RI NSF EPSCoR graduate research fellows

Education & Outreach Graduate students

“As an EPSCoR fellow, I have had the opportunity to participate in enriching outreach activities, and have made use of the facilities at the Genomic and Sequencing Center and the Marine Life Science Facility at URI, without which my research would not be possible. I have also mentored alongside bright and promising undergraduates, who have helped me become a better scientist and teacher.”

Kerry Whi)aker Graduate fellow University of Rhode Island

Rebecca Helm, Dana Lord, Gordon Ober, Kerry Whitaker

Dana Lord Graduate student, Brown University Education: BS in Biochemistry, University of Rochester

“This research will benefit the scientific resource base of the Ocean State.”

Graduate work: Ph.D. candidate in Molecular Pharmacology & Physiology, Brown University

Focus/thesis: Using Structure and Genetics to Understand how Biofilms Form and their Role in Parasitic Life Cycles

Major professor: Dr. Rebecca Page Expected completion: Spring 2014 Career path: Continue using protein structure as a tool to investigate function in either an academic or industrial setting

In her own words ...

My thesis focuses on the biochemical, structural, and molecular understanding of both aerobic and anaerobic microorganisms and their role in biofilms. This work integrates the NSF-EPSCoR research foci of marine life sciences, bioinformatics and genomics and proteomics. I have two aims that together will advance our understanding of biofilm stability and parasitic lifecycles.

My primary focus is to elucidate how bacterial biofilms assemble and are regulated. Biofilms are complex, multicellular bacterial communities that are highly tolerant to antibiotics and important for microbial survival. One well-recognized, but poorly understood mechanism used by bacteria to survive environmental stress is through the formation of persister cells. Persister cells are a subpopulation of metabolic quiescent cells that exhibit multidrug tolerance. I focus on the gene mqsR, the most highly upregulated gene in persister cells vs. non-persister cells. I am investigating the role MqsR plays in Escherichia coli physiology in an effort to eradicate harmful biofilm infections In collaboration with Dr. Avelina Espinosa at Rodger William University, I also have investigated mechanisms of survival of the virulent human parasite, Entamoeba histolytica. Recent evidence suggests that the E. histolytica lifecycle is intimately coupled to intestinal biofilms, and one protein essential for their survival is the bifunctional alcohol/aldehyde dehydrogenase, EhADH2. In most organisms, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) are two separate enzymes. However, in E. histolytica, they constitute a single enzyme and very little is understood about how each domain (ADH/ALDH) affects the activity of the other. Moreover, many questions remain about the molecular and/or genetic adaptations of EhADH2 to host luminal environments.

This research will benefit the scientific resource base of the Ocean State by enhancing and strengthening the collaboration between two scientific research groups (Page and Espinosa) and two Rhode Island institutions (Brown and RWU). The research outlined here focuses on the proteins that play a central role in biofilm formation, and also the AdhE family of enzymes in pathogenic protozoa.

Our efforts to identify novel protein targets to treat biofilms and the infections caused by these organisms have an enormous potential for economic development in Rhode Island.

Gordon Ober Graduate student, URI

“EPSCoR funding has allowed me to build my experimental design from the ground up.”

Education: BS Ecology and Evolutionary Biology, University of Connecticut, May 2009

Graduate work: Ph.D. candidate in Ecology and Ecosystems Science, University of Rhode Island

Dissertation topic: The response of marine communities to ocean acidification and eutrophication

Major professor: Dr. Carol Thornber Expected completion: Spring 2016 Career path: Ideally, I would like to remain in academia, but other realms are intriguing to me.

In his own words ...

I entered into this Ph.D. program with the intent to study marine community ecology and climate change.

After a few months of working closely with my advisor, I settled on a dissertation topic: How ocean acidification and other factors of global change impact the structure, function, and trophic interactions of local marine communities.

Climate change continues to threaten our globe and while we are beginning to describe its effect, there remain plenty of unknowns. While we may be able to describe how one organism responds to stress, it is much harder to quantify how an entire community will respond.

Broadly stated, my research aims to answer this question and to provide insight as to how communities may shift and relationships may change. The interconnectedness of marine organisms infers that changes at one trophic level will have a ripple effect on the rest of the ecosystem. If we can quantify that effect, we can project how other organisms will be impacted.

In a lab setting I am manipulating both carbon dioxide and nutrient content of seawater and exposing primary producers (macroalgae), herbivores (snails), and predators (crabs). In this mesocosm-based experiment, I aim to describe how these different trophic levels respond both on their own, and in conjunction with one another, to changes in environment.

EPSCoR funding has allowed me to build my experimental design from the ground up.

The established system is self-sufficient and has the ability to run long-term studies. The design is effective and simple, allowing future experiments to transition smoothly.

Kerry Whittaker

“This work is important for our understanding of climate change, and our ability to predict its effect.”

Graduate student, URI Education: BA in English & Environmental Science, Colby College

Graduate work: Ph.D. candidate in Oceanography, Graduate School of Oceanography, University of Rhode Island

Focus/thesis: Exploring the global distribution of genetic diversity in the marine diatom Thalassiosira rotula to better understand the intersection between diatom evolution and the marine environment

Major professor: Dr. Tatiana Rynearson Expected completion: Fall 2013 Career path: Use molecular techniques to advance our understanding of ecology and evolution in the ocean. I’m also interested in gaining a perspective on the interaction between marine science and policy.

Whittaker colle cts Antarctic sediment on a recent oceanographic re hopes of finding search cruise in diatom resting spores. In May, she spent a mon on a research th vess Western Antar el off of the ctic Peninsula, exploring phyt oplankton dyna mic in the region, an d their role in s the feeding ecolog y of krill. Web site: www.krillcruis e.wordpress.com

In her own words ...

My work investigates the intersection between diversity, evolution, and the ocean environment.

The organisms that I study are diatoms; powerhouses of production in our earth system, absorbing CO2 from the environment, fixing it into carbon that fuels marine life, and releasing oxygen. I use molecular tools to explore how diversity nested within diatom species is distributed and subdivided throughout the globe, and how this diversity relates to differences in the functional contribution of diatom populations to unique ecosystems. By doing this, I can begin to piece together the environmental and physical factors influencing the generation of new species, and the subdivision of those species into functionally distinct populations.

This work is important for our understanding of climate change, and our ability to predict its effects. Biodiversity has a lot to do with the ability of a species, or an ecological community, to adapt to changes in the environment. Greater diversity often relates to a greater resiliency and tolerance to environmental change. Unfortunately, we know very little about the extent of diversity in diatoms, or its relationship to their functional role in the environment.

By exploring the extent and distribution of diversity in a diatom species over space, I hope to better understand the resiliency and adaptability of diatoms to a changing climate. Also, I'm very interested in the ways in which climate change will affect diatom evolution, which is ongoing and driven by complex variables of environment, hydrography, behavior, and resource competition.

As an EPSCor fellow, I have had the opportunity to participate in enriching outreach activities, and have made use of the facilities at the Genomic and Sequencing Center and the Marine Life Science Facility at URI, without which my research would not be possible. I have also mentored and worked alongside bright and promising undergraduate students, who have helped me to become a better scientist and teacher.

Rebecca Helm Graduate student, Brown University Education: B.S. in Marine Science (Biology Track), Eckerd College

Graduate work: Ph.D. candidate in Ecology &

“Thanks to NSF EPSCoR, Rhode Island now has cutting edge genomics and computations resources, and I’ve been able to tackle questions I didn’t think possible when I started.”

Evolutionary Biology, Brown University

Focus/thesis: Using Structure and Genetics to Understand how Biofilms Form and their Role in Parasitic Life Cycles

Major professor: Dr. Casey Dunn Expected completion: 2015 Career path: Continue working as a researcher and educator, preferably in an academic setting

In her own words ...

I focus on the role development plays in the evolution of life cycles. I'm particularly interested in a group of animals called cnidarians, which contains many economically and ecologically important species, including corals, sea anemones and jellyfish. (Blog — http://jellybiologist.com/) When I first entered graduate school, I planned to study this group using methods that have been around for decades. Thanks to the NSF EPSCoR, Rhode Island now has cutting edge genomics and computations resources, and I've been able to tackle questions I didn't think possible when I started. I've expanded my thesis into areas with important implications for understanding not just evolution, but ecology as well. With these resources I have developed a thesis that can be divided into two major themes on life cycle evolution and ecology.

First, I used the EPSCoR-funded sequencing and computational facilities at Brown University to examine gene expression through development in a locally occurring sea anemone. I quantified gene expression through multiple developmental stages, discovering the timing for many important developmental milestones. This research lays the foundation for asking comparative questions about life cycle evolution and the response of this species to future climate changes. These results were published earlier this spring in the journal BMC Genomics.

Next, I'm conducting a similar study in a locally occurring scyphozoan jellyfish species. This species, as with many jellies, first starts life looking much like a sea anemone, and only when conditions are right does it produce medusae (jellyfish). Molecular data from this species will be used in a comparative study with data collected from the sea anemone to uncover molecular features associated with complex life cycles. They will also highlight genetic pathways involved in environmental sensing, as jellies are only produced naturally in response to temperature changes.

Funding from EPSCoR has allowed me to conduction genomic studies of non-model species.

Providing detailed information on how these animals change over the course development, and what these changes can tell us about their ecology and evolution.