Year 3

Grant Number: CL1-00519
PI Name: David V. Schaffer
Project Title: The Berkeley Human Embryonic Stem Cell Shared Research Laboratory
a. Scope of Research Taking Place in the Facility
The central mission of our Berkeley CIRM Shared Stem Cell Facility (SSCF) is to provide our East Bay users with knowledge, expertise, training, and equipment to advance scientific knowledge of human embryonic stem cells, as well as other stem cells. Our facility focuses on providing imaging, flow cytometry, and sorting.
To date, 90 students and postdoctoral fellows from the laboratories of 21 PIs use the facility. We list some examples here:

Irina Conboy (BioE). The Conboy lab studies the intersection of aging and stem cell science. If age-imposed decline in the regenerative capacity of stem cells was understood, the debilitating lack of organ maintenance in the old could be ameliorated and perhaps, even reversed. They used the SSCF confocal microscope and flow cytometer in their studies.

Paliwal P, et al. (2012) Age dependent increase in the levels of osteopontin inhibits skeletal muscle regeneration. Aging 4(8):553.

Paliwal P, Conboy IM. (2011) Inhibitors of tyrosine phosphatases and apoptosis reprogram lineage-marked differentiated muscle to myogenic progenitor cells. Chem Biol 18(9):1153.

Sanjay Kumar (BioE). The Kumar Lab’s interests center around the macromolecular basis of cell shape, mechanics, and adhesion, with special emphasis on the nervous system. Specifically, they seek to understand how elements of the cytoskeleton and adhesion machinery physically interact to form a three-dimensional architecture that drives cell shape and shape-dependent behavior and transduces biochemical signals. The SSCF swept field confocal was used to document changes in soft ECMs (MacKay). This microscope was also used by researcher Amit Pathik, who developed paradigm for investigating matrix regulation of invasion (Pathak).

J. L. MacKay, et al. (2012). A genetic strategy for the dynamic and graded control of cell mechanics, motility, and matrix remodeling. Biophysical Journal 102: 434.

A. Pathak and S. Kumar (2012). Independent regulation of tumor cell migration by matrix stiffness and confinement. PNAS 109 (26): 10334.

David V. Schaffer (ChemE, BioE, and Helen Wills Neuroscience Institute). One recently-completed CIRM-funded project involved directed evolution and engineering of new viral gene delivery vehicles capable of highly efficient delivery to human embryonic and induced pluripotent stem cells. This Adeno-associated virus (AAV) variant study involved heavy usage of the flow cytometer and the ImageXpress Micro to quantitate the number of successfully infected (and gene-targeted) cells and colonies (Asuri). In a current CIRM-funded project, we are engineering synthetic materials for the scaleable expansion and dopaminergic differentiation of human ESCs and iPSCs (Keung). Also, we are developing optogenetic tools to investigate signaling pathways involved in stem cell fate decisions (Bugaj). Finally, we discovered a novel signaling pathway that regulates the differentiation of adult neural stem cells into neurons (Ashton).

Asuri, P., et al. (2012) “Directed Evolution of Adeno-Associated Virus for Enhanced Gene Delivery and Gene Targeting in Human Pluripotent Stem Cells.” Molecular Therapy 20:329.

Bugaj, L.J., et al. (2013) “A Modular Optogenetic Platform for Inducible Protein Clustering and Signaling Activation in Mammalian Cells.” Nature Methods 10:249.

Keung, A.J., et al. (2012) “Soft Microenvironments Promote the Early Neurogenic Differentiation but not Self-renewal of Human Pluripotent Stem Cells.” Integrative Biology 4:1049.

Ashton, R.S., et al. (2012) “Astrocytes Regulate Adult Hippocampal Neurogenesis Through Ephrin-B Signaling.” Nature Neuroscience 15:1399.

b. Management and Use of the Laboratory
The overall management of the CIRM Shared Stem Cell Facility CIRM SSCF is coordinated by the management oversight committee.CIRM SSCF is managed by Dr. Mary West. The facility is open to qualified researchers from 9:30 am to 5 pm with controlled access afterhours.
c. Activities of Hired Laboratory Personnel
The CIRM Shared Stem Cell Facility is managed by Dr. Mary West who is responsible for training, equipment function and maintenance. CIRM is also funding an operator, Alma Faleros, for the BD FACS instrument, who works from 12:30 to 9:30pm.
d. Activities of the Oversight Committee
The oversight committee is composed of Facility Director David Schaffer and Profs. Kevin Healy, Song Li, Sanjay Kumar, Irina Conboy, and Astar Winoto. The committee meets regularly with the Facility Manager to obtain updates on the facility, discuss prioritization for new equipment purchases, facility finances, and policies for access.
e. Plans and Any Expected Changes for the Next Reporting Period
In the next year we anticipate busy operation of the facility with no major changes.