Post List

  • September 24, 2009
  • 01:06 PM

The cutting edge…

by Jim Caryl in mental indigestion

I HAD barely started reading this week’s edition of Nature when in the Research Highlights1 section a study really piqued my interest. Surgeons operating to remove malignant tumours can often struggle to differentiate such tumours from surrounding healthy tissues. To ensure complete tumour removal, surgeons also need to remove some of the surrounding healthy tissue [...]... Read more »

Nature editors. (2009) Analytical chemistry: Evaporating flesh. Nature, 461(7263), 451-451. DOI: 10.1038/461451d  

Schäfer, K., Dénes, J., Albrecht, K., Szaniszló, T., Balog, J., Skoumal, R., Katona, M., Tóth, M., Balogh, L., & Takáts, Z. (2009) In Vivo, In Situ Tissue Analysis Using Rapid Evaporative Ionization Mass Spectrometry. Angewandte Chemie International Edition. DOI: 10.1002/anie.200902546  

  • September 24, 2009
  • 12:17 PM

Use enumerated constants in Java

by Yingliang Du in Yingliang Du's Blog

In the article “Create enumerated constants in Java” , Eric point out static final constants like this:
static final int YELLOW = 0;
static final int GREEN = 1;
static final int BLUE = 2;
had the following drawbacks:

The major drawback is the lack of type safety. Any [...]... Read more »

Eric Armstrong. (1997) Create enumerated constants in Java. info:/

  • September 24, 2009
  • 12:08 PM

No T-cell left behind, an explanation to why we sleep and more in my picks of the week from RB

by Alejandro Montenegro-Montero in MolBio Research Highlights

Another week has gone by and some very interesting molbio blog posts have been aggregated into Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that ... Read more »

van Heijst, J., Gerlach, C., Swart, E., Sie, D., Nunes-Alves, C., Kerkhoven, R., Arens, R., Correia-Neves, M., Schepers, K., & Schumacher, T. (2009) Recruitment of Antigen-Specific CD8 T Cells in Response to Infection Is Markedly Efficient. Science, 325(5945), 1265-1269. DOI: 10.1126/science.1175455  

Ascher, M., Sheppard, H., Jr, W., & Vittinghoff, E. (1993) Does drug use cause AIDS?. Nature, 362(6416), 103-104. DOI: 10.1038/362103a0  

Siegel, J. (2009) Sleep viewed as a state of adaptive inactivity. Nature Reviews Neuroscience, 10(10), 747-753. DOI: 10.1038/nrn2697  

  • September 24, 2009
  • 12:00 PM

Capture and Illumina Sequencing of Human Exomes

by Daniel Koboldt in Massgenomics

This month in Nature, a group from Jay Shendure’s lab reported perhaps the most ambitious targeted resequencing study to date - the whole exome sequences of 12 individuals.

Using an array-based hybridization capture method (2 microarrays, 10 g of input DNA), Ng et al selectively targeted CCDS regions totaling 26.6 Mb of sequence (~0.83% of the [...]... Read more »

Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE.... (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461(7261), 272-6. PMID: 19684571  

  • September 24, 2009
  • 11:37 AM

Paint the Town Green

by Journal Watch Online in Journal Watch Online

Planted rooftops can sequester significant amounts of carbon

... Read more »

Getter, K., Rowe, D., Robertson, G., Cregg, B., & Andresen, J. (2009) Carbon Sequestration Potential of Extensive Green Roofs. Environmental Science , 2147483647. DOI: 10.1021/es901539x  

  • September 24, 2009
  • 09:15 AM

The Next Steps in Synthetic Biology

by Tim Sampson in The Times Microbial

The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."... Read more »

Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759  

  • September 24, 2009
  • 09:15 AM

The Next Steps in Synthetic Biology

by Tim Sampson in The Times Microbial

The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."More than 20 years later, this description is being realized. With the great minds and funds of the Venter Institute, we have seen the d........ Read more »

Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759  

  • September 24, 2009
  • 07:43 AM

Science News: Week of September 20, 2009

by Susan Steinhardt in BioData Blogs

Our weekly compilation of science news for the week of September 20, 2009.... Read more »

  • September 24, 2009
  • 05:47 AM

More progress in understanding prostate cancer genetics

by Cancer Research UK in Cancer Research UK - Science Update

Understanding the causes of cancer is one of the key aims of organisations like Cancer Research UK. But although we’ve made huge progress in identifying risk factors for cancers such as breast and bowel cancer, for others the underlying causes aren’t as clear cut. Prostate cancer is one of these.
To find out more, scientists around [...]... Read more »

Eeles, R., Kote-Jarai, Z., Al Olama, A., Giles, G., Guy, M., Severi, G., Muir, K., Hopper, J., Henderson, B., Haiman, C.... (2009) Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nature Genetics. DOI: 10.1038/ng.450  

Al Olama, A., Kote-Jarai, Z., Giles, G., Guy, M., Morrison, J., Severi, G., Leongamornlert, D., Tymrakiewicz, M., Jhavar, S., Saunders, E.... (2009) Multiple loci on 8q24 associated with prostate cancer susceptibility. Nature Genetics. DOI: 10.1038/ng.452  

Gudmundsson, J., Sulem, P., Gudbjartsson, D., Blondal, T., Gylfason, A., Agnarsson, B., Benediktsdottir, K., Magnusdottir, D., Orlygsdottir, G., Jakobsdottir, M.... (2009) Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nature Genetics. DOI: 10.1038/ng.448  

Yeager, M., Chatterjee, N., Ciampa, J., Jacobs, K., Gonzalez-Bosquet, J., Hayes, R., Kraft, P., Wacholder, S., Orr, N., Berndt, S.... (2009) Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nature Genetics. DOI: 10.1038/ng.444  

  • September 24, 2009
  • 04:00 AM

Rehabilitating logged rainforests...

by Rob Goldstein in Conservation Maven

A new study explores the practice of forest rehabilitation and measures the impacts that this carbon sequestration strategy can have on habitat for more... Read more »

EDWARDS, D., ANSELL, F., AHMAD, A., NILUS, R., & HAMER, K. (2009) The Value of Rehabilitating Logged Rainforest for Birds. Conservation Biology. DOI: 10.1111/j.1523-1739.2009.01330.x  

  • September 24, 2009
  • 02:05 AM

Unprofessional Online Content By Medical Students

by Dr Shock in Dr Shock MD PhD

60% of Medical Schools in the US participated in an anonymous electronic survey to assess online posting of unprofessional content by medical students.
Of these schools 60% (47/78) reported incidents of students posting unprofessional online content.

Sexual-Relational Content. Provocative photographs of students, requesting inappropriate friendships with patients on Facebook
Negative comments on specific medical schools using profanity or [...]

Related posts:Negative attitude in medical stud........ Read more »

Chretien, K., Greysen, S., Chretien, J., & Kind, T. (2009) Online Posting of Unprofessional Content by Medical Students. JAMA: The Journal of the American Medical Association, 302(12), 1309-1315. DOI: 10.1001/jama.2009.1387  

  • September 23, 2009
  • 08:39 PM

Accelerated Immune System Aging That Illustrates Normal Immune System Aging

by Reason in Fight Aging!

The study of forms of accelerated aging often provides insight into the biochemical processes of normal (and equally undesirable) degenerative aging. Here, we'll look at the aging of the immune system, a comparatively structured form of degeneration that might be viewed as the natural consequence of evolutionary selection: Evolution is a harsh but efficient mistress; you can consider yourself surprisingly well optimised as a piece of machinery, but your warranty only goes so far as the number of........ Read more »

Sauce, D., Larsen, M., Fastenackels, S., Duperrier, A., Keller, M., Grubeck-Loebenstein, B., Ferrand, C., Debré, P., Sidi, D., & Appay, V. (2009) Evidence of premature immune aging in patients thymectomized during early childhood. Journal of Clinical Investigation. DOI: 10.1172/JCI39269  

  • September 23, 2009
  • 06:14 PM

Predicting eLearning Dropout

by Kristen DiCerbo in Connections Research Blog

Despite its promise, a continuing challenge to online learning/ distance learning/ and eLearning is student dropout. Studies have consistently found higher student dropout rates in these courses than in in-person courses. There have been numerous studies attempting to predict dropout, but few have gotten to the holy grail of being able to identify students who [...]... Read more »

  • September 23, 2009
  • 04:55 PM

Flight of the remote-controlled cyborg beetle

by Mo in Neurophilosophy

REMOTE-CONTROLLED insects may sound like the stuff of science fiction, but they have already been under development for some time now. In 2006, for example, the Defense Advanced Research Projects Agency (DARPA, the Pentagon's research and development branch) launched the Hybrid Insect Micro-Electro-Mechanical Systems project, whose ultimate aim is turn insects into unmanned aerial vehicles.Such projects provide proof of principle, but have met with limited success. Until now, that is. In the ope........ Read more »

Sato, H., et al. (2009) Remote Radio Control of Insect Flight. Front. Integr. Neurosci. , 3(24). info:/

  • September 23, 2009
  • 04:16 PM

Final post on mirror neurons

by Greg Hickok in Talking Brains

I'm kicking the mirror neuron habit after just one more puff (don't worry, I never inhale). I got to page 100 in Rizzolatti & Sinigaglia's Mirrors in the Brain (2008, Oxford Press) and had to stop. The logic just became so incoherent and one-sided that I decided it is a waste of time even to consider the arguments seriously. Here's what they wrote (italics theirs):...these [mirror] neurons are primarily involved in the understanding of the meaning of 'motor events', i.e., of actions performed ........ Read more »

Catmur C, Walsh V, & Heyes C. (2007) Sensorimotor learning configures the human mirror system. Current biology : CB, 17(17), 1527-31. PMID: 17716898  

  • September 23, 2009
  • 04:00 PM

Treating the Obesity Epidemic

by sciencebase in Sciencebase Science Blog

Drugmaker Vivus saw its experimental weight-loss medication, Qnexa, pass two Phase III clinical trials C&EN reported on September 10, and the company’s share price skyrocket.
The rewards of developing a safe and effective anti-obesity medication will be in the tens of billions of dollars, according to Bloomberg. Of course, such apparent breakthroughs are going to hit [...]Treating the Obesity Epidemic is a post from: Sciencebase Science Blog
... Read more »

Andreas G. Anastasiou, & Athanasios Anastasiou. (2009) The effects of current dietary trends and consumption patterns on health: evidence from the UK. Int. J. Behavioural and Healthcare Research, 1(3), 318-333. info:/

  • September 23, 2009
  • 01:52 PM

Swimming in Ethanol's Ethos

by Kristopher Hite in Tom Paine's Ghost

The Arizona Chemical wood pulp mill in Panama City, Florida sits within a stone's throw of the Gulf of Mexico.By Kristopher Hite Walking on a balance beam, the idea of ethanol powering America's future took a shove from the scientific community this week. A new study published in the Journal of Environmental Science and Technology indicates that no matter the starting material whether it be corn kernels or the wood chips, switch grass, and corn stover (all forms of cellulose), the environmental........ Read more »

Heinzelman, P., Snow, C., Smith, M., Yu, X., Kannan, A., Boulware, K., Villalobos, A., Govindarajan, S., Minshull, J., & Arnold, F. (2009) SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability. Journal of Biological Chemistry, 284(39), 26229-26233. DOI: 10.1074/jbc.C109.034058  

  • September 23, 2009
  • 01:20 PM

Catalytic Wittig

by Rik in NNNS chemistry blog

The Wittig reaction, discovered in 1954 by George Wittig, couples ketones and aldehydes with phosponium ylides to alkenes. Although this organic reaction is extensively used in organic chemistry, it suffers from one major drawback: removal of the phosphonium oxide waste product. O'Brien et al. think they have the solution: a Wittig reaction that is catalytic in the ylide.
... Read more »

O'Brien, C., Tellez, J., Nixon, Z., Kang, L., Carter, A., Kunkel, S., Przeworski, K., & Chass, G. (2009) Recycling the Waste: The Development of a Catalytic Wittig Reaction. Angewandte Chemie International Edition, 48(37), 6836-6839. DOI: 10.1002/anie.200902525  

  • September 23, 2009
  • 01:06 PM

Fisheries in Peril: The Evolution of Exploitation

by Johnny in Ecographica

What happens when the commercial fishing industry and recreational fishers target certain species for size? Do these practices of selective harvest equate to active artificial selection for smaller fish? Do these practices reverberate in the fish DNA in such a way that humans can be said to be manipulating the evolutionary trajectory of marine life? Thanks to the journal of Evolutionary Applications, here’s your chance to find out!... Read more »

  • September 23, 2009
  • 12:34 PM

Indications of failure

by Jeremy in Agricultural Biodiversity Weblog

A group of over 20 biodiversity experts from a slew of international conservation agencies have a paper out in Science bemoaning the state of the biodiversity indicators agreed in 2006. These indicators are important because they are supposed to be used to track progress towards fulfillment of the promise made by Parties under the Convention [...]... Read more »

Walpole, M., Almond, R., Besancon, C., Butchart, S., Campbell-Lendrum, D., Carr, G., Collen, B., Collette, L., Davidson, N., Dulloo, E.... (2009) Tracking Progress Toward the 2010 Biodiversity Target and Beyond. Science, 325(5947), 1503-1504. DOI: 10.1126/science.1175466  

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