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I'm a graduate student at UC Berkeley in the Department of Molecular and Cell Biology.

I'm interested in the use of self-patterning organoids to recapitulate developmental events unique to humans and to model complex tissue architecture. I have training in stem cell biology, 2D and 3D culture systems, molecular biology, and bioinformatics.

Learn more about me below:

Education & Training

Education
Academic
    University of California, Berkeley

    Ph.D. (in progress), Molecular and Cell Biology

    2022 - present
    Tufts University

    M.S., Biology (Genetics, Molecular and Developmental Biology)

    2018 - 2020
    Brown University

    Sc.B. (Honors), Neuroscience

    2008 - 2012
Training
Research Appointments
Graduate Student Researcher (GSR)@ University of California, Berkeley
Principal Investigators: Megan Martik, Ph.D. (Assist. Prof) & Dirk Hockemeyer, Ph.D. (Assoc. Prof)
Present
I'm studying the role of cardiac neural crest cells in the the human heart using hiPSC and hESC-derived cardiac organoids (cardioids). Neural crest cells, a migratory population of cell, comes into an otherwise majority mesoderm-derived tissue during development to form structures such as major arteries, septa, and valves. They also differentiate into a small subset of cardiomyocytes. Cardiomyocytes derived from this stem cell population have been shown to respond to injury in teleost fish — de-differentiating, proliferating, and re-differentiating to reform the lost tissue. I'm studying the gene regulatory networks that govern this species-specific regenerative process in a human cardioid/NCC co-culture system that I am developing, multiomics, and CRISPRa/i.

Fulbright Research Fellow@ Institute of Molecular Biotechnology - Austrian Academy of Sciences (IMBA)
Principal Investigator: Jürgen Knoblich, Ph.D. (Prof of Synthetic Bio; IMBA Scientific Director)
Mar 2021 - Aug 2022
I worked with cerebral organoids (three-dimensional tissues that model the core cellular makeup and cytoarchitecture of the brain) to study the role of exogenous and endogenous extracellular matrix (ECM) in dorsal-ventral patterning, polarization of the neuroepithelium and neural rosette, generation of proper cortical cytoarchitecture, and specification of different cell populations.
I also used cerebral organoids to examine how haploinsufficiency of ARID1B, a subunit of the SWI/SNF chromatin remodeling complex, can lead to abnormal development of callosal projection neurons (CPN) and to corpus callosum agenesis. We uncovered abnormal axonal pathfinding and impaired axonogenesis in various mutants of ARID1B.
Research Associate@ Massachusetts Institute of Technology (MIT)
Principal Investigator: Mriganka Sur, Ph.D. (Newton Prof of Neuroscience; Simon Center Director)
Sep 2016 - Mar 2021
I worked with cerebral organoids to elucidate early neurodevelopmental deficits that arise in autism spectrum disorders, specifically in the X-linked disorder Rett Syndrome (RTT). In organoids produced from Rett patient-derived induced pluripotent stem cells (iPSCs) harboring either mutant MeCP2 or their respective isogenic wild-type copy (obtained from X-inactivated clones or gene editing), we showed that MeCP2 deficiency was associated with an increase in neural progenitor proliferation and concomitant decrease in neurogenesis and neuronal migration and maturation. This phenotype was due to dysregulation of the AKT/ERK pathway. My project was to further investigate the molecular mechanism of this migration deficit. Using proteomic techniques, I found an increase in GSK3β/β-catenin signaling, downstream of AKT, in RTT organoids. Using multi-photon and confocal microscopy of virally labeled and immunostained organoids, I also found that, although the morphology and polarity of radial glial cells are mostly preserved, adhesion molecules were dysregulated and neuronal migration trajectory and speed were disrupted in MeCP2-mutant organoids.
Research Assistant@ Massachusetts General Hospital/Harvard Medical School (MGH/HMS)
Principal Investigator: Sanja Sever, Ph.D. (Associate Prof of Medicine)
Sep 2013 - Sep 2016
I studied the protein dynamin and its interactions with actin and other scaffolding proteins. IS discovered that when dynamin was promoted to oligomerize into higher-order structures, it was protected from cleavage by calpain, a protease associated with dendritic pruning. Through confocal and electron microscopy, I then demonstrated that these dynamin oligomers can influence the architecture of the actin cytoskeleton by both stimulating actin polymerization and crosslinking/bundling actin filaments. I also demonstrated through biochemical assays that this stimulation was direct, as genetic manipulation of cytoskeletal adaptor proteins had no effect on the ability of dynamin oligomers to influence the actin cytoskeleton. Finally, to bridge cell structure to cell function, I examined what effect different dynamin mutants and dysregulated cytoskeletal dynamics had on not just endocytosis and intracellular trafficking (canonical roles of dynamin) but also cell adhesion and migration.
Research Assistant@ Brown University
Principal Investigator: Wayne Bowen, Ph.D. (Upjohn Prof of Pharmacology)
May 2011 - Aug 2013
Because calcium can mediate a diversity of cellular responses, cells prevent off-target effects by utilizing the duration, localization, and magnitude of calcium signals to specify certain outcomes. My project was to resolve the paradoxical observation that some classes of Sigma-2 (σ2) Receptor ligands could lead to cell death while others lead to cell proliferation. Through pharmacological manipulation and calcium imaging, I discovered that σ2R activation induced changes in sphingolipid metabolism, which, in turn, encoded different phasic calcium signatures. Therefore, depending on the kinetics and binding affinities of the ligand, there can be a metabolic shift to either a family of sphingolipids that produced a transient rise in calcium responsible for cell growth or to another family of sphingolipids that produced a latent and sustained rise in calcium responsible for cell death/apoptosis.

Publications

Scientific Publications
Peer-reviewed Articles
Articles @ IMBA - Knoblich lab
“Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous ECM.” Martins-Costa C, Pham VA, Sidhaye J, Novatchkova M, Peer A, Möseneder P, Corsini NS, Knoblich JA.
The EMBO Journal, 2023 Oct. Epub 2023 Oct 16. doi: 10.15252/embj.2022113213

Articles @ MIT - Sur lab
“Label-free three-photon imaging of intact human cerebral organoids: tracking early events in brain development and deficits in Rett Syndrome.” Yildirim M*, Delépine C*, Feldman D, Pham VA, Chou S, Ip J, Nott A, Tsai LH, Ming GL, So P, Sur M.
eLife, 2022 Jul. Epub 2022 Jul 29. doi: 10.7554/eLife.78079
“GSK3-β inhibitor CHIR 99021 modulates cerebral organoid development through dose-dependent regulation of apoptosis, proliferation, differentiation and migration.” Delépine C, Pham VA, Tsang HWS, Sur M.
PLOS One, 16(5), 2021 May. Epub 2021 May 05. doi: 10.1371/journal.pone.0251173
“A low-cost 3D printed microfluidic bioreactor for simultaneous live-organoid imaging and long-term culture with drug delivery support.” Khan I*, Delépine C*, Tsang HWS, Pham VA, Sur M, Prabhakar A.
Biomicrofluidics (American Institute of Physics), 15, 024105. 2021 Apr. Epub 2021 Apr 06. doi: 10.1063/5.0041027
  • Highlighted in New Scientist (link) and EurekAlert (link)

Articles @ MGH/HMS - Sever lab
“Pharmacological targeting of actin-dependent dynamin oligomerization ameliorates chronic kidney disease in diverse animal models.” Schiffer M*, Teng B*, Gu C*, Shchedrina VA, Kasaikina M, Pham VA, Hanke N, Rong S, Gueler F, Schroeder P, Tossidou I, Park J, Staggs L, Haller H, Erschow S, Hilfiker-Kleiner D, Wei C, Chen C, Tardi N, Hakroush S, Selig M, Vasilyev A, Merscher S, Reiser J, Sever S.
Nature Medicine, 21:601-9. 2015 Jun. Epub 2015 May 11. doi: 10.1038/nm.3843
  • Highlighted in Nature Reviews Drug Discovery (link) and Nature Reviews Nephrology (link)
“Regulation of dynamin oligomerization in cells: the role of dynamin-actin interactions and its GTPase activity.” Gu C, Chang J, Shchedrina VA, Pham VA, Hartwig JH, Suphamungmee W, Lehman W, Hyman BT, Bacskai BJ, Sever S.
Traffic, 15:819-38. 2014 Aug. Epub 2014 Jun 24. doi: 10.1111/tra.12178
Pre-prints and Manuscripts
Pre-prints @ IMBA - Knoblich lab
“ARID1B controls transcriptional programs of axon projection in the human corpus callosum.”
Martins-Costa C, Pham VA, Wiegers A, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Moeseneder P, Stuempflen M, Chow SA, Seidl R, Prayer D, Hoeftberger R, Kasprian G, Ikeuchi Y, Corsini N, Knoblich JA.
BioRxiv, 2023 May. doi: 10.1101/2023.05.04.539362
“Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous ECM.” Martins-Costa C, Pham VA, Sidhaye J, Novatchkova M, Peer A, Möseneder P, Corsini NS, Knoblich JA.
BioRxiv, 2022 Dec. doi: 10.1101/2022.12.06.519271

Awards

Honors*, Fellowships, and Scholarships
2023 – 2025
NIH/NIGMS T32 Predoctoral Training Program in Genetics †
(Genetic Dissection of Cells and Organisms, GDTP)
2020 – 2021
J. William Fulbright Open Study/Research Award (Fulbright scholar) †
Fulbright-Austrian Marshall Plan Foundation Award in Science and Technology †
2018 – 2020
Tufts Graduate School of Arts & Sciences (GSAS) Merit Scholarship ‡
2019
Tufts Graduate Student Travel Award
2016
American Association for the Advancement of Science (AAAS)/Science Program for Excellence in Science *
2012
Brown University Departmental Honors in Neuroscience *
2008 - 2012
Brown University Institutional Scholarship ‡
Albert L. Barbour Memorial Scholarship ‡
2008
Elaine R. Croston Scholarship ‡
Massachusetts Department of Education (DoEd) Stanley Z. Koplik Certificate of Mastery (declined) * ‡

Science Media

Videography
Digital Video and Editorial Intern @ NOVA - Public Broadcasting Service (PBS)

In the Fall of 2018 I had the opportunity to work on the Digital Video team at NOVA, the popular science programming series produced by the PBS member station, WGBH. There, I researched, fact-checked, and wrote articles and scripts; created graphics and animations; and developed and edited videos. The videos I worked on were part of NOVA’s News & Analysis project funded by the Diversity and Innovation Grant (DIG), which aims to produce timely web video and social media content that considers science in the news cycle. While working on smaller digital videos and articles throughout my internship, my long-term project was an interactive multimedia website that served as a companion piece to a NOVA documentary on the opioid crisis. For this project, I not only assisted in media production, I also conducted research on the neurobiological mechanism underlying addiction, given my background in neuroscience. I also transcribed and summarized interviews for the human-interest angle of the project.

Why Hurricane Florence Caused So Much Flooding
Fireproofing Our Future through Better Design

Teaching

University/College Level
University of California, Berkeley
BIO 1A - General Biology
Fall 2023
University level course that covers core concepts in biology – structure and function, transformation of energy & matter, information flow (central dogma), systems, and evolution.
  • Lead weekly sections, which include lecture review and practice problems
  • Hold office hours, moderate discussion forum, and grade exams/assignments
Harvard University
BIOS 50 - Foundations of Neuroscience
Student evaluation: 4.8/5.0
Summer 2021
University level course that covers basic concepts in neurobiology – cells and gross anatomy; electrical signaling, synaptic transmission, ion channels, and neurotransmitters; sensory and motor systems; cell and circuit development; memory, emotions, and mental illness.
  • Lead weekly sections, which include lecture review, practice problems, and discussion/presentation of primary literature
  • Hold office hours, moderate discussion forum, and grade exams/assignments
BIOS 52 - Neurobiology of Pain
Student evaluation: 4.8/5.0
Fall 2021
University level course that explores neurobiological nociceptive/sensory systems, peripheral & central pain neural circuits, molecular basis of pain pathologies, pharmacological & non-pharmacological treatments.
  • Lead weekly discussion section; help students prepare presentations of primary literature
  • Hold office hours and grade exams/assignments
Pre-college Level
MIT Museum
MIT Museum
.
  • Co-taught and facilitated seminars in robotics, genetics and cell biology, and structural engineering for school groups and the general public
  • Taught basic principles of programming through the Lego Mindstorms NXT and NXT-G programming environment developed by the MIT Media Lab and the Lego group
  • Led guided hands-on activities with Lego DNA kits and digital models to teach DNA replication and the flow of genetic information from DNA to RNA to protein
  • Designed, prototyped, and delivered demonstrations and activities teaching optics and its interface with holography

Information

Links & Profiles
Contact & Connect

vincent dot pham @ berkeley.edu
@vincent_a_pham
LinkedIn

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