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Capabilities and Services

The core labs at the University of Kansas support to investigators by providing assistance and training on specialized instrumentation, experimental design and data analysis.  Each lab has experienced professionals to support you throughout your project. Specific examples each of the labs offers is listed below:
MMC Core
Advanced Computing Facility
  • Computer modeling and simulation
  • High dimensional data processing
  • Knowledgeable staff with expertise in data-intensive research
  • Servers are available for researchers and general access
Analytical Proteomics
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  • Intact protein molecular weight determination
  • High resolution LC-MS analysis
  • Protein identification in complex mixtures
  • Identification of posttranslational modifications
  • MALDI-TOF MS analysis
Animal Care Unit
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  • Animal procurement
  • Husbandry
  • Training
  • Technical Services
Applied Bioinformatics
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  • Data analysis and mining in proteomics, genomics and chemistry
  • Systems biology approaches such as pathway, network and interaction analyses
  • Large scale statistical and machine learning studies
  • Protein structure, function and stability prediction, sequence and domain analyses
  • Design and implementation of relational databases and software programs
  • Workshops and one-to-one sessions for training in software programming and data analysis
BIO Center
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  • Chemistry
  • Physicochemical profiling
  • Dosage form development
  • Bio-availability and pharmacokinetics
  • In vivo screening
  • Analytical tools
  • Bio-molecular assays
  • Cell based assays
Biological Irradiation
In vitro studies: 
  • cultured mammalian cells 
  • establishment of feeder layers 
  • induction of DNA strand breaks 
  • cell survival studies 
In vivo preclinical studies: 
  • rodent tumor therapy studies 
  • spontaneous animal tumor studies 
  • normal tissue radiation tolerance and pathophysiology studies 
  • radiation physics /development studies
Biomolecular NMR
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  • Fragment library screening by STD-NMR
  • Training for new instrument users
  • Consultation on proposal preparation
  • 1D-4D NMR Data Collection.
  • Data processing, analysis, and interpretation.
  • Structure determination.
  • Heteronuclear relaxation measurements and data analysis
  • H/D exchange measurements by NMR 
  • NMR titration measurement
Center for Research Computing
  • Computer modeling and simulation
  • High dimensional data processing
  • Knowledgeable staff with expertise in data-intensive research
  • Servers are available for researchers and general access
Chemical Methodologies and Library Development
  • Computational resources for managing chemical structures and data
  • Predicts key physicochemical properties of compounds to be synthesized
  • Provides guidance in the design of diverse libraries
  • Delivers automated, high throughput mass spectrometry and NMR analyses for confirming the identity and purity of compounds in libraries
Synthesis formats
  • Solution-phase
  • Solution-phase using solid-phase reagents or scavengers
  • Solid-phase
Synthesis Capabilities
  • Serial
  • Parallel
  • Combinatorial
  • Microwave
Analysis, Purification and Compound Management
  • High-throughput analytical-scale RP HPLC/photodiode array UV/HRMS
  • High-throughput mass-directed preparative-scale RP HPLC/dual-wavelength UV/LRMS/ELSD
  • Medium-throughput, automated, 5mm tube-based 1H and 13C NMR
  • Compound formatting available in a variety of formats (vials, plates (96/384)) and solvents
Experimental and Preclinical Imaging
  • Measure drug efficacy by monitoring tumor growth of orthotopic/xenograft models by luminescence or fluorescence.
  • X-ray imaging in order to observe development of metastases in intracardiac injection or orthotopic transplantation models.
  • Bone Density Software for studying bone diseases, such as arthritis and osteoporosis, and measuring efficacy of drugs and other treatment options that may affect bone mineral and other densities. 
  • Monitor near IR fluorescent dyes in order to assess drug delivery via nanoparticles.
  • Delivery of near IR expression vectors to track gene of interest and/or tumor growth and in vivo target validation of molecular therapies.  
Genome Sequencing
  • Provides education, lab training, and assistance to researchers in experimental design, data handling, and new method development
  • High output (more data, longer wait time) and rapid run (quicker turnaround, less data) available
  • Library preparation
Genomics and Bioinformatics
  • RNA-seq analysis
  • Genome assembly (via a reference sequence or de novo)
  • Variant calling and mutation detection
  • ChIP-seq analysis
  • Restriction-site Associated DNA sequencing (RAD-seq) analysis
  • Train junior researchers in bioinformatics techniques
Genomics Facility
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  • Provides consultation for sample and experimental design
  • Microarray data generation, quality monitoring and analysis
  • MIcroarray data confirmation by real-time PCR
High Throughput Screening
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  • Discussion on screening goals, assays and instrument compatibility
  • Primary assay optimization and data analysis including protocols and selection of controls
  • Validation screening of a small library with a robust optimized assay
  • Screening the complete library of compounds
  • Data analysis and storage
  • Secondary screen development and/or screening of primary hits
  • Plating various dilutions of compounds and siRNA libraries
Immunology
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  • Assay standardization
  • Analysis of results
  • Experiment optimization
  • Analysis of multicolor flow cytometry
  • Detection of antibody interactions
  • Detection of cytokines and other soluble proteins
Instrumentation Design
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  • Laboratory automation design and development
  • Sensor and actuator implementation
  • Fabricate electronic and computer-based instrumentation and programmable mechanical devices
  • Printed circuit board layouts, machine shop plans and documentation preparation
Mass Spectrometry
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  • Gas and liquid separations
  • Biomolecule projects
  • Training on selected instruments to self-run samples
Medicinal Chemistry
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  • Preparing targeted libraries for screening and lead optimization
  • Synthesizing organic compounds on various scales (from mg to multi-gram)
  • Providing extracts from natural products
  • Assisting COBRE investigators, if requested, in the design of novel ligands and in the development of practical synthetic routes
Microfabrication and Microfluidics
The Microfabrication and Microfluidics Core (MMC) is designed to facilitate the construction and implementation of:
  • Novel devices that can be used for imaging model organisms including C. elegans, Drosophila, and zebrafish
  • Fluidic systems that can be used to study the physical properties and transport of biological fluid
  • The development of novel electrochemical based sensors for monitoring release of biomolecules from slices, cells and live animals, and (4) assistance with the development of analytical methods.
  • Capabilities and services include photolithography,  plasma (dry) etching,  wet etching, metal and dielectric material thin film deposition, electron microscopy, ellipsometry, device characterization,  laser ablation and engraving, 3D printing and CNC machining.
Microscopy and Analytical Imaging
  • Assay development, analysis and data exploration
  • Image analysis and computational processing
  • Sample prep
  • Light, electron, and scanning probe microscopy
  • 2-D DIGE Scanning & Analysis and Microarray Scanning
Molecular Graphics and Modeling
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The Molecular Graphics and Modeling Laboratory provides a number of computational services aimed toward chemical biology and translational science in biomedical research. For example:
  • Machine learning and data mining for large scale, multidimensional chemical biology data sets
  • Docking and virtual screening of small molecule ligands against protein targets of interest
  • Molecular dynamics simulation and modeling of small/macro molecules, proteins, and biomolecular systems
  • Analysis of structure-activity relationships
  • Visualization and graphics of biomolecules and biomolecular systems
  • Custom algorithm/software development along with databases and web applications
Molecular Probes
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  • Synthesis of a wide variety of molecular probes including small molecules, peptides, and protein conjugates
  • Assay development
  • Generation of zebrafish embryos, larvae, and adults
Nuclear Magnetic Resonance
  • Maintain the high field NMR spectrometers
  • Supervise training of new users
  • Assist users with design, execution, and interpretation of NMR experiments
Protein Production Group
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  • Biacore label-free binding studies
  • Fragment library screening by SPR
  • Advice on experiment design and protocol development
  • Access to FPLCs and other instrumentation for trained users
  • Consultation on proposal or manuscript preparation
  • Molecular biology in support of protein expression (cloning, mutagenesis, tagging, chimeragenesis) Design and construction of expression systems (E. coli and insect cell systems)
  • Expression and re-folding of proteins (large and small scale)
  • Protein characterization and analysis (electrophoresis, chromatography)
  • Biacore label-free binding studies
Protein Structure Lab
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  • Crystallization of an investigator’s target proteins
  • Collection of complete X-ray diffraction data sets locally and at synchrotron
  • Phase determination (experimentally or through molecular replacement)
  • Model building and refinement of structures deduced from diffraction data
  • High throughput crystallography with protein-ligand complexes
  • Publications and grant applications involving X-ray crystallographic issues
Solid State NMR
  • Expertise in interpreting solid state NMR spectra
  • Five different probe setups available allowing a broad range of accessible nuclei
  • Mixtures of molecular species can be analyzed in order to identify what species are present and how much of it
  • Determination of the degree of crosslinking in polymers, the degree of incorporation of metals into catalysts and the change in composition of plant materials from different treatments
Specialized Chemistry Center
Synthesis formats
  • Solution-phase
  • Solution-phase using solid-phase reagents or scavengers
  • Solid-phase
Synthesis Capabilities
  • Serial
  • Parallel
  • Combinatorial
  • Microwave
  • SAR expansion
  • Hit to lead
  • Probe development
Analysis, Purification and Compound Management
  • High-throughput analytical-scale RP HPLC/photodiode array UV/HRMS
  • High-throughput mass-directed preparative-scale RP HPLC/dual-wavelength UV/LRMS/ELSD
  • Medium-throughput, automated, 5mm tube-based 1H and 13C NMR
  • Compound formatting available in a variety of formats (vials, plates (96/384)) and solvents
Cheminformatics
  • Virtual compound library enumeration and screening
  • In silico property calculation, including ADME, toxicology, and metabolic profiling
  • Pharmacophore perception and docking
  • Hit clustering and data mining
  • 1D/2D/3D QSAR including COMFA, COMBINE
Center-driven projects
  • Target identification and localization using affinity labeling of probe compounds
  • Yeast three-hybrid systems as tools for identification of protein targets of probe compounds
X-Ray Crystallography
  • Utilizes diffraction methods to determine high-precision, three-dimensional solid-state structures of crystalline organic, inorganic and biological molecules and identify polycrystalline materials
  • Small-molecule single crystals can be studied with molybdenum or copper radiation
  • Macromolecular single-crystal studies
  • Qualitative powder diffraction studies
  • Analyze the textures of materials
  • Determine structures for twinned samples with multiple domains when single-domain crystals cannot be obtained

LINKS TO LAB WEBSITES

Biochemistry & Protein Science

Bioinformatics & Modeling

Cross-Disciplinary

Materials Characterization

Molecular Structures

Translational Biology

EVENTS
Ability to set up 24 NMR experiments at one time and eliminate periodic user intervention
Screen up to 100,000 compounds in two days for endpoint assays
Next-generation genome sequencing
Near-infrared and bioluminescence imaging instrumentation to track gene of interest and/or tumor growth
Expertise in the design and stability of various pharmaceutical dosage forms
More than 40 computational chemistry software programs and databases
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