BMB Graduate Students
Amber M. Jones Brunette
Greg grew up in the heartland and attended Iowa State University in Ames, Iowa, his hometown. He graduated with a degree in Biology in 2010, and as many young people these days, was unsure of his next step. However, he did know that he had an indelible curiosity and a nagging incapacity to just leave well enough alone, thus he knew science was for him. He soon landed the prestigious position of Research Associate at his alma matter in Genetics, Development, and Cell Biology. There, he studied mechanisms of neuronal diversity in the mammalian retina, specifically with regards to how retinal ganglion cells are produced and what makes certain ganglion cells not like those other ganglion cells. It was interesting work but was focused on whole-cell and even whole tissue-mechanisms, and Greg wanted to know exactly what was happening down to the atom. He has always had a fascination with chemistry, and a passion for biology, thus he knew that biochemistry was indeed his cup of tea. He escaped from the Midwest and landed in Portland for graduate school in the fall of 2012. He chose Dr. Show-Ling Shyng as a mentor and is now happily studying atomic-level mechanisms of KATP channel trafficking and gating regulation. Upon graduation, he hopes to pursue a life in academic science by first landing a post-doc somewhere studying more atomic-level mechanisms, likely in another membrane protein, as he has decided that membrane proteins are the bees-knees.
Born and raised in Richland, Washington—home of the Hanford Nuclear Site—Jessica was surrounded by science at a young age. Despite a blossoming career in hazardous and radioactive waste clean up, she decided to pursue a degree in Biochemistry, Molecular Biology at Washington State University in Pullman, WA. While at WSU, Jessica worked as a research assistant in Dr. Tom Okita's laboratory, studying the mechanism of RNA localization in rice.
Upon completion of her degree, she took a position in Dr. Richard Smith's Biological Separations and Mass Spectrometry group at Pacific Northwest National Laboratory. Here, Jessica was part of a multi-institutional team lead by Dr. Joshua Adkins that utilizes systems biology approaches (proteomics, transcriptomics) to comprehensively characterize Salmonella typhimurium and identify potential therapeutic targets. Her research focused on the differential profile of outer membrane proteins of S. typhimurium through accurate mass and time tag (AMT tag) proteomics approaches to gain insight into virulence mechanisms and host-pathogen interactions. She was also part of a team that used mass-spectrometry approaches to annotate post-translational modifications of the S. typhimurium genome.
Jessica joined the Dr. Buddy Ullman's laboratory in the Department of Biochemistry and Molecular Biology in 2010. Under the mentorship of Dr. Nicola Carter, Jessica's Ph.D. thesis work is focused on delineating the adaptive response of a protozoan parasite and purine auxotroph, Leishmania donovani, to the naturally-encountered purine limitation stress. Through a combination of global studies (proteomics, RNA-seq, and metabolomics) as well as targeted biochemical, genetic, and molecular biology techniques, her work aims to understand how this parasite thrives in an ever-changing environment. She is interested in how Leishmania sense nutrient changes in the microenvironment, regulate mRNA abundance, translation, and ultimately protein abundance--all mechanisms that allow successful adaptation to environmental insults. The overarching goal, of course, is identification of targets to exploit via therapeutic intervention.
Jessica plans to continue her career in science not only through post-doctoral research, but also participation in global outreach and education programs regarding neglected tropical diseases. She is also interested in advising scientific policy as well as enhancing scientific communication.
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.
Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH,Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN. BMC Genomics. 2011 Aug 25;12:433. doi: 10.1186/1471-2164-12-433. PMID: 21867535
Nathan was born and raised in Portland and attended the University of Oregon in Eugene. While at UO he worked in cognitive neuroscience in the lab of Dr. Michael Anderson and graduated with a BS in Psychology in 2005. Nathan intended to pursue a doctorate in neuroscience after finishing his undergrad but felt that he needed a stronger foundation in cellular biology and biochemistry to proceed, so he decided to attend Portland State University to further his undergraduate education. While at PSU his interest shifted to Biochemistry.
In 2009 Nathan started the PMCB program at OHSU, joining the lab of Hans-Peter Bächinger in 2010. The Bächinger lab employs approaches broadly from structural and biophysical, to organismal level biology to examine the complex and unique cellular machinery required for folding of collagen, which is involved in the etiology of connective tissue disorders. Nathan's project involves biochemically characterizing post-translational modifications of basement membrane collagen, underlying all epithelial cells, and to examine their role in protein-protein interactions.
After graduating, Nathan plans to pursue a post-doctoral fellowship in biochemistry outside of the beautiful pacific northwest, and expand the scale of his biological understanding, through education in bioinformatics, systems biology, or proteomics.
Ben grew up in New Jersey and went on to attend Skidmore College in Upstate New York. He is an avid ultimate frisbee player and musician, but his greatest passion is science. In 2009 Ben joined the Department of Chemistry at the University of California, Santa Barbara as a PhD student. After two years he followed his advisor, Dr. John Perona, to Portland and transferred to the Department of Biochemistry & Molecular Biology at OHSU. Ben has been working towards characterizing an ancient metabolic strategy for sulfur assimilation that persists today in anaerobic microorganisms. His research, which combines elements of bioinformatics, genetics and biochemistry, has successfully identified three novel protein-coding genes with roles in homocysteine biosynthesis and sulfide utilization. Ben is nearing the completion of his PhD, and plans to apply his skills in the growing field of synthetic biology after he graduates.
While a native Oregonian, Danielle spent many of her formative years abroad, and graduated from the International School of Bangkok, in Bangkok, Thailand. She chose to return to the Pacific Northwest to attend Whitman College in Walla Walla, Washington for her undergraduate degree in Biochemistry, Biophysics and Molecular Biology. Danielle was involved in several research projects during her time at Whitman, from fish genetics to parasite biochemistry, but it was her work in Buddy Ullman's lab at OHSU on enzymes in the Leishmanial purine salvage pathway that drew her into the world of research. Danielle completed her undergraduate thesis on a novel nucleoside hydrolase in Leishmania, and after after graduating, moved to Portland to take a position as a research assistant in the lab of Gary Thomas at the Vollum Institute. In the Thomas lab her research focused on the role of the PACS proteins in driving apoptosis and cancer. Danielle began the OHSU MD-PhD program in 2009, and after completing the first two years of medical school, joined Ujwal Shinde's lab in the department of Biochemistry and Molecular Biology. Her PhD thesis work is primarily focused on the role of the unique propeptides in regulating the folding and activation of the proprotein convertase family of serine proteases. After completing her PhD thesis, she will complete her MD and plans to enter a residency in Internal Medicine.
Williamson DM, Elferich J, Ramakrishnan P, Thomas G, Shinde U. "The mechanism by which a propeptide-encoded pH sensor regulates spatiotemporal activation of furin."J Biol Chem. 2013 Jun 28;288(26):19154-65. doi: 10.1074/jbc.M112.442681. Epub 2013 May 7. PMC3696687
Elferich J, Williamson DM, Krishnamoorthy B, Shinde U. "Propeptides of eukaryotic proteases encode histidines to exploit organelle pH for regulation."FASEB J. 2013 Aug;27(8):2939-45. doi: 10.1096/fj.12-226886. Epub 2013 Apr 12. PMC3714588