The Departmental Roadmap

II. Overview of Basic Research Activities

New Technologies and Expansion of Core Facilities

In the NIH Roadmap, there was a clear understanding that substantial resources must be designated for new technology development. Initiatives will be made to fund core facilities providing such technologies to large groups of researchers, rather than to individual scientists. Within the Department, we have a tradition of developing such core facilities, and plan to expand and augment these existing programs with new equipment and/or expertise. Currently, the Department has dedicated cores for DNA Sequencing & Genotyping, Animal Pathology, Microscopy, and Mass Spectroscopy & Proteomics. These Cores have obtained substantial NIH funding and service researchers throughout the Institution. These Cores will need to be maintained, updated and expanded as our research enterprise grows. Our specific plans for each of these core facilities is described briefly below:

1. DNA Sequencing and Genotyping Core
2. Mass Spectroscopy/Preteomics Core
3. Animal Pathology Core
4. Microscopy Core

1. DNA Sequencing and Genotyping Core

DNA Sequencing: At present, the DNAcore provides for the DNA sequencing needs of MSSM researchers. Our current throughput of about 50,000 sequences per year is easily managed on our two ABI 3700 96 capillary array instruments. We anticipate a continued increase in resequencing as investigators screen for mutations in human diseases, generate recombinant constructs requiring sequence validation, and pursue comparative genomics in other organisms. The DNAcore’s recent acquisition of a Beckman Biomek FX robotic workstation obtained by a equipment grant from the NIH (NCRR), will facilitate high-throughput genomics. The robotic will speed the accurate preparation of cycle sequencing reactions, automated dye terminator removal, determine DNA concentrations, and normalize samples for optimal read-length and quality.

Oligonucleotide Synthesis and Purification: The DNAcore can synthesize up to 12 oligonucleotides per day on its ABI 394 DNA synthesizer and companion Savant OligoPrep for automated deprotection and lyophilization. This service is primarily used by investigators who need faster turnaround time than possible from commercial vendors or who need special services such as modified oligos and oligo purification. We have an HPLC system for rapid purification of large quantities of oligonucleotides.

LOH and Linkage Analyses: The DNAcore supports LOH and linkage studies and by analysis of microsatellite markers on ABI 3100 and ABI 377 sequencers.

Mutation/SNP Screening: The DNAcore provides mutation and SNP screening using a Transgenomic WAVE™ denaturing high-performance liquid chromatography (DHPLC) instrument with a 192 tube autosampler. This instrument is particularly useful in mutation identification, SNP discovery, and analysis of candidate genes in target populations as it is nearly as sensitive as sequencing, but about 1/5th the cost.

Bioinformatics: The DNAcore and the Department of Genetics and Genomic Sciences also supports Bioinformatics initiatives through its support of linkage analysis software on the DNAcore Xserve server, discount distribution of the MacVector program, and support of Genotyping and Sequence analysis programs.

Future Goals of the DNAcore: The DNAcore foresees the need for investments in new technology to support the research endeavors of Departmental and Institutional Investigators, particularly in genomics, proteomics, and bioinformatics in the following areas.

Gene Association Studies: In the next five years, the genetic analysis of complex traits will become a greater focus of research, and therefore, there will be a need for high-throughput SNP analyses for association studies. Several expensive technologies are available; the equipment investment will be $100,000 - $500,000. The DNAcore is well-positioned to be able to achieve the high-throughput sample preparation and handling required by these technologies due to the recent acquisition of a Beckman-Coulter Biomek robotic liquid handler with both 96 tip and variable span 8 heads.

Proteomics: In addition, the Biomek FX will support high-throughput proteomics endeavors, particularly in concert with the Beckman 2D profiler and Mass spec instruments in the Department of Genetics and Genomic Sciences.

Bioinformatics: The DNAcore and the Department of Genetics and Genomic Sciences also supports Bioinformatics initiatives through its support of linkage analysis software on the DNAcore Xserve server, discount distribution of the MacVector program, and support of Genotyping and Sequence analysis programs.

2. Mass Spectroscopy/ Proteomics Core

Proteomics encompasses systematic studies of the identity, changing abundance, distribution, modifications, interactions, structure and function of large sets of proteins, as well as their involvement in disease. Since multiple proteins can be obtained from each gene, there are more proteins in the human proteome than the 30,000–40,000 genes estimated for the genome. As a technology, proteomics provides tools to study proteins in more comprehensive and systematic ways. It can be used as an analytical means to discover biomarkers of human disease, potentially identify new targets for drug discovery, and elucidate molecular mechanisms of disease pathology.

There is a growing need to further enhance our existing Mass Spectrometry/Proteomics Core to serve better both basic and clinical research. The Mass Spectrometry/Proteomics Core in the Department currently provides state-of-the art proteomic analysis. The core has 2D-gel electrophoresis equipment, an Applied Biosystems Voyager-DE STR matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS), a Thermo Finnigan LCQ electrospray ionization ion trap mass spectrometer (ESI-IT-MS), and a new Applied Biosystems QSTAR Hybrid LC/MS/MS quadrupole TOF mass spectrometer. The goal of the core is to remain state-of-the-art in proteomics and protein analysis. To that end, additional equipment is needed, including a 2-dimensional protein chromatography system, a 2-dimensional fluorescence differential gel system for quantitative proteomic research, as well as the next generation of mass spectrometers.

3. Animal Pathology Core

Our Animal Pathology Core is a Departmental facility equipped with two dissecting microscopes, a paraffin embedding station, microtome and cryostat. Departmental staff members are trained in the use of this equipment, and can prepare tissue sections for routine, light microscopic analysis, as well as in situ hybridization. Having such a facility on site has greatly enhanced our translational research projects using animal models, and we anticipate that the need for this facility will increase over the next five years as more translational research is undertaken. Thus, the Committee recommends that this facility be expanded by purchasing one additional light microscope and a second embedding station for histological analysis. In addition, the Committee feels that this core may be of considerable service to the Institution at large since many investigators routinely working with rodent models do not have access to equipment needed to prepare materials for histological analysis. Thus, discussions should be undertaken with the Dean of Research to investigate whether these services should be offered outside of the Department on a fee-for-service basis.

4. Microscopy Core

Our Microscopy Core currently has a Nikon Eclipse fluorescence microscope equipped with a deconvolution software package. To expand this Core, the Roadmap Committee recommends that we purchase a confocal microscopy system capable of exciting in the UV range so that fluorochomes we are currently unable to use with our current system can be utilized. This system needs to be equipped with software and hardware that would allow for calcium, pH and other cellular function indicator measurements. In addition, it is critical that the system is equipped to carry out fluorescence resonance emission transfer (FRET) analyses.