All speaker abstracts and talk titles will be posted as they become available.
Title: Mechanisms of Development and Regeneration in Hydra (recommend reading)
The adult Hydra continually renews all cells using lineage-restricted adult stem cells and can regenerate its entire body from a small piece of tissue. Both homeostatic maintenance and regeneration requires the coordination of three non-overlapping stem cell differentiation pathways. This complexity of cell fate specification pathways is combined with a simple tissue structure and a small number of total cell types. This unique combination of traits in Hydra allows us to use single cell RNA sequencing (scRNA-seq) to capture the spectrum of cell states at high molecular resolution and use this information to decipher the stem cell differentiation pathways of multiple distinct lineages. We sequenced the transcriptomes of ~25,000 Hydra cells and identified the molecular signatures of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each lineage and identified the transcription factors expressed along these trajectories, thus creating a multi-lineage map of an adult organism. These data provide a significant starting point to unravel the gene regulatory networks (GRNs) that control cell differentiation in the homeostatic Hydra. To understand how these GRNs are triggered by the conserved injury response during regeneration, we have collected RNA-seq and ATAC-seq data on regenerating tissues. These data reveal that injury-induced transcription factors may directly activate the transcription of Wnt pathway genes, which are key factors in establishing a new head organizer. Altogether, we provide a comprehensive molecular description of Hydra homeostatic and regenerative development, which is a valuable resource for tackling fundamental questions in developmental and regenerative biology.
Title: The role of DNA quadruplex structures in telomere biology: Finding a Black Cat in a Dark Room (recommend reading)
The Stone Research Group at UC Santa Cruz employs a combination of biophysical and biochemical methods to study the structure and function of telomeres and telomerase. Telomeres cap the ends of linear chromosomes and promote genome stability by protecting these natural DNA ends from illicit repair and recombination processes. In continually dividing cell types, including the majority of human cancers, telomere length is maintained by the specialized telomerase reverse transcriptase enzyme. Telomerase
is a protein-RNA complex that directs synthesis of guanine-rich (G-rich) telomere DNA repeat sequences at chromosome termini using its integral RNA subunit as a template. These short G-rich telomere repeat sequences have a propensity to fold into noncanonical DNA structures called G-quadruplexes (GQs). Despite mounting evidence that telomere DNA and other repetitive G-rich sequences readily fold into GQ structures in vitro, whether these structures form in cells and play a direct role in biological processes continues to be actively debated. In spite of this ongoing debate, many research groups are actively pursuing the development of novel GQ binding ligands for use in diverse therapeutic settings. In this seminar, I will describe recent work in the Stone Research Group that explores the impact that GQ folding can exert on several transactions that occur at telomeres. Our results support the notion that GQ folding is indeed a functional property of telomere DNA that is exploited by telomerase and other telomere-associated factors in order to maintain telomere homeostasis.
Title: Software Without Algorithms? Deep Learning Meets The Stuff Of Life. (recommend reading)
Abstract: Deep Learning, a recent development in neural network technology, has become a prominent commercial and research tool. My research group combines neural networks with traditional bioinformatic and marine ecology techniques, in order to gain insight into effects of climate change on ocean environments. I will present 3 current projects: (1) Assessing coral reef biodiversity through Deep Learning analysis of settlement plates, with citizen scientist crowdsourcing. (2) Studying increasing success of sponge reefs when coral reefs declined during historical climate change events. (3) Data mining GenBank for specific genes of interest.
Title: Fluid-structure interaction in biological fluids (recommend reading)
This talk will review mathematical and computational challenges in studying fluid-structure interaction in biological fluids. Applications to modeling drug-eluting stents for coronary angioplasty with stenting, optimal design of bioartificial pancreas for the treatment of Type 1 diabetes, optimal design of micro-swimmers, and to the study of emergent behaviors of colloidal suspensions, will be addressed.