Chemistry posts
- February 9, 2011
- 02:01 AM
- 1,117 views
Chemical data curation: yes, it is that bad.
by egonw in Chem-bla-ics
The readers of Antony's blog know enough about the problem. And many in the QSAR community know it too (and many other do not). Chemical structure data is noisy. I haven't recently created a new local data set for analysis, so I have not taken time to blog about it much, but the ambiguity in chemical databases is enormous. Just yesterday, Antony and I had a good discussion about tautomers and in particular how things are linked together.
If we are in the field of property prediction, knowing wh........ Read more »
Porter, W. (2010) Warfarin: history, tautomerism and activity. Journal of Computer-Aided Molecular Design, 24(6-7), 553-573. DOI: 10.1007/s10822-010-9335-7
- February 8, 2011
- 10:20 PM
- 988 views
The many relationships of leaf-cutter ants
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Trying to capture the movement of a colony of leaf-cutter ants in a single photo is nearly impossible in my (amateur) experience. The queues of ants follow a worn-down trail in the ground that they themselves made with the impact of their little ant feet. There are ants moving in both directions, between the food [...]... Read more »
Currie, C., Scott, J., Summerbell, R., & Malloch, D. (1999) Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature, 398(6729), 701-704. DOI: 10.1038/19519
Schoenian, I., Spiteller, M., Ghaste, M., Wirth, R., Herz, H., & Spiteller, D. (2011) Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proceedings of the National Academy of Sciences, 108(5), 1955-1960. DOI: 10.1073/pnas.1008441108
- February 2, 2011
- 11:36 PM
- 783 views
Colonoscopy for everyone! ..or Gonna Buy Me A Dog
by Aurametrix team in Olfactics and Diagnostics
New research from Japan brings good news: dogs can be almost as accurate as a colonoscopy exam.In patients with colorectal cancer (CRC) and controls, the sensitivity of canine scent detection of breath samples compared with conventional diagnosis by colonoscopy was 0.91 and the specificity was 0.99. The sensitivity of canine scent detection of watery stool samples was 0.97 and the specificity was 0.99. The ........ Read more »
Sonoda H, Kohnoe S, Yamazato T, Satoh Y, Morizono G, Shikata K, Morita M, Watanabe A, Morita M, Kakeji Y.... (2011) Colorectal cancer screening with odour material by canine scent detection. Gut. PMID: 21282130
- January 28, 2011
- 12:00 PM
- 811 views
Red blood cells can tell time?
by Brooke N in Smaller Questions
Brief introduction to the new research identifying how red blood cells run their circadian rhythm without transcription & translation.... Read more »
O'Neill JS, & Reddy AB. (2011) Circadian clocks in human red blood cells. Nature, 469(7331), 498-503. PMID: 21270888
- January 21, 2011
- 08:41 PM
- 1,688 views
The Universe and Life is asymmetric: Chirality
by The Astronomist in The Astronomist.
The shadow of symmetry haunts physics. Symmetry is invoked to understand nature concisely, but broken symmetry is invoked to understand nature completely. Physics is filled with examples of shattered symmetries: there is more matter than antimatter, neutrinos only come in the left handed spin flavor, and quantum processes break symmetries constantly, but nature also violates symmetry in chemistry and biology in a very clever manner. Chemistry and biology are subjects I do no normally touch ........ Read more »
Robert N. Compton, Richard M. Pagni, & Volume 48, 2002, Pages 219-261. (2002) The chirality of biomolecules. Advances In Atomic, Molecular, and Optical Physics, 219-261. info:/
- January 20, 2011
- 08:53 PM
- 739 views
Kudos to the Fagnou Group
by Crystallinity in Chemical Crystallinity
I am continuously impressed by the publications that have appeared since Prof. Keith Fagnou's shocking passing a little over a year ago. The chemical community still mourns; it is clear from these post-mortem publications that Fagnou's - and his clearly dedicated and talented graduate students and post-docs - brilliance lives on. The chemistry that Fagnou has truly spearheaded, direct C-H functionalization, is a method of forming C-C, C-N, C-B, etc bonds without having to prepare one of the c........ Read more »
Lapointe, D., Markiewicz, T., Whipp, C. J., Toderian, A., & Fagnou, K. (2011) Predictable and Site-Selective Functionalization of Poly(hetero)arene Compounds by Palladium Catalysis. Journal of Organic Chemistry. info:/10.1021/jo102081a
- January 17, 2011
- 11:35 AM
- 805 views
Salmon, scent and going home again
by GrrlScientist in Maniraptora
Did you know that salmon rely on their sense of smell (olfaction) for nearly every aspect of their lives, from locating food to avoiding predators? ... Read more »
Arthur Hasler, & Warren Wisby. (1951) Discrimination of Stream Odors by Fishes and Its Relation to Parent Stream Behavior. The American Naturalist, 85(823), 223. DOI: 10.1086/281672
W.J. Wisby, & A.D. Hasler. (1954) Effect of olfactory occlusion on migrating silver salmon (O. kisutch). Journal of the Fisheries Research Board of Canada, 472-478. info:/
Yamamoto, Y., Hino, H., & Ueda, H. (2010) Olfactory Imprinting of Amino Acids in Lacustrine Sockeye Salmon. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008633
Tierney, K., Sampson, J., Ross, P., Sekela, M., & Kennedy, C. (2008) Salmon Olfaction is Impaired by an Environmentally Realistic Pesticide Mixture. Environmental Science , 42(13), 4996-5001. DOI: 10.1021/es800240u
Sandahl, J., Baldwin, D., Jenkins, J., & Scholz, N. (2004) Odor-evoked field potentials as indicators of sublethal neurotoxicity in juvenile coho salmon (Oncorhynchus kisutch) exposed to copper, chlorpyrifos, or esfenvalerate. Canadian Journal of Fisheries and Aquatic Sciences, 61(3), 404-413. DOI: 10.1139/f04-011
- Ecology / Conservation
- Biology
- Chemistry
- homing
- Cell Biology
- Evolutionary Biology
- olfactory pits
- Anatomy
- pheromone hypothesis
- Behavioral Biology
- olfaction
- Biochemistry
- Ecology
- Zoology
- Chemical Biology
- Ichthyology
- salmonidae
- fish
- pesticides
- salmon
- Environmental Chemistry
- Salmonidae
- Environmental Health
- migration
- Conservation
- January 17, 2011
- 11:12 AM
- 1,064 views
Darwin meets Gibbs: thermodynamics of natural selection
by Vasili Hauryliuk in stringent response
In order to perform its function, protein should be properly folded. Therefore stability of this proteins’ native state is crucial for its function. Denatured protein can be toxic the cell and requires specialised machinery to degrade it, thus compromising cells fitness. Having a denatured protein is not equal to just not having a functional one, it is equal to not having a functional one and hiving some costly junk.Since stability is so crucial for proteins function, it must leave its trace i........ Read more »
Fu H, Grimsley G, Scholtz JM, & Pace CN. (2010) Increasing protein stability: importance of DeltaC(p) and the denatured state. Protein science : a publication of the Protein Society, 19(5), 1044-52. PMID: 20340133
Franzosa EA, & Xia Y. (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Molecular biology and evolution, 26(10), 2387-95. PMID: 19597162
Drummond DA, & Wilke CO. (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell, 134(2), 341-52. PMID: 18662548
Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, & Drummond DA. (2011) Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proceedings of the National Academy of Sciences of the United States of America, 108(2), 680-5. PMID: 21187411
Loladze VV, Ermolenko DN, & Makhatadze GI. (2001) Heat capacity changes upon burial of polar and nonpolar groups in proteins. Protein science : a publication of the Protein Society, 10(7), 1343-52. PMID: 11420436
DePristo MA, Weinreich DM, & Hartl DL. (2005) Missense meanderings in sequence space: a biophysical view of protein evolution. Nature reviews. Genetics, 6(9), 678-87. PMID: 16074985
- January 10, 2011
- 11:55 AM
- 601 views
Environmentally Friendly Alkyl Halide Synthesis from Alcohols
by Michael Long in Phased
A very common chemical conversion (important to pharmaceutical and other syntheses), which in its most gentle application generates much waste, has now been rendered far more environmentally friendly.... Read more »
Dai, C., Narayanam, J. M. R., & Stephenson, C. R. J. (2011) Visible-light-mediated conversion of alcohols to halides. Nature Chemistry. DOI: 10.1038/NCHEM.949
- January 7, 2011
- 06:00 AM
- 1,126 views
Finding an Alzheimer’s Drug From Scratch
by Sharon Neufeldt in I Can Has Science?
Pharmaceutical companies sometimes get a bad rap, but most people don’t realize just how labor/money-intensive the process of drug discovery is. A recent paper offers a little glimpse at the process – although this research was done by chemists at … Continue reading →... Read more »
MacMillan, K., Naidoo, J., Liang, J., Melito, L., Williams, N., Morlock, L., Huntington, P., Estill, S., Longgood, J., Becker, G.... (2011) Development of Proneurogenic, Neuroprotective Small Molecules. Journal of the American Chemical Society. DOI: 10.1021/ja108211m
- January 5, 2011
- 09:45 PM
- 603 views
Genetically Damaged Bacteria Grow via Synthetic Proteins
by Michael Long in Phased
Bacteria which possess genetic damage that normally prevents reproduction in a nutrient-deficient medium can be saved by expression of artificial proteins, an important step towards constructing artificial life.... Read more »
Fisher, M. A., McKinley, K. L., Bradley, L. H., Viola, S. R., & Hecht, M. H. (2011) De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0015364
- January 4, 2011
- 04:51 PM
- 753 views
Happy New Year, Self-Repair, Bananas, and Remembering the Future!
by Paul Vallett in Electron Cafe
Happy new year! I hope 2011 brings us everything 2010 promised but failed to deliver. Namely jetpacks and first contact. But in the meantime we will have to enjoy these other exciting discoveries! Self-repairing solar cells. One of the advantages that plants have over man-made solar cells is that whenever one of the dye molecules [...]... Read more »
Choi, J. (2010) Biomimetic light-harvesting optical nanomaterials. SPIE Newsroom. DOI: 10.1117/2.1201007.003130
- January 3, 2011
- 07:27 AM
- 1,041 views
A nanoscale biofuel cell for self-powered nanotechnology devices
by Michael Berger in nanowerk
Nanotechnology researchers working on self-powered nanodevices - nanoscale systems that scavenge energy from their surrounding environment - have been experimenting with various power sources ranging from piezoelectric systems to sound. However, the most abundant energy available in biosystems is chemical and biochemical energy, such as glucose. Researchers in China have now reported an nanowire-based biofuel cell based on a single proton conductive polymer nanowire for converting chemical energ........ Read more »
Pan, C., Wu, H., Wang, C., Wang, B., Zhang, L., Cheng, Z., Hu, P., Pan, W., Zhou, Z., Yang, X.... (2008) Nanowire-Based High-Performance “Micro Fuel Cells”: One Nanowire, One Fuel Cell. Advanced Materials, 20(9), 1644-1648. DOI: 10.1002/adma.200700515
- December 27, 2010
- 07:19 AM
- 1,347 views
2010 – twelve months of great science
by Joerg Heber in All That Matters
The past year has been a great year for science with major advances in several areas. Too many exciting results to mention here. Instead, to reflect about the past year I have chosen a representative paper for each month of the year that I hope can serve as an example of the great science going [...]... Read more »
Chuang, T., Allan, M., Lee, J., Xie, Y., Ni, N., Bud'ko, S., Boebinger, G., Canfield, P., & Davis, J. (2010) Nematic Electronic Structure in the "Parent" State of the Iron-Based Superconductor Ca(Fe1-xCox)2As2. Science, 327(5962), 181-184. DOI: 10.1126/science.1181083
Lin, Y., Dimitrakopoulos, C., Jenkins, K., Farmer, D., Chiu, H., Grill, A., & Avouris, P. (2010) 100-GHz Transistors from Wafer-Scale Epitaxial Graphene. Science, 327(5966), 662-662. DOI: 10.1126/science.1184289
Kelzenberg, M., Boettcher, S., Petykiewicz, J., Turner-Evans, D., Putnam, M., Warren, E., Spurgeon, J., Briggs, R., Lewis, N., & Atwater, H. (2010) Enhanced absorption and carrier collection in Si wire arrays for photovoltaic applications. Nature Materials. DOI: 10.1038/nmat2635
Ergin, T., Stenger, N., Brenner, P., Pendry, J., & Wegener, M. (2010) Three-Dimensional Invisibility Cloak at Optical Wavelengths. Science, 328(5976), 337-339. DOI: 10.1126/science.1186351
Liang, Y., Xu, Z., Xia, J., Tsai, S., Wu, Y., Li, G., Ray, C., & Yu, L. (2010) For the Bright Future-Bulk Heterojunction Polymer Solar Cells with Power Conversion Efficiency of 7.4%. Advanced Materials, 22(20). DOI: 10.1002/adma.200903528
Yu, X., Onose, Y., Kanazawa, N., Park, J., Han, J., Matsui, Y., Nagaosa, N., & Tokura, Y. (2010) Real-space observation of a two-dimensional skyrmion crystal. Nature, 465(7300), 901-904. DOI: 10.1038/nature09124
Chadov, S., Qi, X., Kübler, J., Fecher, G., Felser, C., & Zhang, S. (2010) Tunable multifunctional topological insulators in ternary Heusler compounds. Nature Materials, 9(7), 541-545. DOI: 10.1038/nmat2770
Lin, H., Wray, L., Xia, Y., Xu, S., Jia, S., Cava, R., Bansil, A., & Hasan, M. (2010) Half-Heusler ternary compounds as new multifunctional experimental platforms for topological quantum phenomena. Nature Materials, 9(7), 546-549. DOI: 10.1038/nmat2771
Bae, S., Kim, H., Lee, Y., Xu, X., Park, J., Zheng, Y., Balakrishnan, J., Lei, T., Ri Kim, H., Song, Y.... (2010) Roll-to-roll production of 30-inch graphene films for transparent electrodes. Nature Nanotechnology, 5(8), 574-578. DOI: 10.1038/NNANO.2010.132
MAIMAN, T. (1960) Stimulated Optical Radiation in Ruby. Nature, 187(4736), 493-494. DOI: 10.1038/187493a0
KLEMENT, W., WILLENS, R., & DUWEZ, P. (1960) Non-crystalline Structure in Solidified Gold–Silicon Alloys. Nature, 187(4740), 869-870. DOI: 10.1038/187869b0
Kim, R., Kim, D., Xiao, J., Kim, B., Park, S., Panilaitis, B., Ghaffari, R., Yao, J., Li, M., Liu, Z.... (2010) Waterproof AlInGaP optoelectronics on stretchable substrates with applications in biomedicine and robotics. Nature Materials, 9(11), 929-937. DOI: 10.1038/nmat2879
Toyabe, S., Sagawa, T., Ueda, M., Muneyuki, E., & Sano, M. (2010) Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality. Nature Physics, 6(12), 988-992. DOI: 10.1038/nphys1821
Wunderlich, J., Park, B., Irvine, A., Zarbo, L., Rozkotova, E., Nemec, P., Novak, V., Sinova, J., & Jungwirth, T. (2010) Spin Hall Effect Transistor. Science, 330(6012), 1801-1804. DOI: 10.1126/science.1195816
- December 22, 2010
- 12:02 PM
- 792 views
New place, new view, slow reactions and the origins of life
by The Curious Wavefunction in The Curious Wavefunction
I have been unable to blog for the past few days because I was busy moving to Chapel Hill for a postdoc at UNC Chapel Hill. I am very excited about this move and my upcoming research which is going to involve protein design and folding. Regular blogging will resume soon. Until then, happy holidays, and I will leave you with the following interesting paper published by a group from my new institution.One of the abiding puzzles in the origin of life is to explain how life arose in the relatively s........ Read more »
Stockbridge, R., Lewis, C., Yuan, Y., & Wolfenden, R. (2010) Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes. Proceedings of the National Academy of Sciences, 107(51), 22102-22105. DOI: 10.1073/pnas.1013647107
- December 22, 2010
- 11:21 AM
- 793 views
Happy Christmas Lectures 2010
by Duncan Hull in O'Really?
As Tom Lehrer once sang on his winterval carol: “Christmas time is here, by golly, Disapproval would be folly, Deck the halls with hunks of holly, Fill the cup and don’t say ‘when.’ Kill the turkeys, ducks and chickens, Mix the punch, drag out the Dickens, Even though the prospect sickens, Brother, here we go [...]... Read more »
Mark Miodownik. (2005) Facts not opinions? Devoloping both the physical and aesthetic properties of materials. Nature Materials, 4(7), 506-508. DOI: 10.1038/nmat1416
- December 22, 2010
- 06:00 AM
- 752 views
Trespassing Viruses Will Be Killed on Contact
by Sharon Neufeldt in I Can Has Science?
It’s the holiday season, which means it’s time to start thinking about the flu! The flu is notoriously tricky to prevent with vaccines, partly because there are so many strains of influenza virus, and each strain is constantly undergoing genetic … Continue reading →... Read more »
Bryan B. Hsu, Sze Yinn Wong, Paula T. Hammond, Jianzhu Chen, and Alexander M. Klibanov. (2010) Mechanism of inactivation of influenza viruses by immobilized hydrophobic polycations. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1017012108
- December 21, 2010
- 10:36 PM
- 972 views
Ergot in the Rye
by Matthew DiLeo in The Scientist Gardener
Stopping at the charity field on the way back from pollinating, I noticed a ripening rye cover crop the next field over - and decided to look for my friend, ergot.*
I couldn't believe my luck! There were little black pods sprouting from rye spikes all over the edge of the field. This is a very exciting creature to a plant pathologist - and one that's had quite an impact on European history...
Ergot is a plant disease caused by Claviceps purpurea, a member of one of my favorite fungal families........ Read more »
Schumann, G. (2000) Ergot. The Plant Health Instructor. DOI: 10.1094/PHI-I-2000-1016-01
Stone, R. (2008) MYCOLOGY: Last Stand for the Body Snatcher of the Himalayas?. Science, 322(5905), 1182-1182. DOI: 10.1126/science.322.5905.1182
Roberts, C., & Andrae, J. (2004) Tall Fescue Toxicosis and Management. Crop Management. DOI: 10.1094/CM-2004-0427-01-MG
- December 21, 2010
- 04:22 AM
- 616 views
re: Commercial or Proprietary?
by egonw in Chem-bla-ics
OK, the second paper I ran into today is a perfect match for the paper by Khanna and Ranganathan I just dicussed in the Commercial or Proprietary? post. So perfect, in fact, that it I should have really combined them. But since the other post is already infecting the WWW, I'll have to post this update.
Yap wrote up a paper on PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints (doi:10.1002/jcc.21707), and Table 2 is quite like Table 1 in the paper by Kh........ Read more »
Yap, C. (2010) PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry. DOI: 10.1002/jcc.21707
- December 18, 2010
- 03:30 PM
- 622 views
Long-Term Efficacy of an Artificial Wetland for Wastewater Treatment
by Michael Long in Phased
An artificial wetland in central Florida greatly improved municipal and industrial wastewater quality for at least 18 months.... Read more »
Lazareva, O., & Pichler, T. (2010) Long-term performance of a constructed wetland/filter basin system treating wastewater, Central Florida. Chemical Geology, 269(1-2), 137-152. DOI: 10.1016/j.chemgeo.2009.06.006
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