These days, if you want to conduct research in the life sciences, you need more than a magnifying glass and a dissecting kit. You need much more sophisticated equipment. You need a mass spectrometer. A gene sequencer. An electron microscope. You need super-computing power. You need lots and lots of money!
Not to worry. In Delaware, scientists have access to the most advanced research tools, thanks to a system of shared resources known as the “core centers.” A core center is a laboratory that functions around a particular instrument or a related set of instruments, where scientists from around the state can reserve time to use these tools and receive expert assistance from the staff that operate the center. The centers generally operate on a fee-for-service basis, although initial consultations are often free of charge.
The Delaware EPSCoR Research Infrastructure Improvement grant includes funds for purchasing and upgrading core center instrumentation, as well as providing small grants to individual researchers enabling them to use the core centers. Many, but not all, of the core centers are housed at the Delaware Biotechnology Institute in Newark. To learn more about the core centers and what type of work goes on at each one, click on the following links:
The Bioimaging Center contains state-of-the-art electron, atomic force, confocal, and light microscopes. The laser capture microdissection microscope uses a tiny laser beam to cut out and remove the precise portion of a sample (a thin slice of plant tissue, for example) that is of interest. In addition to these powerful microscopes, the center offers specimen preparation equipment, digital imaging equipment, and computerized image analysis and enhancement workstations.
The center is jointly housed at the Delaware Biotechnology Institute and in the Department of Biological Sciences at the University of Delaware in Newark.
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, and the staff is available for project consultations and can train users in equipment operation.
Also known as the microarray core facility, the Functional Genomics Center offers technology for gene expression research. A microarray — often called a “gene chip” — consists of thousands of tiny bits of genetic material arranged in a grid, usually a chemically treated glass slide. Each spot on the slide represents a single gene. The entire genetic make-up of a bacterium can fit on a single gene chip. Microarrays are used to determine which genes are active under certain conditions. The active genes result in spots that light up on the gene chip when viewed with special scanners. A computer keeps track of which gene is contained in each spot and analyzes the patterns of activity.
Researchers can take advantage of the center’s custom fabrication and testing services or use a pre-existing platform. An important aim of the microarray core facility is to assist researchers that are new to the technology. Faculty and students are encouraged to tour the facility, and to discuss their research projects. Training sessions are required on all equipment that is available to core facility users. Some of the instrumentation may only be operated by the center’s personnel, but users of the facility are welcome to observe and to learn about the operation of all pieces of equipment in the laboratory.
The Structural Biology Core Center offers nuclear magnetic resonance (NMR) and x-ray crystallography equipment for analyzing the structure of biological molecules. The NMR facility is located in Brown Laboratory, the home of the Department of Chemistry and Biochemistry on the University of Delaware main campus in Newark. It houses six nuclear magnetic resonance (NMR) spectrometers for use in analyzing samples in both solid and liquid states. The X-ray Crystallography Laboratory is located in UD’s Drake Hall and is used to analyze solid-state samples.
NMR takes advantage of the magnetic properties of atomic nuclei to provide very precise and reliable analyses that reveal physical, chemical, electronic, and structural information about molecules. NMR spectrometers can identify individual atoms in a molecule and in many cases quantify the number of each type of atom in a sample. NMR spectroscopy can also provide very detailed information about the three-dimensional structure of molecules, which is important in understanding large biological molecules such as proteins and nucleic acids. NMR spectroscopy works best when the atoms in a sample are somewhat free to move, such as in a solution. X-ray crystallography, which can determine the exact position of each atom in a molecule, works better when the atoms are held still, as in a rigid crystalline structure. Researchers grow these crystals in the lab using a variety of methods.
Both facilities provide consultation, equipment training, and sample analysis services to university researchers and collaborators. Outside industry users are accommodated on a fee-for-service basis as scheduling permits.
The BioIT Center at the Institute houses a compute cluster, a database cluster, a visualization studio, along with multiple specialized servers.
The Visualization Studio, one of the first in the country to be dedicated primarily to life-sciences research and education, is essentially a darkened room with a 100-ft2 screen, providing an interactive, immersive, 3D graphics environment for up to ten researchers and students. A pair of digital projectors that are positioned behind the 15ft x 7ft screen deliver a rear-projected, edge-blended image with a total resolution of 2240x1024 pixels. Ultrasonic sensors mounted in the ceiling of the studio track the motion of the lead researcher's head and of a handheld 3-D wand, allowing for an experience where the team members can literally immerse themselves within the data. The display is driven by two servers. An eight-processor Silicon Graphics Prism visualization supercomputer with four graphics pipelines provides a Linux environment with the power of the SGI graphics software. A dual-core HP AMD64 with a high-end NVidia graphics processor will allow the wealth of Windows software to be utilized.
In September 2003, the BioIT Center installed a Sun Microsystems SunFire V60x Linux Compute Cluster, featuring 128 dual processor 2.8 GHz Xeon CPUs, a 48-Node Myrinet Switch, 160 Gigabyte of Memory, and over a Terabyte of disk storage. Since that time, the cluster has been upgraded to include seven quad-processor Sunfire X4100M2 nodes. Funded jointly by the NIH-BRIN/INBRE grant and the NIH-COBRE “Structural and Functional Genomics” grant, this computational capacity will allow researchers to significantly reduce processing time for CPU-intensive research related to genomics, proteomics and biophysical chemistry.
In support of the organization and analysis of the rapidly growing amount of genomic and proteomic data, a cluster of six Sun Microsystems SunFire X4200M2 systems is available as a database server. Each system has 4 AMD64 cores, 16GB memory, and 300GB local disk space. In addition, an Apple 10.5TB RAID array, a 840GB Sun RAID array, and a 480GB Sun JBOD array are available as shared storage across all servers.
MySQL and Oracle database systems are available on the SunFire X4200's to organize, store and evaluate the rapidly growing amount of data, both from external databases as well from internal sources such as the microarray center, the mass spec facilities in the proteomics center, the bioimaging center and from several DNA sequencers in the DBI Network.
Complementing its computational resources, the Bioinformatics Center offers access to a variety of bioinformatics analysis tools, with state-wide licenses in place for Vector and Xpression NTI, and Sequencher as well as a broad number of publicly available sequence analysis programs. In addition, several software tools used for biomolecular modeling and visualization, including Gaussian, MOE, Amira, and Spider, have been installed at the BioIT Center to meet the needs of the biochemistry community for protein simulation and analysis.
DNA Sequencing and Genotyping
The DNA Sequencing and Genotyping Center provides genetic analyses for university research groups and outside users on a fee-for-service basis. The genetic analyzer housed in the center is a state-of-the-art instrument capable of moderate- to high-throughput sequencing (up to 656 samples/day). From a pure preparation of DNA, the center performs all the steps (cycle sequencing, purification, capillary electrophoresis, and base calling) needed to obtain the sequence of nucleotides — the As, Ts, Cs, and Gs — that make up the genetic code. The resulting sequence data is accessible to the investigator from a Web-accessible file server. The DNA Sequencing and Genotyping Center is housed in the Charles H. Allen, Jr. Biotechnology Laboratory on the campus of the College of Agriculture and Natural Resources at the University of Delaware.
The Proteomics Core Center is actually a group of instrumentation centers dedicated to the analysis of proteins. Protein molecules are composed of chains of amino acids linked together in a particular order as specified by an organism’s genetic code. The order in which the amino acids are linked gives each protein a three-dimensional structure which determines the properties and function of that protein. Some proteins are common to many forms of life, while others are unique to a particular species. Proteomics studies are generally aimed at isolating and identifying proteins and determining the sequence of amino acids that make up those proteins.
The proteomics facilities include the following:
- Mass spectrometry facilities — A mass spectrometer analyzes a chemical compound by breaking the compound down into its component ions and then exploiting the differences in mass and charge of the various ions to separate them and record their relative abundances. Located in the Lammot du Pont Laboratory at the University of Delaware, the “mass spec” facility includes both open-access, user-friendly instruments that are available for researchers to use 24/7, after training, as well as high-performance instruments for more detailed and precise analyses conducted with the assistance of technical staff.
- Protein production facility — This facility, located at the Delaware Biotechnology Institute (DBI), is designed for large-scale protein expression and purification research. It includes reactors and fermentors for cell culture, centrifuges for cell harvest and separations, homogenizers and filters for processing cell lysate (products obtained by rupturing cell membranes), and high-performance liquid chromatography equipment for protein and peptide purification.
- Protein/peptide sequencing facility — As its name suggests, this equipment, housed at DBI, determines the sequence of amino acids in proteins and peptides.
- Protein characterization facility — The protein characterization facility at DBI consists of an analytical ultracentrifuge, which can characterize a variety of biophysical properties of large organic molecules, or “macromolecules.” The abundant information provided by the analytical ultracentrifuge can help the researcher assess the sample’s heterogeneity (aggregation and purity), molecular conformation (folded or unfolded), composition (assembled or unassembled), and thermodynamic properties. Its ability to run many different samples at the same time allows researchers to study biomolecules of interest under various conditions.
Scientific research often involves observing what happens when one factor, called a variable, is changed while all other factors remain the same. For plant researchers, this amount of control requires special rooms where variables such as light, temperature, and humidity can be carefully set and monitored. The Delaware Biotechnology Institute maintains two walk-in growth chambers that are shared by multiple research groups. Conditions in the growth chambers are tracked at all times by a computer that can notify a staff member if the growth conditions stray from specified limits.
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