Gregory Watson (James Cook University, Australia) and coworkers have discovered small-scale architecture on termite wings that imparts remarkable water-repelling properties, while adding only minimal weight to the wings, enabling a species of weak fliers to readily fly in rain. This news feature was written on February 2, 2010.... Read more »
Watson, G. S., Cribb, B. W., & Watson, J. A. (2010) How Micro/Nanoarchitecture Facilitates Anti-Wetting: An Elegant Hierarchical Design on the Termite Wing. ACS Nano, 4(1), 129-136. DOI: 10.1021/nn900869b
For something as widely used for as long as general anesthetics (GAs), one would think that their molecular mechanism of action would have been fairly understood. Far from it. From Linus Pauling's theory of gases like xenon acting at high concentrations by forming clathrates to more recent theories of GA action on lipids and now on proteins, tantalizing clues have emerged, but speculation remains rife. In a recent Acc. Chem. Res. review, a group of researchers explains some recent studies on GA action. Now there's a field that to me seems primed for computational studies. This is for two reasons. Firstly, experimental information on GAs is hard to come by. Consider their chemical features; halogenated, apolar small molecules lacking polar hydrogen bonding and other interactions, binding to their targets with low affinity (it's interesting that halogenation seems to be a key criterion for GA action). In addition most GAs do not bind to a highly specific active site but instead influence protein action indirectly. Such features make any kind of NMR or x-ray structure determination an enormous challenge. Secondly, molecular dynamics simulations (MDS) have come of age. With recent programs augmented by tremendous gains in hardware and software, microsecond to millisecond simulations have gradually become a reality. This particular field seems to provide a classic and worthy challenge for MDS, since GAs seem to interact indirectly and subtly with proteins by influencing their local and global dynamics rather than binding to well-defined active pockets. Such dynamic perturbations would fail to be captured during the pico to nanosecond timescales typically sampled by MDS. For instance, the most prevalent belief for GAs right now is that they interact with ligand-gated ion channels like the GABA and NMDA receptor and with potassium ion channels. One hypothesis for the mode of action of halothane is that it binds to the open conformation of a potassium ion channel. The channel stays open for milliseconds, thus thwarting experimental study. However, a millisecond transition provides a robust and respectable challenge for long time-scale MD simulations. At the same time, caveats abound in the field. For instance it's easy to infer that a GA molecule binds to a certain site and obstructs the motion of a tyrosine residue, thus providing support to fluorescence quenching and other studies. But the results of such studies as well as the all-important site-directed mutagenesis studies are notoriously hard to interpret; indirect influences on protein motion may be construed as direct binding to particular sites. Plus, it seems to me that one can read too much into the mere, rather obvious observation that a molecule binding to a protein site inhibits the motion of some residues; whether that observation translates into a realistic phenomenon may be much harder to glean. So yes, it seems that GA action provides a fertile field for computer simulation. Long MD simulations generally seem to me to be a solution looking for problems; after all most interesting molecular interactions in the body take place on the order of micro to milliseconds. There is a huge number of important problems waiting to be tackled with such tools. However, interpretations of the results will always have to be guided by the sure hand of experiment, with the always important caveat that when it comes to interpretation, one computational study and one experiment can have several offspring.Vemparala, S., Domene, C., & Klein, M. (2010). Computational Studies on the Interactions of Inhalational Anesthetics with Proteins Accounts of Chemical Research, 43 (1), 103-110 DOI: 10.1021/ar900149j... Read more »
Vemparala, S., Domene, C., & Klein, M. (2010) Computational Studies on the Interactions of Inhalational Anesthetics with Proteins. Accounts of Chemical Research, 43(1), 103-110. DOI: 10.1021/ar900149j
Luigi Dei (University of Florence, Italy) and coworkers have investigated the chemical rationale underlying the degradation of some nineteenth century photographs, relevant towards preserving historically valuable photographs for future generations. This news feature was written on January 31, 2010.... Read more »
Carretti, E., Milano, M., Dei, L., & Baglioni, P. (2009) Noninvasive physicochemical characterization of two 19th century English ferrotypes. Journal of Cultural Heritage, 10(4), 501-508. DOI: 10.1016/j.culher.2009.02.002
Titan, it’s the farthest place humans have ever landed a robotic probe and one of the most intriguing moons in the solar system, resembling a cryogenic version of our own planet when it was still young. Because it has an active cycle of organic compounds, a thick atmosphere, lakes of liquid natural gas and geologic [...]... Read more »
Tokano, T. (2009) Limnological Structure of Titan's Hydrocarbon Lakes and Its Astrobiological Implication. Astrobiology, 9(2), 147-164. DOI: 10.1089/ast.2007.0220
Dominique Mazier (Universite Pierre et Marie Curie-Paris, France) and coworkers have used mass spectrometry to rapidly and unambiguously diagnose a blood-based fungal infection, faster than is possible through conventional diagnostics. This news feature was written on January 27, 2010.... Read more »
Marinach-Patrice, C., Fekkar, A., Atanasova, R., Gomes, J., Djamdjian, L., Brossas, J.-Y., Meyer, I., Buffet, P., Snounou, G., Datry, A.... (2010) Rapid Species Diagnosis for Invasive Candidiasis Using Mass Spectrometry. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008862
tags: evolutionary biology, behavioral ecology, biochemistry, biophysics, magnetoreception, photochemical mechanism, cryptochromes, geomagnetic fields, butterflies, Monarch Butterfly, Danaus plexippus, birds, migration, Cryptochrome, bpr3.org/?p=52,peer-reviewed research, peer-reviewed paper
Every autumn, millions of monarch butterflies, Danaus plexippus, each weighing less than one gram (one US penny weighs 2.5 grams), migrate nearly 4000 kilometers (3000 miles) between their summer breeding grounds in the United States and their wintering areas either in southern California or in the mountains of Mexico (Figure 1).
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Gegear, R., Foley, L., Casselman, A., & Reppert, S. (2010) Animal cryptochromes mediate magnetoreception by an unconventional photochemical mechanism. . Nature. DOI: 10.1038/nature08719
tags: evolution, evolutionary biology, evolutionary ecology, plumage color,carotenoid-based colour, carotenoids, lipid peroxidation, oxidative stress, sperm motility, sperm quality, sperm velocity, birds, ornithology, Great Tit, Parus major, bpr3.org/?p=52,peer-reviewed research, peer-reviewed paper
Great Tit, Parus major.
Image: Luc Viatour, Creative Commons/Wikipedia [larger view]
In some species of birds, males are more brightly colored than females. This phenomenon is due to female choice: females choose to mate with males that have the brightest plumage colors and most elaborate ornaments. But these characters are more than mere glitzy advertising, they are an example of honest signals because the brightest plumage and most elaborate ornaments are worn only by those males who have managed to procure enough resources necessary to grow them. But what is the link between plumage brightness and male quality? According to a newly published study of Great Tits, Parus major, males with more intensely colored breast plumage produce faster and more motile sperm.
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Helfenstein, F., Losdat, S., Møller, A., Blount, J., & Richner, H. (2010) Sperm of colourful males are better protected against oxidative stress. Ecology Letters, 13(2), 213-222. DOI: 10.1111/j.1461-0248.2009.01419.x
Philip Power offers a new insight into the chemistry of some of the heavier main group elements - that square in the periodic table cornered by aluminium and tellurium - in a recent review in Nature. In it he proposes that based on the type of bonding and reactivity compounds containing elements in this square can really behave as transition metals. ... Read more »
The duck-billed Platypus is such an odd creature that one could get the idea that its survival depends on potential predators laughing themselves to death, but in fact it can rely on a far more potent defense. It carries a venomous sting on its hind legs. Envenoming by a male Ornithorhynchus anatinus causes not only [...]... Read more »
Kita, M., Black, D., Ohno, O., Yamada, K., Kigoshi, H., & Uemura, D. (2009) Duck-Billed Platypus Venom Peptides Induce Ca Influx in Neuroblastoma Cells . Journal of the American Chemical Society, 131(50), 18038-18039. DOI: 10.1021/ja908148z
One of the really great things about science is its potential for self-correction. If you have an hypothesis, a result (strange or otherwise), a set of data, it can be tested by anyone. This is encouraged, in fact: when you publish you’re not just saying ‘look how clever I am’ but also ‘here’s something new! [...]... Read more »
Beloqui, A., Guazzaroni, M., Pazos, F., Vieites, J., Godoy, M., Golyshina, O., Chernikova, T., Waliczek, A., Silva-Rocha, R., Al-ramahi, Y.... (2009) Reactome Array: Forging a Link Between Metabolome and Genome. Science, 326(5950), 252-257. DOI: 10.1126/science.1174094
The last three issues of the 2009 volume of L'Anthropologie are dedicated to prehistoric art, and one the papers contained in that special volume concerns five vault fragments from Fumane Cave (Veneto region, Italy) that were recovered during excavation and that bear designs made in red ochre. The art itself is already well known and has been published in great detail as part of a monograph a few years ago (Broglio and Dalmieri 2005), but this study presents some new data on the likely age of the fragments, as well as on the composition of the pigments from which they're made.View of the inside of Fumane Cave.http://www.grottadifumane.it/FOTOGALLERY-DELLA-GROTTA.htmlThe issue with these fragment has been to precisely determine how old they are, since they are in secondary position, that is to say, they were not found where they were painted. It seems that during a cold snap following the moment on which the designs were painted on the cave, the vault surface spalled off and the fragments fell on deposits that were, logically, more recent than the paintings themselves. The oldest fragment (Fragment I in the figure below) bears a representation of some kind of quadruped was recovered in Unit A2, which is the base of the Aurignacian deposits at the site, whereas Fragment II ("the shaman", so called because the anthropomorphic figure it bears also shows some horn-like features) was recovered from the a pile mound of stones located at the cave's mouth, while the other decorated blocks were recovered in later (i.e., more recent) Aurignacian and Gravettian layers. In Italy, the Gravettian is securely attributed to modern humans, who are also widely thought to be the makers of the Aurignacian, and its earliest expression, the Protoaurignacian.The five decorated vault fragments from Grotta di Fumane.From: Broglio et al. (2009:756, Plate 2).The main issue, chronologically speaking, has been to determine when the figures were painted on the cave vault, since the layers in which they were recovered only provide a terminus ante quem for their age, in other words, an upper limit for their age. So, at first glance, there is no evidence for the age of these paintings beyond that of the layers in which they were recovered. However, in this study, Broglio et al. (2009) make the case that all the paintings date to the earliest Aurignacian at the site, that is to level A2. Historically, the dating of the earliest Aurignacian at Fumane has been hotly debated, but the authors present new dates for previously dated charcoal samples that have undergone, for the new dates, a new, more thorough pretreatment (i.e., ABOx SC). This has provided two statistically equivalent age determinations of 35,640 +/- 220 and 35,180 +/- 220 BP for level A2. Interestingly, and fittingly in light of my recent post on the presentation of calibrated and uncalibrated radiocarbon dates, they conclude that, by reference to the calibration curve based on the Cariaco Basin data and the GISP2 Greenland ice core, that "the chronological data show that Protoaurignacian Unit A2 dates to between 43,250 to 40,500 BPGISP2, with an age of 41,000BPGISP2 being statistically more likely" (Broglio et al. 2009:760; my translation, emphasis added).What allows them to tie the paintings to that age determination is the study of ochre found in Unit A2. The base and top of that layer include conspicuous concentrations of red ochre, and some ochre crayons were also recovered from A2. The clincher is that these crayons are made of the same ochre as that which was used for the parietal art. This is demonstrated by a brief compositional analysis of the pigments using various methods, that also indicates that these ochres are circum-local in provenience, being found in the Lessini Mountains, at the southern edge of which Fumane sits.In sum, while the decorated pieces themselves were not dated directly, this study provides some strong circumstancial evidence for their being of early Aurignacian age. If this attribution is correct, it provides us with some solid data about some of the iconographic canons and artistic techniques used by early Aurignacian foragers in northern Italy and some insights into the variability in artistic behavior within this cultural tradition at the beginning of the Upper Paleolithic.ReferencesBroglio, A., and G. Dalmieri (eds.). 2005. Pitture paleolitiche nelle Prealpi venete: Grotta di Fumane e Riparo Dalmieri. Memorie del Museo Civico di Storia Naturale di Verona, 2 serie. Sezione Scienze dell'Uomo. Verona, Italy.Broglio, A., De Stefani, M., Gurioli, F., Pallecchi, P., Giachi, G., Higham, T., & Brock, F. (2009). L’art aurignacien dans la décoration de la Grotte de Fumane L'Anthropologie, 113 (5), 753-761 DOI: 10.1016/j.anthro.2009.09.016... Read more »
Broglio, A., De Stefani, M., Gurioli, F., Pallecchi, P., Giachi, G., Higham, T., & Brock, F. (2009) L’art aurignacien dans la décoration de la Grotte de Fumane. L'Anthropologie, 113(5), 753-761. DOI: 10.1016/j.anthro.2009.09.016
Osato et al. have signed on for Oseltamivir total synthesis number 27 even though it is clear by now that the drug Tamiflu is totally ineffective against the dreaded swine flu. Nevertheless this particular synthesis has several interesting features notably its start from humble and widely available ribose ... Read more »
Osato, H., Jones, I., Chen, A., & Chai, C. (2010) Efficient Formal Synthesis of Oseltamivir Phosphate (Tamiflu) with Inexpensive -Ribose as the Starting Material . Organic Letters, 12(1), 60-63. DOI: 10.1021/ol9024716
Young-Tae Chang (National University of Singapore) and coworkers have synthesized a molecule which will be very useful for probing mitochondrial dysfunction, implicated as a factor in neurodegenerative diseases, cancers, diabetes, and other serious medical conditions. This news feature was written on January 14, 2010.... Read more »
Kim, Y. K., Ha, H.-H., Lee, J.-S., Bi, X., Ahn, Y.-H., Hajar, S., Lee, J.-J., & Chang, Y.-T. (2010) Control of Muscle Differentiation by a Mitochondria-Targeted Fluorophore. Journal of the American Chemical Society, 132(2), 576-579. DOI: 10.1021/ja906862g
There have been many new developments in quantum computing during the last few years, but last Sunday a paper appeared in Nature Chemistry that shows how far the area really has come. It seems that now things are getting really interesting: American and Australian scientists just built a quantum circuit that calculated the energy Eigenvalues [...]... Read more »
Xing-Fang Li (University of Alberta, Canada) and coworkers have added to concerns that unknown carcinogens may be lurking in treated water. This news feature was written on January 14, 2010.... Read more »
Qin, F., Zhao, Y.-Y., Zhao, Y., Boyd, J. M., Zhou, W., & Li, X.-F. (2009) A Toxic Disinfection By-product, 2,6-Dichloro-1,4-benzoquinone, Identified in Drinking Water. Angewandte Chemie International Edition. DOI: 10.1002/anie.200904934
The late, great Linus Paul, twice Nobel laureate (chemistry and peace) and advocate of mega doses of vitamin C for beating disease and extending life (he died at the ripe old age of 93) was one of the most influential scientists of the 20th century.
He worked out how nature’s catalysts, proteins known as enzymes, speed [...]... Read more »
Simón, L., & Goodman, J. (2009) Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes. The Journal of Organic Chemistry, 2147483647. DOI: 10.1021/jo901503d
Adam Kristensson (Lund University, Sweden) and coworkers have begun to unravel the chemical basis of cloud seeding by small amino acid particles, helping to understand the possible contribution of a natural aerosol to global climate. This news feature was written on January 12, 2010.... Read more »
Kristensson, A., Rosenørn, T., & Bilde, M. (2010) Cloud Droplet Activation of Amino Acid Aerosol Particles. The Journal of Physical Chemistry A, 114(1), 379-386. DOI: 10.1021/jp9055329
Jianhua Qin, Bingcheng Lin (Dalian Institute of Chemical Physics, China), and coworkers have fabricated a cheap biomedical device that will find much use in resource-limited and emergency situations. This news feature was written on January 12, 2010.... Read more »
Lu, Y., Shi, W., Qin, J., & Lin, B. (2010) Fabrication and Characterization of Paper-Based Microfluidics Prepared in Nitrocellulose Membrane By Wax Printing. Analytical Chemistry, 82(1), 329-335. DOI: 10.1021/ac9020193
This is the spring without end
This is the summer of malcontent
This is the winter of your mind
M. E. Smith, 1992
Actually Mark, this is the Winter of Malcontents. In case you had failed to notice, the Angles are unhappy with the recent weather that has afflicted Albion’s Plain.
All this snow and ice is [...]... Read more »
Hellstén PP, Salminen JM, Jørgensen KS, & Nystén TH. (2005) Use of potassium formate in road winter deicing can reduce groundwater deterioration. Environmental science , 39(13), 5095-100. PMID: 16053115
Kuchnir Fygenson (University of California, Santa Barbara) and coworkers have gained physical insights relevant towards rendering planar lipid bilayers more useful for practical biological and engineering applications. This news feature was written on January 8, 2010.... Read more »
Weirich, K. L., Israelachvili, J. N., & Fygenson, D. K. (2010) Bilayer Edges Catalyze Supported Lipid Bilayer Formation. Biophysical Journal, 98(1), 85-92. DOI: 10.1016/j.bpj.2009.09.050
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