Chemistry posts
- November 26, 2012
- 06:39 PM
- 196 views
CHARGE, traffic pollution and autism
by Paul Whiteley in Questioning Answers
The headline reads "Traffic fumes linked to autism". The by-line describes how babies who were exposed to traffic air pollution during their first year of life "are more likely to become autistic". Welcome to the study by Heather Volk and colleagues* on traffic pollution, particulate matter and risk of autism.Motorbiking... @ Wikipedia Before heading into the paper, the discerning autism research reader will no doubt remember that this is a topic which has already cropped up in autism rese........ Read more »
Volk, H. (2012) Traffic-Related Air Pollution, Particulate Matter, and AutismAir Pollution, Particulate Matter, and Autism. Archives of General Psychiatry, 1. DOI: 10.1001/jamapsychiatry.2013.266
- November 24, 2012
- 06:50 PM
- 285 views
Cosmic refinery
by Perikis Livas in Tracing Knowledge
What sounds like science fiction is actually reality: using the 30m-telescope of the Institute for Radio Astronomy for astronomical observations in the millimetre range of wavelengths, astronomers have detected, for the first time, the interstellar molecule C3H , in our galaxy. It belongs to the hydrocarbon family and is thus part of major energy resources of our planet, i.e. petroleum and natural gas. The discovery of this molecule at the heart of the famous Horsehead Nebula in the Constellatio........ Read more »
Max Planck. (2012) Cosmic refinery. Max Planck Gesellschaft - Research News - Astronomy - Astrophysics - Chemistry. info:/
- November 23, 2012
- 08:28 PM
- 335 views
The protein folding problem
by Perikis Livas in Tracing Knowledge
The protein-folding problem was first posed about one half-century ago. The term refers to three broad questions: (i) What is the physical code by which an amino acid sequence dictates a protein’s native structure? (ii) How can proteins fold so fast? (iii) Can we devise a computer algorithm to predict protein structures from their sequences? We review progress on these problems. In a few cases, computer simulations of the physical forces in chemically detailed models have now achieved the ........ Read more »
Tracing Knowledge. (2012) The protein folding problem. Tracing Knowledge. info:/
- November 18, 2012
- 03:39 PM
- 229 views
DHSs and histone modifications: methylation, acetylation, citrullination, and phosphorylation
by egonw in Chem-bla-ics
One day on, and still struggling with the chemistry behind gene regulation. Let no biologist ever tell me again not to use acronyms (yes, I am looking at you!). But it is interesting. I learned a lot about ChIP, histone modifications, etc, etc. This is an amazing world, where specific histone complex protein residues get methylated, acetylated, citrullinated, and phosphorylated. Of course, all this is in the context of the ENCODE meeting we have tomorrow at BiGCaT, where I will try to ........ Read more »
Thurman, R., Rynes, E., Humbert, R., Vierstra, J., Maurano, M., Haugen, E., Sheffield, N., Stergachis, A., Wang, H., Vernot, B.... (2012) The accessible chromatin landscape of the human genome. Nature, 489(7414), 75-82. DOI: 10.1038/nature11232
Felsenfeld G, Boyes J, Chung J, Clark D, & Studitsky V. (1996) Chromatin structure and gene expression. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9384-8. PMID: 8790338
- November 17, 2012
- 12:02 PM
- 199 views
The chemistry of DNA modifications for gene regulation
by egonw in Chem-bla-ics
I have started learning about epigenetics, and particularly the regulatory effects of DNA methylation and acetylation. It's cool, it's hot, it's everything we hope will explain genetics, because genes certainly did not.
The chemistry behind this involves interesting pathways, involves storage of information that passes from one generation to another... epigenetic effects down to the grandchild generation have repeatedly been shown now. I likely candidate are mRNAs that persist beyond the cell d........ Read more »
Donohoe, D., Collins, L., Wali, A., Bigler, R., Sun, W., & Bultman, S. (2012) The Warburg Effect Dictates the Mechanism of Butyrate-Mediated Histone Acetylation and Cell Proliferation. Molecular Cell. DOI: 10.1016/j.molcel.2012.08.033
- November 16, 2012
- 10:09 AM
- 135 views
Sweaty Criminals Beware
by Arielle D. Ross in Salamander Hours
Sweaty Criminals BewareA new way to lift fingerprints left behind by sweat-laden paws. Continue reading →Salamander Hours - A Science Blog with a Mighty Name... Read more »
Jaber, N., Lesniewski, A., Gabizon, H., Shenawi, S., Mandler, D., & Almog, J. (2012) Visualization of Latent Fingermarks by Nanotechnology: Reversed Development on Paper-A Remedy to the Variation in Sweat Composition. Angewandte Chemie International Edition. DOI: 10.1002/anie.201205259
- November 16, 2012
- 08:56 AM
- 182 views
Airships: The Future of Air Travel?
by Jason Carr in Wired Cosmos
Considering the fact that airships have been around for a while now, it’s hard to believe that they are thought of as emerging technologies today. But that’s exactly the case given recent advances in this arena. Hydrogen airships have a troubled history due to several significant historical disasters. However, new technologies could help reduce this [...]... Read more »
Michele Trancossi, Antonio Dumas, Mauro Madonia, Jose Pascoa, & Dean Vucinic. (2012) Fire-safe Airship System Design. SAE Int. J. Aerosp. , 11-21. info:/10.4271/2012-01-1512
- November 13, 2012
- 05:28 PM
- 279 views
Stealing nature’s photosynthetic secrets
by Perikis Livas in Tracing Knowledge
The prospect of creating clean, renewable hydrogen fuel is closer than ever after a breakthrough in our understanding of photosynthesis.
Professors Rob Stranger and Ron Pace from the Research School of Chemistry in the ANU College of Physical and Mathematical Sciences used computer modelling to reveal the molecular structure of the photosynthesis reaction site in plants. This is where sunlight is used to convert water into its components – hydrogen and oxygen.
For the first time, the........ Read more »
Australian National University. (2012) Stealing nature’s photosynthetic secrets. Australian National University. info:/
- November 13, 2012
- 02:45 PM
- 159 views
The perfect combination: wine, intrinsically disordered proteins and mass spectrometry
by Clay Clark in Biochem Blogs
After spending a great deal of time and energy on cancer research everyday, sometimes I like to go home and down a glass of red wine (or two, depending on the day). Then, I am left to ponder the simpler … Continue reading →... Read more »
GAWEL RICHARD. (1998) Red wine astringency: a review. Australian Journal of Grape and Wine Research, 4(2), 74-95. DOI: 10.1111/j.1755-0238.1998.tb00137.x
Pascal Christine, Poncet-Legrand Céline, Imberty Anne, Gautier Catherine, Sarni-Manchado Pascale, Cheynier Véronique, & Vernhet Aude. (2007) Interactions between a Non Glycosylated Human Proline-Rich Protein and Flavan-3-ols Are Affected by Protein Concentration and Polyphenol/Protein Ratio. Journal of Agricultural and Food Chemistry, 55(12), 4895-4901. DOI: 10.1021/jf0704108
Canon Francis, Ballivian Renaud, Chirot Fabien, Antoine Rodolphe, Sarni-Manchado Pascale, Lemoine Jérôme, & Dugourd Philippe. (2011) Folding of a Salivary Intrinsically Disordered Protein upon Binding to Tannins. Journal of the American Chemical Society, 133(20), 7847-7852. DOI: 10.1021/ja200534f
- November 12, 2012
- 07:07 PM
- 176 views
Competition in flatland
by Joerg Heber in All That Matters
Move over graphene, there is competition in town. A new type of two-dimensional materials – with the far less appealing family name, transition metal dichalcogenides – are increasingly gaining attention. Well, at least they’re giving it a shot. Graphene, a sheet of carbon atoms only one atomic layer thick, still has plenty going for itself [...]... Read more »
Wang, Q., Kalantar-Zadeh, K., Kis, A., Coleman, J., & Strano, M. (2012) Electronics and optoelectronics of two-dimensional transition metal dichalcogenides. Nature Nanotechnology, 7(11), 699-712. DOI: 10.1038/nnano.2012.193
- November 11, 2012
- 04:48 PM
- 405 views
Scientists Discover Possible Building Blocks of Ancient Genetic Systems in Earth’s Most Primitive Organisms
by Perikis Livas in Tracing Knowledge
Scientists believe that prior to the advent of DNA as Earth’s primary genetic material, early forms of life used RNA to encode genetic instructions. What sort of genetic molecules did life rely on before RNA?
The answer may be AEG, a small molecule that when linked into chains forms a hypothetical backbone for peptide nucleic acids, which have been hypothesized as the first genetic molecules. Synthetic AEG has been studied by the pharmaceutical industry as a possible gene silencer to st........ Read more »
ScienceDaily. (2012) Scientists Discover Possible Building Blocks of Ancient Genetic Systems in Earth's Most Primitive Organisms. ScienceDaily. info:/
- November 10, 2012
- 09:45 PM
- 193 views
Detecting bacteria with fluorescent nanoparticles
by Cath in Basal Science (BS) Clarified
pH indicators are more than just tools for helping students visualize the differences between acids and bases. They can also be used in sensors to monitor bacterial growth in packaged [...]... Read more »
Wang, X., Meier, R., & Wolfbeis, O. (2012) Fluorescent pH-Sensitive Nanoparticles in an Agarose Matrix for Imaging of Bacterial Growth and Metabolism. Angewandte Chemie. DOI: 10.1002/ange.201205715
- November 9, 2012
- 02:46 PM
- 331 views
Caffeine Helps Us Recognize Positive Words
by Elizabeth Preston in Inkfish
Does anyone still say "full of beans"? The phrase is supposed to describe someone who's upbeat and energetic. Maybe we can revive the expression by attaching it specifically to coffee beans, as in, "I just had a double-shot cappuccino and boy, oh boy am I full of beans!"
Caffeine lovers know the feeling of finishing a well-timed cup of coffee or tea: positive, alert, ready to go. (And maybe ready to go to the bathroom.) New research suggests that our brains also process language differently........ Read more »
Kuchinke, L., & Lux, V. (2012) Caffeine Improves Left Hemisphere Processing of Positive Words. PLoS ONE, 7(11). DOI: 10.1371/journal.pone.0048487
- November 8, 2012
- 04:29 PM
- 204 views
Science on Crack, 5: The science of weed
by Puff the Mutant Dragon in Puff the Mutant Dragon
Of all our country's illegal drugs, cannabis is by far and away the most popular. Depending on where you live, it may not even be illegal for much longer.... Read more »
Grotenhermen, F. (2003) Pharmacokinetics and Pharmacodynamics of Cannabinoids. Clinical Pharmacokinetics, 42(4), 327-360. DOI: 10.2165/00003088-200342040-00003
- November 6, 2012
- 09:32 AM
- 177 views
Retreating to Ocean Isle
by Clay Clark in Biochem Blogs
When you think of Italy you may conjure up images of fine wines, food hearty enough to suppress the most insatiable appetite or natural beauty only a poet could describe, but I think of a birthplace. The birthplace of an … Continue reading →... Read more »
Alon Uri. (2009) How To Choose a Good Scientific Problem. Molecular Cell, 35(6), 726-728. DOI: 10.1016/j.molcel.2009.09.013
Bourne Philip E., & Friedberg Iddo. (2006) Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Computational Biology, 2(11). DOI: 10.1371/journal.pcbi.0020121
Walters Jad, Schipper Joshua L., Swartz Paul, Mattos Carla, & Clark A. Clay. (2012) Allosteric modulation of caspase 3 through mutagenesis. Bioscience Reports, 32(4), 401-411. DOI: 10.1042/BSR20120037
- November 1, 2012
- 11:23 AM
- 205 views
Honey Bees, Whiskey, and Juicy Fruit Gum
by Dan Bailey in Smells Like Science
For a blog called Smells Like Science, you might have noticed that I haven’t written much about smelly science. That all changes here as I get to the bottom of the “Juicy Fruit: which fruit does it taste like?” debate. Plus, what do Juicy Fruit Gum and honey bees have in common?... Read more »
BOCH R, SHEARER DA, & STONE BC. (1962) Identification of isoamyl acetate as an active component in the sting pheromone of the honey bee. Nature, 1018-20. PMID: 13870346
Collins, A., & Blum, M. (1982) Bioassay of compounds derived from the honeybee sting. Journal of Chemical Ecology, 8(2), 463-470. DOI: 10.1007/BF00987794
- October 30, 2012
- 01:09 PM
- 201 views
The Bcl-2 family of proteins: A life or death situation
by Clay Clark in Biochem Blogs
If you’ve taken a biochemistry class, you’ve probably heard the structure-function paradigm for proteins: amino acid sequence dictates how the protein will be folded, and the ordered 3D structure of the protein is necessary for function.(1) For example, proper formation … Continue reading →... Read more »
Dunker A.Keith, Lawson J.David, Brown Celeste J, Williams Ryan M, Romero Pedro, Oh Jeong S, Oldfield Christopher J, Campen Andrew M, Ratliff Catherine M, & Hipps Kerry W. (2001) Intrinsically disordered protein. Journal of Molecular Graphics and Modelling, 19(1), 59. DOI: 10.1016/S1093-3263(00)00138-8
Rautureau Gilles J. P., Day Catherine L., & Hinds Mark G. (2010) Intrinsically Disordered Proteins in Bcl-2 Regulated Apoptosis. International Journal of Molecular Sciences, 11(4), 1824. DOI: 10.3390/ijms11041808
Rodi Diane J, Janes Robert W, Sanganee Hitesh J, Holton Robert A, Wallace B.A, & Makowski Lee. (1999) Screening of a library of phage-displayed peptides identifies human Bcl-2 as a taxol-binding protein. Journal of Molecular Biology, 285(1), 203. DOI: 10.1006/jmbi.1998.2303
- October 25, 2012
- 02:53 PM
- 346 views
Why You Should Reject the “Rejection Improves Impact” Meme
by caseybergman in I wish you'd made me angry earlier
Over the last two weeks, a meme has been making the rounds in the scientific twittersphere that goes something like “Rejection of a scientific manuscript improves its eventual impact”. This idea is based a recent analysis of patterns of manuscript submission reported in Science by Calcagno et al., which has been actively touted in the [...]... Read more »
Calcagno, V., Demoinet, E., Gollner, K., Guidi, L., Ruths, D., & de Mazancourt, C. (2012) Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns. Science. DOI: 10.1126/science.1227833
- October 24, 2012
- 11:32 AM
- 392 views
The Smell of Fear
by Miss Behavior in The Scorpion and the Frog
Several animals, many of them insects, crustaceans and fish, can smell when their fellow peers are scared. A kind of superpower for superwimps, this is an especially useful ability for prey species. An animal that can smell that its neighbor is scared is more likely to be able to avoid predators it hasn’t detected yet. Who can smell when you're scared? Photo provided by Freedigitalphotos.net.“What does fear smell like?” you ask. Pee, of course. I mean, that has to be the answer, right? It........ Read more »
Brown, G.E., Jackson, C.D., Malka, P.H., Jacques, É., & Couturier, M-A.,. (2012) Disturbance cues in freshwater prey fishes: Does urea function as an ‘early warning cue’ in juvenile convict cichlids and rainbow trout?. Current Zoology, 58(2), 250-259. info:/
- October 22, 2012
- 03:47 PM
- 133 views
Free energy in the woods
by Clay Clark in Biochem Blogs
The Gibbs Conference on Biothermodynamics recently held its 26th annual meeting in Carbondale, IL. The Gibbs conference began in 1986 with a meeting to discuss the discipline of thermodynamics in biological systems. How does one apply the rigorous techniques utilized … Continue reading →... Read more »
Ackers Gary K., & Bolen D.Wayne. (1997) The Gibbs conference on biothermodynamics: Origins and evolution. Biophysical Chemistry, 64(1-3), 5. DOI: 10.1016/S0301-4622(96)02246-6
Vogt Austin D., & Di Cera Enrico. (2012) Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism. Biochemistry, 51(30), 5902. DOI: 10.1021/bi3006913
Shea Madeline A., Correia John J., & Brenowitz Michael D. (2011) Introduction: Twenty five years of the Gibbs Conference on Biothermodynamics. Biophysical Chemistry, 159(1), 5. DOI: 10.1016/j.bpc.2011.07.002
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