Research Interests
The Division of Quantitative Sciences includes the laboratories of Analytical, Cellular, and Molecular Microscopy (ACMM), Microarray Technology, Computational Biology, Molecular Epidemiology, and Mass Spectrometry and Proteomics. The Division’s laboratories use objective measures to define pathophysiologic events and processes.
The ACMM laboratory prepares samples by either paraffin or frozen methods and has programs in pathology, histology, and imaging to describe and visualize changes in cell, tissue, or organ structure. Our imaging instruments allow us to visualize cells and their components with striking clarity, and they enable researchers to determine where in a cell particular molecules are located. An archive of pathology tissues in paraffin blocks (Van Andel Tissue Repository, or VATR) is being accumulated with the cooperation of local hospitals. The archive currently has approximately 250,000 paraffin blocks representing 150,000 cases. In collaboration with Tom Barney from VAI-IT, clinical data is being added into VATR for hundreds of the samples each week by digital parsing of pathology report texts sent electronically from the hospital files. VATR is used to track samples coming from the hospitals, along with all of the data and images generated from research. Images from the Aperio ScanScope are automatically imported into VATR and associated with the appropriate sample. The ACMM lab also carries out research that will improve our ability to quantify images. We are able to image using either fluorescent (e.g., FITC, GFP) or chromatic agents (e.g., DAB, H&E) and separate the components using our confocal, Nuance, or Maestro instruments.
The Laboratory of Microarray Technology provides gene expression arrays, miRNA arrays, and array CGH using the Agilent microarray platform and cDNA platform capability. Samples can be prepared from a variety of species. Genomic DNA or total RNA from a wide range of tissues including blood and fresh or frozen tissues have been analyzed. A recent gene expression discovery was made using archived newborn blood spots, in collaboration with Dr. Nigel Paneth at MSU. We showed that thousands of gene signatures can be obtained using low-resolution gene expression arrays, enabling clinical research into the origins, epidemiology, and diagnosis of human pediatric diseases. Feature extraction software reads and processes the raw microarray image files in an automated mode. Application-specific QC reports summarize the results and provide an accurate quality assessment. The output files are compatible with statistical analysis packages such as R and GeneSpring. Microarray technology plays an important part in the discovery of genetic signatures, copy number variations, and biomarkers for therapeutic purposes.
Other highlights
Our GRAPCEP mentorship program continues for the ninth year and is now funded by Schering Plough. In 2008 we had two students from GRAPCEP, several undergraduate summer interns, and a graduate school student rotation.
