text:
The genetic and physiological origins of laughter?
This Wikipedia article  defines laughter in many terms, such as...

"a visual expression of happiness, or an inward feeling of joy"

and

"a part of human behavior regulated by the brain, helping humans clarify their intentions in social interaction and providing an emotional context to conversations".

Note: the emphasis was added by myself.
The article also states that laughter is "probably genetic", and that

"Scientists have noted the similarity in forms of laughter induced by tickling among various primates, which suggests that laughter derives from a common origin among primate species."

According to this report which the Wikipedia referenced, the expression of laughter in general is present among other great apes. Phylogenetic trees were reconstructed to represent the evolution of this trait among primates (which concludes that the ability to laugh must have a genetic basis, at least to some degree).
Note: I also found this WikiAnswers post, but it clearly can't be that reliable.
A search on the OMIM database yielded this result, where children with Angelman syndrome were characterized with "excessive laughter", this result, in which Charles Bonnet syndrome was characterized with "inappropriate laughter", as well as many other genetic mutations which resulted in some sort of uncontrollable laughter.
I understand that laughter is a complex psychological expression of emotion likely associated with more abstract thought, and that there simply can't be "a laughter gene", but my question is:
Is there any known genetic or physiological origin of laughter? What is biologically different in great apes which allows for laughter, in comparison with a panoply of other animals? I'm looking for more of a molecular answer rather than an ecological or psychological one.

this question (or any follow ups you might have) would also find a good home at CogSci.SE.

I recommend this article: The Evolution and Functions of Laughter and Humor: A Synthetic Approach by M Gervais and DS Wilson, 2005, University of Chicago Press.
For your question about the origin, firstly they explain that all laughter is induced by stimuli which are unexpected or unpredictable, experienced in a non-serious (unthreatening, safe) context. Given examples include peek-a-boo, which can make a child laugh but also cry if the child is not perceiving the situation as safe. Also that we can't tickle ourselves and tickling is induced by stimulating vulnerable body areas. Similarily, apparently in apes laughter is mainly induced by "tickling in conjunction with mock aggression and chasing".
They explain the function of (Duchenne, that is stimulus-driven "honest" as opposed to voluntary) laughter to be propagation of "positive affect" in a group, as it utilises the chameleon effect (it is contagious) which apparently has been shown to exist for its "cooperative value". Other studies seem to have shown that a) we are thirty times more likely to laugh in a social context than by ourselves and b) the contagiousness of laughter response increases with group size, making it an efficient tool for coordinating a group and getting everyone into the same emotional state.
As for other animals, the article doesn't address that. It does seem like a different question to me so I would consider separating that into a second one.

Informative and relevant response, but I'm also looking for some sort of a more "molecular" explanation as well. Any more insight?

Molecular in what sense? The neural pathways, anatomy?

Hmm. Signalling pathways, anatomy as well, but I'm mostly interested in the molecular genetics of it. Your answer is certainly a fine one, but doesn't quite cover that area.

Could you give a different (unrelated if you wish) example that could explain what you mean by molecular genetics in relation to a pattern of behaviour?

Rather than the behavioural act of laughing itself, I'm more concerned with the biological ability to laugh that humans and some great apes have, according to the report. As laughter also has some sort of genetic component, there must be some genes being expressed within specifically primates that allows us to laugh. I'm thus interested in the expression of these genes, and how they interact to create the phenotype of being able to laugh.

@LanceLafontaine The road from genes, to proteins, to neurons, to neural systems, to behavior is a very long one. It has not been parsed out yet so what you're asking for can not yet be delivered. Keep in mind that laughter (like all behavior) is an extremely complicated emergent property of many underlying systems. It's never as simple as "having some genes for X". Basically, the question your asking is too vast.

@Preece, notice that I mention exactly that in the question. I'm not looking for the impossible, but rather what's already known, if anything. And if nothing is known, an answer explaining why would be sufficient.


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Why can't we breed watermelons without any remaining seeds in the flesh?
Watermelon is just starting to come in season in the northeastern U.S., and having a seedless watermelon is convenient.  The only downside is, the "seedless" almost always still have the immature, sterile white seeds in them.
What is the mechanism for breeding these watermelons so that only these white seeds remain?  What is the genotype that results?  Could the genetics be modified so that there are virtually no seeds (short of any minor aberrations) left in the flesh of the fruit?

The seedless watermelons, like bananas, are a crop that are specifically bred to be trisomic (three copies of a chromosome). The consequence is the seeds are non-viable.

What, if anything, would be required to eliminate the seeds altogether?  Or are you saying this is as far down that road as we can go?

That I can't comment on.

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How long do your eyes need to adapt to darkness and reach full contrast?
I heard you should wait some time until your eyes adapt to darkness and are able to see smallest luminosity differences, otherwise you might overlook faint objects in the ocular. Are there any rules of thumb here?
What about looking for 5 minutes on your bright laptop, do you have to wait again the same time or wear some sunglasses? ;)

Thirty two minutes on an average

Actually, the US Army and Air Force (and I assume the Navy) teach their life support troops about this (as well as the aviators), since so many missions are conducted at night.  It is actually some very interesting physiology involved in this.  This Army Instructional manual should be of help (PDF File).

On an average it takes 30 to 45 minutes for your rods to be fully dark adapted to night vision.

It also covers things such as Mesopic vision and Scotopic vision, eye health, and how to actually dark adapt.  I suggest it as a good read.  It's less than 14 pages.

It should be mentioned that dark adaptation occurs in two phases. Your pupils dilate in a few seconds, then your rods adjust over many minutes. Try this demo!: Take off your glasses/contacts or borrow someone else's in a brightly lit room at night. View a row of LEDs. I use a cable modem in a home office for this. Stand where you can just barely focus on the LEDs, then flip off all the lights. You start out with tiny pupils that make a lens with a wide depth of focus, so you can see the LEDs. When your pupils contract, the lens enlarges, the DOF shrinks, and the LEDs go blurry.

An old camping trick, for after someone's shone a flashlight in your face -- put your hands over your eyes, and stare into the palms of your hands for 5 to 10 seconds.  Your pupils will fully dialate, so you'll restore your basic night vision in seconds, not the 3-4 minutes they mention.  (but not something you'd want to do when flying an aircraft, I'm guessing).  You still have to wait to get back any color sensitivity, though.

@Joe, Uh, any citations or simply old wives' tale?

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Below which temperature human muscles don't work?
When one exposes theirs body parts to cold environment (especially foot and hands), they may be numb, with temporarily blocked both muscles.
What is typical body temperature below which human muscles don't work properly?
Moreover, what is the mechanism behind it?
EDIT:
Interested in case when muscles almost cease to work (e.g one is not able to grasp a cup), not just in small perturbations to strength.

If you dissect striated muscle out of most-any organism, the actual contractile apparatus works over a wide range of temperatures. So that's at the single-muscle-fiber scale. The muscle itself continues to work at all (thawed) temperatures below body temperature -- the problem comes with its regulation.
The shivering response -- a centrally controlled  involuntary contractile pattern -- overwhelms voluntary muscle control. So the mechanism behind loss of muscle coordination in hypothermia is the same as the shivering mechanism. When the core temperature drops, the midbrain starts over-riding voluntary control of the muscles. When the core temperature drops far enough; around 32C, the shivering often slows down or stops. Voluntary movement becomes compromised probably because the brain simply isn't working; neuron firing rates are so slow that sensation, processing, and motor responses are all critically impaired.
The feeling of numbness does not actually directly accompany a loss of muscle contractility. You can walk pretty much indefinitely on frozen feet if you can keep your balance (and you keep your core temperature up.) Lots of people survive severe frostbite of their feet (their feet do not often survive, however.) The reason why it seems your hands don't work when they get cold is that you can't feel what you're doing (note; your hands can be much colder than your core body temperature.) But the muscles themselves work right up until they freeze solid.
UPDATE:
 Here's a paper that directly addresses the scenario posed by OP -- the decrease in grip strength with temperature.   Figure 1 of that paper illustrates their experimental setup; they measure the contractile strength of the index finger while manipulating the temperature of the rest of the hand. They show that contractile function is impaired with temperature and look at temperatures as low as 12C.
They measure as much as a 50% impairment on twitch tension upon cooling to 12C. It's interesting that they review results suggesting that some of this effect is intrinsic to the muscle fiber (not neurological), showing that I should refine what is meant by "continuing to work" in my opening paragraph. (I meant having an ability to generate contractile force when equilibrated in solution containing sufficient ATP and Ca$^{2+}$, not the ability to contract optimally.) For fun, I linearly extrapolated the final arm of Figure 5 and found that the 'voluntary tension' approached 25% at 5C. This suggests that total failure of the voluntary contraction happens somewhere below the freezing point of water (muscle would freeze at a temperature lower than 0C because of colligative effects.)

http://www.jacklondons.net/buildafire.html

Thanks, especially for the last link. (I thought also about possibility that capillaries contract to much at lower temperatures, to support demand of muscles.)

Regarding the capillaries, you're right they that they greatly constrict, but the muscles have enough blood supply to continue functioning. Muscles are also good at tolerating anaerobic conditions (lactic acidosis.)

Was going to write an answer based on shivering, interesting read!

This seems complicated, but I found a reference that might answer these questions (if its right).
Sports physiology common wisdom is that human muscles regularly work in the range of 37C to 40C which is basically body temperature.  Since the muscles generate quite a bit of heath when they function, they are usually not functioning in colder temperatures and hyperthermia starts setting in.
Thomas et al. put this to the test by cooling down some muscles in volunteers!
They say that the core body temperature is more important than the peripheral temperature in restoring muscle strength (torque produced).  Hypothermia makes the victim weaker and weaker apparently and it sets in below 37C pretty quickly apparently.  They speculate that the cooling might actually impair the nervous system from activating the muscles, which might be an answer to your question.
This is probably not the final word, but its as far as I got...

Nice, but a quick skim says that they showed only small deviations. I am the most interested when muscles strength is only fraction (say, <25%) of the maximal one, or they are not working at all.

@Piotr As you can imagine, a specfic study of this nature might be difficult to get past an ethics review.  There probably are some case write ups of individuals, but they would tend to be anecdotal "then I couldn't move my arms!".  Perhaps someone can find a clinical review.. but there will usually be cause to complain when you are reviewing the limits of human physiology.

I am not talking about anything damaging, rather about a common experience for anyone doing winter sports, or even hiking in the rain.

If bulk or major muscle groups have an internal temperature of much less than 37C these authors imply that this is not a common experience - the circulatory system and the functional heat of the muscles will keep the temperature stable.  you will still feel uncomforatable, but until hyperthermia or frostbite sets in the main tissue temperature will be stable.


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Why do neurons die so quickly (relative to other cells) when deprived of oxygen?
This question could be considered a follow-up question to Why is a lack of oxygen fatal to cells?, although the top answer there does not address why damage starts to pop in.
The answer says this:

Neurons are also highly metabolically active, which means they
  generate more waste products. A buildup of nitrogenous waste products
  in the cell (and bloodstream) can be potentially fatal due to it's
  effects on pH (screws up enzymes and a whole slew of biochemical
  reactions)

But when the brain is deprived of oxygen, metabolism shuts down. So waste products aren't being generated anymore.
====
Basically I'm wondering - what causes neurons, in particular, to die so quickly (relative to other cells, like kidney cells) after they're depleted of energy?

who said anything about metabolism shutting down when the brain is deprived of oxygen? Brain cells die, sure, is that what you mean by "shut down"? Are you implying that they go into some kind of dormant state before they die?

Doesn't metabolism shut down before death occurs? Or does the metabolism start causing damage, which causes death in the process?

this isn't very scientific, but metabolism shutting down is death in some sense. Our neurons aren't designed to be shut down, so if that happens they start to fall apart (die).

FYI: I've opened a related question on how much our brains' metabolic rate varies. My guess is that since neurons consistently use lots of energy, they are totally unprepared to exist in a low-metabolism state.

But on the other hand, some organisms can be frozen and revived. In that case, metabolism is shut down but death does not occur.

There is a good review in the Journal of Experimental Biology (Bickler and Donohoe 2002, JEB 205, 3579–3585) I will just summarize for those that do not have access to the review.
Neurons use lot of energy to maintain their polarized state, this is not required to other cells. When O2 or blood flow is reduced, the neuronal ATP levels breaks down very fast, with 90% ATP depleted in less than 5 minutes. Without ATP, the neuron can not maintain the correct ion flux, so depolarization occurs causing glutamate excitotoxicity, cell swelling and finally cell death.

+1. Neurons use a lot of active transport pumps that consume ATP to maintain ion gradients and to shuttle neurotransmitters.

What about cardiac myocytes? They also need to maintain a depolarized state for synchronized contraction


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Reaction mechanism and substrate interaction of dopamine beta-hydroxylase
The reaction in which dopamine beta-hydroxylase catalyses the conversion of dopamine to norepinephrine is shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves structural biology?
Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else. I'm really wondering what in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. In other words, what is the structural mechanism behind substrate specificity?

Maybe I'm misunderstanding, but the product obviously has to be epinephrine, so the enzyme will add the OH to that specific place that results in the right product. If you're asking how the enzyme does that, you might want to be more specific about which parts of the mechanism you're interested in.

Evolutionarily speaking - yes - the enzyme has evolved to add OH to that specific place. I'm really wondering what in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. I'll just edit the question to include that now.

It's still not clear what you're asking. At the moment, I would answer: "The enzyme has evolved to do that and the body has evolved to use that molecule. That's just how it is, for some reason that exact molecule was convenient." Or are you asking about the reaction mechanism of the active site? In that case you should say that.

Okay I changed it to say that.

I think he is asking about what is the structural mechanism behind substrate specificity.

May be a good start is at BRENDA database http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.17.1

Dopamine beta hydroxylase is not really substrate specific, it will affect many different compounds.

There are various studies on the mechanism of action of dopamine beta-hydroxylase (DBH).
This review (sorry, non-free article) by Kaufman and Friedman was written less than 10 years after the discovery of the reaction of conversion of tyrosine into [nor]adrenaline in the adrenal gland:
DOPAMINE BETA-HYDROXYLASE - Kaufman S., Friedman S. - Pharmacol Rev. 1965 Jun;17:71-100.
It makes for an interesting read, as they start detailing the history of our knowledge on adrenaline synthesis (well, at least at that point in time!), the various hypotheses and models that were thought of, experiments with radioactive labeled precursors and so on.
They then procede to talk about the mechanism of the enzyme. Without going too much in detail, they report experiments showing that oxygen, ATP and Mg++ stimulate dopamine beta-hydroxylase enzymatic activity, with the following note on Mg++:

[...] Mg++ is required for the uptake of catecholamines by the adrenal vesicles. EDTA inhibits the uptake of the precursor, hydroxytyramine, but does not inhibit the enzymatic conversion to norepinephrine if the vesicles are intact.

They also list the requirement for two cofactors: ascorbate and copper

The first indication that Dopamine-beta-hydroxylase is a mixed-function oxidase was the demonstration of a requirement for ascorbate. It was found that this reducing agent
could stimulate the hydroxylation reaction even in adrenal particles, and the requirement for ascorbate became more pronounced as the enzyme was purified.

Bringing to the reaction:

Dopamine + ascorbate + O2 → L-norepinephrine + dehydroascorbate + H2O

For the Cu:

Only recently, however, was the enzyme obtained in a pure state and the metal characterized by direct analysis. The metal is copper and it is present in a concentration of 0.65 to 1.0 ug per mg enzyme (4 to 7 moles of copper per mole of protein). It can be removed by treatment with concentrated potassium cyanide. This copper-free enzyme is inactive but can be reactivated by addition of Cu<sup++.

They then proceed to detail some basic mechanism of action, which I will not report here for briefness.
A few years later, researchers from the same group authored a book chapter for the American Chemical Society entitled:
The Mechanism of Action of Dopamine β-Hydroxylase - Kaufman S., Bridgers W.F., Baron J - in Oxidation of Organic Compounds, Chapter 73, pp 172–176, 1968 - Chapter DOI: 10.1021/ba-1968-0077.ch073
From the abstract (I do not have access to the full text of this):

Dopamine β-hydroxylase catalyzes the side-chain hydroxylation of dopamine and other phenylethylamine derivatives. Ascorbic acid serves as a specific electron-donating cofactor. The enzyme from bovine adrenal glands contains Cu2+ and a smaller amount of Cu+. When the enzyme oxidizes ascorbate to dehydroascorbate, most of the Cu2+ is reduced to Cu+. Added substrate is hydroxylated, and Cu+ is reoxidized to Cu2+.

To get to some more recent years...
In this review
New insights into copper monooxygenases and peptide amidation: structure, mechanism and function. - Prigge ST, Mains RE, Eipper BA, Amzel LM. - Cell Mol Life Sci. 2000 Aug;57(8-9):1236-59.
A mechanism for Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3) is proposed, and

Since PHM is homologous in sequence and mechanism to dopamine beta-monooxygenase (DBM; EC 1.14.17.1), the enzyme that converts dopamine to norepinephrine during catecholamine biosynthesis, these structural and mechanistic insights are extended to DBM.

A structure of PHM along with a modeling of DBH is shown in Fig 14. You can see the two catalytic copper atoms and the possible binding of dopamine to the site.

They also show a mechanism of action for PHM. Essentially, through the oxydation of ascorbate the Cu++ becomes Cu+ and can then bind an oxygen molecule that will be used to hydroxylate the product:

Finally, a detailed computational model of the enzyme, and its active site is shown in this paper:
Structural Insight of Dopamine β-Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms - Kapoor A, Shandilya M, Kundu S - PLoS One. 2011;6(10):e26509. Epub 2011 Oct 20.
The active site is shown in Fig. 7, where you can clearly see the two copper atoms in purple and green, the most important aminoacids at the active site and two water molecules in red:

(source: plosone.org
Figure 10C shows the interaction of dopamine with the aa of the active site (Fig 10A and B show superposition between rat and human enzymes and Fig 10D shows the interaction of a drug with the enzyme):

(source: plosone.org)

Finally, a remark on your question. You say:

Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else.

As I said somewhere else: not everything has an evolutionary explication, and evolution is not finalistic. This specific enzyme structure appeared at some point and it was evidently working fairly well, and at the time the rest of the pathway may or may not have been like it is at present, but the important thing is that the enzymatic network managed to work together. It could had well evolved to hydroxylate another position, but probably in that case we would have different enzymes downstream. The important thing to remember is that the enzyme did NOT evolve with the finality of oxidizing the beta carbon.

great answer nico, and excellent fair-use quoting to help those without access to the article.

As an aside, I think it's crazy that copyright covers scientific articles for this long - I think copyright expiry should be much shorter for papers.

@Richard Smith: that is very true, and it makes life very difficult for researchers sometimes... (anyway, luckily the last two articles I quoted are free, the last one is under CC license).

The likely catalytic mechanism of dopamine β-hydroxylase, based on molecular modelling and the actual structure of peptidylglycine α-hydroxylating mono-oxygenase, was presented ten years ago in the extensive answer of @nico. The key point is that two copper ions are almost certainly involved in the chemical oxidation mechanism.
However the crux of the question, removing the reference to evolution is:

…the enzyme … add(s) OH to the beta-carbon rather than somewhere else.
I'm really wondering what in the enzyme’s shape makes the OH added to
the beta carbon, rather than somewhere else. In other words, what is
the structural mechanism behind substrate specificity?

which can be stated more succinctly as:
What structural factors in the enzyme determine the position in dopamine where the hydroxyl group is added?
The answer from @nico does not  address this point, and, indeed he appears to dismiss this in a comment in which he writes:

Dopamine beta hydroxylase is not really substrate specific, it will
affect many different compounds.

This, I maintain, is quite misleading: whatever other substrates it may oxidize, dopamine β-hydroxylase is absolutely specific for a single carbon atom when dopamine is a substrate.
So how does the substrate interact with the enzyme?
Ever since the analogy of enzymes and substrates fitting like lock and key, the idea was that the amino acids at the enzymes active site bound the substrate in such a way that the appropriate atoms on the substrate were brought into proximity to the catalytic components of the enzyme, amino acid residues or non-protein co-factors. This has been borne out by the countless protein structures that have been determined subsequently and, indeed, in this respect the question appears rather naïve, despite its chemical sophistication.
Obviously, the interest in this case is in identifying which residues of the enzyme interact with dopamine — perhaps binding the hydroxyl and amino groups and interacting with the aromatic ring. At present we do not know the answer as the single experimental structure available for dopamine β-hydroxylase does not include a substrate or substrate analogue. In this respect the most that comes out of this study (published in Science Advances in 2016 — i.e. since @nico posted his answer) is identification of the active site cleft where Cu is located and which is presumed to bind dopamine, and the modelling of the substrate, as shown below. This is from Fig. 6 of that paper, with the Cu ions shown in blue and the modelled substrate in yellow.

No apologies for posting 10 years after the question first appeared. It was bumped up recently for some reason and I felt it worth providing a different viewpoint and some more up-to-date info.

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Is it plausible that eukaryotic organelles like flagella and cilia are the result of endosymbiosis with spirochetes?
This was a claim by Lynn Margulis explained over at this link.

The sense organs of vertebrates have modified cilia: The rods and cone
  cells of the eye have cilia, and the balance organ in the inner ear is
  lined with sensory cilia. You tilt your head to one side and little
  calcium carbonate stones in your inner ear hit the cilia.  This has
  been known since shortly after electron microscopy came in. Sensory
  cilia did not come from random mutations. They came by acquiring a
  whole genome of a symbiotic bacterium that could already sense light
  or motion. Specifically, I think it was a spirochete [a
  corkscrew-shaped bacterium] that became the cilium.

And why would our bodies incorporate spirochetes as part of our basic functionality?

There are many kinds of spirochetes, and if I’m right, some of them
  are ancestors to the cilia in our cells. Spirochete bacteria are
  already optimized for sensitivity to motion, light, and chemicals… If
  I’m right, the whole system—called the cytoskeletal system—came from
  the incorporation of ancestral spirochetes.

You can find this on Wikipedia: http://en.wikipedia.org/wiki/Evolution_of_flagella#Symbiotic.2Fendosymbiotic.2Fexogenous_models. In lectures we have also been made aware of the fused membrane of cilia with the cell rather than the separate membranes of endosymbionts. There were more (better) reasons but I've forgotten.

Well, since all cells in a multi-cellular organism originally come from the same precursor cells, it’s hard to argue that some of them have endosymbiotic compartments that are missing in others, and notably their precursor.
Notably, there are species which possess both ciliary and rhabdomeric photoreceptor cells, and their precursor is non-ciliary. This is incompatible with Margulis’ endosymbiosis hypothesis.
PZ Myers has a good summary of the relevant papers [1, 2].

[1] D. Arendt, K Tessmar-Raible & al., Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain, Science 306, 2004.
[2] D. Arendt, Evolution of eyes and photoreceptor cell types, Int J Dev Biol. 47, 2003.

To play devil's advocate, I'd say that the fact that cilia in modern cells are fully encoded by nuclear genes (and thus that non-ciliary cells can develop cilia) does not entirely rule out the possibility of an endosymbiotic origin: transfer of endosymbiote genes to the nucleus does occur, with e.g. mitochondria having a highly reduced genome, and with some eukaryote species actually possessing mitochondria (or organelles derived from them) that have no DNA at all. That said, there does seem to be other evidence against the endosymbiotic origin of cilia.

@Ilmari You are right, it’s not a definitive proof. But to specify, what I’m arguing isn’t about nuclear genes, it’s that cell development, which does to some extent recapitulate phylogeny, doesn’t show this evolution. The endosymbiosis hypothesis would imply a non-parsimonious evolution on the gene regulatory level, which first induces a loss-of-function and later a gain-of-function in one sister cell type but not the other. The more parsimonious explanation, a single gain of function (again, on the regulatory level) in one cell type, is incompatible with the endosymbiosis hypothesis.


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How much does a human brain's metabolic rate vary?

Possible Duplicate:
How does brain energy consumption depend on mental activity?

Our brains consume about 20% of our energy when we're at rest. How variable is a human brain's energy consumption? Will thinking harder consume more energy? Does this change significantly when we sleep?

Related: http://biology.stackexchange.com/questions/839/how-does-brain-energy-consumption-depend-on-mental-activity

maybe even duplicate.


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Did we first have swimming birds or flying birds?
Looking at the swimming birds building nests just across my garden, I suddenly wondered how evolution came to swimming birds and whether flying birds started swimming or whether swimming bird like animals started flying.
What came first and when and why?

Wouldn't we have had running birds first?

Flying came first, as far as we know. The earliest known bird (currently), Archaeopteryx lithographica, already had aerodynamic feathers (Feduccia and Tordoff, 1979). The Solnhofen Limestone, where it was discovered, is ~145 million years old, so we can place the "when" flight evolved to greater than or equal to that time.
Gansus yumenensis is regarded as the earliest aquatic bird and is dated from ~120 million years ago. The Hesperornithiformes are the sister taxon of Gansus (less derived) and also aquatic. However, they date from ~85 million years ago. It is not clear whether the ancestors of Hesperornithiformes were also aquatic. Because they branched off the main line of birds before Gansus, these ancestors would likely predate Gansus, but those relatives have not yet been discovered.

Thanks for the extensive answer, so there's a gap of at least ~25 million years, considering the current state of knowledge.

Another way to look at this is: How do you evolve flight when you're aquatic? There are three proposed models (or even five) for the evolution of flight:

wings helped predators to better jump at prey from high positions
wings helped a jumping animal to make longer jumps
wings helped a tree-living animal to get around

All of these models assume that you have a high or solid surface to start flying from. Water, in contrast, is a difficult underground to start flying from (being flat and soft).
In contrast, to evolve swimming for "terrestrial" bird seems much more straightforward.

Ok, seems a fair line of thought, but if this were true, why do we have flying fish (ok, not really flying, but still, they could have evolved from there)?

Fish have been around for 500 million years, and no true flying fish has evolved during that time. However, in tetrapods (which evolved from fish), flight has evolved in bats, birds, and pterosaurs. In contrast, "flying fish" are actually gliding fish that accelerate in the water (and not in the air, as birds do).


text:
Did animals evolve from plants?
Did animals evolve from plants? Did animals' ancestors have chloroplasts in their cells?

Why do you think that animals evolved from plants?

@Michael Kuhn because animals and fungi (uniconts) evolved from biconts. Biconts currently represented only by plants.

I see! The relation of the eukaryote ancestor to the unikont/bikont split is still debated. Here's one option supported by rare genomic changes: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817406/figure/fig4/ where a chloroplast-less ancestor acquires a chloroplast on the way to plants

Based on your comments to the answers and above... it seems that your question is "Did the common ancestor of plants and animals have chloroplasts?" In my opinion, this is quite distinct from "Did animals evolve from plants?"

See this paper "Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi" for information on the divergence estimates (I'm not sure if there are more recent papers discussing this).
Plants, animals and fungi are eukaryotes, distinct from eubacteria and archaebacteria, which are prokaryotes. The difference being in the composition of the cell, particularly a nucleus contained within a membrane for eukaryotes, along with other membrane bound organelles, e.g. chloroplasts. They all share a common ancestor, according to this paper, that split 1.576 Bya (billion years ago) +/- 88 Mya (although it states the relationships are unresolved - it is often difficult to resolve relationships so deep in a tree). They form distinct groups known as Kingdoms under Linnaean based biological classification; the Fungi, Plantae and Animalia. Thus, in answer to your question, no, animals did not evolve from plants.
Plants have chloroplasts in their cells, which provide the ability to produce energy via photosynthesis. It is thought that the chloroplast resulted from a symbiotic relationship between early plants and a cyanobacteria in that they both relied on each other for survival and so coevolved. Animals don't contain chloroplasts and instead contain an organelle called the mitochondria (although most plants also have mitochondria), which is also thought to have been a bacterial endosymbiont, probably related to rikettsias.
Protists also contain chloroplasts. The protists are intermediate between all three groups and have been notoriously difficult to classify, being placed into a fourth Kingdom, the Protozoa, although this grouping has been contested. The current Cavalier-Smith system was proposed in 2004 and classifies life into 6 Kingdoms.
Chloroplasts are thought to have evolved from a single endosymbiotic event in Archaeplastida, although there are evidence to suggest some secondary endosymbiotic events. Check out this paper for more information; figure 1 shows the relationships between the different groups and the endosymbiotic events. The Opisthokonts are the origin of the Fungi and Animalia kingdoms.

This does not answer the question: did ancestors of animals have chloroplasts?

Ancestors of animals had mitochondria (hence the "animal equivalent of the chloroplast is the mitochondria), as did the ancestors of plants have chloroplasts. Although, it is a common misconception, that plants don't respire and in fact most plants also have mitochondria.

Edited my question to include chloroplast origin information. Hope that helps?

I wonder. Wikipedia says that Chromalveolata derivd from red algae, but your diagram shows the opposite.

As I mentioned in my post, resolving the relationships of the organisms at the base of the phylogenetic tree is particularly difficult. I'm all for taking a multi-gene phylogenomic approach to this, but the more genes we add the more computationally intensive the analysis. Also, incomplete lineage sorting and other issues can compound resolution of the tree. I should imagine these things were so similar, that determining relationships is even more difficult. As we have no sequences for these organisms, we must perform ancestral state reconstruction in order to, infer the hypothetical nodes.

Here's a cool phylogenomics paper by Eugene Koonin "The origin and early evolution of eukaryotes in the light of phylogenomics" - http://genomebiology.com/2010/11/5/209

I think it's misleading to say mitochondria are the animal equivalent of chloroplasts. All plants, not just 'most', have mitochondria. Chloroplasts are only similar to mitochondria in that they are both endosymbiotic organelles. Metabolically and evolutionarily they are very different.

Also, whilst this answer has excellent phylogenetic detail, it doesn't explicitly answer the question.

Thanks for the comments @RichardSmith :) I have updated my post accordingly.

No. Animals form the kingdom Animalia (or Metazoa) which is distinct from the Plantae kingdom.
Both evolved independently from single-celled eukaryotes.
In fact, animals are more closely related to fungi than to plants.

Did those single-celled eukariotes have chloroplasts?

@Anixx No. Chloroplasts originally developed in green algae, after divergence from the single-celled common ancestor of plants and metazoa.

Which implies that multi-cellularity evolved independently at least twice, once in plants and once in animals (and possibly in fungi as well). Interesting.

@Keith Ha! Actually, “Multicellularity has evolved independently at least 46 times …”

@KonradRudolph: Wow. That could have some interesting implications for extraterrestrial life. Planets where life has developed but hasn't evolved beyond single-cell organisms might be less common than I would have assumed. (Unless there's something special about terrestrial single-celled organisms that makes the development of multi-cellularity unusually easy.)

@KeithThompson Indeed, it does have these implications: There are potential hard-to-cross thresholds to higher life forms, which prevents their abundance in the Universe (and may help explain the Fermi paradox), but evolution of multicellularity is not one of them.

@Konrad Rudolph What are these "potential hard-to-cross thresholds"? What are they called (or what should I google for)?

@user17915 Such a threshold is usually called a “Great Filter”. There’s a good overview of the argument on Wait but Why.


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Determine which gene is in the middle complementation

Possible Duplicate:
Crossing mutant strains on minimal media problem

I'm studying this problem for my genetics final:

My Attempt:   The answer for part B is met2 and the answer for part C is Df1.  Met2 and met 1 both have 1 no so i'm not sure how met2 is in the middle.  I didn't even know complementation tests could tell gene location. I think the answer to part C is because df1 has the most NOs, which means it's missing the most DNA.  (If it had that DNA, it would complement).

Please don't ask a duplicate question, you can just edit your own posts to add more information. I copied the content of this question into your older one, and will delete this one soon.


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Why doesn't yearly screening for lung cancer decrease mortality rates?
In a large trial, screening yearly for lung cancer hasn't reduced mortality rates. Why is this? Isn't cancer best treatable when caught early? Is this because lung cancer is hard to treat anyway, because yearly is not frequent enough, or why?

Not necessarily the root of what you are asking, but Diagnostic follow-up of positive screening results was determined by participants and their health care practitioners -- essentially, this leaves what to actually do with the positive result to the patient and/or the doctor.  Some patients may refuse care and some doctors may not be equipped to deal with the problem or hesitate to farm out to specialists.

Is lung cancer effectively treatable? The common theme with cancer is that although lots of “treatments” exist, not all of them do actually prolonge life expectancy after diagnosis …

This question is a bit vague. Rather than asking why screening doesn't prevent mortality, maybe you should ask yourself why screening would prevent mortality.

Shep I answered this on the topic. It should prevent mortality by giving a patient a chance to start a treatment earlier, which is said to increase dramastically the odds of recovery.

You'll get better answers if you make it clear what you're asking. I assume it's not whether cancer is easier to treat if it's caught early, or if lung cancer is hard to treat anyway, I think we both know those things are true. Do you want to know why we don't screen more? Why lung cancer is hard to treat even when we've found it? Why we typically don't catch lung cancer earlier? These are all questions that can be answered. Overall it's a good question, though.

There are a number of reasons, generally, why a screening test may fail to decrease cancer mortality rates:

The screening test may not be very good. I know this seems like an obvious one, but its something of a problem - a screening test will only reduce mortality if it catches cases that are both treatable and wouldn't be detected in time to treat using other methods. For example, it may be that even if caught slightly later by other methods, lung cancer is equally treatable (or equally difficult to treat).
Mortality from false positive tests and subsequent procedures in non-cases offsets any gain in survival among cases.
Diagnosis is only one step toward treating a disease. Even if detected, if a disease is not treatable or isn't treated, knowing you have the disease doesn't change your mortality risk.

In this case it appears that a chest radiograph isn't good enough at detecting lung cancer to manifestly improve mortality outcomes. The author's of the paper don't really specify why this is - though since they're just looking at lung cancer mortality, it's likely not #2.


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Primary function of the enzyme lipoprotein lipase
I read here and here that the function of lipoprotein lipase is to facilitate fat uptake and storage in adipose tissue. Could anyone provide a slightly more expanded explanation, without going into too much detail, and without the use of too much jargon (I am not a biologist). I have read the wikipedia page, but sadly I didn't understand it....Thanks !
Edit: One of the things that is confusing me is what "fat uptake" means in this context.

Haven't read yet Stahl et al.,  Identification of the Major Intestinal Fatty Acid Transport Protein. To facilitate may mean no more than break down of triglycerides, as uptake mechanism is not known yet.

Fat uptake means cells eating fat.
I'll try to keep it simple, so forget the many approximations. You need first to consider that most fat circulates in the blood under the form of triglycerides (TG). TG are not soluble in water, so how do they circulate? They are hidden inside cargo vehicles called lipoproteins. When a circulating lipoprotein touches a cell, if the cell expresses lipoprotein lipase (LPL), first LPL would trap the lipoprotein cargo, and then will start to catabolize the TG.
Importantly, there are no efficient TG cargoes inside the cell, so the function of lipoprotein lipase is to make fat easy to move inside the cell. TG are a chemical assembly of one glycerol and three fatty acids. Of note, there are good fatty acid cargoes inside the cell, so LPL will break TG into glycerol and fatty acids so that they can be further metabolized depending on the cell type.
Heart and muscle cells will bring fatty acids to mitochondria where they will be oxidized to produce energy. With reference to your question, adipocyte cells will bring fatty acids to other cellular compartments where they will be converted back to triglycerides and stored as fat. That's why you read that LPL facilitates fat uptake and storage in adipose tissue.

Great answer. Thank you ! I would upvote, but I don't have sufficient rep myself (yet). Just a further query: when I read: "facilitate fat uptake and storage" would I be right in saying the /primary/ function is fat uptake, which then results in fat storage (in adipocytes).

No. All cells need fats, primarily to build membranes and to store in vesicles for later conversion to energy. Storage is not restricted to adipocytes.

@Larry_Parnell Sorry, by writing "(adipocytes)" I meant to query whether the /primary/ function of LPL in adipose tissue is fat storage ? I took home from the answer is that LPL performs fat uptake and thereby facilitates fat storage.

Haven't read much - it might be that the mechanism of uptake of  free fatty acids (produced by lipoprotein lipase, outside the cell) is yet unknown. Thus, LPL should not perform uptake at all. Free fatty acids might even freely diffuse through membrane.

Adipocytes are fat cells. On their outer surface are enzymes called lipoprotein lipase abbreviated as 'LPL' . the major function of LPL is to break down triglycerides into soluble fats and facilitate their transportation into adipocytes. So as more triglycerides are broken down, the fat cells increase in number by almost thousands times and in by 20 times. This means the more the energy intake, the higher the rate at which at which fat cells get enlarged thereby making an individual to be extensively obese

Maybe you can add some references to your answer to attract more upvotes.


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List of species recently found of economic value
Is there a website or organization cataloging lists of biological species to have been recently found of great economic value? For example, a plant that wasn't of economic relevance a while ago but has been found recently to be important, due to advances in breeding varieties and more crops being planted. The same for species that were already important but have turned to be even more important in the last few years.

Are you looking for a business idea? The most clever use of SE I've seen recently. ;)

Perhaps the Biofuel Ecophysiological Traits and Yields Database would be of some help?

I can only answer for plants. The short answer is no, there is no central source of information of that kind.
You are basically asking about the sub-classifications economic botany and ethnobotany, which cover the economy and human uses of plants respectively. Neither field is particularly fast-paced, so you could simply keep up to date with the latest issues of journals like Economic Botany or Ethnobotany.
One key area of development for new valuable crops is in crop wild relatives, but there is no particular publication you should watch for that. Keep an eye on the Crop Trust as they will shortly be releasing, in collaboration with us (the Millennium Seed Bank) some reports and data about this.
If I wanted to keep up to date with all those things over time, I would set up some saved search alerts on Google Scholar for key search terms like 'emerging crop', 'new crop', 'crop wild relative', etc. Just perform a search on Scholar and then click the envelope button to the right of the search field to create a recurring search alert.
One other potential source of information would be to check FAOSTAT each year. You can examine global and local data about area under cultivation, yield, investment, commodity value, etc. of most crops. If something new were to emerge as a big player, it would appear on there.


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What exactly is meant by the expression "differentially expressed"?
As far as I've seen, this expression is almost always used in relation to gene expression profiling. Unfortunately, I have no background in this area. Can someone please explain this in layman terms?

Although each cell of your body essentially contains the same DNA and the same genes, cells in different tissues express (turn on) different genes under different conditions. Measuring differential gene expression involves looking at the amount of expression for a gene (or set of genes) in two contrasting scenarios. The contrast could be across different times, different tissues, different conditions, different related species, etc.
When, you say a gene is "differentially expressed", this is very context-specific. The phrase means nothing by itself, and it is only useful in terms of the applicable contrast. For example, the statement "gene A is differentially expressed" is uninformative, while the statement "gene A is differentially expressed in liver and muscle tissue" is descriptive--it tells you that liver tissues and muscle tissues have a significantly different level of gene A products. Often the terms "up-regulated" and "down-regulated" are also used to provide additional detail. In the context of the previous example, the statement "gene A is up-regulated in muscle tissues" tells you that the level of gene A products is higher in muscle tissues than in liver tissues.


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How many, and how severe, are known single gene polymorphisms for obesity?
A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (Peng et al., 2011). The paper looked at 59 studies and concluded that, "FTO may represent a low-penetrance susceptible gene for obesity risk", although the association was weaker (or non-existent) for some ethnic groups.
Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?

I was always wondering whether detecting such SNPs links to diseases (risk) is of significance. Sometimes, I think biology is so complex, even for diagnosis SNPs don't help very much. I am just chattering.

I think there are some statistical issues with this - such as multiple testing and family-wise error, but most of the studies in the meta-analysis I linked to seem to be quite solid and found odds ratios with confidence intervals comfortably above 1. Clearly it is well known that obesity etiology is multi-factorial and genetics plays a relatively smaller part (compared to the environment), but the evidence does seem clear that there are some genetic components, and gene-environment interactions are also likely.

MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see Thorleifsson et al. (2009), Elks et al. (2010) and Willer (2009)

Yes, FTO is the strongest thus far in the populations thus far tested. If Asians or African populations were to be tested as deeply, as often as European populations, other genes certainly may be added to the list.


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Molecularly, why can you straighten or perm hair?
I'm aware that hair can be curly because of the disulfide bond interactions in between cysteine amino acids in alpha-keratin filaments. However, I'm curious as to the biochemistry involved in straightening hair with a straightening iron, as well as with "perming" hair.
What happens at the molecular level? I suspect that a straightening iron simply disrupts the present disulfide bonds, but I'm only speculating.

Pretty much yes. However, temporary things like wetting your hair or using an iron merely disrupt the hydrogen bonding network. http://www.ccmr.cornell.edu/education/ask/index.html?quid=708

Related: https://biology.stackexchange.com/questions/42760/how-do-disulphide-bonds-in-hair-cause-curling

For straightening hair with a flat iron:
This source provided by bobthejoe states that temporarily straightening hair involves the breaking of hydrogen bonds between keratin molecules within hair.

One of the reasons hair is curly is because of hydrogen bonds between the proteins (keratin) that make up your hair [...]. Another way to alter hydrogen bonds is with heat; electric straighteners work because of this principle. The platters on electric straighteners are flat so that when your hair cools it takes the shape of "flat" as the hydrogen bonds reform. The same thing occurs with curling irons, but since the heating element is circular, the hair stays curled as it cools. The effect of heat, however, is temporary, over time the hydrogen bonds eventually return to their original form and the hairs goes back to the way they were. This rearrangement happens because moisture in the air hydrates the proteins.

This source provides a similar explanation.

Running a flat iron through blown-dry hair breaks the hair’s hydrogen bonds. It flattens hair until water or water vapor (from humidity, drizzle or the shower) penetrates the hair fiber and allows the hydrogen bonds to revert to their natural positions.

Thus, the straightening of hair with an flat iron does not involve the breakage of disulfide bonds as I had originally hypothesized.
For perming hair:
This article suggests that perming involves the chemical treatment of hair with reducing agents to break the present disulfide bonds between cysteine amino acids, followed by the reformation of the disulfide bonds in the desired curled shape.

In a standard “cold” perm, hair is put into curlers and the reducing agent ammonium thioglycolate is added. The disulfide bonds break and keratin molecules are now free to move around and adjust to the shape of the curl. Then a “neutralizer,” such as hydrogen peroxide, is added to reverse the effect of the reducing agent. New disulfide bonds form so the keratin molecules are locked into the shape of the curls.

This Wikipedia article also suggests that the chemical straightening of hair is obtained with the same process.

When disulfide bonds break it leads to hydrogen bonds, which then changes the shape of the alpha keratin protein. Therefore, that is why the hair changes from straight to curly or vice versa. It's the ability of the hydrogen hydrogen weak force that allow the protein to fold differently.

Welcome to Bio and thanks for your answer. +1 could you add a reference?

Both actions- whether by heat or drying naturally by moisture evaporation break and restructure the ionic hydrogen bonds.
This is why a wet roller set has staying power despite no heat and when using heat esp., if the hair is damaged or if temp. Gets too hot, it will denature the hair and will not be able to be set to the desired shape. (Damaged hair can not longer hold moisture-- hair is made of a protien, keratin)

Hi welcome to Bio.SE! Short answers are not typically well received on this SE site. We also ask that all answers provide citations or other kind of reputable support. Please add more context and support to your answer to avoid having it deleted. Thanks.


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How do nuclear receptors locate each other to form a DNA loop?
Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (Rubina et al.; J Mol Bio 2004).
I am not sure how exactly the receptors first attach to the DNA (dimers on each site first or the whole complex on one site), but in any case they will need to attach to one response element, then loop the DNA and bind the other response element. It seems like something that should be obvious, but I cannot stop wondering: How do the receptors locate the other site?
Normally I would simply say: diffusion - it just randomly happens. But I imagine bending DNA in such a way would require a lot of energy; too much to just randomly waste it trying to find another site.

Not sure NR are actually bending a linear DNA into a loop. The loop, as Shigeta points, could already form by random coiling. Then, NR would stabilize the loop recruiting other coregulators. All together they will act like a glue.

This probably isn't the complete answer as I don't know so much about eukaryotic transcription, but maybe I can start the answer.
First of all DNA bending can be sequence dependent - the double helix is not intrinsically straight.  DNA is also pretty easy to bend - it spends most of its time coiled pretty easily around histones, and eukaryotes, supercoiled into chromatin.
In transcription though, there are proteins that come along and effect bends in the DNA or even tight loops, so that the transcription initiation complex (TIC) can be activated by transcription factors (TFs) upstream as the DNA flops over.
see this happening in this video at about :40:
http://www.youtube.com/watch?v=5MfSYnItYvg&feature=related
I think in some cases there might be other proteins bound upstream of the TIC to make the influence of various TFs greater.   I know in highly regulated genes (such as developmental genes in animals) transcription regulation can be impossibly complicated with lots if internal logic.  The classic example is ENDO16 from sea urchin (see second image) which has scores of protein binding sites in front of it.
I was told that DNA binding proteins find their binding sites at a rate faster than diffusion.  The prof told me that she thought that there might be a tendency to diffuse along the length of the DNA because of its charge.  I have no reference for this, but it might help answer your question as to how the NRs pair up so quickly.

What a funny coincidence, I once sent that video (rather, the "advanced" one) round my course colleagues when we had biochem XD Thanks for the info and references about DNA! It's unfortunate that the most important part (your last paragraph) was only word of mouth though, because that's actually what I'm wondering :/


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If a non-mammal is starved of oxygen for some time, how long would it take the animal's neurons to die?
This is a follow-up question to Why do neurons die so quickly (relative to other cells) when deprived of oxygen?.
I'm particularly interested in the case of reptiles, octopuses, and other invertebrates. Could it be that mammalian neurons are especially oxygen-demanding compared with the neurons of other animals?

I believe, it mostly depends on external parameters rather then organism type. The humans could revive after up to 72 hours of clinical death with specific treatment, while under normal conditions irreversible damage occurs after 5-10 minutes. Some frogs, for example, can survive being frozen for several months.

Medically, recovery of brain function after 3 minutes of oxygen deprivation at body temperature is rare.
Further down here in 1 it indicates that at lower temperatures the time can be much longer.  At 13C, the record is 80 minutes for people.  Animals cooled to 0C have a record of recovery of three hours!  Not sure how much like themselves they feel after that though...


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Is the "Great Pacific Garbage Patch" beneficial for marine wildlife?
A study was just released by researchers at Scripps Institute of Oceanography revealing a drastic increase in the amount of plastic adrift in the Pacific Ocean. According to the paper, the amount of plastic in the North Pacific Subtropical Convergence Zone has increased 100-fold over the last 40 years.
But most of the news stories coming out about this discovery are thin on facts about the dangers of plastic. And the research even suggests marine wildlife may be benefiting from the artificial flotsam.
Clearly this increase in trash can't be good. Can it?

There are very few things in the world that aren't beneficial to some lifeform.  Even if you were to, say, spill a mixture of persistent broad-spectrum poisons on an area that killed off 99.9% of all species there, the remaining 0.1% that did survive would benefit from the lack of competition.
The "great garbage patch" is hardly so extreme a phenomenon, but similar effects can be seen there: some species suffer, others benefit.  In that sense, it's no different from any other changing habitat.
From a conservation viewpoint, there are two issues here that one might find worrying:

First, novel, extreme or rapidly changing habitats tend to have lower than average biodiversity, at least initially: the few species that thrive in the new environment tend to proliferate at the expense of others, forming a relatively simple (and often not very stable) food web.  Of course, over evolutionary timescales we'd expect the surviving species to adapt and diversify and the ecosystem to settle into a more stable state, but that tends to take a long time compared to the human timescale on which such novel habitats are created.
Also, the effects of the "garbage patch", or ecological changes in general, are not limited to the directly changed area.  Creating a new habitat in one part of the ocean is one thing; disrupting the ecosystem of the entire ocean is something else, as doing so leaves no unaffected refuge for the species that are harmed.
For example, fish, birds and marine mammals passing even just occasionally through the patch might end up swallowing plastic and accumulating it in their gut; meanwhile, even for less motile organisms, the patch might act as a population sink, depleting their population density in nearby areas.  And if some organisms, such as the sea skaters mentioned in the article you cite, thrive in the patch, the increased population will likely spill into other areas, potentially harming their competitors or prey species.

As for why the news are focusing on the beneficial effects of the garbage to the sea skaters, well, that's what the study that prompted this current batch of news stories was about.  It's also seen as newsworthy precisely because it seems so unexpected: we've all heard stories of plastic flotsam harming wildlife, so finding out that some species are actually benefiting from it has some "man bites dog" style news value.
Also, it's a lot easier and more convincing to observe something that is there than something that isn't: we can directly see these insects laying their eggs on the bits of plastic, giving direct and incontrovertible proof of a causal connection.  Meanwhile, simply observing that some species used to be more common in the area of the patch than it is now is a lot less direct and informative: we might never be sure just how the patch is harming that species, and it always leaves skeptics an opening to claim that the decline might be caused by other factors.  With the sea skates, on the other hand, we're not just observing the effect, but the direct mechanism as well.

References? especially for the effects of habitat on biodiversity?

@David: I'll see if I can dig up some.


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How similar are Circulating Tumor Cells and Cancer Stem Cells?
Circulating Tumor Cells (CTCs) are linked with metastasis and their presence can be used to indicate the onset of metastatic cancer. Likewise, the Cancer Stem Cell (CSC) hypothesis suggests that tumorigenic stem cells are the source of cancer. However, microscopy experiments and cytometry have suggested that the morphology of CTCs and CSCs are quite different. Essentially, we have not been able to find Circulating Cancer Stem Cells (asides Myeloma since they are circulating anyways).
My question is how similar are these cells? If they are different, is relapse caused by the CSCs from the primary tumor or CTCs in metasises that have become CSC-like?

There are several competing models of metastasis, and this question does go right to the differences between them.
The primary thing to remember about CSCs is that all evidence suggests that they are a tiny, tiny subset of tumor cells.
CTCs, meanwhile, consist of whichever cells manage to acquire the right combination of motility, invasiveness, and resistance to anoikis (apoptosis caused by lack of attachment to neighboring cells or extracellular matrix).
So, one possible explanation is that CTCs are drawn from the whole population of tumor cells, and that CSCs therefore make up a very small, nigh-undetectable subset of CTCs-- but that this is the subset that ends up founding the distant metastases while the rest of the CTCs get cleaned up by the immune system or lie dormant in the target tissue. You could call this the stochastic model: CSCs form some small, randomly determined fraction of the CTCs, but they preferentially survive and found secondary tumors.
Another model posits that the cells undergo substantial changes in phenotype driven by responses to their microenvironment. CSCs, like normal stem cells, presumably require a pretty specific niche to maintain their stemness. CTCs, meanwhile, acquire their invasiveness and anoikis-resistance in response to conditions in the tumor, such as hypoxia. So, another possiblity is that, in response to stimulus from the microenvironment, a cell with the potential to be a CSC undergoes some phenotypic changes and becomes a CTC. It circulates for a while, finds a target tissue, extravasates, invades the target microenvironment, then starts re-setting up the microenvironmental niche to re-establish its stem-like properties. Call this the dynamic hypothesis: it's a single potential CSC the whole time, but it looks like a CTC while it's circulating and like a CSC only in its niche.

Actually people have been able to isolate circulating tumour cells that show the phenotypic hallmark of a CTC - the ability to give rise to an entire tumour and successfully implant in serial transplantation / dilution assays.
See http://gut.bmj.com/content/early/2016/07/25/gutjnl-2016-311447.full
There is also some elegant work in mice showing that you can trace metastatic populations derived from clusters of polyclonal cancer cells in circulation and through to eventual metastasis, showing that circulating tumour cells with stemness certainly exist at least in model organisms.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763783/


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Protein construct design
I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying start/end sites have ended up being aggregated in E coli (while the full length protein expresses reasonably well). My question is what considerations one should use to determine start/end sites to maximize chances of getting soluble, purifiable protein. The criterion I used were:

Preferably loop region in known x-ray structure
Use hydrophobicity plots to minimize hydrophobic residues at both termini
3-4 residue linker between protein and affinity tag (GST/6xHis)

From personal experience with an earlier construct, this can turn out to be an idiosyncratic exercise but I was wondering if I was missing any crucial parameters.
EDIT: I also played around with the PDB file of the non-truncated protein to check whether huge hydrophobic patches were exposed on deletion of the domain(s), and I didn't find any such patches that could potentially be exposed and lead to aggregation

Did you identify structural domains in the protein using Pfam or some other domain detecting peptide search?
It's pretty useful to cut your constructs at the boundaries of structurally independent domins in the protein if you know where they are.  Hydrophobicity plots might lead you to cut right in the middle of a protein fold, only exascerbating inclusion body formation/protein precipitation.

I used the x-ray structure to determine known loop regions that connect structured domain regions (pt #1)

I see - if this is a series of independent folding domains like SRC, what you have done makes sense.  In this case what you call 'loops' would be more like linker peptides.  In this case, sometimes things that look independent actually are not.  Its also possible to get precipitated protein for more conventional reason - problems with heterologous expression or codon choice when moving from human to e coli for instance.  its hard to be more specific without details.  does seem as if you made a reasonable effort.


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determining genome-wide exogenous binding of pathogens to host genome?
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice genome to the advantage of the pathogen.
It's an interesting concept but left me wondering how one would determine de novo the binding of these pathogen effectors into the host if one didn't know them. What would be the steps to determine where are the pathogen's TFs binding the host genome?
Edit: there is the possibility of not knowing which proteins bind to the host genome, so what would be the way of developing the antibodies in this case?
Reference:

 Li T, Liu B, Spalding MH, Weeks DP, Yang B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology 30: 390–2.

The techniques used to do this are ChIP-seq and ChIP-chip.
Basically, you

let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to their original location on the genome.

Wikipedia has a nice picture explaining this process in a little more detail:

A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix).
Now that the specificities have been determined, identifying TAL effector target sites is simply a matter of measuring the probability of that TAL effector's RVD sequence aligning to a novel sequence. Some applications are described here and here.
The TALENT 2.0 server (invited paper under review) provides tools for designing custom TAL effectors to target specific DNA sequences, or for identifying potential off-target binding sites in a given sequence or genome.
References:

 Moscou MJ, Bogdanove AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science (New York, NY) 326: 1501.
 Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757–61.
 Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research 39: e82.


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Do gene expression levels necessarily correspond to levels of protein activation?
I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid?
My problem with the assumption that RNA levels correlate with that of the active product (i.e. the protein) is that a lot of post translational regulation occurs, including co-factor binding and phosphorylation, to name but 2. Does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and active protein?
It makes sense to me that RNA would correlate with protein certainly, but whether this relates to the proteins active function is what I wonder - i.e. there could be a pool that is replenished as and when the protein levels drop, but the proteins are only actually active for short periods in response to specific stimuli. So, does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and active protein?

Update (04.07.12)
I have not accepted any answers as yet because none address my question about levels of protein activation, but I concede to Daniel's excellent point that proteins are not all activated in the same way; some are constantly active, some require phosphorylation (multiple sites?), some binding partners... etc! So a study looking at 'global' activation is not yet possible. Yet I was hoping that someone may have read some specific examples.
I today found an unpublished review by Nancy Kendrick of 10 studies that have looked at the correlation between mRNA and protein abundance - still not relating to activation. However she finishes the paper as follows;

The conclusion from the ten examples listed above seems inescapable:  mRNA levels cannot be
  used as surrogates for corresponding protein levels without verification.

If this is her conclusion about protein levels, then any correlation between protein activation and mRNA abundance seems unlikely (as a rule. Some protein levels do correlate with the RNA - see the paper).
I am still interested in any answers that give any information about specific examples of protein activation and mRNA levels - it seems highly unlikely there are no such studies, but I have been as yet unable to find any!

Good point: also you can imagine that if some mutation results in (for example) protein X being ubiquitylated you'd be likely to see an increase in the RNA that codes for X while the level of X drops. In this case the RNA would make a pretty lousy proxy.

To be frank, if you can't find a correlation between mRNA and protein abundance, why would you bother to ran the next experiment to find correlations between mRNA and protein activation?

@bobthejoe it does seem like it would be a fruitless experiment - doesn't mean no one has looked though (in fact I am surprised there isn't more literature on it). If no one else has found any then I will either accept one of the answers already given or post my own combining the evidence against any correlation.

@LukeTheDuke, I'm cautiously excited about your hypothesis.

A more recent review paper about this topic: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654667/pdf/nihms395043.pdf

It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. This paper on yeast and this paper on cancer both establish this, although using older techniques (SAGE and microarrays, respectively), while this more recent review discusses the topic in light of more recent technologies (e.g. RNA-seq).
Perhaps the difficulty with exploring the correlation between mRNA levels and levels of active, mature proteins is that we still know so little about so many proteins and and what makes them active and mature versus inactive, premature, etc. Not all proteins need post-translational modifications to be active, but some do. Currently, this is investigated on a very detailed protein-by-protein basis (as far as I know), so gathering enough data for a large-scale study could take a long time. On the other hand, there are a variety of (increasingly affordable) high-throughput methods for measuring the abundance of thousands of RNA species simultaneously. I think people are using mRNA levels to estimate expression not because it's the most biologically cogent course of action, but rather because it is much easier, more affordable, and more high-throughput (which is all the rage these days).

It's interesting that the RNA doesn't even correlate well with protein abundance it that example, let alone activation state. I agree that the reason RNA is measured is for the comparative ease with which its abundance is quantified, however my issue is with the conclusions drawn in many papers based on the assumptions that RNA levels are at least indicative of protein abundance/activation! Thanks for the links and your reply

@Daniel: +1 for ending it at "..high throughput (which is all the rage these days)"!

Sometimes, overproduction of mRNA is a response to low concentrations of the expressed protein. Great answer.

I think that overproduction of mRNA in response to low protein is potentially what studies are looking for, as it implies the protein is in demand at that time (compared to a protein that does not need replenishing). This is of course confounded by that fact that proteins will have different lifespans! Thanks for your answer, I am hoping for more answers that might address the link between mRNA and protein activation, if there is any at all. If there isn't, then I fear that many studies may be reporting false claims!

I think you'll find very few papers that demonstrate changes in mRNA levels by microarray, claim that an increase in the gene product's activity is responsible for the biological effect, and then stop. mRNA data is complicated, not useless. Almost anywhere that mRNA upregulation is reported, it will be followed by a measurement of the protein levels and other follow-on experiments to confirm the protein's involvement.

This study in E.coli is useful in setting out some additional issues at play here, in a system where post-translational modifications are basically a non-issue.  The authors see clearly a correlation between mRNA and Protein levels (Fig. 3C) and theorize that differences translation rate and protein turnover are responsible for differences in protein level for two genes with similar mRNA level.
They investigate the issue on a single-cell level and find no correlation between a single cell's mRNA level and protein level for a given gene (Fig. 4).  This is attributed to the time-scale separation between mRNA turnover (usually a few minutes) and protein turnover (in many cases degradation is so slow, protein turnover is driven by dilution/cell division).  One way to understand this is there are several "generations" of mRNA contributing to a the population of protein at a given moment, which is not inconsistent with the central dogma.  However this result raises serious problems for using mRNA as a proxy for protein in comparing single-cells.
However generally, in populations of bacteria, using mRNA as a proxy for protein works pretty well, especially when comparing levels of a gene under perturbations.  Unless we believe translation or protein degradation is affected mRNA level should be a good proxy, though there can be issues with using this quantitatively because regulation is often not linear (i.e. double mRNA doesn't produce double protein).  See, for example, sRNA regulation.

Thanks for the answer, and link to the study. It makes sense that mRNA and protein levels correlate to some degree, for the reasons you mention there will never be complete concordance. I am interested to know of any studies that have looked into whether mRNA levels are at least indicative of protein activation - I am particularly interested with regard to the relevance to humans. Many thanks.


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Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?
There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it could be interpreted.
While this agrees with my understanding of the subject, I wonder whether there could be any use to perform full sequence of one's genome for means of personal health care?
The only effect I recall which affects individual's health and could not be caught by SNP genotyping is DNA methylation, but complete sequencing procedure does not detect it either, as far as I know.

Our group does Whole Exome Sequencing. While not as exhaustive as whole genome sequencing, it does offer more coverage than SNP genotyping and can provide more useful data.

Not my field, but I guess most DNA methylation and other epigenetic modifications would be organ specific. I wonder if a buccal swab could give useful information in this context.

If that were true, why do scientific projects bother with sequencing then? It’s way more expensive, and in general most labs don’t have money to waste.

Sequencing gives the researcher data on rare or private mutations that are not on the genotyping arrays.

This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient.
In terms of health risks based on SNP genotypes, the data are far from complete. Sure, some level of risk can be assigned to a variant (SNP), say at certain markers within the FTO gene and risk of obesity. However, the complete list of risk alleles for this and numerous other complex traits is not fully described. Furthermore, the impact of environmental factors (EF), or lifestyle choices, on those genetic variants is only beginning to gain wider attention. For example, a risk allele may not show itself as risk until the EF, such as amount of physical activity or percent energy from dietary polyunsaturated fat, passes a certain threshold. Such gene-environment interactions are thought to contribute to the variance in traits (phenotypes), but to what degree is not known.
Added in edit 15 May 2012: Epistasis, or gene-gene interactions, also are important but far from being cataloged for humans. A situation could arise where one allele elevates risk for a certain condition, but compensatory alleles elsewhere in the genome decrease that risk. We don't know the full extent of epistasis in humans.
Thus, in terms of personal healthcare outside of something like cancer and monogenetic disorders, there may be little that is gained from genotyping or complete genome sequencing, little that is compared to other advice you already know. I carry risk alleles for certain conditions, but there is not really any advice one can give me that is specific for those alleles that I have, where that advice is different than or goes beyond general advice health care providers already have dispensed.

Genotyping only tests for SNPs in predetermined locations. If you have SNPs in other places in your genome, genotyping won't tell you that, but whole genome sequencing will (by comparing your genome to a reference genome available at NCBI). Also, there are other variants such as copy number variations, repeats, insertions and deletions that genotyping can not capture, but all of those can contribute to disease.

Genotyping can tell you more information than just SNP, for instance you could easily amplify a region of a gene for sequencing to determine if there are more serious errors.


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How to DIY preserve pet DNA today so that it can be used in 20 years
I know that there are companies that offer a kit+storage of your pet DNA for around $2k.
My question is if there is any other option for doing this yourself with a thought in mind that in 20+ years the technology will get so advanced that even this DIY sample can be utilized.
Any ideas? Maybe drying a blood drop or mixing blood with alcohol/acetone?
Also, I read somewhere that it is better if the pet is still very young, because if you take old pet DNA the clone will exhibit mature signs even as a youngster. Is this true? If yes then what is the top age that is safe?

Make it have babies?

If DNA is all you want, there are pretty easy extraction methods that you can do at home. You would then have to freeze it in a conventional home freezer. I can't guarantee that the DNA would not degrade after 20 years. In fact, I don't even know how stable DNA extracted in the lab is stable for.

Freezing sounds kinda primitive.

You asked for DIY methods. Surely that means you are looking for as "primitive" methods as possible?

Heard a news story a couple of days ago about a couple who had their dog cloned after it died. @leonardo Amy had some brief suggestions.  Also your last paragraph might be better posed as a seperate quesiton.

@RegisteredUser Hmm. How else would you store DNA? Dehydration? As far as I know, freezing (at very low temperature, way below home appliance freezers) is what’s done in “professional” labs.

I can't consider freezing as a long term option. What will happen if I get a power outage or will have to move apartment...

Well it is DNA and it is stable at 37°C, (and warmer) otherwise we wouldn't exist. Freezing is meant to slow chemical reactions resulting from any DNAase contamination.

@leonardo DNA requires constant maintenance to remain 'stable' in your cells at 37 degrees, although DNA can be found in fossil remains, so a synthetic version of this may be theoretically possible. Typically we store extracted samples at -80 degrees celcius, which you're unlikely to be able to achieve at home, unless you invest in a specialist freezer - this is unlikely to be cheaper than the company the OP refers to. And RegisteredUser, I'm afraid that freezing is the only long-term option that I'm aware of! Certainly when you're considering 20 years

Freezing in TE buffer might also help (10 mM Tris pH 8, 1mM EDTA). If you have a biologist friend, I'm sure you can get him or her to let you "borrow" some.

Any idea if this work for blood as well? http://www.ncbi.nlm.nih.gov/pubmed/10620236

preserving DNA for cloning is entirely a different issue than just any old DNA - making sure all the chromosomes are there and intact and useful for injection for in vitro insertion makes this a difficult question...

For the impatient, I'm going to say that probably if you only have a regular home freezer, its unlikely that you will be able to do this. If you have access to a -80C or liquid nitrogen storage its possible, but also less likely.
Cloning an animal typically starts with the transplantation of a nucleus into an egg cell whose nucleus has been removed.  So unless things change drastically in the next 20 years, just purifying DNA and keeping it in a tube of the fridge is not enough - you need to preserve epithelial (skin cells) or some other tissue in a state which can be revived to produce a live and intact cell when you want to do the cloning.
Its possible that we will have machines that can take DNA from a DNA prep and produce a living cell - this is what we hope to do with the mammoth and other extinct animals from fossil tissue some day.  But whether that will be the case in 20 years is just a guess, whether it is affordable is also just a guess.
So from what we know now, you will need to preserve a piece of tissue from the animal when it is alive.  I'm not an expert on how to do this, but you might be able to get the skin cells to sort of turn into a cell line and then freeze them for not too much money.
If you do this, regular freezers are not cold enough to prevent freezer burn.  This is what happens when you put a steak in to the freezer, wrapped in plastic even it will shrivel up and start to dry out as the water in the ice starts to sublime out of the package (the dry air in the freezer basically sucks the water out of the food).  If this happens to your animal tissue, its probably not going to revive.
Scientific labs use -80C freezers and liquid nitrogen storage because the water turns into a glass and all biochemical reactions are basically stopped. (besides drying out, the enzymes like DNAse are still nominally functioning in the cells at -20C and even simple bacterial cells don't live for more than a year at -20C, much less mammalian cells).  For preserving cell lines, liquid nitrogen is much more preferred.  I would say that properly produced cell lines can theoretically revive after indefinite liquid nitrogen storage.
So that's a quick answer.  Sorry to be a party pooper - things could change quite a bit in the next 20 years, but we just don't know how much.  popping a paw in a baggie or some DNA extract into the freezer might work, but its hard to say for sure.
As far as the choice of where the DNA comes from in the animal, its true that skin cell lines are often producing imperfect animals - the DNA may be modified in the skin in various ways that cause the animal to be smaller, weaker, or even deformed compared to the donor.  At this time all the protocols I see (and i could be wrong) are skin cells.  I would expect that there is a better tissue to preserve, but that might be just a guess at this point.  Its likely that in the next 20 years the choice of cell line from the donor will change quite a bit as well.

I don't have a -80C freezer and was hoping for some type of room temp preservation, but thanks anyway.

sorry I couldn't be more positive.  we still have a ways to go before we are like "Bladerunner".  i'm trying to help a biohacker lab get started and the cost of -80C refrigeration is a stumbling block to citizen bioscience.

Well if you are optimistic, which isn't outrageous, you could store some skin tissue taken from the pet.  flash freeze in liquid N2, then seal it in a solid piece of plastic (keeping cold) and pop it in the freezer.  Might work... store in the ice cube tray so that defrost cycles in the fridge don't heat the sample up.

Its possible that we will have machines that can take DNA from a DNA prep and produce a living cell... well, we can do that for bacteria!

If you believe that all you would need is a DNA sample, then I suggest that you store a decent amount of hair in a -20 freezer and hoe for the best. The reason I recommend hair is that it has previously been used to obtain the genome of an 4500year old human. If left at room temperature hair may still produce a genome but probaly only for a couple of hundred years with the current sequencing technology.

To clone something you need a living cell, not just DNA. Although DNA could someday be used to make a clone, it would require technology that is a long way off. You can store DNA indefinitely by extracting it from a cell and storing it in alcohol.
To preserve a live cell indefinitely requires very cold temperature, below -50F, otherwise the cell will deteriorate in various ways. Normal freezing temperatures will damage the cell due to the way water crystallizes at near freezing temperatures. If a cell is fully dessicated somehow without damaging it, then possibly it could be preserved in alcohol at room temperature, but it would be hard to dessicate the cell without damaging it.
You can, of course, experiment to try to do it. Get some cells, and first learn how to grow them so they reproduce. Once you can do that, try freeze drying them with different solvents. Once the cell is dried, store it in alcohol, then try to revive the cell by re-hydrating it. If you can cause the cell to divide again after re-hydration then, congratulations!, you have figured out how to preserve a live cell indefinitely at room temperature and can potentially publish a paper about it. Obviously, this would require many weeks of devoted effort to accomplish.

This is an old Q/A; an answer discussing cryopreservation techniques is missing and would improve it if you want something to work on here.


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What is the effective relatedness of inbreeding?
If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?

The easiest and most simplistic way to look at it is to assume that the amount of genetic material halves each generation.  On average, humans are about 0.1% to 0.15% different from each other, so in order to get that you'd need around $1/2^{10}=0.0976\%$ and $1/2^9=0.1953\%$. The exponent numbers $2^9$ and $2^{10}$ are 512 and 1024, respectively.
Armatus' Dawkins bit is almost word-for-word what he actually said:

By the time we get to third cousins, "we are getting down near the baseline probability that a particular gene possessed by A will be shared by any random individual taken from the population".

Dawkins was ball-parking that a bit, although he was really talking only about a specific gene.  The inbreeding coefficient is properly defined as:

The probability that an individual carries two identical-by-descent alleles at a locus.

Which takes care of some of the fudging.  With that in mind, though, within eight generations the odds are less than even you even share any genetic material with an ancestor/offspring. That's actually a mathematical analysis (with plenty of assumptions!) from the mid-80s but it's an interesting read: you can look up values for certain relations going back a bit.  The answer will vary depending on the background "average" you care about.  Europeans, for example, are particularly closely related.
Indeed, "[g]enetic variation is geographically structured, as expected from the partial isolation of human populations during much of their history."  If you want a perhaps easier-to-read explanation of some of the math, I would suggest this 2006 review, in particular box 2.  From that, a silly back-of-the-envelope calculation from 0.1% related gives a path of around 10 individuals, which is a little more distant than your third cousin.

In "The Selfish Gene" Dawkins claims a relatedness factor of 1/128 to be pretty much the same as the baseline chance for the rest of the population to have the same gene, so that would be a third cousin. (Or your great great great great great grandparents, though an incestuous relationship with them is quite unlikely I think.)
I'm not sure where he got that from though.


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How long is DNA stable in a freezer?
Inspired by the post about extracting pet DNA, how long would genomic DNA be stable for in a -20°C freezer? It is common practice to store DNA (double-stranded, plasmid) in a -20°C freezer in the lab, but would genomic DNA last longer in a -80°C freezer? With either method, how long would it be stable for?

It depends on your concentration. More concentrated DNA is more stable.

Closely related to this question - if not dupe?

If the DNA is pure, it should last quite a long time.  If there are enzymes and other biological molecules in there, -80C will work much better.
I think you could keep pure DNA at -20C practically indefinitely.
Purity is the main issue there, also pH stabilized, sealed properly, etc.  That makes all the difference.

I would say that even at 4°C the stability is fairly high

I usually keep plasmid minipreps at 4C for months its true.  I think the difference is if the ends of the DNA are sheared or ragged, as in a typical gDNA prep, then it might not be so great to leave it unfrozen.

You can store your DNA for 1 week at -4C and for one month at -20C but with storing DNA over these period of time there is a deduction of 10-15% of yield from your DNA sample.

Can you provide a citation for this? I am skeptical, because I routinely transfect cells using DNA stocks frozen years ago.