The Nebraska Center for Virology Core Facilities

Microscopy Core
UNL Center for Biotechnology
Director: Dr. You (Joe) Zhou

The facility provides all NCV members with microscopy imaging systems, technical support in bio-imaging, and is helping develop strong collaborations with NCV biological researchers.

Activity/Service/Equipment Available:
• Confocal laser scanning microscope (Olympus FV500 inverted & FV500 upright)
• Olympus FMs (upright)
• Nikon FM (inverted)
• PixCell IIe Laser-Capture Micro-dissection system (LCM)
• Photo-printer (Codonics) for high quality color prints
• H-7500 Transmission electron microscope (TEM)
• S-3000N Variable Pressure SEM
• S-4700 Field Emission SEM
• Sample preparation, sectioning for TEM and SEM
• Immunohistochemical processing
• Image analysis
• Expertise in cell biology and microscopy for grant proposals
• Training for graduate students and postdocs in microscopy

Structural/Protein Core
UNL Department of Chemistry
Director: Dr. Ronald Cerny

This core supports all aspects of protein work, from purification to structural analysis. The structural biochemists from this core are contributing innovative molecular approaches for studying viral-host interactions, broadening the Center's research tools to carry inter-disciplinary research.

Activity/Service/Equipment Available:
• Exact Mass Measurement – Electron Ionization MS
• Low Resolution Fast Atom Bombardment (FAB) MS
• Exact Mass Measurement – FAB MS
• Direct Injection (single component) Electrospray Ionization (ESI)
• Liquid Chromatography – Mass Spectrometry (LC/MS)
• Matrix Assisted Laser Desorption Ionization MS (MALDI) Peptide
• Matrix Assisted Laser Desorption Ionization MS (MALDI) Protein
• 2D gel Image Analysis
• Robotic Gel Excision
• In-gel enzymatic digestion (1D and 2D Gels)
• Protein Identification (LC/MS-MS and database searching)
• Mapping Post-Translational Modifications
• Assistance in the development of LC/MS methods for biomolecules

Bioinformatics Core
UNMC Eppley Institute
Director: Dr. Simon Sherman

This core supports users in several activities: sequence analysis, molecular modeling, and generation and analysis of databases. It provides the Center's investigators with state-of-the-art tools and the computational techniques and support for solving problems related to the structure and function of biologically important molecules and will be an integral component of the studies proposed in all four projects.

Activity/Service/Equipment Available:
• Molecular Modeling - Protein structure/property analysis; conformational analysis of small molecules; molecular dynamic simulations; QSAR analysis; molecular docking; secondary and tertiary structure prediction; homology modeling of proteins; protein engineering; NMR analysis of peptides.
• DNA Microarray Analysis - Image analysis: optimization of data extraction with variety of software tools; customization for specific applications. Statistic inference: normalization/filtering/visualization; cluster analysis; data transformation; data integration.
• Genetic Sequence Analysis - Sequence alignments and consensus calculation; RNA folding and secondary structure prediction; phylogenetic analysis; searching for sequence-structure-function correlations; pattern analysis in DNA and protein sequences; gene finding and exon, intron, start and stop codon location; promoter region searching; gene identification and prediction; genome mapping; cloning project fragment assembly.
• Immunoinformatics – Potential antigenic epitope finding by predictions of proteosomal cleavage sites and binding to MHC.
• Database Developing and Mining – Database design; data warehouses.

DNA Microarray Core
UNMC Eppley Cancer Center
Director: Dr. David Kelly

This core can provide the resources, infrastructure and support to allow the rapidly evolving technology of DNA microarrays to be applied to a wide spectrum of biomedical research. The Core is a centralized state-of the-art facility that offers expertise in the design, production, use, and analysis of DNA microarrays.

Activity/Service/Equipment Available:
• Human Oligonucleotide Arrays
    - Set of two 10K chips that interrogate the full 18K+ Compugen Human oligonucleotide
    - 12.5K chip interrogating only known genes
• Mouse Oligonucleotide Arrays
     - Two 11.5 K chips that interrogate the full 22K Compugen Mouse oligonucleotide
• RNA isolation and purification
• Fluorescent probe synthesis, hybridization, washing and scanning
• Data acquisition and analysis including image segmentation, normalization, ratio determinations and gene selection
• MagnaSpotter robot
• ScanArray 4000 confocal laser scanner
• Beckman Coulter Biomek FX liquid handling system