Core Descriptions for Grants

Biomedical Research Supply Store
(Category: Research Support Services)

Leadership:

• Carol McKissick, MBA, Program Administrator
• Sanjay Uchil, MS, Manager, Applications Development

Mission: To conserve time, money, space and effort for the University of Maryland, Baltimore (“UMB”) and UMB BioPark researchers, by maintaining a central supply core facility, e-commerce web site and expediting service which thrives upon its ability to innovate and re-create itself in accordance with the requirements of the University and its research staff. BIORESCO enables scientists to “do science” instead of procurement and accounting. We endeavor to become a “one-stop shop” for researchers and their staff.

Services:

All products purchased through BIORESCO are at the lowest possible prices and the researchers pay no Shipping or Handling charges. The BIORESCO web site hosts catalogs from over 45 Vendors. Customers can search and order from over 1.5 million discounted products.

In addition to our Core purpose as stated above, we offer:

• Two large annual vendor shows that bring over 50 vendors and 1200 members from the research community together
• Collaboration with UMB Environmental Health and Safety to minimize the volume and variety of dangerous chemicals on campus by maintaining years of searchable campus purchasing data
• Calibration for pipettors and balances
• Peptide and Oligonucleotide Synthesis
• Emergency Freezer Storage (-20 degrees C,-80 degrees C)
• Free packing and shipping materials for all temperatures
• Dry ice for sale

Additional Information:

Based on a 10 year analysis:

• Average savings from List — 27% • Savings in shipping and handling charges — $16.1 million
• Administrative Cost per purchase is around $4, which is much below the national average for a procurement purchase ($60) or P-card purchase ($20)
• We take the hassles out of replacements, backorder substitution

Biosensor (Category: Structural Biology)

Leadership:

• Robert Bloch, PhD, Director

Mission: The Biosensor Core Facility’s objective is to provide the faculty, staff and students on the University of Maryland, Baltimore, with the latest technology for the quantitative study of binding reactions in real time, specifically with an approach that is versatile, highly sensitive, and “user friendly,” with a wide range of biomolecules  that are label-free.

Services:

Biacore® instruments utilize the optical method of “surface plasmon resonance” (SPR), small changes in the interaction of monochromatic light with a metallic surface that occur when a protein or other molecule binds to that surface. Using the T200 or 3000, the core and its staff can provide accurate determinations of “on” and “off” rates for binding reactions, as well as determine affinity constants for binding. Because our instruments use SPR, many different kinds of binding reactions can be studied, often robotically, and a wide range of biological molecules can be examined, including proteins, nucleic acids, carbohydrates and lipids, as well as small molecules. Typical studies can:

• Determine if pairs of molecules bind to each other.
• Determine kinetic constants, binding constants, and specificity of binding.
• Determine if several molecules can bind simultaneously to the same ligand or if they compete for binding.

Equipment:

Biacore 3000:

The Biacore 3000 is designed to study binding of macromolecules to each other, with the possibility of examining molecules as small as ~2 kDa. The instrument accepts a chip with 4 flow cells that can be used in pairs, to compare flow cell 2 with flow cell 1 and flow cell 4 with flow cell 3, or in a single set of 4, to compare flow cells 2, 3 and 4 each with flow cell 1. Software is designed to optimize curve fitting and calculation of kinetic and binding constants.

Biacore T200:

The Biacore T200 operates very similarly to the 3000 but it has a very stable baseline signal which allows it to be used to study the binding of small molecules as well as macromolecules. The instrument accepts a chip with 4 flow cells that can be used in pairs, to compare flow cell 2 with flow cell 1, or flow cell 4 with flow cell 3. The software has been adapted to facilitate kinetics studies in a single cycle, by introducing low to high concentrations over the surface of the chip without intervening wash or regeneration steps

Biostatistics (Category: Biostatistics and Statistics )

Leadership:

• Søren M. Bentzen, MSc, PhD, DMSc, Director

Mission: Quantitative biomedical research is a team sport. The biostatistician brings a strong foundation in statistics, mathematics and computational methods, augmented by knowledge of the field of application and familiarity with biomedical concepts and terminology.

Services:

We collaborate on all aspects of design, analysis, interpretation, and reporting of quantitative biomedical research.

• Problem Formulation
• Study Design
• Data Collection
• Data Analysis
• Interpretation and Reporting

Equipment: n/a

Clinical and Translational Research Informatics Center (Category: Biostatistics and Statistics )

Leadership:

• J. Kathleen Tracy, PhD, Director

Mission: The purpose is to accelerate the translation of scientific discoveries from the basic science bench to clinical studies, bedside practice, and community intervention, through use of information technologies (IT) and informatics. CTRIC[TR1]  enables and advances research through various services which support clinical and translational research. CTRIC offers a variety of services to assist University of Maryland Baltimore faculty with their research needs at any stage in the process.

Services:

• Research Design: CTRIC staff is trained to make recommendations on appropriate study design, selection of suitable measures and variables, and data analytic strategies. CTRIC can also give assistance with power and sample size calculations.

• Data Management: CTRIC maintains each project’s relational database throughout the study including an IRB approved audit log of any data changes. Data can be prepared in tables in a readable format upon request, either at intervals during the study or at the end. Data reports, detailing enrollment, missing values, or other specifications can be created as needed. Access to data in the University of Maryland Medical System (UMMS)

• Clinical Data Repository: Across various facilities, UMMS has more than 600,000 visits every year, with much of the resulting data stored in the data repository. Researchers who are interested in accessing this vast resource can be provided with guidance through the process of obtaining IRB approval, submitting a data request, and analytic strategies.

• Quality Assurance/Control: CTRIC staff can design a quality assurance plan specific to a researcher’s study database and run regular reports to indicate improbable and impossible values in the database.

• Data Analysis: CTRIC staff is available to provide a wide range of data analysis services, from t-tests and analysis of variance with repeated measures to complex regression analysis. CTRIC provides annotated documentation of the analysis results, ensuring clear understanding of both the statistical tests used and proper interpretation of the results; CTRIC can also prepare graphs and tables, as well as draft appropriate portions of the Results section for a manuscript or scientific poster.

COMMON TOOLS USED BY CTRIC

• TeleForm®
• REDCap®
• Microsoft Access®
• MySQL®
• FreezerPro®
• Manual keying of data is also an option

Center for Translational Research in Imaging @ Maryland: CTRIM (Category: Imaging)  

Leadership:

• Rao Gullapalli, PhD, MBA, Director

Mission: To foster a collaborative environment that facilitates novel innovations in animal[TR1]  imaging and image guided therapeutics that can be translated to the clinic.

Services:

The staff of C-TRIM provides consultation on all animal imaging related research. Assistance is available for the design of experiments and to optimize imaging techniques. Image processing and analysis expertise is available within the core and training is provided upon request. The core also conducts an annual retreat where specific areas of research are highlighted. One aspect of the core is to develop new diagnostic imaging technologies and to develop image guided therapeutic interventions to remain at the state-of-the-art.

• High-resolution anatomic imaging for CNS and body applications (MR/CT)
• Tumor kinetics using receptor specific exogenous agents (MR/ PET)
• Multi-nuclear MR spectroscopy (H-1, C-13, Na-23, P-31, F-19 etc.)
• Metabolomic studies (MR/PET)
• High-resolution Diffusion Tensor Imaging for detecting microstructural and cellular changes (MR) • Vascular studies (CT/MRI)
• Cerebral blood flow studies using endogenous contrast (MR)
• Cardiac functional analysis (MR/PET/CT)
• Investigation of Blood-Brain Barrier disruption for various particle delivery (MR/MRgFUS)
• Neuromodulation using low energy ultrasound (MRgFUS)
• Ablative image guided surgery
• Focal image guided body and neuro thermal therapy applications. (MRgFUS) • Bone density measurements (CT)
• Cardiac metabolism (MR/PET)
• Musculoskeletal studies (MR/CT)
• Detection of novel fluorophores (Xenogen)
• GFP and Luciferase imaging (Xenogen)
• Monitoring tumor growth (CT/MR/PET/Xenogen)

Equipment:

• Bruker BiospecAvance III 7 Tesla Small Animal MRI Scanner
  • High-resolution qualitative and quantitative assessment of structure and function for CNS and various body applications
  • Multi-nuclear spectroscopy (H-1, C-13, Na-23, P-31, F-19 etc)
  • High-resolution Diffusion Tensor Imaging for detecting microstructural and cellular changes
  • Vascular studies, cerebral blood flow, cardiac function analysis
  • Siemens Inveon Small Animal PET- CT Imaging System
    • Dockable PET-CT for combined anatomic and functional imaging
    • High specificity radionuclide uptake
    • Metabolic imaging
    • High resolution system, (50 μm for CT and 1.2 mm for PET) with extended FOV
    • Xenogen IVIS-200 Optical in vivo imaging System
      • Rapid whole-body optical images of mice, rats or rabbits
      • Wide range of fluorescence excitation and emission filters
      • Wide array of molecular biology assays including GFP and luciferase
      • Measures proteasome activity, monitor tumor growth, drug efficacy
      • MRI-guided Focused Ultrasound (MRgFUS) System
        • Integrated with MR for image guidance
        • Tumor ablation studies, blood brain barrier disruption and neuromodulation

Confocal Microscopy (Category: Imaging)  

Leadership:

• Thomas Blanpeid, PhD, Director
• Joseph Ryan H. Mauban, PhD, Core Manager

Mission: The Confocal Core’s mission is to provide researchers with a wide array of state-of-the-art confocal imaging equipment to enable acquisition of high resolution images (both in vivo and in vitro). The Confocal Core offers training and assistance in the use of multiple confocal microscopes housed in our facility. Optimization of data acquisition and image processing are both part of the training, thus enabling researchers to efficiently design studies, acquire image data and extract relevant data features. The confocal facility is available to all UMB researchers and extramural users on a fee-for-service basis.

Services: The facility provides individual instruction on an array of confocal microscopes. The needs of the researcher are considered in choosing which microscope will best suit the experimental design. Facility users can be trained to utilize the machine best matching their respective imaging requirements. In general, imaging of fixed samples, cultured cells, organ slices and small animals can be accommodated. Imaging techniques including FRET, FRAP, photoactivation and uncaging are readily implemented. The microscopes have excitation sources that cover most fluorophores with excitation ranging from 355- 633 nm. Multiphoton excitation of fluorophores is also available on select instruments. An image analysis workstation equipped with software packages is available to users. The Core also has a culture room with an incubator, culture hood and a widefield fluorescence microscope for use in preparation of cultured and live samples. Preparation of live animals for imaging experiments can also be done in this newly renovated space.

Equipment:

• Zeiss 710 NLO
  • Upright confocal microscope with single photon and multiphoton excitation capabilities for imaging live cells, slices and whole animals
  • Electrophysiology and other types of data acquisition can be incorporated
  • Zeiss 7MP
    • Upright multiphoton microscope for in vivo imaging
    • Excitation wavelengths 730 to 1300 nm; 2 PMT and 2 sensitive GaAsP detectors
    • Can be combined with electrophysiology or other measures
    • Zeiss 5Live
      • Combined point-scanning and slit-scanning confocal microscope
      • Fast acquisition frame rates for studying dynamic cellular processes at physiological temperatures
      • Dual scan heads allow simultaneous imaging and optical manipulation
      • Zeiss 510
        • Conventional laser scanning confocal microscope
        • Acquisition of multiple fluorophores
        • Excitation (488, 543, 633, Ti:Sapphire laser)
        • Imaging of fixed, labeled tissue/cells
        • Olympus LCV Incubated Microscope
          • Widefield inverted microscope allowing continuous imaging of cells for hours or days
          • Fluorescence and DIC imaging
          • Motorized stage for multiple dishes and many positions
          • Cell migration, cell division, wounding and repair processes, phagocytosis

Cytogenetics (Category: Nucleic Acid and Genomics)

Leadership:

• Ying Zou, MD, PhD, FACMG, Director

Mission: This Core offers cytogenetic and molecular genomic diagnosis for both constitutional and acquired chromosome abnormalities. We focus on the detection and characterization of subtle chromosome abnormalities in hematological malignancies/ stem cells, as well as roles of telomere biology

Services:

The Cytogenetics Laboratory is a CLIA-certified and CAP accredited facility that offers comprehensive cytogenetic diagnosis for both constitutional and acquired chromosome abnormalities. It provides conventional karyotype analysis and fluorescence in situ hybridization (FISH) studies for the detection and characterization of chromosome abnormalities in clinical specimens and in established cell lines. The Cytogenetics Laboratory includes an American Board of Medical Genetics-certified clinical cytogeneticist/clinical molecular geneticist, highly knowledgeable laboratory supervisors, and experienced staff.

• Chromosome Studies on multiple sample types including peripheral blood, bone marrow, fibroblasts and solid tissues (Karyotype).
• FISH testing
  • Whole chromosome painting
  • Centromere probes
  • Subtelomere probes
  • Microdeletion probes
  • Cancer probes
  •  Other locus-specific probes
  • Microarray analyses (Data analyses)

Equipment:

• Metasystems Metafer Slide Scanner and Ikaros/ Isis Analysis Software
•  Nikon TMS microscope w/Fluorescence
• Olympus AX-70 microscope
• Olympus BHSM microscope
• Olympus BX-41 microscope
• Olympus BX-41 w/Fluorescence
• Zeiss Axiophot microscope
• Zeiss Axioskop microscope

Cytokine Core Laboratory  (Category: Cytometric & Bioassay)

Leadership:

• Jeff Hasday, MD, Director

Mission: The UM SOM Cytokine Core Laboratory (CCL) is an academic-based, fee for-service laboratory dedicated to providing a high-quality, low-cost cytokine, chemokine and growth factor measurement service for both intramural and extramural investigators

Services:

• The CCL offers an extensive list of human, mouse, and rat cytokine, chemokine and growth factor assays. We offer two assay platforms, ELISAs and Multiplex. Both platforms have their own unique advantages and disadvantages.
• The lab offers in-house ELISA protocols utilizing validated commercial reagents and have the ability to order commercial kits for those less common biomarkers. Using in-house protocols allows us to greatly reduce costs while still upholding high standards in quality.
• We utilize a Luminex™ 100 system for our multi analyte assays using high quality fully customizable commercial kits from the country’s leading vendors in multiplex technology.
• The CCL is here for every investigator from beginning to end. We are happy to help with experimental design all the way through to data interpretation.
• Our turnaround time is approximately 10 business days, and data are emailed to the investigator in a user-friendly Excel format.

Equipment:

• Luminex™ 100 Multi-analyte System: This system allows for the simultaneous measurement of up to 100 analytes in a single well. The machine utilizes two lasers, a reporter laser at 532 nm and a classification laser at 635 nm, to detect and measure fluorescently dyed microspheres. This allows for smaller sample requirements with a larger data output. Bio-Rad’s Bio-Plex Manager Software is used for data requisition and analysis.

• Molecular Dynamics Precision Microplate Reader:  The reader is used for all ELISA applications. It has 8 filters with the ability to change to others as required to read plates at multiple wavelengths. It reads 96-well plates in a matter of seconds and paired with the SoftMax Pro software it becomes a powerful machine to cover all ELISA needs.

• BioTek ELx50 Plate Washer: BioTek’s ELx50 Microplate Washer is a fully programmable instrument that allows for full control of plate washing required for ELISA assays. Automated plate washers allows for higher throughput and for lower CV%’s over standard manual washing.

Electron Microscopy  (Category: Imaging)

Leadership:

• Ru-ching Hsai, PhD, Director

Mission: The Electron Microscopy Core Imaging Facility provides electron microscopy related research, consultation and imaging services to all faculty and staff of the University of Maryland Baltimore campus and the academic and industrial community in the Washington, D.C. and Baltimore areas. The objective of this facility is to provide affordable electron microscopy research services using the modern EM techniques and state-of the-art instrumentation from sample processing.

Services:

• Conventional TEM sample preparation, including embedding in various types of resin and ultrathin sectioning
• Conventional SEM sample preparation, including chemical dehydration, critical point drying and sputter coating
• Cryo-sample preparation for both TEM and SEM, including high pressure freezing, freeze substitution, cryo-ultramicrotomy, plunge freezing and freeze fracture
• Immuno electron microscopy using pre-embedding, post embedding or Takuyasu methods
• Negative staining of purified macromolecular complexes, bacteria, viruses, liposomes, nanoparticles, or viral like particles (VLP)
• Advanced microscopy techniques, such as cryoEM, correlative LM/EM (CLEM) and 3D EM
• Electron microscopes imaging for trained or novice users
• Advanced consultation and training of electron microscopy related techniques and equipment usage
• Annual Current Electron Microscopy Techniques workshop
• Annual Ultramicrotomy Minicourse
• Instrument demonstration

Equipment:

• Transmission Electron Microscope
  • FEI tecnai T12 is a high performance, high resolution transmission electron microscope equipped with a tungsten filament. It is well suited to be a general purpose instrument in a multi-user facility. The tecnai T12 is also equipped with a Gatan 626 cryo transfer holder for observing frozen hydrated biological sample at liquid nitrogen temperature.
  • Scanning Electron Microscope
    • The FEI Quanta 200 is a versatile high performance, low-vacuum scanning electron microscope with a tungsten electron source. It can be operated in three different vacuum modes, High Vacuum (HV), Low Vacuum (LV) and Environmental Mode (ESEM), thus accommodate a wide range of sample of any SEM system. The Quanta 200 is also equipped with a Gatan Cryo transfer unit (ALTO2100) for cryo SEM imaging and freeze fracture
    • Cryo Sample Preparation Instruments
      • High Pressure Freezer
      • Automated Freeze Substitution
      • Plunge Freezer
      • Cryoultramicrotome
      • Gatan TEM Cryotransfer Holder
      • Gatan SEM Alto Cryo Chamber

Flow Cytometry UMCCC  (Category: Cytometric & Bioassay)

Leadership:

• Xiaoxuan Fan, Ph.D. Director
• Karen F. Underwood, BS Research Specialist

Mission: The University of Maryland Greenebaum Comprehensive Cancer Center’s Flow Cytometry Shared Service (FCSS) offers equipment and technical expertise to members of the UMGCCC, members of the campus and small business, in conducting research in cancer biology and other areas of basic and applied science. 

The objective of this facility is to provide a full-scale; state-of-the art Flow Cytometry services from sample acquisition through data analysis to cell sorting.

Services:  The facility makes available state-of-the art instrumentation and techniques, while developing new ways of answering questions about the nature and function of cells.

The facility is interested in contributing to all Aspects of the research process including consultation in experiment design, technical assistance, and distribution of raw data files, and analyzing and interpretation of results.

The facility also provides training and individual instruction can be provided as needed for operation of LSRII and CANTO analytical instrumentation.

Analysis of cell populations based on fluorescent surface staining and light scatter.

Analysis of cells expressing combinations of fluorescent reporter proteins.  As well as analysis of apoptosis and cell cycle stage based on DNA content.  As well as intracellular metabolism, ion concentration and DNA damage response.

High speed and single cell sorting on up to 9 parameters/7colors.

Advance consultation, strategic plan, development and expert data analysis.

Users can analyze their own data on Flow Jo Software; we have mac and pc dongles and have an onsite work station.

Equipment:

The facility has state-of-the-art analysis instruments used for quantitative analysis.

• BD LSRII Flow Cytometer with High Throughput Sampler Option
• BD FACS CANTO Cytometer
• Amnis Flow Sight

The facility is also equipped with two state-of-the-art high-speed cell sorters.

• BD FACSAria I
• BD FACSAria II

Flow Cytometry & Mass Cytometry CVD  (Category: Cytometric & Bioassay)

Leadership:

• Marcelo Sztein, MD, Director

Mission: To ensure that University of Maryland investigators have access to flow cytometry and mass cytometry services for their research. A facility with dedicated operators ensures well-performing instruments and optimal results with a minimal outlay of expenses. Established in 1991, this facility has state-of-the art equipment and a highly trained and experienced staff.

Services:

• Multichromatic flow cytometry

Including markers for:

• Lineage
• Maturation
• Activation
• Homing
• Intracellular cytokines
• Serum/supernatant cytokine levels using bead kits (e.g., BD Pharmingen CBA kit)
• Cell cycle analysis (PI, DAPI)
• Cell proliferation (CFSE, PCNA, BrdU and Ki67)
• Apoptosis (Annexin V vs. PI; TUNEL; subG0/G1 peak analysis)
• Green fluorescence protein (GFP) (eukaryotic and prokaryotic)
• Cell sorting (2 and 4-way) based on GFP and/or multichromatic staining
• Mass Cytometry (>35 parameters)
• Advice with experimental design and data analysis

Equipment:

• BD LSR II Flow Cytometer
  • 4 lasers: 407, 488, 552, and 641 nm
  • 16 parameters (14 colors plus forward and side scatter)
  • Beckman Coulter MoFlo Legacy Cell Sorter
    • 3 lasers: 407, 488, and 641 nm
    • 12 parameters (10 colors plus forward and side scatter)
    • 2- or 4-way high speed sorting (based on 10 parameters)
    • CyCLONE single cell sorting
    • Fluidigm CyTOF Mass Cytometer
      • >35 parameters based on mass spectrometry detection of metal isotope-labeled antibody staining
      • No need for single color controls or fluorescence compensation

Fluorescence Spectroscopy (Category: Imaging)

Leadership:

• Joseph R. Lakowicz, PhD, Director

Mission: The Center for Fluorescence Spectroscopy (CFS) provides state-of-the-art fluorescence instrumentation for studies of structure, function, and dynamics of biological macromolecules. CFS also provides the expertise on applications of fluorescence for bioassays and cellular imaging.

Services:

• The CFS makes available state-of-the art spectroscopic instrumentation and techniques for fluorometric bioassay development and cellular imaging. Techniques include:
  • Fluorescence energy transfer (FRET)
  • Fluorescence polarization (FP)
  •  Fluorescence correlation spectroscopy (FCS) •
  • Single molecule detection (SMD)
  • Time-resolved spectroscopy
  • Fluorescence lifetime imaging microscopy (FLIM)
  • Facility also provides technical expertise on all aspects of fluorescence techniques used in basic science and biological/medical applications.
  • Cell imaging and studies of biomolecule interactions of assemble molecules and on single molecule basis are available with fluorescence microscopies.

Equipment:

• Fluorescence Lifetime Imaging Microscope State-of-the-art imaging system, Alba V (FLIM and FCS) is designed for cellular imaging and bioassay readout and quantitative analysis. The system is equipped with multiple lasers, multiple channels, dual scanners and dual lifetime imaging capability (TD and FD).
• Single Molecule Fluorescence Microscope
  • Multiple lasers
  • Lifetime capability
  • FCS
  • Time-Resolved Fluorescence Spectrometer 
    • Super Continuum Laser
    • Automated system
    • Atomic Force Microscope and NSOM WITec alpha300S
      • Contact Mode
      • AC Mode
      • Confocal capability

Genomics: Research Genomics and Translational Genomics (Category: Nucleic Acid and Genomics, Clinical Resources)

Leadership:

• Nick Ambulos, PhD, Director, Research Genomics Lab
• Linda Jeng, MD, PhD, Director, Clinical/ Translational Genomics (CLIA LAB)

Mission: The mission of the Genomics Laboratory is to provide the expertise, state-of-the-art resources and training necessary to promote cutting edge basic, translational and clinical genomic research, as well as clinical testing under Clinical Laboratory Improvement Amendments (CLIA).

Services:

• CORE SERVICES (RGL[TR1] )
  • Cytogenomic Arrays 
  • Extraction of Nucleic Acid
  • DNA
  • RNA
  •  Gene Expression Arrays
  • Global Expression Profiling
  • miRNA Expression Profiling
  •  Transcriptome Analysis
  • Genotyping
  • Taqman Assays
  • SNP Arrays (targeted or GWAS studies)
  • Next Generation Sequencing (NGS) of Gene Panels
  • Sanger DNA Sequencing
  • CLINICAL TESTING (TGL[TR2] ) CLIA LAB
    • APOB Genotyping
    • Confirmation of a Research Finding
    • CYP2C19 Genotyping
    • CYP2C19 Sequencing
    • ytogenomic Microarray
    • Extract and Hold
    • IDH1 R132_IDH2 R140 and R172

Equipment:

• Affymetrix GeneChip 3000 systems
• Agilent Bioanalyzer model 2100 
• Applied Biosystems Model 3730XL DNA Sequencers
• Applied Biosystems Model 7900 rtPCR System
• Illumina iScan
• Ion Torrent Personal Genome Machine (PGM) Sequencers
• MiSeqDX (to arrive Spring 2015)
• Nanodrop single-channel and 8-channel spectrophotometers

Genomic Research Center, Institute for Genome Science (Category: Nucleic Acid and Genomics)

Leadership:

• Lisa DeShong Sadzewicz, PhD, Administrative Director
• Luke J. Tallon, Scientific Director

Mission: The Genomics Resource Center (GRC) is a high-throughput core laboratory and data analysis group supporting the scientific programs of the Institute for Genome Sciences, University of Maryland Baltimore and its collaborators utilizing state-ofthe-art technology to generate high quality genomic data in a cost effective manner.

Services:

Sequencing Applications

• DNA/RNA Extraction
• Library Preparation
• Genomes/Metagenomes
• Exomes and Custom Capture
• Transcriptomes/ Metatranscriptomes
• Epigenomes
• Microbiome Amplicons
• Single Cell Sequencing
• Custom Amplicons
• Digital Molecular Profiling
• Custom Applications

Analysis Services

• Assembly & Annotation
• Comparative Genomics
• Variant Analysis
• Transcriptome Analysis
• Epigenome Analysis
• Microbiome Profiling
• Pathway & Network Analysis
• Microarray Analysis
• Cloud Based Pipelines
• Customized Analysis

Equipment:

• Illumina NovaSeq 6000
• Illumina HiSeq 2500 & 4000
• Illumina MiSeq and iSeq
• PacBio Sequel & Sequel II
• Oxford Nanopore MinION
• NanoString nCounter MAX
• 10x Genomics Chromium System

Informatics Research Center (Category: Biostatistics and Statistics )

Leadership:

• Anup Mahurkar, Director
• Michelle Gwinn Giglio, PhD, Associate Director
• Owen White, PhD, Associate Director

Mission: To enable basic and translational research by leveraging expertise in genome-scale analysis tools and high performance computing.

Services:

The Institute for Genome Sciences Informatics Resource Center engages in fee-for-service (FFS) and collaborative research projects and proposals. For this purpose two cores were created: the Genome Informatics Core (GIC) and the High-Performance Computing Core (HPC). The following are some of the major services available through these IRC cores.

GENOME ANALYSIS The GIC has a talented group of researchers and staff with expertise in the following analyses:

• Genome Annotation
• Comparative Genome Analysis
• Metagenome Analysis
• Metatranscriptome Analysis
• Microarray Analysis
• Transcriptome Analysis
• Epigenome Analysis
• Variant Analysis
• Pathway Analysis S

SOFTWARE AND TOOL DEVELOPMENT GIC software engineers are available to develop custom software solutions that include:

• Web site Development
• Custom Programming/Scripting
• Research Data Capture Systems
• Database Design

RESEARCH COMPUTING The HPC computational infrastructure is available to researchers to conduct their own analysis. The following are some of the ways researchers can access this infrastructure.

• Cloud Computing
• Pre-packaged Genome Analysis Pipelines
• Command-line tools

Additional Information:

VISUALIZATION TOOLS The IRC has developed a number of genome visualization and curation tools that are available to the research community. In addition we have also deployed third-party open source tools. Some of these include:

• SYBIL – A browser for comparative genomics results that provides views for ortholog groups, synteny gradients, genomic regions, and more.
• Circelator – A circular genome visualization tool providing compact figures showing diverse types of information that can be used to compare features of multiple genomes.
• Manatee – A genome annotation query and curation tool that allows users to browse annotations by gene location, function, and biological role. Annotations can be revised by users as well as downloaded in a variety of standard formats.
• Integrative Genome Browser (IGV) – A tool that provides simultaneous visualization of multiple types of genome-associated information including gene models, ortholog data, RNA-Seq alignments, and more.
• JBrowse – A Web-based genome visualization tool.

COMPUTATIONAL INFRASTRUCTURE Supporting informatics at IGS/IRC is a state-of-the-art computational infrastructure that includes a computational grid, an internal 10-gigabit network, database servers, and a hierarchical storage management system.

The infrastructure includes:

• Twenty-five high-performance high-memory multi-processor machines (128- 1024 GB RAM, 4-8 CPU multi-core processors)
• Over eighty high throughput computational nodes (24-128 GB RAM, 2 CPU multi-core Intel Xeon processor machines)
• A 4-tier enterprise-class high-performance storage system with 1.5 petabytes
• A tape library with a capacity to store 1 petabyte of data

The IRC has recently deployed one of the largest public academic clouds, the Data Intensive Academic Grid (DIAG), to enable bioinformatics analysis to be conducted remotely by researchers in the community. The scientific community can access this resource as a traditional grid, as a computational cloud like Amazon EC2, or through Ergatis, a pipeline management system.

The DIAG includes:

• Eight high-performance high-memory multi-processor machines (128-1024 GB RAM, 4-8 CPU multi-core processors)
• Over one hundred twenty five high throughput machines (48 GB RAM 2 CPU multi-core Intel Xeon processor machines)
• 500 TB of shared high-performance storage

Nuclear Magnetic Resonance: NMR (Category: Structural Biology[TR1] )

Leadership:

• David Weber, PhD, Director

Mission: The objective of the UMB NMR Center is to promote the use of nuclear magnetic resonance spectroscopy for use in ongoing and new research projects at the University of Maryland School of Medicine.

Services:

We offer assistance and training for:

• Collecting NMR data
• Processing NMR data
• Analysis of NMR data

ADDITIONAL CORE SERVICES:

• Linux and Apple workstation access for data processing and analysis
• Lab space for sample handling
• Assistance with NMR-related computer software including Bruker Topspin, NMRView, nmrPipe, nmrDraw, xplor-NIH, and several others

Equipment:

• 600 MHz Bruker Avance III NMR Spectrometer with TCI cryoprobe
• 800 MHz Bruker Avance Spectrometer with TXI cryoprobe and BACS 60 automatic sample changer
• 950 MHz Bruker Avance III Spectrometer with TCI cryoprobe

Pathology Biorepository (Category: Clinical Resources)

Leadership:

• Olga Ioffe, MD, Director
• Paul Staats, MD, Co-Director
• Ashley Cellini, PA (ASCP), Manager

Mission:

• Pathology Biorepository Shared Service (PBSS) provides access to a collection of high quality banked patient samples while maintaining patient confidentiality.  PBSS provides pathology, histology, and histotechnology services to assist with procurement, analyses, and clinicopathologic correlations of human tissue specimens.  Access to a high-quality bank of patient samples permits UMGCC investigators to perform studies aimed at understanding the biology of normal and diseased tissues with an ultimate goal of translating this knowledge into diagnostic and clinical applications.

Services:

The Pathology Biorepository Shared Service was established by University of Maryland Greenebaum Cancer Center (UMGCC) in 2006 as a developing core. PBSS has both the unique advantage of the long-standing expertise gained under the well-established relationship with the NCI as well as the existing expertise and archives within the Pathology Department. PBSS is the only tissue bank shared service for specimens removed at the time of surgery on the campus. We have an integrated relationship with the Anatomic Pathology Department, which is essential for obtaining well-characterized tissue samples as well as for pathology and histology expertise. Frozen tissue archives of PBSS consist of more than 8,000 frozen tumor samples, 6,900 of which are paired with normal tissue from the same patient, and more than 22,000 frozen mononuclear cell isolates, plasma, and serum samples.

Tissue Procurement and Processing Services:

• Fresh or Frozen tissue
• Plasma and serum collection
• Bone marrow and peripheral blood mononuclear cell isolation
• Biospecimen storage and retrieval
• Rapid collection and storage methods
• Project/protocol-specific procurement

Translational Research Support:

• Histology Services
  • Tissue processing and embedding
  • Sectioning and staining
  • Immunohistochemistry (IHC), including antibody work-up and control tissues
  • Special Stains
  • Tissue Microarray (TMA) Construction
  • Digital Image Analysis Services
    • Aperio digital IHC and TMA software
    • Quantitative IHC

• Data Services
  • Association of archived and prospectively collected tissue with clinical data
  • Prospectively maintained and queryable database for all collections
  • Consultation Services
    • Pathology consultations
    • Interpretation support
    • IRB application assistance
    • Material Transfer Agreement (MTA) submission support

Equipment:

• n/a

Physiological Phenotyping (Category: Animal Model Resources)

Leadership:

• Ling Chen, MD, PhD,  Manager, Associate Professor of Physiology and Medicine

Mission: The Physiological Phenotyping Core (PPC) provides cutting edge small animal phenotyping services with a focus on cardiovascular and respiratory systems in rodents. The core has a 10-year track record of services, including microsurgery, telemetry recordings, high-frequency ultrasound, and pressure volume loop analysis

Services:

• Microsurgery and animal models: catheter and device implanting; coronary artery ligation; aortic banding; artery wire denudation or ligation; chronic hypoxia
• Biomicroscopy (high frequency ultrasound) imaging of adult or fetal hearts, large or small vessels, tumors, or abdominal organs; ultrasound-guided micro-injection
• Acute in vivo measurements: hemodynamics, pressure volume loop analysis, respiratory mechanics, sympathetic nerve activity, and etc.
• Long-term recordings: blood pressure, aortic or organ blood flow, sympathetic nerve activity, ECG, EEG, EMG, temperature
• Equipment Rent

Equipment:

• Vevo 2100 High-frequency Ultrasound System (VisualSonics), the most updated system for high resolution imaging under B-, M-, color and pulse-wave Doppler mode, 3-D construct, and Vevo strain. (Figures: Mouse Echo; Tumor Imaging)

• Telemetry System (DSI) allows long-term recordings of blood pressure, biopotential (ECG, EEG, EMG), sympathetic nerve activity, and blood glucose concentration. It can be interfaced with flowmeters (Transonic), e.g., for simultaneously long-term recordings of blood pressure and cardiac output (Figure: Long-term BP and CO)

• MP150 Acquisition System (BioPac): 16-channel modular system interfaced with various transduces or amplifiers of pressure, volume, flow, biopotential, and temperature, as well as Mikro-tip catheters (Millar), flowmeters (Transonic), and cardiac output computer (Columbus Instruments)

• Environment System (Kent Scientific) allows customized exposure of hypoxia or hyperoxia (Figure: CIH setup)

• Pressure-volume loop system (Transonic) for comprehensive analysis of cardiac function in vivo or in isolated heart preparation

• Tailcuff Blood Pressure System (SC1000, Hatteras)

Protein Analysis (Category: Structural Biology)

Leadership:

• Brian Hampton, Director

Mission: The Protein Analysis Lab provides multiple technologies for the purification and analysis of proteins, peptides and small molecules.

Services:

• Protein Identification: from immunoprecipitation, affinity pull-downs even complex samples in solution or in-gel.
• Protein Profiling: determine which proteins are differentially expressed. Compare two conditions from tissues to cultured cells using chemical labeling or SILAC.
• Targeted Quantification: directly detect and quantify specific proteins of interest. Useful when working with species where antibodies are not available or useful.
• Mass Determination: of proteins is performed on an ESI-FTICR-MS instrument that provides high resolution and mass accuracy. Useful for structural analysis of proteins, quality control of purified or engineered proteins, and can be used for confirming small molecule binding to the target protein if that interaction is stable to the ionization technique.

Equipment:

Thermo LTQ Linear Ion Trap Mass Spectrometer:

• LEAP PAL HTS robotic autosampler with cooled sample compartment holding up to 576 vials
• Two Thermo Surveyor 4-channel solvent delivery HPLC pumps
• Ion sources include ESI and nanoESI • Fully automated with control under Xcalibur software
• Resolving power ~15,000 (FWHM) in enhanced zoom scan mode
• m/z range 150 to 4000

Waters Quattro Micro Triple Quadrupole Mass Spectrometer:

• Waters 2695 HPLC and 2996 photodiode array detector
• Electrospray ion source
• Scan modes include: Parent ion and Product ion scans, Multiple Reaction Monitoring (MRM) also known as SRM, and Constant Neutral scan
• MassLynx 4.0 Data system
• m/z range 50 to 2000

Waters 2695 HPLC System:

• Waters 2695 4-channel solvent delivery system
• 96 vial capacity cooled sample management
• 2996 photo diode array detector
• Flow rate capability from 0.01 to 5mls/min
• Fraction collectors
• Waters Empower Data system

Genomics: Research Genomics and Translational Genomics (Category: Nucleic Acid and Genomics, Clinical Resources)

Leadership:

• Nick Ambulos, PhD, Director, Research Genomics Lab
• Linda Jeng, MD, PhD, Director, Clinical/ Translational Genomics (CLIA LAB)

Mission: The mission of the Genomics Laboratory is to provide the expertise, state-of-the-art resources and training necessary to promote cutting edge basic, translational and clinical genomic research, as well as clinical testing under Clinical Laboratory Improvement Amendments (CLIA).

Services:

• CORE SERVICES (RGL[TR1] )
  • Cytogenomic Arrays 
  • Extraction of Nucleic Acid
  • DNA
  • RNA
  •  Gene Expression Arrays
  • Global Expression Profiling
  • miRNA Expression Profiling
  •  Transcriptome Analysis
  • Genotyping
  • Taqman Assays
  • SNP Arrays (targeted or GWAS studies)
  • Next Generation Sequencing (NGS) of Gene Panels
  • Sanger DNA Sequencing
  • CLINICAL TESTING (TGL[TR2] ) CLIA LAB
    • APOB Genotyping
    • Confirmation of a Research Finding
    • CYP2C19 Genotyping
    • CYP2C19 Sequencing
    • ytogenomic Microarray
    • Extract and Hold
    • IDH1 R132_IDH2 R140 and R172

Equipment:

• Affymetrix GeneChip 3000 systems
• Agilent Bioanalyzer model 2100 
• Applied Biosystems Model 3730XL DNA Sequencers
• Applied Biosystems Model 7900 rtPCR System
• Illumina iScan
• Ion Torrent Personal Genome Machine (PGM) Sequencers
• MiSeqDX (to arrive Spring 2015)
• Nanodrop single-channel and 8-channel spectrophotometers

Translational Core Laboratory (Category: Clinical Resources, Animal Model Resources)

Leadership:

• Rena Lapidus, PhD, Director

Mission: The University of Maryland Greenebaum Comprehensive Cancer Center’s Translational Shared Service (TLSS) offers pre-clinical and clinical experimental support to basic researchers and physicians in the UMGCC community. We work in areas across the entire spectrum: cell biology, in vitro, in vivo and human trials.

Services:

In Vitro Assays

• IC50 generation
• Cell cycle (propidium iodide)
• Viability (trypan blue exclusion)
• Apoptosis
• Potentiation/Synergy
• ROS
• Western Analysis
• Angiogenesis
• Mycoplasma testing

Xcelligence

• Real time proliferation/invasion/migration

In Vivo Assays

• IACUC approved umbrella protocol
• Tolerability
• Tumor Growth
• Pharmacokinetics: generation of plasma
• Efficacy (flank models)
• Efficacy (orthotopic models)
• Pharmacodynamic Endpoints
• Imaging of cells with Xenogen System

Pharmacodynamic (PD) Endpoints

• in-patient samples, tumor or surrogate tissues,preclinical samples
• Endpoint dependent on target (e.g., ELISA, flow cytometry, Western, unique assay)

Equipment: n/a

CORE RESOURCES

• Access to 70+ human cell lines
• Luciferase-expressing breast, leukemia, ovarian, colon and prostate cancer cell lines
• IACUC approved umbrella protocol
• Access/Knowledge in Using Xenogen/IVIS Imaging Mice
• Primary Xenograft Models
• Breast
• Leukemia (under development)
• Ovarian (under development)
• Access to IRB approved protocol for tissue acquisition

Clinical Trial Support

We isolate:

• Plasma
• Serum
• Tumor Biopsy
• Whole Blood (isolation of PBMC, DNA, RNA, protein)
• Bone Marrow (isolation of marrow cells)
• Buccal Mucosa

Veterinary Services (Category: Animal Model Resources)

Leadership:

• Louis DeTolla, VMD, PhD, DACLAM, Director
• E. Douglas Allen, BS, LATg, Deputy Director

Mission: Our mission is to study the characterization of animal models of human disease; provide accredited services for laboratory animal care through collaborative research, professional development of veterinarians through specialty training with American College of Laboratory Animal Medicine (ACLAM); achieve continuous certification through compliance with The Association for Assessment and Accreditation of Laboratory Animal Care International (AAALACi), the United States Department of Agriculture (USDA); and the Office of Laboratory Animal Welfare (Public Health Service, NIH) and to act as a resource for information and instruction on the use of laboratory animals

Services:

• Wide range of animal models from mice to non-human primates for biomedical research
• GLP support for FDA/EPAregulated studies
• Generation of polyclonal/ monoclonal antibodies and induced pluripotent stem cells
• Maintain mouse colonies (SCID-NOD/NSG/NRG, nude, C57BL/6)
• Pre-research consultations with researchers on development of animal models
• Technical services provided for rodent procedures such as: blood withdrawal, anesthetic support, and weaning
• Hands on training course to investigators and staff on humane handling of laboratory animals

Equipment:

• In Vivo Imaging System 200 Series- IVIS- Xenogen
  • Superior bioluminescent and fluorescent imaging
  • Spectral imaging
  • Single view three-dimensional imaging

• Applications:
  • Localization and quantitation of infectious agents
  • Tracking metastatic tumor cells Gene expression localization

μQUANT Core Facility  (Category: Cytometric & Bioassay)

Leadership:

Ping-Hsin Rex Lin, MS

Mission: The μQUANT Core Facility housed within the Institute of Human Virology provides quality immunological analyses of biological analytes to researchers at the UM SOM, as well as other collaborators locally and nationally. Our aim is to provide consistent service that allows researchers to compare results generated this week with those gathered last month or a year ago

Services: Include, but are not limited to:

• ELISAs
• Immunoassay setup & protocol establishment
• Luminex assays
• Mycoplasma & endotoxin testing
• Monoclonal antibody and recombinant protein screening, production, purification, & labeling
• HIV, SIV, & SHIV culture
• TCID50 and neutralization assays
• Quantitative PCR

Equipment:

• SpectraMax M2 6-96 well Plate Reader
  • 6-well to 96-well plate reading capability ·
  • Built-in absorbance and fluorescence
  • Absorbance wavelength between 200 nm and 1000 nm, excitation wavelength between 250 nm and 850 nm, and emission wavelength between 360 nm and 850 nm
  • Wallac Victor 2 Multi-analyte plate reader
    • Complete platform for quantitative detection of lightemitting or light absorbing markers
    • Luminescence, fluorescence, time-resolved fluotescence (DELFIA), and photometer
    • Veritas Microplate Luminometer
      • Read glow and flash luminescent reactions in 96-well plates
      • Bio-Plex 200 System
        • Simultaneously quantitate up to 100 analytes per sample from culture media and serum
        • Automatically analyze up to 96 samples in 30 min
        • Instantly customize your assay by mixing Bio-Plex assay, or create your own assays
        • Dramatically increase the amount of useful data obtained from a single sample
        • BioRad IQ5 Real-time PCR system
          • Detection Range: 515–700 nm
          • Excitation Range: 475–645 nm
          • Multiplexing of up to 5 fluorophores in each reaction vessel conserves precious samples and reagents
          • StepOnePlus Real-time PCR system
            • 96-well Real-Time PCR instrument with sensitive 4-color optical LED recording system
            • SimpliAmp PCR Thermal cycler