Biotechnically Speaking

A newly approved class of anti-cholesterol medications could be the latest in a long line of ‘biopharmaceutical blockbusters’. These drugs not only produce big revenue for pharmaceutical companies, but also represent employment opportunities for early-career scientists who want to develop cutting-edge therapies. To get into the game, aspiring young researchers must tailor their training and skills to the industry… Read more at Nature.

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Thanks to the boom in next-generation DNA sequencing technology, hundreds of thousands of genomes and exomes have been sequenced, with more rolling off sequencers every day. Yet the majority of these data sets lie in distributed databases, hidden behind firewalls and user authentication schemes that make it impossible (or at least very difficult) for researchers to access them. And those that are freely available typically are divorced from the phenotypic data that makes genomic data useful to geneticists in the first place. The developers of a new genetic search tool are hoping to change all that… Read more at BioTechniques.

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Biological science these days is all about Big Data. Whether it’s in the form of DNA sequences, photomicrographs, or mass spectra, researchers increasingly need to collect, integrate, manipulate, and interpret enormous pools of information. For many biologists, that can be pretty intimidating. Traditional training programs tend to focus on scientific fundamentals and experimentation, not computer programming and statistics. As a result, when many researchers find themselves confronted by massive data sets, they have no idea how to tackle them… Read more at The Scientist.

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When Marilyn Goudreault received a request for plasmids stored in the repository of the laboratory she manages at the Lunenfeld–Tanenbaum Research Institute in Toronto, Canada, there was never any question whether she would honour it. Reagent sharing is typically a precondition of publication in peer-reviewed journals, and is fundamental to the scientific process. But first, Goudreault would have to find the plasmids… Read more at Nature. (PDF)

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To minimize complexity, researchers often study cellular proteins or nucleic acids in isolation. But sometimes—when testing a drug’s efficacy and safety, for instance, or monitoring tumor progression—ex vivo just won’t do. The only way to know how a compound or cells will behave in the body is to put them into an animal and watch what happens live. The results are easily recognizable in the pages of your favorite journal: the ghostly outline of a mouse, with a telltale multicolored heat bloom indicating where the action is… Read more at Science. (PDF)

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Eukaryotic genes don’t generally act alone. Their expression typically is driven by interactions with proximal promoters, promoters who are themselves influenced by the concerted action of distal enhancer and repressor sequences often located hundreds of kilobases away. In short, eukaryotic gene expression is a complex and intricate business. Cartoons and diagrams usually portray these interactions as simple loops, with transcription factors binding to regulatory sequences, acting as bridges to tweak the activity of distant gene promoters. Yet it’s clear that in reality, the nucleus must be loaded with such loops: Mammalian genomes, notes Job Dekker, Professor and Co-director of the Program in Systems Biology at the University of Massachusetts Medical School, are chock full of regulatory sequences, some constitutive, others transmitting subtle developmental cues. Given the genetic cacophony this situation can produce, how can cells limit genetic “distractions” to ensure regulatory sequences act only where they’re supposed to? Read more at BioTechniques. (PDF)

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Three years ago, Jennifer Doudna and Emmanuelle Charpentier launched a molecular biology revolution by unraveling the CRISPR/Cas system. Their seminal paper, published in June 2012 and cited over 900 times according to Google Scholar, describes a mechanism by which the Cas9 enzyme can cleave any segment of DNA, guided by a short RNA molecule complementary to the sequence of interest. Scientists quickly took note and have since exploited the finding to rewrite the genomes of cultured cells and model organisms, tweak gene expression programs, and drive drug development and disease etiology research… Read more at BioTechniques. (PDF)

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When Mary Alikian, a clinical scientist and “part-time PhD student” at Imperial College London, began her doctoral research, she decided to use digital PCR (dPCR). Alikian, who was interested in investigating RNA biomarkers associated with chronic myelogenous leukemia, quickly realized she had a problem though: no one in the lab had experience with dPCR, so no one could teach her how to do it correctly. “I had no clue what things I should consider and what things I should not.” Read more at BioTechniques. (PDF)

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Arguably, there is no hotter area in life science research today than induced pluripotent stem (iPS) cells. With applications in basic research, drug discovery, and cell therapeutics, iPS cells—essentially embryonic stem cells without the embryo—have attracted tremendous excitement from academics, funding agencies, and pharmaceutical companies alike. The first clinical trial based on an iPS cell–derived product has launched in Japan, less than a decade removed from Shinya Yamanaka’s discovery of the iPS cell process in 2006. Yet as iPS cell R&D speeds towards the clinic, a nagging question remains: Just how easy is it to replicate findings between labs? Read more at BioTechniques. (PDF)

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What if scientific journals were like hotels, restaurants and holiday operators — easy to compare online and reviewed by those who use them? That thought occurred to conservation biologist Neal Haddaway two years ago: frustrated by a bad experience publishing his work with a journal he prefers not to name, he decided to launch Journalysis.org, a journal-review site that he likens to TripAdvisor. “I wanted to basically reward the journals that were doing a good job and, within reason, name and shame the ones that weren’t doing so well,” he says… Read more at Nature.

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