ISG Graduate Student Members | Institute for Systems Genomics

Katelyn Denegre
Department of Molecular and Cell Biology, UConn

Advisor: Michael O'Neill
Entered Graduate Program: 2017
Research Interests: genetics, epigenetics

I am involved in two projects as part of my research. The first project is a detailed exploration of our gene of interest, Xlr3 and its involvement in male reproduction. In short, this work uses wild type and Xlr3 transgenic mice to perform a gross histological assessment of the testis and meiotic spermatocyte surface spreads to take a detailed look at Xlr3’s involvement in Meiotic Sex Chromosome Inactivation (MSCI) during prophase I. The second project I am involved with, uses a novel breeding scheme to track transmission of the X chromosome across generations and explores the consequences of disrupting meiosis in one generation and the downstream effects on behavior and neurodevelopment in the next two generations. Xlr3b imprint is disrupted in the brains of female mice whose fathers have disrupted MSCI because of the Xlr3 transgene. It is the sperm from these fathers that possess an epimutated X chromosome which they are passing on to the daughters. Additionally, the grandsons of these male mice have behavioral differences when compared to wild type counterparts. Overall, this project explores transgenerational epigenetic inheritance and suggests that disrupted MSCI leads to the production of epimutated sperm which then affects neurodevelopment and behavior in subsequent generations. This work is important because it proposes a clearcut mechanism by which transgenerational epigenetic inheritance is occurring in this system. Most studies on transgenerational epigenetic inheritance are observational in nature and thus lack a mechanism to explain the phenomenon.

Katherine Fleck
Department of Molecular and Cell Biology, UConn

Advisor: Jelena Erceg
Entered Graduate Program: 2021
Research Interests: 3D Genome Organization, Genome Structure and Function, Gene Evolution, Gene Regulation

My research interests include the evolution of human genes along with their function and regulation in the context of 3D genomic organization. Additionally, how the interplay between these gene features may change with disease states in order to better understand genome structure and function.

Lucas Jones
Department of Marine Sciences, UConn

Advisor: Hannes Baumann
Entered Graduate Program: 2019
Research Interests: Population Genomics, Transcriptomics

Research currently involves leveraging novel genomic approaches to gain a mechanistic understanding of organismal response to climate change. Lucas is particularly interested in low-coverage, whole genome sequencing approaches and bioinformatic tools to process large data sets which will help us better understand how organisms will deal with environmental stressors.

Urvi Kaul
Department of Anthropology, UConn

Advisor: Deborah Bolnick
Entered Graduate Program: 2021
Research Interests: anthropological genomics; population genetics; epigenetics

My dissertation research is an interdisciplinary project, utilizing population genetics, epigenetics, and qualitative methods to assess the impact of politically-induced mass migration on communities. In particular, I look at how sociopolitical events trigger displacement from ancestral homelands, resulting in migration and the formation of new diasporic communities elsewhere, and consider both the biological and social effects of these movements. Currently, I work with a particular Kashmiri ethno-religious group (Kashmiri Pandits), within the United States. My research utilizes population genetics to consider how historical events producing changes in community composition may be reflected in the genomic record; epigenetic methods are used to assess the potential biological impact of displacement; qualitative methods are utilized to consider how community members narrate and make sense of their displacement and its impact on their identity within the United States.

Mengjia Lin
Department of Molecular and Cell Biology, UConn

Advisor: Stacey Hanlon
Entered Graduate Program: 2021
Research Interests: Genetics

B chromosomes are extra, non-essential chromosomes that have been found in hundreds of different species including plants, insects, and mammals. In Drosophila, B chromosomes are heterochromatic and are transmitted in a biased manner during female meiosis. However, the mechanism behind the biased transmission is currently unknown. Therefore, my goal is to understand the dynamics of the B chromosomes during the meiotic divisions in females.

Rachael Massey
Biomedical Science, UConn Health

Advisor: Stefan Pinter
Entered Graduate Program: 2022
Research Interests: Cytogenetics, Chromosome Biology, Molecular Genetics, Clinical Genetics, Human Pathology

Rachael Massey is a clinically certified cytogenetic technologist (ASCP) and graduate student in Dr. Stefan Pinter's lab. From a young age, Rachael's family history fostered her interest in studying human disease pathology. She expanded her love for chromosomes while working as a cytogenetic technologist at a clinical diagnostic laboratory. She later joined the ISG's Health Care Genetics PSM program, working as a program representative and graduate assistant for Dr. Judy Brown. She completed her M.S. capstone project in Dr. Alexander Jackson's laboratory, identifying diverse neuronal cell types in the mouse hypothalamus. In the year before starting her Ph.D., Rachael worked in the lab of Dr. Rachel O'Neill, assisting with karyotyping and assembling human and non-model genomes. Rachael now studies genes that escape X chromosome inactivation and the implications these genes have on sex differences and sex chromosome disorders in the Pinter lab.

Kaylah Samuelson
Department of Molecular and Cell Biology, UConn

Advisor: Stacey Hanlon
Entered Graduate Program: 2020
Research Interests: Genetics, Meiotic Drive, Chromosome Segregation

I study the mechanism behind drive suppression of the B chromosomes in Drosophila melanogaster, particularly a protein named Matrimony (Mtrm) that is crucial to ensure the proper segregation of chromosomes. My work looks at uncovering how Mtrm functions to prevent the biased segregation of the B chromosomes using classical Drosophila genetics and microscopy.

Saren Springer
Department of Physiology and Neurobiology, UConn

Advisor: Rahul Kanadia
Entered Graduate Program: 2020
Research Interests: Epigenetics, Transcriptomics, and Developmental Biology

My research aims to understand how layers of gene expression regulation, such as epigenetic modifications, RNA processing mechanisms, and transcription, are coordinated to regulate RNA abundance across development. My work leverages an knockout model for the minor spliceosome to understand how impairing this fundamental step in gene expression alters parallel layers of gene expression regulation. Through analysis of epigenetic and transcriptomic data collected from embryonic limb buds across time, I've discovered that loss of the U11 small nuclear RNA (a component of the minor spliceosome) causes dramatic transcriptomic divergence linked to the mis-splicing of minor intron-containing genes embedded within epigenetic, transcriptional, and RNA processing regulation steps. Together, the disruption of these core regulatory processes stalls transcriptomic progression and contributes to defects in limb progenitor cell differentiation. My work bridges omics and developmental studies to understand how the minor spliceosome regulates gene expression during limb development, with broader implications towards understanding congenital diseases associated with defects in splicing.

Cynthia Webster
Department of Ecology and Evolutionary Biology, UConn

Advisor: Jill Wegrzyn
Entered Graduate Program: 2022
Research Interests: Conservation Genomics, Bioinformatics, Transcriptomics

As a graduate student in the Plant Computational Genomics lab, I frequently utilize machine learning and computational statistics to optimize the identification of protein-coding genes. Specifically, I lead the development of EASEL (Efficient, Accurate, Scalable Eukaryotic modeLs), a tool that employs generalized hidden Markov models and random forest algorithms to improve gene prediction accuracy in eukaryotic genomes. With EASEL, I have successfully annotated genomes of non-model organisms, including Magicicada septendecula and Inga vera. In addition to software development, I mentor undergraduates in the Biodiversity and Conservation program which focuses on generating long read data for de novo genome assembly of species listed on the IUCN Red List, such as Juglans cinerea.