Clark student studying in lab Undergraduate Research

Undergraduate Research

Undergraduates considering careers in the biological sciences obtain practical experience by taking advantage of the many opportunities offered in the biology department to engage in faculty-sponsored research projects. Please visit the Undergraduate Research Projects page to see the sorts of research projects our students have undertaken.

Undergraduate Research Profiles

Amanda Fragata

Threespine stickleback fish are an excellent model organism to study since populations have formed an adaptive radiation, as their ancestral oceanic counterparts repeatedly colonized freshwater lakes. Dependent on the conditions of the environment they inhabit, stickleback tend to evolve in similar ways. In some populations female foraging groups will opportunistically feed on other stickleback eggs, forcing gravid females to retain their clutch leading to a state of chronic stress. The presence of cannibalism is an ecological stressor which impacts the hormone levels of reproductive females, thus providing the opportunity to investigate the potential impact that population and enforced egg retention have on circulating levels of stress hormones, development and behavior of fry and levels and localization of stress related genes in the brain.

During the summer of 2015, with the support of the Beavers Research Fellowship, I began collecting data on reproductive female stickleback to prepare to study how the vertebrate stress response system evolves under changing environments. My efforts are currently focused on exploring which specific genes in the brain play a role in regulating the stress response system in reproductive females with and without the presence of an ecologically relevant stressor. I anticipate that in the coming year my focus may veer towards studying the impacts that stress and other ecologically relevant factors have on fry growth and behavior. My research at Clark thus far has strengthened my aptitude for deep scientific inquiry and has continuously provided me with many wonderful opportunities to explore my interests.

Sam Kovaka: Comparative Fungal Genomics

Genome sequencing is now widely used across all fields of biology, and the time and cost of sequencing a genome is decreasing rapidly. It is particularly useful for fungi, a diverse kingdom that includes important model organisms which can be manipulated using classical genetic methods, as well as many species that cannot be grown in the lab. There are currently over 500 sequenced fungal genomes, some of which were generated in part by researchers at Clark. The development of a fungus from a single cell to a complex fruiting body (mushroom) is a poorly understood process, especially compared to our understanding of plant and animal development, the other two major multicellular kingdoms.

My research has primarily focused on using comparative genomic methods to identify genes involved in fruiting body development. Using bioinformatics methods, I have identified genes that may play a role in development in different fungal genomes, and I have assessed if they are regulated in similar ways. My research at Clark has given me the opportunity to attend scientific conferences, led to great summer research programs, and made me very excited for my future as a biologist.

Nicholas Pagan: A Novel, Integrative Method for Assessing Lake Macroinvertebrate Communities

Building on the basic principles of lake bioassessment, my project employs a novel sampling technique to sample macroinvertebrate communities in eastern Massachusetts lakes. The Chironomid Pupal Exuvial Technique (CPET) differs from conventional benthic macroinvertebrate sampling because it focuses on the discarded skins of chironomid (flies and midges) pupae as opposed to the living larvae in the substrate of a lake’s littoral zone. This allows for rapid assessment of a multitude of habitats because exuviae found in collection points such as weed beds and leeward lake shores represent communities from many different lake habitats. This allows for a more complete and efficient sampling than the conventional benthic technique, which samples small, spatially restricted bottom habitats only.

During the summer of 2014, supported by a Carlson Summer research fellowship, I partnered with Robert Nuzzo of the Massachusetts Department of Environmental Protection to train in CPET sampling and identification. Thanks to a Geller research fellowship, the following summer I used CPET to conduct biomonitoring on 25 lakes in Worcester County that are affected by varied levels of human disturbance. My project focuses on understanding how human disturbance in Massachusetts lakes affects chironomid community structure, and I hope to establish a system of reference lakes for the DEP’s coming probabilistic lake survey. I am currently focusing my efforts on sorting and identifying exuviae in samples. This research partnership with Bob Nuzzo from the DEP potentially opens the door for future research collaborations between Clark Environmental Science students and State agencies such as the DEP.


Below: Listen to Clark biology undergraduates talk about their research.

Cell and Molecular Biology

Lincoln Muhoro, Class of 2007

Lincoln Muhoro talks about his research in Dr. Lazo’s lab on epidermolysis bullosa, a skin disorder that causes blistering on the skin. Listen Now

Ecology & Evolution

Katie O'Brien, Class of 2007

Katie O'Brien talks about her research on stickleback in Professors Susan Foster's and John Baker's lab. She is trying to understand all the interactions that go into what a female chooses when she makes her eggs. Watch Now


Peter Stein, Class of 2007

Peter Stein, a computer science major, talks about being recruited by Professor David Hibbett to do research on bioinformatics. Watch Now