Director: B. Marc Bissonnette, M.D.
Phone: (773) 702-8597
e-mail: mbisson@medicine.bsd.uchicago.edu

The Molecular Biology and Biochemistry Core of the DDRCC provides services vital to the study of the basic building blocks of cellular molecules of the digestive systems in the context of normal physiology, immune/inflammatory conditions, microbial interactions, and inflammatory bowel diseases. These include services to characterize DNA, RNA, proteins and lipids. This Core was revised in 2001 when the services and facilities of the Functional Genomics Laboratory were added, and again in 2003 when the services and facilities of the Proteomics Component were included to meet the growing and changing needs of Core users.

There are five major components: (1) DNA analysis, (2) RNA expression (3) Proteomics, (4) Lipid Composition and lipid raft preparation; (5) Specialized services and training. Specific services include:

• DNA sequencing, and non-sequencing analyses for ras and CTNNBI (coding for ?-catenin) DNA mutations.
• Gene expression studies by DNA arrays and real time PCR, including Taqman design.
• Protein studies, including proteomic analyses: MALDI-TOF, Mr determination, protein ID, and post-translational characterizations (phosphorylations, glycosylations etc); design and assistance with signal transduction experiments.
• Analysis of membrane lipid composition and lipid raft preparation.
• Specialized services, training and shared resources

1. Training: Training of laboratory personnel in each of these Core components, including real time PCR, array technology, proteomics, lipid analysis etc., are major undertaking by the Molecular Biology and Biochemistry Core staff. For example, great emphasis is placed on rigorous adherence to RNase free conditions to prevent RNA degradation or contamination for array and real time PCR studies. Similarly, the protein component provides training to obtain non-degraded proteins free of contamination (for example, keratin) for proteomic studies. Proper training in each of these areas is essential for maintaining quality control. Quarterly workshops are advertised with links on the DDRCC web page and are provided for a variety of services, including real time PCR, DNA arrays, and proteomics to all with interests in these techniques.

2. Maintenance of Shared Resources: The real time PCR component of the Molecular Biology and Biochemistry Core maintains and monitors a light cycler PCR workstation. The DNA array facility is maintained by the Functional Genomics component and the protein mass spectrometry facilities are maintained by the Proteomics Core. Each of these facilities routinely runs controls to ensure high reliability and sensitivity of their assays (see specific descriptions above for details of controls and quality assurance). All users are trained to exercise safe and appropriate laboratory procedures.

3. Discounted services and supply costs: The real time PCR component is able to provide its users with discounted purchases of Taqman probes and real time PCR supplies. This is possible through large volume purchases that significantly reduce the costs of molecular biologic reagents, including probes, DNA polymerase and reverse transcriptase. In addition, purchase from single lots helps standardize conditions needed to maintain consistent real time PCR results. Active inventory maintenance of a large number of tested Taqman probes further reduces the cost of this technique if appropriate probes are available. In the case of signal transduction studies, a large inventory of available tested antibodies reactive to total proteins and phospho-active proteins enhances the utilization of this component. As described in detail above, the DDRCC is helping to underwrite the costs of the powerful but relatively costly DNA array and proteomic technologies. DDRCC members receive substantial subsidies, amounting to a 50% reduction in sample run costs when using the DNA array or proteomics facilities.

The Molecular Biology and Biochemistry Core Director, Dr. Marc Bissonnette, and Co-Director, Dr. Judy Cho oversee the operations of all components. Dr. Xinmin Li is the Director of the Functional Genomics component. Dr. Alex Schilling is the Director of the Proteomics component. Directors are responsible for ensuring proper scientific direction and efficient use of services and facilities of their respective sections.

Preference for services and facilities are given to a) NIDDK-funded investigators, b) recipients of current pilot and feasibility funds, c) non-funded junior investigators in digestive diseases, and d) established investigators outside of the area of digestive diseases who are interested in extending their research into this area.

All components offer training and consultation as part of their services. Users are encouraged to take advantage of this if they foresee extended or heavy use of facilities. Users are asked to acknowledge the DDRCC in all publications utilizing the DDRCC Cores.

Utilization of Services and Facilities: Use of facilities and services will be subject to approval by the Core Director and Executive Committee.