Chemistry posts
- April 12, 2012
- 07:11 AM
- 557 views
There Might Be Evolved Dinosaurs in Other Planets: Research
by United Academics in United Academics
The study by American chemist Ronald Breslow, at Columbia University, is actually about the conditions that made life possible on earth. But its conclusions are stunning.... Read more »
Breslow R. (2012) Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth. Journal of the American Chemical Society. PMID: 22444622
- April 9, 2012
- 12:53 AM
- 375 views
Mycology Symposium, Poster Session
by csoeder in Topologic Oceans
It is a lovely spring day and I am absorbing some sunlight, hanging out in the tail end of the Carrboro Really Free Market while I type up my notes on the Duke Mycology Symposium. There were a couple of posters which really caught my eye. One thing that I think is very interesting about [...]... Read more »
Cohn, J. (2008) Citizen Science: Can Volunteers Do Real Research?. BioScience, 58(3), 192. DOI: 10.1641/B580303
Randolph Nesse, & George Williams. (1994) Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books: New York. info:/
- April 7, 2012
- 04:47 AM
- 471 views
A typical QSAR study (cite:citesAsAuthority)
by egonw in Chem-bla-ics
I use CiTO to keep track of how the CDK is cited and used, and just looked at a typical QSAR paper. Here are my comments on "Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship", by Lu et al (doi:10.1016/j.chemolab.2011.11.011). Normally, I am fairly short in these reviews which I publish via the CDK Google+ page, briefly describing what CDK functionality is being used. But this time the post became a more substantial r........ Read more »
Lu, X., Ji, D., Chen, J., Zhou, X., & Shi, H. (2012) Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship. Chemometrics and Intelligent Laboratory Systems. DOI: 10.1016/j.chemolab.2011.11.011
- April 6, 2012
- 09:42 PM
- 311 views
Mycology Symposium, Day 2
by csoeder in Topologic Oceans
Day 2 of the Duke Mycology Symposium has wound to a close, [DAY 1 HERE] and I am sitting on my porch contemplating the afternoon’s lectures: “Pathogen recombination during the amphibian Chytridiomycosis pandemic: Why change what’s working?” A genetics perspective on Bd, a fungus responsible for widespread amphibian mortality. Apparently one of the factors in [...]... Read more »
Dadachova E, Bryan RA, Huang X, Moadel T, Schweitzer AD, Aisen P, Nosanchuk JD, & Casadevall A. (2007) Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi. PloS one, 2(5). PMID: 17520016
- April 5, 2012
- 11:53 PM
- 331 views
Mycology Symposium, Day 1
by csoeder in Topologic Oceans
When I’m not too busy raging at skuptaloids online, I enjoy molecular biology and mycology, the study of fungi. Towards those ends, I’m visiting the Duke Symposium in Celebration of Mycology and Mycologists. I was only able to attend a few afternoon lectures on the first day of this conference, but am enjoying it greatly! [...]... Read more »
Randolph Nesse, & George Williams. (1994) Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books: New York. info:/
Trick, C., Bill, B., Cochlan, W., Wells, M., Trainer, V., & Pickell, L. (2010) From the Cover: Iron enrichment stimulates toxic diatom production in high-nitrate, low-chlorophyll areas. Proceedings of the National Academy of Sciences, 107(13), 5887-5892. DOI: 10.1073/pnas.0910579107
Turnbull, J., & Field, R. (2007) Emerging glycomics technologies. Nature Chemical Biology, 3(2), 74-77. DOI: 10.1038/nchembio0207-74
- April 5, 2012
- 02:23 PM
- 324 views
Another reason to love mass spectrometry
by Clay Clark in Biochem Blogs
Many scientists out there want to know about the dynamics of a protein or how a protein binds to small molecules. But sometimes that information is hard to get using classical techniques such as X-ray crystallography or NMR. Maybe … Continue reading →... Read more »
Zhang, X., Chien, E., Chalmers, M., Pascal, B., Gatchalian, J., Stevens, R., & Griffin, P. (2010) Dynamics of the β -Adrenergic G-Protein Coupled Receptor Revealed by Hydrogen−Deuterium Exchange . Analytical Chemistry, 82(3), 1100-1108. DOI: 10.1021/ac902484p
Landgraf, R., Chalmers, M., & Griffin, P. (2011) Automated Hydrogen/Deuterium Exchange Electron Transfer Dissociation High Resolution Mass Spectrometry Measured at Single-Amide Resolution. Journal of The American Society for Mass Spectrometry, 23(2), 301-309. DOI: 10.1007/s13361-011-0298-2
Wales, T., & Engen, J. (2006) Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrometry Reviews, 25(1), 158-170. DOI: 10.1002/mas.20064
- March 30, 2012
- 04:36 AM
- 571 views
Researchers One Step Closer to Giving Robots the Ability to “Feel”
by Jason Carr in Wired Cosmos
A particular area of interest I have is the the use of robots in space exploration so I try to keep an eye out for interesting developments within the robotics field to share with you guys. I came across a recently released research paper dealing with mechanical stimuli and thought this might be of interest to [...]... Read more »
Chen, I., Kuksenok, O., Yashin, V., Balazs, A., & Van Vliet, K. (2012) Mechanical Resuscitation of Chemical Oscillations in Belousov-Zhabotinsky Gels. Advanced Functional Materials. DOI: 10.1002/adfm.201103036
- March 26, 2012
- 11:43 AM
- 495 views
Bioplastics in Bloom
by Whitney Campbell in Green Screen
When imagining the world without a dependence on petroleum, I tend to think of objects like solar panels, electric cars, and wind turbines — the things that could potentially replace the parts of the current oil-energy infrastructure. But what about the other items made from petroleum that could be replaced by alternative materials? What about bicycle tires, nail polishes, compact discs, surf boards, lipsticks, tool boxes, and shower curtains?... Read more »
Torres Galvis, H., Bitter, J., Khare, C., Ruitenbeek, M., Dugulan, A., . (2012) Supported iron nanoparticles as catalysts for sustainable production of lower olefins. Science, 835-838. DOI: 10.1126/science.1215614
- March 23, 2012
- 11:24 AM
- 715 views
How Stress Makes Oranges Better for You
by Elizabeth Preston in Inkfish
Though Sicily may seem like a relaxing oasis, it's really a stressful climate where rogue elements can turn you bloody--whether you have a run-in with the mafia, or you're an orange. New research shows why the Italian blood orange prefers this hostile environment to your backyard. With a little coercion, though, we might someday convince this extra-healthy fruit to move abroad.
Citrus sinensis is an orange with eerie red flesh that's grown most successfully around Sicily. To develop the........ Read more »
Butelli, E., Licciardello, C., Zhang, Y., Liu, J., Mackay, S., Bailey, P., Reforgiato-Recupero, G., & Martin, C. (2012) Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges. THE PLANT CELL ONLINE. DOI: 10.1105/tpc.111.095232
- March 20, 2012
- 11:37 AM
- 822 views
The Amazing Story of Alexander Shulgin: The chemist who discovered hundreds of psychedelics from his humble garden shed
by Neurobonkers in Neurobonkers
A beautiful new film tells the story of Alexander Shulgin, the chemist who re-discovered MDMA (after it was synthesised and abandoned by Merck) and went on to discover hundreds of psychedelic drugs such as the 2C*family. He is famous not only for independently discovering and developing so many psychedelics but for testing them extensively on himself and for writing the core textbooks of the psychedelic literature, PiHKAL (‘Phenethylamines I Have Known and Loved’) and TiHKAL (‘........ Read more »
Benzenhöfer U, & Passie T. (2010) Rediscovering MDMA (ecstasy): the role of the American chemist Alexander T. Shulgin. Addiction (Abingdon, England), 105(8), 1355-61. PMID: 20653618
- March 15, 2012
- 09:31 PM
- 1,006 views
Caramel Color Carcinogens -- Bring Back Crystal Pepsi Part 2
by DJ Busby in Astronasty
Recently in the news, 4-MEI in cola's caramel coloring includes a carcinogen. I explain the severity, and follow it up with my proposal for the resurrection of Crystal Pepsi.... Read more »
Chan, P., Hills, G., Kissling, G., & Nyska, A. (2007) Toxicity and carcinogenicity studies of 4-methylimidazole in F344/N rats and B6C3F1 mice. Archives of Toxicology, 82(1), 45-53. DOI: 10.1007/s00204-007-0222-5
National Toxicology Program (NTP, 2007). (2007) Chemical Meeting The Criteria For Listing As Causing Cancer Via The Authoritative Bodies Mechanism: 4-Methylimidazole. NTP Technical Report Series. info:other/NIH: 07-4471
Gardener, H., Rundek, T., Markert, M., Wright, C., Elkind, M., & Sacco, R. (2012) Diet Soft Drink Consumption is Associated with an Increased Risk of Vascular Events in the Northern Manhattan Study. Journal of General Internal Medicine. DOI: 10.1007/s11606-011-1968-2
- March 14, 2012
- 03:43 PM
- 372 views
Genetically programmed death pathways in bacteria
by Clay Clark in Biochem Blogs
A new paper published in PLoS Biology characterizes two bacterial death pathways Programmed cell death (PCD) in eukaryotes is a well-studied process that is used by organisms to maintain homeostasis. The mechanisms of PCD are under intense study because altered … Continue reading →... Read more »
Erental, A., Sharon, I., & Engelberg-Kulka, H. (2012) Two Programmed Cell Death Systems in Escherichia coli: An Apoptotic-Like Death Is Inhibited by the mazEF-Mediated Death Pathway. PLoS Biology, 10(3). DOI: 10.1371/journal.pbio.1001281
Vesper, O., Amitai, S., Belitsky, M., Byrgazov, K., Kaberdina, A., Engelberg-Kulka, H., & Moll, I. (2011) Selective Translation of Leaderless mRNAs by Specialized Ribosomes Generated by MazF in Escherichia coli. Cell, 147(1), 147-157. DOI: 10.1016/j.cell.2011.07.047
Belitsky, M., Avshalom, H., Erental, A., Yelin, I., Kumar, S., London, N., Sperber, M., Schueler-Furman, O., & Engelberg-Kulka, H. (2011) The Escherichia coli Extracellular Death Factor EDF Induces the Endoribonucleolytic Activities of the Toxins MazF and ChpBK. Molecular Cell, 41(6), 625-635. DOI: 10.1016/j.molcel.2011.02.023
- March 14, 2012
- 10:58 AM
- 666 views
Plant Neurons? Sensation and action in the Venus Flytrap
by TheCellularScale in The Cellular Scale
Plants are more electric than you might think. (Venus Fly Trap by Nick Ford at nickpix2012)While they don't have neurons in the proper sense, they have sensory receptors, ion channels, action potentials, and can process information. One of the most remarkable feats of plant information processing occurs in the venus flytrap. The venus fly trap is remarkable among plants because it has very fast and very specific information processing capabilities. It can ........ Read more »
Benolken RM, & Jacobson SL. (1970) Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56(1), 64-82. PMID: 5514161
Volkov AG, Adesina T, & Jovanov E. (2007) Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling , 2(3), 139-45. PMID: 19516982
Forterre Y, Skotheim JM, Dumais J, & Mahadevan L. (2005) How the Venus flytrap snaps. Nature, 433(7024), 421-5. PMID: 15674293
- March 13, 2012
- 12:39 PM
- 642 views
Childbirth and C-Sections in Bioarchaeology
by Kristina Killgrove in Powered By Osteons
Basically since we started walking upright, childbirth has been difficult for women. Evolution selected for larger and larger brains in our hominin ancestors such that today our newborns have heads roughly 102% the size of the mother's pelvic inlet width (Rosenberg 1992).
Yes, you read that right. Our babies' heads are actually two percent larger than our skeletal anatomy.
Fetal head and mother's pelvic inlet width
Photo credit: Evolution-of-man.info
Obviousl........ Read more »
D.W. Amundsen, & C.J. Diers. (1969) The age of menarche in Classical Greece and Rome. Human Biology, 41(1), 125-132. PMID: 4891546
J.P. Boley. (1991) The history of caesarean section. Canadian Medical Association Journal, 145(4), 319-322. info:/
C. Cruz, & S. Codinha. (2009) Death of mother and child due to dystocia in 19th century Portugal. International Journal of Osteoarchaeology, 491-496. DOI: 10.1002/oa.1069
W. Gilbert, D. Jandial, N. Field, P. Bigelow, & B. Danielsen. (2004) Birth outcomes in teenage pregnancies. Journal of Maternal-Fetal and Neonatal Medicine, 16(5), 265-270. DOI: 10.1080/14767050400018064
K. Hopkins. (1965) The age of Roman girls at marriage. Population Studies, 18(3), 309-327. DOI: 10.2307/2173291
K. Rosenberg. (1992) The evolution of modern human childbirth. American Journal of Physical Anthropology, 35(S15), 89-124. DOI: 10.1002/ajpa.1330350605
C. Wells. (1975) Ancient obstetric hazards and female mortality. Bulletin of the New York Academy of Medicine, 51(11), 1235-49. PMID: 1101997
A. Willis, & M. Oxenham. (2011) A Case of Maternal and Perinatal Death in Neolithic Southern Vietnam, c. 2100-1050 BCE. International Journal of Osteoarchaeology, 1-9. DOI: 10.1002/oa.1296
Zlas, J., Stark, H., Seligman, J., Levy, R., Werker, E., Breuer, A., & Mechoulam, R. (1993) Early medical use of cannabis. Nature, 363(6426), 215-215. DOI: 10.1038/363215a0
- March 12, 2012
- 07:44 AM
- 462 views
Measuring nucleotide concentrations inside the living cells
by Vasili Hauryliuk in stringent response
Taking biological system apart and doing experiments in vitro is a very powerful approach. However, Nature has loads of dirty tricks up her sleeve, so doing experiments in vivo is more kosher - at least you get all the concentrations rights and will have all of the components present in the system.Cells use a whole plethora of nucleotide-based messengers (Pesavento and Hengge, Curr. Opin. Microbiol. 2009), and following concentrations of these in vivo is something microbiologists would love........ Read more »
Paige JS, Nguyen-Duc T, Song W, & Jaffrey SR. (2012) Fluorescence imaging of cellular metabolites with RNA. Science (New York, N.Y.), 335(6073), 1194. PMID: 22403384
Paige JS, Wu KY, & Jaffrey SR. (2011) RNA mimics of green fluorescent protein. Science (New York, N.Y.), 333(6042), 642-6. PMID: 21798953
Christen M, Kulasekara HD, Christen B, Kulasekara BR, Hoffman LR, & Miller SI. (2010) Asymmetrical distribution of the second messenger c-di-GMP upon bacterial cell division. Science (New York, N.Y.), 328(5983), 1295-7. PMID: 20522779
Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta-Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A.... (2007) The structural basis of cyclic diguanylate signal transduction by PilZ domains. The EMBO journal, 26(24), 5153-66. PMID: 18034161
- March 10, 2012
- 03:10 PM
- 634 views
Calcium: for more than just your bones
by TheCellularScale in The Cellular Scale
You have probably heard that calcium is good for your bones, but what you might not know is that your brain can't function without it. Broccoli is rich in calcium (source)We have previously discussed the electrical properties of neurons. Much like the sodium ion (Na+) and the potassium ion (K+), the calcium ion (Ca2+) can flow into and out of the cell to modulate its electrical activity. Grienberger and Konnerth 2012, Figure1Calcium has an even bigger role, however.&nb........ Read more »
Grienberger, C., & Konnerth, A. (2012) Imaging Calcium in Neurons. Neuron, 73(5), 862-885. DOI: 10.1016/j.neuron.2012.02.011
- March 8, 2012
- 07:00 AM
- 623 views
Blood Pressure Pills to Combat Racism: Research
by United Academics in United Academics
Researchers from the Oxford University have found that people consuming a common heart disease drug, propranolol (40 mg), show less implicit racism than those who don’t consume the medicine. The drug acts on the mechanisms that activate fear, which, according to the scientists, is the main cause of racism.... Read more »
Terbeck, S., Kahane, G., McTavish, S., Savulescu, J., Cowen, P., & Hewstone, M. (2012) Propranolol reduces implicit negative racial bias. Psychopharmacology. DOI: 10.1007/s00213-012-2657-5
- March 7, 2012
- 08:27 PM
- 370 views
A genetically encoded site-specific label for protein imaging
by Clay Clark in Biochem Blogs
sciseekclaimtoken-4f580c3179515 Rapid bioorthogonal labeling of proteins By Clay Clark, @biochemprof There are a number of current methods for labeling proteins for imaging either in vitro and/or in live cells and organisms, including fusions with fluorescent proteins, dyes, tags (such as SNAP, … Continue reading →... Read more »
Lang, K., Davis, L., Torres-Kolbus, J., Chou, C., Deiters, A., & Chin, J. (2012) Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nature Chemistry. DOI: 10.1038/NCHEM.1250
Chen, I., & Ting, A. (2005) Site-specific labeling of proteins with small molecules in live cells. Current Opinion in Biotechnology, 16(1), 35-40. DOI: 10.1016/j.copbio.2004.12.003
Best, M. (2009) Click Chemistry and Bioorthogonal Reactions: Unprecedented Selectivity in the Labeling of Biological Molecules. Biochemistry, 48(28), 6571-6584. DOI: 10.1021/bi9007726
- March 6, 2012
- 11:50 AM
- 627 views
Nairobi bugs: WMD or Cancer cure?!
by Colin Beale in Safari Ecology
15 times more toxic than cobra venom, you really shouldn't eat a Nairobi beetle! Nairobi bugs (also known around East Africa as Nairobi Eye, Nairobi Fly, Nairobi beetles, Blister Beetles and a whole range of other names) are not the best loved creatures out here. This year they've come out in greater number than the last few years, presumably thanks to some relatively good rains, and whilst they're not loved, they're certainly fascinating wee beasties. But before we go into the details, let's st........ Read more »
Kellner, R. (2002) Molecular identification of an endosymbiotic bacterium associated with pederin biosynthesis in Paederus sabaeus (Coleoptera: Staphylinidae). Insect Biochemistry and Molecular Biology, 32(4), 389-395. DOI: 10.1016/S0965-1748(01)00115-1
Jewett, J., & Rawal, V. (2007) Total Synthesis of Pederin. Angewandte Chemie, 119(34), 6622-6624. DOI: 10.1002/ange.200701677
Brega, A. (1968) STUDIES ON THE MECHANISM OF ACTION OF PEDERINE. The Journal of Cell Biology, 36(3), 485-496. DOI: 10.1083/jcb.36.3.485
- March 3, 2012
- 03:42 PM
- 365 views
A new assay to study small GTPase interactions
by Clay Clark in Biochem Blogs
Let there be { if (RhoGTP + Effector == ProteinComplex) { Luc1 + Luc2 = ActiveLuciferase; LIGHT = 1; } else if (RhoGTP + GAP == RhoGDP) { RhoGDP + Effector = NoProteinComplex; LIGHT = 0; } else if (RhoGDP … Continue reading →... Read more »
Anderson, E., & Hamann, M. (2012) Detection of Rho GEF and GAP activity through a sensitive split luciferase assay system. Biochemical Journal, 441(3), 869-879. DOI: 10.1042/BJ20111111
Jaiswal M, Dubey BN, Koessmeier KT, Gremer L, & Ahmadian MR. (2012) Biochemical assays to characterize Rho GTPases. Methods in molecular biology (Clifton, N.J.), 37-58. PMID: 22144266
Massoud, T., Paulmurugan, R., De, A., Ray, P., & Gambhir, S. (2007) Reporter gene imaging of protein–protein interactions in living subjects. Current Opinion in Biotechnology, 18(1), 31-37. DOI: 10.1016/j.copbio.2007.01.007
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