Synteny and Genetic Conservation of the Nicotinamide Amidase Gene in the Drosophilawillistoni and Drosophila bipectinata Species as Compared to Drosophila melanogaster
Presenter: Colbie Lacina Group Members: Maria Eduarda Cunha Faculty Sponsor: Jessica Crowley School: Quinsigamond Community College Research Area: Genetics Location: Poster Session 1, 10:30 AM - 11:15 AM: Campus Center Auditorium [A10]
This project was done as part of the Genomics Education Partnership’s Pathways Project to catalog trends in evolution in the oxidative stress pathway in varying species of Drosophila fruit flies compared to Drosophila melanogaster. Signaling pathways are crucial for an organism's adaptation to the environment and for regulating oxidative stress. The NAD+ salvage pathway is responsible for defending against oxidative stress. The nicotinamide amidase gene produces an enzyme responsible for sustaining intracellular NAD+ levels required for metabolic homeostasis and cellular stress responses. We examined this gene and its genomic neighborhood in Drosophilawillistoni and Drosophila bipectinata in reference to the location within the well-annotated Drosophila melanogaster to determine the extent to which the gene is conserved within both species. This research was conducted by annotating genetic features within the DNA sequence, such as transcription start sites, intron-exon boundaries, protein coding regions, 5’ and 3’ untranslated regions, using UCSC Genome Browser, NCBI BLAST, and FlyBase. By annotating genes across multiple species, we can measure the rate of molecular evolution and discern the variation and constraints in the target gene. The research contributes to the understanding of how pathway genes are structured and how related species change over time.
Evolutionary Divergence of the JNK Regulator puckered: A Comparative Genomic Analysis of Drosophila willistoni and Drosophila pseudoobscura to Drosophila melanogaster
Presenter: Jadyn Kiley Group Members: Anna Galoyan Faculty Sponsor: Jessica Crowley School: Quinsigamond Community College Research Area: Genetics Location: Poster Session 1, 10:30 AM - 11:15 AM: Campus Center Auditorium [A12]
Signaling pathways are fundamental biological systems that regulate how cells respond to environmental stressors, such as oxidative stress, and how these cells influence processes involved in aging. The Jun N-terminal Kinase (JNK) signaling pathway mediates stress responses that regulate tissue morphogenesis, wound healing, regeneration, and apoptosis. The Puckered gene encodes a dual-specificity phosphatase that functions as a critical negative regulator of the JNK signaling pathway. During oxidative stress, increased JNK activity induces puckered expression, and the resulting phosphatase attenuates JNK signaling to maintain cellular homeostasis under stress. This project aims to annotate the puckered (puc) gene in the fruit fly species Drosophila willistoni and Drosophila pseudoobscura by comparing them to the well-annotated D. melanogaster reference genome. Using evidence collected from Genomics Education Partnership (GEP) tools (including the UCSC Genome Browser, NCBI BLAST) our analysis will determine how the puc gene has been conserved or altered over evolutionary time. By comparing D. willistoni and D. pseudoobscura with D. melanogaster we will identify shifts in genomic neighborhood and gene architecture. This research contributes to a broader understanding of how signaling pathway genes evolve and how species-specific adaptations to oxidative stress are reflected in JNK pathway regulation. This project is part of the Genomics Education Partnership (GEP) Pathways Project.
Evolutionary Conservation of the Mrp4 Transporter Gene in Drosophila
Presenter: Meghana Kesavan Group Members: Baaba Swanzy Essuman Faculty Sponsor: Jessica Crowley School: Quinsigamond Community College Research Area: Genetics Location: Poster Session 1, 10:30 AM - 11:15 AM: Campus Center Auditorium [A16]
Multidrug Resistance Protein 4 (Mrp4) is an ATP‑Binding Cassette transporter gene found in the Drosophila fly species which works to move substrates across cell membranes. Expression of the Mrp4 gene has been linked to increased lifespans in flies due to its help in removing toxic foreign materials from the cell, protecting the organism from harmful chemicals, drugs, and oxidative stress. The conservation of this gene can differ among fly species, and by studying this variation, we can understand how the gene has evolved over time. Through the Genomics Education Partnership (GEP) Project, we compare this gene in the species D. willistoni and D. mojavensis to assess how it has evolved in relation to the reference genome, D. melanogaster. The Drosophila phylogenetic tree suggests that D. willistoni and D. mojavensis would have very different genomic characteristics compared to D. melanogaster, due to their distant evolutionary relationship. This initial hypothesis is tested by annotating the Mrp4 gene in the UCSC Genome Browser, where we identify the changes in its sequence and genomic neighborhood, and ultimately determine the extent to which the gene has diverged. The overall results from this analysis of the Mrp4 gene will contribute to the broader GEP Pathways Project by helping refine predictions about how signaling genes evolve.
Synteny of the Enigma Gene in Three Different Drosophila Species
Presenter: Justin James Whelan Faculty Sponsor: Christine Battle School: Quinsigamond Community College Research Area: Genetics Location: Poster Session 1, 10:30 AM - 11:15 AM: Campus Center Auditorium [A17]
Signaling pathways are crucial to keeping any organism’s internal balance in check, being responsible for everything from response to environment to maintaining balance within any living organism. Oxidative stress is a situation that disrupts an organism’s balance, resulting in an increase in the amount of unstable molecules known as free radicals. The damage free radicals cause is vast, typically shortening an organism's lifespan or contributing to chronic illnesses. A gene known as Enigma encodes a protein located within the mitochondria classified as oxidoreductase, which prevents oxidative stress from occurring and is responsible for regulating the homeostasis of lipids. Mutations in the Enigma gene can cause lost or reduced functions of the production of oxidoreductase. The objective of this project is to research the presence of Enigma in other Drosophila species that are not as well annotated as D. melanogaster. The two species of interest in this research project are D. bipectinata and D. willistoni. After the necessary data is collected, a model will be constructed to show all three of the annotated genes of the species, showing how Enigma manifests across different species under the same genus. The Genomics Education Partnership online database will be used to annotate genomes of interest in the research of this project. This research on the synteny of D. melanogaster with D. bipectinata and D. willistoni is a contribution to the 2026 Genomics Education Partnership Pathways project, exploring how genes in pathways evolve.
The Role of ceh-43 and rnt-1 in C. elegans Health
Presenter: Lizmary Vidal-Sanchez Zoe Vidal-Sanchez Faculty Sponsor: Joslyn Mills School: Bridgewater State University Research Area: Genetics Location: Poster Session 2, 11:30 AM - 12:15 PM: Room 163 [C26]
Oral health is essential and determines overall well-being. Craniofacial anatomy can impact oral health, so it is imperative that genetic disorders disrupting craniofacial development, such as Amelogenesis Imperfecta (AI) and Cleidocranial Dysplasia (CCD), are studied to optimize treatments. AI is a genetic disorder that causes tooth enamel malformation, and CCD is a genetic bone disorder that causes hypoplastic clavicles, open skull fontanelles, and dental anomalies. Although C. elegans do not have teeth or bones, they have genes homologous to those associated with these disorders. This allows us to investigate the cellular and molecular contributions of these gene products to study AI and CCD to better understand the mechanisms and improve treatments in humans. The nematode gene ceh-43, which is responsible for neuronal cell differentiation and embryonic development, is homologous to AI-associated DLX3. The nematode gene rnt-1, which is responsible for male-tail, body length, and hypodermal cell development, is homologous to CCD-associated RUNX2. Although the importance of these genes in nematode development has been highly studied, little research has been conducted on the genes’ impact on overall health in adult C. elegans. Determining the role of these genes in the health of C. elegans will further the understanding of these homologs and how they can be used to better understand AI and CCD. Experiments to test stress responses, lipid metabolism, and frailty were used to determine the health of C. elegans with knockdown of these genes using RNAi.
Improving Undergraduate Student Genetics Literacy Through a Case Study Addressing Central Dogma Misconceptions
Presenter: Michelle Letowska Faculty Sponsor: ROSA A. MOSCARELLA School: UMass Amherst Research Area: Genetics Location: Poster Session 6, 4:15 PM - 5:00 PM: Campus Center Auditorium [A50]
Misconceptions about foundational genetics concepts, like the central dogma (CD), are keeping many undergraduate students from attaining genetics literacy. It is crucial to help students overcome these misconceptions not only because genetics unifies many important biological concepts but also because it has revolutionized medicine and changed society. For example, through genetics we have developed cancer treatments and created genetically modified organisms. To help students achieve genetics literacy, this project has two main goals: 1- the creation of a case study on the CD to serve as a supplemental learning tool, and 2- gather information to gain further insight into student CD misconceptions. The case study was designed for students in Introductory Genetics courses, a sophomore level course, to practice CD concepts by connecting how a DNA mutation can lead to a rare disease called immune dysregulation, polyendocrinopathy, X-linked syndrome (IPEX). Additionally, pre- and post-assessments were created to not only measure the effectiveness of the case study but to also gain further insight on student mental models regarding the flow of genetic information. Participants also took a survey inquiring about factors that may be influencing their learning such as grade level and previous, related courses. The case study will provide students an opportunity to not only strengthen their critical thinking skills by applying their knowledge but to also recognize and address any misconceptions they may have. Thus, I hypothesize that instruction followed by a case study will have an impact on students’ understanding of the CD.
Virophages are a group of double-stranded DNA viruses that hijack the replicative machinery of giant viruses (GVs), limiting their overall DNA replication and gene expression. So far, they have been primarily studied in aquatic environments and little is known about their role in soil ecosystems. To bridge this gap in research, 33 different virophage viral operational taxonomic units (vOTUs) were discovered from the Barre Woods soil warming experiment with one vOTU existing solely in the heated plot with significant overrepresentation (p = 0.00029). We termed this vOTU “Imagivirus” since a majority of its identified proteins are hypothetical. Apart from these hypothetical proteins, four major conserved genes: major and minor capsid, cysteine protease, and ATPase, were identified across all vOTUs. Phylogenetic analysis using conserved genes in high quality genomes and from reference virophage genomes show Imagivirus genomes forming a distinct clade. Virophages are surprisingly abundant in soil samples, compared to the limited collection of GVs and protists. The purpose of this study is to examine this relative abundance of virophages and better understand their significance in the soil microbiome. A similar overrepresentation of a potential protist host or giant virus in warming plots samples was not detected and hence, the virophage may exist as free particles in the soil or more numerically abundant replicons inside a host cell.
Meiotic Homolog Pairing in Polyploid Yeast
Presenter: David Bai Faculty Sponsor: Tadasu Nozaki School: UMass Amherst Research Area: Genetics Location: Poster Session 6, 4:15 PM - 5:00 PM: Concourse [B16]
Diploid (2n) organisms contain two sets of homologous chromosomes, each of which must spatially pair during meiosis for crossover formation. In polyploid organisms (>2n), pairing becomes more complicated, as 3 or more homologous chromosomes must each pair during meiosis. The question of how these chromosomes pair and how polyploidy affects the progression of meiosis in vivo remains unsolved. To observe pairing in polyploid cells, budding yeast containing tagged fluorescent loci on chromosome II were prepared. Triploid (3n) and tetraploid (4n) yeast strains were constructed by disrupting the MATa or MATα locus and repeatedly mating. Ploidy level was then confirmed by flow cytometry and number of fluorescent spots. After meiotic induction, long timelapse live-cell imaging of the polyploids allowed for observation of chromosomal pairing during meiotic prophase I. The resulting imaging data showed that bivalent pairing occurs in the majority of cases, with trivalent and quadrivalent pairing being much less frequent. This suggests that chromosomes, once paired, employ a protective mechanism to prevent further pairing, even if there are still unpaired chromosomes in the nucleus.
