Biotechnically Speaking

When Fernando Cagua was preparing to write up his findings on the economics of whale-shark tourism, he didn’t fire up Microsoft Word. He opened his web browser. Cagua, an ecologist at King Abdullah University of Science and Technology in Thuwal, Saudi Arabia, was keen to try out an online writing environment that would allow him and his three co-authors to work on the same paper simultaneously. Over the past few years, a small cadre of tools have sprung up expressly for this purpose… Read more at Nature.

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As a child in Nigeria, Onyx Adegbola contracted malaria. She would come down with the typical symptoms—fever and body aches, nausea, and headaches—and to ease her suffering, she would take anti-malarial tablets. But here’s the thing. One isn’t supposed to self-diagnose malaria; there are simple tests you can perform instead to confirm it is malaria and not some other disease. The definitive one involves examining a blood smear under a microscope, but microscopes were—and are—relatively scarce in that part of the world. So are clinical laboratories… Read more at NOVA Next.

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Microfluidics, the science of moving and manipulating nanoliter or microliter volumes through micron-scale channels, is playing an increasingly outsize role in the life sciences. For some researchers, microfluidics holds the key to low-cost diagnostics. Others use the technology to evaluate the quality of nucleic acid preparations or to drive targeted DNA sequencing. But for an ever-larger pool of researchers, microfluidics offers a way to reduce biology to a fundamental unit, the cell… Read more at The Scientist.

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At the north end of the Utah State University (USU) campus in Logan, Utah, Randy Lewis’ lab in the new USTAR Bioinnovations Center is on the cusp of a materials science gold rush.

Lewis’ gold isn’t hidden deep in the snow-capped peaks just beyond his corner office though; it’s buried in the bacteria, silkworms, genetically modified alfalfa sprouts, and even goat’s milk found in his lab. These are the recombinant biofactories that Lewis and his colleagues have harnessed to generate what many hope will be a new bioengineering treasure: spider silk… Read more at BioTechniques.com. (PDF)

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On Jan. 29, 2014, the scientific community was stunned by the news that, with a simple 30-minute dip in acid, mouse pluripotent stem cells could be efficiently generated from adult precursor cells.  If reproduced and extended to human cells, the findings, detailed in a pair of papers in the journal Nature, promise to be a game changer for stem cell therapeutics, as they offer inducible pluripotent stem cell-like flexibility with none of the concomitant technical difficulty.

“The result is ‘shocking,’ ‘astounding,’ ‘revolutionary,’ and ‘weird,’ said scientists not accustomed to using such exuberant words to describe research findings,” wrote Carolyn Johnson in the Boston Globe.

But within days, excitement over what the researchers called STAP (stimulus-triggered acquisition of pluripotency) cells moved to dismay amid reports of difficulty in reproducing the method and allegations of scientific misconduct… Read more at BioTechniques.com. (PDF)

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“Like finding a needle in a haystack” is an overused expression, but when it comes to some biological scavenger hunts, it fits. Researchers studying rare variant biomarkers often find themselves on the lookout for faint genetic signals against an overwhelming background, sometimes as little as a single positive in 100,000 negatives or more. Such a situation cries out for polymerase chain reaction (PCR), a technique uniquely capable of capturing the proverbial needle. But standard PCR won’t do—it is a qualitative technique—and neither will quantitative real-time PCR (qPCR), which often lacks the necessary accuracy and sensitivity. These days, there’s a third and increasingly popular option: digital PCR (dPCR). By discretizing those 100,000 molecules in a large number of individual reactions, dPCR makes the rare positive surprisingly easy to find… Read more at sciencemag.org (PDF).

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Imagine you’re just starting in a lab. Your new PI decides to test your mettle at the bench with a simple project: Replicate some immunohistochemistry results from a recent publication. No problem, right? Not necessarily. Immunohistochemistry relies on antibodies, and antibodies, says Anita Bandrowski of the University of California, San Diego, “are extremely messy.” Unlike many reagents in today’s molecular biology lab, antibodies are far from the turnkey solutions commercial vendors would have you believe… Read more at BioTechniques.com. (PDF)

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Time was when mass spectrometry was the province of white-coated chemistry Ph.D.s with a secret language all their own. Terms like ion trap and post-source decay, mass-to-charge, and MALDI made the field inaccessible to others. Today, the technique has pushed beyond those narrow confines and entered the biology lab, where it underlies proteomics and biomarker research. But you can also find mass specs in airports and warehouses, and even at the bottom of the ocean. In many cases those instruments are being run not by specially trained researchers, but by TSA agents, soldiers, and first responders. Chalk that up to miniaturization. Researchers have finally figured out how to compress benchtop systems into portable, sometimes handheld gadgets. In so doing, they have created devices that empower not only themselves, but the wider world… Read more at sciencemag.org (PDF).

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You know those high-speed cameras on the television show Mythbusters, the ones the hosts use to slow a bullet to a crawl or catch an explosive shock wave in mid-flight? Imagine using a camera like that to capture molecular dynamics. You could catch the motion of enzymes as they flex to bind ligands, watch photoreactive proteins change shape in response to light, or map a virus’s topology. Turns out, imaging at that level isn’t science fiction… read more at BioTechniques.com (PDF)

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The YouTube video opens on a researcher studying an agarose gel on a UV light box. He slumps in resignation—clearly, his clones are a bust. He slowly shuffles over to the whiteboard, drops to his  knees, and notches yet another failure under the heading “Assembly Attempts.” Tally total: 33.  Anyone who has tried his or her hand at DNA cloning can relate. So simple in theory, yet persnickety in practice, cloning causes many headaches and sleepless nights. Cryptic restriction sites, unexpected fragment toxicity, phases of the moon—all seemingly play a hand… read more at BioTechniques.com (PDF)

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