Current Lab Members
Chris Amemiya, PhD
Professor of Molecular and Cell Biology
Chair, Quantitative Systems Biology Graduate Program
President, Pan-Am Society for Evolutionary Developmental Biology, PASEDB
Faculty Equity Advisor, UC Merced
Elected Fellow, AAAS
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.
Khan Hassan, MD, PhD
Research Specialist & Instructor
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 system inters 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.” 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.
I am a graduate student at the University of Washington now conducting my thesis work at UCM after our lab moved from Seattle in 2017. For the first part of my PhD thesis, I characterized the presence of chitin within the viscous hydrogel that fills the electrosensory organs, or Ampullae of Lorenzini, of cartilaginous fish, 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 is currently under review and can be found on BioRXiv here: https://www.biorxiv.org/content/10.1101/687301v1
Now, I am working to understand the evolution and function of chitin within these unique and fascinating structures. I am also exploring the molecular organization of chitin within the gel using various microscopic techniques.
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.
I am using the popular CRISPR-Cas9 gene editing method to understand the role of the polysaccharide, chitin in developing zebrafish. Chitin is present in fungi and the exoskeletons of arthropods but for many decades it was assumed to be absent in vertebrates. Excitingly, we discovered that zebrafish are indeed endogenously producing chitin in several anatomic locations, including their guts! This led us to ask, why is chitin in the gut of the fish? How did it evolve in zebrafish and do other fish exhibit this phenomenon as well? CRISPR-Cas9 is an excellent tool used to knock out gene activity and is known for its relatively simple use. I have created guide RNAs (gRNAs) targeted to chitin synthase genes and when the Cas9 endonuclease cleaves the gRNA target it will, in theory, deactivate chitin production. I will then screen for any changes in phenotype and development in order to investigate the role that chitin plays in zebrafish.
UCM Undergraduate Researcher
Under the mentorship of Dr. Hassan and Dr. Amemiya, I have worked on identifying the Kern Brook lamprey (Lampetra hubbsi) as a local species in the Central Valley. I am currently working with Dr. Hassan to develop mono-clonal or poly-clonal antibodies from Kern Brook Lamprey as an alternative to the sea lamprey (Petromyzon Marinus) which has a conserved usage of the variable lymphocyte receptor B (VLRB). The usage of the VLRB, or what we call, “lampribodies”, could be more cost effective as compared to their mammalian counterparts with greater use within biomedical/biotechnology sciences.
Past Lab Members
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 – Faculty 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