|
FACILITIES AVAILABLE TO CEPCEB FACULTY, STUDENTS, &
POSTDOCS
Renovation was recently completed of the UCR Core
Instrumentation Facility in the newly named Noel T. Keen Hall located in the
north wing of Batchelor Hall (please search for Noel Keen Hall on the campus
map). The Core Instrumentation Facility is a state-of-the-art, 10,000 square-foot
shared-use facility providing instrumentation suites in microscopy and imaging,
bioinformatics, proteomics, and DNA sequencing and molecular biology. CEPCEB
Microscopy and Imaging Core Facility Confocal
microscopy is a robust technology for querying the structure and function of living
cells, producing optical sections of a sample at the theoretical limit of light
resolution. This benefit is also its weakness, since only a tiny volume of sample
space is visible at any time. The microscopy core facility provides a comprehensive
suite of confocal microscopes, with a wide selection of special features which
make it easier to navigate specimen space, and capture the most important data.
Under the supervision of a full-time, imaging expert and Academic Coordinator,
Dr. David Carter, the Center is developing
high throughput imaging capability, and is pioneering a range of optical imaging
applications for use in plant systems. Three confocal microscopes, a laser ablation
system, an imaging analysis system and two dissecting scopes are available for
demanding and routine imaging. Use of equipment in the CEPCEB microscopy facility
can now be booked online.
CEPCEB
Small Research Grants Awarded for Microscopy and Imaging The
Center for Plant Cell Biology awarded two seed grants of $2,000 to the following
recipients for projects using the Microscopy and Imaging resources in the core
facility: | Name: | Juan
Dong, Graduate Student | Christian
Lytle, Associate Professor | | Department: | Botany
& Plant Sciences | Biomedical
Sciences | | Project: | Localization
of chemocyanin in the lily pistil and on in vitro grown pollen tubes | The
kinetics of intraluminal acidification of gastric glands |
These
grants will be administered as a 12-month line of credit to be spent at the CEPCEB
core facility on billable equipment. The following equipment is available: - Leica
SP2 UV confocal microscope with 9 laser lines and spectral detection
- Meridian
InSight ocular viewing confocal with Ar and Kr lasers and Hamamatsu C4880 camera
- Atto
Pathway HT fully automated confocal imaging system, now with montage capability
- Leica
MZIII fluorescence stereo scopes with Combi turret, SPOT b/w and JVC color cameras
- MCID
Elite image analysis system with motorized Zeiss Axiovert microscope
- Photonic
Microsystems pulsed laser on a motorized laser ablation microscope platform
- Leica
Ultracut T with EM FCS cryo unit for preparing TEM samples (Expert users only)
- Sorvall
MT 6000 ultramicrotome for preparing TEM samples
- EMS 5000 oscillating
tissue slicer for live tissue sectioning under water
- Hacker 5030 microtome
for routine plastic and wax histological sectioning
- Microm HM500 OMV motorized
cryostat with "vacutome" feature for cutting flat cryosections
- BioRad
PDS1000/He Biolistic gene gun with Hepta adaptor for wide area coverage
Back to Top 
| |
Leica
TCS SP2 Confocal Microscope |
| | | | |
|
| | 1) Leica
TCS SP2/UV Confocal Microscope. This is a top-of-the-line, advanced
confocal microscope that is best suited for high-resolution imaging of live or
stained cells labeled with multiple markers and fluorescent resonance energy transfer
(FRET) experiments. It is equipped with nine laser lines (including UV, blue,
green and red) and has a fully flexible 4-channel spectral detection system. The
system allows co-localization of proteins tagged with multiple fluorescent proteins
with overlapping excitation and emission wavelengths (e.g., CFP/GFP/YFP), and
can simultaneously perform bright field, reflection and multichannel fluorescence
confocal imaging. | | 2)
Atto Pathway HT. The Pathway HT automated imaging workstation is a fully integrated
system for performing high throughput confocal imaging experiments on slides,
dishes or multiwell plates. It has on board fluid handling and climate control,
and by moving the optics below a stationary sample is especially suited to work
on non-adherent cultured cells or large bulky samples. | | |
| |
Laser
Scanning Confocal Microscope Light Path | | | | | |
| |
| | 3) Insight
Point Confocal Microscope. This is a real-time confocal microscope that is
useful for rapid visual screening of large amounts of material. It has advanced
application-driven software for collecting kinetics and z-series, performing image
and histogram analysis, and creating top quality 3D reconstructions. |
| 4)
Photonics Instruments MicroPoint Pulsed Laser. A laser ablation system is
available for knock-out studies of cells and tissues. It uses a high resolution
motorized stage for burning precise patterns in heat absorbant media; and can
be used for isolating individual cells, chromosomes, and chromosome fragments.
This system can also be used for photoactivationi and Fluorescence Recovery After
Photobleaching (FRAP) experiments. | |
| |
| | |
| |  |
5) Two Leica MZ FLIII Fluorescence
Stereomicroscopes equipped with two different cameras: a commercial grade
digital color camera and a SPOT RT scientific grade cooled CCD camera. One system
is equipped with a Fluo Combi turret and 10x objective, which allows screening
to be performed on whole plants at subcellular resolution. |
| 6)
Microtomes. The Microscopy Core also houses several microtome systems (a Leica
EM FC S Low-Temperature Sectioning System, a Leica Ultracut T and an EMS 5000
oscillating tissue slicer) and other equipment necessary to prepare material for
TEM analysis. The TEM is housed in the campus Central
Facility for Advanced Microscopy and Microanalysis (CFAMM). |
| | | Back
to Top |
|
| |
| | | | Back
to Top CEPCEB
Bioinformatic Core Facility The CEPCEB Bioinformatic
Core houses several terminals and Linux server(s), which are dedicated to providing
the community with state-of-the-art bioinformatics tools for high-throughput sequence
analysis, data mining, integration of relational databases, etc. The center is
supervised by a full-time Academic Coordinator, Dr.
Thomas Girke. The role of this group is to actively develop research collaborations
with other scientists, to keep them informed about new bioinformatics resources
and to build user-specific data mining tools and databases. Due to the group's
extensive hands-on expertise in the plant functional genomics area including transcriptional
profiling, functional gene characterization and high-throughput sample handling,
it can provide truly discovery-oriented bioinformatics solutions by creatively
interacting between different research disciplines. For more
information on the facility, please see the Bioinformatics
Core Site | Research
focus of the bioinformatics core:
- Data mining: RNA, protein and
metabolic profiling
- Large-scale sequence analysis: ESTs, genomes,
etc.
- Sequence motif finding: promoter, proteins, etc.
- Database
construction
- Integration of databases from different research disciplines
- Modeling of metabolic and signaling pathways
|  |
Back to Top
CEPCEB W.M. Keck Proteomics
Core Facility
Mass spectrometry (MS) based approaches have
emerged as a major tool in proteomics research for characterization of cellular
proteins. Our core facility lab is equipped with state-of-the-art mass spectrometers
such as Q-TOF and QSTAR that are complementary in system configuration for high
sequence coverage and can perform high throughput peptide mass analysis with high
sensitivity and mass accuracy. Under the supervision of the Proteomics Academic
Coordinator, Dr. Songqin Pan, the Center is developing
MS capabilities for analysis of protein complexes, protein modifications, organelle
proteomes, and discovery of protein-ligand interactions, protein markers for diseases
and mutants.
| |
| |
| 
| The
QSTAR XL oMALDI MS/MS is one of top-of-the-line instruments made
by Applied Biosystem Inc., a major mass spectrometers manufacturer. With oMALDI
ionization source, this instrument analyzes peptide samples in solid phase and
allows the investigators to reanalyze the same sample multiple times with different
methods in order to confirm findings. It can generate peptide mass fingerprinting
(PMF) for initial protein identification and then allow targeted MS/MS analysis
to deduce amino acid sequences in a very efficient high-throughput manner. It
is very useful for less complex samples that do not require peptide separations.
It is relatively easy in sample preparation and instrument operation, and therefore,
this system is good for education purpose for beginners who wish to gain experiences
in proteomics research. |  |
| Q-TOF
ESI MS/MS | | |
The Q-TOF ESI MS/MS is made by
Micromass, a subsidiary of Waters Corporation. Complementary to QSTAR, the Q-TOF
system is configured with an ESI ionization source. It is coupled with a capillary
HPLC system to automatically integrate peptide separation, MS/MS analysis, data
interpretation, and database search into a single run using a single centralized
software control. It is particularly useful for complex samples containing a number
of proteins. The option of ESI nano-spray and nano-flow (0.2-1 ul/min) HPLC available
in the system is critical to analysis of the low-abundant proteins that require
high instrument sensitivity. Q-TOF can be operated in either standard V-mode with
10,000 resolution or W-mode with 17,000 resolution, which is used only when ultra-high
mass resolution and accuracy is needed. Since it uses electro-spray ionization
(ESI) to charge the peptides, the Q-TOF data set would be complementary to that
generated by the QSTAR oMALDI, therefore increasing peptide coverage and the number
of proteins that can be identified.
|  |  |
| Capillary
HPLC |
| LC-MALDIprep |
| | This
Waters capillary HPLC is used for peptide separation only and directly coupled
with Q-TOF ESI MS for continuous MS/MS data acquisition. Dependent on sample volumes
and column sizes, the flow rate of HPLC can range from 1-20 ul/min for wide range
of application. For very small amount of samples that are derived from low-abundant
proteins, high MS sensitivity is needed. In such cases, HPLC flow rate can be
further reduced to 0.2-1ul/min range by using a flow splitter that can be an optional
use in the HPLC configuration. |  | MALDI
MS is a convenient method for simple samples containing one or few proteins such
as those from 2D-gel spots. For complex samples such as those from 1D-gel bands
that may contain many proteins, it may lack specificity in database search. In
such cases, LC-MALDIprep can allow HPLC offline separation and spot samples directly
on individual wells of MALDI sample plate for MS and MS/MS analysis. Peptide separation
by HPLC offline can reduce sample complexity and ion suppression to increase peptide
coverage, and therefore, more proteins can be identified from a complex mixture
sample. |  |
CEPCEB
PROTEOMICS SERVICES
Rate
Schedule 2006-07
Services | Per | Internal
Rates | External
Educational Rates | External
Commercial Rates | | Mass
Spectrometer: Q-TOF | unit | $ 149.91
| $ 371.45
| $
506.58 | | Mass
Spectrometer: Q-STAR XL |
hour | 19.14 | 67.60 | 92.19 | | LC-MALDI
Prep | unit | 112.84 | 207.14 | 282.50 | | 2D-gel
Electrophoresis | unit | 49.25 | 94.45 | 128.81 | | Training
and Consultation Services | hour | 4.72 | 55.83 | 76.14 |
Back
to Top
The
UCR Institute for Integrative Genome Biology Core Instrumentation Facility
The Genomics Core Facility at the Institute for Integrative Genome Biology (IIGB) provides technical, instrument, and professional development. The Genomics Facilities is supervised by an Academic Administrator, Glenn Hicks, and a Specialist is currently being recruited to manage day-to-day operations. The Core has two suites of instrumentation.
In the Genomics suite, automated colony picking (Genetix QPix), extraction and purification of plasmids from bacterial cultures in deep-well plates (Beckman Mutimek robot), handling of liquids for DNA sequencing reactions (Multiprobe II robot, Perkin Elmer) and PCRs (Dyad, Biorad, Eppendorf thermocyclers). For routine sequencing the facility has a 96-capillary sequencer (ABI 3730xl). For genotyping, amplified microsatellites can be detected with a 16-capillary instrument (ABI 3100) and appropriate computer software (ABI GeneMapper).
In the Gene Expression suite, custom and commercial microarrays services are available. For custom arrays, the core offer two arrayers, a macroarrayer with 96 pins (Genetix Qpix) and a microarrayer with 1~48 pins (Biorad VersArray ChipWrite Pro spot arrayer). Three scanners are available for arrays, one for macroarrays and two for microarrays. For macroarrays, a Typhoon scanner (GE) with a resolution of 10~500uM can generate images from a variety of fluorophores and phosphoimage screens. For microarrays, the core offers two different scanners, the GenePix 4000B (Molecular Devices) and the ScannArray Express (Perkin Elmer) along with appropriate software for analysis. For commercial Affymetrix arrays, hybridization (Hybridization Oven 640), staining and washing (Fluidics Station 450), and scanning for processing RNAs (quality control with Bioanalyzer, Agilent) as offered. For array data analysis, two software packages (Moleculat Devices Acuity and Strategene ArrayAssist) are available. To validate gene expression, we house quantitative PCR (ABI-7700 & BioRad-iQ5) thermocyclers. For fluorescence cytometric and sorting applications with whole cells, the facility houses an advanced cell sorter (BD FACSAriaT) which is a high-speed sorter with fixed-alignment cuvette flow cell and three air-cooled lasers (488nm, 633nm, and 407nm).
For further information on the facility's services, protocol
and rates, please see the Institute
for Integrative Genome Biology Core Instrumentation Facility site. Back
to Top
Other
Campus Facilities
Botany & Plant Sciences Department
Shared Equipment The Department of Botany and Plant Sciences has cold rooms,
X-ray film processor, dark rooms, word-processing services, printing facilities,
a Molecular Dynamics PhosphoImager facility, automated DNA sequencers, Arabidopsis
growth facilities, reach-in and walk-in growth chambers, and incubators for growing
plants on sterile media. The department has HPLC equipment and a Hewlett-Packard
5890 Series II gas chromatograph with a 5971A mass-selective detector. The staff
in the Department of Botany and Plant Sciences is suberb, providing services from
preparing grant proposals to managing growth facilities and mechanics and electronics
shop support (see Botany
and Plant Sciences).
Analytical Chemistry Instrumentation Facility (ACIF) The ACIF
has a MALDI/TOF mass spectrometer. An Academic Coordinator, Dr. Kangling Zhang,
supervises the proteomic aspect of ACIF. For more information
on the facility, please see the Analytical
Chemistry Instrumentation Facility (ACIF) site.
Arabidopsis
Growth Facilities
The Department has several shared Arabidopsis growth
rooms with a total of approximately 2600 sq.ft. of growth space and several small
greenhouses designed for year-round Arabidopsis growth. In addition, a new transgenic
plant facility to be completed by the end of 2001 will have 640 sq.ft. of Arabidopsis
growth space.
Central Facility for Advanced Microscopy and
Microanalysis (CFAMM) The campus Central
Facility for Advanced Microscopy and Microanalysis is equipped with TEM (Phillips
CM300) and SEM (Phillips XL30-FEG) systems, a critical-point-dryer (Balzers CPD0202),
a cryofixation system (Reichert-Jung KF80), and two ultramicrotomes (RMC XT-X
and Sorval MT2). The facility houses a state-of-the-art Zeiss LSM 510 confocal
microscope. This equipment is available on a user fee basis. Fore
more information on this facility, please see the
Central Facility for Advanced Microscopy and Microanalysis (CFAMM) site Back
to Top
|
