genetics - What does phasing mean?

This refers to haplotype phase (aka gametic phase). This essentially means knowing which allele belongs to which copy of the chromosome, or alternatively, which alleles appear together on the same chromosome.

In short-read sequencing, for example, it is difficult to resolve the haplotype of two heterozygous SNPs if they have not been covered by the same read. If you observe A/a and B/b, you do not know whether you have AB + ab or aB + Ab. So you would say you do not know the phasing.

See the Wikipedia links for more information.

neuroscience - Systems identification in small neural network

For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically.

While it is true that whole organism optical recording is technically possible in C. elegans, I'm not aware of any published work where all neurons were identified and recorded from simultaneously and then combined with connectivity data in a systematic way.

I should note, that this isn't limited to C. elegans. Florian Engert's lab has published whole-organism recordings from zebrafish as well. At the moment, though, there are still technical challenges to work out before we get the input-output relationships you desire on a whole organism level. First off, the recordings aren't truly simultaneous, in the sense that it still takes time to build up 3D images from z-stacks. Second, the image processing to label neurons is not yet robust. And finally, the most popular optical indicators are based on calcium levels and thus provide only a proxy for membrane potential and furthermore they have limitations in time resolution, range and accuracy.

The field, however, is progressing rapidly and I suspect that these challenges will be overcome in the next few years.

What are the best databases to ask such questions?

There are no database yet for C. elegans neural activity, likely because the number of groups publishing optical recordings in C. elegans is still fairly small. But as more labs pick up the technique, I think the value of a database will become more obvious to the community and the OpenWorm project is providing some well-needed leadership in this area.

Finally, I should point out that in the end we may find that neural activity and connectivity provide only one part of the story. It is likely that in C. elegans neuromodulators and other "unwired" connections between neurons could play very important roles as well.

senescence - Do crocodiles age?

Well, this needs to be broken down into two parts. Do Crocodilians age (undergo senescence), and are Crocodilians immortal (will only die of external causes)?

Are Crocodilians immortal?
- No. They appear to live about as long as humans before they die.

Measuring crocodile age is unreliable, although several techniques are used to derive a reasonable guess. The most common method is to measure lamellar growth rings in bones and teeth—each ring corresponds to a change in growth rate which typically occurs once a year between dry and wet seasons. Bearing these inaccuracies in mind, the oldest crocodilians appear to be the largest species. C. porosus is estimated to live around 70 years on average, with limited evidence of some individuals exceeding 100 years. One of the oldest crocodiles recorded died in a zoo in Russia. A male freshwater crocodile at the Australia Zoo is estimated to be 130 years old. He was rescued from the wild by Bob Irwin and Steve Irwin after being shot twice by hunters. As a result of the shootings, this crocodile (known affectionately as "Mr. Freshy") has lost his right eye.

Do Crocodilians undergo senescence (show signs of aging)? Well, if this study from "Gerontology" written by Patnaik BK in 1994 is to believed... Maybe not.

Evidences and mechanisms of rapid or negligible senescence in reptiles are still fragmentary and unclear... neither the increase in mortality rate and accumulation of lipofuscin nor the reproductive senility have been shown conclusively in ageing reptile populations.

So, while Crocodiles and Alligators (both Crocodilians) definitely have a finite lifespan, because they just continue to grow it's hard to tell how long they have left until the day they die.

biochemistry - Can jellyfish improve Black Sea environment?

According to this study, cited by many popular science magazines, jellyfish and other, smaller animals can contribute to the vertical ocean stir as much as currents do.

Black Sea chemistry and biodiversity is highly coupled with the lack of vertical currents, present in oceans or bigger seas. (Some ) effects are limited salinity in the top layers - and many ocean fish species cannot live in black sea - and limited space for life (under 50 meters there is no oxygen)

Can the jellyfish population (which is exploding now) change the stratification of water layers enough that the highly saline waters from bottom go up, and oxygen goes down, allowing a completely new ecosystem here?

If yes, what are the outcomes of such prospects? Besides the potentially catastrophic release of hydrogen sulphide form the bottom, can it be an improvement for the biodiversity here?

zoology - Why would the Camargue horses have a white coat while the foal have a dark coat?

Our own hair will also turn gray (indeed, yours seems to be on its way, if you don't mind me saying so) but there need not be an advantage to that; if it doesn't affect our ability to have successful children it probably doesn't matter much to evolution or selection. When it comes to animals that interact with humans, though, many traits are selected for, even those without an advantage, in fact often we select for disadvantageous traits (if they were advantageous, we might not need to select for them in the first place).

As this 2008 paper from Nature Genetics goes into, the "graying with age [phenotype] is an autosomal dominant trait" overwhelmingly caused by "a 4.6-kb duplication in intron 6 of STX17 (syntaxin-17) that constitutes a cis-acting regulatory mutation". To answer your question, though:

The Gray horse provides a notable example of how humans have cherry-picked mutations with favorable phenotypic effects in domestic animals... The prestige of riding a white horse has thus led to selection of the Gray-causing mutation by humans; this mutation is by far the most common cause of white color in horse.

This phenotype is actually often detrimental, as white/gray horses can have eye problems and higher rates of skin cancer; Camargue's are particularly susceptible to melanomas, present in around 70% of horses by age 15. There does seem to be some benefit, though, as the second paper I linked suggests these horses are subject to fewer fly attacks.

EDIT: I seem to have been unclear and you seem to have misunderstood my answer. Let me break it down:

That is an example of why something negative or pointless might persist, as would a dominant inheritance pattern that is fixed in a population: negative traits that are only weakly deleterious have a non-negligible chance of fixation. Asking what the advantage is is somewhat of a moot question because every single Camargue horse has the trait; asking what caused a seemingly-negative phenotype to become fixed is a good question, but likely an unanswerable one as it occurred long ago.

As a side note, how long a breed has been in an area does not simply imply breed purity. Here's a quote from the International Museum of the Horse:

Through the centuries many armies have passed by the Camargue, including the Greeks, Romans and Arabs. The horses brought with these armies influenced the Camargue over time. It has even been suggested that the Camargue has had some influence on the early breeds in Spain as armies took them back home.

mammals - How compatible are mammalian digestive systems?

I think this would depend entirely on the diet of the host and donor mammal.

Assuming they are of similar size and diet, I don't see any reason why this wouldn't work. The gut tends to absorb more or less everything in the food.

If the diet of the two mammals differed significantly, I could see some problems with eating the correct foods. Herbivores with the significantly shorter carnivore gut would have trouble killing and eating things without carnivore teeth/claws/what have you, and the plants would not provide enough nutrition on their own. Rabbits, for instance, have a two-pass digestive system, so in order to use a rabbit gut the mammal would have to eat their own feces regularly. (Rabbits have digestive bacteria in their colon, but grass has to travel to the colon and then back 'upstream' to the absorptive part of the gut. So this is achieved by going around again.)

biochemistry - Chemical structure prediction

I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure with optimal geometry of random small chemicals (say 30 atoms)? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a command line UNIX program which computes mols from formulas.

---

Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction.
http://www.mti.univ-paris-diderot.fr/fr/downloads.html

skin - Why Do Healing Wounds Feel Warmer To The Touch?

I fell over on my bicycle trying to avoid running over a rattlesnake, and ended up badly skinning my knee. It immediately began to bleed, but soon clotted.

It has been 2 days now and it has formed a thin scab and is healing well as far as I can tell. I was chilly from the air conditioning, and I noticed the wounded knee was much warmer than the healthy knee. It was very warm, while the other was rather cold to the touch.

I read here about skin healing, and thought, maybe it is because the blood rushed there to clot the wound. But, the wound is already clotted and sealed and the worst is over. So my question is:

• Why is my wound and the area around it so much warmer days after the injury?

structural biology - Isotropy of sarcomere bands in skeletal muscle cells

As seen under a polarization microscope, the A-Band in skeletal muscle fibres is so named because it is anisotropic in its refractive index which is a characteristic of orderly crystalline structure. On the other hand, the I-Band is so named because of its isotropic nature, as far as its refractive index is considered, which is characteristic of Amorphous substances or substances which lack long-range order. Both are filamentous (as opposed to globular) in the sarcomere (Actin is present as F-Actin).

But then why this difference in the characteristics of refractive index,
which is indicative of order (i.e crystalline or amorphous?) in their
molecular structure?

Moreover, is the H-Band anisotropic?

If not, then the anisotropy of the remaining part of A-Band must be a consequence of the relative arrangement of Actin and Myosin which are independently isotropic, and hence cannot give a possible isotropic arrangement.

If yes, then that indicates that the myosin filaments are anisotropic in themselves and actin filaments are isotropic. But, in the region of their overlapping (A-Band minus H-Band), the overlap is between an anisotropic (myosin) and an isotropic (actin) component which shouldn't be anisotropic because the randomness of actin filaments (i.e. its isotropicity) should make the entire configuration isotropic?

I am sorry if I am wrong in my understanding of isotropic and anisotropic characteristics, or if my question sounds too "physics-related", but this has been bothering me for quite some while now.

Here is a directly related question I asked on physics.se. It partly solves the problem of possible arrangement of isotropic elements to generate anisotropy.

biochemistry - How to prevent protein precipitation?

Alas, the great problems with protein formulation. I assume that the labeling chemistry forces you to use the 8.5 pH. (I don't think this is necessarily true since succinimidyl chemistry does work at pH=7.2 and the NHS ester is fairly unstable above pH=8.6)

We usually tackle this problem entirely by brute force ie. testing multiple buffer condition with different bases and different salt concentrations. First attempt would be to try out all of the Good's Buffers notablely HEPES, TRIS, MOPS, Tricine, Maybe you should look at both zwitterionic buffers and non-zwitterionic buffers. In your case, the succinimidyl is vunerable to primary amines so avoid things like Tris/Glycine.

The second thing to test would be various salt concentrations. Since you're already dumping in Sodium Bicarb, NaCl should be great. Unfortunately, this is where things get tricky since it is hard to know if your protein precipitates at low salt or high. A test from 20 mM, 50 mM, 100 mM, 150 mM, 200 mM, 500 mM should cover most of the interesting regimes.

Alternatively the sudden change in the ionic environment around your protein may be causing it to precipitate. You probably should dialyze or purified your protein in PBS to allow it to refold appropriately.

human genetics - What is a Mitochondrial Eve and Y-chromosomal Adam

When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men?

Kind of, yes. The concept behind Mitochondrial Eve and Y-Chromosomal Adam has to due with cell replication and basic genetics.

The Mitochondria ("Power Generators" of the cell) are directly inherited from mother to daughter cell. That is, new cells do not start with 0 and are forced to make them de novo. Some Mitochondria are replicated before division and some are 'given' to the daughter cell to start with.

Because of the unique way that Mitochondria are inherited, when it comes to creating new humans it means that only the Mother's Mitochondria are given to any children she gives birth to regardless of the sex of the child. So I, being male, have my Mother's Mitochondria - which the same as my Grandmother's - and the same as my Great-Grandmother's - etc. etc. etc. until you can trace that line back to "Mitochondrial Evel" whose Mitochondria are the origin for all humans on the planet and are inherited Maternally.

In that sense it is an unbroken lineage of genetic information as inherited from mothers, though not exclusive to women.

"Y-Chromosomal Adam" is a similar concept - Women do not have a "Y"-Chromosome, so every Y-Chromosome men have today had to originate from somewhere. It's trickier to do than tracing Mitochondrial DNA because while Mitochondria are inherited exclusively from mother to child, there could have been multiple Fathers to Mitochondrial Eve's children and other similar complications that muck things up.

How is the specific "identity" or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today?

For "Y-Chromosome Adam" it's still more or less in the data-gathering phase as far as I was last aware. It's not as concrete as "Mitochondrial Eve", which has a very solid body of work supporting her.

The "identity" is known because the more in common a person's genes have with the genes of another, the more closely they are related. The researchers took a lot of genes from very divergent populations, and compared them. The researchers were then able to tell which portions were common among all of the Mitochondrial DNA, which had changed the most, and which had changed the least from each other. Using that data, you can construct a rough image of what the originator (or LCA - Last Common Ancestor) had for their own genetic makeup.

You can construe a time period because portions of your DNA (either Mitochondrial or Nuclear) acquire/tolerate mutations at an expected rate - say 1 mutation every 1.5 Million Years. So as long as you have a rough idea of what your LCA's genes looked like (see above), then a modern day sample with 5 mutations is 7.5 M.Y. away from the LCA.

how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?

They didn't when they started testing. That's part of the fun of the project.

The "Out of Africa Hypothesis" rose in prominence partially due to the findings of the research. It basically posits that the ancestors of humans evolved once in Africa, and then spread from Africa to the rest of the world. Because the Mitochondrial Eve research concludes that "Eve" was around before we spread throughout the rest of the world, it implies that every ancestor already had Eve's legacy when they started migrating into Europe, Asia, the Philippines, etc. Thus every human on Earth, no matter where they are today, shares traits with Mitochondrial Eve.

For the Amazonian tribes, they would have inherited it from their ancestors in North America, which were ancestors of tribes in Asia who crossed an ice bridge into North America, and the tribes in Asia came out of Africa.

zoology - How do animals/plants change for each season?

There are various parameters that describe change of seasons such as day length, temperature, humidity. But it can be assumed that most of these parameters ultimately depend on one parameter- day length.

The response of plants towards the length of day/night cycle is called photoperiodism (which dictates spring flowering).

This article explains the effect of a gene called CONSTANS(CO) on spring flowering. CO is post transcriptionally regulated by cryptochromes and phyochromes.

The circadian rhythm in CO mRNA abundance was proposed to represent a photoperiod response rhythm, in which exposure to light coincides with CO expression only under LDs (Long Day) and thereby triggers flowering.

......

We propose that early in the day phyB promotes the degradation of CO whereas in the evening cryptochromes and phyA antagonize this degradation and stabilize CO protein,

However, my knowledge of plant molecular biology is not that great and I would advise that you refer the mentioned article and the cross references cited in that.

human biology - How does the body measure dehydration?

From Wikipedia entry on thirst:

In the mammalian brain, the posterior surface of the hypothalamus
forms the front wall of the third ventricle (a cerebrospinal
fluid-filled cavity) and clusters of cells (osmoreceptors) on this
surface, notably in the organum vasculosum of the lamina terminalis
(OVLT) and subfornical organ (SFO), signal this cellular dehydration
to other parts of the brain, and thirst is experienced. Destruction of
this part of the hypothalamus in humans and other animals results in
partial or total loss of desire to drink even with extremely high salt
concentration in the extracellular fluids.1

The entry on osmoreceptor says in part:

When the osmotic pressure of blood changes (i.e. it is more or less
dilute), water diffusion into and out of the osmoreceptor cells
changes. That is, they expand when the blood plasma is more dilute and
contract with higher concentration.

It also describes how the kidney measures chlorine anion flow through some nephrons, which triggers a cascade of messenger molecules resulting in increased blood levels of the hormone angiotensin, which also results in thirst messages originating in the hypothalamus.

1Derek A. Denton (8 June 2006). The primordial emotions: the dawning of consciousness. Oxford University Press. pp. 118–19. ISBN 978-0-19-920314-7.

2Walter F., PhD. Boron (2005). Medical Physiology: A Cellular And Molecular Approach. Elsevier/Saunders. ISBN 1-4160-2328-3. Page 872

endocrinology - Steroid Hormone Signalling

Note: Since my area of expertise is with peptide hormones, I will offer a partial answer.

Steroid hormones are carried through the circulation by binding to globular proteins. When these hormones are released from binding proteins, the classical route of action is by free diffusion through the cell membrane. This diffusion is due to their aromatic structure. You rightly point out that the classical receptors of these hormones are found in the cytoplasm or nucleus. For example, estrogen signalling as a classic signalling template which has genomic (DNA) and non-genomic (protein) targets to exert its effects.

Non-canonical signalling can occur through at least one G-protein coupled receptor (GPCR). Unlike most GPCR's which are localized to the cell membrane, GPR30 appears to be localized to the endoplasmic reticulum, which means steroid signalling still occurs through canonical means and also this newer pathway.

Then again, there are also steroid effects that modulate ion channels, for example GABA receptors. These are not specific receptors where only a steroid hormone can have an effect, yet they can activate or inhibit the effects (along with other drugs).

microbiology - Where would Saccharomyces cerevisiae be found in highest concentrations in environment?

Here is a link to an interesting article which reports a survey of wild isolates of Saccharomyces cerevisiae in China.

Wang, Qi-Ming, et al. (2012) Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol 21: 5404-5417

A relevant quotation from the article:

In addition to grapes and oak tree (Quercus spp.) bark, S. cerevisiae was successfully iso-lated from a variety of damaged fruit collected in orchards or markets in different provinces of China; from the bark of different deciduous trees; forest soil and rotten wood collected in primeval, original secondary and planted forests located in different regions covering temperate, subtropical and tropical climate zones from northern to southern China. Unexpectedly, the success rate of S. cerevisiae isolation from fruit samples (6.5%) was lower than that from tree bark (16.5%), soil (10.8%) and rotten wood (9.2%) samples. S. cerevisiae was more frequently isolated from forest soil samples (success rate 13.7%) than from orchard soil samples (success rate 9.1%). Among the fruits giving positive S. cerevisiae isolation, grape samples showed the lowest success rate.

Table S2 in the supplemental information records isolates as follows:

climatic zone    sites   isolates
__________________________________
tropical           5       20
subtropical        2       14
temperate          13      51

Superficially, from this it looks as if there would probably be little difference between New York state (humid, continental) and Florida (humid, subtropical).

gene regulation - How does the enzyme Dicer function in the RISC complex?

Dicer is an endo-ribonuclease belonging to the RNAse-III class. Dicer is not a part of the RISC. It however helps in the formation of RISC by cleaving dsRNA or the stem of hairpin RNA on two ends which liberates a small dsRNA product. Then one of the strands is loaded into the RISC.

There are several reviews on this topic and there is a video as well which you can find on youtube.

human biology - When was the purpose of bone marrow discovered?

I'm currently reading William Cheselden's book Osteographia or The Anatomy of the Bones, which was published in 1733 (for the pretty pictures, naturally; not up to date anatomy). When he addresses the topic of bone marrow, he says,

Every cylindrical bone has a large middle cavity, which contains an oily marrow, and a great number of lesser cells towards their extremities, which contain a bloody marrow. [...] The bloody marrow is also found in all spongy cells of the bones. [...] The use of the first kind of marrow I imagine is to soften, and render less brittle, the harder fibres of bones near which it is seated; and that the other marrow is of the same use to the less compact fibres, which the more oily marrow might have made to soft; and that for this reason, there is less of the oily marrow, and more of the bloody in young bones than in old ones.

Which strikes me as completely incorrect -- though correct me if I'm wrong. So, when was the purpose of marrow in hematopoiesis discovered, and by whom?

ecoli - Can Escherichia coli survive on glucose and water alone?

Yes, but no. In other words, this quote is not probably not true in the ways you'd think. Bacteria can survive on practically nothing for long periods of time, but whether you call that life is subjective.

Nitrogen is necessary for all the co-enzymes and proteins to sustain life. In order to get energy, if E coli. needs to metabolize nitrogen to waste at all, all the bacteria would eventually all die out. The same feat for human beings would be to add a little sugar into sewage and surviving on it. Nobody would die right away, but its hard to call that living maybe.

Unless a medium is exchanged, E coli in a laboratory culture will start a massive die off. When the E coli culture becomes terminal in this way, a portion of the bacteria go into stationary phases where the bacteria can survive for very long times - for months or possibly years. So some of the bacteria would survive, but they would be dormant. You might not call this survival, but tens of thousands of bacteria are still alive and can generate colonies if transferred to fresh media.

Laboratory cultures and media are of course artificial conditions which don't reflect the environment which bacteria are adapted. In their life cycle, they typically have other sorts of behavior and experience low nutrient conditions often enough. Bacteria are also different in that a 99.99% die off can be considered a typical event in some cases.

ethology - Tool use by animals: research history

I was under impression that data about quite a lot different species using different tools is a fairly modern phenomenon, i.e., all of the research is fairly recent.

Around 50 years ago it was widely believed, by scientists too, that it was only apes that are able to use tools. I was recently told that it's basically nonsense and scientists have been studying different tool-using animals since the beginning of the 20th century or earlier.

Where could I get more info on research done in this area? I'd be especially thankful for those done in USSR, since it used to be my country and my knowledge on everything was basically limited by the Iron Curtain. However, I am also interested in research done worldwide as well.

genetics - Which X-Y chromosomes have the developmental genes for mammals?

First, while half the chromosomes come from each of the two parents, these two sets of chromosomes are not termed X and Y (they would usually be called maternal and paternal). The terms X and Y refer to potential members of just one pair of the 23 pairs (in humans) of chromosomes, and X chromosomes can come from either the mother or the father. The presence or absence of a Y chromosome determines sex in mammals.

The Y chromosome contains one gene, SRY, which determines sex, and almost no nother genes. SRY simply switches on the "make a male" program in the cells.

Essentially all other genes, including any toolbox genes, come from both parents, one copy from each. (An exception, in males, are those genes on the X chromosome, which in males are present in only one copy and which came from the mother. Another exception is mitochondrial genes.)

entomology - Is it possible for parasitic wasp to alter the behaviour of it's host after emerging from it?

In the study by Whitfield 1990 (1) I found the information that the parasitic wasp from family Ichneumonidae have interesting symbiotic viruses called polydnaviruses. This virus stay as provirus in the wasps genome and is transmitted vertically between subsequent generations of parasitoid. It does not harm the wasp and it is transmitted to the wasps hosts (usually caterpillar). The virus does not replicate in the caterpillar, but alter it's physiology: supress immune response and metamorphosis and increases the amount of nutrients in caterpillars hemolymph.

Still, I have not found any references about this kind of virus altering the behaviour of the caterpillar after the emergence of wasps larvae.

[1] Whitfield, J. B. (1990). Parasitoids, Polydnaviruses and Endosymbiosis. Parasitology Today, 6(12), 381-384. (free PDF)

cardiology - What would life expectancy be in the western world in the absence of Ischemic heart disease?

This paper from 1991 is intervention-based, so it reports the effects of behavior modification on lifespan in people who turned 35 in 1990. The authors report the gains for each individual behavior and then say:

Eliminating coronary heart disease mortality is estimated to extend the average life expectancy of a 35-year-old man by 3.1 years and a 35-year-old woman by 3.3 years

Which they feel is a modest increase but I rather disagree. This report estimates the that reduction in death due to heart disease of over 50% between 1950 and 1995 gained around 3.5 years, although most of that is probably due to better medical treatments. This 2004 study used 1998 data from the UK and estimated that:

The average gain in life expectancy from the elimination of cardiovascular disease risk as a cause of death was 4.0 years for all the 35 year-old men in the sample (n = 24), and 1.8 years for all the 35 year-old women in the sample (n = 32).

Although I would note the low sample size. I didn't expect to find much, so I was surprised to find these... and with similar results! One big issue is that a lot of the more recent research has focused on smoking, weight/BMI, and blood pressure reduction, rather than all IHD/CHD/CAD; I found tons of those. As a side note, simply reducing TV watching to less than two hours a day can lead to a gain of almost 1.5 years.

What is Luc Montagnier's research on electromagnetic signals from DNA about?

I think that ymar poses an excellent set of questions that should be discussed on these forums. It brings back memories (sic) of the memory of water controversy.

I'll quote from Andy Coghlan's excellent article published in New Scientist in 2011

Draw your own conclusions. (The emphases are mine).

... So what have
Montagnier and his team actually found? Full details of the
experiments are not yet available, but the basic set-up is as follows.

Two adjacent but physically separate test tubes were placed within a
copper coil and subjected to a very weak extremely low frequency
electromagnetic field of 7 hertz. The apparatus was isolated from
Earth's natural magnetic field to stop it interfering with the
experiment. One tube contained a fragment of DNA around 100 bases
long; the second tube contained pure water.

After 16 to 18 hours, both
samples were independently subjected to the polymerase chain reaction
(PCR), a method routinely used to amplify traces of DNA by using
enzymes to make many copies of the original material.

The gene
fragment was apparently recovered from both tubes, even though one
should have contained just water (see diagram).

DNA was only recovered
if the original solution of DNA - whose concentration has not been
revealed - had been subjected to several dilution cycles before being
placed in the magnetic field. In each cycle it was diluted 10-fold,
and "ghost" DNA was only recovered after between seven and 12
dilutions of the original. It was not found at the ultra-high
dilutions used in homeopathy.

Physicists in Montagnier's team suggest
that DNA emits low-frequency electromagnetic waves which imprint the
structure of the molecule onto the water.

This structure, they claim,
is preserved and amplified through quantum coherence effects, and
because it mimics the shape of the original DNA, the enzymes in the
PCR process mistake it for DNA itself, and somehow use it as a
template to make DNA matching that which "sent" the signal

I always knew there was something suspect about genetics! Stick to biochemistry, that's what I say :-)

evolution - Is there theory that connects longevity, time-scale of environmental disturbance, and adaptation?

Not exactly matching your question, but I think that the idea (from stochastic demography) that life histories should be buffered against environmental variability in influential vital rates (Pfister, 1998, Morris & Doak, 2004) can be related to this issue, even if it is mainly (originally) dealing with stationary environmental fluctuations.

In general, fluctuations in vital rates cause the stochastic population growth rate to decrease. This can be described by Tuljapurkar's approximation (Tuljapurkar, 1982):

$$log \lambda_s = log \lambda_d - \frac {1}{2\lambda_d^2} \sum_{i,j} V(a_{ij})S^2_{ij}-\phi$$

where $\lambda_s$ is the stochastic growth rate, $\lambda_d$ is the deterministic growth rate based on average conditions, $V(a_{ij})$ is variance in vital rates (here matrix entires) and $S^2_{ij}$ is sensitivity in vital rates. $\phi$ represents covariances between rates, which can be important, but can sometimes be ignored for simplicity. This equation shows that the effect of variability in vital rates on stochastic growth rate (which can be interpreted as a measure of fitness) is a product of sensitivity to change and the amount of variability.

Because of the negative consequences on stochastic population growth, selection is expected to minimize variance in population growth rate. Pfister (1998) predicted (based on an evolutionary argument and the equation above) that a species should have smaller temporal variances in the life history traits it is most sensitive to. Therefore, across species, there should be a negative correlation between the sensitivity and the temporal variance of vital rates. This also means that the evolution of life histories and the tolerance of species to variability in environmental conditions are shaped by their life-history patterns.

A consequence of this is that in a long-lived species (as an example), you should find larger variabilty in juvenile survival than in adult survival, since population growth rate is more sensitive to variability in the latter. The lower variability in adult survival can then be seen as an expression of "hardiness" to variability in environmental conditions, and this theory can therefore be used to understand likely evolutionary trajectories of different species, also under a climate change scenario. The ways to minimize the negative effects of variability in population growth in this theory is to either be hardy in important traits (change in environmental conditions doesn't translate much into variability in vital rate) or to decrease the sensitivity in vital rates that vary a lot (which amounts to modifying the life-history pattern of the species). Your question mainly deals with longevity, and this is influenced by both maturation age and adult survival. Therefore, this theory can be useful to think about which species should develop a "hardy" strategy.

However, this answer completely ignores tipping-points in environmental tolerances, nonlinear responses and the genetic variation that selection can act on.

Related articles you might want to check out are Van de Pool et al (2010), Morris et al. (2008) and Doak et al 2005.

neuroscience - Do people with colorblindness have less cones or no cones of a certain type?

This is a complicated case, as it can have multiple causes.
The genes which are coding for the long (L, yellow) and medium (M, green) wavelength photopigments are located head-to-tail on the X chromosome. This is the reason why this colors are affected much more and especially in men (which only have one copy of this chromosome).

What seems to happen mostly is that the photopigment of one type of cone cells (and their neuronal connectivity) is missing, while the density of the cone cells is still the same. This means that the cells are they, but are not functioning. See these publications (when you have problems getting the articles, let me know in the comments, I can help):

What can additionally happen in some cases is that these cones have a different pigment than they should have. See the third paper above for details.

botany - What's the name of the fibrous strands that hold the seeds in a pumpkin?

If you cut open a pumpkin, the seeds are suspended inside the pumpkin by some fibrous, slimey strands. You can see them in the middle of this sliced-open pumpkin:

I'm writing a post for the Cooking.SE blog, and am trying to find out the proper botanical term. Someone suggested that might be called the endocarp, but I want to make sure and also see if there is a more specific term.

Edit

In "Morpho-Physiological Aspects of Productivity and Quality in Squash and Pumpkins (Cucurbita spp.)" §C.1, I see this:

In the central portion of the fruit, a mass of tough fibers, together with vascular strands connected to the seeds, comprise the placental tissue. The endocarp is made up of small, thin-walled cells that form a membranous tissue that adheres to seed, becoming a transparent skin on dried seeds. (emphasis added)

Am I reading correctly that the name for this part of the pumpkin is "placental tissue", and that the endocarp is just a thin layer on the seeds themselves?

human biology - How does the brain's energy consumption depend on mental activity?

I answered on the facts of this question already on skeptics.SE, here and here. You should read both papers very carefully, I highlighted the most important facts but this is a very tricky question, esp. when it comes to defining what mental activitiy is. The papers also give an explanation of how fMRI signal is linked to NEURONAL activity, as far as I remember there is no strong direct link.

You assume in your question that a mathematician solving a differential equation needs higher mental activity than a child reading a book. Is this legitimate? It seems intuitive but also very subjective. In the paper they mention that for the highest and lowest energy consumption we lose consciousness. I will not draw conclusions from this. However, you are talking about conscious mental activities so this may answer your question. To me it means more that the understanding of the human brain in neurobiololgy is on the level of the Rutherford Atomic Model in Physics at the beginning of the 20th century. We have not really got a clue how information is processed and how it's constrained by physical laws and principles of entropy and energy. By reading the 2 papers it looks more like the human brain is not raising energy consumption as a computer would (the computer analogy pretty much fails when compared to the human brain). Most of the energy is used for unconscious processes in "standby mode".

As in physics, extreme cases such as savants and the mentally disabled are probably the best starting point to exclude possible models of human brain and physical boundary conditions as we cannot approach the questions of human brain in a reductionistic way. How can savants like Kim Peek process such huge amounts of information AND save it. He is able to scan books pages just once and know them by heart thereafter. His brain does not, however, consume more energy than an average human brain. So mental activity is probably not a very good term, quantity, or even really suited to be scientifically used. Does neuronal activity mean mental activity (in the sense of your definition?) Reading the papers, the problem is the separation of mental and neuronal activities. At first you have to know what are the basic brain functions and processes that are consuming most of the energy. However the brain is not built in modular way like a computer (most energy is used here for constantly refreshing RAM). So there is not really a objective way to analyse and separate this modular energy consumption, if it even is modular.

In my opinion, most models about information processing in human brain are intuitive guessing (again Rutherford). We need much more detailed experiments and data (Blue Brain Project). fMRi is like analysing a atom with a magnifying glass. Also, the more prosperous approach from a biophysical perspective is probably not the level of "mental activity" but the hard-based amount of information processed by human brains and linked energy consumption (Kim Peek). But therefore we need a model of how this information is saved in human brain. Do normal humans save the same information as Kim Peek scanning a page or are we just unable to recall it consciouscly? When solving a differential equation, how much energy do you consume when recalling facts and is that experience not similar to reading a book? How much is mental logical tasks and is there really a difference at all?

I will stop here, hope you gained some insight that the question is of course important but too early to be definitively answered. I think we will learn a lot more from projects like Blue Brain as we have from fMRI experiments.

biochemistry - Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?

My recollection is that the formation of a phospholipid normally involves acylation of glycerol 3-phosphate. Glycerol 3-phosphate is a glycolytic intermediate, and so there is no actual phosphorylation of a glycerol; the phosphate on the glycerol will have come from the phosphorylation of glucose or of fructose 6-phosphate.

In a kinase reaction the oxygen of the -OH in the acceptor acts as a nucleophile at the P of the phosphate, so in terms of your question the O atom comes from the acceptor, not the donor. Presumably if there was a glycerol kinase (I expect there is) it would have the same mechanism so the O would come from the glycerol.

human biology - Does difference in expected life duration between men and women have biological nature?

It is known that men in most countries live less than women. I wonder whether it is due to different life conditions or because male and female organisms differ?

For example, I heard that testosterone may cause cardiovascular deceases. Is it true? Are there other biological mechanisms that can shorten men's lifespan?

biochemistry - Why can't the brain and red blood cells use fuels other than glucose?

The question is rather straight forward: I have always been curious as to why, but cannot find an explanation online.

I can imagine that the mechanism is different for each, but why does brain tissue and red blood cells use specifically and only glucose for energy metabolism?

evolution - When did vision evolve for the first time?

I'll address the question in the title "At which time did sight evolve for the first time?" by assuming that by the evolution of vision, we mean the evolution of the eye.

Molluscs are an excellent phylum to investigate this question because they exhibit a wide range of eye designs and levels of complexity.

At the most basic level, limpets such as Patella exhibit small patches of photoreceptor cells lying in a relatively flat configuration. Slightly more advanced is Pleurotomaria which has photoreceptors and pigmentation cells held in an eyecup. We then have the pinhole camera style eye as seen in Nautilus (see this post), and more complex eyes with a cornea, retina, and lense such as those seen in squid (e.g. Loligo).

Assuming that "a patch of photoreceptors" in an animal counts as an eye, then we should probably looking for marine invertebrates. The problem here is that if they had only soft body parts we might struggle to identify the oldest examples in sediments.

One candidate for the "earliest eye" might be urbilatarians - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be Kimberella (described here) which might or might not have been a mollusc and might or might not have had photoreceptors!

(credit : wikipedia)

zoology - Will a garter snake eat unusual prey if made to smell like something normal?

Yes, changing the scent has been accepted by most snake breeders as a method to feed stubborn snakes (reference). For example, if your snake prefers chicken, and wont accept mice, rub a chick on a pre-killed mouse and this may trick it into eating the mouse (reference). With regard to garter snakes, the diet may change based on its habitat, its age and even being kept in captivity can change its diet. This article should provide you information with feeding your garter snake if it is stubborn (reference).

gel electrophoresis - How do SDS-PAGE gels differ in a Bis-Tris system vs. a Tris-Glycine system?

SDS PAGE system rely on the fact that protein is denatured and surrounded by the SDS negatively charged detergent micelle. This eliminates most of the charge and idiosyncratic solubility differences from one protein to another and gives a reasonable separation based only on size of the protein which is related to the size of the SDS micelle around each molecule.

Bis-Tris and Tris-glycine buffers have quite different charge shielding characteristics. Bis (also known as 2-[Bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)-1,3-propanediol) has a tertiary amine with a pKa of 6.46 and a pKb of 7.54. glycine is a zwitterion at any pH between 2.3 and 9.6. This creates a difference in the way that the buffer shields the SDS PAGE micelles from the rest of the electrical field, slowing down (probably glycine slows things down a bit) the time to resolution, but also giving the micelles more time to migrate.

So for SDS PAGE systems, the resolution of the gel has at least as much to do with the size of the gel pores (based on the acrylamide and bis-acrylamide percentages), the amount of protein you are putting into a given volume of loading well, and the size differences of the bands you are tying to separate. (you need to get pretty lucky to separate a 100.54 kda band from a 100.85 kDa band, but 1.5 to 1.8 kDa is easier 10 to 14 kDa is even easier). Also consider adjusting the current or voltage of the power supply. The buffer system is only one consideration in planning your experiment and often not the primary factor of quality.

cell biology - What is the title of Darwin's paper on cellular structure?

Darwin had written lots of papers which dealt with fertilization (which involves single cells), as he primarily dealt with the reproduction, continuation and thus evolution of a species, but these did not deal with cell biology specifically.

After a closer look at the complete list of all his publications, I found that he did have two cell-related publishings, specifically about the size of cells, one entitled Bees in Jamaica increase the size and substance of their cells, and the other, Bee-cells in Jamaica not larger than in England, in which he retracts the statement he had made in the previous article.

Ultimately, to answer your question, it seems as though none of his works dealt with cellular structures.

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References

• Charles Darwin. "Bees in Jamaica increase the size and substance of their cells". Journal of Horticulture (15 July): 305.




• Charles Darwin. "Bee-cells in Jamaica not larger than in England." Journal of Horticulture (22 July): 323.

evolution - How many times did life emerge from the ocean?

I presume you mean how many times did life emerge from the ocean? ("how often" implies you want to know the regularity). Anyway, great question. I really enjoyed reading and thinking about it.

I doubt we know the precise number, or even anywhere near it. But there are several well-supported theorised colonisations which might interest you and help to build up a picture of just how common it was for life to transition to land. We can also use known facts about when different evolutionary lineages diverged, along with knowledge about the earlier colonisations of land, to work some events out for ourselves. I've done it here for broad taxonomic clades at different scales - if interested you could do the same thing again for lower sub-clades.

As you rightly point out, there must have been at least one colonisation event for each lineage present on land which diverged from other land-present lineages before the colonisation of land. Using the evidence and reasoning I give below, at the very least, the following 9 independent colonisations occurred:

• bacteria


• cyanobacteria


• archaea


• protists


• fungi


• algae


• plants


• nematodes


• arthropods


• vertebrates

Bacterial and archaean colonisation
The first evidence of life on land seems to originate from 2.6 (Watanabe et al., 2000) to 3.1 (Battistuzzi et al., 2004) billion years ago. Since molecular evidence points to bacteria and archaea diverging between 3.2-3.8 billion years ago (Feng et al.,1997 - a classic paper), and since both bacteria and archaea are found on land (e.g. Taketani & Tsai, 2010), they must have colonised land independently. I would suggest there would have been many different bacterial colonisations, too. One at least is certain - cyanobacteria must have colonised independently from some other forms, since they evolved after the first bacterial colonisation (Tomitani et al., 2006), and are now found on land, e.g. in lichens.

Protistan, fungal, algal, plant and animal colonisation
Protists are a polyphyletic group of simple eukaryotes, and since fungal divergence from them (Wang et al., 1999 - another classic) predates fungal emergence from the ocean (Taylor & Osborn, 1996), they must have emerged separately. Then, since plants and fungi diverged whilst fungi were still in the ocean (Wang et al., 1999), plants must have colonised separately. Actually, it has been explicitly discovered in various ways (e.g. molecular clock methods, Heckman et al., 2001) that plants must have left the ocean separately to fungi, but probably relied upon them to be able to do it (Brundrett, 2002 - see note at bottom about this paper). Next, simple animals... Arthropods colonised the land independently (Pisani et al, 2004), and since nematodes diverged before arthropods (Wang et al., 1999), they too must have independently found land. Then, lumbering along at the end, came the tetrapods (Long & Gordon, 2004).

Note about the Brundrett paper: it has OVER 300 REFERENCES! That guy must have been hoping for some sort of prize.

References

• Battistuzzi FU, Feijao A, Hedges SB. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4: 44.


• Brundrett MC. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275–304.


• Feng D-F, Cho G, Doolittle RF. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proceedings of the National Academy of Sciences 94: 13028 –13033.


• Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB. 2001. Molecular Evidence for the Early Colonization of Land by Fungi and Plants. Science 293: 1129 –1133.


• Long JA, Gordon MS. 2004. The Greatest Step in Vertebrate History: A Paleobiological Review of the Fish‐Tetrapod Transition. Physiological and Biochemical Zoology 77: 700–719.


• Pisani D, Poling LL, Lyons-Weiler M, Hedges SB. 2004. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol 2: 1.


• Taketani RG, Tsai SM. 2010. The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes. Microb Ecol 59: 734–743.


• Taylor TN, Osborn JM. 1996. The importance of fungi in shaping the paleoecosystem. Review of Palaeobotany and Palynology 90: 249–262.


• Wang DY, Kumar S, Hedges SB. 1999. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc Biol Sci 266: 163–171.


• Watanabe Y, Martini JEJ, Ohmoto H. 2000. Geochemical evidence for terrestrial ecosystems 2.6 billion years ago. Nature 408: 574–578.

physiology - Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?

The answer really depends on what aspect of the urine and feces one is considering.

On the atomic level, no, urine and feces are composed entirely of atoms taken from our environment. As one would expect, as there is no "Humanium" on the periodic table. In fact, all the atoms in urine and feces were originally created by stars.

On the molecular level, yes. The body produces molecules that we do not ingest, or that we ingest in minute quantities, such as urea and bile.

On the cellular level, yes. The body produces, for instance, red blood cells even if the person eats a vegan diet with no blood intake. The proteins that make up the cells are created by breaking down ingested proteins into their constituent amino acids, which are then used to construct new proteins.

Also at the cellular level are the huge amount of bacterial cells that we support. Estimates of the number of bacterial cells in our body range from ten to 100 times the number of our own cells. The bacterial component in feces is massive - up to 1/3 of feces by weight are bacteria. Urine, being produced from the blood by the kidneys, is relatively sterile.

pcr - When designing primers how important is the GC clamp?

I will offer my own (empirical) account of primer design. A GC-clamp aids in specificity of the priming and therefore contributes to the overall efficiency of the PCR reaction. In the past, I have (out of necessity) designed primers that had both too much GC-clamping on the 3' end, and used primers without any GC-clamping. These PCR reactions were performed successfully, with differing levels of primer-dimer formation and overall efficiency.

In my experience, GC-clamping is nice, but not strictly required for good PCR. My general rule-of-thumb is to terminate my primers with 2 G/C wherever possible. If something is going to fail, it is not usually the PCR.

entomology - Are mosquitoes repelled by high frequency sound?

After seeing your question, I decided to do a bit of research on the topic.

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http://www.eurekalert.org/pub_releases/2007-04/jws-mrt041607.php

"Mosquito repellents that emit high-pitched sounds don't prevent
bites"

Some key-points from the webpage:

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A Cochrane Systematic Review of the use of electronic mosquito repellents (EMRs) failed to find any evidence that they work.

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To test these claims a team of Cochrane Researchers conducted a systematic review looking for trials conducted with EMRs. They located ten field trials that had been carried out in various parts of the world. None of these trials showed any evidence that EMRs work.

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All ten studies found that there was no difference in the number of mosquitoes found on the bare body parts of the human participants with or without an EMR

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http://en.wikipedia.org/wiki/Insect_repellent

These electronic devices have been shown to have no effect as a mosquito repellent by studies done by the EPA and many universities.

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http://www.cbc.ca/news/story/2007/04/18/mosquito-repellent.html
Key points from the article:

"There was no evidence in the field studies to support any repelling effects of EMRs, hence >no evidence to support their promotion or use"
           
-Ahmadali Enayati, researcher

This is a major point as well:

The study also said that in 12 of the 15 experiments, the landing rates of mosquitoes on subjects was in fact higher than in control groups.

The article also points out that female mosquitoes can't hear very well- Which supports the idea that high-frequency repellents are ineffective; Much more than you probably think. Why? Well, it's pretty simple:

Female Mosquitoes are the only Gender that Bite.

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Overall, when you consider the countless studies and research put in to the effects of high-frequency sounds on mosquitoes, it's pretty obvious that:

High Frequency Sounds do NOT repel mosquitoes

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eyes - Are there specific conditions that allow humans to see ultraviolet wavelengths

It is fairly common knowledge that the lens in its normal state absorbs ultraviolet (UV) radiation. An interesting notion has come up from time to time in my reading that suggests there are a small number of conditions that result in humans being able to 'see' ultraviolet.

What conditions may cause this? Also, those affected, would they 'see' it has a different shade of violet?

lab techniques - Measuring fitness / lifetime reproductive success (LRS) in Drosophila

I haven't done LRS but I don't see a reason why you couldn't make that measurement over only a few days, if you keep this method consistent through out all your populations. Just as a control you might have to do a complete LRS to see if you get any patterns in their egg laying behaviour, which I assume/believe is a decreasing pattern over time but just check the pattern of your WT and make sure your food is the same throughout all your experiments as changes in yeast % can completely distort your results as fly lay eggs like crazy when given yeast!! so use the same batch of fly food.

Although I'm no expert at this, if you look at female ovaries and do some molecular/phenotypic characterisations, you might get some interesting data if you are already observing a huge difference between your populations although you would have to look at the literature for this but having played around with these stuff a little, you find a surprising amount of data! This is in a way nice since you take the males out of the equation as the reproductive fitness could be compromised by either males or females in a population. To determine this you need to cross the males and females of your population of interest to WT flies and count the embryos (although this is slightly dangerous since if males are not performing well, females can lay lots of unfertilised eggs, blanks, and they are indistinguishable from fertilised egg so maybe count the hatched offspring and immediately discard them although that presents its own set of challenges and variables and to be honest its not likely to happen since you usually get this blanks in virgin females that have not yet courtshiped). If you observe lets say no changes in embryo numbers when your male populations are crossed to WT females but significant changes when females are crossed to the WT males, you would know the problem is with the males in your population.

Hope this helps!

EDIT: So I looked a bit further into this and came across this paper (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024560). If you look at Fig 6, I think it answers your question. I'm basically quoting the paper here. They measured the correlations between adult LRS and cumulative and short-time measures of fecundity and offspring production. Correlations of the short-time measures of fecundity and offspring production with adult LRS were highly dependent on the time of measurement. For young females the correlations were low, but when measured from older females, the correlations were much higher (up to 0.67 for short-time fecundity and 0.83 for short-time offspring production). For both short-time fecundity and short-time offspring production the highest correlations with adult LRS were reached when the female age was about 50 to 80 days. The length of the time frame had only a minor effect: the correlation of the 10-day measure with adult LRS was generally only slightly higher than that of the 2-day measure. The short-time measures performed well in comparison to the cumulative measures of fecundity and offspring production. So in short if you let your females age a bit and measure their fecundity, then it should be representative of their LRS.

botany - Root hair formation in Arabidopsis

In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.

The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one cortical cell do not develop root hair.

What is the advantage of this ?

biochemistry - Raphide toxicity in Pothos plant

Recently I found out that the common houseplant Pothos (Epipremnum aureum) is toxic to cats and dogs due to the presence of "insoluble raphides." I have a lot of these plants around my house and my cat drinks water from the vase that they are in (I put drinking water into the vase that he always drinks from). He doesn't chew the Pothos leaves, he only drinks the water, is it still dangerous? I tried several times to give him water in an ordinary bowl, but he prefers the water that's associated with the Pothos plant, so I thought that maybe the roots of the plant excrete something nutritious (but I guess that's not the case, apparently...).
Is it harmful for an animal (cat) to drink water that has a Pothos plant immersed in it?
Also, my other cat does chew on the Pothos leaves (he goes crazy for them). Is it possible to have immunity and not be affected by the toxic chemicals? I read that chewing is supposed to provoke stomach irritation, but I would think that if the cat that chews the leaves suffered from irritation he wouldn't keep getting excited about chewing the leaves...
So what is going on? Many thanks!

evolution - Why do sloths come down from the trees to defecate?

I'm under the impression that most sloths exhibit this behavior, but why? They are slow moving and so have no way of escaping from predators when on the ground. Not to mention the energy they expire to break from their normally sedentary lifestyle.

They may only have to defecate and urinate once a week, but it strikes me as an unnecessary risk. Why not let gravity do all the hard work?

Can a brain be transplanted?

"Is it possible" has a carefully conditional "yes". Do we have the expertise or technology to do it now? No. One of the biggest difficulties is that nerve tissues (the connections between brain and rest of body) will take time to heal... time during which the brain cannot sufficiently give commands to the rest of the body to keep autonomic functions running.

Head transplants, however, have been "successfully" completed using monkeys. The monkey lived for sometime after the transplant, but eventually died. China has also been known to do a similar procedure with dogs.

Caution, this may be too explicit for some; I'm not sure ethics boards would allow it nowadays:
Monkey Head Transplant

Alternatives to TBE buffer for denaturing polyacrylamide gel electrophoresis of DNA and RNA?

I just stumbled upon an article promoting 10 mM sodium borate as an alternative to the well-known TAE and TBE buffers for agarose gel electrophoresis of DNA (Brody & Kern, 2004). They claim that sodium borate outperforms TBE and TAE at high-voltage conditions due to the significantly lower heat development.

I'm currently using TBE buffer and gels with 7M urea for my denaturing PAA gels, and I'm wondering if there are similar alternative conditions for those denaturing PAA gels of nucleic acids?

I couldn't find anything on using sodium borate for denaturing PAA gels, so I'm wondering if it should work the same as for the agarose gels or if it just isn't a good buffer for that kind of gel.

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

What is the relationship between sexual and and natural selection?

To Darwin's point of view, sexual and natural selection are two different mechanisms. Then, we tended to consider that sexual selection is part of natural selection. The part of natural selection that is not attributed to sexual selection is sometimes called ecological selection. Today, our understanding of these mechanisms brought us to consider the meaning of these words slightly differently.

Natural selection is not anymore the result of a struggle for survival. It is any process yielding to a change in allele frequency through a long-enough term difference in fitness. Fitness is a index of how much an individual, a gene or whatever, leave copies of itself after a long and short enough amount of time (one might not agree with this definition I guess). Take two strains of bacteria in two petri dish, consider they are one population and let the bacteria grow. One strain will grow faster and the allele frequency will vary over time. It is the result of natural selection although there were no competition, no struggle at all given that they were not in contact.

Sexual selection is a type of natural selection that involves sexual competition. There are two types of sexual competition, the so-called inter- and intra-sexual competition. Inter-sexual competition means that one sex chose the other one, while for intra-sexual there is no choice from the other sex. For example, if you see two animals fighting, they either fight to have the physical acces to the other sex (intra-) or they fight and then, let the female decide which one is the best to mate with (inter-). These two concept of intra- and inter-sexual competition might somehow overlap in some specific case. I would argue that the concept of sexual competition and therefore of sexual selection have never been accurately defined. Therefore, I would not complain if one prefers to give up the concept of sexual selection to use only the concept of natural selection.

Many articles state that sexual and natural selection act on a trait with the same or opposite directions. Given the above argumentations, you could as well say that there are two different forces of natural selection. if the trait is at state 'A', then the individual is very attractive to the other sex but is likely to not be able to escape a predator. This is the case of most of the trait we think of when talking about trait evolving through sexual selection. See Zahavi's handicap principle for more information.

physiology - Would my hands sweat this much if I wasn't wearing gloves?

Hand sweating has been fairly well-studied, both because sweating from the hands is one of the main mechanisms of heat dissipation at higher temperatures and because there is a significant effect on palmar sweating by the autonomic nervous system (the main cause of hyperhydrosis of the palms).

Disregarding autonomic effects (stress response), the single most important determinant of hand and foot blood flow is the thermal status of the body core. Heat dissipation is more marked in the hands than feet, and remains so as temperature increases.

Studies have been done of palmar sweating in extremes of temperatures, palmar sweating changes with aging (decreases), palmar sweating in disease, etc. But what has not been studied is the effect of localized heat on sweating of the palms, which would be of interest to you if sweating was a result of the insulating capacity of the gloves.

What is known about palmar sweating is that it is an ongoing and important process in both genders, at all temperatures, and at all ages. The most reasonable assumption then, given the limits of the literature, is that your hands sweat continuously and steadily at a given temperature, and it is highly likely that you are noticing it when wearing gloves only because the vapor barrier caused by the gloves prohibits evaporation.

_{The roles of hands and feet in temperature regulation in hot and cold environments
OBSERVATIONS ON THE ACTIVITY OF SWEAT GLANDS WITH SPECIAL REFERENCE TO THE INFLUENCE OF AGEING
Why do I get sweaty palms?}

biochemistry - Do humans have chemosensors for nutrients or chemicals?

I'm reading about chemoreceptors on Wikipedia, and see that the typical ones are mentioned: taste, smell, CO₂. I would like to learn more about the other kinds of chemoreceptors that humans may possess. I'm particularly interested if these can detect chemical compounds, or lack of thereof in food.

Here's an example:
Do omnivore mammals vary food preferences based on dietary needs?

There's "rapid recognition of Indispensible Amino Acid(IAA) depletion in the rat brain's IAA chemosensor, the anterior piriform cortex (APC)"

Reading the article above, it appears that at least rats and birds can develop aversion to food that does not contain indispensable amino acids. This is done through chemosensors in the brain. Do humans possess any similar chemosensors?

Thank you for your input!

lab techniques - What are good practices with reusing desalting columns

Regardless of what protocol you use, and what the advertised efficacy of that protocol might be, in any situation like this I think the important thing to consider is: what would happen if the material taken from a re-used column was contaminated by a previous application? Can you live with the consequences of such contamination?

If you are preparing DNA for further use (PCR and/or cloning and/or transformation) then you run the risk of propagating a contaminant through subsequent steps and getting into a real mess. I worked in a lab once where one postgrad ended up spending several weeks working with a cloned fragment that was actually derived from someone else's work in the same lab (although not due to re-use of a column as far as I remember).

If you are preparing protein samples then the risks are possibly reduced, but if the protein sample is going to be subjected to sensitive methods (blotting, MS) then again, could get messy.

genetics - How to compare SNP from genotyping results for multiple people with a known phenotype?

Each rsid identifies a unique SNP in the genome. Thus there should not be any entry in the files that have the same rsid but different chromosomes and/or positions. If you do find this, it is likely that you have data from different versions of the assembled genomes.

To find genetic variants associated, i.e. correlated, with your trait, you need to focus on the genotype at each of the SNPs. For example, SNP rs3094315 is an A/G polymorphism, i.e. an individual can either have the genotype AA, AG, or GG. To find if it is associated with tongue rolling, you would count the number of AA, AG, and GG individuals (alternatively you could sum the number of A and G alleles) in the group that can roll their tongue and compare those numbers to the group that cannot. You would then repeat this for each SNP that you want to test. For most SNPs, there will be no difference in proportion.

That being said, this is not a modest undertaking as this a cornerstone of human and statistical genetics. There are many issues that could strongly bias your results (e.g. population stratification, genotyping error, linkage disequilibrium, multiple testing). To learn more, you can read about the Cochrane-Armitage Trend Test and the PLINK software. If you are really serious I recommend Applied Statistical Genetics with R by Andrea S. Foulkes.

genetics - Do spouses begin to share genes over time?

Microchimerism (Mc) is an interesting concept, and

refers to the harboring of a small number of cells (or DNA) that originated in a different individual. Naturally acquired Mc derives primarily from maternal cells in her progeny, or cells of fetal origin in women.

In women, it has nothing to do with transfer during/after sex but rather is due to the presence of the developing fetus. There is definite long-term persistence of microchimerism, although not much is yet known about its effects. Here is a nice and free review from 2010 dealing with the subject. Most if not all of the effects have to do with immune function, in particular autoimmunity. It is definitely not a mechanism by which couples begin to look similar. That is social, in particular a result of living in the same environment with similar activities and tastes. Male contribution to cellular content in the embryo is almost nil, as sperm die and the transcript count in the successful sperm is puny compared to the egg. Most RNA content in the embryo is maternal until it switches to embryo.

genetics - How are there multiple varieties of the potato?

Well, uvesten is correct in saying that potatoes are flowering plants and as such they can reproduce sexually. However, as everyone mentions potatoes can, like many plants, reproduce asexually by putting out clones.

Since clones are (by definition) genetically identical to the parent plant, this would seem to rule out the possibility of producing different varieties (or even species) from clonal propagation.

But! this very interesting study by Jiang et al. looked at Arabidopsis lineages (Brassica family). They found:

"in vitro regeneration of Arabidopsis plants results in a high frequency of heritable phenotypic variation "

That is, regenerant Arabidopsis plant lineages displayed extensive phenotypic somaclonal variation - the cloned "offspring" were not genetically identical. They attributed most of this genetic variation to an increased base substitution frequency in the regenerant offspring but there may also be unknown epigentic factors as well.

Jiang et al. summarise:

...

... somatic mutation rates are characteristically higher than germline rates in multicellular organisms [26] and has important particular potential consequences for the evolution of plants, given that they frequently adopt life cycle strategies that involve regeneration from somatic tissues.

So, perhaps some of the variation we see in plant species which commonly propagate asexually actually arose during this process and not via sexual reproduction ... ? This would be good news for houseplants which are nearly always propagated asexually.

However, I am not sure whether this extends to potatoes.

Jiang et al. 2011, Current Biology, 21, 1385, Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes

pigmentation - How do animals perform detailed active camouflage?

We often see videos of octopuses and chameleons changing their color to suit their surroundings. If it was a simple color change from white to red, it'd be understandable, but some of these animals can change colors while incorporating a lot of detail.

How do they process so much information and mimic it. Is this a subconscious action, or do they actually draw a picture in their head and then 'print' it on their bodies? Does this ability come from birth or does it get better over time?

biochemistry - How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?

5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product slowly degrades over periods of time within the cell, allowing for cells to lose their blue coloration.

What mechanisms can explain the degradation of 5,5'-dibromo-4,4'-dichloro-indigo within cells?

genomes - Examples of intracellular parasites of medical or economic importance?

As Armatus pointed out above, all viruses are obligately intracellular, and their medical and economic importance cannot be overstated.

Many bacterial species live intracellularly. The arthropod specific Wolbachia has a wide variety of consequences for its host, including alteration of reproduction and sex ratios, induction of reproductive isolation possibly driving speciation, and conferring protection from some viral infections.

Eukaryotes can be intracellular parasites as well: Malaria is a well-known example. Toxoplasma gondii is another intracellular parasite that uses cats as a primary host, but can use other warm-blooded animals (such as humans, rats, and birds) as intermediate hosts. T. gondii infection has been shown to induce behavioral changes in rats, causing an attraction to cats (thereby increasing the chance that the parasite will infect the cat and sexually reproduce). There is also some evidence that T. gondii infection in humans causes behavioral and psychological changes such as decreased reaction times, and links to depression and suicide.

genetics - Possible Genotypes of 4 Alleles of Adh

Those Hardy-Weinberg equations are the general case, used for only two alleles. This question is basically answered here, for three alleles; you've got a situation of four alleles. That means you need to have:

$(p+q+r+s)^2=1$

Where $p$, $q$, $r$, and $s$ are the frequencies of your respective alleles. This expands out to the rather unwieldy:

$p^2+2pq+2pr+2ps+q^2+2qr+2qs+r^2+2rs+s^2=1$

Now it becomes a plug 'n chug assignment; simply assign the frequencies and calculate.

Assuming $p$ is Adh-1, $q$ is Adh-2, etc., $p^2=0.0121$, $2pq=0.1848$, and so on.

dna - Are all body atoms really recycled several times during a life?

Rudolf Shoenheimer and David Rittenberg were key figures in introducing the isotopic tracer technique to biology.

This technique, which may be dated to the discovery of deuterium by Urey in 1933, produced a revolution in biological thought.

Much of the early work was done at the Department of Biological Chemistry at Columbia University under the chairmanship of H. T. Clark.

Up to this time it was thought that the components of tissues were relatively stable, and that ingested food was metabolized immediately to provide a source of energy.

The first experiments showed that when deuterated fatty acids were fed to mice, most of the label was initially deposited in adipose tissue.

It was concluded that adipose tissue acts a 'fuel depot' that is in a state of metabolic flux and is the direct source of fatty acids burned as a fuel (see here for refs). Fats present in food are not primarily used an an immediate energy source.

When a stable isotope of nitrogen became available (N¹⁵), it was found that proteins were also 'in a state of dynamic flux' and were being continuously regenerated and broken down.

The first experiments were done with N¹⁵-labeled tyrosine and it it worth quoting from the paper (Studies in Protein Metabolism. VII The metabolism of tyrosine by D Rittenberg Rudolf Schoenheimer & S. Ratner)

The results indicate that in our rat the nitrogen of at least one
amino acid, tyrosine, was only partly excreted in the urine, while
almost half of it was retained in the body proteins.

Of this deposited nitrogen only a fraction was found attached to the original
carbon chain, namely to tyrosine, while the bulk was distributed over other
nitrogenous groups of the proteins

Shortly after giving a series of lectures at Harvard University in 1941, Shoenheimer took his own life. The lectures were published posthumously as a classic book called The Dynamic State of Body Constituents.

Further information about the early work on isotopes, their role in changing completely the way we think about metabolism, and the role of Columbia University in shepherding in this great era, may be found in the following open-access article by Eugene. P. Kennedy:

Hitler’s Gift and the Era of Biosynthesis

Another good reference on the work of Schoenheimer may be found here

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So are all proteins broken down and regenerated? I know of any one exception and that is the lens crystallins where there is virtually no turnover
throughout the life of an individual.

The crystallins in our lens are synthesized at birth and remain with us virtually unchanged for life.

There is a very nice open-access paper on this published in PLOS One:

Radiocarbon Dating of the Human Eye Lens Crystallines Reveal Proteins without Carbon Turnover throughout Life

(Lynnerup et al. 2007)

human biology - What happens when we know that there is something that we forgot but we can't remember what it was?

It is a phenomenon known as room amnesia, some research has shown that your brain may use physical barriers like the room and doorways as a way to compartmentalize thoughts.
One article summarizes it here:

The researchers say that when you pass through a doorway, your mind
compartmentalizes your actions into separate episodes. Having moved
into a new episode, the brain archives the previous one, making it
less available for access. It’s as if you slam a mental door between
what you knew and…what was I saying?

This is the research.

sleep - How are people able to wake themselves up after a pre-specified amount of time?

There is quite a lot of research on self-awakening (see this search on Google Scholar for self awakening). Hopefully someone else more familiar with this literature can add a more authoritative answer about the mechanisms of self-awakening. In the interem I briefly extract some relevant points from Ikeda and Hashi (2012). The study does not directly address biological mechanisms. However, understanding the reliability of self-awakening and the correlates of the ability to self-awaken is presumably relevant to forming such an understanding.

First they summarise some existing research:

Both the accuracy and success rate of self-awakening have been
experimentally examined. More than half of the people who have the
ability to self-awaken suc- cessfully awakened within 30 minutes of
the predetermined time. For example, seven participants succeeded on
nine of 14 days (64%) in a sleep laboratory, and 15 participants
succeeded on 35 of 44 nights (80%) at their homes. Survey studies
indicate that many people habitually self-awaken in daily life; for
example, 52% of 269 adults (aged 21−84 years) and 10.3% of 643
university students6 reported habitu- ally self-awakening. People who
have a habit of self-awakening in the morning have regular sleep/wake
schedules, tended to have a morningness chronotypology, awakened
comfortably in the morning, and had less daytime dozing.

In their own study they found:

The present study investigated self-awakening, both habitual and
inconsistent, compared to awakening by external means in relation to
sleep/wake schedules for five consecutive years in 362 students
(starting at mean age 15.1 ± 0.3 years). Students who self-awakened
consistently for five consecutive years (5% of all students) went to
bed earlier than those who inconsistently self-awakened (mixed group,
40%) or consistently used forced awakening by external means (56%).
Awakening during sleep was more frequent and sleep was lighter in the
consistently self-awakened group than in the mixed and consistently
forced-awakened groups. However, daytime dozing was less frequent and
comfort immediately after awakening was greater for the consistently
self-awakened group than for the mixed and consistently
forced-awakened groups.

Reference

• Ikeda, H., & Hayashi, M. (2012). Longitudinal study of self-awakening and sleep/wake habits in adolescents. Nature, 4, 103-109. PDF


• Bell CR. Awakening from sleep at a pre-set time. Percept Mot Skills. 1980;50(2):503–508.


• Lavie P, Oksenberg A, Zomer J. “It’s time, you must wake up now.” Percept Mot Skills. 1979;49(2):447–450.


• MoorcroftWH,KayserKH,GriggsAJ.Subjectiveandobjectiveconfir- mation of the ability to self-awaken at a self-predetermined time without using external means. Sleep. 1997;20(1):40–45.


• ZepelinH.REMsleepandthetimingofself-awakenings.BullPsychon Soc. 1986;24(4):254–256.


• Zung WW, Wilson WP. Time estimation during sleep. Biol Psychiatry. 1971;3(2):159–164.


• Matsuura N, Hayashi M, Hori T. Comparison of sleep/wake habits of university students with or without a habit of self-awakening. Psychiatry Clin Neurosci. 2002;56(3):223–224.

human biology - Why can't you taste food when you have a cold?

There are many factors that contribute to the flavor of food - the five "traditional" tastes (sweet, sour, bitter, salty, umami), smell, texture, spiciness, "coolness" (like peppermint), temperature, etc. Smell and taste are detected in similar ways, by chemoreceptors expressed in taste pores by specialized cells of the lingual epithelium (tongue), and in the nose by the olfactory epithelium. Both are affected by upper respiratory tract infections like colds and the flu, leading to diminished senses of taste and smell, and a corresponding reduction in the overall flavor of food.

reproduction - Parthenogenesis in Bees

Parthenogenesis is defined as:

"A type of asexual reproduction in which egg develops without fertilization to form a new individual."

If parthenogenesis takes place in bees, a drone or male bee is produced.

My question is that parthenogenesis is the development of EGG into new individual so, how can egg be developed into male because egg won't have that "Y" chromosome required for male offspring?