Podrabsky Laboratory

Current Laboratory Members

Principle Investigator

Dr. Jason E. Podrabsky

  • Graduate Affairs Committee Chair
  • Professor of Biology (2004-current)
  • B.S. Biology, Oregon State University, PhD Biology, University of Colorado, Postdoctoral fellowship, Stanford University
  • Publications and CV available on PDXScholar

Research Areas of Interest

I am interested in how embryonic development can be altered by environmental and ecological factors. I enjoy using integrative approaches to understand the molecular mechanisms that drive organismal responses to the environment. Most of my work focuses on regulation of metabolic dormancy and stress tolerance associated with diapause in embryos of annual killifishes.

Fun Fact!

I enjoy the art of bonsai.

Contact

Email: podrabsj@pdx.edu

Instagram: @jpodpdx

 

Dr. Podrabksy fishing

Postdoctoral Researchers

Dr. Amie L. T. Romney

  • Interim Director of the Center for Life in Extreme Environments (CLEE)
  • B.S. Zoology, Weber State University, M.S. Integrative Physiology, University of Nevada, Ph.D. Biology, Portland State University
  • Publications and CV available on PDXScholar and Google Scholar

Research Areas of Interest

My current research is examining the role of maternal provisioning in alternative life history strategies in A. limnaeus. I hypothesize that maternal programming of developmental trajectory is likely accomplished by the differential packaging of escape- or diapause-specific gene products into the oocyte prior to fertilization.

Keywords: Developmental and Cellular physiology, embryology, regulation of gene expression, phenotypic plasticity

Fun Fact!

I have held a human heart while it was still beating in someone's chest. BPM was about 146.

Contact

Email: arom2@pdx.edu

 

Dr. Gazal Kalyan

  • Research Associate, Oregon Data Science Collaborative (ODSC)
  • B.Tech. Biotechnology, Lovely Professional University, M. Tech. Bioinformatics, Indian Institute of Information Technology, Ph.D. Bioinformatics, Indian Institute of Technology
  • Publications available on Google Scholar

Research Areas of Interest

My research is multidisciplinary, intersecting computer science and biology. I am passionate about developing scalable, reproducible computational biology tools and algorithms using in-silico techniques.  My current research focuses on streamlining the proteomics and transcriptomics analysis of the annual killifish, Austrofundulus limnaeus. This is an incredible species that could withstand anoxia and has signature gene patterns that contribute to understanding how they survive in extreme conditions.

Keywords: Multi-omics, computational biology, gene co-expression, algorithms, organism health

Fun Fact!

I like playing board-games!

Contact

gazal@pdx.edu

Gazal taking selfie

Graduate Students

Chelsea Hughes, Ph.D. Candidate

  • B.A. Biology, Wake Forest University, M.S. Biology, University of Wisconsin Oshkosh
  • Publications available on PDXScholar and Google Scholar

Research Areas of Interest

My dissertation work focuses on identifying mechanisms of epigenetic and post-translational controls during anoxia tolerance and ischemic recovery, and how these changes alter the proteomic landscape of the cell. I have A) developed a Python proteomic analysis pipeline to quantify changes in histone PTMs, B) identified multiple histone post-translational modifications in normoxic and anoxic embryos, C) identified and quantified histone post-translational modifications and histone isoform abundances in normoxic, anoxia-recovered, and anoxic WS40NE cells, D) used label free proteomics to identify differential protein expression and molecular pathways associated with anoxia and recovery, and  E) used 3mM sodium lactate and lactic acid preconditioning to determine how preconditioning can impact the transcriptome and cellular growth rates in normoxic, anoxia-recovered, and anoxic WS40NE cells. 

Keywords: Epigenetics, Proteomics, Post-translational Modifications, Lactate Preconditioning

Fun Fact!

I have a scar on my chin from pretending to be a polar bear as a child.

Contact

Email: chugh2@pdx.edu
 

 

Chelsea using anoxic chamber

Riley Roth-Carter, Ph.D. Candidate

  • B.S. Biology, University of Portland
  • Publications available on PDXScholar and Google Scholar

Research Areas of Interest

Some of my current projects are using Quantitative Image Based Cytometry (QIBC) to assess cell cycle dynamics during anoxic exposure and its relation to DNA damage accumulation, using LA-qPCR to quantify levels of DNA Damage and assess repair capacity after anoxic exposure and reoxygenation, using DNA Strand Assay to assess replisome stability and protection of nascent DNA during anoxic exposure, and using RAD-Seq to quantify mutational burden after anoxic exposure. 

Keywords: DNA repair and replication, immunocytochemistry, cell cycle, stress-response

Fun Fact!

I love to be outdoors whenever possible. Hiking, camping, snowshoeing, whatever gets me out into nature. 

Contact

Email: rothcar2@pdx.edu
 

 

Riley using anoxic chamber

Patrick Clouser, Ph.D. Candidate

  • B.S. Clinical Laboratory Science, Oregon Health and Science University 
  • Publications available on PDXScholar

Research Areas of Interest

My work is focused on the response of embryos to anoxic stress and recovery using transcriptomics. This has lead to the development of a bioinformatic pipeline to prepare differential analysis, gene ontologies, transcription factor analysis, and cluster analysis using non model organisms. In addition to my current project I enjoy anything -omics,  and have been enhancing the labs genome via ONT long read sequencing. 
 

Keywords: -omics, stress tolerance, bioinformatics, molecular biology, cancer biology.

Fun Fact!

I enjoy scuba diving.

Contact

pat6@pdx.edu
 

Pat posing

Rosalia (Rosy) Tanori, M.S. Candidate

  • B.S. Biology, Oregon State University
  • Publications available on PDXScholar and Google Scholar

Research Areas of Interest

My current project aims to use a CUT&RUN assay to identify the genomic locations where vitamin D receptor (VDR) proteins bind to DNA and alter gene expression, under conditions that induce diapause and those that do not. I use custom anti-VDR A. limnaeus antibodies and validate for CUT&RUN through western blotting, and in situ hybridization, confirming its ability to specifically interact with the VDR protein in vivo.

Keywords: Gene expression, development, molecular physiology

Fun Fact!

I have a pet hamster named Nugget.

Contact

Email: rosy@pdx.edu

Rosy holding a micropipette

 

Undergraduates

Jaden Villacrusis, Biology Major

  • Class of 2026

Research Areas of Interest

My current project is to stage and sample embryos incubated at twenty degrees Celsius (which induces diapause) and examine Vitamin D concentrations. We want to understand how these concentrations differ across diapause and escape embryos, and the role they play in developmental trajectory. 


Keywords: gene expression, molecular biology, phenotypic plasticity

Fun Fact!

My research journey started with studying birds, specifically the Mariana Fruit Dove. 
 

 

Jaden wading in water

Angel Santos, Environmental Science Major

  • Class of 2026

Research Areas of Interest

My current project involves developmental staging and sampling of killifish embryos incubated at thirty degrees (induces the escaped trajectory) to examine Vitamin D concentrations. The goal is to determine if concentration levels differ across the different morphological stages of the embryos, and the role they play in developmental trajectory. 
 

Keywords: organismal physiology, conservation biology, phenotypic plasticity

Fun Fact!

My two older sisters inspired me to go down the environmental field with initial interest in Ornithology (specific to the Northern Mariana Islands).

Angel posing with a shovel and shellfish

Lori Tran, Biochemistry Major

  • Class of 2025

Research Areas of Interest

My current project examines if environmental stress can lead to histone post-translational modification (hPTM) in killifish embryo cells and if this response is unique to killifish. Our goal is to see if artificial selection from repeated extracellular lactate exposure can induce hPTMs in the cells and eventually lead to an increase in anoxia tolerance. 

Keywords: cell biology, epigenetics, post-translational modifications, gene expression

Fun Fact!

I love drinking tea, but classic green tea is the best.

Lori abroad!

Jaina Canlas, Science Major

  • Class of 2025

Research Areas of Interest

My current project is on the killifish embryo cells. We are studying how mutations in the genes will affect the expression and concentration of DNA replicated after PCR. We want to understand how the killifish cells can produce DNA where we would normally see other organisms halting expression or undergoing apoptosis.

Keywords: animal biology, gene expression, cell biology, epigenetics

Fun Fact!

When I'm not studying like a madwoman, I enjoy playing badminton, video games on my Nintendo Switch, or watching a period piece or K-Drama.

Jaina posing

Ace Morris, Environmental Science Major

  • Class of 2026

Research Areas of Interest

My current project consists of the molecular control of dormancy and stress tolerance in annual killifish.

Keywords: transcription factors, gene expression

Fun Fact!

I used to compete in western-style horseback riding competitions. My favorite event was figure 8.
 

Ace taking a selfie