Upcoming Seminars

ZOOM Link

https://ucsc.zoom.us/j/91784487738?pwd=bXZMRVFHYmRzQVF3WDlhaGJ2cW9GZz09

Meeting ID: 917 8448 7738

Passcode: 625688

Speaker

Laura Cook, Binghamton University - "Mucosal colonization by pathogenic streptococci"

Laura has been an Assistant Professor at Binghamton University since the Fall of 2018. Her postdoctoral studies focused on quorum sensing in streptococci and the role of cell-cell signaling in colonization of the host. Projects like this have influenced the work currently done in her lab.

Registration:
Register for the webinar here

Speakers

(1) Ed Monuki, M.D., Ph.D.

(2) Albert La Spada, M.D., Ph.D.

Title

"Did You Know Your Brain Floats? Molecules, Cells, and Fluids That Create a Healthy Brainyard Pool"

About the Speakers
Ed Monuki - After growing up in Los Angeles, Dr. Monuki received his BS from MIT, then his MD and PhD degrees from UC San Diego. As a PhD student, he worked on developing glial cells with Greg Lemke at the Salk Institute. He then moved to Boston for residency and fellowship training in Anatomic Pathology and Neuropathology. While attending at the Brigham & Women’s Hospital and Boston Children’s Hospital, he carried out postdoctoral research on the developing forebrain with Chris Walsh at the Beth Israel Deaconess Medical Center before joining UCI in 2001.

Albert La Spada - Dr. La Spada graduated Summa Cum Laude from the University of Pennsylvania with a degree in Biology in 1986. As a M.D. - Ph.D. student at the University of Pennsylvania School of Medicine, he identified the cause of X-linked spinal & bulbar muscular atrophy (SBMA) as an expansion of a trinucleotide repeat in the androgen receptor gene. As the first disorder shown to be caused by an expanded repeat tract, this discovery of a novel type of genetic mutation led to the emergence of a new field of study.

WHEN
Thursday, December 1, 2022 - 12:00pm

WHERE

Location: PSB 305 and Zoom - https://ucsc.zoom.us/j/98347094038?pwd=WGZvUUVlbm9MaE91NEd3MkZDZ1ZWZz09; Passcode: 628845

SPEAKER

Lucas Seninge, PhD Candidate, Biomolecular Engineering & Bioinformatics; Advisor: Joshua Stuart

Title: Integrating Prior Biological Knowledge And Machine Learning For Single-Cell Transcriptomics Analysis

Abstract: Single-cell RNA sequencing (scRNA-Seq) has offered a unique window into studying cellular identity at unprecedented scale and resolution. However, the process of revealing this cellular identity remains challenging. For example, the annotation of each assayed cell with a cell type label indicating its functional identity still relies on manual examination, which is rate-limiting and poses reproducibility issues. Similarly, inferring the activity of gene regulatory pathways specifying cell state relies on methods designed for bulk RNA sequencing data and do not make use of the important amount of data generated by single-cell experiments. Here, I describe my work to combine prior biological knowledge about cellular entities contained in curated databases and machine learning to shed light on the cellular identity of single cells.

Specifically, I developed statistical frameworks for the automated annotation of single-cell transcriptomes with cell type labels by integrating prior cell ontology information and cell type-specific marker gene sets. Then, I developed a method to infer pathway activity in single cells by using recent progress in the field of deep generative modeling as well as prior knowledge from gene annotation databases. I discuss potential future direction to design generative model architectures to approach the more ambitious task of modeling targeted perturbation of pathways or transcription factors to perform in-silico experiments and alter cellular state at the single-cell level. This body of work contributes to the growing literature of methods incorporating prior knowledge about biological systems into complex machine learning frameworks, as well as highlights the challenges met in such integration.

Location:
Sinsheimer Building, Room 123, 4:00PM

ZOOM Link

https://ucsc.zoom.us/j/99660744134?pwd=bmc0OHJ3aXlSMWR4d1VEcnJUbDlBUT09

Speakers

(1) Michael Lawson, Puglisi Lab, Stanford - “Basis of Speed and Fidelity in Eukaryotic Translation Termination"

(2) Nicole Martinez, Martinez Lab, Stanford - "Uncovering new functions of RNA modifications in mRNA processing”

Location:
Physical Sciences Building, Room 240, 3:30 - 5:00PM

Speakers

(1) Anna Gillespie, Ph.D., Frank lab; UCSF - “A novel approach to modulating hippocampal memory replay”

(2) Max Turner, Ph.D., Clandinin lab; Stanford - “Self motion signals dynamically shape a population code for visual feature detection in Drosophila”

About the Speakers
Anna Gillespie hails from Loren Frank's lab at UCSF, where she is currently finishing up her post-doc work, however we have the distinct pleasure of hosting Anna just before she starts her own lab at University of Washington. She is actively recruiting graduate students, post-docs, and technicians, so please encourage your lab members and students to connect with her if they are interested in any of those positions. Her talk is entitled, "A novel approach to modulating hippocampal memory replay".

Max Turner comes to us from Thomas Clandinin's lab at Stanford University. He will be presenting a talk titled "Self motion signals dynamically shape a population code for visual feature detection in Drosophila" which will feature data primarily from this preprint perhaps with some new data from recent months added in.

Registration: https://www.activemotif.com/chromatin-club-bay-area

Invited Speakers:

(1) Bradley Colquitt, Assistant Professor MCD
"Gene Regulatory Mechanisms of Birdsong Neural Circuit Development"

(2) Albert Li - Jiangbin Ye Lab, Stanford University
"Metabolic and Epigenetic Reprogramming During Breast Cancer Progression"

(3) TBD - UC Davis
Presentation Title TBD

In Vivo Imaging Of Human Neuronal Development At Single Cell Resolution In Chimera Models
Yi Zuo, Ph.D., UCSC; Krishnan Padmananbhan, Ph.D.

When: Wednesday, Oct 26, 1:05 PM, Biomed200

While the structural changes that human neurons undergo during development are key to understanding neural circuit function, there are currently limited ways to study these dynamic processes. To address this challenge, we developed a novel method for time-lapse in vivo two-photon imaging of GFP-labeled human neural precursor cells (hNPCs) derived from induced Pluripotent Stem Cells (iPSCs) transplanted into the visual cortex of a mouse. By imaging over both short periods (~1 hour) and long intervals (~1 week), we were able to uncover features of hNPC proliferation, migration and growth dynamics across different times scales of development for up to 8 months. In transplants with large numbers of engrafted hNPCs, we observed extensive cell proliferation and migration. Migrating cells tended to travel towards and accumulate around blood vessels, with neurites surrounding and ultimately ensheathing these vessels. By contrast, in transplants with small numbers of engrafted hNPCs, we could identify individual neurites that were tracked for up to 8 months. In these engrafts, we observed extensions and retractions of neurites, often as great as 100s of um within a 24-hour period. Furthermore, neurites tended to form fascicles, with extensions favoring the direction of established neurites, suggesting that cells that extend together, stabilize together. Interestingly, these processes often grew along blood vessels, suggesting that the host vasculature plays a critical role in guiding development, possibly as an energy source to supporting both migration and neurite maturation. Taken together, our data allowed us to track the diversity of developmental programs, including proliferation, migration, and neurite maturation from the hNPC state to putative cortical neurons. Our new method thus provides a platform for modeling both normal human development as well as modeling developmental and psychiatric disorders.

In Vivo Imaging Of Human Neuronal Development At Single Intersectional Environmentalism: The key to Fighting Racism and Climate Change Through a Lens of Science and Community Building

Emily Pinckney, Marine Biologist, Science Equity advocate, Diversity, Equity, and Inclusion Strategist, Policy Analyst, Intersectional Environmentalist Thought Leader

Tacoma Commission

When: Wednesday, Oct 26, 1:05 PM, Nat Sci Annex 101 + Zoom
https://ucsc.zoom.us/j/94395754442?pwd=MG9TODh4dWNZWEVSSEJib3NNTmJpUT09

Meeting ID: 943 9575 4442

Passcode: MCD

Cell-type-specific roles of androgen receptor in prostate homeostasis and cancer
Zhu Wang, Department of MCD Biology, UC Santa Cruz

When: Friday, Oct 21, 12-1:05 PM, Nat Sci Annex 101 & Zoom

Zoom Link: https://ucsc.zoom.us/j/94223430506?pwd=dXBHdkpSejNvMVI4Y0RjUElKcjZ4UT09

Meeting ID: 942 2343 0506

Passcode: MCD

Intellectual Property Wars: The Battle for Access to Medicines
Tahir Amin, LL.B., Dip. LP; Anna Maria Barry-Jester

When: Tuesday, Oct 18, 7:00 PM, Kuumbwa Jazz Center

REGISTER HERE

Genetic insights into quality control of gene expression
Joshua Arribere, Ph.D., Assistant Professor of MCD Biology, UC Santa Cruz

When: Friday, Oct 14, 12-1:05 PM, Nat Sci Annex & Zoom

Zoom Link:https://ucsc.zoom.us/j/95430874685?pwd=T1FNRm1hUStEb1FrZ1JsRnB2cFo4dz09

Meeting ID: 954 3087 4685

Passcode: MCD

Cell Cycle Dynamics that Ensure Genome Stability
Jeanette Gowen Cook, Ph.D.
Professor and Chair, Department of Biochemistry & Biophysics, UNC School of Medicine, Professor, Department of Pharmacology
Member, Lineberger Comprehensive Cancer Center

When: Monday, Oct 10, 12-1:05 PM, Nat Sci Annex & Zoom

Host: Doug Kellogg

Zoom Link:

https://ucsc.zoom.us/j/97724169680?pwd=QzBRTlg5UnNkaUVoZy9GYnl5Mis4QT09

Meeting ID: 977 2416 9680

Passcode: MCD