Metagenomic profiling, also called metagenomic shotgun sequencing (MSS) represents a powerful application made possible by the digital nature of next-generation sequencing technologies. In it, one basically sequences a sample isolate obtained from somewhere — a shovelful of dirt, a scoop of plankton, or anything else that contains living organisms. MSS has proven particularly useful to studies of the human microbiome, or in layman’s terms, all of the bacteria/viruses/fungi that live in our bodies.


Many such microbiota are beneficial or simply commensal (not doing harm) with us. Others, like methicillin-resistant Staphylococcus aureus (MRSA), can cause severe disease. Most efforts to chart the human microbiome have focused on bacteria, whose relatively stable genomes make them amenable to assay development. Viruses, in contrast, are somewhat under-studied. Part of that is due to the small size and highly variable nature of viral genomes.


A new study in Genome Research showcases a capture-based enrichment strategy to improve virome sequencing. The ViroCap panel was developed by Todd and Kristine Wylie, who happen to be colleagues of mine at the McDonnell Genome Institute. The panel enriches for nucleic acids from 34 families of DNA or RNA viruses that infect vertebrate hosts, beautifully illustrated in a figure from the paper (see above).


At the time of the ViroCap design, NCBI GenBank contained the sequenced genomes of around 440 viral species, for a total of about 1 Gbp (billion base pairs) of sequence. After considerable bioinformatics efforts, the authors produced a ~200 Mbp sequence target and worked with Nimblegen to have it designed.


References
Wylie TN, Wylie KM, Herter BN, & Storch GA (2015). Enhanced virome sequencing through solution-based capture enrichment. Genome research PMID: 26395152


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Agricultural biotech giants are starting to make moves into CRISPR gene editing, saying they’ll be selling seeds engineered with the technology by the end of this decade.

DuPont said today it entered an agreement with Caribou Biosciences, a spin-off from the laboratory of Jennifer Doudna at the University of California, Berkeley, who carried out key work on CRISPR-Cas9, a technology that provides something like a find-and-replace feature for DNA.

DuPont says it is already growing corn and wheat plants edited with CRISPR in greenhouses and that field trials will start next spring.

“We are talking about bringing products to market in five to 10 years,” says Neal Gutterson, vice president for agricultural biotechnology at Pioneer Hi-Bred, part of DuPont’s $11-billion-per-year crop chemicals and biotech seed business. “That is a pretty damn good time line compared to other technology.”

DuPont is testing CRISPR to make drought-resistant corn as well as wheat genetically altered so it will breed like a hybrid, rather than self-pollinate as it typically does. Hybrid plants are vigorous, and yields can jump by 10 or 15 percent.

A growing list of plant types have already been genetically engineered with CRISPR-Cas9 in academic laboratories, including soybeans, rice, and potatoes. Last month, a Japanese team used gene editing to turn off fruit-ripening genes in tomato plants.

As part of their collaboration, DuPont said it had made an investment in Caribou, a small startup that holds commercial rights to patents Berkeley has applied for on CRISPR-Cas9. DuPont will have exclusive rights to those patents in crops like corn and soybeans, should they be approved.


Currently, most GMOs are transgenic plants that have been engineered by adding bacterial genes to the plants so that they poison insects or survive weed sprays. Thanks to biotechnology, the seed business has ballooned to about $40 billion a year, and companies like Monsanto, Dow, DuPont, and Syngenta have come to dominate it. But the need to invest millions more in a sweeping technology shift hits as depressed commodity markets have made the profitability of biotech seeds less certain.


Gutterson says DuPont thinks gene editing will kick off a new wave of products and profits. “We have no doubt that genome editing is going to have a material impact on the value proposition,” he says. “We think another whole cycle could come from genome editing.”


Gene editing could lead to some surprising creations in agriculture. For instance, peanuts have a number of proteins responsible for allergies. Getting rid of them is challenging, but allergy-free peanuts might be possible with the new technology.

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Have you ever given someone a business card and never heard back from them? That’s actually quite common. What if I tell you that I have a business card alternative that will get you a response almost 100% of the time. Yes it is possible, and I have been using this power networking trick for …

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CAMBRIDGE, Mass. (AP) — The Massachusetts Institute of Technology has offered free online courses for the last four years with one major downside: They didn’t count toward a degree. That’s about to change.
In a pilot project announced Wednesday, students will be able to take a semester of free online courses in one of MIT’s graduate programs and then, if they pay a “modest fee” of about $1,500 and pass an exam, they will earn a MicroMaster’s credential, the school said.
The new credential represents half of the university’s one-year master’s degree program in supply chain management. As part of the pilot project, students who perform well in the online half can take an exam to apply for the second semester on campus. Those who get in would pay $33,000, about half the cost of the yearlong program.
“Anyone who wants to be here now has a shot to be here,” MIT President L. Rafael Reif said. “They have a chance to prove in advance that they can do the work.”

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