The RCMI Cell and Molecular Biology Core (CMB Core) provides focused services using cell and molecular biological techniques. It also provides access, upkeep and training on “state of the art” equipment. Funding by the RMCI allows these services to be offered at minimal cost to users of the core. Technical services and necessary consumable supplies are provided to support cancer research projects at Xavier University. The long term goal of the Cell and Molecular Biology Core is to enhance the overall biomedical research capabilities at Xavier University.
Skripnikova, Elena, Ph.D.
Role: Research Associate
"The MyiQ Optical Module, builds upon the strengths of the iCycler thermal cycler, and provides an easy and efficient means for single-color experimentation. The CCD detector allows for simultaneous imaging of all 96 wells. This results in a comprehensive data set illustrating the behavior of the reactions during each cycle. Simultaneous image collection ensures that well-to-well data may be compared reliably. The MyiQ system reports data on the PCR in progress in real-time, allowing immediate feedback on reaction success. All of these features found in the MyiQ system hardware were built to promote reliability and flexibility"
"The Rotor-Gene Q combined with optimized QIAGEN real-time PCR kits and assays offer reliable results in all real-time PCR and high-resolution melt applications, including:
* Gene expression analysis
* Pathogen detection
* DNA methylation analysis
* Mutation scanning
* High Resolution Melting analysis"
1. Cell Viability Assay
2. Proliferation Assay
1. Maintain Cell and plate as requested
2. Freeze Away stocks
1. Heatmap generation
2. Gene Ontology Analysis
3. Pathway analysis and custom pathway creation
Studies offered include:
1. Kinase Assays - IC50 (Invitrogen)
2. Nuclear Receptor Binding Assays
3. RNAi or shRNA
4. Cell-Based Assays (transfection plates)
1. Real time rt-PCR (SABiosciences)
a. Commercial PCR Arrays
- Pathway/ disease focused
- miRNA screen
b. Custom real time rt-PCR
2. Other PCR Arrays
a. DNA Methylation Array
b. DNA Somatic Mutation Array
Mass Spectrometry based Global Scale Protein Profiling:
- TMT Mass Tagging (for quantitative protein expression analysis)
- Phospho-protein Profiling (in development)
1. Protein extraction, purification and quantification
2. DNA/RNA extraction, purification and quantification
3. Cloning (Primer design, PCR, Ligation, DNA product production and validation)
4. Recombinant Protein expression (Bacterial, Mammalian cell culture)
5. Gel electrophoresis and Western Blotting
6. Immunoprecipitation/affinity interactions
"Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data."
"MeV is a desktop application for the analysis, visualization and data-mining of large-scale genomic data. It is a versatile microarray tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. Thousands of biologists have downloaded and used MeV to examine their data with an easy-to-use, graphical interface.
MeV generates informative and interrelated displays of expression and annotation data from single or multiple experiments. A huge array of alrogithms are included in MeV modules, and are available at a button-click, such as K-means clustering, Hierarchical clustering, t-Tests, Significance Analysis of Microarrays, Gene Set Enrichment Analysis, and EASE."
"The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists according to:
- Gene families and subfamilies, including annotated phylogenetic trees
- Gene Ontology classes: molecular function, biological process, cellular component
- PANTHER Protein Classes
- Pathways, including diagrams
PANTHER is part of the Gene Ontology Reference Genome Project. "
"PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing."