UAB Institutional Research Core Program

UAB Institutional Research Core Program (IRCP)

Supporting Research Excellence at the University of Alabama at Birmingham

An Overview of UAB's Core Facilities

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Background and Mission

IRCP Overview

The UAB Institutional Research Core Program (IRCP) serves as a cornerstone of UAB's commitment to advancing research and scholarship across various disciplines.

Mission

  • Promote the development and operation of outstanding core facilities to serve UAB investigators
  • Assist cores in developing sound business plans
  • Implement robust standard operating and quality assurance procedures
  • Provide customer-focused services that facilitate research advancement
  • Maintain financial stability of core facilities

Vision

UAB will be a regional, national and world leader in academic research infrastructure and environment making it the institution of choice for research scientists.

Structure and Organization

IRCP Organizational Structure

Oversight

  • Vice President for Research - Chris Brown
  • the IRCP Executive Committee
  • IRCP Directors - Michael Bertram, PhD, MBA and Mark Bolding, PhD

Core Selection Criteria

  • Strategic alignment with UAB's research mission
  • Accessibility to all UAB faculty
  • Proper oversight and management structure
  • Documented research productivity and user satisfaction
  • Sound financial management practices
Core Facilities Overview

UAB IRCP Core Facilities

The UAB IRCP encompasses 18 core facilities across a wide range of scientific disciplines:

  • Advanced Materials Characterization Core (AMCC)
  • Animal Behavioral Assessment Core (ABAC)
  • Bio-Analytical Redox Biology (BARB) Core
  • UAB Biological Data Science Core (U-BDS)
  • Cryo-Electron Microscopy Facility (CEMF)
  • Flow Cytometry and Single Cell Core Facility (FCSC)
  • Genomics Core
  • High Resolution Imaging Facility (HRIF)
  • Human Imaging Shared Facility (HISF)
  • Mass Spectrometry/Proteomics Shared Facility (MSP)
  • Metabolism Core
  • Microbiome Core
  • MMR-CBPR-QR Core
  • Nuclear Magnetic Resonance Facility (NMR)
  • Preclinical Imaging Shared Facility (PISF)
  • Research MRI Core (RMRIC)
  • Social Determinants of Health (SDH) Core
  • Transgenic & Genetically Engineered Models Core
Core Facility: AMCC

Advanced Materials Characterization Core (AMCC)

Provides comprehensive analytical services for a wide array of materials, catering to UAB researchers, external educational institutions, and industries.

Directors: Dr. Paul Baker, Dr. Vinoy Thomas

Purpose

The AMCC facilitates research and development of materials by offering detailed characterization of fundamental properties including elemental composition, chemical bonds, crystal structure, surface features, and overall chemical structure.

Key Services

  • Elemental composition analysis
  • Chemical bonding characterization
  • Crystal structure determination
  • Surface imaging at microscopic scale
  • Chemical structure analysis

Key Equipment

  • X-ray photoelectron spectroscopy (XPS)
  • X-ray diffraction (XRD)
  • Scanning electron microscopy (SEM) with EDX
  • Raman spectroscopy
  • Nanoindenter for material hardness testing
Core Facility: ABAC

Animal Behavioral Assessment Core (ABAC)

Dedicated facility for comprehensive behavioral testing of mice and rats to evaluate neurological function, cognitive abilities, and behavioral traits.

Director: Dr. Craig Powell | Managing Director: Dr. Ayanabha Chakraborti

Purpose

The ABAC facilitates understanding of relationships between genetic conditions, environmental/chemical exposures, anatomical lesions, and their behavioral consequences. The core provides critical behavioral data for preclinical intervention trials.

Key Services

  • SHIRPA neurological screening battery
  • Motor skills testing (Rotorod, Rotometer)
  • 24-hour activity monitoring
  • Emotional and exploratory behavior assessment
  • Learning and memory tests (T-maze, Y-maze, Morris water maze)
  • Running wheel monitoring for activity and circadian rhythms

Key Equipment

  • Specialized mazes (Morris water maze, 8-arm radial maze)
  • Video tracking systems for activity quantification
  • Shuttle boxes for basic memory skills testing
  • Forced running wheel and running wheel cages
Core Facility: BARB

Bio-Analytical Redox Biology (BARB) Core

State-of-the-art facility providing comprehensive services in mitochondrial metabolism, oxidative stress assessment, and analysis of psychological/physiological stress.

Director: Dr. Doug Moellering | Operational Director: Dr. Melissa Sammy

Purpose

The BARB Core serves as a central hub that facilitates and promotes the development of multidisciplinary research projects among independently funded research programs both within UAB and at institutions worldwide.

Key Services

  • Hormonal chronic stress analysis (cortisol in hair/nails)
  • Mitochondrial DNA damage-associated molecular patterns
  • Electron transport chain kinetics analysis
  • Mitochondrial bioenergetics (Seahorse XFe96)
  • High-quality mitochondrial isolation
  • Redox assays for oxidative stress measurement

Key Equipment

  • Multiple Oroboros Oxygraph-2k fluorometers
  • Seahorse XFe96 Bioanalyzer
  • Equipment for standardized mitochondrial isolation
Core Facility: U-BDS

UAB Biological Data Science Core (U-BDS)

Provides cutting-edge computational biology capabilities for identifying, characterizing, and quantifying molecular variation and its impact on biological systems.

Director: Dr. Liz Worthey | Managing Director: Dr. Lara Ianov

Purpose

The U-BDS provides exceptional computational analysis and method development support to the UAB research community, with the goal of identifying, characterizing, and quantifying molecular variation and its impact on biological systems.

Key Services

  • Genomics data analysis and interpretation
  • Transcriptomics data analysis (RNA-Seq, miRNA-Seq)
  • Single-cell/single-nuclei RNA-Seq analyses
  • Systems biology approaches for translational medicine
  • Grant application assistance

Key Equipment

  • High-performance computing clusters
  • Specialized bioinformatics software
  • Secure data management systems
  • Custom analysis tools (e.g., SEAS1, PAGER)
Core Facility: CEMF

Cryo-Electron Microscopy Facility (CEMF)

Provides access and training in cutting-edge cryo-electron microscopy for characterizing biological samples from cellular to atomic resolution.

Director: Dr. Terje Dokland | Facility Manager: Dr. James Kizziah

Purpose

The CEMF advances UAB's research mission by supporting the application of cryo-electron microscopy (cryo-EM) in scientific discoveries. The facility enables detailed characterization of biological samples at resolutions ranging from cellular to atomic scale.

Key Services

  • Sample preparation for negative staining and cryo-EM
  • Room temperature and cryogenic imaging
  • Data collection and processing
  • 3D reconstruction and structural analysis
  • Comprehensive user training

Key Equipment

  • Thermo Fisher Glacios 2 electron microscope (200kV)
  • Talos F200C G2 electron microscope
  • FEI Vitrobot Mark IV for sample vitrification
  • PIE Scientific Tergeo EM Plasma Cleaner
  • Specialized cryo sample holders
Core Facility: FCSC

Flow Cytometry and Single Cell Core Facility (FCSC)

Internationally recognized facility providing advanced cell analysis and single-cell technologies to significantly advance basic and clinical research.

Director: Dr. Troy Randall | Associate Director: Dr. Vidya Sagar Hanumanthu

Purpose

The FCSC provides state-of-the-art equipment and services designed to advance both basic and clinical research endeavors. The facility empowers UAB investigators with sophisticated cellular analysis, sorting, and single-cell genomic/transcriptomic studies.

Key Services

  • High-parameter cell analysis
  • Precise cell sorting based on multiple parameters
  • Single-cell RNA sequencing
  • Spatial transcriptomics
  • Multiplex immunofluorescence

Key Equipment

  • BD FACSymphony S6 six-way cell sorter
  • BD FACSymphony A5 high-parameter cell analyzer
  • 10x Xenium single-cell spatial transcriptomics platform
  • Lunaphore COMET multiplex immunofluorescence instrument
Core Facility: Genomics Core

Genomics Core Laboratories

Central resource offering comprehensive genomic services, from basic sequencing to complex genotyping and gene expression studies.

Directors: Dr. Michael Crowley, Dr. David Crossman

Purpose

The Genomics Core provides UAB investigators with the necessary tools and support to conduct a wide range of genomic analyses, from basic sequencing to complex genotyping and gene expression studies for diverse research applications.

Key Services

  • Standard Sanger sequencing
  • Next-Generation Sequencing (NGS)
  • Custom genotyping (single SNP to >5 million SNPs)
  • Whole genome linkage and association studies
  • Gene expression analysis
  • Methylation analysis for epigenetic studies
  • Bioinformatic analysis services

Key Equipment

  • Illumina NextSeq500 instrument
  • Illumina MiSeq sequencer
  • Applied Biosystems 3730xl DNA Analyzer
  • Real-Time PCR systems
Core Facility: HRIF

High Resolution Imaging Facility (HRIF)

Central hub providing state-of-the-art imaging resources and comprehensive technical support for a wide range of biological and biomedical research applications.

Director: Dr. Alexa Mattheyses

Purpose

The HRIF facilitates high-quality imaging for a wide range of biological and biomedical research applications, offering both electron microscopy and light microscopy capabilities with expert support and training.

Key Services

  • Confocal microscopy for high-resolution optical sectioning
  • Live cell imaging for dynamic biological processes
  • Multi-photon microscopy for deep tissue imaging
  • Widefield microscopy for general imaging needs
  • Super-resolution microscopy to overcome diffraction limits
  • Electron microscopy for ultrastructural details
  • Advanced image analysis

Key Equipment

  • Zeiss Lightsheet 7 microscope
  • Nikon A1R HD confocal microscope
  • Leica Stellaris 5 confocal microscope
  • Nikon SIM and dSTORM super-resolution microscopes
Core Facility: HISF

Human Imaging Shared Facility (HISF)

Vital resource providing advanced medical imaging resources and comprehensive services for clinical studies, with a special focus on oncologic research at the O'Neal Cancer Center.

Directors: Dr. Sam Galgano, Dr. Elainea Smith

Purpose

The HISF fosters excellence in both patient care and research by offering world-class imaging and analysis capabilities for clinical trials and validation of novel imaging biomarkers across a range of medical disciplines.

Key Services

  • Coordination of clinical trials with imaging endpoints
  • Validation of novel imaging biomarkers
  • Support for first-in-human to phase I-III clinical trials
  • Standardized imaging research protocols
  • Coordination of non-routine imaging services

Key Equipment

  • X-rays and computed tomography (CT) systems
  • Magnetic resonance imaging (MRI) scanners
  • Positron emission tomography-CT (PET CT)
  • Positron emission tomography-MRI (PET MRI)
  • Mammography and ultrasound equipment
Core Facility: MSP

Mass Spectrometry/Proteomics Shared Facility

State-of-the-art facility providing comprehensive capabilities for the identification, characterization, and quantification of proteins and their post-translational modifications.

Director: Dr. James A. Mobley | Operations Director: Dr. Kyoko Kojima

Purpose

The MSP supports the diverse research needs of UAB Cancer Center members by enabling the identification, characterization, and quantification of proteins and their post-translational modifications from various biological samples, including cells, biological fluids, and tissues.

Key Services

  • Single and complex protein identification
  • Quantitative proteomics (label-free, iTRAQ, TMT, SILAC)
  • Post-translational modification (PTM) analysis
  • Advanced statistical and systems biology analysis
  • Comprehensive experimental design guidance

Key Equipment

  • High-Resolution Q Exactive HF-x Orbitrap Mass Spectrometer
  • Thermo Fisher Orbitrap Velos Pro mass spectrometer
  • Agilent 1260 Infinity nano-HPLC stack with auto-sampler
  • BioTek Microplate Spectrophotometer
Core Facility: Metabolism Core

Metabolism Core

Specialized facility providing state-of-the-art assessments of various metabolic parameters for research purposes.

Director: Dr. Barbara A. Gower

Purpose

The Metabolism Core promotes multidisciplinary research and comprehensive training in clinical nutrition and obesity across the UAB campus, offering accurate measurement of energy expenditure, substrate metabolism, body composition, body fat distribution, and bone quality in human subjects.

Key Services

  • Total energy expenditure (doubly-labeled water method)
  • Resting energy expenditure (indirect calorimetry)
  • 24-hour energy expenditure (whole-room indirect calorimetry)
  • Body composition analysis via DXA
  • Body density measurements in infants (PeaPod system)
  • Body composition via multi-compartment models
  • Exercise and physical activity assessment

Key Equipment

  • Isotope Ratio Mass Spectrometer (IRMS)
  • Resting and whole-room indirect calorimeters
  • iDXA instruments for body composition
  • Peripheral quantitative computed tomography (pQCT)
  • Parvo Medics TrueOne® 2400 metabolic system
Core Facility: Microbiome Core

Microbiome Core

Specialized facility focused on providing comprehensive services for the analysis of microbial communities through 16S rRNA gene sequencing.

Director: Dr. Casey D. Morrow

Purpose

The Microbiome Core enables researchers to investigate the complex roles of the microbiome in various physiological and pathological processes through comprehensive analysis of bacterial communities in biological samples.

Key Services

  • 16S rRNA gene sequencing of biological samples
  • Standardized procedures for sample collection and storage
  • Secure data transfer and storage
  • Quantitative assessment of microbiome populations
  • Comparative analysis between different samples
  • Advanced analyses including ecological modeling
  • Prediction of metagenomic content and metabolic pathways

Key Equipment

  • DNA extraction and quantification equipment
  • Next-generation sequencing platforms
  • Access to UAB High Performance Computing cluster
  • Specialized software for microbial community analysis
Core Facility: MMR-CBPR-QR Core

Mixed Methods Research-Community Based Participatory Research-Qualitative Research Approaches (MMR-CBPR-QR) Core

Supports innovative applications of mixed methods research, community-based participatory research, and qualitative research approaches in social and behavioral sciences.

Directors: Dr. Nataliya Ivankova, Dr. Ronit Elk

Purpose

The MMR-CBPR-QR Core empowers UAB investigators to develop applied knowledge and essential skills in mixed methods, community-based participatory research, and qualitative methodologies to address complex social and health issues and promote health equity.

Key Services

  • Guidance on mixed methods research design
  • Support for community-based participatory research partnerships
  • Expertise in qualitative research approaches
  • Training in study conceptualization and design
  • Grant writing assistance
  • Abstract and manuscript preparation support
  • Qualitative data collection protocol development
  • Data analysis and visualization

Key Equipment

  • Qualitative data analysis software
  • Resources for community engagement
  • Mixed methods research toolkits
  • Training materials and resources
Core Facility: NMR Facility

Nuclear Magnetic Resonance (NMR) Facility

Critical university-wide resource supporting research in structural biology and drug discovery through Nuclear Magnetic Resonance spectroscopy.

Directors: Dr. William Placzek, Dr. Richard Dluhy

Purpose

The Central Alabama High-Field NMR Facility provides access to and expertise in NMR spectroscopy, making this powerful analytical technique readily available to researchers throughout UAB and within the broader scientific community.

Key Services

  • NMR expertise for submitted sample analysis
  • Structural elucidation of biological macromolecules
  • Support for drug discovery research
  • Design and development of novel biomaterials
  • NMR-metabolomics studies
  • Training on NMR applications for specific research

Key Equipment

  • Seven high-field NMR spectrometers
  • Bruker Avance III-HD 850 MHz NMR Spectrometer
  • Bruker Avance II 700 MHz NMR Spectrometer
  • Bruker Avance III-HD 600 MHz NMR Spectrometer
Core Facility: PISF/SAIF

Preclinical Imaging Shared Facility (PISF)

aka Small Animal Imaging Facility (SAIF)

Offers comprehensive multimodality imaging approach specifically designed to provide a molecular-level understanding of disease processes in animal models.

Director: Dr. Anna Sorace

Purpose

The PISF/SAIF supports sustainable and responsive preclinical imaging, primarily in oncology models, enabling therapeutic assessment of treatment responses and facilitating translational research at UAB.

Key Services

  • Ultrasound imaging for real-time assessments
  • Magnetic resonance imaging (MRI) for high-resolution studies
  • Computed tomography (CT) for detailed structural imaging
  • Nuclear imaging (PET and SPECT) for molecular imaging
  • Optical imaging techniques
  • Data analysis and image processing
  • Radioactive biodistribution studies

Key Equipment

  • MILabs uSPECT6/CT/OI system
  • Bruker Biospec 9.4 Tesla Preclinical MRI system
  • Siemens Inveon PET/CT Multimodality System
  • iThera MSOT inVision 256-TF
Core Facility: RMRIC

Research MRI Core (RMRIC)

aka Civitan International Neuroimaging Laboratory (CINL)

State-of-the-art facility dedicated to providing comprehensive magnetic resonance imaging experiments and analyses for detailed examination of brain and body in health and disease.

Directors: Dr. Virendra Mishra, Dr. Jane Allendorfer

Purpose

The RMRIC supports a wide range of research endeavors, from fundamental studies of MRI physics to complex multisite clinical trials, offering advanced imaging capabilities for understanding structure and function throughout the body.

Key Services

  • Advanced MR imaging and spectroscopy
  • Physics support for technique development
  • Protocol development assistance
  • Hardware and software development support
  • Pilot and feasibility studies
  • Whole body imaging with expertise in brain, spinal cord, eye, liver, skeletal muscle, heart, and kidney

Key Equipment

  • Siemens MAGNETOM Prisma 3.0 Tesla scanner
  • GE Premier 3.0 Tesla wide bore scanner
  • GE SIGNA PET/MR 3.0 Tesla model
  • 0.55 Tesla Siemens Freemax
  • Vera mock MRI scanner for patient preparation
Core Facility: SDH Core

Social Determinants of Health (SDH) Core

Dedicated to empowering UAB investigators to rigorously evaluate the significant impact of social and environmental factors on a wide spectrum of health outcomes.

Directors: Dr. Gabriela Oates, Dr. Elizabeth Baker

Purpose

The SDH Core facilitates innovative investigations into the complex interplay between biological, clinical, economic, educational, structural, and social factors that contribute to health and disease, with the ultimate aim of promoting health equity for all.

Key Services

  • Expert consultations on SDH measures and data sources
  • Methodology for selection, acquisition, and analysis of SDH data
  • Statistical models for nested data (geographic and longitudinal)
  • Integration of area-level SDH measures with other data sources
  • Geospatial analysis and mapping for presentation/publication
  • HIPAA-compliant geocoding of location data
  • Support for grant proposals addressing SDH

Key Equipment

  • ArcGIS Pro 3.1 and StreetMap Premium
  • Secure HIPAA-compliant computing environment
  • Esri ArcGIS products for visualization and analysis
  • Interactive mapping tools for study eligibility determination
Core Facility: TGEM Core

Transgenic & Genetically Engineered Models Core (TGEM)

Centralized facility dedicated to providing efficient and high-quality services for the production of genetically modified animal models, including mice, rats, and zebrafish.

Directors: Dr. John Parant, Dr. Courtney Haycraft

Purpose

The TGEM Core offers UAB investigators and external researchers access to specialized services performed by trained professionals, adhering to the highest standards of quality and efficiency in the generation of genetically engineered models for research.

Key Services

  • DNA microinjection techniques
  • Embryonic stem (ES) cell microinjection
  • Generation of mouse models of disease
  • Production of genetically modified rat models
  • Zebrafish genetic engineering
  • Consultation on model design and strategy

Key Equipment

  • Microinjection equipment
  • CRISPR/Cas9 gene editing tools
  • Embryo cryopreservation equipment
  • In vitro fertilization (IVF) equipment
  • Specialized animal housing facilities
Impact and Benefits

Overall Impact of the UAB IRCP

Contribution to the Research Landscape at UAB

  • Facilitates successful grant applications and prestigious awards
  • Attracts and retains top-tier researchers
  • Enhances overall research productivity and impact
  • Supports higher volume of impactful publications

Impact on Broader Scientific and Clinical Communities

  • National and international recognition for excellence (e.g., FCSC recognized by ISAC)
  • Services provided to external institutions and industries
  • Contributions to broader scientific knowledge and technological advancements

Role in Fostering Innovation

  • Enables high-risk, potentially high-reward research projects
  • Development of new methodologies and techniques
  • Critical support for translational research
  • Bridges gap between basic science and clinical applications
Collaborative Potential

Synergies and Collaborative Potential within IRCP

Combining Core Capabilities: Example Research Pathway

Cancer Therapeutics Development Pipeline:

  1. TGEM Core: Generate mouse model of specific cancer
  2. SAIF: Monitor tumor growth and treatment response in vivo
  3. FCSC: Analyze immune cell populations within tumor microenvironment
  4. BARB Core: Investigate drug effects on cellular metabolism
  5. MSP: Identify key protein changes induced by treatment

IRCP's Role in Facilitating Collaboration

  • Central access point for information about all cores
  • Helps researchers identify complementary core services
  • Organizing workshops and networking events
  • Encourages interdisciplinary research partnerships
  • Strategic coordination of equipment and expertise
Conclusion

UAB Institutional Research Core Program: A Critical Research Asset

The UAB IRCP stands as an invaluable and indispensable asset to the university's research enterprise, providing essential support to scientists, students, and clinicians across multiple disciplines.

Key Contributions

  • Provides access to cutting-edge technologies that would be inaccessible to individual labs
  • Fosters collaborative research environments that spark innovation
  • Offers essential training opportunities for the next generation of researchers
  • Enables researchers to pursue innovative and high-impact projects
  • Significantly contributes to the advancement of scientific knowledge
  • Supports translational research for improving human health

As UAB continues to strive for excellence in research and innovation, the Institutional Research Core Program remains a critical driver of scientific discovery, fostering collaboration, and enhancing the university's reputation as a leading research institution.