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Links 1 through 10 of 411 by Charlie Schick tagged science

"Bacteriophage could be an alternative to conventional antibiotic therapy against multidrug-resistant bacteria. However, the emergence of resistant variants after phage treatment limited its therapeutic application. Our data showed that the phage cocktail was more effective in reducing bacterial mutation frequency and in the rescue of murine bacteremia than monophage suggesting that phage cocktail established by SBS method has great therapeutic potential for multidrug-resistant bacteria infection."

Biologic warfare at the bacterial level. In some developed countries antibiotic misuse has caused the rapid development of antibiotic-resistant bacteria. Bacteriophage therapy has therefore taken a more important role. Except, it has its issues. In this paper, they work to avoid phage resistance with a multi-phage approach.

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"Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans."

A broad survey to understand the nature of this pesky and increasingly common pathogen.

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"The Broad isn't alone: Mount Sinai School of Medicine in New York City, the Allen Institute for Brain Science in Seattle, the Salk Institute in San Diego, and University of California, San Diego, are also launching major efforts to study cell circuitry, says UCSD computational biologist Trey Ideker. He suggests that eventually these groups should form a "big, coordinated science project" so that they can divide up the task of mapping circuits in different cell types. "This is a very big goal and in a sense the logical successor to the Human Genome Project," Ideker says."

Mapping cellular circuits - very interesting.

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"For decades, Robert Daum has studied the havoc wreaked by methicillin-resistant Staphylococcus aureus. Now he thinks he can stop it for good."

Excellent story of the fight against MRSA by the guy who first made us aware of it.

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"The first challenge that OSDD's cyber-community assigned itself was to glean more information from the M. tuberculosis genome. It was sequenced in 1998, but researchers had clues to the functions of only a quarter of its 4000 genes. In December 2009, OSDD set out to reannotate all possible genes. Some 500 volunteers got the job done in a mere 4 months. Now OSDD is trying to exploit these data. “The more people you put to work on the problem, the more chances you will have to identify the set of compounds that will likely make it through compound optimization, animal models, preclinical, and, eventually, clinical trials. If you increase your success chances, then your overall costs decrease,” says Marc Marti-Renom of the National Center for Genomic Analysis in Barcelona, Spain."

FoldIt, GalaxyZoo, now this. Is the next phase of computing networked human computing?

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"The Earth Microbiome Project (EMP) is the most ambitious attempt to provide a systematic characterization of the microbial world that dominates this planet. The ecosystem services provided by microbes in every environment (including the human body) are fundamental to the survival of life on this planet and the continued economic and physical health of the human race. The pilot study of the EMP started in March 2011 and is now reaching its zenith."

This session has four interesting talks on handling the data deluge, a field guide, why we should care, and mathematical modeling. Cool. Can't wait for the speaker notes and the like.

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"Many yoghurts are loaded with live bacteria, and labelled with claims that consuming these microorganisms can be good for your health. But a study published today shows that such yoghurts have only subtle effects on the bacteria already in the gut and do not replace them."

Yes, but the paper goes to point out that both in humans and mice, there was an upregulation of polysaccharide metabolism genes in the existing gut microbes. Hm, there are some serious implications there.

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"Now, a new study by Eric Martens, David Bolam, and colleagues has looked into how a pair of the most common species of gut bacteria metabolize polysaccharides, showing that each bacterium is highly specialized. Using a high-throughput system for feeding the bacteria dozens of kinds of carbohydrates, one at a time, and tracking the bacteria's gene expression, they were able to see how these microbes have tailored themselves to fill specific niches in the gut."

This is a really good study. For me, a better understanding of the gut metabolic ecology will allow for the development of better probiotics. One interesting finding in this study is that some bug don't grow well on simple sugar because their sensors are built for complex sugars. Made me think of folks in developed world and what effect eating more simple sugars (high-fructose corn syrup) has on gut flora and any consequential obesity.

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"This study has identified the first bacterial genes required for induction of settlement and metamorphosis of a marine invertebrate animal."

This is an interesting genetic study as to what in the bacteria cause the induction of settlement and metamorphosis. Hooray for Nature for making this paper open so that I could read it. Though the paper focused on the genetic aspects and didn't speculate (unless I missed it) how this connection arose evolutionarily. My speculation is that the bacteria is an environmental marker, telling the worm where to settle and grow.

Cool, huh?

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"Horizontal gene transfer — the exchange of genetic material between different species or lineages — is an important factor in bacterial evolution. A study of human microbiome data comprising more than 2,000 full bacterial genomes shows that this environment is a hotbed of horizontal gene transfer: pairs of bacteria isolated from the human body are 25-fold more likely to share transferred DNA than pairs from other environments. Thus microbial ecology — rather than phylogeny or geography — is the most important driver of the patterns of horizontal gene exchange. Further analysis revealed 42 unique antibiotic-resistance genes that had been transferred between human and agricultural isolates, and 43 transfers across national borders."

This paper sets me spinning due to it being about microbes, microbes on humans, human microbial ecology, and horizontal gene transfer. The other thing that is intriguing about this paper is the mention of unique antibiotic-resistance genes.

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