Core Facilities

The University of Delaware maintains a growing network of facilities to support an expanding life sciences research agenda. Some shared instrumentation cores are located in College of Earth, Ocean, and Environment (Sharp Campus in Lewes, DE), Chemistry/Biochemistry (Brown Laboratory), Biological Sciences (Wolf Hall), and the College of Agriculture and Natural Resources (Worrilow and Townsend Halls). A significant number of shared cores have been located at the Delaware Biotechnology Institute (DBI).

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The Delaware Biotechnology Institute Core Facilities:
(http://www.dbi.udel.edu/coreinstrumentation.html)

The Delaware Biotechnology Institute (DBI)
DBI is a government-academia-industry partnership focused on positioning Delaware as a center of excellence in biotechnology and life sciences. One of the key objectives of the Institute is to provide a network of state-of-the-art research equipment for the University of Delaware and the region.

The Institute is housed in a new 72,000 ft² research laboratory located in the Delaware Technology Park adjoining the University. This facility is designed to house 150-180 interdisciplinary researchers (University faculty, their research groups and professional support). The laboratory contains individual laboratory spaces (23 @1000 ft e²ach), offices, conference rooms, interactive spaces and over 15,000 ft² of shared equipment and instrumentation areas.

The DBI facility provides access to six core instrumentation centers and specialized facilities, each under the direction of an experienced researcher or administrator. Faculty also may access other core facilities located in laboratories throughout campus.

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

Bioimaging Center
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.

CBCB Bioinformatics Core: Dr. Shawn Polson, Coordinator, DBI Suite 205

The mission of the CBCB Core Facility is to provide scientific expertise and core infrastructure support in Bioinformatics and Computational Biology for the Delaware research and education community. The CBCB is under the direction of Dr. Cathy Wu, and the activities of the Bioinformatics Core are coordinated by Dr. Shawn Polson.  Drawing on the combined resources of the CBCB, the Delaware Biotechnology Institute (DBI), and the Protein Information Resource (PIR), the Core provides both computing infrastructure and knowledgeable personnel with significant hardware, software and professional support for bioinformatics and computational needs. Four Research Faculty with broad expertise encompassing various areas of bioinformatics analysis provide both bioinformatics/computational services and/or research collaborations. The core staff also includes a Network and Information Systems Manager and a full-time IT associate.

A special focus of the Bioinformatics Core has been the expansion of next generation sequencing (NGS) analysis pipelines available as fee-for-service to support the growing number of investigators utilizing the advanced NGS capabilities of UD's Genotyping and Sequencing Facility for genomic and transcriptomic-based discovery.  The facility also has substantial capabilities built upon its close relationship with the Protein Information Resource (PIR) that have been successfully applied to a number of research projects including proteomic analysis using tools such as iProXpress and literature and data mining capabilities of iProLINK.  These combined omic analysis and data integration pipelines form the nucleus of a broader bioinformatics framework that CBCB is actively developing to provide a user portal for dynamic analysis and visualization of genomic, transcriptomic, and proteomic data to its users at UD.

The Center's in-house High-Performance Computational hardware includes over 500 processor cores supporting bioinformatic analysis.  Included are approximately 250 cores freely accessible by researchers as part of our Linux-based Torque PBS cluster, BioHen.  A combination of system types allows the choice of systems best suited for the particular needs of a given analysis. Included are numerous nodes configured for memory intensive computing applications with 128 - 512GB of RAM per machine.  The data center currently hosts in excess of 100 TB of usable disk space.  The CBCB is also a stakeholder in the campus-wide Mills Community Cluster providing access to an additional 5000 processor cores. CLC Genomics Workbench/Server, CLC Main Workbench, JMP, JMP genomics, Matlab, and a suite of other commercial and open source Bioinformatic and Statistical Software packages are supported and maintained on Center hardware.  Our Database Cluster is composed of 6 Sunfire X4100M2 servers and acts 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. Data security is a high priority and access to results other than through these methods is strictly limited.  Our 3-D Visualization Studio is an immersive 3D graphics room with a 7'x15' rear-projection screen, delivering rear-projected, edge-blended images with total resolution of 2240 x 1024 pixels.  Other resources and services include secure FTP server, file servers, on and off-site data backup servers, email server, streaming video server, web hosting, cloud-based storage interface, large format printing, administration of researcher-owned servers, and bioinformatics software license support.

Proteomics Facility

Mass Spectrometry: 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.

OPEN ACCESS INSTRUMENTS:

  • Agilent 5973 GC-MS, AutoSampler, Split/splitless injection
  • ThermoFinnigan LCQ LC-MS, Electrospray
  • Bruker Omniflex MALDI, Linear and Reflectron modes

HIGH-PERFORMANCE INSTRUMENTS:

  • Waters Double Focusing AutospecQ
    EI, CI, ESI, LSIMS.
    Accurate mass, high resolution
    4000 amu at 8kV acceleration
    Positive and negative ions
    MS-MS capabilities
  • Waters Q-TOF
    LC-MS-MS for proteomics
    QqTOF geometry
    Data dependant MS to MS-MS switching
    de novo sequencing
    Library searching

FTMS:

  • ThermoFinnigan T-30. 3 Tesla
    EI, CI, ESI, CO2 Laser Desorption,
    Accurate mass capabilities
    MS-MS
  • Bruker Bioapex 70e. 7Tesla
    EI, CI, ESI, MALDI
    Accurate mass capabilities
    MS-MS
  • MALDI-TOF
    Bruker BIFLEX III
    384 well sample plate
    Linear and reflectron modes

Protein Production Core Facility

Protein Producton 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.

DNA Sequencing & Genotyping Center

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.

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College of Earth, Ocean, and Environment

Hugh Sharp Campus, Lewes, DE

Marine Environmental Genomics

The Marine BioSciences program has several faculty with research in the area of environmental genomics. These faculty primarily work out of the laboratory facilities on the marine campus in Lewes, DE. Equipment on site includes:

  • ABI 7500 qPCR
  • ABI 310 capillary sequencer
  • Spectrumedix 2410 capillary sequencer

Eppendorf Robotic pipetting station, epMotion 5075

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College of Agriculture and Natural Resources facilities

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.

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UD Library

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 Marine Studies Library

The Marine Studies Library is a branch library serving the faculty, staff, and students of the Graduate College of Earth, Ocean, and Environment. 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.

The Agriculture Branch Library

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

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.