Chemistry posts
- March 12, 2012
- 07:44 AM
- 463 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
- 635 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
- 372 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
- 630 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
- 370 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
- February 26, 2012
- 06:10 PM
- 326 views
“Watch” lysozyme chopping bacterial cell wall
by Clay Clark in Biochem Blogs
When nano first met biology by Xun Lu Lysozyme is an enzyme that helps to protect us from getting bacterial infections because it can degrade and utilize the sugars in the bacterial cell wall. A good source of lysozyme … Continue reading →... Read more »
Choi, Y., Moody, I., Sims, P., Hunt, S., Corso, B., Perez, I., Weiss, G., & Collins, P. (2012) Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit. Science, 335(6066), 319-324. DOI: 10.1126/science.1214824
- February 26, 2012
- 11:40 AM
- 889 views
Friday Roundup-Eating Roadkill and Turtle Troubles in Canada
by David Steen in Living Alongside Wildlife
A New York Snapping Turtle
Protecting Snapping Turtles in Canada. The distribution and range of a species is often heavily influenced by climate and habitat. If an area does not have suitable climate or habitat for a species, they cannot occur there. It's that simple. Polar Bears would not be comfortable in tropical jungles and you will not find Green Iguanas basking on icecaps. It gets a ... Read more »
Cedervall, T., Hansson, L., Lard, M, Frohm, B, & Linse, S. (2012) Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish. PLoS ONE, 7(2). info:/
de Solla SR, Bishop CA, Lickers H, & Jock K. (2001) Organochlorine pesticides, PCBs, dibenzodioxin, and furan concentrations in common snapping turtle eggs (Chelydra serpentina serpentina) in Akwesasne, Mohawk Territory, Ontario, Canada. Archives of environmental contamination and toxicology, 40(3), 410-7. PMID: 11443374
Allender MC, Dreslik M, Wylie S, Phillips C, Wylie DB, Maddox C, Delaney MA, & Kinsel MJ. (2011) Chrysosporium sp. infection in eastern massasauga rattlesnakes. Emerging infectious diseases, 17(12), 2383-4. PMID: 22172594
- February 24, 2012
- 03:29 PM
- 602 views
Your Sunscreen Makes Fish Anorexic
by Elizabeth Preston in Inkfish
Infinitesimal particles inside our cosmetics, drugs, and processed foods are making their way into streams and oceans. There, they become a whole new food group for fish and other aquatic life. Although we treat them as harmless, the nanoparticles added to fish's diets may put them off their lunch altogether.
Manmade nanoparticles--bits of material built to be 300 microns across or smaller--have been booming over the last 10 to 15 years. In pharmaceuticals, they carry tiny doses of drugs int........ Read more »
Cedervall, T., Hansson, L., Lard, M., Frohm, B., & Linse, S. (2012) Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0032254
- February 22, 2012
- 10:09 AM
- 651 views
Video tip of the week: Updated Introductory Tutorial on the RCSB PDB
This post is part of OpenHelix's "Tip of the Week" blog feature. For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. ... Read more »
Berman, H., & et al. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
- February 18, 2012
- 09:27 PM
- 463 views
Why buying recreational drugs online is not a great idea
by Mutant Dragon in Puff the Mutant Dragon
... Read more »
Centers for Disease Control and Prevention (CDC). (2012) Severe Methemoglobinemia and Hemolytic Anemia from Aniline Purchased as 2C-E (4-ethyl-2,5-dimethoxyphenethylamine), a Recreational Drug, on the Internet - Oregon, 2011. MMWR. Morbidity and mortality weekly report, 85-8. PMID: 22318470
- February 17, 2012
- 10:46 AM
- 948 views
A Scientist’s Worst Nightmare
by Neurobonkers in Neurobonkers
A detailed analysis of a new infographic dealing with the issue of falsification in scientific research.... Read more »
Ioannidis, J. (2005) Why Most Published Research Findings Are False. PLoS Medicine, 2(8). DOI: 10.1371/journal.pmed.0020124
Moonesinghe, R., Khoury, M., & Janssens, A. (2007) Most Published Research Findings Are False—But a Little Replication Goes a Long Way. PLoS Medicine, 4(2). DOI: 10.1371/journal.pmed.0040028
Young NS, Ioannidis JP, & Al-Ubaydli O. (2008) Why current publication practices may distort science. PLoS medicine, 5(10). PMID: 18844432
Fanelli D. (2009) How many scientists fabricate and falsify research? A systematic review and meta-analysis of survey data. PloS one, 4(5). PMID: 19478950
- February 15, 2012
- 08:16 AM
- 314 views
Apple Pie, Hold the Apples
by Dan Bailey in Smells Like Science
There aren’t many foods that are as closely tied to American identity as apple pie. And Americans love apple pie so much that, at times, we’ve felt compelled to make it even when we don’t have any apples. I’ve heard about a recipe for apple-less apple pie from a number of people over the years, but I’ve never talked to anyone who’s actually eaten it. So this past weekend, I decided to give it a try.
... Read more »
Spence, C., Levitan, C., Shankar, M., & Zampini, M. (2010) Does Food Color Influence Taste and Flavor Perception in Humans?. Chemosensory Perception, 3(1), 68-84. DOI: 10.1007/s12078-010-9067-z
- February 12, 2012
- 02:01 PM
- 536 views
Chemical Ghosts in the Machine
by Cris Campbell in Genealogy of Religion
If we think deeply about evolution, we eventually will ask questions not about the origin of species but about the origin of life. For some theistic evolutionists, this is the point of Designer intervention. They find it hard to imagine that chemicals could combine in way that gives rise to life. For those less inclined [...]... Read more »
Urey, Harold. (1952) On the Early Chemical History of the Earth and the Origin of Life. Proceedings of the National Academy of Sciences, 38(4), 351-363. DOI: 10.1073/pnas.38.4.351
Peretó J. (2005) Controversies on the origin of life. International microbiology : the official journal of the Spanish Society for Microbiology, 8(1), 23-31. PMID: 15906258
Joyce, G. (1989) RNA evolution and the origins of life. Nature, 338(6212), 217-224. DOI: 10.1038/338217a0
Orgel LE. (1998) The origin of life--a review of facts and speculations. Trends in biochemical sciences, 23(12), 491-5. PMID: 9868373
- February 11, 2012
- 03:30 PM
- 321 views
Searching for E.T., III: Arsenic, DNA and alien life
by Mutant Dragon in Puff the Mutant Dragon
For those unfortunate enough to inherit it, sickle cell anemia is a devastating disease. Victims suffer from symptoms like frequent infections, persistent fatigue and bouts of crippling pain. It’s a little surprising to realize all this havoc stems from a single and seemingly minor change in the hemoglobin protein — exchanging one amino acid called glutamate for another called valine. That swap creates a pocket on the surface of the protein that can bind other hemoglobin molecules wh........ Read more »
Tackett, A. (2002) Non-Watson-Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase. Nucleic Acids Research, 30(4), 950-957. DOI: 10.1093/nar/30.4.950
- February 10, 2012
- 05:23 AM
- 429 views
Forming crystals from supercooled liquids with lasers
by DundeePhysics in Dundee Physics
One of the things that we are working on in the lab is the study of ice nucleation making use of optically trapped droplets. Nucleation is in the starting point for processes such as freezing and crystallization, and so obviously is of great scientific and industrial importance. Another of the things that my group is [...]... Read more »
Ward, M., McHugh, S., & Alexander, A. (2012) Non-photochemical laser-induced nucleation of supercooled glacial acetic acid. Physical Chemistry Chemical Physics, 14(1), 90. DOI: 10.1039/c1cp22774b
- February 6, 2012
- 08:39 AM
- 461 views
A perfect couple for designing chemical reactions
by Joerg Heber in All That Matters
We are all familiar with the basic ways in which light interacts with matter, when light absorption causes atoms to move and creates heat, or when light gets absorbed by the outer electrons of atoms so that they move into energetically excited states, which is how electricity in solar cells is created. Common to both [...]... Read more »
Schwartz, T., Hutchison, J., Genet, C., & Ebbesen, T. (2011) Reversible Switching of Ultrastrong Light-Molecule Coupling. Physical Review Letters, 106(19). DOI: 10.1103/PhysRevLett.106.196405
Hutchison, J., Schwartz, T., Genet, C., Devaux, E., & Ebbesen, T. (2012) Modifying Chemical Landscapes by Coupling to Vacuum Fields. Angewandte Chemie International Edition. DOI: 10.1002/anie.201107033
- February 4, 2012
- 06:55 PM
- 362 views
Searching for E.T., II: Ammonia-drinking aliens
by Mutant Dragon in Puff the Mutant Dragon
In the movies, lab chemicals are usually blue, green or some other startling color. In reality, most of the chemicals you encounter in a lab are colorless or have fairly boring colors. There are exceptions, however, and this is one of them.... Read more »
Benner, S., Ricardo, A., & Carrigan, M. (2004) Is there a common chemical model for life in the universe?. Current Opinion in Chemical Biology, 8(6), 672-689. DOI: 10.1016/j.cbpa.2004.10.003
- January 27, 2012
- 10:10 AM
- 743 views
Oxford University Censor First Broadcast of Lecture That Resulted in Censuring of Prof. Nutt, Former UK Government Drugs Advisor
by Neurobonkers in Neurobonkers
Watch the full video of the lecture and uncover what was in the slides censored for "copyright reasons"... Read more »
Nutt, D., King, L., & Phillips, L. (2010) Drug harms in the UK: a multicriteria decision analysis. The Lancet, 376(9752), 1558-1565. DOI: 10.1016/S0140-6736(10)61462-6
Nutt, D. (2009) Estimating drug harms: a risky business?. Centre for Crime and Justice Studies. info:/
Halpern JH, Sherwood AR, Hudson JI, Gruber S, Kozin D, & Pope HG Jr. (2011) Residual neurocognitive features of long-term ecstasy users with minimal exposure to other drugs. Addiction (Abingdon, England), 106(4), 777-86. PMID: 21205042
Carhart-Harris, R., Erritzoe, D., Williams, T., Stone, J., Reed, L., Colasanti, A., Tyacke, R., Leech, R., Malizia, A., Murphy, K.... (2012) Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1119598109
Editorial team. (2010) The EMCDDA annual report 2010: the state of the drugs problem in Europe. The European Monitoring Centre for Drugs and Drug Addiction, also published in Euro surveillance :European communicable disease bulletin, 15(46). PMID: 21144426
- January 27, 2012
- 10:00 AM
- 484 views
Watermarking molecules
by Aaron Sterling in Nanoexplanations
I’ve posted twice about Anonymous hacking into Stratfor — and, more generally, their hacktivism has been making bigger and bigger waves. CNN recently ran a fairly positive story on the support hacktivists are providing the Occupy movement. Many of these … Continue reading →... Read more »
Joachim J. Eggers, W.D. Ihlenfeldt, & Bern Girod. (2001) Digital Watermarking of Chemical Structure Sets. Information Hiding, 200-214. DOI: 10.1007/3-540-45496-9_15
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