Core B: Research Support Core
The RSC (RSC) of the University of Kentucky Superfund Research Center (UK-SRC) provides vital access to expertise, research resources and state of the art instrumentation to researchers engaged in all aspects of the biomedical and environmental science research projects. The RSC enhances the productivity, quality and consistency of these projects by providing a formalized mechanism for access to expert investigators and professional staff and by enabling efficient use of expensive and sophisticated instrumentation that would otherwise be beyond the capabilities of individual laboratories to acquire and support. The RSC provides services in “Quantitative Biology” encompassing biostatistics support for experimental design and computational infrastructure for data management, analysis and sharing. Bioanalytical services provide technologies for quantitation and structural analysis of toxins, nutritional protectants and markers and mediators of oxidative stress and inflammation. The RSC is now also developing advanced mass spectrometry-based strategies for identification of biomarkers of PCB toxicity and nutritional protection from PCB exposure.
Establishment of a coordinated effort in the form of the Research Support Core maximizes both the research and cost effectiveness of our SRP investigators. This Core is divided into two major components directed by an expert in each area:
- Bioanalytical Component - Directed by Dr. Andrew Morris
- Quantitative Biology Component - Directed by Dr. Arnold Stromberg
The overall activity of the Research Support Core is managed by Dr. Morris in close collaboration with the coordinators of individual components, Dr. Hennig (the Director of UK-SRC) and the Administration Core, and the Project Leaders of all individual grants.
- Provide unified infrastructure for data management that can be used to share information between the component projects enabling integration of observations that will illuminate common pathways of PCB toxicity and nutritional protection.
- Provide expertise in biostatistics that is vitally necessary for the design and interpretation of experiments conducted by all of the participating investigators and to continue to expand and refine these capabilities to encompass informatics approaches to management of large data sets necessary for application and implementation of gene expression profiling and mass spectrometry.
- Provide access to state of the art mass spectrometry based methods for detection and quantitation of PCBs, nutritional protectants and other small molecules and mediators that are of shared importance to the participating investigators for calibration, validation and monitoring of PCB sensing and remediation technologies by the environmental science projects and for ensuring consistency and relevance to human exposure of PCB doses used in studies with cultured cell and animal models.
- Leverage recent institutional investments in advanced mass spectrometry instrumentation and research infrastructure for the further development of the metabolomics capabilities of the bioanalytical component of the RSC.
- Provide a conduit for synergistic interactions between the UK-SRC Center and Clinical and Translational researchers at the University of Kentucky who are engaged in studies of nutritional protection in case controlled clinical studies of cardiovascular and metabolic disease
The Research Support Core is directed by Dr. Andrew J. Morris, who also oversees the Bioanalytical Component. Dr. Morris is a Professor of Cardiovascular Medicine. Dr. Morris’s personal research program concerns studies of pathways of lipid metabolism involved in inflammation, cardiovascular and metabolic diseases. Professional staff of the Research Support Core includes Ms. Manjula Sunkara and and Dr. Sony Soman, who are responsible for day to day operations of the core. Drs. Sunkara and Soman have extensive backgrounds in analytical chemistry with experience in the design and implementation of tandem mass spectrometry assays for small molecules gained in both academia and industry. Dr. Arnold J. Stromberg directs the Quantitative Biology Component. Dr. Stromberg is the Chair of the Statistics Department and has published extensively in the area of computational analytical methods for large scale analysis of gene expression data.
- AB Sciex 4000 Q-Trap hybrid triple quadrupole linear ion trap mass spectrometers
- ABSciex 5600 “Triple TOF” hybrid quadrupole time of flight mass spectrometer.
- Agilent 6890 gas chromatograph/ electron capture detector and Agilent 5975 inert mass selective detector.
- Biorad Bioplex 200 suspension array reader and MAGPIX multiplex analyzer.
- Nikon TE200/Nikon A1R resonance scanning confocal microscope.
- LiCor Infra-Red Blot Imaging System.
- HPLC systems with fluorescence and electrochemical detection capabilities.
- Seahorse XF24 Extracellular Flux Analyzer.
- Thermo LTQ Velos Orbitrap Mass Spectrometer with Electron Transfer Dissociation and Eksigent Nano LC system.
- Bruker EMX ESR spectrometer.
- Routine Assays, Services and Representative Collaborative Studies
- SRC-Wide PCB measurements to ensure inter project consistency and relevance to human exposure.
- Quantitation of lipids, metabolites, small molecule toxins and therapeutics.
- Targeted Metabolomics/Lipidomics.
- Unbiased Metabolomics/Lipidomics for biomarker discovery.
- Confocal Microscopy.
- Suspension array analysis of inflammatory mediators.
- Free Radical Biology Core Services.
- Analysis of markers of oxidative and nitrosative stress
- Measurements of mitochondrial function and cellular phenotypes associated with oxidative stress
- Redox Proteomics.
- Electron paramagnetic resonance (EPR) detection of free radicals.
Intellectual Property (IP) Development and Technology Transfer
The University of Kentucky strives to provide an atmosphere where the spirit of inquiry flourishes and where this scholarly inquiry, in the form of research and other creative activity, ultimately leads to tangible benefits for society. The University of Kentucky Intellectual Property Development Guide is to assist all faculty, clinicians, staff and students who make a discovery or conceive or develop an innovation while at the University of Kentucky.
- how to make the IP office aware of an invention or innovation,
- a flowchart of UK’s IP disclosure and protection process,
- a commercialization pathway designed specifically for inventions and innovations that arise from clinical practice,
- information about patents, copyrights, trademarks, and trade secrets, and
- Intellectual Property Committee meeting dates and members,
- UK’s royalty structure.
The guide also contains FAQs and a table of whom to contact about various IP issues. The Website for the Office of Intellectual Property Development and Technology Transfer is http://www.research.uky.edu/ip/. The IP guide is also available here.
Routine Assays, Services and Representative Collaborative and Developmental Studies
SRC-Wide PCB measurements to ensure inter project consistency and relevance to human exposure.
- Quantitation of lipids, metabolites, small molecule toxins and therapeutics. We have developed methods for detection and quantitation of toxins, metabolites, and nutrients that are of broad importance to the SRC researchers including neutral lipids (sterols, cholesterol esters, oxysterols, mono- di and tri- glycerides), free fatty acids, prostaglandins and fatty acid derived mediators (Prostaglandin F1 alpha, Tetranor prostaglandin E metabolites, Thromboxane B2, 15-keto Prostaglandin E2, Prostaglandin D2, Prostaglandin E2, 6-Keto Prostaglandin F1 alpha, F and J type Isoprostanes, resolvin D1, resolvin D2, maresin, DiHDoHE, HETE, Lipoxin A4), all major classes of glycro- and sphingo- phospholipids, polyphenols and nutritional protectants (ECGC and Resveratrol) and PCBs and their metabolites including oxidized species and glucuronide conjugates.
- Targeted Metabolomics/Lipidomics. We are working with UK-SRC investigators to develop and apply mass spectrometry based methods for lipid and metabolite profiling that we hope could lead to the identification of biomarkers of PCB toxicity and the protective effects of nutrition and exercise.
- Unbiased Metabolomics/Lipidomics for biomarker discovery. This approach uses our AB Sciex 5600 instrument to provide unprecedented depth and coverage of analytes and is highly suitable for unbiased metabolite profiling and is being used to identify lipid and metabolite signatures associated with PCB exposure or protective effects of nutrients, diet and exercise.
- Confocal Microscopy. Confocal microscopy is of broad importance to the biomedical research projects for imaging proteins, markers and mediators of PCB toxicity and nutritional protection in cultured cells and tissues. For example, this includes studies of experimentally induced atherosclerosis in mice and the impact of PCBs and nutritional protectants on the organization and subcellular localization of proteins involved in PCB sensing and protection from oxidative stress in cultured vascular endothelial cells.
- Suspension array analysis of inflammatory mediators. Measurements of peptide and protein cytokines and inflammatory mediators in plasma (and some cases tissue samples) from human subjects and mice. The core personnel are responsible for instrument calibration and validation and can assist users with sample collection and preparation. Routinely measured analytes of direct relevance to the biomedical SRC investigators include IL-6, IL-1beta, IL-10, MCP-1, VEGF, TNFalpha, RANTEs, IFNgamma, G-CSF and adiponectin.
Free Radical Biology Core Services. A partnership with the Free Radical Biology Core (FRBC) of the University of Kentucky Markey Cancer Center provides the following capabitlies:
- Analysis of markers of oxidative and nitrosative stress is accomplished using immunological approaches coupled in some cases with direct measurements using HPLC methods with fluorescence or electrochemical detection that we are also working to conduct using HPLC MS/MS. Available assays include measurements of protein carbonyls and 3-nitrotyrosine and protein-bound 4-hydroxy-2-trans-nonenal, HNE as indices of protein and lipid oxidation. Measurements of 8-hydroxy-2 deoxy-guanosine or 8-hydroxy-2-guanosine as indices of DNA and RNA oxidation. Analyses of antioxidant enzyme activities and levels. Analyses of reduced and oxidized glutathione (NAD+/NADH, NADP+/NADPH).
- Measurements of mitochondrial function and cellular phenotypes associated with oxidative stress are accomplished by measurements of changes in oxygen consumption and pH in intact cells using the Seahorse flux analyzer, measurements and manipulation of the expression of antioxidant or redox-related proteins (including those that regulate the redox status of cells, scavenge free radicals, and repair oxidative/nitrosative damage) in cultured cells.
- Redox Proteomics. Identification of proteins with differential expression in systems of interest using standard proteomics approaches (protein separation, digestion, ESI-MS/MS sequence analysis of tryptic peptides using a Thermo LTQ-Orbitrap mass spectrometer whic can be extended to encompass so called “redox proteomics” in which proteins containing oxidized or nitrosylated residues or adducts formed by reaction with products of lipid oxidation are targeted for analysis either directly or after chemical derivatization.
- Electron paramagnetic resonance (EPR) detection of free radicals. EPR is the only technique that can directly detect and quantitate free radicals in live experimental systems. These services are provided using state-of-the-art equipment for detection and quantitation of free radicals, antioxidants, and pro-oxidants using spin trapping approaches.
Detailed Research Support Core Instrumentation Database
- Two AB Sciex 4000 Q-Trap hybrid triple quadrupole linear ion trap mass spectrometers with Shimadzu automated HPLC systems for small molecule quantitation by selective reaction monitoring mode tandem mass spectrometry. One of these instruments can also be operated with an Advion Nanomate Chip based nano ESI source for direct infusion mass spectrometry. One these instruments can also be operated with an ABSciex Flashquant Vacuum MALDI source for high throughput quantitation of small molecules and tissue imaging mass spectrometry.
- ABSciex 5600 “Triple TOF” hybrid quadrupole time of flight mass spectrometer. The instrumentis operated with an Eksigent micro flow HPLC system which incorporates a low dispersion ESI electrode for capillary HPLC and automated flow infusion of samples or a Shimadzu HPLC system. This instrument offers high mass accuracy and mass resolution at fast scan speeds making it a uniquely powerful tool for targeted and unbiased metabolite profiling and metabolism studies using stable isotope tracers
- An Agilent 6890 gas chromatograph/ electron capture detector and Agilent 5975 inert mass selective detector. Is used primarily for routine analysis of PCBs by well documented EPA compliant methods particularly in environmental samples where unbiased identification of PCBs cannot be accomplished using our HPLC ESI MS/MS methods.
- Instrumentation for sample preparation. Systems for automated solid phase extraction, solvent evaporation and sample concentration are available.
- Data Analysis capabilities are provided by workstation computers running a variety of software packages.
- A Biorad Bioplex 200 suspension array reader and MAGPIX multiplex analyzer. For measurements peptide hormones, inflammatory cytokines, adipokines and other relevant classes of mediators in human and mouse tissue samples including blood plasma using multiplexed fluorescence antibody based assays.
- A Nikon TE200/Nikon A1R resonance scanning confocal microscope. Is used to acquire confocal images at video frame rates as well as perform standard imaging of fixed specimens.
- Access to the following instrumentation is provided through our arrangement with the Markey Cancer Center Free Radical Biology Core:
- LiCor Infra-Red Blot Imaging System. For immunochemical analysis of markers of oxidative and nitrosative stress by western blotting with adduct specific antibodies.
- Two HPLC systems with fluorescence and electrochemical detection capabilities. For determination of Redox-coupled reduced glutathione and oxidized glutathione, NAD(P)H and NAD(P)+ .
- Seahorse XF24 Extracellular Flux Analyzer. For measurements of mitochondrial status and respiration that are altered under conditions of oxidative and nitrosative stress.
- Thermo LTQ Velos Orbitrap Mass Spectrometer with Electron Transfer Dissociation and Eksigent Nano LC system. For identification of proteins that are subject to oxidation or nitrosylation including MS/MS based sequence analyses of tryptic peptides to identify oxidatively modified amino acids.
- Bruker EMX ESR spectrometer. For identification of transient and reactive free radicals by spin trapping.