Steve Koch

After thinking about it all day, I still think this is the best presentation I have ever seen, by far. Highly recommend seeing him give this talk if you have the chance. - Steve Koch

Rated 5 Stars for Style. I know little about yeast or pathogens, but still found this article fascinating. I learned a lot from the well-written abstract, author summary, and introduction. Also, the authors take care in the results section to explain things such as synthetic lethal mutations and theories for general kinds of gene interactions, which I found very accessible to a non-expert. Links to tools such as FuncAssociate also helpful. And of course, the overall story of finding a mammalian pathway affected by the pathogen effector protein, starting with yeast studies is exciting. Kudos to the authors for a great paper. - Steve Koch

Science (New York, N.Y.), Vol. 79, No. 2042. (16 February 1934), pp. 151-153. Gilbert Lewis - Steve Koch

Interesting thoughts from Lewis in his 1934 Science paper on biological effects of heavy water (relevant to the FEBS paper I read a couple weeks ago http://friendfeed.com/steveko...): "It is not inconceivable that heavy hydrogen, which exists in small amounts in all natural water, may actually be essential to some plants or animals. A... more... - Steve Koch

He also gave a significant amount of D2O to a mouse to drink. He wrote that he regretted the experiment because he wasted so much D2O without setting up the experiment to achieve maximum information. But he did get a little data: "During the course of three hours the mouse received, in three doses, a total of 0.54 g of 87 per cent. and 0.26 g of 71 per cent. heavy water, containinig... more... - Steve Koch

The role of naturally occurring D in living organisms has been examined by using deuterium-depleted water (30-40 ppm D) instead of water containing the natural abundance of D (150 ppm). The deuterium-depleted water significantly decreased the growth rate of the L929 fibroblast cell line, and also inhibited the tumor growth in xenotransplanted mice. Eighty days after transplantation in 10 (59%) out of 17 tumorous mice the tumor, after having grown, regressed and then disappeared. We suggest that the naturally occurring D has a central role in signal transduction involved in cell cycle regulation. - Steve Koch

Interesting thoughts from Lewis in his 1934 Science paper on biological effects of heavy water (relevant to the FEBS paper originally linked in this thread): "It is not inconceivable that heavy hydrogen, which exists in small amounts in all natural water, may actually be essential to some plants or animals. A supply of water almost completely freed from the heavy isotope is now being prepared for the purpose of conducting such studies." - Steve Koch

Biophysical journal, Vol. 96, No. 12. (17 June 2009), pp. 5040-5049. Magnetic tweezers are a powerful tool to manipulate single DNA or RNA molecules and to study nucleic acid-protein interactions in real time. Here, we have modeled the magnetic fields of permanent magnets in magnetic tweezers and computed the forces exerted on superparamagnetic beads from first principles. For simple, symmetric geometries the magnetic fields can be calculated semianalytically using the Biot-Savart law. For complicated geometries and in the presence of an iron yoke, we employ a finite-element three-dimensional PDE solver to numerically solve the magnetostatic problem. The theoretical predictions are in quantitative agreement with direct Hall-probe measurements of the magnetic field and with measurements of the force exerted on DNA-tethered beads. Using these predictive theories, we systematically explore the effects of magnet alignment, magnet spacing, magnet size, and of adding an iron yoke to the... - Steve Koch

Science, Vol. 78, No. 2034. (22 December 1933), pp. 566-571. Doesn't appear to have an abstract, but here is the second paragraph: "Since the heavier isotope of hydrogen was discovered about two years ago, some seventy-five papers and notes have been published dealing with its properties. It would be difficult to give an adequate review of the subject in the time available for this talk, and therefore I shall confine myself to a few topics which have interested us at Columbia, giving them in detail and referring only briefly to other interesting and valuable work. I shall discuss methods of separation and the properties of the hydrogens. The method of discovery is history now and need not be reviewed." HC Urey - Steve Koch

Good quote from the letter by Urey: "It is interesting to consider one obvious but easily overlooked difficulty in working with this water. It must be very hygroscopic. Hygroscopic water! This is really something new!" - Steve Koch

Tsitologiia, Vol. 6, No. 6. (c 1964), pp. 667-679. Abstract: In the literature there are data on the increase in the temperature of transition of native proteins to denaturated state when H2O is changed for D2O in the medium. It was of interest to learn whether D2O can produce a stabilizing effect on living cells. Results obtained from experiments on living cells, glycerized models and actomyosin allowed the following conclusion: Change of H2O for D2O in the medium increases heat resistance of Campanula persicifolia leaf epidermis cells, of ciliated cells of the frog palate mucosa and of glycerized models of ciliated cells as well as resistance of ATP-ase activity of actomyosin of frog's skeletal muscles. These results confirm data obtained by Deshcherevski and Kornienko (1964) concerning deuterization of frog muscles. Change of H2O for D2O increases high hydrostatic pressure resistance of Campanula persicifolia leaf epidermis cells, of the frog ciliated cells, and resistance of... - Steve Koch

Biofizika, Vol. 9 (1964), pp. 315-320. Abstract: Dissected sartorius muscles from Rana temporaria were kept in Ringer's solution (without Na2CO3) for about 1 hour and then stained for 40 minutes at 18-19C in 0.02% neutral red diluted with Ringer's solution containing 50-90% D2O or with conventional Ringer's solution. Stain was extracted with acidified alcohol and the color measured in a photoelectric colorimeter. Muscles adsorbed less of the vital stain in D2O than in H2O, which indicates that D2O produces no paranecrotic changes in muscle tissue but increases stability of the intracellular structure. As measured by the minimum temperature at which the muscle began to contract, thermal stability of the contracting structure averaged 5.6[degree]C higher in 95% D2O than in H2O and was independent of the time for which the muscle had been kept in D2O. When placed in D2O at 38[degree]C, which is below the average thermal stability in D2O (41 [degree]C), muscles contracted only 1/15 as... - Steve Koch

Proceedings of the National Academy of Sciences of the United States of America, Vol. 71, No. 2. (February 1974), pp. 540-543. Deuterium oxide, DO, increases the temperature-tolerance of when it is administered to adult flies as a sucrose solution. The effect is very rapidly exerted; it is detected within 10 min after the flies have a brief (10 min) opportunity to drink. This increased resistance to heat-death surely implies an increased resistance of macromolecules to thermal denaturation. DO is known to exert such an effect on protein solutions. The speed with which the increased stability develops clearly implicates a solvent action of DO, and is most easily understood if the effect is traceable to enhancement of the hydrophobic interactions which contribute to conformational stability. The increased strength of deuterated hydrogen bonds cannot be excluded however. The possible bearing of these results on the hypothesis that DO always increases the period of circadian oscillations... - Steve Koch

Pittendrigh & Cosbey in 1974 show that drinking 25% D2O for only 10 minutes confers heat tolerance onto fruit flies within 10 minutes. That is, they acquire heat tolerance very quickly. They attribute this to a solvent effect on protein stability, either through increase of the hydrophobic effect, increased strength of protein hydrogen bonds, or some other solvent effect. - Steve Koch

1973 study of D2O on circadian rhythms. A good quote from introduction: "Many subsequent studies, the most important of which are those of Suter and Rawson (2) and Enright (3), indicate this effect of D20 is widespread: it lengthens r in unicellulars (1), green plants (4), isopods (3), insects (Caldarola, in preparation), birds (5, 6), mice, and hamsters (2, 5, 7, 8). The effect is clearly widespread and since no exceptions have been found in 12 cases, it is likely to be truly general. As several authors have noted, it therefore merits closer study as a potential clue to the physical nature of the cellular oscillation responsible for circadian rhythmicity." - Steve Koch

Thanks, Bora! - Steve Koch

This looks like the best early reference for index of refraction data on mixtures of D2O / H2O. By Luten, who worked some with Lewis on heavy water at Berkeley. - Steve Koch

Show ability to cut a specific, single region of human genome. Probably an incredibly useful technology, related to what Cameron was telling us about last week. Linked to me by F1000 and reviewed there by Scott K Silverman - Steve Koch

This is a half page letter to Nature in 1934, reporting measurements of the index of refraction of gaseous D2O as essentially the same as for gaseous H2O (light water). He says, "I hope to complete measurements of the refraction and dispersion and to publish the results before November." I am not sure if I'm interpreting the results correctly (or if they were later confirmed), but it seems to say that the refractive index of gaseous H2O and D2O are indistinguishable, wherease liquid D2O has a lower index than H2O (even lower than expected based on increased D2O molecular volume). Would this be explained by the stronger hydrogen bonding in D2O, and less polarizability because of that? This is a very incomplete thought. - Steve Koch

Actually, I found the later paper, and I think it has a different conclusion (http://www.jstor.org/stable...) . It's somewhat fascinating that Cuthbertson in 1936 does not cite his 1934 letter to Nature, which had an opposite conclusion (as far as I can tell). So that shit was going on, even way back then. Huh. - Steve Koch

Feynman has a cute derivation of the index of refraction of gases in vol. 1 of Lectures. It is a classical (non-quantum) derivation, but it still gives useful intuition about the way (n-1) scales with mass, charge and density, and the dependence on mass is like 1/m, consistent with what you say about D2O vs. H2O. Unfortunately his model of the gas consists of atoms with harmonically... more... - mkz

Seems to confirm other measurements of liquid heavy water (Lewis and others). However, contradicts Cuthbertson 1934 letter to Nature, which is amazingly not cited here, or anywhere else. Seems a bit fishy. - Steve Koch

Do you think Nature would correct the online version if I wrote them a quick note saying the 1934 Nature letter by Cuthbertson was contradicted by the 1936 Royal Society letter by Cuthbertson and Cuthbertson? I doubt it. But it would have saved me a bit of thinking if they had already done that. - Steve Koch

A 1949 list of over 2000 references to "heavy hydrogen" (deuterium mostly, I think) research. I think resulting from end of Manhattan project. The PDF is searchable, and a quick search for "refractive" was productive for me, so I think it's probably useful. - Steve Koch

I've just started reading this, but does look like a gold mine. Feel silly for not looking at NIST sooner. Here's a cool thing I just learned. There's such a thing as "Standard Mean Ocean Water" (SMOW). It's defined as: 0.999 842 mole fraction 1H; 0.000 158 2H; 0 3H; 0.997 640 16O; 0.000 371 17O; 0.001 989 18O ... SO: "pure heavy water" at least as NIST is concerned has more than 0.2% heterogeneity in oxygen isotopes! - Steve Koch

Actually, the introduction is great source of some background. However, rest of paper is heavily focused on very precise equations for various physics parameters of D2O. I don't see dielectric constant or index of refraction, though. - Steve Koch

Lewis writes, "Sir: Even before I had succeeded in concentrating the isotope of hydrogen, I predicted that H2H2O [D2O] would not support life and would be lethal to higher organisms. As soon as heavy water became available experiments to test this idea were begun, but it was necessary to choose an experiment which would require the minimum of biological technique and also very small quantities of water. The minute seeds of tobacco..." - Steve Koch

@mkz, I agree! I too was surprised. And it's even more amazing how he casually says "lethal to higher organisms." And it turns out that indeed it's more lethal to eukaryotic than prokaryotic cells. And I think actually more lethal to multicellular than unicellular. Where did he get that insight? Amazing. - Steve Koch

Urey, Brickwedde, and Murphy. According to Lewis & Macdonald in 1933, this paper marked the discovery of deuterium. - Steve Koch

From Johnathan Eisen's twitter: http://twitter.com/phyloge... - Steve Koch from Bookmarklet

Try: http://twitter.com/phyloge... - Jim Till

Thanks, corrected - Steve Koch

Fun to watch someone so passionate and happy about his life work. From Daniel Lemire on friendfeed: http://friendfeed.com/lemire... - Steve Koch

Is now a good time to mention the myth about how D2O can cause neurological disorders. Its very popular amongst the neutron scattering community because we swim in the stuff. - Cameron Neylon

Don't even get me started on the deuterium dreams I've been having lately :) - Steve Koch