Post List

  • November 30, 1999
  • 12:00 AM
  • 2,443 views

New GPCR Structure: Dopamine D3 Receptor

by Peter Nollert in Protein Crystallization Blog

Yay – another GPCR structure to look at! I just noticed that the 2.9A Dopamine D3 Receptor (in complex with Eticlopride) coordinates 3PBL have been released by the PDB earlier this week. This one will take some time to digest. My congratulations go again to the Stevens lab at TSRI. This is a great achievement, well done.... Read more »

Chien, E., Liu, W., Zhao, Q., Katritch, V., Won Han, G., Hanson, M., Shi, L., Newman, A., Javitch, J., Cherezov, V.... (2010) Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist. Science, 330(6007), 1091-1095. DOI: 10.1126/science.1197410  

  • November 30, 1999
  • 12:00 AM
  • 2,343 views

New GPCR structure: CXCR4 Chemokine Receptor (HIV and cancer target)

by Peter Nollert in Emerald BioStructures Blog

Congratulations to Ray Stevens and team to determining and publishing the crystallographic structure of the CXCR4 Chemokine receptor in Science. The diffenent binding areas for the small molecule and peptide antagonist are nicely resolved and show extensive interactions with binding pocket residues in the 2.5 – 3.1 A crystal structures... Read more »

Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC.... (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (New York, N.Y.), 330(6007), 1066-71. PMID: 20929726  

  • November 30, 1999
  • 12:00 AM
  • 2,233 views

Mixture Models for Ordinal Data

by Christopher Winship in SMR Blog

Cumulative probability models are widely used for the analysis of ordinal data. In this article the authors propose cumulative probability mixture models that allow the assumptions of the cumulative probability model to hold within subsamples of the data. The subsamples are defined in terms of latent class membership. In the case of the ordered logit mixture model, on which the authors focus here, the assumption of a logistic distribution for an underlying latent dependent variable holds within ........ Read more »

Breen, R., & Luijkx, R. (2010) Mixture Models for Ordinal Data. Sociological Methods , 39(1), 3-24. DOI: 10.1177/0049124110366240  

  • November 30, 1999
  • 12:00 AM
  • 1,758 views

Rethinking Circadian Clock Machinery

by Allison in Dormivigilia

Chronobiologists at Cambridge have discovered circadian rhythms in peroxide oxidation in HUMAN blood cells. That sounds cool, right? But what if I told you that this research will forever make us rethink the innerworkings of the circadian clock because this is the first documentation of non-transcriptionally driven circadian rhythms... Read more »

O'Neill JS, & Reddy AB. (2011) Circadian clocks in human red blood cells. Nature, 469(7331), 498-503. PMID: 21270888  

  • November 30, 1999
  • 12:00 AM
  • 1,983 views

Let’s Get Cellular: Meth Metabolism

by Dirk Hanson in Addiction Inbox

We know from the work of Nora Volkow and others that meth abusers have chronically low levels of dopamine D2 receptors in their brains. But what is going on in the rest of the body when methamphetamine addiction is running full force?... Read more »

Sun, L., Li, H., Seufferheld, M., Walters, K., Margam, V., Jannasch, A., Diaz, N., Riley, C., Sun, W., Li, Y.... (2011) Systems-Scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine. PLoS ONE, 6(4). DOI: 10.1371/journal.pone.0018215  

  • November 30, 1999
  • 12:00 AM
  • 1,924 views

Minding As and P: Can Arsenic Substitute for Phosphorus or Not?

by Sara Klink in Promega Connections

Back in December 2010, there was a press conference held by NASA to announce the discovery of a bacterium found in a high salt, high pH lake with high concentrations of arsenic that seemed to have substituted arsenic for phosphorus in the bacterium’s biomolecules. This set off a wave of response in the blogosphere regarding what Felisa Wolfe-Simon and her team did nor did not do to confirm arsenic was incorporated into DNA molecules. Controversy ranged from the ability of arsenic to form a sta........ Read more »

Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P.... (2011) Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus". Science. DOI: 10.1126/science.1202098  

  • November 30, 1999
  • 12:00 AM
  • 1,901 views

The Comeback Cove

by Whitney Campbell in Green Screen

Great news for conservation is always exciting, so when I read about a remarkable wildlife rebound in this month's issue of PLoS ONE, I couldn't resist sharing it here. ... Read more »

  • November 30, 1999
  • 12:00 AM
  • 2,830 views

2011: The Year in Drugs Deaths and data fraud

by Neurobonkers in Neurobonkers

A look at the biggest drugs news stories of the year and a statistical analysis of drugs deaths this year.... Read more »

Measham,F. Moore, K. Østergaard, J. (2011) Mephedrone, ‘‘Bubble’’ and unidentified white powders: the contested identities of synthetic ‘‘legal highs". DRUGS AND ALCOHOL TODAY, 137-146. info:/

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  

  • November 30, 1999
  • 12:00 AM
  • 2,622 views

The Nano-ear: 'Hearing' with optical tweezers

by David McGloin in Dundee Physics

Discusses a recent paper in Physical Review Letters which describes a way to create a sensitive acoustic detector with an optical tweezers.... Read more »

  • November 30, 1999
  • 12:00 AM
  • 2,598 views

Is this journal for real?

by Neurobonkers in Neurobonkers

This year 134 suspect new journals have appeared from the abyss, all published by the same clandestine company “Scientific & Academic Publishing, USA“... Read more »

Morrison, Heather. (2012) Scholarly Communication in Crisis. Freedom for scholarship in the internet age. Simon Fraser University School of Communication. info:/

  • November 30, 1999
  • 12:00 AM
  • 2,167 views

The Fragile Monument of Hominin Diet

by Matt Sponheimer in Originus

Hominin Diet... Read more »

  • November 30, 1999
  • 12:00 AM
  • 1,907 views

Parody: How to Synthesise Pseudoephedrine From N-Methylamphetamine

by Neurobonkers in Neurobonkers

Over in the US it has apparently become so difficult to get hold of pseudoephedrine (Sudafed), that one researcher has published a satirical paper explaining how to manufacture it out of crystal meth (PDF). The paper describes how “in the past most stores were able to sell pseudoephedrine”, the US’s most popular decongestant but new laws require only pharmacies, often with restricted opening hours to sell the medicine only to those carrying government issued ID. The paper argue........ Read more »

Hai, O. Hakkenshit, I.B. (2012) A Simple and Convenient Synthesis of Pseudoephedrine From N-Methylamphetamine. Journal of Apocryphal Chemistry. info:/

  • November 30, 1999
  • 12:00 AM
  • 2,058 views

Some Members of the Parliament Should Be Selected By Lottery, According to Research

by United Academics in United Academics

What if democracy works better with some members of parliament chosen at random? This is what Athenians used to do in the past, and what a team of Italian researchers at the Università di Catania defend in a paper, now brought back to attention by Marc Abrahams in his weekly column ‘Improbable Research’ at the The Guardian.... Read more »

Pluchino, A., Garofalo, C., Rapisarda, A., Spagano, S., & Caserta, M. (2011) Accidental politicians: How randomly selected legislators can improve parliament efficiency. Physica A: Statistical Mechanics and its Applications, 390(21-22), 3944-3954. DOI: 10.1016/j.physa.2011.06.028  

  • November 30, 1999
  • 12:00 AM
  • 2,050 views

How to spot exo-Earths...

by Invader Xan in Supernova Condensate

It seems like we’re not going to stop discovering new exoplanets anytime soon. Around one sixth of all exoplanets currently known can be observed transiting their star’s disk. Given that transits are precisely what NASA’s Kepler mission is going to spend the next three years looking for, that number is certainly set to increase over the coming months. But with exoplanet transits comes a unique opportunity to study them…... Read more »

Pallé, E., Osorio, M., Barrena, R., Montañés-Rodríguez, P., & Martín, E. (2009) Earth’s transmission spectrum from lunar eclipse observations. Nature, 459(7248), 814-816. DOI: 10.1038/nature08050  

  • November 30, 1999
  • 12:00 AM
  • 1,581 views

Detecting Gene Doping in Sports: MicroRNA biomarker sought

by Nicole Kelesoglu in E3 Engaging Epigenetics Experts

WADA funds research into developing detection methods for the emerging threat of gene doping in sports.... Read more »

Elmo W.I. Neuberger, Magdelena Jurkiewicz, Dirk A. Moser and Perikles Simon. (2012) Detection of EPO gene doping in blood. Drug Testt. Analysis. DOI: 10.1002/dta.1347  

  • November 30, 1999
  • 12:00 AM
  • 1,850 views

Violent Video Games May Favor Cooperation, Researchers Say

by Jaime Menchén in United Academics

Two recent studies refute the idea that violent video games make players more aggressive and antisocial. Actually, researchers argue, playing cooperatively may result on just the opposite.... Read more »

  • November 30, 1999
  • 12:00 AM
  • 2,197 views

Genes Dealt Made Asians Svelte

by nooffensebut in The Unsilenced Science

Early genome-wide association studies suggest a genetic propensity to thinness in Asians. I review how these kinds of studies might be able reveal genetic racial differences in obesity and intelligence, and I address a few of the challenges to doing so.... Read more »

Belsky DW, Moffitt TE, Houts R, Bennett GG, Biddle AK, Blumenthal JA, Evans JP, Harrington H, Sugden K, Williams B.... (2012) Polygenic risk, rapid childhood growth, and the development of obesity: evidence from a 4-decade longitudinal study. Archives of pediatrics , 166(6), 515-21. PMID: 22665028  

Hsu FC, Lenchik L, Nicklas BJ, Lohman K, Register TC, Mychaleckyj J, Langefeld CD, Freedman BI, Bowden DW, & Carr JJ. (2005) Heritability of body composition measured by DXA in the diabetes heart study. Obesity research, 13(2), 312-9. PMID: 15800289  

Kilpeläinen TO, Zillikens MC, Stančákova A, Finucane FM, Ried JS, Langenberg C, Zhang W, Beckmann JS, Luan J, Vandenput L.... (2011) Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile. Nature genetics, 43(8), 753-60. PMID: 21706003  

Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R.... (2008) Proportionally more deleterious genetic variation in European than in African populations. Nature, 451(7181), 994-7. PMID: 18288194  

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB.... (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.), 335(6070), 823-8. PMID: 22344438  

Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Lango Allen H, Lindgren CM, Luan J, Mägi R.... (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature genetics, 42(11), 937-48. PMID: 20935630  

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G.... (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science (New York, N.Y.), 337(6090), 64-9. PMID: 22604720  

Zuk O, Hechter E, Sunyaev SR, & Lander ES. (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proceedings of the National Academy of Sciences of the United States of America, 109(4), 1193-8. PMID: 22223662  

  • November 30, 1999
  • 12:00 AM
  • 1,319 views

More evidence that antibiotics are over-prescribed - How should that change?

by Rogue Medic in Rogue Medic

Today Lancet Infectious Diseases posted an early release of an article that shows that the antibiotic amoxicillin still does not work on viruses.

Many doctors still routinely prescribe antibiotics for viral infections.

Bias, perhaps the biggest confounder in medical research, is controlled for very well.

What does the study show?... Read more »

  • November 30, 1999
  • 12:00 AM
  • 1,561 views

Tet1 Enzyme Based Enrichment Method for Methylome Sequencing: TamC-Seq

by Nicole Kelesoglu in E3 Engaging Epigenetics Experts

Summary of a recent Nature paper that details a new inexpensive, enzyme based enrichment method for methylome sequencing. ... Read more »

Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR.... (2013) Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature communications, 1517. PMID: 23443545  

  • November 30, 1999
  • 12:00 AM
  • 1,504 views

A field guide to whole-genome analyses

by Mauro Mandrioli in The aphid room

Genome sequencing projects have been for long time possible goals for few model organisms and required the concerted effort of large consortia, but now...... Read more »

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