Bite Size Research Talk (Julie Wiedemann, Jonathan Rodriguez, Thao Nguyen)
Date: Thursday, October 6th at 10:00 AM
Location: ISEB 6610
Remote attendance: https://uci.zoom.us/j/98759668414 (Zoom Meeting ID: 987 5966 8414)
Speaker: Julie Wiedemann
Lab Affiliation: Bogi Andersen Lab
Title: Cell Atlas of the Mouse Eyelid
Abstract: Meibomian gland dysfunction is associated with 80% of cases of dry eye disease, a common eyelid disorder. Using single cell and spatial transcriptomic approaches, we plan to identify mechanisms controlling Meibomian gland progenitor cell survival and renewal, as well as define transcriptional programs in the normal murine eyelid epithelia, epidermis and conjunctiva. In addition, we aim to characterize fibroblast heterogeneity in the eyelid in relation to skin fibroblast heterogeneity.
Speaker: Jonathan Rodriguez
Lab Affiliation: John Lowengrub Lab
Title: Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy
Abstract: Chronic myeloid leukemia (CML) is a blood cancer characterized by dysregulated production of maturing myeloid cells driven by the product of the Philadelphia chromosome, the BCR-ABL1 tyrosine kinase. To discover novel strategies to improve tyrosine kinase inhibitor (TKI) therapy in CML, we developed a nonlinear mathematical model of CML hematopoiesis that incorporates feedback control and lineage branching. The resulting quantitative model captures most of the dynamics of normal and CML cells at various stages of the disease and exhibits variable responses to TKI treatment, consistent with those of CML patients. To capture other important experimental results, such as treatment free remission, we augment our model with the addition of feedbacks or new stochastic elements.
Speaker: Thao Nguyen
Lab Affiliation: Fangyuan Ding Lab
Title: Systematic Characterize Protein-Nucleic Acid Binding Kinetics
Abstract: The molecular interactions between nucleic acids and proteins influence the essential and regulatory processes of the cell. Yet, well-established techniques such as DNA ChIP-seq and RNA CLIP can only provide a snapshot of interactions, such as the consensus sequence motif and the probability of protein binding. Comprehensive measurement of protein-nucleic acid interaction dynamics—the binding and dissociation kinetics—will provide key missing insights into the cellular function of these molecules and allow engineering of their behavior. However, the current kinetics measurement methods, such as population-based or single-molecule works, have technical challenges because of the stochastic nature of nucleic acid-protein interactions. Each protein can rapidly bind and dissociate from its target DNA/RNA, and the sequence of bound-motif is variable. Hence, we are developing a single-molecule high-throughput platform based on magnetic tweezers—with the ability to identify at least 100 distinct molecules simultaneously and quantify their interactions in real-time. To test the method, we plan to characterize the binding kinetics of RNA-modifying proteins. This quantitative information will help explore their functions in various biological settings, such as cancer progression, and lay a foundation for potential therapeutics.