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Links 1 through 10 of 255 by Charlie Schick tagged biology

"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 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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"The Original EcoSphere® is the world’s first totally enclosed ecosystem - a complete, self-contained and self-sustaining miniature world encased in glass. Be wary of inferior and lower quality imitations. Easy to care for, an EcoSphere is an incredible learning tool that can provide powerful insights about life on our own planet... and provide a glimpse of technology that's shaping the future of space exploration."

So cool. Will have to get one some day. [via @curisma]

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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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"Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology."

Hm. Some really practical uses of microbes - impregnating fabrics to provide bioactive activity.

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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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"Molecular diagnostics and molecular biology in general are becoming more pervasive every day in a range of applications but are still seen by many as being an arcane science. Many undergraduate science curricula cover only the basics of theoretical components without exposure to laboratory practice, due to perceived cost and complexity of laboratory facilities needed. With this in mind, I recently set out on a quest to see whether a non-specialist, $500 complete molecular biology laboratory was possible."

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