News & Highlights: Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal disease characterized by premature aging. In their recent collaboration, YRC researcher John Yates and collaborator Juan Carlos Izpisua Belmonte found induced pluripotent stem cells from HGPS patients lacked molecular characteristics associated with the disease, which were restored upon differentiation. See their paper in Nature to learn more. [Read Article]
News & Highlights: YRC researcher Stan Fields used the model organism Saccharomyces cerevisiae to probe the effects of nutritionally acquired metabolites on statins, a cholesterol-lowering drug widely prescribed to prevent heart disease. He found that copper and zinc ions impair the effect of statins by upregulating genes related to sterol production. Please read his paper in Molecular BioSystems to learn more. [Read Article]
News & Highlights: YRC researchers David Baker and Stan Fields have developed new technology for examining how a protein's sequence affects its function. This new technology is large-scale and may be applied to many in vitro or in vivo protein assays, providing a general means for studying the functional consequences of protein variation. Please read their paper in Nature Methods to learn more. [Read Article]
News & Highlights: The YRC collaborated with Sue Biggins at the Fred Hutchinson Cancer Research Center in Seattle to examine centromeres, whose proper function is critical to prevent conditions associated with cancer and some birth defects. This work, performed in yeast, was recently published in Molecular Cell, where Dr. Biggins proposes a new pathway for the regulation of centromeric function. [Read Article]
News & Highlights: Multidimensional protein identification technology (MudPIT) developed by the YRC was used in a recent collaboration with David Drubin at the University of California, Berkeley, to examine the assembly of actin networks in yeast. In his recent paper in Current Biology, Dr. Drubin describes the nucleation and assembly of these large protein complexes, and how MudPIT was used to characterize their composition. [Read Article]

Quantitative Phenotyping


Chemostat array (click photo to enlarge)
The Dunham lab in the YRC is interested in developing technologies for understanding the functional consequences of protein variation in yeast and human. We are currently part of a group of YRC labs studying a panel of very diverse yeast strains collected from around the globe. These strains have been subjected to a battery of high throughput assays, including gene expression, proteomics, metabolomics, and microscopy characterization. From these data, we hope to learn about variation at the phenotype level and develop new technologies to connect back to sequence variation. Given the difficulties in making similar genotype-phenotype connections in complex diseases, we hope our model system will help inform approaches in humans. Since much of this approach relies on next generation sequencing, we have focused on developing methods and collaborations using DNA sequencing data.
We are also interested in improving yeast culture technologies to provide better control over growth parameters. As part of this project, we are developing an inexpensive, small footprint fermenter array. We are seeking collaborators interested in using this device.