Research in the Department of Physiology depends on the availability of animal models and technologies that aid in the dissection and elucidation of human physiology and pathophysiology. Researchers in the department have recently completed the construction of inbred consomic rat strains for each chromosome. Technologies are available for chronic blood pressure measurement by indwelling catheter, tail-cuff or telemetry methods. Facilities have been constructed in-house for high-throughput chronic whole animal hypoxia exposure. In addition, the entire institution is supported by a state-of-the-art Biomedical Resource Center for the efficient and safe housing and maintenance of experimental animals.
The department has had a longstanding involvement with bioinformatics and related technologies. The advent of physiological genomics and the widespread trend towards large-scale analyses and the resulting data management has driven this need. Bioinformatics research in the department ranges from individual databases and software applications that support internal research projects to large-scale public databases that provide data and bioinformatics tools for users worldwide. The Bioinformatics Program plays a central role in the bioinformatics projects, providing the core software and database development expertise that supports many other efforts.
Large-scale public programs
- Rat Genome Database
Online model organism database for the laboratory rat, Rattus norvegicus.
- PhysGen Program for Genomics Applications
PhysGen generates large quantities of physiological data linked to specific consomic rat strains. The PGA bioinformatics component is responsible for the database, website and statistical tools that enable researchers to utilize this rich data set.
- NHLBI National Proteomics Center
MCW houses one of ten U.S. proteomics centers. Its bioinformatics component focuses on data analysis and algorithms for MS/MS proteomics experiments.
Recent papers featuring bioinformatics
DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. Nucleic Acids Res. 2005 Jul 1;33 (Web Server issue):W376-81.
Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant". J Am Soc Mass Spectrom. 2005 Jun;16(6):916-25. Epub 2005 Apr 15.
The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D485-91.
Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. 2004 Apr;14(4):651-60.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.
A more recent development in the department has been the establishment of research in the area of Computational Biology. The broad goals of this discipline include developing computational technology for predicting and analyzing the behavior of biological systems and guiding engineering-based manipulations of these systems. Physiological systems are created and maintained and destroyed by the interactions of complex networks of biological components. Traditional wet-lab science strives to identify these components and observe their interactions in vivo or in vitro. Computation biology adds mathematical modeling and offers the promise of being able to model the experimental observations and create, test and refine hypotheses in silico.
Current computational biology research in the department includes projects designed to predict the behavior of large-scale biochemical networks, developing computational models of the transport and biochemical reaction of metabolites and other substances in the myocardium systems, and multiscale modeling of the heart in health and disease.
The Department of Physiology at MCW has a reputation for consistently developing new and important technologies in experimental physiology to further our understanding of whole animal physiology. From in vivo techniques such as site-directed drug infusions, muscle stimulation for induction of angiogenesis and innovative models of stroke to in situ models such as renal micropuncture and television microscopy for vessel reactivity studies, Physiology Department faculty members have developed a large arsenal of tools for conducting cutting-edge research.
A technology platform is comprised of both the research expertise and the technology needed to enable virtually any investigator at MCW to conduct state-of-the-art research in the area of functional genomics, particularly as it relates to human disease. Each of these technology platforms is being used by faculty members both inside and outside the Human and Molecular Genetics Center at MCW. Numerous technology platforms are being used by members of the department to further studies in physiology and genetics. Platforms are available to other Physiology Department faculty members and their laboratories within core facilities in the department and the HMGC.
High-throughput technologies for comprehensive proteome analysis are available through the National Proteomics Center at MCW, part of the Marquette University and Medical College of Wisconsin Department of Biomedical Engineering. Instrumentation and technologies currently available and used for research include a semi-automated two-dimensional gel electrophoresis system, chromatography systems for protein fractionation, and different mass spectrometers for mass analysis of peptides.
The 2-D gel system utilizes an Ettan IPGphor II (GE Healthcare) unit for gels of all sizes up to 24 cm. A Typhoon 9400 Scanner is equipped to use fluorescent dyes for quantitative analysis of proteins using DIGE technology. Protein identification is facilitated by an Ettan Spot Handling Workstation 2.1, which employs automated robotics for picking, digesting, drying and dispensing of the protein spots originating from the 2-D electrophoresis gels. The resulting peptides can be spotted from microplate wells or containers onto MALDI-TOF targets for identification. The workstation automatically processes up to 1152 samples per batch. An Ettan MALDI-Time-of-Flight (TOF) mass spectrometer is used for protein identification.
Additional proteomic analyses can be performed using a LCQ Deca XP Proteomics workstation (Thermo Finnigan), an electrospray ionization-ion trap mass spectrometer which allows the chromatographic separation of complex peptide mixtures, and the subsequent identification and amino acid sequence characterization using tandem mass spectrometry. Finally, an electrospray micro-TOF mass spectrometer (Agilent) is available to facilitated peptide fingerprinting as well as the mass spectrometric analysis of small molecules and metabolites.