March 5, 2020

159 Boyer Hall

Trent Northen, Ph.D.
Chemist Senior Scientist, Environmental Genomics and Systems Biology, DOE Joint Genome Institute

"Exploring the chemistry of microbiomes with mass spectrometry"

Sponsor: MBI - Thursday Research Seminar Series

February 27, 2020

154 BSRB

Matteo Pellegrini, PhD

"What Can We Learn About Our Health From DNA Methylation"

Sponsor: OHRC

February 20, 2020

159 Boyer Hall

Janet Rossant, Ph.D., FRS, FRSC
University of Toronto, Professor, Molecular Genetics, Obstetrics and Gynecology

"Defining totipotency- from embryos to stem cells"

Sponsor: MBIDP
Thursday Seminar Series

February 20, 2020

154 BSRB

Michelle Chan, Ph.D.
University of California, San Francisco

"From one cell to many: Deciphering regulation in mammalian development"

Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. In mammals, this field is particularly challenging due to the indeterminate relationship between self-renewal and differentiation, variation of progenitor field sizes, and internal gestation. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins. Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for understanding developmental processes.

Thursday, February 20, 2020
11:30am in 154 BSRB
(Biomedical Research Science Bldg.)
Hosts: Dr. Alexander Hoffmann and Dr. Bill Lowry

Light refreshments

February 18, 2020

12pm (noon)
158 Hershey Hall (Grand Salon)

Manu Setty, Ph.D.
Sloan Kettering Institute, New York, NY

"Characterization of lineage decisions in developmental trajectories using single-cell data"

How a cell decides its lineage is a long-standing and enigmatic question in molecular biology. I will present my research to characterize lineage decisions in developmental trajectories by computational modeling of high throughput data such as single-cell RNA-seq. I will describe Palantir, the first single-cell trajectory detection algorithm to model continuities in lineage decisions. Palantir models differentiation as a Markov process to compute the lineage biases and differentiation potential, a measure of plasticity, for all cells. Palantir modeling enables an accurate identification of lineage decision regions and associated gene expression and regulatory dynamics. I will then describe our study to characterize the spatial and temporal trajectories of mouse endoderm development. Combining Palantir modeling with a large-scale single-cell data, we uncovered an unexpected plasticity of embryonic epiblast cells to differentiate to the surrounding extra-embryonic endoderm at implantation and the concomitant emergence of the spatial signal in the endoderm. Our analysis further demonstrated the convergence of embryonic definitive and extra-embryonic visceral endoderm cells into spatially organized organ territories in the gut-tube at mid-gestation.

February 13, 2020

159 Boyer Hall

Mitchell Lazar, M.D., Ph.D.
University of Pennsylvania

"Transcriptional Regulation of Circadian Rhythms and Metabolism"

Sponsor: MBIDP - Thursday Research Seminar Series

February 12, 2020

1357 Gonda

Zeba Wunderlich, Ph.D.
Assistant Professor, Department of Developmental and Cell Biology, University of California, Irvine

"The Connections Between Enhancer Architecture and Function"

To carry out an enormous diversity of tasks, proteins can assume a variety of structures or disordered states, and years of work have made the connection between protein sequences, structures, and functions. Enhancers and other pieces of regulatory DNA regulate gene expression in highly disparate biological processes, but we still lack general principles that can help us connect enhancer sequence, transcription factor binding site arrangement (or architecture), and function. In my seminar, I will share two projects that seek to make connections between the way enhancers are built and the tasks they carry out in two biological settings: early development and the innate immune response in Drosophila. In the first part, I will describe a mechanism by which redundant (shadow) enhancers control expression noise, and in the second, I will describe the patterns of evolution that drive divergence in the expression response to bacterial infection.

February 3, 2020

158 Hershey Hall (Grand Salon)

Johannes Schöneberg, PhD
UC Berkeley

"Adaptive Optics Lattice Light-Sheet Imaging and AI Powered Big Data Processing of Live Stem Cell-Derived Organoids"

New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue-scale 4D cell biology but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome- edited human embryonic stem cells, which were differentiated into intestinal epithelial organoids. Lattice light-sheet imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70 × 60 × 40 μm xyz) at 5.7 s/frame. We developed an open-source data analysis package termed pyLattice to process the resulting large (∼60 Gb) movie data sets and to track clathrin-mediated endocytosis (CME) events. We then expressed fluorescent protein fusions of actin and tubulin in genome-edited induced human pluripotent stem cells, which were differentiated into human cortical organoids. Using the AO-LLSM mode on the new MOSAIC (Multimodal Optical Scope with Adaptive Imaging Correction) allowed us to image neuronal migration deep in the organoid. We augmented pyLattice with a deep learning module and used it to process the brain organoid data.

January 23, 2020

1pm - 2pm
154 BSRB

Dan Cohn, PhD
Professor, Molecular, Cell & Developmental Biology and Orthopaedics Surgery

"The TRPV4 Skeletal Dysplasias: Genetics, Mechanism, Mouse Models and Prospects for Therapy"

OHRC Musculoskeletal Research Seminar Series
Seminar title: The TRPV4 Skeletal Dysplasias: Genetics, Mechanism, Mouse Models and Prospects for Therapy

Speaker: Dan Cohn, PhD
Professor, Molecular, Cell & Developmental Biology
and Orthopaedics Surgery,
UCLA College of Letters & Sciences,
David Geffen School of Medicine at UCLA
Contact – Gloria Kiel –

January 23, 2020

5pm - 6pm
27-200C CHS

Andrew Goldstein, PhD
Assistant Professor-in-Residence, Molecular, Cell & Developmental Biology and Urology; UCLA College of Letters & Sciences and David Geffen School of Medicine at UCLA

"Prostate Aging, Tumorigenesis and Metabolism"