CORE Grant - Vision Science at UC Berkeley

Core Grants, National Eye Institute (NEI): The primary objective of Core Grants for Vision
Research is to provide groups of investigators who have achieved independent National Eye Institute
(NEI) funding with additional, shared support to enhance their own and their institution's capability
for conducting vision research.
Secondary objectives of this program include facilitating collaborative studies and attracting other
scientists to research on the visual system.
Core Grants are subdivided generally into discrete units or modules, with each devoted to a specific
activity that would be impractical or less-efficient to support on an individual research project grant.
The primary purpose of each module is to support a service or resource that enhances or facilitates
the research efforts of a group of investigators, each having independent NEI funding. Some sharing
of Core Grant resources and services with other NIH-funded collaborators and with investigators new
to vision research is encouraged. For more about NEI Core grants, see CORE.
There are several modules currently supported by the CORE Grant: Gene Delivery Module,
Microscopic Imaging Module, Software Development Module, and Translational Research Module.
These modules can be shared by various groups. The Modules cooperate with one another, and they
are also designed to introduce Vision Science researchers to some of the unique resources that are
available on the UC Berkeley campus, including facilities in nanotechnology, fMRI, and other
optical imaging resources. The contact information for each module is given below, along with links
to more information about the purpose of each module.
Gene Delivery Module
Contact: Mei Li , Room 592, Minor Hall, School of Optometry
Email: [email protected]
Imaging & Instrumentation Module
Contact: Chris Gainer, School of Optometry
Email: [email protected]
Software Module
Contact: Akhila Raman, Room 587, Minor Hall, School of Optometry
Email: [email protected]
Translational Research Module
Contact: Zakia Young, School of Optometry
(510) 642-0687
Email: [email protected]
The main goal of this Module is to provide DNA constructs and viral vectors for expressing genes in
tissues of the visual system, enabling precise molecular manipulation of proteins involved in visual
function. The Gene Delivery Module is the only campus facility that provides viral vectors for
introducing genes in vivo.
The viral vectors help deliver genes to the area of interest using viruses as carriers — Adeno
Associated Virus (AAV) or Lentivirus (LV). These viruses are replication incompetent viruses. They
can infect target cells and transmit target genes; however, they cannot replicate within target cells
because the viral structure genes are absent. These recombinant viruses have reduced or no immune
response in the host and have cloning capacity of up to 4.7 kb for AAV and up to 10 kb for LV. The
recombinant viral vectors are packaged by helper virus free approaches, e.g. triple plasmids
transfection into HEK293T cells to generate AAV vectors. The triple plasmids are transgene plasmid,
RC (rep & cap) plasmid and helper plasmid. Individual researchers submit their own transgene
plasmids, in which gene of interest and AAV inverted terminal repeats (ITRs) are included. The
GDM provides the RC plasmids and helper plasmids required to generate the serotypes of viral
vectors that meet the individual researcher’s needs.
Once the transgene plasmid (100-200 μg) has been submitted to the GDM, the GDM will start
culturing a large amount of HEK293T cells; packaging and purifying viral vectors with triple
transfection, iodixanol gradient ultracentrifugation and affinity column purification; and at last,
measure the viral titers by fluorescent probe labeled quantitative PCR. It takes around three to four
weeks to complete generating 1-2 purified viral vectors with the higher titer of 10^11 to 10^14 vg/ml
(viral genomes per ml) and a total volume of 150-200 μl for in vivo use. These recombinant viral
vectors have reduced or no immune response in the host. These viral vectors generated in the GDM
are expected to provide good efficiency. The transgene expression depends on the promoter used, the
target cells and the serotype used.
For more details or questions please contact:
Mei Li, M.D. Ph.D.
Gene Delivery Research Specialist
Vision Science Core, Gene Delivery Module
University of California, Berkeley
School of Optometry
592 Minor Hall
Berkeley, CA 94720
[email protected]
The Software Module provides custom programming support for physiological, psychophysical, and
brain-imaging applications that are important for understanding visual system function. The Software
Development Module is unique in providing new software to solve stimulation, acquisition, and
analysis problems that have existed for years, but cannot be solved with commercially available
The module supports the development of shared software tools (and some computer hardware) that
will be of use to many members of the UC Berkeley Vision Science community. Development
focuses in a variety of areas, including Eye Monitoring Tools, Display Tools, Neuroimaging Tools,
and Psychophysics/Physiology Software Development.
Examples of software development in this module include (a) Design and implementation of
software in Matlab and C language; (b) Signal processing algorithms for vision science and
neuroscience projects; (c) Eye Tracker data analysis, (d) Pupil tracking in wavefront sensor; (e)
Retinal motion tracking; (f) Cardiac, respiratory and ultrasound data analysis; (g) neural spike sorting
software; (h) Monitor gamma estimation by visual contrast method; and (i) orientation sensor
For more details or questions, please contact:
Akhila Raman
Room 587, Minor Hall
School of Optometry
University of California
Berkeley, CA 94720-2020
Email: [email protected]
The School of Optometry’s newest CORE Unit is the Translational Research Core Facility (TRCF).
The TRCF has been established to provide research design and implementation, in conjunction with
organizational and statistical resources, to support investigators in their patient-oriented translational
research. The TRCF has on staff a Clinical Research Coordinator who can facilitate IRB submissions
and assist with subject recruitment. The Newest member of the TRCF staff is Dr. Shaokui Ge, a biostatistician.
Shaokui has a background in quantitative biology, specializing in data analysis for biomedicine and
environmental health related issues. He earned his PhD in quantitative biology from Chinese
Academy of Sciences in Beijing, China. From 2011 to 2013, Shaokui was an NIH-sponsored Senior
Training Fellow for both the Departments of Biostatistics and Epidemiology at the University of
Washington. He served as a Statistical Research Associate for Fred Hutchinson Cancer Research
Center in Seattle. Through his education and training, Shaokui has been able to develop and hone
his skills in following data analysis areas: sample size calculation and power analysis, generalized
linear models, longitudinal data analysis, categorical data analysis, survival analysis, classification
and prediction, and infectious disease modeling. Shaokui is excited to join the TRCF and is looking
forward to getting to work on his first TRCF project. If the TRCF’s staff can be of assistance to you,
please call (510) 642-0687 or email [email protected] with any questions.
Zakia Young
Clinical Research Coordinator
Translational Research Core Facility
School of Optometry
Telephone: (510) 642-0687
Email: [email protected]
Shaokui Ge
Translational Research Core Facility
School of Optometry
Telephone: (510) 642-0687
Email: [email protected]
Dennis M. Levi, OD, MS, PhD, FAAO
Professor of Vision Science and Optometry
Email: [email protected]
Meng C. Lin, OD, PhD, FAAO
Associate Professor, Clinical Optometry and Vision Science
Email: [email protected]
The Microscope Imaging Module provides expert technical support for the assembly, modification,
and use of advanced microscopic system for imaging cells and tissues of the visual system. the
Microscopic Imaging Module is unique in providing technical expertise for users to customize their
own microscopes for functional imaging, including in vivo. It also serves to subsidize the very high
hourly costs of shared-use microscopes. The three main goals of the module are to:
Encourage Vision Science researchers to utilize existing advanced imaging methods on
Customize existing microscopes to satisfy individual research needs.
Assemble new microscopes from component parts to bring advanced multiphoton imaging
technologies to the Core.
Please consult the CORE Microscopy Specialist, Chris Gainer ([email protected]) before using
the facility so that he can advise you of available microscopes best suited for your research needs.
2 Locations: 251 Life Sciences Addition, 361 Li Ka Shing Center
Zeiss LSM 780 NLO AxioExaminer
Zeiss LSM 710 AxioObserver
Zeiss LSM 510 NLO AxioVert with FLIM
Zeiss LSM 510 Meta NLO AxioImager
Zeiss LSM 510 META AxioPlan
Zeiss 5‐LIVE AxioSkop
Andor/Nikon Spinning Disk
3i Upright SDC with SLM
Nikon PALM with AO and SDC
3iSutter In Vivo SLM
Zeiss AxioZoom Fluorescent Stereoscope
Leica Fluorescent Stereoscope
TRAINING – You must register for training if this is your first time using the MIC. Register for
training on the MIC Training site at Remember to mention
“Opto‐Core” as your billing account to ensure that your training and usage costs are subsidized.
RESERVING EQUIPMENT – All equipment can be reserved via online calendars at
BILLING – To ensure your costs are subsidized, please mention the “Opto‐Core” account when
registering for training and usage. The Special Projects Coordinator, Donna Lee, at the School of
Optometry will need to receive your bills to process the subsidy. If there’s any confusion at the MIC
about account access and billing to Opto‐Core, please have them contact Donna Lee
at [email protected]
*Please note that a new iLabs training and reservation system will roll out sometime in 2014
replacing the current sign‐up methods above.