-3. Therefore, the only sensitive part of insects is the intestinal epithelium which gets renewed on a regular basis (similar to that of humans, also a known target of radiation), but...

Insects (and generally the arthropodes) are known to have exoskeleton. This potentially serves as a good "armor" for vulnerable intestine cells, filtering out the most heavy particles (like alpha- and in some respect also the beta-particles).
EDIT: This seems not to be real protection, see the discussion in comments.

Therefore it is not a surprise that insects generally show much higher resistance against radiation.
EDIT:
As it was correctly added in the comments, there are also gamets, that are most sensitive to radiation (because they bear only the half of the normal genetic information and cannot repair mutations). Even though the lesions in gamets do not lead to immediate death, the potential sterility can easily cause the extinction.
However, cockroaches (and insects generally) are known to be r-animals, meaning that they favor the quantity (r) over quality (K) of their off-spring. This strategy is optimal when dealing with radiation-induced changes in gametes: the high number of offsprings compensates for the genetic imperfections in gametes.

[a] -- meaning that is has secreted peptides in their hemolymph that protect them
[b] -- there are phagocytes, somewhat similar to tissue magrophages in humans, but the rest of the cell chains in immune response in vertrebrates, like T- and B-cells, are completely missing. Those are responsible for the mediation and amplification of the immune response in vertebrates and are the cells that are most susceptible to radiation damage.

It is a very good answer. However, I have reservations when it comes to the last point (i.e. exoskeleton). First, I would bet that thin exoskeleton screen radiation much less than human skin (the total amount is proportional to cross-section, i.e. ~mass/area (given the same atomic composition), which is greater for the skin). Second, alpha particles are likely to be stopped by both (a few cm of air suffices), beta needs a few cm of flesh (depending on its energy) so it is likely harm all volume of insect but not of human and gamma radiation won't be stopped by neither exoskeleton nor skin.

@PiotrMigdal You are probably right. What I was taking into account is that chitin can be likened to polysacharides that are known to have higher roentgenologic density compared to flesh. Can you confirm or disprove it?

While it's not my main topic I bet that (as I said) for all typical organic substances the shielding is ~mass/area. And as chitin has density of ~1.5g/cm^3 (ref) 1 cm of flesh is equivalent to  ~7mm of chitin. So for radiation which is neither stopped nor transmitted by both, insects (unless they are extremely large) are less shielded. However, there may be some nuances and I think it makes I good question for http://physics.stackexchange.com.

Humoral and cellular immune system are parts of adaptive immune system, which is present only in vertebrates. Insect have only innate immune system that contain phagocytes and peptides (secreted by cells in fat body). You didn't mention about gametes, probably the most sensitive cells to radiation (becouse they are haploid).

@MartaCz-C I use the words "humoral and cellular" in their direct meaning here, rather than referencing to the parts of adaptive immune system: this usage is acceptable and can be found in many research papers on insects (example). But thank for your suggestion, I will edit my answer.

Also they don't live very long, so cancer is not as big a problem.

Studies of Deinococcus radiodurans, the most radioactively tolerant microorganism we know, show that it has many genes for DNA repair.
In the case of the cockroach, I would assume that in addition to repairing genes, and maybe some antioxidants produced in the cells to quench free radicals produced by radiation, the fact that the roaches lay many, many eggs is also useful. If the radiation kills 99.99% of the roaches, you will still have some insects coming from the egg clutches.
Selection is the insect's friend when you are a k-limited animal!


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What are the clotting factors' effect on avascular necrosis development?
Do clotting factors tpa and pai-1 lead to degenerative osteoarthritis in the same way that lupus anticoagulant and prothrombin might? Is one of these pathways particularly detrimental during formation of osteoarthritis or avascular necrosis (if these factors are inhibited or modified in some way)?

First of all we should distinguish between the physiological clotting factors that are parts of the normal clotting pathways, and those that might affect clotting pathways but are not observed under healthy conditions.
TPA (tissue plasminogen activation), PAI-1 (plasminogen activator inhibitor) and prothrombin are normal clotting factors that are essential for blood clotting. Any deficiency (congenital or acquired) might cause certain pathologic conditions, including the osteoarthritis and avascular bone necrosis.
Lupus anticoagulant, however, is an antibody against cell membrane that is common for Lupus. This antibody can intervene into the process of clotting and increase the prothrombine time (the common lab method to test blood clotting properties), hence the name "anticoagulant". But this effect is just a sort of "side-effect" of this antibody, that leads to certain symptoms in case of auto-immune attack against different target organs.
So, after this introduction I can rephrase your first question as: "Does the deficiency of clotting factors TPA and PAI-1 lead to degenerative arthritis in the same way that lupus anticoagulant and prothrombin deficiency might?"
The part of the answer is already in this question: yes, the deficiency of these factors might and under certain conditions, leads to the development of osteoarhritis and avascular necrosis.
I must confess, I found no evidence whether the underlying mechanism is different or not. Papers just prove that these factors are discovered in the affected joins, and see the correlation in mice models between the factors and the articifially induced arthritis. But I found no study which would try to address the mechanisms of these actions or to show, whether these are different.


text:
Do large animals often evolve into smaller animals?
There are several examples where the largest animals were killed off preferentially due to a major ecological shift:

The KT extinction event
The Holocene extinction, as well as the major megafauna humans killed off

The common ancestor of modern mammals is thought to be "shrew-like" in size, and it differentiated into most of the large animal species in the world today.  I imagine that a similar statement can be made for dinosaurs.  In general it seems that a major extinction event is likely to be best weathered by smaller creatures which can later, over time, increase in size to fill the niche that larger animals, and evolution dictates it will be profitable to do so.
Does this limit large animals to only the branches of the tree of life?  Any given set of (Multicellular) species obviously share a common ancestor that is much smaller than them.  Is it possible for many species to share a common ancestor that is considerably larger than any of them?

To give another example: insects from the Carboniferous period were huge (e.g. Meganeura). Nowadays, apart from some stick insects, I don't think there are other big terrestrial arthropods...

@J.M. That would be a counter-example to my examples, and it could answer the question as yes, they do.  But we also need to establish that modern insects actually evolved from the past's large insects, instead of evolving from small insects that lived among the large insects.

I'm not up to date with whether Meganeura is phylogenetically related to modern-day dragonflies, so maybe we have to wait for a (palaeo-)entomologist to chime in on that subject.

Define "often"; island dwarfism is a seemingly-repeatable effect.

@Nick: sounds like an answer to me. :)

As written, it is confusing as to what you are asking.  In one sense you seem to be asking about the environmental factors that would drive the evolution of size but since evolution is never progressive then there can be no expectation of a evolution-based temporal trend.  I am not sure if the idea that large animals are more vulnerable to extinction is completely accepted, but if we accept it, then it reduces your question to a truism if applied to mass extinctions - if only small animals remain then non-directional evolution would give the impression of progression.

@DQdlM Is it common that an animal species decreases in size then differentiates into many other species?

@Zassounotsukushi I don't think there is much support for those kinds of generalizations.  Different ecological contexts would tend to apply selection pressure for body size in different ways and those ecological contexts will vary in space and time.  As Kevin points out in his answer the potential for large changes in body size have been shown so it is a plastic trait but it will respond to the selection pressures at hand (as Nick T points out in his comment on island dwarfism).

Your question brings up several important issues with regards to the evolution of body size. The rationale for concluding that the ancestral mammal had a small body size is that all of the taxa in that area of the tree tend to be small. In contrast, if all of those taxa had been cow-sized, then the most parsimonious conclusion would be that the ancestral mammal was cow-sized.
Identification of ancestors is difficult
Identification of a fossil species as the most recent common ancestor of a pair of sister taxa is exceedingly difficult. The way that different species are diagnosed in fossils in by their unique derived characteristics (autapomorphies). So if a fossil is found with no autapomorphies, then it is plausibly an ancestor (i.e., at the split between two sister taxa). Some would argue that if you don't find any autapomorphies, then you just haven't looked closely enough.
Cope's Rule
The idea that lineages tend to evolve toward larger body size is known as Cope's Rule, named for the paleontologist Edward Drinker Cope. The success of Cope's Rule has been highly variable, with some lineages following and others not (Polly, 1998).
Some clades following Cope's Rule

Early reptiliomorphs (Laurin, 2004)
Pterodactyloidea (Hone and Benton, 2007)
Most Cambrian-Devonian marine invertebrates (Novack-Gottshall, 2008)
North American canids (Van Valkenburgh et al., 2004)
Mesozoic birds (Hone et al., 2008)

Some clades not following Cope's Rule

Early stegocephalians (Laurin, 2004)
"Rhamphorhynchoid" pterosaurs (Hone and Benton, 2007)
Mesozoic birds (Butler and Goswami, 2008)

Note that many results depend on the methods used.
Evidence from experimental evolution
Several studies have addressed body size evolution in vertebrates both directly and indirectly. MacArthur (1944a, 1944b) directly selected for large and small body mass in laboratory mice. Within 8 generations, mean body masses had increased or decreased by over 50%. Even when body mass is not directly selected upon, mass can change in a correlated way. Selection for high levels of voluntary activity has led to an approximately 25% reduction in body mass.
Based on these studies, evolution of body size (larger or smaller) is certainly possible within relatively few generations.

i'd heard that miniaturization of animals is also a recognized effect of subpopulations on islands.  gigantism can also occur, but is the result of the organism differentiating into new niches.  the hobbits are examples of this effect, do i remember right?

It probably goes equally both ways. Examples of miniturization are balanced by examples of gigantism (e.g., lots of South American taxa during its "island" period).

yes - i think its a matter of niches being open for just a few critters to fit into and sizes can change drastically. in crowded systems, the time it takes to change size would be prohibitive.


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Good source that explains the evolution of single-celled organisms "from scratch"
Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?

Origin of Life: Chemical Approach is an edited volume by Piet Herdewijn and M. Volkan Kisakürek.
here is the book's description from the webpage:

Dedicated to the fond memory of two great pioneers of this science, Leslie E. Orgel and Stanley L. Miller, this compilation of reviews and original manuscripts provides an overview of the current state of the art, written by some of the eminent "players" in this creative domain of "explorative chemistry".
  Since we are still far from finding a definitive answer to the most fundamental of questions in science, "chemistry" here is defined in its broadest sense. It is against this background that the contributions cover such a wide range of theories, including chemistry and selection, evolution of the pioneer organism, chemical aspects of synthetic biology, ribozyme catalysis of metabolism in the RNA world, intractable mixtures and the
  origin of life, the chemical etiology of nucleic acids, interstellar amino acids, and even the chemistry that preceded life's origin.

Pricy, but it's on order. Will let you know if it fits the bill.

Cool. I have the luxury of being at university with a pretty good library but I definitely found it useful for teaching origin of life concepts in a fairly robust manner.

@C.LawrenceWenham Did it fit the bill?

I quite like the account given in Early evolution without a tree of life, where alkaline hydrothermal vents (like "Lost City") are theorized to have formed pre-biotic compartments with a proton gradient (i.e. an energy source) from which cells could have evolved.

From a more geology-oriented perspective:
Robert M Hazen (2007) - Genesis: The Scientific Quest for Life's Origins
Noam Lahav (1999)- Biogenesis: Theories of Life's Origin
J William Schopf (2001) - Cradle of Life
I have watched Hazen's nice "Origins of Life" DVD/Video Course. There he says that the Miller-Urey stuff has gotten less popular. Their atmosphere contains too much Nitrogen, Hydrogen  and focuses on the water surface and the open water body.
More recent research points to a more CO2-rich atmosphere, and that life evolved deeper in hot water at the bottom of the ocean.

+1 - Hazen's course is an excellent introduction.


text:
How can I produce milligram quantities of an isotope-labeled DNA oligomer?
I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs.
I'm also only interested in the single-stranded DNA, so a method that produces double-stranded DNA without any way to easily separate the strands would also not be useful.
What methods are there to produce labelled DNA that fulfill these requirements?

You can also design a plasmid that has your 35mers and raise the bacteria with isotopic carbon and nitrogen C13 acetate and N15 ammonium sulfate will work with E coli in a minimal medium.
this is not cheap, but the cheapest available sources of the isotopes can be used.

That doesn't give me single-stranded DNA. It's also very inefficient as I only use 1/200 of the plasmid DNA (30bp single-strand of a 3kb plasmid), so a Megaprep with 2.5 mg yield would still only give me 0.0125 mg of my DNA. I can't reasonably make 100 Megapreps to isolate 1mg of my sample.

I found a couple of methods using M13 phage growing on E coli:

Reddy P, McKenney K. Improved method for the production of M13 phage and single-stranded DNA for DNA sequencing. Biotechniques. 1996 May;20(5):854-6, 858, 860.
I Jupin and B Gronenborn. Abundant, easy and reproducible production of single-stranded DNA from phagemids using helper phage-infected competent cells.Nucleic Acids Res. 1995 February 11; 23(3): 535–536.

You could easily adapt these protocols to grow on 13C, 15N-containing medium. Then you could use a restriction enzyme able to cut ss DNA and purify your fragment through a PA gel. Clontech's gigaprep kit (up to 50 mg of DNA) will cost you $546 (in the US, before any quote).
Disclaimer: I've never done any of this!

The cheapest way to make that large quantity of DNA without the need of the whole oligomer being label would be to produce 34 nucleotides by chemical synthesis. The 35 nucleotide can be labeled and ligated to the remaining strands. This should reduce the costs of producing the oligomer since the most expensive stage, the labeling is limited to just the final nucleotide.

I need all of the nucleotides labeled, only the last one is not enough unfortunately.

I realized that the other suggested ideas are pretty effect. I would culture the plasmids with non-labeled bacteria and using a cesium gradient, you should be able to separate half-labeled DNA from unlabeled and fully labeled DNA. After a restriction digest, you should be able to isolate single stranded DNA by density centrifugation.

What about PCR using labeled nucleotides? Might have to run several reactions to get miligram quantities you need, but 35 nucleotides seems really really small for growth in bacteria, and purification would be extremely difficult. But 35 bases might even be too small for PCR, hardly bigger than your primers.
If you do need to grow in e coli, it might make sense to create a plasmid with multiple repeats of the 35 base sequence separated by the same restriction site. You can grow e coli in c13 n15 media, but it's expensive and you have "train" the cells over several generations because the heavier isotopes create differences in chemical kinetics that make the labeled nutrients hard for enzymes to use, but I've seen people do this for making proteins for NMR.
I bet you need this labeled DNA for NMR, don't you?
Have you considered phosphate NMR? No need to label it, P-31 is already NMR active.
If it must be C13 N15, I highly recommend having it synthesized, it will be expensive, but that 35 base length and the requirement for single strandedness are ideal for chemical synthesis.


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Can I elute my GFP-tagged protein off anti-GFP antibody using a peptide?
I would like to perform a modified co-immunoprecipitation assay using a GFP-tagged protein.  We are going to bind the tagged protein to anti-GFP antibody then bind that to protein A/G beads, however we want to be able to selectively elute the tagged protein off the beads.  I know that you can elute a FLAG tagged protein off of M2 anti-FLAG antibody by adding excess FLAG, so can I use the same approach with my GFP tag?  If so, does anyone know a commercially available GFP monoclonal antibody who's epitope has been mapped so I can use excess epitope to elute my protein?  Or possibly a source of recombinant GFP?

I found a paper that describes a method to purify GFP fusion proteins using affinity chromatography: "Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography" (1). Unfortunately I don't have access to the full text, so I can't check how exactly they elute the GFP fusion protein from the column. They describe a specific monoclonal antibody they use, there should be information on how to obtain it in the paper.
Abstract:

GFP has often been used as a marker of gene expression, protein
  localization in living and fixed tissues as well as for protein
  targeting in intact cells and organisms. Monitoring foreign protein
  expression via GFP fusion is also very appealing for bioprocess
  applications. Many cells, including bacterial, fungal, plant, insect
  and mammalian cells, can express recombinant GFP (rGFP) efficiently.
  Several methods and procedures have been developed to purify the rGFP
  or recombinant proteins fused with GFP tag. However, most current GFP
  purification methods are limited by poor yields and low purity. In the
  current study, we developed an improved purification method, utilizing
  a FMU-GFP.5 monoclonal antibody (mAb) to GFP together with a
  mAb-coupled affinity chromatography column. The method resulted in a
  sample that was highly pure (more than 97% homogeneity) and had a
  sample yield of about 90%. Moreover, the GFP epitope permitted the
  isolation of almost all the active recombinant target proteins fused
  with GFP, directly and easily, from the crude cellular sources. Our
  data suggests this method is more efficient than any currently
  available method for purification of GFP protein.

(1) Zhuang R. et al., Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography. Protein Expr Purif 2008, 59(1), 138-43

In the reported paper the authors used an affinity matrix carrying a covalently coupled mAb. They then eluted the bound proteins using the standard low pH glycine buffer.


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How do I prepare and clone from E. coli DNA?
I'm looking for a protocol to get genomic DNA from an E. coli sample so that I can clone a small portion of it using PCR into a plasmid.  (< 500 bp in this case).
It seems OWW (Open Wet Ware) only discusses preparation of fragmented DNA. Does this mean I have to cut it up before I can clone from it?  Any pointers would be really appreciated.

What is OWW? Acronym expansion or a link would be helpful.

It's a wiki for describing consensus protocols and organizing lab webpages: http://openwetware.org

@shigeta could you elaborate on what you mean by cloning?  Do you want to incorporate a fragment of the E. coli genome into a plasmid and then transform the plasmid for cloning?

thanks Mac - edit added Kevin. @ Mac That's right - in this case I want to clone a < 500 bp segment from the genome and pop it into a plasmid like pGLO.

Is anyone still looking for an answer to this? Phenol/chloroform extraction is the gold standard. And here's a protocol specific to E. coli genomic DNA that doesn't use phenol/chloroform: http://bio.classes.ucsc.edu/bio105l/EXERCISES/DNA/genomic.pdf

The answer I got from a colleague is that to PCR from a bacterial sample, you can add bacteria right to the PCR tube without even lysing it.  maybe this so obvious nobody thought to say this....

@shigeta Oh yeah, I do that often when screening colonies following a ligation/transformation. Stick a colony with a toothpick, stir in some water, use the water for PCR. I increase the first 95C step of a PCR protocol from 2 min to 4 min. These reactions aren't the cleanest though - if you amplifying a gene for downstream cloning, I'd still recommend purifying the DNA first.

Hey all I think I didn't know how to word this question properly.  After asking a colleague I was told that I don't need to prepare the DNA at all for this tiny non-library scenario.
She told me to just take a little smear of bacteria on a toothpick and put it into the PCR reaction with the master mix and the enzyme and the heating cycles would do the rest.
Maybe this question was too simple - sorry if it was.
( Sure enough it worked fine.  )

Yes, you must fragment the genome in order to insert it into a vector for cloning; you can't "insert" the whole 5 Mbp genome of E. coli into a vector.  It's difficult to transform cells with huge plasmids, 2-20 kbp is an optimal range.  In any case, if you want a clone of the whole genome, wait 30 minutes and the cell will happily oblige you.
Most procedures that isolate genomic DNA will fragment it in the first place, as it is much too large and fragile to stay together, and if it did it, the majority would be caught up in other cell debris and discarded.  Vortexing with glass beads is a typical first step to randomly fragment it.  After this, you can digest the DNA and your vector to place matching ends on it, ligate it, and transform host cells.
If you want a targeted approach (to extract a specific gene, a technique with which I am unfamiliar), you may be able to use PCR on your extracted, fragmented DNA, as there would hopefully be one intact segment spanning what you want.

To clone a specific gene, you have to design PCR primers that will amplify the gene and also with specific restriction sites flanking your gene. The restriction sites should correspond with the restriction sites found in the poly-linker of your plasmid. For ligation, digest your plasmid, treat with CIP (to reduce vector background), and ligate it with your purified and digested PCR product. Needless to say, this is probably an oversimplified explanation of cloning; let me know if you want more details.

@JamesPan I've subcloned genes between vectors, I just didn't know if there was any differences between vector->vector and genome->vector.  It's all DNA so in theory there isn't anything new, but I don't know about the practical considerations.

i thought cloning meant to PCR a fragment of the genome - i've never head of popping the genome fragments into a plasmid directly - you would have to have a lot of genomic DNA to do this - sounds hard.

@NickT I think genome->vector should still be the same general principle. Amplifying genes from genomic DNA should still be straightforward (I amplify genes from human DNA all the time). I find that sometimes, at least in human DNA, it can get fussy at you, so I try different PCR additives like DMSO or Betanine. Use ~50ng of E. coli genomic DNA for your template, amplify, get your products, and insert it into a vector just like anything else.

@JamesPan feel free to post another answer; your experience and depth of knowledge seems better than mine.  The more answers, the better.

feel like you are telling me how to PCR something off genomic DNA while i am hoping for a protocol to purify the chromosomal DNA in order to copy it by PCR...


text:
What are good resources for self-learning modern molecular biology concepts?
My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to be a molecular biologist, I do aspire to better understand modern approaches better.
Short of going back to school and taking classes, what are good resources for learning on my own? I'd like to get to the point of being able to understand Nature, Science, Cell, etc. Is this even a feasible goal?

I've voted to close because this (the title much more-so than the rest) is very subjective so doesn't have a "right" answer. If you can narrow the scope to a particular issue it would be much improved.

I think this is going to come up often, so I raised an issue on meta: http://meta.biology.stackexchange.com/questions/24/should-questions-without-definitive-answers-be-closed

Just convert to a wiki.

@Poshpaws community wiki is not a crutch for extremely subjective questions.

@Nick T I wasn't suggesting it was. However, rather than chucking it out as "too subjective" if you change it to CM people can freely give their experience and suggestions which might turn into a useful resource.

Questions rarely, if ever, need community wiki. If the question needs this level of collaboration and discussion, it's probably not a good for for the site.  If calls for community wiki seem to somehow "fix" that, it's probably not a good fit for the site. http://blog.stackoverflow.com/2011/08/the-future-of-community-wiki/

Sure it's feasible! Of course, there are lots of papers that I can't read even with a recent education, but you should be able to make a good dent by:

Getting a good modern textbook like Molecular Biology of the Cell by Alberts et al. This is becoming a standard text and gives pretty good coverage of the field. I find that it doesn't always get as detailed as I would like, but such is the nature of textbooks I think. Another textbook that some people like is Molecular Cell Biology by Lodish et al, although I don't have experience with it myself.
Watch online lectures. MIT OpenCourseWare has a pretty good molecular biology course. It may get basic for you at times, but the lecturers are well-respected molecular biologists and geneticists.
Read reviews in things like Nature Reviews to get a 30,000-foot view. Review authors often touch on concepts that primary literature assume you know. Armed with a good text, you should be able to get a good idea of what people are talking about. On a similar note, the "News and Views" commentary articles that accompany "high-impact" papers are great for giving people unfamiliar with the field a taste of why a certain paper deserves attention.
Come back here and ask!

By far the best resource mentioned here is the first textbook, Molecular Biology of the Cell published by Garland Science. It's one of a few truly great modern textbooks, with some high-school biology and that book you can learn modern molecular biology to a high level.

You can watch the iBioSeminars, which are given by some of the best cell and molecular biologists out there.

Drop by the diybio.org mailing list, which is home to a bunch of autodidactic free thinkers like yourself.  They always can suggest fun projects and learning resources.
Also check out Nature's Scitable education resource ("A collaborative learning space for science")

conflict of interest: I helped start diybio.org

Sorry, I just couldn't help but point out the following book:

Joking aside, every book from this series I read was fantastic. I didn't read this particular one, but I would nonetheless recommend to give it a try.


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What is the morphological difference between Leydig cell in human and pig?
The pig is only an example, just an animal. Leydig cells have protein inclusions (Reinke crystals) that are mostly made of crystallised lipofuscin. They are secretory inclusions i.e. cells formed in secreting cells.
An example of Leydig cell in pig's testicle:

My teacher told me that there is a difference in the existence of some cells between humans and animals.
However, I cannot find such a difference. I have not been provided a slide of human Leydig cell so I have not been able to compare.
What is the morphological difference between Leydig cell in human and pig?

Perhaps what your teacher meant was not so much a difference in Leydig cell morphology, but in interstitial tissue morphology, ie. tissue which occupies the space in between seminiferous tubules. Leydig cells are its most interesting component, others being small blood vessels (a lot of them), nerves and connective tissue (mostly fibroblasts, mastocytes, lymphocytes and macrophages). In different species interstitial tissue looks differently, for example:

Leydig cells form clumps around blood vessels, and are surrounded by fibroblasts (which makes them more difficult to isolate) in guinea pig, but not in mice or rat;
in human a lot of interstitial tissue is extracellular matter, Leydig cells are not so frequent, but more active;
and, last but not least, in pig, there is little extracelluar matter and a lot of Leydig cells that are very easily isolated (and produce large amounts of estrogen).

I found all this in some old lecture notes; I couldn't dig up any sensible reference, though.

I have studied all available (via University library) literature on the Leydig cells and I think your teacher might have this article summarizing the morphological studies on Leydig cells in different animal models in mind.
To put it straight, the most common animal models for studying Leydig cells are rats, mice and pigs.
The development of Leydig cells in rats was shown to be bi-phasic: development of the Leydig cell population in fetus and its degradation while transforming into the mature cells. It has been believed for quite long that this is also true for human Leydig cells. However, some studies performed on pigs and monkeys delivered an evidence for an additional phase of cell degradation sometimes between the fetal and neonatal development shifts. These data are summarized on the following Figure (taken from the referenced paper):

So, by comparing the Leydig cells of rats and humans from the same fetus age or shortly after the birth (neonatal time) you might see the degradation of Leydig cells -- they decrease in size and many of them eventually die -- compared to normal state of these cells in rats.


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Latency to audition in human beings?
On average, in a human being with no neurological deficits, how long does it take for a sound which is sensed in the ear to reach the cortex?
Which brainstem structures are most responsible for the delay?
(I'm interested in things like the effect of the Olivary n.)

There are several ways to infer into the propagation delays of auditory system in vivo that is applicable to humans (i.e. leaves the subjects intact).
One of them is so-called ABR that stands for Auditory Brainstem Response. As it is clear from its name this method allows you to derive the brainstem response to an auditory stimulus (so, you can track the auditory pathway up to its input into thalamus), but its resolution is so fine that you can separate single components ("waves") for the following path segments (from Wikipedia):

Wave I – generated by the peripheral portion of cranial nerve VIII
Wave II – generated by the central portion of cranial nerve VIII
Wave III – generated by the cochlear nucleus
Wave IV – generated by the superior olivary complex/lateral lemniscus
Wave V – generated by the lateral lemniscus/inferior colliculus

So, it takes only 10 ms for the signal to reach the input into thalamus. This correlates well with some auditory signal based activities, like startle reflex, which was also shown to have about 10 ms latency.
I tried to search for some electrophysiological recordings from auditory cortex (temporal lobe) paired with auditory stimuli, but the first paper I came accross that is available for free (and which I can also link from my answer) is this work done on monkeys.
If you look at Figure 1:

This is the results from multiunit recordings and you see that the initial activity in the cortex starts approximately 20 ms after the stimulus onset with a short activity pattern, followed by some short break and then longer period of activity with broader frequences spectrum.
In my opinion the delays in signal propagation are not due to complex signal processing in the olivary nucleus or any other brainstem structures, rather they are due to electro-chemical transformations in CNS synapses.
The initial arrival of the signal into the cortex does not mean the perception of the sound, it definitely takes hundreds of millisecond until the conditioned cortex-mediated response to this stimulus.


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What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?
What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?

Anyway... here is one relevant paper on human olfactory receptors.

here's another paper that might shed light on the second part of your question... http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002224

personally i find ethanol and its closest homologs smell 'sweet'

That make some sense just looking at the mocules. They both bind to the olfactories in a similar way. using the H-OH side.

The smell of dry erase markers come from the chemicals ethanol, butanol and isopropyl alcohol. Like all chemicals inhaled through the nose, they bind to the Receptor neurons in the located in the back of the nose. The neurons interpret the chemicals using a 'lock-and-key' model but the specific way its coded and perceived in humans is still being researched and the process is not completely understood.


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Can siRNA induce DNA methylation in mammalian cells?
Some years ago Hiroaki Kawasaki and  Kazunari Taira published an article called "Induction of DNA methylation and gene silencing by short interfering RNAs in human cells" in Nature:

In plants, dsRNAs targeted to CpG islands within a promoter can also
  induce RNA-directed DNA methylation3, 4, 5, 6, 7, 8; however, it
  remains unclear whether gene silencing mediated by DNA methylation can
  be induced by dsRNAs in mammalian cells. Here, we demonstrate that
  short interfering RNAs (siRNAs; 21–25-nucleotide RNA molecules) induce
  DNA methylation and histone H3 methylation in human cells.

This paper seemed to show that siRNA can also induce long-term silencing of genes by DNA methylation in mammalian cells, which hasn't previously been observed. Unfortunately, the paper was retracted later, calling the results into question.
I found the paper very exciting at the time, as it suggested the possibility to perform gene therapy, to silence specficic genes, just by using RNA interference.
What is the current scientific consensus here, is there any convincing evidence that siRNA-induced DNA methylation is possible in mammalian cells? Was anyone able to replicate the results from Kawasaki and Taira?

From a brief survey of the literature, it seems Kawasaki and Taira have been largely vindicated by the community before and since their paper. The retraction was by Taira alone, Kawasaki refused to co-sign because he maintained the data were valid. From the retraction it seems the reason for the retraction was a lost lab book.
Prior to the Kawasaki and Taiga paper, there were already several other papers describing RNAi-induced epigenetic modification in mammals:

Castanotto, D., Tommasi, S., Li, M., Li, H., Yanow, S., Pfeifer, G.P. & Rossi, J.J. (2005) Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther. 12 (1), 179–183.
Morris, K.V., Chan, S.W.-L., Jacobsen, S.E. & Looney, D.J. (2004) Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells. Science. [Online] 305 (5688), 1289 –1292.

Then there was another paper the next year by Kawasaki & Taira, which was not retracted:

Kawasaki, H. & Taira, K. (2005) siRNA Induced Transcriptional Gene Silencing in Mammalian Cells. Cell Cycle. [Online] 4 (3), 442–448.

And it seems the idea is now generally accepted and supported by quite a few other studies, mainly looking at germline cells. For example:

Carmell, M.A., Girard, A., Kant, H.J.G. van de, Bourc’his, D., Bestor, T.H., Rooij, D.G. de & Hannon, G.J. (2007) MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline. Developmental Cell. [Online] 12 (4), 503–514.

There is no review that I could find which really ties it all together convincingly, but there are several reviews on RNAi directed histone and chromatin modification in general which mention that the fact is now established in mammals:

Joshua-Tor, L. & Hannon, G.J. (2010) Ancestral Roles of Small RNAs: An Ago-Centric Perspective. Cold Spring Harbor Perspectives in Biology.
Volpe, T. & Martienssen, R.A. (2011) RNA Interference and Heterochromatin Assembly. Cold Spring Harbor Perspectives in Biology. 3 (9).

The germ cell reference (Carmell et al., 2007) does not describe siRNA, instead it deals with entirely different class of small RNAs, called piRNA (in the paper they referred to them as rasiRNA, but piRNA now is a commonly used nomenclature). There are crucial differences between siRNA and piRNA (size distributions and proteins with which they associate) and they shouldn't be mixed up.

I browsed through Joshua-Tor and Hannon (2010) review that you cited and I haven't noticed any mentioning of siRNAs directing DNA methylation (or histone modification) in mammals. Sorry if I missed it, can you please quote the relevant sentence?

@Sergei you're right! That paper actually mentions piRNA-directed methylation, rather than siRNA. I'll leave it in the answer as it is still of relevance to the question.


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How can I keep HEK cells alive while expressing NMDA receptors?
I am trying to express functional NMDA receptors in HEK293 line cells for single channel recording experiments.
The HEK cells are maintained in the standard way (Thomas & Smart 2005) and transfected with NR1 and NR2x subunit cDNAs and also GFP, using either lipofectamine or calcium phosphate precipitation. GFP expression suggests successful transfection, but cells exhibiting green fluorescence are uniformly swollen and dead and it's more or less impossible to obtain a successful patch. Untransfected cells seem to remain perfectly viable.
On the basis that the toxicity might be a consequence of Ca2+ influx through open NMDARs, I've tried including a cocktail of blockers in the growth medium, including AP5, kynurenic acid and Mg2+, but the transfected cells continue to die.
Can anyone suggest anything else I should be doing to keep the cells alive? Or am I just on a hiding to nothing? Other researchers seem to have managed this (eg Medina et al 1995, Vicini et al 1998) and do not seem to be doing anything substantially different, so I'm a bit at a loss.

You need to block NMDARs with 200 uM AP5 or 1 mM kynurenic acid. We have also used 10 mM MgCl2.

Try perhaps lowering the level of expression of your construct. HEK cells are notorious for expressing large quantities of your transfected insert. Do you have it under a CMV promoter? Try a milder one, such as an ubiquitin promoter or similar or, even better, a doxycyclin-inducible system (e.g., clontech's tet off) so you can manage the expression levels through the dox concentration/time of induction.

It is indeed using a CMV promoter, so that would be something to look at. One suggestion I've seen is to co-transfect with a high ratio of an "empty" pcDNA plasmid as a competitor to reduce expression. That sounds a bit Heath Robinson, but it would be an easier test than splicing into a new vector...

Sure, you can give that a try. I would expect that to lower the transfection efficiency rather than the level of expression per cell, but it's easy enough to try it right away. Good luck! BTW: I had to google "Heath Robinson": nice one!


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Why is there an extended delay before G.M. liver cells are attacked by the immune system?
In this BBC article a trial is described where patients with B-Haemophillia are infected with modified Adeno-associated Virus 8 which contained the genes for Factor IX clotting protein.  Trials seemed to be successful, however the article later mentions

There was an immune response against the infected liver cells around seven to nine weeks after the virus was injected.

I am interested to know why there was a delay period of such length?  Would this be true of all cells and is it due to a long duration of clonal selection in the humoral immune response or is something else at play?  Also, I'm presuming that the Adeno Virus would be attacked long before the cells it has infected?

The delay in immune attack is common for many viral infectious deceases where auto-immune response plays substantial to significant role in pathogenesis of the decease. The classical example here are the viral hepatitis B, C and D where it is auto-immune attack that causes the massive death of liver cells (hepatocytes).
The delay in immune attack is explained by the following mechanisms:
The immune attack is developed against the surface antigen, in case of hepatitis it is the HbS Antigen. "Surface" means that this antigen has to appear on the cell surface in order to elicit immune response: the virus itself as well as the parts of destroyed cells are not immunogenic enough for this.
The second point explaining why the attack takes so long to develop is that it is primarily cell-mediated attack, the humoral factors play the secondary role here.
So, the usual "workflow" in this case is the following:

Contamination with hepatitis virus.
Virus propagation to hepatic cells and their infection.
Processing of the viral DNA (either as DNA or first reversed-transcripted from RNA) so that it is integrated into cell normal processing pathways.
Expression of viral proteins (=antigenes) and their anchoring in the cell membrane.
Surface antigenes are detected by macrophagues, processed and expressed on their membrane for T-helpers
... (continuation of the usual cell-mediated immune response via T4 and T8 lymphocytes).

Every stage takes some time, the total duration can sum up to 4 to 12 weeks depending upon the viral activity and the immune system status.

I've encountered cell mediated and humoral pathways as part of my studies so far, so I understand most of your answer.  However why is it that the response to this pathogen is more cell-mediated than humoral?

There is no clear answer here, possible causes are high mutability of the RNA hepatitis viruses (similar to that of AIDS) and the positioning of many viral antigens deeply within the liver cells, so that they cannot be accessed by antibodies. Humoral response is also here, but during the successful course of therapy it is supposed to go down, not up.


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Are there dextral/sinistral higher animals?
For example, almost every dog I've met in my life (more than 20 subjects) uses their right paw touching one while asking for attention. Can it be used as a criterion for calling them dextral? If not, what?
However, I realize that even those dogs who live in the street might get influenced by dextral people:

There is no domestic animal which has so radically altered its whole
  way of living, indeed its whole sphere of interests, that has become
  domestic in so true a sense as the dog (Konrad Lorenz)

Is there any research about it?

Related: Do animals exhibits handedness (paw-ness?) preference?

Handedness has been studied in several different species of toads. As basal tetrapods, the authors argue that these taxa are unlikely to be influenced by human hand dominance and are thus a better model for studying the evolution of handedness.
Bisazza et al. (1997) studied "pawedness" in Bufo bufo, B. viridis, and B. marinus in wild-caught animals by determining which forelimb was used to remove a piece of paper from the animals' snout or a balloon placed over its head.
The results were mixed. B. bufo preferred the right forelimb in both tests, but B. viridis and B. marinus did not. B. marinus did preferentially turn its head left in another experiment, using the right forelimb for support.
A subsequent study by Malashichev and Nikitina (2002) showed that Bombina viridis is "lefthanded," while Bombina bombina is "ambidextrous."
So based on these studies, lateralization appears to have a long evolutionary history.


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How do biological communities at deep-ocean hydrothermal vents migrate between vents?
Much interest in the astrobiology community has been generated by the discovery of biological communities populating deep-ocean hydrothermal vents (i.e. "black smokers"). (1) These ecosystems rely on chemoautotrophic bacteria/archaea extremophiles as primary producers living at 40-80 C temperatures.
However, the lifetimes of these black smokers have been estimated to be of order 25 years. How  are these biological communities able to migrate to newer, active vent systems in conditions of extreme cold and high pressure?
(1) Lonsdale, P., 1977, Deep Sea Research, 24, 9

Interesting question.  I don't think the pressure would be a problem unless they have an air-filled cavity equalized to a lower pressure (which I can't imagine these organisms would have) or if the dispersal required rapid movement to other depths.  As far as I understand it, if you live in water and are filled with water then pressure is no big deal.

Yes, I am sure that the temperature would be more of a challenge.

I did some research on the topic and came accross this paper by Johnson et al. I am not a zoologist, so everything I write here is taken from the references paper.
The authors used genetics to estimate gene flow between different populations of limpets Lepetodrilus fucensis which is considered to be an endemic hydrothermal vent animal. They used a mathematical demographic model "isolation with migration" to estimate the migration of the animals across different biotopes.
The vents are distributed along the ridge segments and can be seen as small islands isolated by tens of kms from each other along the same ridge segment and thousands of kilometers between distinct ridges.
The results suggest that there is certain migration between the adjacent vent locations, that means that the flora of one vent can indeed survive the distance towards the next most proximal vent.

So, from now on is my pure speculation. Since the distance between single vents along the same ridge segment seems not be to so high we can suggest that these organisms are capable to resist the pressure and temperature on the ocean bottom while travelling from one vent to another...

I think you mean "fauna of the vent" rather than "flora".

Following up on Alexander's response, I read a little more on the subject by looking at some of the references in the Johnson et al. paper.
This paper  discusses an interesting case where researchers could study a hydrothermal vent ecology before and after a catastrophic eruption giving a "natural clearance" experiment. Since endemic organisms were eradicated, any pioneer species must come from other vent systems.
A number of species, in the form of larvae caught in larval traps, were observed to arrive at the vent. These species, including Cyathermia naticoides, Lepetodrilus spp and Gorgoleptis spiralis, arrived at a significantly different (P < 0.05, MANOVA and ANOVA) rate to the pre-eruption larval source population rate. Larvae of one gastropod species, Ctenopelta porifera, which had been seen only once pre-eruption, arrived in significant numbers post eruption. The source of these larvae may have been from a vent 300 km away.
These authors associate this change in the populations pre- and post-eruption with the specifics of the hydrodynamic transport processes operating in the region.
A more general sequence of vent re-population is given in this article.
However, the interesting thing for me was the significant, but changing fluxes of larval species at these deep-sea vents.


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When does BLAST fail to align 2 DNA sequences?
This is an assignment that had confused me for a long time.  So I think you guys who study computational biology might be interested. The original question is:

Find the two most similar DNA sequences of length 20 that Blast using a word length of 5 will fail to align.

BLAST works by finding a perfect match between sequences of a length equal to this "word length" and then enlarging it in a standard way -- yet there will be no alignment without this perfectly matched word.
So in your case, you must look for two 20bp sequences with no common 5bp sub-sequence; for instance:
AAAAAAAAAAAAAAAAAAAA

and
AAAACAAAACAAAACAAAAC

Yeah, this is the standard answer.  But note that BLAST works  different with Protein. That's why it confused me for a while.

Is "word length" == k-tuple?

@StudentT Precisely k in k-tuple.

I am not sure I understand BLAST correctly.
When using BLAST in DNA and protein, they are different. There is a threshold T in protein "seeding" step, which means the seeding sequence is not perfectly matched. However, it seems there is no T in seeding step and we are looking for perfect match and extend them to neighbouring sequence.
So, if there is no word length 5 exact match between these 2 sequence, BLAST will fail.

I am afraid i don't understand what you are trying to say here. Could you please clarify?