The struggle with image glut

•April 29, 2016 • Leave a Comment

As the fruit-fly larva wriggles forwards in the video, a crackle of neural activity shoots up its half-millimetre-long body. When it wriggles backwards, the surge undulates the other way. The 11-second clip, which has been watched more than 100,000 times on YouTube, shows the larva’s central nervous system at a resolution that almost captures single neurons. And the experiment that created it produced several million images and terabytes of data… Read more at Nature.

Democratizing mass spectrometry

•April 15, 2016 • Leave a Comment

As a postdoctoral researcher at the University of Wisconsin, Madison, Kevin Clark spent a lot of his time synthesizing peptides. Mass spectrometry (MS) was the key to Clark ensuring that those peptides were what he thought they were. “You have to do mass spectrometry to test your work,” he says. Clark would end up using MS—specifically, matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) MS—for the bulk of 2 decades. Nevertheless, when he took up proteomics research at the University of Georgia in 2010, he felt like an MS newbie all over again… Read more at BioTechniques. (PDF)

Immunohistochemistry for the 21st century

•March 8, 2016 • Leave a Comment

Immunohistochemistry (IHC) dates back decades, but that doesn’t mean it’s stagnant. Automated sample processors, digital slide scanners, image analysis software, and more have given the aged procedure a decidedly 21st century flair… Read more at Science. (PDF)

Xenotransplantation makes a comeback

•February 24, 2016 • Leave a Comment

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.

When two is better than one

•February 11, 2016 • Leave a Comment

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)

The bacteria among us

•December 18, 2015 • Leave a Comment

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)

Annotating the scholarly web

•December 2, 2015 • Leave a Comment

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.