Bioimaging: Dr. Kirk Czymmek, Director, DBI Suite 117

The Bioimaging Center is a multi-user facility, which provides state-of-the-art microscopic imaging instrumentation and technology, located in room 117 Delaware Biotechnology Institute, and is equipped with:

• Transmission Electron Microscope (TEM) – Zeiss CEM 902 with a Mega View II digital camera from Soft Imaging Systems;
• Field Emission Scanning Electron Microscope (FE-SEM)– Hitachi S4700 with a Gatan Alto 2500 Cryotransfer System and an Oxford INCA Energy (EDS) System; The FE-SEM has collaborative capabilities via the Internet.
• Multiphoton/Confocal Microscope – Zeiss LSM 510 NLO with a PECON Environmental Incubation System;
• High Speed Sprectral Confocal – Zeiss LSM5 DUO, with META and Live Scanhead
• Atomic Force Microscope (AFM) – Veeco Nanoscope IIIA with Phase capabilities;
• Laser Capture Microdissection Microscope (LCM) with a PALM MicroBeam Laser System;
• Zeiss Axioskop2 and Zeiss M2BIO microscopes using either the Zeiss AxioCam or Hamamatsu Orca-ER digital camera;
• Microtomy tools include the Reichert-Jung Ultracut E microtome and the LKB 7800 Knifemaker. 
• Specimen preparation equipment includes a Leica EM PACT for high-pressure freezing, Leica EM AFS for automated freeze substitution and a Denton Bench Top Turbo III for Carbon or Gold/Palladium coating. 
• Image analysis and enhancement workstations: two Dell computer systems which have an array of image processing and analysis software, a Fujifilm Pictography 4000 Printer with publication quality print capability, a Nikon Coolpix 5700 digital camera and an Agfa Duoscan T2500 scanner.  In addition, the center has a facility for specimen preparation and a darkroom with a Kodak X-Omat.

The center is open to university researchers and collaborators on a fee-for-service basis; outside industrial users are accommodated when scheduling permits.  Access to the center is available through a web-based reservation system. The staff is available for project consultations and provides regular user training.  The center is staffed full time by a Director, Dr. Kirk Czymmek, and Research Associate Deborah Powell. 

Contact:

Dr. Kirk Czymmek, Bioimaging Center Director,
DBI Suite 117
kirk@udel.edu
To schedule use of Bioimaging Center Facilities, go to the online calendar, at:
http://cgi.bisc.udel.edu/webcal/index.php3?calendar=coremicro

For information on rates, go to: http://www.dbi.udel.edu/bioimgrates.html

Bioinformatics: Dr. Douglas O'Neal, DBI Suite 209

The BioIT Center supports the computational and data management needs of the DBI research community and is anchored by three major systems:

• High-Performance Compute Cluster

  The core of DBI's HPC offering is a linux-based beowulf cluster with 122 compute nodes providing 286 computer cores. A mix of system types allows the choice of systems best suited for the particular of the computation. The nodes include:

  113 x Sunfire V60x dual-processor 2.8GHz Xeons (64-bit)/ 2GB memory
  7 x Sunfire X4100M2 quad-processor Opterons (64-bit)/ 8GB memory
  1 x Sunfire X4600M2 16-processor Opterons (64-bit)/ 64GB memory
  1 x Sunfire X4600M2 16-processor Opterons (64-bit)/ 128GB memory

  All compute nodes are connected via gigabit ethernet and have access to a 1.1TB shared RAID array. An parallel Myrinet network connects 48 of the nodes allowing low-latency data transfers.

  The HPC cluster is commonly used for protein sequence alignment (NCBI BLast, EMBOSS) and molecular modeling (Gaussian, GAMESS), but also supports other bioinformatics applications as well as custom applications suited for parallel processing. Fair-use scheduling of resources is provided by the Sun Grid Engine queue management system.

• Database Server Cluster

  The BioIT Center uses a cluster of six Sunfire X4100M2 servers, each with quad-processor 64-bit Opteron CPUs and 16GB memory, as a repository of experimental data in relational databases. Both MySQL and Oracle database systems are available, allowing researchers to organize, store, and evaluate their data. An Apple 10.5TB RAID array, a Sun 840GB RAID array, and a Sun 480GB JBOD array provide ample storage space for current data.

  While direct access to stored data via command line and web-based clients is provided, general access to share results is usually though customized web pages. Data security is a high priority and access to results other than though these methods is strictly limited.

• 3-D Visualization Studio

  The Visualization Studio is an immersive 3D graphics room with a 7'x15' rear-projection screen, delivering a rear-projected, edge-blended image with total resolution of 2240 x 1024 pixels. The display is driven by two servers; an eight-processor Silicon Graphics Prism visualization supercomputer with four graphics pipelines provides a Linux environments with the power of the SGI graphics software, and a dual-core HP AMD 64 with a high-end NVidia graphics processor allows a variety of Windows software to be utilized. An integrated tracking system allows the graphics software to follow the motion of a researcher and adjust the display so that the researcher can walk around or through 3D objects. Both systems are available for molecular and biological modeling projects.

The BioIT Center also supports multiple special-purpose servers. Among these are web servers, a secure ftp server for data transfer, streaming video servers, and an email server. The BioIT staff will work with researchers to design and purchase servers dedicated to specific groups or projects. These systems can be physically located in the BioIT computer room and managed by the center's staff if desired.

The BioIT staff bring several types of expertise to the center to aid researchers. Dr. Doug O'Neal is the manager of the BioIT Center and is experienced in scientific computing and system administration. Dr. Mihailo Kaplarevic provides database and scientific programming support for the Center's researches. Combining scientific training with information technology experience, both can provide the needed interface between research needs and the computer hardware and software resources at DBI. Web site support and desktop computing support is handled by Eric Garrison.

Contact:

Dr. Douglas O’Neal, BioIT Manager, DBI 210, oneal@dbi.udel.edu, (302) 831-3456

Transgenic and Gene Targeting Facility
Kimmel Cancer Center, Thomas Jefferson University

The Transgenic and Gene Targeting Facility of Thomas Jefferson University at the Kimmel Cancer Center is available to University of Delaware Investigators for transgenic, gene targeting, and cryopreservation projects, and also offers a suite of assisted reproductive technologies useful for such tasks as strain rescue, expansion, and rederivation.

Contact:

Director of the TJU Transgenic and Gene Targeting Facility

Carlisle P. Landel, Ph.D.
Kimmel Cancer Center
Thomas Jefferson University
233 S. 10th Street, BLSB 619
Philadelphia, PA 19107
E-mail: clandel@jci.tju.edu
Phone: (215) 503-4539

UD Coordinator for Transgenic Animal Transfers

Frank M. Warren
Manager of the Office of Laboratory Animal Medicine
University of Delaware
Newark, DE 19716
E-mail: fwarren@udel.edu
Phone: (302) 831-2400

UD Coordinator for New Projects

Catherine B. Kirn-Safran, Ph.D.
University of Delaware
Department of Biological Sciences
Newark, DE 19716
E-mail: ckirn@udel.edu
Phone: (302) 831-3249

Proteomics Facility: John Dykins, Lamott DuPont Laboratory

Located in the Department of Chemistry & Biochemistry, the Proteomics/Mass Spec Facility is grouped on the first floor of Lamott DuPont Laboratory. There are three open access, user-friendly instruments that are available, after training, for researchers to use 24/7.  The high performance instruments are for more detailed and precise analyses as detailed below.

Contact:

Mr. John Dykins, Mass Spec Facility Manager
122 Lamott DuPont Lab
(302) 831-3578
dykins@udel.edu

For a consultation, or to reserve time on an instrument contact Mr. John Dykins, facility manager, via email or at (302) 831-3578.

Center for Translational Cancer Research: Dr. Mary C. Farach-Carson, Wolf Hall

The Center for Translational Cancer Research is a multi-user facility, located in 006, 007, 345 Wolf Hall and 226 McKinly Lab, provides access to services including protein profiling, protein identification, HPLC, and flow cytometry (including cell cycle/apoptosis analysis), to university researchers and collaborators on a fee-for-service basis.  Outside industrial users are accommodated when scheduling permits.

The Center for Translational Cancer Research Core Facility currently consists of:

• CTCR Research Laboratory is located in Wolf 006, the CTCR Research Laboratory provides a shared  site for interdisciplinary research. Under the direction of Dr. Chu Zhang, CTCR Research Coordinator, this laboratory is fully equipped with common laboratory equipment that is shared by students, fellows,  residents, clinicians and faculty who wish to conduct state of the  art research projects utilizing cell culture, molecular, genetic  and physiological approaches. In addition, the Research Core will provide assistance with mechanisms to obtain human subjects training,  protocol development, and safe laboratory practices.The Research Laboratory is adjacent to room 006 which houses the CTCR Core and close to surgical suites and pathogen free barrier facility for pre-clinical studies.
• Beckman 126/166 High Performance Liquid Chromatograph (HPLC)
• Becton Dickinson FACSCalibur Flow Cytometer
• Bio-Rad SELDI-TOF-Mass Spectrometer
• GE Healthcare eXplore Locus Pre-Clinical in Vivo MicroCT Scanner
• Billups-Rothenberg Incubator Chambers
• Dynex MRX ELISA Plate Reader
• Dynex MLX Luminometer
• Molecular Dynamics Phosphorimager
• ABI Prism 7000 Real-Time PCR

Access the facility online, at: http://www.udel.edu/ctcr/core/

Contact:

Faculty oversight of this facility is a joint responsibility of Mary C. Farach-Carson, Ph.D.   Please contact Rob Long, the Center for Translational Cancer Research Core Facility Director, if you have any questions regarding facility usage.

Rob Long
Dept. of Biological Sciences
309 Wolf Hall
University of Delaware
Newark, DE 19716E-mail: rlong@udel.edu
Phone: (302) 831-0266
Fax: (302) 831-6100

Structural Biology Facility, 015 Brown Laboratory: Dr. Steve Bai

The NMR facility offers a suite of spectrometers in Brown Laboratory, and is open to university researchers and collaborators. 

For liquid-state  and solid state NMR spectroscopy:

• Bruker AMX360 spectrometer (011A BRL).  This spectrometer equipped with a 5-mm QNP probe and a 5-mm broadband probe. Variable temperature ranges from -70 C to +150 C.
• Bruker AV400 spectrometer (208 LDL).  The AV400 is scheduled to be installed Spring 2005. AV400 will be equipped with an auto-sampler which handles 60 samples.  Remote access capability will facilitate use by other institutions of higher education in the region.
• Bruker DRX-400 spectrometer (021 BRL).  This spectrometer equipped with a 5-mm QNP probe and a 5-mm broadband probe. Variable temperature ranges from -70 C to +150 C.
• Bruker AV600 spectrometer (015BRL).  The AV600 spectrometer is equipped with a 5-mm inverse triple resonance CryoProbe, a conventional 5-mm inverse triple resonance probe (ATM PTXI probe), and a 5-mm broadband probe.

Data Workstation:

• Dell Precision workstation (Linux Redhat 7.5 and Bruker xwinnmr 3.5) for off-line data processes

In addition, the facility provides spectrometer training and sample services to campus researchers, who may request instrument time or training via an online reservation system.  Outside industry users will be accommodated on a fee-for-service basis when scheduling permits.

Contact:

Dr. Steve Bai, Facility Manager
025 Brown Lab
(302) 831-8901
bais@udel.edu

For a consultation, contact Dr. Steve Bai.  To find more information about the facility, reserve time on an instrument, or request instrument training, sign up online at http://www.nmr.udel.edu/nmr/.

Protein Production Facility: Dr. Yu-Sung Wu, Director, DBI Lab 143

This facility is designed for large scale protein expression and purification, and is equipped with:

• Fermentor - New Brunswick Scientific BioFlo 4500 (22L capacity for bacteria and yeast cell growth)
• Bioreactor -  New Brunswick Celligen Plus (7.5L capacity for insect and mammalian cell growth)
• High Pressure Cell homogenizer - Avestin EmulsiFlex C5.  This instrument is designed for processing large volume cell lysate.
• High capacity centrifuge rotor – Beckman Coulter JLA 8.1000 for cell culture harvest
• High performance liquid chromatography - GE AKTA Explorer 100 and Purifier 10.

The unique features of the AKTA system include (1) a single platform for large and small scale protein/peptide purification (2) a wide variety of commercial chromatographic media and/or columns available (3) user friendly software to customize method development. 

• Analytical ultracentrifuge - The facility also features a Beckman Coulter XL-I analytical ultracentrifuge, which can characterize a variety of biophysical properties of macromolecules such as molecular weight, sedimentation coefficients, diffusion coefficients, equilibrium constants and stoichiometry.  This instrument was funded by the NIH NCRR Delaware BRIN grant.

The protein production core is funded by a COBRE (Center of Biomedical Research Excellence) grant from NIH (Abraham Lenhoff, Chemical Engineering, P.I.) Dr. Yu-Sung Wu, Core Director, works closely with multidisciplinary research groups to make optimum use of the protein production facilities system for specific research projects.

Contact:

Dr. Yu-Sung Wu, Director
DBI Lab 143
wu@dbi.udel.edu
302-831-3441(office) or 302-831-4687(lab)

For a consultation, contact Dr. Yu-Sung Wu.  To reserve time on an instrument, or request instrument training, sign up online at https://www.engr.udel.edu/cgis/webevent/publish2.72a/webevent.cgi

DNA Sequencing Core Facility – Charles C. Allen, Jr. Biotechnology Laboratory

The UD DNA Sequencing & Genotyping Center is equipped with the following instrumentation:

• ABI Prism 3130XL Genetic Analyzer – The 3130XL system is a fully automated, fluorescence-based capillary electrophoresis platform that simultaneously analyzes 16 samples. The system provides automated polymer loading, sample injection, separation and detection, and data analysis. The instrument can run unattended for up to 24 hours.
• Apple G5 Server – The Xserve G5 offers dense power in a 1U server with dual 64-bit G5 processors at speeds of 2.3GHz. A UNIX-based server operating system with unlimited clients, up to 1.2TB storage, PCI-X expansion, dual Gigabit Ethernet, fast I/O ports and an optical drive.
• NanoDrop Technologies ND-1000 UV-Vis Spectrophotometer – The NanoDrop® ND-1000 UV-Vis Spectrophotometer enables highly accurate analyses of extremely small samples with high reproducibility. The sample retention system eliminates the need for cuvettes and capillaries. Benefits include full spectrum absorbance (220-750nm) and small sample size (1-2ul).
• ABI GeneAmp PCR System 9700 Thermocyclers – High-performance thermocyclers offer fidelity, accuracy, NIST traceable calibration, and fast response to temperature changes. Heating and cooling is thermoelectric, a heated lid provides for oil-free operation.
• Eppendorf Centrifuge 5804R & 5417– The 5804R centrifuge is capable of high-speed centrifugation (up to 20,800 x g) of tubes and plates using interchangeable swing-bucket and high-speed fixed-angle rotors. Internal temperature settings range from –9°C to 40°C. The 5417, for microcentrifuge tubes only, has similar capabilities without refrigeration.
• Dell Optiplex GX270 workstation – Computer workstation loaded with licensed software for sequence and fragment analysis.
• UVP Ultraviolet transilluminator – Ultraviolet transilluminator for gel imaging and documentation.

The UD Sequencing & Genotyping Center provides state of the art genetic analysis for university research groups and outside users on a fee-for-service basis. Bruce Kingham (brucek@udel.edu) is available for troubleshooting and consultation.

Contact:

Bruce Kingham, Director/Associate Scientist
Allen Laboratory, room 157
(302) 831-0823  Laboratory
(302) 831-8177  FAX
brucek@udel.edu

Growth Chambers: Robert Pekala, DBI Building Engineer, DBI Lab 170

• Common use growth chambers

Two common use growth chambers are shared by multiple research groups who utilize a single growth shelf or multiple shelves while growing plants with similar light, temperature and humidity conditions.   Both are Conviron Walk-in Growth Chambers, Model MTPC 144, with 144 ft² growth space each, located in DBI Room 170.

The growth chambers are maintained through annual contracts with Conviron, and are monitored by a dedicated computer which tracks growing conditions and will alarm and page the building manager if the growth conditions go out of specification.

Contact:

Mr. Robert Pekala, DBI Engineering and Operations Manager
(302) 831-3439
pekala@dbi.udel.edu

Macromolecular X-ray Crystallography Facility: Drake Hall

The X-ray Crystallography facility offers state-of-the-art instrumentation to solve structures of biological macromolecules from single crystals, and is open to university researchers and collaborators. 

Rotating Anode X-ray Generator

• Rigaku/MSC RU-H3R rotating anode X-ray generator offering a high brilliance 300 micron X-ray beam.  The generator located in 314 Drake Hall is equipped with Osmic optics, which give the beam a more tightly focused and monochromatic beam.

R-axis IV Image Plate Area Detector

• Rigaku/MSC R-axis IV image plate area detector is located in 314 Drake Hall.  The detector collects images that are 3,000 square pixels with a 100 micron pixel resolution.  Data to a resolution of 1.4 Å has been collected on this X-ray system.

X-stream Cryo-System for Data Collection at –180 °C

• Data are typically collected under cryo conditions using this self-contained X-stream cryo-system that includes an air compressor, gas separation filter bank, He-refrigerated cryo system, and nozzle.  Data is collected with an inverse phi, which allows easy mounting of liquid nitrogen frozen samples.

Data Workstation

• Dell Precision workstation (Linux Redhat 7.5, HKL2000, and CrystalClear software) for data processing.

The protein crystallography core is funded by a COBRE (Center of Biomedical Research Excellence) grant from NIH (Abraham Lenhoff, Chemical Engineering, P.I.) Dr. Brian Bahnson, Core Director, works closely with multidisciplinary research groups to make optimal use of the macromolecular crystallography facilities for preliminary studies of specific research projects.   Outside industry users will be accommodated on a fee-for-service basis when scheduling permits.

Contact:

Dr. Brian Bahnson, Associate Professor of Chemistry & Biochemistry
312 Drake Hall
(302) 831-0786
bahnson@udel.edu

For more information regarding this facility online at http://www.udel.edu/chem/bahnson/

Fischer Greenhouse Laboratory:

Includes headhouse containing equipment room, growth chamber room, media preparation room, fertilizer, pesticide and pot storage rooms, classrooms, student laboratory and manager's office, and over 10,000 sq. ft. of glasshouse space for a total of 24,037 sq. ft. A new, $1.5 million plant growth facility, including state-of-the-art growth chambers, seed drying and storage and autoclave capabilities, will be built in spring 2002.

DBI Common Laboratory Equipment: Robert Pekala, DBI Building Engineer

DBI provides common access to standard equipment maintained and overseen by the DBI building manager. Equipment includes two Beta Star Autoclaves; six Class II B1– Nuaire Biological Safety Hoods; two cold rooms (4°C Temperature-controlled environment); centrifuges including three Eppendorf 5415D; one refrigerated and one non-refrigerated Eppendorf tabletop centrifuge, five Beckman Coulter Optima and two Beckman Coulter Avanti superspeed centrifuges.

Shared equipment further includes two Beckman Coulter DU 7400 Diode Array Spectrophotometers; a Beckman Coulter CEQ 2000XL DNA Analysis System; two freezer farms; two Lancer Glassware Washers; two Alpha Innotech 2200 Gel Documentation Stations.

Common equipment incubators include a Precision Automatic CO2 Incubator; two Yamamoto IC 600 Bacterial Incubators; two Forma Scientific Seri-Cult 200 incubators; VWR Scientific 1535 and VWR Scientific 1540 incubators; two Nuaire NU 3500 TS Autoflow CO2 Water-Jacketed Incubators; and a Queu QWJ 5005 CO2 Water-Jacketed Incubator.

Additional common equipment includes an Amersham Pharmacia MD Typhoon® 6500 Variable Mode Imager; a Nikon Ellipse TE200 inverted microscope; a Beckman Coulter LS 6500 Multi-Purpose Liquid Scintillation Counter; a Beckman Coulter DU 640 UV/VIS Spectrophotometer; two Spectroline UV Transilluminators; a New Brunswick C-24 Benchtop Platform Shaker; and three New Brunswick C-25 Floor Platform Shakers; and Barnstead NANOpure Diamond Water Purification Units provided in each lab.

College of Agriculture and Natural Resources facilities:

Worrilow Hall Facility: Facilities in Worrilow Hall include a cell culture laboratory (400 sq. ft.), cold room (100 sq. ft.), histology laboratory (500 sq. ft.), a dark room (100 sq. ft.), and a glassware kitchen (400 sq. ft.). Each research faculty member in Worrilow occupies approximately 1000 sq. ft. of laboratory space and individual labs are well equipped to conduct research. Worrilow Hall is connected to Townsend Hall, which houses the administrative offices for both the Department of Animal and Food Sciences and the College of Agriculture and Natural Resources. The renovation of Townsend Hall was completed in March 2000.

Charles C. Allen, Jr. Biotechnology Laboratory:

The Charles C. Allen, Jr. Biotechnology Laboratory is a 16,635 sq. ft. facility located in the Townsend/Worrilow Hall complex. This state-of-the-art facility, specifically designed for in vivo studies on chickens, was completed in 1998. This building has two large BL-3 level biocontainment laboratory suites with adjoining animal rooms and an additional six animal rooms that function independent of the laboratories. All animal rooms are entered through airlocks to prevent the introduction or release of infectious agents. These rooms are equipped with either modified, custom-designed HEPA-filtered isolation cabinets or Montaire-Andersen (glove-port) isolation cabinets.

University of Delaware Library Facilities

The University of Delaware Library System includes the Hugh H. Morris Library housing the main collection and four branch libraries. The libraries contain over 2 million volumes, about 500,000 government publications, and 3 million microforms. Subscriptions are held to over 20,000 journals, many of which are on-line, and articles from other journals are obtainable by on-line ordering and fax-back service. DELCAT, the University of Delaware Library online catalog, can be accessed via the University of Delaware computing network, the Internet, or by modem from anywhere in the world. The University of Delaware web page provides gateway access to electronic resources on the World Wide Web and electronic access to locally licensed, networked and electronic information, including journal article references and abstracts, full-text journal articles and government information and maps. Library Networked Databases include more than 150 databases containing hundreds of thousands of references and summaries of the contents of journals, including large full-text databases of entire articles online, which are available to faculty, staff and students of the University of Delaware.

The Agriculture Branch Library, located in Townsend Hall adjacent to the Department of Animal and Food Sciences, provides a specialized collection of 22,000 books and bound periodicals on animal and food sciences, plant and soil sciences, entomology, wildlife management, agricultural engineering technology, biotechnology, and food and resource economics. The branch subscribes to over 225 periodicals and scholarly journals and has reserve materials available. The library has seating for 24, including six computer stations.

The Chemistry Library is a branch library serving the faculty, staff and students of the Department of Chemistry and Biochemistry and the Department of Chemical Engineering. It is located on the second floor of Brown Laboratory on the main campus of the University in Newark. It provides a specialized collection of approximately 28,000 books and bound periodical volumes on many areas of chemistry and related fields. The Chemistry Library subscribes to over 230 periodicals and scholarly journals, and provides access to many more journals and World Wide Web pages in electronic format through the University of Delaware Library home page. Seating is available for approximately 50 users including spaces at public terminals for access to library and World Wide Web resources in chemistry and related subject areas. Microform reader printers are available for access to the early years of Chemical Abstracts, with more recent years of this resource available via SciFinder Scholar.

The Marine Studies Library is a branch library serving the faculty, staff, and students of the Graduate College of Marine and Earth Studies. It provides a specialized collection of approximately 15,000 books and bound periodicals on marine biology and biochemistry; chemical, physical and biological oceanography; marine geology; and aquaculture. Seating is available for approximately 50 users including spaces at public terminals for access to library and World Wide Web resources in marine studies and related subject areas. This branch library is located on the Hugh R. Sharp Campus in Lewes, Delaware, in the Cannon Marine Studies Laboratory.