Biotechnically Speaking

A newly announced genome-editing experiment—the largest documented to date—is the latest in a series of advances reinvigorating the field of xenotransplantation. In October, Harvard University geneticist George Church and colleagues at Boston-based startup eGenesis described the use of CRISPR-Cas9 to disrupt all 62 genomic copies of porcine endogenous retrovirus (PERV) in cultured pig kidney epithelial cells. That feat, which dwarfs the greatest number of simultaneous DNA changes ever recorded using genome editing, removes one potential hurdle facing use of pig xenotransplants in human patients—zoonosis. But eGenesis is not the only company actively exploring the commercial prospects of xenotransplantation… Read more at Nature Biotechniques.

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Hardly a day goes by without the announcement of a newly sequenced genome. Whatever the DNA source—animal or plant, fungus or bacterium—genome sequencing has become so commonplace, the feat no longer amazes. It may shock younger readers to learn that not so long ago completed genomes merited journal covers and press conferences. Perhaps lost in all this familiarity and access is the recognition that, a decade after the first next-gen sequencing instruments went online and more than a decade since the completion of the Human Genome Project, sequence assembly remains a challenge… Read more at BioTechniques. (PDF)

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When Jack Gilbert, Microbial Ecology Group Leader at Argonne National Laboratory in Argonne, Illinois, wanted to lose some weight, he didn’t try traditional dieting. Instead, he tried sequencing. One of a growing number of researchers investigating the human microbiome—the collection of bacteria that live in and on us—Gilbert sequenced the bacterial flora in his own gut and used those data to design a specific diet suited to his internal microbial species diversity and its metabolic potential… Read more at BioTechniques. (PDF)

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Would researchers scrawl notes, critiques and comments across online research papers if software made the annotation easy for them? Dan Whaley, founder of the non-profit organization Hypothes.is, certainly thinks so. Whaley’s start-up company has built an open-source software platform for web annotations that allows users to highlight text or to comment on any web page or PDF file. And on 1 December, Hypothes.is announced partnerships with more than 40 publishers, technology firms and scholarly websites, including Wiley, CrossRef, PLOS, Project Jupyter, HighWire and arXiv… Read more at Nature.

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Flow cytometers guide fluorescently labeled cells one by one past a series of lasers and detectors in order to record their physical and molecular characteristics. Researchers using these techniques can survey tens or even hundreds of thousands of cells, garnering information that allows them not only to enumerate known cell types (such as CD4+ and CD8+ T cells) but also to identify novel subpopulations they may never have known were there. But data collection is only the first part of the story… Read more at The Scientist.

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Adam Rocker didn’t expect the software that managed his digital reference library to flag up better ways he could be doing his research. But his electronic filing system of choice, ReadCube, periodically scans his library and suggests related papers, rather as some music-file-management programs highlight recommended tunes. And that feature, he says, has brought up some unexpected gems… Read more at Nature.

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Advertising campaigns notwithstanding, few people are under the illusion that diet soda is actually good for them. But for a rare group of individuals suffering from phenylketonuria (PKU), a genetic disorder affecting the body’s ability to process the amino acid phenylalanine, the drink can be downright devastating.

Phenylalanine is one of the building blocks of proteins, and if allowed to accumulate to high concentrations, as in the case of PKU, it can cause mental retardation in children, which is why newborns are routinely screened for the disease—and why cans of diet soda labeled, “Phenylketonurics: Contains Phenylalanine.” … Read more at BioTechniques. (PDF)

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Pick a paper, any paper. If it involves the protein, nucleic acid, or metabolite content of bacterial or eukaryotic cells, there’s likely a section detailing how those cells were grown in culture. Cell culture is how researchers expand cells to harvest macromolecules or to interrogate their responses to changing conditions or chemical treatment. Inherent in such work is the assumption that all the cells in a dish are identical—by growing them in culture, the researcher is simply amplifying the signal. But that isn’t always true. Subtle differences at the molecular level can yield significant variation in cellular behavior, but until recently researchers had no way to probe that variability. Today, they do… Read more at Science. (PDF)

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There’s much to marvel at when it comes to viruses. But what University of California at Berkeley professor Carlos Bustamante chooses to study may at first not seem like one of them. Bustamante researches the seemingly mundane process of how virus particles are loaded with their nucleic acid payload, and for the better part of 15 years, he has been chipping away at the so-called ring ATPase assembly found at the base of a virus called bacteriophage phi29… Read more at BioTechniques. (PDF)

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Between alternative transcription start sites, alternative splicing, and post-translational modifications, a given gene may produce dozens of protein variants, each with a different biological activity. Teasing apart those structure-function relationships requires mapping specific variants to their associated biological functions, and the tool of the trade for doing so is mass spectrometry. But not just any mass spec will do. Researchers need a holistic view of protein structure, data that is lost with the popular “bottom-up” proteomics strategy. Powered by today’s ultrahigh-resolution, high massaccuracy mass specs, protein biochemists are increasingly turning bottom-up upside-down. Their new alternative: top-down proteomics… Read more at Science. (PDF)

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