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Stanford Genome Technology Center retreat highlights interdepartmental synergy

IMG_0108The recent Stanford Genome Technology Center retreat drove home for me why it’s a great idea to put biochemists, geneticists, engineers, and physicians in a lab together.

Set up in 1989 to establish automated methods for the Human Genome Project, SGTC works to increase the speed, accuracy, and cost-effectiveness of genomic, biomedical, and diagnostic technologies. The center integrates personnel from Stanford’s departments of genetics, biochemistry, medicine, and electrical engineering. At the two-day retreat, researchers presented their latest work in areas like synthetic biology, genome sequencing applications, single-cell approaches, and devices for cellular and molecular detection.

Since I joined SGTC this summer, I’ve gotten a firsthand view of the benefits of combining engineers and biologists. As our engineer Rahim Esfandyarpour, PhD, told me, “We have a lot of solutions – you biologists just need to tell us what the problems are.” The solutions presented at the retreat ranged from ‘sequencing by seeing’ – literally reading DNA molecules under an electron microscope – to a nanopipetting technology that noninvasively takes tiny samples from individual cells, to electrical ‘needles’ that can detect interactions between individual cells or even molecules, to wearable devices that quantify molecules in sweat.

Another recurrent theme was the central role of baker’s yeast S. cerevisiae (as in, the yeast that make bread, wine, and beer) in developing genome technologies. This species is a powerful workhorse for synthetic biology: it’s fast, cheap, and easy to study the function of genes, mutations, and even entire pathways by engineering them in yeast. In fact, one of SGTC’s biggest projects is doing the latter to boost the discovery of natural products (NPs), chemicals made from enzymes encoded by clusters of genes in bacteria, fungi, and plants.

“What’s interesting about NPs is that they’re used in something of a ‘chemical warfare’ among microorganisms and plants in the wild, and they’ve been honed by millions of years of evolution,” said Maureen Hillenmeyer, PhD, who leads the NP team at SGTC.

NPs have therefore been the source of two-thirds of the antibiotics we use to kill pathogens and fight disease. Given the current antimicrobial resistance crisis, the largely untapped potential of the NP universe is ever more attractive. Because of genome technologies, researchers can now reverse the traditional methods of discovery, starting with genes we can sequence, analyze, and engineer to see what NPs they produce. Hillenmeyer’s team is developing yeast as a synthetic host for potential NP gene clusters, so that we can discover new NPs and enable others to do the same.

Our director, Ron Davis, PhD, talked about his son, who has a severe case of chronic fatigue syndrome (CFS) – a disease struggling to be treated, understood, and even acknowledged by the medical community. Davis is hopeful that the technologies being developed at SGTC will help to demystify his son’s disease and maybe even point towards a cure.

“Open biological questions and diseases are an opportunity for us to integrate and apply this toolbox of technologies we’ve developed,” Lars Steinmetz, PhD, center co-director, told us. “Let’s keep pushing the limits of what we can measure.”

Raeka Aiyar, PhD, is the communications director at the Stanford Genome Technology Center. She is trained in genomics and bioinformatics. Follow SGTC on Twitter @StanfordGenome.

Previously: "This is probably one of the last major diseases we know nothing about": A look at CFS, Stanford team develops technique to levitate single cells and Cancer's mutational sweet spot identified by Stanford researchers
Photo courtesy of Raeka Aiyar

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