People

CURRENT LAB MEMBERS

I have always been interested in how the information in the genome gives rise to evolutionary adaptation and innovations in the long term, and disease in the short term. I got my PhD with John Gold, a fly geneticist (turned fish systematist and population geneticist) with a direct evolutionary lineage to Thomas Hunt Morgan and H. J. Müller. I worked on North American cyprinid fishes and their relationships. From there I did a postdoc with Gary Litman, a comparative immunologist, where I learned molecular genetics. I did a second postdoc at the Lawrence Livermore National Lab working on the Human Genome Project and helped develop large-insert cloning methods with Pieter de Jong. My first faculty job was in the Center for Human Genetics (Department of Pediatrics) at the Boston University School of Medicine; it was in Boston where I was reintroduced to cyprinid fishes (zebrafish) working in collaboration with Len Zon at Harvard Medical School. I was a Member of the Benaroya Research Institute in Seattle from 2001-2017 and ran an NIH-NSF genome center for a while and conducted research in comparative genomics and developmental genomics. I also did a stint as an NSF Program Director (Integrative Organismal Systems) in 2007-2008. I moved the lab in the fall of 2017 to the University of California, Merced. We have finally set up shop. Our work is a continuation of our previous studies, focusing on four areas of research: (1) programmed genome rearrangement in development and immunity of a basal vertebrate; (2) development of the lamprey system for generating monoclonal antibodies, “lampribodies”; (3) characterization of vertebrate chitin in evolution and development; and (4) use of comparative genomics for studying novelties and innovations during terrestrialization.

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Lamprey and hagfish (agnathans) have a unique adaptive immune system. In response to antigens, these agnathans produce an antibody molecule using leucine rich repeat cassettes available in the genome. The antibody properties of these single chain molecules are comparable to immunoglobulin based adaptive immune systems in terms of binding affinity and diversity. The general nomenclature of this new class of molecules is variable lymphocyte receptors (VLR). Under Dr. Amemiya’s mentorship, I have developed a screening system to specifically target, lymphocyte receptor B (VLRB) from immunized lampreys using the phage display technique. We call them “lampribodies.” You can find a publication about this topic here. I am dedicated to seeing the success of this technology and its widespread use at both UC Merced and across the wider biomedical/biotechnological community.

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I recently finished my PhD thesis at the University of Washington (UW) and am a researcher in private industry in Redwood City, CA. My research was conducted both at UW and the University of California, Merced (UCM) after our lab moved to California from Washington in 2017. For the first part of my PhD thesis, I characterized the presence of chitin within the hydrogel that fills the electrosensory organs, or Ampullae of Lorenzini, of cartilaginous fishes, such as sharks, skates, and rays. I identified chitin synthase genes within the little skate (Leucoraja erinacea) and showed that these genes are expressed by cells that appear to be synthesizing and excreting chitin into the lumen of the organs. A manuscript detailing this work has been published in Current Biology and can be found at this link

I also characterized the development of the Ampullae of Lorenzini and examined the onset of chitin synthesis in little skate embryos. Further, I explored the molecular organization of the components within Ampullae of Lorenzini gel using various techniques including atomic force microscopy (AFM), scanning electron microscopy (SEM), and small angle x-ray scattering (SAXS). This work was done in collaboration with researchers in the departments of Physics and Materials Science at UCM and has been published in iScience and can be found at this link

We are currently working on a few more manuscripts from my time in the Amemiya lab.

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My research involves using genome and transcriptome data together with bioinformatic tools to study the evolution and molecular bases of vertebrate innovations. I have previously studied the evolution of neuronal and neuroendocrine systems for my doctoral thesis. By combining genomic analyses with molecular phylogenetics, my research has shown that the ancient whole-genome duplications in vertebrates likely contributed greatly to the evolution of processes such as vision, neural communication, body growth, the control of water balance, and social behaviours. Currently I am studying the evolution of chitin synthases in vertebrates and the molecular mechanisms of chitin synthesis and organization in the ampullae of Lorenzini. I am also interested in the evolution of proteins that modify the extracellular matrix, such as sulfotransferases. Papers are currently being submitted from my time in the Amemiya lab.

I am a second year PhD student in the QSB graduate program. I am currently working on a synthetic biology project to generate monoclonal antibodies using the lamprey as a vehicle. The goal is to generate these monoclonal antibodies (lampribodies) in a system whereby the lampribodies are displayed on the surface of E. coli in order to facilitate library construction and screening. In addition, I wish to use this platform to help understand the EvoDevo of vertebrate chitin.

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PAST LAB MEMBERS

Leesa Hagerman, BS – PhD Student, UC Merced

Kyle Rekedal, BS – PhD Student, Univ. Pennsylvania

Haley Harkness, BS – Bioengineering student, San Diego State Univ, CA

Lauren Vandepas, PhD – NOAA Postdoctoral Fellow, Seattle, WA

Joyce Tang, MS – University of Washington, Seattle, WA

Mike Rego, BS – Benaroya Research Institute, Seattle, WA

Murat Kaya, PhD – Faculty, Aksaray University, Aksaray, Turkey

Jeramiah Smith, PhD – Associate Professor at University of Kentucky, Lexington, KY

Joel Sohn, PhD – Research Fellow, Harvard University, Cambridge, MA

Nil Ratan Saha, PhD – Data Scientist at Accenture Applied Intelligence, Seattle, WA

Mark Robinson, PhD – Research Division, Amazon.com, Seattle, WA

Tatsuya Ota, PhD – Faculty, Graduate University of Advanced Studies, Hayama, Japan

Asaf Halevi, MS, MBA – Senior Director, Eli Lilly and Co., Indianapolis, IN

Tsutomu Miyake, PhD – Visiting Professor, Jikei University, Tokyo, Japan

Allan Force, PhD – out of science

Thuy-Ai Nguyen, PhD – Scientist at NIH (NIEHS), Research Triangle, North Carolina

Hirohide Kawasaki, MD, PhD – Kansai Medical University, Osaka, Japan

Thomas Powers, PhD – out of science

David Garrity, PhD – deceased

Joshua Danke, BS – Bellingham Police Department, Seattle

Andrew Stuart, BS – Lab Manager, Fred Hutchinson Cancer Center, Seattle