NIH
P30 - Core Grant For Vision Research
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I.
Imaging Support Module - computer-aided image analysis;
production of graphics for data analysis, presentation and
publication, including poster printing (see
more details)
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David
Copenhagen
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Matthew
LaVail
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Suling Wang,
514-0679, wangs@vision.ucsf.edu
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| II.
Molecular Biology and Genetic Analysis Service Module -
PCR and Southern blot genotyping of transgenic
animals and in situ hybridization (see
more details) |
David
Sretavan |
Todd
Margolis
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Elizabeth
Hawkes,
(415) 476-4135,
HawkesE@vision.ucsf.edu
Tony Tran,
(415) 476-4135,
TranT@vision.ucsf.edu |
III.
Confocal and Digital Microscopy Support Module -
digital data acquisition using confocal microscopy and optical
brightfield, darkfield, phase contrast or fluorescence microscopy
(see more details)
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Hilary
Beggs
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David
Copenhagen
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IV.
Computer/IT Support Module - assistance
in computer and information technology hardware and software
selection, installation, instruction in use, maintenance
and minor repairs, networking, and programming for custom
research needs (see more details)
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Jonathan
Horton
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Joan
O'Brien
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V.
Electrical and Machine Shop Service Module - design,
manufacture, maintenance and repair of specialized research
instruments and devices (see more details)
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Stephen
Lisberger
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Juan
Korenbrot
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The broad
objective of the Core Vision Research Grant is to facilitate study
of the structure, development and function of the visual system in
health and in blinding diseases, with the aim of preventing, mitigating
or curing such diseases through the application of the most sophisticated
available techniques, including the methods used in molecular biology
and molecular genetics.
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Details
on each module is found below:
Module
I. Imaging Support Module Details
please
see http://vision.ucsf.edu/graphicimagingmodule
A. Services Offered/Technician:
A key attribute of the Imaging Support Module is the availability of
the Module Technician, Suling Wang. Many of the Core investigators
have some experience with imaging software. However, few know many
of the fine details of the software and, consequently, do not use
it to its full capacity. Moreover, some Core investigators are unfamiliar
with the software applications. Ms. Wang is available to instruct
Core investigators and their junior colleagues in the best use of
software applications. With Ms. Wang’s extensive computer
graphic arts background this both improves the output images and
saves time for the research groups in learning the software applications.
She can also instruct in the use of all hardware that includes the
photo printer, slide scanner, flatbed ADF scanner, etc. Suling
is the sole operator of the poster printer. If you need to print
a poster, contact Suling as early as possible by email at wangs@vision.ucsf.edu,
or call 514-0679. Suling is here Wednesdays and Fridays.
There is also a website for this office with help guides and information
on hardware, software, and poster printing: http://vision.ucsf.edu/graphicimagingmodule
B. Module Resources:
-Laboratory/Office
The Graphics Imaging Module (GIM) is located in Room K-123 on the first
floor of the Koret Vision Research Laboratory Building. This 140 sq.
ft. room is dedicated to imaging functions only and is located between
the office and laboratory of the Module Director, Dr. David Copenhagen,
and the Principal Investigator (and former Imaging Module Director),
Dr. Matthew LaVail. The room contains a desk for the Module Technician,
four computer workstations with all of the necessary input and output
devices needed for graphic imaging (see below) and bookshelves. There
is storage space for printing supplies, software discs and manuals,
computer discs and administrative records.
-Computer Workstations:
The main components of the Module are four workstations, two Mac Pro
Intel computers with 30” cinema display monitors, one Mac Pro
G5 with a 20” monitor, and a Dell Precision with Windows XP
Pro. All are high quality products to enable you to work on graphic
data and prepare presentation and publication graphics. The installed
software includes Adobe Creative Suite CS4 (Photoshop, Illustrator,
Acrobat Pro, InDesign, Flash and Dreamweaver), Microsoft Office 2004
/ 2008 (Mac), Microsoft Office 2003 / 2007 (Windows), iWork ‘09,
Quicktime Pro, iMovie, Imaris 3D Imaging, Image J, Meta Morph, Premiere
6.0, Final Cut Pro, and Canvas 8, Each computer is networked to a
black & white laser printer and
Color Laserjet printer. Both printers can also be networked from the
labs.
Other input and output devices are:
• Workstation GIM3 (Mac G5):
This computer is primarily used by the graphics imaging technician
(Suling Wang), all website
editing software is installed --Flash, Dreamweaver, and InDesign.
• Workstation GIM1 (Mac Intel): HP Scanjet 8250. This scanner has an
Automatic Document Feeder (ADF), which can scan up-to 50 sheets of
paper at one time. This scanner is used to scan multiple pages into
a PDF. Imaris 3D software is also on this computer.
• Workstation GIM5 (Mac Intel): Epson Stylus R1800 Photo Printer. This
printer is used to produce prints for publication, or for data analysis.
The Canon CanoScan 8800F has an adapter to scan slides.
• Workstation GIM4 (Windows): Has Meta Imaging and an older version of
Imaris 3D software (4.2).
• MacBook (Intel): BootCamp is installed with Windows XP Pro. Adobe Creative
Suite CS4 and Microsoft Office are also installed.
In addition, there are two Panasonic LCD projectors to practice and
give (local) presentations. A Canon Powershot Digital Elph camera is
also available.
-Access, Location and Availability:
The door to the Imaging Module is secured with an electronic combination
lock. Individual access codes have to be assigned to personnel associated
with the labs of all the Core investigators by the technician. The
room is accessible 24 hours a day, 7 days a week. The electronic
lock system records each entry, so we can track usage. Sign-in logs
are attached to each computer workstation. The graphics Imaging Technician
(Suling Wang) is present from 9:00 am - 5:00 pm. If you have
questions outside this time you can send an email to; wangs@vision.ucsf.edu.
Personnel from other, non NEI-funded vision labs are also welcome
if and when the facilities are not in use by Core investigators or
members of their labs. In all cases, use of the facility is restricted
to research-related activities.
C. Module
Supervision: David Copenhagen, Ph.D., is an NEI-funded retinal neurobiologist
who supervisesthe Module. He has had substantial experience in computerized
graphics, and he has worked closely with the former Module Director,
Dr. Matthew LaVail, as Assistant Module Director in the previous
grant period in the design, construction, development of policies
and recruitment of technical staff for the Module. Dr. Copenhagen
is responsible for the fiscal and day-to-day activities of the Module,
as well as supervising the Module Technician. Dr Copenhagen’s
lab and office are very close to the main imaging facility on the
first floor of the Koret Vision Research Building. This proximity
enables Dr. Copenhagen to maintain close contact with the facility
and the Module Technician. As in the past, Dr. Copenhagen meets at
least once weekly with the graphics imaging Module Technician. In
addition, he meets with her any other time that problems arise or
questions about the operation of the module need to be discussed.
In the event that Dr. Copenhagen is out of town, Dr. LaVail, the
former Module Director and now, Assistant Director, is willing to
supervise and answer questions.
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Module
II. Molecular Biology & Genetic Analysis Service Module Details
A. Services Offered/Technician
This module is designed to assist our community of scientists in
the use of molecular and genetic analysis in vision research.
Specifically,
this module provides two essential services, 1) PCR & Southern
blot analysis/genotyping of transgenic and gene knockout animals, and
2) Analysis of gene expression using in situ hybridization methodologies.
The Module’s functions will be divided between two research
technicians. The two technicians know at least the basics of the
other's job, so
they can cover for each other for emergency work or monitor studies
in progress when one is away on vacation or due to illness.
-Genotyping Service: The genotyping services will require individual
investigators and lab personnel to submit a work request form. These
are collected and reviewed to determine the level of work from different
laboratories. Individual investigators requesting this service will
be instructed to provide the PCR protocol including primer information
and expected PCR results. Users are also requested to provide a short
description of the research project using module services. Results
are emailed or print versions are made available to investigators.
The module technician will be available to users for discussions of
the results, especially if any genotyping problems are encountered.
For each line of mutant animal, the details of the breeding program
are typically established and carried out by a member of a given lab
who is the primary investigator on that project. The Core Module technician
will perform tail tissue digests, DNA extraction, and PCR or Southern
blot genotyping necessary for the production of experimental animals
and the continual renewal of each breeding colony.
-In situ hybridization: The in situ hybridization service will help
with specific and effective use of probes in anatomical analyses of
cellular and subcellular localization of gene expression. Individual
investigators will supply the DNA template for probe synthesis as well
as a working in situ hybridization protocol. The module will then carry
out template synthesis, quality control and in situ hybridization.
Limited assistance with protocol optimization will also be provided.
B. Module Resources
-Access and Availability: The services provided by this module are
available to all Core vision researchers at UCSF. Vision investigators
requiring services provided by the module will contact the technical
personnel during working hours and submit samples for analysis.
-PCR/Southern blot genotyping: components of the module are housed
in a dedicated laboratory suite located on the first floor of the Koret
Vision Research Laboratory..
C. Module Supervision
The Module Director is David Sretavan, M.D., Ph.D., a NEI-funded independent
investigator whose areas of specialty are development of the visual
system, axonal injury and glaucoma. His laboratory has made extensive
use of multiple molecular techniques to investigate the basis of embryonic
retinal ganglion cell axon pathfinding during early development and
mechanisms of axon damage in glaucoma.
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Module
III. Confocal and Digital Microscopy Support Module Details
A. Services
Offered/Technician:
This module will provide dedicated space and technical support/expertise for
investigators using confocal microscopy in their studies using a Zeiss LSM
5 Pascal laser scanning confocal microscope which has been installed in dedicated
space at the F.I. Proctor Foundation. The technician, will provide training
on this complex instrument, technical tips, and general oversight of the Module.
Investigators familiar with the instrument would receive just a minimal amount
of training before being certified for its use. Others would require more extended
training. As time permits, Fred will also aid investigators in specific studies
and interface with the Zeiss technical support staff in helping investigators
take advantage of the advanced tools included in the microscope software package.
This module
will also serves those who need to acquire conventional brightfield,
darkfield or fluorescence digital images for data analysis or publication.
For this work, there is a fully equipped Nikon Eclipse E800 microscope
with a Diagnostic Instruments Spot digital camera and computer attached
in the same facility as the confocal microscope. The technician will
maintain the equipment and instruct Core investigators in its use
and, as needed, he will also instruct investigators in the basics
of brightfield and fluorescence microscopy, as well as the fine points
of digital imaging and data acquisition.
B. Module
Resources:
-Equipment:
The Zeiss LSM 5 Pascal laser scanning confocal microscope is equipped
with DIC optics, 10X, 20X and 40 X dry objectives and 40X and 63X
oil immersion objectives. In addition the microscope has lasers and
filter cubes for fluorescein, rhodamine and DAPI fluorescence imaging.
The microscope stage will accept both standard slides and cell culture
dishes. The microscope and imaging software is run on a Fujitsu computer
with internal CD read/write drive and the Windows 2000 operating
system. The objectives, filters and barriers are all computer controlled.
Image viewing and analysis is carried out with twin 22 inch flat
screen displays. A Nikon Eclipse E800 brightfield/fluorescence microscope
with a Diagnostic Instruments Spot digital camera and associated
PC Computer (Dell) is in the same facility. It is fully outfitted
with optics for all brightfield, darkfield and the most commonly
used fluorescence microscopy optics and filters.
-Laboratory/Office: The confocal microscope module will be located in Room
103 of the F.I. Proctor Foundation Building at 95 Kirkham St., immediately
adjacent to the Koret Vision Research Laboratory Building of the Beckman Vision
Center. This room, approximately 200 sq. ft. in size, was just recently remodeled
as a climate-controlled microscopy room for both confocal microscopy and conventional
fluorescence and bright field microscopy. There is a dedicated electrical circuit
specified for the confocal microscope and its associated lasers, as well as
a back-up electrical system to keep the system on line for 20 minutes (for
proper shut down to be carried out) in case of an unexpected break in electrical
service . The room also contains a isolation air table for the confocal microscope,
as well as newly installed ISDN lines, so that data can be downloaded to computers
in individual investigators’ laboratories. This lab space is immediately
adjacent to the laboratory of Dr. Todd Margolis, the Module Director.
-Access,
Location and Availability: Room 103 is located on the ground level
of the F.I. Proctor Foundation Building immediately adjacent to the
Koret Vision Research Laboratory Building of the Beckman Vision Center.
Access to the room is controlled by an electronic lock that keeps
track of the ID numbers of the investigators who make use of the
facility. A log book in the room will be used to track usage . Scheduling
will be carried out using an online calendar and database. The facility
and technical support will be made available to all vision researchers
on a reservation basis. Investigators who wish to make use of the
facility without technical support will first need to be “certified” by
the module director and support staff. The module Director will review
usage on a regular basis in order to assure fair and appropriate
use of the facility.
C. Module Supervision:
Hilary Beggs, Ph.D., an NEI-funded independent investigator, will supervise
this module.
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Module
IV. Computer/IT Support Module Details
See: http://www.ucsfeye.net/coreit
A. Services
Offered/Technician:
Technician/Programmer
is Matthew Feusner. Matt graduated from Cornell University in 2004
and 2005 with a B.S. and M.Eng. in Computer Science. Matt worked
with the Human-Computer Interaction Group at Cornell on eye-tracking
research for web usability. He has extensive coding experience in
a variety of programming languages including C/C++, Java, Matlab,
JSP, PHP, and Perl, and is always willing to learn new languages
if needed. As the core grant IT module programmer analyst, he is
available to help with any programming, or technical support needs
that you may have. The website for the IT module can be found at http://www.ucsfeye.net/coreit .
There is a procedure for filing work requests through the website.
His first priority will always be to address work requests as they
come in. You can also reach him by phone at 514-9338, or come by
his office in person in the Koret Vision Building, K335.
Matt can provide assistance with every aspect of computer technology. Below
are cited a few examples:
1. Assist with creation and programming of computer systems for conducting
laboratory research on the visual system. Develop systems for presentation
of visual stimuli, monitoring of subject responses, and acquisition of neuronal
responses.
2. Assist investigators with use of computers for data collection, analysis,
and display.
3. Advise on purchase of new computer systems, helping to chose components
(processor, memory, hard drives, monitor, graphics card, optical devices, network
card) that best meet the investigator’s needs.
4. Assist with installation, hookup, and configuration of new computer system.
Advise regarding purchase and installation of peripheral devices (printers,
scanners, etc.).
5. Advise on selection of computer software programs, and assist with software
setup and installation.
6. Perform minor repairs on computers; help add components, reconfigure computers,
and salvage usable parts from old computers.
7. Help laboratories to organize local computer networks to link individual
members; assist labs to establish links to main campus computer networks.
8. Assist users in the application of various software programs used in research
work, e.g., Eudora, Excel, Word, Endnote, Acrobat, Easy CD Creator, Canvas,
Matlab, Filemaker, IgorPro. Provide assistance when users find them unable
to understand or apply various software applications.
9. Troubleshoot computer hardware and software bugs and incompatibilities.
10. Assist users to establish and maintain data back-up and archiving systems
11. Maintain anti-virus software and help users to prevent virus infection.
Assist laboratories with computer security.
12. Assist with programming of technical components of individual laboratory
websites.
B. Module
Resources:
-Laboratory/Office:
The Computer/Information Technology Support Module (Computer/IT Module)
will be located in Room K-321 in the Koret Vision Research Laboratory
Building. This 110 sq. ft. room will serve as an office for the computer
programmer/analyst. It will contain a desk, bookshelves, computers,
as well as a small workshop with tools for minor computer repairs
and assembly. The room will be connected by phone and ethernet lines
for verbal and electronic communication with all vision researchers
at UCSF.
-Computer:
We propose to purchase the following computers, or equivalent models,
for the module technician: 1) Dell Dimension 8200 Series: Pentium® 4
Processor at 2.40GHz with 533MHz system bus/ 512K L2 Cache, 512MB
PC800 RDRAM, 128MB DDR NVIDIA GeForce4™ Ti 4600 Graphics Card
w/DVI and TV-Out, 120GB 7200RPM Hard Drive with DataBurst Cache™,
120GB 7200RPM Hard Drive with DataBurst Cache™, Intel® Pro
100 M PCI Ethernet Network Card, Microsoft® Windows® XP Professional,
and 17 in Flat Panel Display, and
2) Power Mac G4 Dual 1 GHz processors, 512MB RAM, 80GB 7200RPM Hard Drive,
Radeon 900 Pro Graphics Card, DVD-R-CD-RW Drive, Gig Ethernet Network Card.
[We have a spare flat panel display for this computer.]
-Access,
Location and Availability: The most important virtue of an effective
Computer/IT support module is accessibility, because when computer
problems arise, the investigator usually needs them solved promptly.
A computer glitch can halt an experiment, jeopardize data collection,
or interrupt office work. Service requests will be submitted electronically
to the Computer/IT technician, and triaged in terms of urgency and
complexity. Top priority will be given to problems that are acute,
and that can be resolved quickly. Because the Computer/IT module
will be situated in a central location within the Koret Vision Research
Laboratory, it will be easy for individual scientists to seek help,
often in person. However, many computer problems must be addressed
on site. Therefore, the Computer/IT technician will often be at work
in the laboratory of a given scientist, and not physically located
in the Computer/IT Support module office. To assure easy and constant
access in this situation, the Computer/IT technician will carry a
cell phone or pager during working hours.
C. Module Supervision
Jonathan
Horton, M.D., Ph.D., an NEI-funded independent investigator, will
supervise the module. During the prior grant period, he shared responsibility
for supervising the combined Imaging and Computer Support Module.
He makes extensive use of computer technology in his neurophysiological
laboratory, and therefore has the appropriate scientific background
to direct the Computer/IT Support Module. His office and laboratory
are located on the same floor of the Koret Vision Research Laboratory,
offering close physical proximity to the proposed Computer/IT Support
Module. He will meet informally on a semi-daily basis with the Computer/IT
Support Module technician to make sure that the unit is functioning
smoothly and that there are no impediments to full utilization of
the module.
Work requests,
even if transmitted verbally to the Computer/IT Support Module technician,
will be logged electronically. This operating procedure establishes
a written record of 1) computing problems that are encountered, 2)
the solution to these problem, 3) the productivity of the Computer/IT
technician, and 4) the time utilized by each investigator, 5) the
time lag between request and solution of each problem. The Computer/IT
Support technician will triage problems and set up an appropriate
work schedule, but the electronic log book will be reviewed regularly
by the Module director. This monitoring will insure that the Computer/IT
Support Module is working productively and completing assignments
in a timely fashion.
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Module V. Electrical and Machine Shop Service
Module Details
A.
Services Offered/Technician: The Electrical and Machine Shop Module
will provide dedicated space and technical expertise to support the
design and manufacture of specialized research instruments that are
required by Core Grant investigators but are not available commercially.
The Electrical Shop, for example, provides the capacity to design and
debug quite complex printed circuit boards, which are then submitted
to an outside agency for cheap manufacture. The Machine Shop, for example,
manufactures custom implants that are both superior to and more suitable
than those available from companies. Both shops provide essential repair
services for equipment that was manufactured in the shops, as well
as equipment that was purchased from outside. In many instances, the
equipment is no longer being made, but is essential to the vision research
of one or more laboratories, making this repair service of utmost importance.
Further, the shops have the capacity to provide immediate service when
things break during an ongoing experiment, and to make lab-calls to
repair equipment that is difficult to bring to the shop. This capacity,
especially, underscores the value of this service module to the vision
research community.
The Electrical
and Machine Shops will provide Core investigators with consultation
on and the design of new equipment, modification of equipment and
repairs free of charge.
B. Module
Resources
-Equipment:
The electrical shop has a full complement of test equipment, including
oscilloscopes, a logic analyzer, and the hardware and software needed
for the design of simple and complex circuit boards. The machine
shop has two lathes, two milling machines, a band saw, a table saw,
sanding and grinding machines, and equipment for cutting and shaping
sheet metal. Both shops have computers that are on the internet,
and the electronics shop uses a web-based system for users to describe
and track jobs they submit.
-Laboratory/Office:
The electrical shop comprises a 300 sq. ft. room located on the 7th
floor of the Health Sciences West Tower of UCSF. The machine shop
comprises two rooms. One is a 400 sq. ft. room that is used for manufacture
and repair, and includes a small desk space used for ordering and
billing paperwork by the shop head. The other is a 80 sq. ft. room
that is available to researchers for their own use, once they have
been trained and examined for knowledge of the use of the machines.
-Access
and Availability: The electrical shop is staffed by an experienced
electronics engineer from 9:30 to 6 PM daily. The machine shop is
staffed by two experienced machinists, one of whom also serves as
the shop head. The machine shop is open from 7 AM to 5 PM daily.
Both shops maintain an open-door policy: customers are expected to
drop in at their convenience. Both are located in space assigned
to the Department of Physiology, and near the laboratories are the
Module Director (Dr. Lisberger) and several extensive users on this
Core Grant (Stryker, Korenbrot, Miller).
C. Module
Supervision:
Stephen Lisberger, PhD, an NEI-funded and independent investigator, will supervise
the Electrical and Machine Shop Module. He has been supervising the Electrical
and Machine Shops for over 10 years for the Department of Physiology, and has
extensive experience in the intricacies of much of the equipment that is manufactured
and maintained by the shops. His laboratory is located near the shops, making
supervision seamless. Dr. Lisberger will be assisted by a shop committee consisting
of himself, Juan Korenbrot (Assistant Director of the module), and one more
person to be chosen from the investigators on this Core grant. With the help
of the shop committee, Dr. Lisberger will have responsibility for monitoring
the workflow through the shops and ensuring that the needs of all Core Grant
users are met with the shortest delay that is possible.
The shops
operate on a three-stream basis. The first stream is emergency work,
defined as unexpected repairs and small jobs that are essential to
research being done on an animal that is already in the experimental
apparatus. Emergency work pre-empts other work and is done immediately
whenever possible. The second stream is work with an identifiable
deadline when it will be needed for ongoing research. This work is
done approximately in order of entering in the shop queue, with adjustments
made for individual needs. The third stream is jobs that are low
priority but that will someday enter the second stream. Users are
responsible for assigning priority to their jobs, and the role of
the module director is to mediate when this proves necessary.
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