REU Faculty Research Profiles
The Syracuse University Biology REU program focuses on using microscopy to explore form and function across biological scales (MicroFFABS). Faculty mentors study how organisms' structures impact their functions, from molecular to organismal levels, using models like poplar trees, mice, and cell cultures. This unified approach allows students to explore diverse fields while connecting through microscopy. The program aims to attract diverse participants and help students from underrepresented institutions discover new research paths. Through collaboration and hands-on experience, students will engage with cross-cutting concepts in biology, preparing them for future research opportunities.
Please review the faculty mentors' research profiles and choose a minimum of 3 the mentors.
Yasir Ahmed-Braimah
Our lab uses advanced fluorescence microscopy and live imaging to uncover mechanisms of reproductive interaction inside the female reproductive tract. By developing fluorescently tagged sperm lines across members of the Drosophila virilis group, we visualize sperm storage, movement, and utilization in real time to understand the cellular and molecular basis of postmating reproductive processes. We combine confocal microscopy, high-resolution live imaging, and quantitative image analysis to track how sperm from different males behave within specialized storage organs, how these dynamics break down in hybrid matings, and how rapid evolution of reproductive proteins shapes these interactions. Students in our lab gain hands-on training in specimen preparation, image acquisition, quantitative image analysis, and experimental design, contributing to projects that connect cell-level processes to the evolution of reproductive isolation and speciation.
Carlos Castañeda
The Castañeda lab studies protein quality control (PQC) mechanisms under physiological and stress-induced conditions focusing on how ubiquitin and polyubiquitin chains regulate the formation and disassembly of biomolecular condensates through phase separation. This process is crucial as many proteins tagged with polyubiquitin are marked for degradation or other cellular pathways. REU students will monitor condensate formation of ubiquitin-binding proteins using microscopy techniques. They will learn to express and purify phase-separating proteins, conduct turbidity assays, and use fluorescence microscopy. Additionally, students will perform single particle tracking and FRAP to quantify protein properties and carry out live-imaging experiments in mammalian cells.
Heather Coleman
The Coleman lab studies plant cell wall formation and the genetic and external factors affecting its characteristics. We also explore how humans can utilize plants for bioproducts and fuel. Poplar is used as a model system, with projects including mapping the transcriptional regulation of hemicellulose production, understanding the role of gene duplicates in wood formation and abiotic stress resistance, and studying the impact of mycorrhizal fungal associations on poplar growth. The REU student will use techniques like plant tissue culture, light microscopy, and molecular biology to analyze secondary cell wall formation, structure, and organization.
Sarah Hall
Epigenetic mechanisms control how early-life stress influences gene expression in C. elegans. These nematodes make a crucial developmental decision based on environmental conditions, entering a dauer stage under stress, which affects gene expression and leads to altered adult phenotypes. The Hall lab has found that RNA interference (RNAi) pathways regulate these gene expression changes due to early stress. The REU student will utilize CRISPR/Cas9 to create strains with fluorescent reporters to study neuronal gene expression in RNAi mutants, correlating these with chemotaxis behavior changes. Techniques include molecular cloning, genetic crosses, fluorescence microscopy, and behavioral analysis.
Heidi Hehnly
Visualizing Centrosome Dynamics During Early Embryonic Development. Centrosomes are key organizers of the microtubule cytoskeleton and play essential roles in cell division, polarity, and signaling during embryogenesis. This project will investigate how specific centrosomal proteins contribute to proper tissue organization in developing zebrafish embryos. The student will use high-resolution fluorescence microscopy to track centrosome positioning, duplication, and dynamics in real time during early developmental stages. They will learn how to generate and stage live embryos, prepare samples for imaging, and use advanced imaging platforms (e.g., spinning-disk or laser-scanning confocal microscopy) to capture centrosome behavior in intact tissues. Quantitative image analysis will be applied to assess how perturbations of individual centrosome proteins alter division orientation and morphogenesis. Through this project, the student will gain hands-on experience in live-cell imaging, quantitative microscopy, and hypothesis-driven experimental design, while contributing to our understanding of centrosome function in vertebrate development.
Jamie Lamit
Imaging and quantifying roots in wetland plants. Mycorrhizal fungi colonize roots of the vast majority of plants, and have important influences on plant growth and ecosystem processes. However, these fungi have been largely overlooked in the saturated soils of wetland habitats. This project will focus on characterizing the fungi colonizing plant roots in different types of wetlands (bogs, marshes, swamps). The student will assist with fieldwork collecting roots of a variety of plant species from wetlands in central New York. In the laboratory, collected roots will be cleaned, sorted, and scanned for computer-based image analysis of root traits, followed by preparation for microscopy by chemical clearing of cellular contents (with potassium hydroxide), staining with a fungal specific stain (Trypan blue, Chlorazol black) and mounted on slides. The intensity of fungal colonization in roots will be quantified with the line-intersect method using a Zeiss compound light microscope. To complement microscopy, a subsample of roots will also be subjected to DNA extraction, PCR and sequencing to identify fungal species.
Chih hung Lo
Tunneling nanotubes (TNTs) are F-actin based membrane extensions that allow for direct intercellular transfer of cargo between cells. TNTs have been recognized as a mechanism for exchange of organelles, like lysosomes, between neurons and glia. While this may be a response to diminishing cellular stress, it may also be a pathway for the propagation of pathological proteins such as tau, beta-amyloid, and α-synuclein in neurodegenerative diseases. This project investigates how lysosomes are trafficked within and between cells through TNTs, and how this process changes under neurodegenerative conditions. Microscopy will be used as the main investigative method, using live-cell confocal imaging to visualize TNT formation and track fluorescently labeled lysosomes and intrinsically disordered proteins (IDP) as they move between neurons, astrocytes, and microglia. Time-lapse microscopy will examine directionality and dynamics of lysosome and IDP transport, as well as quantification of TNT frequency. Students will learn to culture neural cell lines, transfect cells with fluorescent labeling, and use microscopy and image analysis of live and fixed cells to uncover how TNT-mediated lysosomal trafficking contributes to neural communication and propagation of neurodegenerative pathology.
Jessica MacDonald
Disruptions in neuronal development and connectivity within the neocortex, the area of the brain responsible for high cognitive function, are found in many neurodevelopmental disorders (NDDs), including autism spectrum disorders, intellectual disability, and schizophrenia. What causes this atypical development is still poorly understood, but likely includes a combination of genetic, epigenetic, and environmental factors, including maternal nutrition. To tackle this complex biology, the MacDonald lab is currently studying how the nutritional factors vitamin D and folic acid modify neuronal development and function in both normal mice and mice with genetic mutations in epigenetic regulators that model neurodevelopmental disorders such as Rett syndrome and autism spectrum disorders. We are investigating how these genetic, epigenetic, and maternal nutrition factors intersect to regulate two major developmental convergence points for NDDs: the proliferation and differentiation of neuronal progenitors, and the establishment of appropriate local and long-distance neuronal connections. We will employ a combination of immunohistochemistry and fluorescence microscopy to identify changes in neocortical development; viral-based fluorescent axonal tracing with confocal imaging to identify changes in neuronal connectivity; and primary neuronal cell culture with live imaging to identify changes in cell proliferation and neuronal specification.
Heather Meyer
The Meyer Lab investigates how intrinsically disordered proteins (IDPs) enable plants to sense and respond to environmental changes. Because plants cannot move, they rely on environmental cues such as temperature and day length to regulate key developmental processes like flowering. Yet, how cells perceive and convert these cues into specific molecular signals remains unclear. IDPs are especially intriguing as environmental sensors because they can dynamically change their structure and function in response to physical and chemical fluctuations, including temperature, pH, and osmolarity. Many IDPs form reversible protein assemblies called biomolecular condensates under changing conditions, providing a physical means of organizing and regulating cellular processes. Using the model plant Arabidopsis thaliana, this summer's REU student will use advanced live-cell imaging, along with molecular biology and biochemistry, to determine how IDP phase behavior influences plant development in variable environments. This research uncovers fundamental principles of environmental sensing and adaptation with broad implications for understanding how all eukaryotes integrate environmental information to control development.
Melissa Pepling
Cell adhesion in mouse primordial follicle formation (Melissa Pepling SU Biology) The reproductive lifespan of mammalian females is set at birth, when the ovary establishes a finite pool of primordial follicles—single oocytes surrounded by granulosa cells. During the perinatal period, oocyte clusters break apart and become individually encapsulated, a process essential for lifelong fertility. Several signaling pathways, including steroid hormone, KIT, and PI3K signaling, regulate this transition, and estrogen or estrogen-mimicking compounds can disrupt follicle formation. However, the adhesion mechanisms that control oocyte separation and new contacts with granulosa cells are not well understood. Based on findings from hamster ovaries, we hypothesize that distinct cell adhesion molecules (CAMs) mediate these steps: E-cadherin maintains adhesion within oocyte clusters, whereas N-cadherin promotes adhesion between oocytes and granulosa cells as follicles form.This project will examine E- and N-cadherin expression in the mouse ovary during primordial follicle formation and block their function using ovary organ culture to define their roles in follicle assembly. Role of the REU student: The student will examine the expression of E and N-cadherin proteins in mouse ovaries using immunocytochemistry during follicle formation. Samples will be analyzed by taking optical sections through labeled ovaries using the LSM 980 confocal microscope. The student will block the activity of each cadherin in ovary organ culture and examine effects on primordial follicle formation by labeling cultured ovaries with an oocyte marker again followed by analysis with confocal microscopy.
Jayson Smith
Unlike most cells, post-mitotic neurons are non-renewable and must remain functional for decades. They achieve this remarkable feat via “Terminal Selectors”—transcription factors that establish and maintain neuron-type identities and functions throughout life. The Smith lab studies the conserved terminal selector UNC-3/EBF3 in motor neurons (MNs) as a paradigm, using C. elegans and human stem-cell-derived neurons to explore its intrinsic (cell-autonomous) and extrinsic (non-cell-autonomous) roles in development. The REU student will employ confocal microscopy, quantitative image analysis, big data analysis, and classical genetics to investigate how UNC-3 acts in host MNs to influence neighboring MNs.