Pascale Delangle (Institute for Nanoscience
and Cryogenics, France) and coworkers have synthesized a
copper-binding molecule that may be useful for treating
disorders related to copper toxicity.
This news feature was written on May 21, 2009.... Read more »
Pujol, A. M., Gateau, C., Lebrun, C., & Delangle, P. (2009) A Cysteine-Based Tripodal Chelator with a High Affinity and Selectivity for Copper(I). Journal of the American Chemical Society, 131(20), 6928-6929. DOI: 10.1021/ja901700a
Network Tools and Applications in Biology (NETTAB) is a series of workshops in Bioinformatics. It focuses on the most promising and innovative ICT tools and their utility in Bioinformatics. These workshops aim to introduce participants to the evolving network standards and technologies that are being applied to the field of biology.
Since 2001, the NETTAB workshops [...]... Read more »
Cannata, N., Schröder, M., Marangoni, R., & Romano, P. (2008) A Semantic Web for bioinformatics: goals, tools, systems, applications. BMC Bioinformatics, 9(Suppl 4). DOI: 10.1186/1471-2105-9-S4-S1
David Smith (University of York, United Kingdom)
and coworkers have synthesized polymers that form strong
chemical bonds with DNA, yet degrade over time, which enhances
their utility as possible DNA delivery vehicles for gene therapy.
This news feature was written on May 18, 2009.... Read more »
Welsh, D. J., Jones, S. P., & Smith, D. K. (2009) “On-Off” Multivalent Recognition: Degradable Dendrons for Temporary High-Affinity DNA Binding. Angewandte Chemie International Edition, 48(22), 4047-4051. DOI: 10.1002/anie.200900401
As I was reading the post about open access science in which Bora over at A Blog Around the Clock mentions the research paper I posted on this blog, I found one line in particular that expresses the importance of Open Access science in my mind. In the article Bora says:
"In any case, it is much better for data to be out in the open, available to anyone who knows how to use Google search, than gathering dust in some manila folder."... Read more »
Zhen Xi (Nankai University, China) and coworkers
have developed a rapid assay for thiol molecules, which are
implicated in many healthy and diseased cellular functions.
This news feature was written on May 16, 2009.... Read more »
Yi, L., Li, H., Sun, L., Liu, L., Zhang, C., & Xi, Z. (2009) A Highly Sensitive Fluorescence Probe for Fast Thiol-Quantification Assay of Glutathione Reductase. Angewandte Chemie International Edition, 48(22), 4034-4037. DOI: 10.1002/anie.200805693
Partha Basu (Duquesne University, Pennsylvania)
and coworkers have synthesized a molecule that enables lead ion
detection at concentrations below that permitted by
This news feature was written on May 15, 2009.... Read more »
Researchers in Argentina have developed a new approach to testing food packaging for trace amounts of the toxic heavy metal cadmium.
Cadmium is one of several additives used extensively in the manufacture of plastics. Regulations limit the concentration of cadmium allowable, of course. In the European Union that limit is 100 milligrams per kilogram. But, the [...]Post from: Sciencebase Science Blog... Read more »
Martinis, E., Olsina, R., Altamirano, J., & Wuilloud, R. (2009) On-line ionic liquid-based preconcentration system coupled to flame atomic absorption spectrometry for trace cadmium determination in plastic food packaging materials. Talanta, 78(3), 857-862. DOI: 10.1016/j.talanta.2008.12.051
Yuan Kou (Peking University, China), Johannes Lercher
(Technische Universitat Munchen, Germany), and coworkers
have synthesized stable carbon-based fuels from
This news feature was written on May 14, 2009.... Read more »
Zhao, C., Kou, Y., Lemonidou, A. A., Li, X., & Lercher, J. A. (2009) Highly Selective Catalytic Conversion of Phenolic Bio-Oil to Alkanes. Angewandte Chemie International Edition, 48(22), 3987-3990. DOI: 10.1002/anie.200900404
ODAY'S edition of Nature (14 May 2009) features a landmark paper from researchers at the University of Manchester School of Chemistry that describes the synthesis of a pyrimidine ribonucleotide from simple chemicals that may have existed on an early Earth. The research by Matthew Powner, in the laboratory of John Sutherland, represents a major stepping stone in support of the 'RNA World' theory, which describes the origins of life as passing through a stage in which RNA was the sole mediator of ........ Read more »
Powner, M., Gerland, B., & Sutherland, J. (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459(7244), 239-242. DOI: 10.1038/nature08013
By now, many people have read about Angela Belcher, a professor at MIT, and her lab's recent developments in the use of bacteriophages as a componant of batteries. Having had a very distinct privilage to hear her speak yesterday, I wish to share what I have learned.
In a broad sense, the goal of her lab is to give inorganic compounds (batteries, medical devices, solar cells, etc), "genetic intelligence."... Read more »
Lee, Y., Yi, H., Kim, W., Kang, K., Yun, D., Strano, M., Ceder, G., & Belcher, A. (2009) Fabricating Genetically Engineered High-Power Lithium Ion Batteries Using Multiple Virus Genes. Science. DOI: 10.1126/science.1171541
DNA Origami goes 3DImagine sitting down at your computer, typing out a message, and then having that message translated into a tiny self-assembling machine. In essence, this is what a group of Danish German and American researchers have done. Using short bits of DNA to link up distant regions throughout a very long single strand of DNA these folks were able to build six square walls and have them assemble, on their own, to form a sealed box. What's more, they were able to affix several molecul........ Read more »
Andersen, E., Dong, M., Nielsen, M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M., Sander, B., Stark, H., Oliveira, C.... (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243), 73-76. DOI: 10.1038/nature07971
Itaru Hamachi (Kyoto University, Japan) and coworkers
have imaged neurofibrillary tangles, in preference to senile plaques,
in brain tissue samples, with a cheap synthetic fluorescent molecule.
This news feature was written on May 8, 2009.... Read more »
Ojida, A., Sakamoto, T., Inoue, M.-a., Fujishima, S.-h., Lippens, G., & Hamachi, I. (2009) Fluorescent BODIPY-Based Zn(II) Complex as a Molecular Probe for Selective Detection of Neurofibrillary Tangles in the Brains of Alzheimer’s Disease Patients. Journal of the American Chemical Society, 131(18), 6543-6548. DOI: 10.1021/ja9008369
A group of scientists from Taiwan, lead by Chi-Hung Lin,
have rapidly identified and screened living bacteria for
antibiotic resistance, using surface enhanced Raman scattering.
This news feature was written on May 8, 2009.... Read more »
Liu, T.-T., Lin, Y.-H., Hung, C.-S, Liu, T.-J., Chen, Y., Huang, Y.-C., Tsai, T.-H., Wang, H.-H., Wang, D.-W., Wang, J.-K.... (2009) A High Speed Detection Platform Based on Surface-Enhanced Raman Scattering for Monitoring Antibiotic-Induced Chemical Changes in Bacteria Cell Wall. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005470
Chad Mirkin (Northwestern University) and coworkers
have developed an assay for nitrite and nitrate pollutants
that is useful for environmental monitoring in remote locations.
This news feature was written on May 7, 2009.... Read more »
Daniel, W. L., Han, M. S., Lee, J.-S., & Mirkin, C. A. (2009) Colorimetric Nitrite and Nitrate Detection with Gold Nanoparticle Probes and Kinetic End Points. Journal of the American Chemical Society, 131(18), 6362-6363. DOI: 10.1021/ja901609k
Most scientific publications today are accessed online. That is why Johan Bollen and colleagues used nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia to create a high-resolution map of science in an article published on PLoS One. A first-order Markov chain was extracted from the sequence of user interactions recorded and the model was visualized as shown below to describe the relationships........ Read more »
Bollen, J., Van de Sompel, H., Hagberg, A., Bettencourt, L., Chute, R., Rodriguez, M., & Balakireva, L. (2009) Clickstream Data Yields High-Resolution Maps of Science. PLoS ONE, 4(3). DOI: 10.1371/journal.pone.0004803
On Wednesday, the CDC reported that influenza A H1N1 viruses from 13 patients with confirmed diagnoses of swine flu had been tested for resistance to a variety of antiviral drugs. The good news was that all of the isolates were susceptible to the antiviral drugs oseltamivir (Tamiflu) and zanamivir (Relenza). However, all 13 were resistant to adamantane-based drugs (amantadine and rimantadine). Resistance to adamantane drugs (which were developed first) has actually become quite widespread amo........ Read more »
Schnell, J., & Chou, J. (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 451(7178), 591-595. DOI: 10.1038/nature06531
Pielak, R., Schnell, J., & Chou, J. (2009) Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0902548106
Stouffer, A., Acharya, R., Salom, D., Levine, A., Di Costanzo, L., Soto, C., Tereshko, V., Nanda, V., Stayrook, S., & DeGrado, W. (2008) Structural basis for the function and inhibition of an influenza virus proton channel. Nature, 451(7178), 596-599. DOI: 10.1038/nature06528
Stouffer, A., Ma, C., Cristian, L., Ohigashi, Y., Lamb, R., Lear, J., Pinto, L., & DeGrado, W. (2008) The Interplay of Functional Tuning, Drug Resistance, and Thermodynamic Stability in the Evolution of the M2 Proton Channel from the Influenza A Virus. Structure, 16(7), 1067-1076. DOI: 10.1016/j.str.2008.04.011
Ken Dill and David Mobley from UCSF have a really nice review in Structure on computational modeling of protein-drug interactions and the problems inherent in the process. I would strongly recommend anyone interested in the challenges of calculating protein-drug binding to read the review, if not for anything else for the copious references provided. The holy grail of most such modeling is to accurately calculate the free energy of binding. For doing this we frequently start with a known structu........ Read more »
Mobley, D., & Dill, K. (2009) Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”. Structure, 17(4), 489-498. DOI: 10.1016/j.str.2009.02.010
For decades DNA has been regarded as a potential building block for molecular electronics, but random sequences of DNA vary in their conductivity — charge transfer through G–C (guanine–cytosine) pairs is much faster than through A–T (adenine–thymine) pairs. Charge can migrate along an A–T rich sequence by ‘hopping’ between G–C pairs, but this decreases [...]... Read more »
Kawai, K., Kodera, H., Osakada, Y., & Majima, T. (2009) Sequence-independent and rapid long-range charge transfer through DNA. Nature Chemistry. DOI: 10.1038/nchem.171
One of the questions seldom asked when building a model or assessing experimental data is "What's the error in that?". Unless we know the errors in the measurement of a variable, fitting predicted to experimental values may be a flawed endeavor. For instance when one expects a linear relationship between calculated and experimental values and does not see it, it could either mean that there is a flaw in the underlying expectation or calculation (commonly deduced) or that there is a problem with ........ Read more »
Brown, S., Muchmore, S., & Hajduk, P. (2009) Healthy skepticism: assessing realistic model performance. Drug Discovery Today, 14(7-8), 420-427. DOI: 10.1016/j.drudis.2009.01.012
I’ve been mulling over this paper for a few days now. Last week, NASA JPL put out a press release about cool stars having a different mix of life forming chemicals to sun-like stars. The release was immediately picked up by news sites and bloggers alike. With good reason too — the findings could have a lot of implications for future astrobiology searches. With my interest piqued, I thought I’d get hold of a copy of the paper and find out more…... Read more »
I. Pascucci, D. Apai, K. Luhman, Th. Hemming, J. Bouwman, M. R. Meyer, F. Lahuis, A. Natta. (2009) The Different Evolution of Gas and Dust in Disks around Sun-like and Cool Stars. Astrophysical Journal (submitted). DOI: http://arxiv.org/abs/0810.2552v2
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