Georgia Gosnell Seminar Series

From Bench to Bedside: Developing a novel therapeutic against the deadly brain eating amoeba Balamuthia mandrillaris

Kaitlin Marquis, Ph.D. '15 (biotechnology)
Scientist
Chan Zuckerberg Biohub Network

Balamuthia mandrillaris is a free-living amoeba that causes a condition with a mortality rate of 90%. This presentation will focus on our current research efforts to understand the mechanisms of action of nitroxoline, create a high-quality annotated reference genome for B. mandrillaris, and analyze the transcriptional response to nitroxoline as compared to other cellular stressors. These insights will highlight nitroxoline’s potential as a transformative therapeutic agent and advance our understanding of Balamuthia, establishing a foundation for the development of targeted interventions against this pathogen.

Unlocking the Genetic Repertoire of a Cultivated Megaphage

Richard Allen White III, Ph.D.
Assistant Professor
Bioinformatics and Genomics
University of North Carolina at Charlotte

Phage G is the largest known bacteriophage on Earth that we have been able to cultivate. Phage G is one of the largest phage particles >1 um which is half the size of an E. coli and the largest sequenced genome for a cultivated phage at 499 kbp. Phage G has over 650 protein-coding genes, with roughly half being hypothetical proteins, the rest being structural in nature. Its closest known relative in nature was found in the gut of moose but has always been thought to originate from soil. G phage reminds one of the greatest mysteries and stories in all of phage biology with its genome finally unlocked.

T Cell Immunometabolism in Function and Disease

KayLee Steiner (Biotechnology ’20)
Ph.D. Candidate
Cancer Biology
Vanderbilt University

Inflammatory diseases are often driven by imbalanced proinflammatory effector and anti-inflammatory regulatory CD4 T helper cells (Th cells). These T cell subsets rely on distinct metabolic programs, modulation of which can affect Th cell differentiation and disease development. Here multiple in vivo CRISPR/Cas9 screens of lipid metabolic genes identified the mitochondrial fatty acid synthesis (mtFAS) pathway as critical for the fitness and function of proinflammatory Th cells. Mecr, which is the rate limiting enzyme in this pathway to generate mitochondrial lipoic acid, was found to be significantly depleted in models of disease. These results show that mtFAS and Mecr play important roles in T cell immunometabolism and may provide targets to modulate immunological function.

Living on the edge: Pollinating insects and plant communities along highways

Kaitlin Stack Whitney, Ph.D.
Assistant Professor
Department of Science, Technology, & Society
Rochester Institute of Technology

What does the shift towards using roadsides for conservation mean for pollinators and people? This seminar will present on the results of over 5 years of research, conducted in collaboration with many RIT students and land managers across upstate New York. We undertook a landscape-scale experiment to study the potential impacts of altering highway roadside management on pollinating insects, plant communities, and human health. Additionally, we incorporated social psychology surveys, qualitative interviews, and cost-benefit analyses to gain deeper insights into peoples’ perceptions of the project and roadsides as ecosystems.

Building Quantitative Skills in Biology Students

Melissa L. Aikens, Ph.D.
Associate Professor
Department of Biological Sciences
University of New Hampshire

Quantitative skills are an essential core competency for undergraduate life science students. However, learning these skills can be challenging. My research seeks to understand how we can support biology students’ learning of quantitative skills from both a motivational and cognitive perspective.

Co-sponsored with the Center for Advancing Scholarship to Transform Learning (CASTLE).

Advanced Cryotechnologies for Conservation: Ethics and Justice Considerations

Evelyn Brister, Ph.D.
Professor of Philosophy
Rochester Institute of Technology

Advanced biopreservation technologies will prove useful in conservation through scaling up biobanking and restoration activities, including coral reef restoration and de-extinction. This seminar describes how these techniques will facilitate conservation and surveys the ethical issues that arise.

Coastal Wetlands in a Changing World: Impact on carbon sequestration and greenhouse gas release

Inke Forbrich, Ph.D.
Assistant Professor
University of Toledo

Coastal wetlands are important interfaces between land and ocean, storing and exchanging matter with adjacent ecosystems and the atmosphere. With accelerated sea level rise, these systems accrete material to keep elevation relative to mean sea level, migrate inland or submerge. This reconfiguration of the coastal zone impacts carbon pools and fluxes across systems differently. In this seminar, I will discuss examples from two space for time studies, as well as on-going changes in a freshwater estuarine wetland at the coast of Lake Erie.

Determining the socio-ecological impact of field station conservation initiatives

Sydney VanWinkle, M.S. (RIT '19 '21)
Fulbright U.S. Student Fellow
Madagascar Researcher

Madagascar is a global biodiversity hotspot and a priority for worldwide conservation efforts. Many conservation initiatives are associated with field stations, which serve as hubs for conservation research and environmental education programs. A common challenge among field stations is understanding the impacts of the initiatives they undertake. In this study, we developed and piloted an assessment tool that we used to evaluate a Conservation Club program. Overall findings provide insight into the challenges and successes of community-based conservation and show the long-lasting impacts of the Conservation Club program in Madagascar.

Biology Without Walls: Student Research Presentations

Biology Without Walls is an immersive field course. The students will present research findings from a glaciated, protected field site to understand the impacts of climate change and humans on ecosystems.

Microbial Assembly: Using ecology to deconstruct pandemics and build healthy amphibian microbiomes

Dr. Elle Barnes
Assistant Professor
Thomas H. Gosnell School of Life Sciences
RIT

Amphibians are the most endangered group of animals due to climate change, habitat degradation, and the global spread of disease. These stressors have been linked to changes in the structure of the amphibian microbiome. In the MEGA (Microbial Ecology & Genomics in Amphibians) lab at RIT, we ask BIG questions about tiny organisms. When does history matter for the assembly of disease-resistant amphibian microbiomes? By combining genomics and ecological theory, we explore how human-induced environmental degradation and pathogen spread can drive the persistence of alternative states of microbial diversity with important consequences for function.

New Strategies for Antibiotic Dosing in the Age of Multidrug-Resistance

Zackery P. Bulman, PharmD
Assistant Professor
University of Illinois Chicago
College of Pharmacy

Dr. Bulman’s team aims to devise novel therapeutic approaches that are capable of successfully treating infectious diseases while also suppressing the amplification of new resistance mechanisms. This presentation will identify new approaches to combat clinically relevant multidrug-resistant bacteria such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Different approaches to dosing antibiotics, use of unique antibiotic combinations, and consideration of molecular mechanisms of resistance in antibiotic selection will be discussed.

The Green Diversity Under Our Feet: Secrets and Surprises of Green Microalgae

Dr. Elena L. Peredo
Assistant Professor
Thomas H. Gosnell School of Life Sciences

Green microalgae are unicellular green plants that share an evolutionary history, basic physiology, and genetic background with terrestrial plants. Despite this close relationship, they continue to conceal many secrets!   Microalgae can be found in a wide range of habitats and exhibit remarkable endurance capabilities. In this seminar, we will delve into the fascinating world of these microorganisms, exploring some of their morphological and physiological adaptations. Additionally, we will investigate the genetic basis of their remarkable desiccation tolerance.

Understanding Learning Strategies and Metacognition in Genetics Students

Dr. Jenny Knight
Associate Professor
Molecular, Cellular & Developmental Biology
University of Colorado Boulder

The practice of metacognition has been correlated with better learning, but there are still many questions to answer. We have been investigating student reports of their learning strategies in an introductory genetics course to determine if strategy use and accuracy in reporting correlate with higher performance. The data suggest that focusing on encouraging students to be aware of their study approaches and to follow through with known effective practices may be instrumental in helping students shift strategies and improve their learning.

Understanding and Modulating Immune Responses to Adeno-associated virus (AAV) Gene Therapy

Dr. Allison Keeler-Klunk
Assistant Professor
Horae Gene Therapy Center
University of Massachusetts
Chan Medical School

Although adeno-associated virus (AAV) is considered a non-pathogenic virus, it still is recognized by both the innate and adaptive immune system and produces a substantial response. Understanding how the immune system sees and responds to the AAV is important for moving clinical gene therapies forward.  Taking knowledge gained from characterizing immune responses observed in AAV clinical trials, we have developed novel tools for modulating immune responses to AAV gene therapy. 

ATOMDANCE: machine learning denoising and resonance analysis for functional and evolutionary comparisons of protein dynamics

Dr. Greg Babbit and Dr. Maureen Ferran
RIT Thomas H. Gosnell School of Life Sciences

Comparative methods in molecular biology and molecular evolution rely exclusively upon the analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from dynamic shifts in machine-like motions induced by molecular interactions. Here, we introduce ATOMDANCE, a suite of statistical and kernel-based machine learning tools designed for denoising and comparing functional motion states of proteins captured in time-series from molecular dynamics simulations. We’ll spend the first half of the talk reviewing the software/methods and we’ll spend the second half as an open discussion of its potential application to problems in virology and immunology.

GSoLS Student Seminars: What I did this Summer

September 13: Part 2

• Hannah DeFelice participated in an REU at the University of New Hampshire. As part of the program, Hannah traveled to norther Sweden to perform vegetation assessments and collect pore water samples in an area of permafrost transition/thaw. Her results showed considerable change in vegetation cover, pH, and methane concentrations between 2015 and 2023.
• Sydney Purcell conducted research at RIT in Dr. Ferran's viral genetics lab. She focused on using targeted molecular imaging agents to image breast cancer cells and infecting C. elegans with VSV to overexpress a specific gene. Zak Azad conducted research in Dr. Thomas' lab at RIT. The research project focused on optimizing parameters that impact phage growth and yield.
• Tori Russell was involved in several research projects in Dr. Ferran's lab at RIT, including a mechanobiology project, a breast cancer imaging project, and a C. elegans/VSV project.
• Maggie Muldoon participated in the RIT Wetlands REU, with her research project focusing on the impact of the Emerald Ash Borer on bird species and habitat in forested wetlands.

August 30: Part 1

• Natalie Siwek completed a co-op with VHB, a company that specializes in civil engineering, urban planning, and environmental consulting. She supported the Natural Sciences team by assisting with wetland delineations, rare species surveys, construction compliance inspections, permit application preparation, and data collection and synthesis.
• Leah Robinson was part of an NSF EFRI REM program in the Material Science and Engineering Department at the University of Michigan, researching how organic vapor jet printed active pharmaceutical ingredients impacted the cell growth and viability of ovarian cancer cell spheroids.
• Zach Black spent the summer doing research at RIT in Dr. Ferran's viral genetics lab. He worked on optimizing two transfection reagents and determined whether transfecting cells activates NF-kB, with the goal of understanding NF-kB regulation in human prostate cancer cells.
• Katie Chrisbacher had an Emerson research fellowship at RIT this summer and completed research in Dr. Skuse's lab. She worked on a chemotherapeutic rhodcyanine dye, MKT-077.

GSoLS Student Seminar: “Closing the gap on sources and sinks of anthropogenic debris across an urban to rural gradient in the Great Lakes Basin”

Speakers:
Paige Arieno ‘23 BS, ’24MS
Evan Batte ‘23 BS, ‘24 MS
Nikki Fuller, ’24 MS
Jayson Kucharek ‘23BS, ‘24 MS
Environmental Science

Plastic pollution is a significant threat to the ecosystem and human health. This research aims to better understand this threat by assessing the sources of plastic pollution from rural to urban regions in the Lake Ontario watershed, evaluating hot spots of debris accumulation and degradation that retain pollution in the watershed, and developing a regional budget for plastic pollution to estimate quantity and identity of debris entering the Lake.

“Pairing is Sharing: Critical thinking improves when working in pairs”

Speaker:
Sam Conflitti '23
Biotechnology and Molecular Bioscience

Analogies are often used by experts to communicate complex ideas in science. In this study, we explored how learners communicate their ideas about genetic information flow using analogies and how different environments (working alone or working with a partner) impact critical thinking skills.

“Isolation, Whole-Genome Sequencing, Annotation and Characterization of Two Antibiotic-Producing and -Resistant Bacteria, Pantoea rodasii RIT 836 and Pseudomonas soli RIT 838, Collected from the Environment.”

Speaker:
Serena Tuytschaevers '25
Bioinformatics and Computational Biology

Several bacterial strains isolated from the environment near the RIT campus were found to be resistant to multiple clinically relevant antibiotics. We found that two strains, Pantoea rodasii RIT 836 and Pseudomonas soli RIT 838, produce bactericidal compounds against Escherichia coli and hope to further analyze their genomes to get insights into the antibiotic resistance and production by these bacteria.

"Unveiling the Signaling Pathways of Mother of Millions, an emerging Crassulacean Acid Metabolism (CAM) model”

Speaker:
Shui Li Eu-Balint '24
Biology

Kalanchoe delagoensis, also known as Mother of Millions, is an obligate CAM plant that rapidly proliferates through plantlet formation on its leaf edges, making it an ideal CAM model species. Despite its unique biology, little is known about its molecular signaling and defense responses. This study aimed to address this knowledge gap by profiling key signaling molecules in response to phytohormone treatment.

Dr. Jacqueline Clark Ludwig, RIT: Can moth muscles make robots move? Examining metamorphosis in the tobacco hawkmoth to identify tissue engineering targets

Speaker:
Dr. Jacqueline Clark Ludwig
Inclusive Excellence Program Manager
RIT

In the tobacco hawkmoth (Manduca sexta), metamorphosis involves restructuring a soft caterpillar with slowly contracting muscles into a rigid adult with flight powered by rapidly contracting muscles. The largest of these, the dorsolongitudinal flight muscles (DLMs), develop from partially degenerated larval fibers, making them identifiable throughout pupa life. This may allow the DLMs to be engineered for use in soft robots or other devices.

Dr. Farid Halim: Unraveling the Role of Formate Dehydrogenase in Methanogenesis: Insights into Microbial Energy Metabolism

Speaker:
Dr. Farid Halim '10 (biotechnology)
Postdoctoral Research Associate
University of Minnesota

Methanogens are a group of anaerobic archaea that produce methane through the process of methanogenesis. One of the key steps in this process is the oxidation of formate, carried out by formate dehydrogenase (Fdh) enzymes. We describe how Fdh can be part of methanogenesis metabolism to carry out formate oxidation to generate methane. These findings shed light on the complex mechanisms of methanogenesis and the functional roles of Fdh homologs in this process.

Dr. Andrew Newhouse: Using Genetic Engineering to Rescue Threatened Native Trees

Speaker:
Dr. Andrew Newhouse
American Chestnut Research and Restoration Project
SUNY ESF

Abstract: 
The American Chestnut Research & Restoration Project aims to produce trees that are well-adapted to thrive throughout their natural range. Our primary focus is on disease tolerance, and we have produced a line of trees with a wheat gene that allows them to tolerate the fungal blight that functionally extirpated these trees from our landscape.  For the American chestnut, genetic engineering offers a unique opportunity to enhance blight tolerance for restoration while minimizing other changes to the genome.

Trevor Penix: Applied Biomedical Genomics and Bioinformatics at the Genomics Research Center

Speaker:
Trevor Penix (Biotechnology ’20)
Ph.D. Candidate
St. Jude Graduate School of Biomedical Sciences
St. Jude Children’s Research Hospital

Abstract: 
Respiratory bacterial pathogens have been known to take advantage of influenza-infected hosts, greatly exacerbating disease and playing a significant role in morbidity and mortality. Through proteomic and genetic approaches, I plan to uncover the molecular players responsible for the direct binding of bacteria and influenza. The goal is to understand this mechanism to help inform the treatment of high-risk influenza patients, hopefully preventing deadly secondary bacterial infections.

Melissa Duhaime

Speaker:
Melissa Duhaime
Assistant Professor
Department of Ecology and Evolutionary Biology
University of Michigan

Abstract:
It is estimated that 4.8-12.7 million tons of plastic enter the ocean in a single year, and this number is expected to increase exponentially. To target major sources and pathways on a global scale, the question remains: What is the physical fate of plastic once in the oceans and major fresh waterways? Our work is to experimentally resolve the knowledge gaps regarding the fate of plastic debris in freshwater systems.

Elizabeth Pritchett and Dr. Dalia Ghoneim: Applied Biomedical Genomics and Bioinformatics at the Genomics Research Center

Speakers:
Elizabeth Pritchett, Operations Director
Dr. Dalia Ghoneim (bioinformatics '07)
Genomics Research Center 
University of Rochester

Abstract:
Drs. Pritchett and Ghoneim will overview the ongoing applied and translational next-generation sequencing (NGS) genomics capabilities at the University of Rochester.

Erik Dopman: Genetic causes and population consequences of behavioral and life history evolution

Speaker: Erik Dopman
Tufts University

Abstract:
While most biologists agree that multiple reproductive barriers are required for new species to form, empirical studies often emphasize single barriers to interbreeding such as hybrid sterility. In my talk I will describe how the two main reproductive barriers seen in the European corn borer moth (Ostrinia nubilalis), temporal and behavioral isolation, are a byproduct of only four genes.

Shawn Fahl: Applications of Cryopreserved Human Dissociated Tumor Cells (DTCs) for Drug and Diagnostic Development

Speaker: Shawn Fahl '05 (biotechnology)
Vice President of Lab Operations, Cell Services, and R&D, Discovery Life Sciences

Abstract:
The acquisition of fresh human tissue is often an impediment to significant research advances. We have developed cryopreserved dissociated human tissues as a viable specimen source for many downstream applications, including immunophenotyping, bulk and single-cell sequencing, and single-cell functionality. Extensive cellular profiling of these samples by flow cytometry revealed indication-specific trends in the composition of the tumor microenvironment, and these specimens provide the opportunity to screen for novel drug targets and biomarkers. We have used the PD1/PDL1 pathway, which is currently therapeutically targeted in numerous solid cancers, to confirm the utility of these samples in evaluating immunomodulatory pathways. These studies have been extended to uncover novel functional immune receptors to target the next generation of immunotherapies.

Dr. Julie Thomas, RIT: Building on “déjà vu” to understand giant phage head assembly and function

Speaker: Dr. Julie Thomas, Associate Professor
RIT Thomas H. Gosnell School of Life Sciences

Abstract:
Phage research is undergoing a renaissance due to the abundance and diversity of phages in the environment, as well as their use to control multi-drug-resistant bacteria. In this seminar, I will discuss our research on the large Salmonella phage SPN3US, whose complex head has déjà vu-like similarities to that of the model E. coli phage T4. Our goal is to define the molecular cues that control proteolytic maturation in T4 and SPN3US so they can be exploited to package non-phage proteins into their heads.

Dr. Daniel Grunspan: Biases and Partnerships: Learning from Student Social Networks

Speaker: Dr. Daniel Grunspan, Assistant Professor
Department of Integrative Biology, University of Guelph

Abstract:
With high student-to-faculty ratios, large classes elevate the importance of relationships and interactions between students. Using social network analysis, Dr. Grunspan will present how peer interactions evolve over the course of a semester. Results indicate that who students study with primarily depends on course structure and shared identities between peers, while who students perceive as strong in the class material follows a strong gender bias.

Douglas Lyles: Trafficking of viral ribonucleoproteins in the cytoplasm of host cells

Speaker: Douglas Lyles, Professor of Biochemistry
Wake Forest School of Medicine

Abstract:
The ribonucleoprotein (RNP) cores of RNA viruses are too large to diffuse through the cytoplasm of eukaryotic cells. Nonetheless, they migrate extensively post-infection to form inclusion bodies and migrate to the plasma membrane for virus assembly. We have shown that vesicular stomatitis virus (VSV) RNPs move through the cytoplasm primarily by rapidly bouncing back and forth within traps and hopping from trap to trap in random directions.

GSoLS Faculty Slide Slam

Speaker: GSoLS Faculty Slide Slam
Thomas H. Gosnell School of Life Sciences, RIT

Abstract:
Join the Thomas H. Gosnell School of Life Sciences community to learn about faculty research and the opportunities for student research. Faculty will be presenting 5-minute summaries of their research.

Stefan Schulze, RIT: Comprehensive prokaryotic glycoproteomics: challenges, solutions, and their application to pathogenic bacteria

Speaker: Stefan Schulze, Assistant Professor
Thomas H. Gosnell School of Life Sciences, RIT

Abstract:
Protein glycosylation, one of the most complex post-translational modifications, plays central roles in a variety of cellular processes in prokaryotes. Therefore, system-wide analyses of glycoproteins are crucial to gain a molecular understanding of biofilm formation, antibiotic resistance, and pathogenicity mechanisms. Yet the challenges posed by the complexity and variability of glycoproteins have prevented their large-scale analyses in most prokaryotes so far. Here, I will present an interdisciplinary approach that combines bioinformatics, comprehensive glycoproteomics, and cell biological characterizations for the functional analysis of prokaryotic glycosylation. For the model archaeon Haloferax volcanii, this approach led to the identification of the largest archaeal glycoproteome described as yet, revealed the concurrence of two independent N-glycosylation pathways that can modify the same glycosylation sites, and indicated the involvement of glycosylation in crucial cellular processes such as cell shape determination. The universal applicability of the developed methods and bioinformatic tools now sets the stage for functional glycoproteomics in bacteria. The first results highlight the importance of glycosylation for biofilm formation in the opportunistic pathogen Pseudomonas aeruginosa. In summary, comprehensive prokaryotic glycoproteomics provides new insights into prokaryotic cell biology and, in turn, opens new avenues for developing novel therapeutics.

Dr. Girish Kumar: Impact of extraction methods, filter pore sizes, and primers on eDNA metabarcoding results

Speaker: Dr. Girish Kumar, Genomics Research Associate
Thomas H. Gosnell School of Life Sciences, RIT

Abstract:
Findings from environmental DNA (eDNA) metabarcoding are strongly influenced by the experimental approach. Yet, the effect of pre-PCR sample processing on taxon detection and estimates of biodiversity across different water types is still poorly resolved. In this presentation, I will discuss the impact of sampling effort, extraction method, filter pore size, and primers on metabarcoding results for fish in water samples.

Dr. Leslie Kate Wright, RIT: Representations and Visualizations in Molecular Biology

Speaker: Dr. Leslie Kate Wright
Professor and Interim Head of Thomas H. Gosnell School of Life Sciences

Abstract:
The field of Molecular Biology relies heavily on visual representations to communicate ideas about unobservable biological processes and molecules. Visual representations are simplified models that appear in biology textbooks, teaching materials, and even as quickly created drawings on paper or whiteboards during discussion. Much evidence suggests, however, that biology learners and experts do not necessarily “see” the same things when deciphering or creating visual representations. This seminar will highlight two recent projects from our laboratory; how visual representations are used to illustrate Molecular Biology concepts and how student-generated drawings can be a window into mental models of Molecular concepts and processes.