Chemistry posts
- August 31, 2010
- 07:00 AM
- 28 views
Chemistry of the Great Big Blue: Metals
by Bluegrass Blue Crab in Southern Fried Science
The ocean is full of metals and minerals that naturally occur such as zinc, copper, and cobalt and many marine organisms therefore depend upon access to those metals in small concentrations. However, inshore marine systems receive inputs from industrial, mining, and stormwater runoff that far exceed what these organisms can use. So what’s the effect? [...]... Read more »
M. Mayer-Pinto, A.J. Underwood, T. Tolhurst, R.A. Coleman. (2010) Effects of metals on aquatic assemblages: What do we really know?. J. Exp. Mar. Biol. Ecol., 1-9. info:/
- August 30, 2010
- 10:05 PM
- 33 views
All Thirteen Priority Elemental Pollutants Emitted via Oil Sand Extraction
by Michael Long in Phased
David Schindler (University of Alberta, Canada) and coworkers have thoroughly destroyed the claim that oil sand extraction, as currently practiced, is safe for the environment. This news feature was written on August 30, 2010.... Read more »
Kellya, E. N., Schindlera, D. W., Hodsonb, P. V., Shortc, J. W., Radmanovicha, R., & Nielsena, C. C. (2010) Oil sands development contributes elements toxic at low concentrations to the Athabasca River and its tributaries. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1008754107
- August 30, 2010
- 05:38 PM
- 35 views
Assessing computationally designed enzymes
by The Curious Wavefunction in The Curious Wavefunction
One of the most promising recent developments in computational biochemistry is the development of potential capability to design entirely new enzymes that can perform reactions inaccessible to naturally occurring proteins. Such enzymes can be of great utility as novel biofuels, synthetic reagents and new drugs. A particularly noteworthy set of publications in this regard were from David Baker’s and Ken Houk’s groups in Seattle and Los Angeles. In 2008, the groups designed an enzyme for perfo........ Read more »
Kiss, G., Röthlisberger, D., Baker, D., & Houk, K. (2010) Evaluation and ranking of enzyme designs. Protein Science. DOI: 10.1002/pro.462
- August 23, 2010
- 09:05 PM
- 55 views
A Web Server for Identifying the "Hot Spot" of Protein-Protein Interfaces
by Michael Long in Phased
Narcis Fernandez-Fuentes (University of Leeds, United Kingdom) and coworkers' web server will greatly accelerate the development of drugs which target protein-protein interfaces. This news feature was written on August 23, 2010.... Read more »
Segura Mora, J. S., Assi, S. A., & Fernandez-Fuentes, N. (2010) Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0012352
- August 22, 2010
- 12:30 AM
- 55 views
Of blood and breath: metabolite-based diagnosis of ovarian cancer
by Irene Gabashvili in Olfactics and Diagnostics
Physicians always knew that breath contains clues to diseases. Chemicals in breath often correlate with chemicals in saliva and blood - be it alcohol, anaesthetics or other metabolites (see, for example, this study by Dr Andreas Hengstenberg).As one of my interests is breath-based detection of ovarian cancer, I took note of the recent paper claiming 99% to 100% accuracy of detecting ovarian cancer by metabolites in blood. The authors used customized functional support vector machine-based machin........ Read more »
Zhou M, Guan W, Walker LD, Mezencev R, Benigno BB, Gray A, Fernández FM, & McDonald JF. (2010) Rapid Mass Spectrometric Metabolic Profiling of Blood Sera Detects Ovarian Cancer with High Accuracy. Cancer epidemiology, biomarkers . PMID: 20699376
- August 20, 2010
- 01:40 PM
- 69 views
Cylons and Smelloscopes: False Positives and False Negatives in the Search for Extraterrestrial Life
by The Astronomist in The Astronomist.
Are there planets outside of our solar system? Is there life on other planets? Is life on other planets like life on Earth? These are questions that astronomers, astrobiologists, chemists, and geologists are trying to answer with current experiments. In order to answer these questions we must observe distant planets and we must determine what life on those planets may be like. Detecting extrasolar planets is tricky enough, but imaging what alien life is like may well be stranger than science fic........ Read more »
Beichman, C. A., Woolf, N. J., & Lindensmith, C. A. (1999) The Terrestrial Planet Finder (TPF) : a NASA Origins Program to search for habitable planets. JPL publication. info:/
- August 19, 2010
- 02:00 PM
- 55 views
Scientists With Data Agree…A Deepwater Oil Plume Exists in the Gulf
by Dr. M in Deep Sea News
BP want’s to deny the presence of a deepwater oil plume in the Gulf of Mexico. The very oil plume both predicted by models published in 2003. The very oil plume that the massive amounts of dispersant injected at depth created to prevent oil from washing ashore. Even the government wants to deny the existence of any . . . → Read More: Scientists With Data Agree…A Deepwater Oil Plume Exists in the Gulf... Read more »
Richard Camilli, Christopher M. Reddy, Dana R. Yoerger, Benjamin A. S. Van Mooy, Michael V. Jakuba, James C. Kinsey, Cameron P. McIntyre, Sean P. Sylva, & James V. Maloney. (2010) Tracking Hydrocarbon Plume Transport and Biodegradation at Deepwater Horizon. Science. info:/10.1126/science.1195223
- August 17, 2010
- 12:31 PM
- 57 views
Spaceballs!
by Invader Xan in Supernova Condensate
Causing quite a big stir in the astrochemical world recently is the astronomical detection of C60, more popularly known as fullerene. This is kind of a big deal. Fullerenes have been known about since the 1980s when Harry Kroto et al first5 created them by vapourising graphite with electrical discharges. Since then, it's been found that C60 molecules are very stable and readily formed molecules. Lots of people have hypothesised them existing in space, but up until now there's been no conclusive........ Read more »
Cami, J., Bernard-Salas, J., Peeters, E., & Malek, S. (2010) Detection of C60 and C70 in a Young Planetary Nebula. Science. DOI: 10.1126/science.1192035
- August 16, 2010
- 07:16 AM
- 51 views
POSS Dendrimers for Drug Delivery
by KJHaxton in Endless Possibilities v3.0
Drug delivery is an area of research on the border of pharmaceutical science and medicinal chemistry. My experience of drug delivery is mainly concerned with using polymers to devise new ways of getting approved drugs into the human body. For example, a drug used in chemotherapy may well have extensive side effects when administered to a patient by intra venous infusion, yet [...]... Read more »
Maeda H. (2001) The enhanced permeability and retention (EPR) effect in tumor vasculature: the key role of tumor-selective macromolecular drug targeting. Advances in enzyme regulation, 189-207. PMID: 11384745
Kaneshiro, T., Wang, X., & Lu, Z. (2007) Synthesis, Characterization, and Gene Delivery of Poly- -lysine Octa(3-aminopropyl)silsesquioxane Dendrimers: Nanoglobular Drug Carriers with Precisely Defined Molecular Architectures . Molecular Pharmaceutics, 4(5), 759-768. DOI: 10.1021/mp070036z
Kaneshiro, T., & Lu, Z. (2009) Targeted intracellular codelivery of chemotherapeutics and nucleic acid with a well-defined dendrimer-based nanoglobular carrier. Biomaterials, 30(29), 5660-5666. DOI: 10.1016/j.biomaterials.2009.06.026
Yuan, H., Luo, K., Lai, Y., Pu, Y., He, B., Wang, G., Wu, Y., & Gu, Z. (2010) A Novel Poly( -glutamic acid) Dendrimer Based Drug Delivery System with Both pH-Sensitive and Targeting Functions . Molecular Pharmaceutics, 7(4), 953-962. DOI: 10.1021/mp1000923
- August 12, 2010
- 02:15 PM
- 60 views
A Safe, Cheap, and Stable Aqueous Lithium-Ion Battery
by Michael Long in Phased
Yong-Yao Xia (Fudan University, China) and coworkers' aqueous lithium-ion batteries exhibit excellent recharge capability, and with further technical development will become commercially viable. This news feature was written on August 12, 2010.... Read more »
Luo, J.-Y., Cui, W.-J., He, P., & Xia, Y.-Y. (2010) Raising the cycling stability of aqueous lithium-ion batteries by eliminating oxygen in the electrolyte. Nature Chemistry. DOI: 10.1038/nchem.763
- August 11, 2010
- 01:51 PM
- 77 views
On cancers and petroleum spills
by Irene Gabashvili in Olfactics and Diagnostics
Researchers have known for years that smell of cancer patients is chemically different from healthy individuals. One more study featured in British Journal of Cancer brings us a bit closer to an inexpensive, easy-to-use, portable device for home diagnostics. Exhaled breath collected from 177 volunteers (patients with lung, colon, breast, and prostate cancers and healthy controls) was examined by gold nanoparticle nanosensor arrays (GNPs) and gas chromatography linked to the mass spectr........ Read more »
Peng G, Hakim M, Broza YY, Billan S, Abdah-Bortnyak R, Kuten A, Tisch U, & Haick H. (2010) Detection of lung, breast, colorectal, and prostate cancers from exhaled breath using a single array of nanosensors. British journal of cancer, 103(4), 542-51. PMID: 20648015
- August 10, 2010
- 06:58 PM
- 78 views
Finding Buckyballs in Space
by Steve W in Bridgehead Carbons
When you hear about molecules in interstellar space or on the moons of Saturn they tend to be small molecules like methane, ammonia or water. A big organic molecule would be something like glycine, the simplest amino acid, with only 5 "big" atoms (carbon, oxygen and nitrogen) and 5 Hydrogen atoms. So finding buckyballs with 60 or 70 carbon atoms is really quite extraordinary. It's a big difference, and buckyballs contain only carbon atoms - no other elements not even hydrogen, the mo........ Read more »
Cami, J., Bernard-Salas, J., Peeters, E., & Malek, S. (2010) Detection of C60 and C70 in a Young Planetary Nebula. Science. DOI: 10.1126/science.1192035
- August 10, 2010
- 01:05 PM
- 67 views
Pheromonal Trickery: Towards Sustainable Invasive Ant Control
by Michael Long in Phased
Max Suckling (New Zealand Institute for Plant and Food Research) and coworkers have worked towards controlling imported red fire ants, a damaging insect pest, in an environmentally-responsible manner. This news feature was written on August 10, 2010.... Read more »
Suckling, D. M., Stringer, L. D., Bunn, B., El-Sayed, A. M., & Vander Meer, R. K. (2010) Trail Pheromone Disruption of Red Imported Fire Ant. Journal of Chemical Ecology, 36(7), 744-750. DOI: 10.1007/s10886-010-9810-6
- August 10, 2010
- 08:00 AM
- 75 views
Ultrasonic plasma bubbles implode
by David Bradley in SciScoop Science Forum
If you’re having a baby scan, rest assured there’s nothing to worry about here, this piece of research is about high-energy ultrasound. The difference is like comparing a research laser beam to the light from a cheap flashlight… Anyway, according to Ken Suslick, when high-intensity ultrasound passes through a liquid, the expansion wave of the [...]... Read more »
Flannigan, D., & Suslick, K. (2010) Inertially confined plasma in an imploding bubble. Nature Physics. DOI: 10.1038/nphys1701
- August 9, 2010
- 02:50 PM
- 54 views
Chemical Ant Language Has Synonyms
by Michael Long in Phased
Ellen van Wilgenburg (University of Melbourne, Australia) and coworkers have shown that ants can sometimes discriminate between highly similar carbon-based compounds, depending on molecular chain length and branching unit position. This news feature was written on August 9, 2010.... Read more »
van Wilgenburg, E., Sulc, R., Shea, K. J., & Tsutsui, N. D. (2010) Deciphering the Chemical Basis of Nestmate Recognition. Journal of Chemical Ecology, 36(7), 751-758. DOI: 10.1007/s10886-010-9812-4
- August 8, 2010
- 05:20 AM
- 67 views
Synthesis of Cylindricines
by Akshat Rathi in The Allotrope
The family of tricylic compounds despite being known to possess no significant biological activity have been a target of many previous syntheses because of it's challenging structure. The paper in discussion today is the synthesis of Cylindricine C synthesised in the Chemistry Research Laboratory at Oxford University which elaborates the use of the recently published methodology by the Donohoe group.
Most of the previously reported synthesis (Snider, Heathcock, Molander, Trost and........ Read more »
Donohoe, T., Brian, P., Hargaden, G., & O’Riordan, T. (2010) Synthesis of cylindricine C and a formal synthesis of cylindricine A. Tetrahedron, 66(33), 6411-6420. DOI: 10.1016/j.tet.2010.05.044
- August 5, 2010
- 10:04 AM
- 94 views
Humans beat computers in predicting protein structures
by The Curious Wavefunction in The Curious Wavefunction
I was going to first describe Rosetta in a post, but a rather cool paper related to the program which appeared in Nature yesterday makes me jump the gun.In a nutshell, Rosetta tries to predict the structure of proteins from amino acid sequence by inserting fragments from known protein structures and doing many rounds of side chain torsional angle and rigid-body energy optimization. It uses a scoring function to rank the resulting structures that uses empirically derived hydrogen bonding, hydroph........ Read more »
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304
- August 5, 2010
- 08:24 AM
- 79 views
Foldit: Innovative Biology for Gamers
by GrrlScientist in This Scientific Life
Guessing how a protein will fold up based on its DNA sequence is often too difficult for even the most advanced computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, an online computer game where computer players do the work. ... Read more »
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304
- August 4, 2010
- 01:15 PM
- 75 views
A Simplified Yet Quantitative Model for Macromolecular Crowding
by Michael Long in Phased
Nikolay Dokholyan (University of North Carolina at Chapel Hill, United States) and coworkers report a primitive theoretical model for protein folding stability in relation to macromolecular crowding, and find that it agrees with experiments as well as theoretical models which are far more complicated. This news feature was written on August 4, 2010.... Read more »
Tsao, D., Minton, A. P., & Dokholyan, N. V. (2010) A Didactic Model of Macromolecular Crowding Effects on Protein Folding. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0011936
- August 4, 2010
- 01:10 PM
- 76 views
Determining the structure by looking at the molecule
by Lars Fischer in EuCheMS 2010 Blog
In many cases it is notoriously difficult to determine the exact structure of a molecule, especially with larger ones. Stereocenters tend to make things worse, and interesting molecules tend to have several of them. Have you ever sat up to the neck in a pile of inconclusive spectra and wished you could just hold it [...]... Read more »
Gross, L., Mohn, F., Moll, N., Meyer, G., Ebel, R., Abdel-Mageed, W., & Jaspars, M. (2010) Organic structure determination using atomic-resolution scanning probe microscopy. Nature Chemistry. DOI: 10.1038/nchem.765
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