Research and Infrastructure Core

Core 1

The Shareable Instrumentation Facility

听听听听听听听听听听听听听听听 Core I provides 快活视频's researchers with the necessary equipment to conduct flexible and thorough studies. This facility allows on-site use of an array of equipment that would otherwise be inaccessible to individual researchers due to budgetary constraints. The instrumentation is divided between two locations: Williams-Bowie Research Building and Carver Research Building. Additionally, two full-time employees ensure that all users are properly trained and that equipment stays in a ready-to-use state.听听

听听听听听听听听听听听听听听听 Resources within this core offer the following capabilities: Digital Wide-field and Confocal Microscopy, Gene Expression Analysis, Flow Cytometry, Microplate Reading (Absorbance, Fluorescence and Luminescence), Gel Imaging, Tissue Culture, HPLC, GC/MS, Pulsed Field Gel Electrophoresis, Electroporation, Ultra-High-Speed Centrifugation, Film Processing and InVivo Imaging.听

Available Instruments Include:听

1. Digital Imaging:

路Two Confocal Fluorescent Microscopes: 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听 听听听

• Olympus Laser Scanning Confocal (Fluoview Software)听

• Olympus Spinning Disk Confocal (MetaMorph Software)听

搂Capable of imaging live cell experiments

路Two Wide-Field Fluorescent Microscopes: (CellSens Software)

• Leica Upright

• Leica Inverted

路Two Olympus Wide- Field Fluorescent Microscopes: (CellSens Software)听

• 滨苍惫别谤迟别诲听

• Upright

• 路One IHC Microscope:

• Upright (CellSens Software)

An IVIS Lumina XR is housed on the 1st floor of WB Hall :听 Multimodal imaging Fluorescence, bioluminescence, x-ray and photography Compatible with rats, mice, cell cultures, bacterial cultures, and microplates Operated using Living Image software

Three Flow Cytometers are available:听

路A Sony iCyt EC800 system is located in WB Hall room 2055Operated using EC800 Software 听

路A FACSCalibur system is located in WB Hall room 2055.

• Operated using FlowJo software

路An Accuri C6 is located in Carver Research Building room 31.听

• Operated using CFlow software

2. Gene Expression听

Five plate readers are distributed between WB Hall and CRB:听

路WB Hall Room 2017:

• One BioWave XS (absorbance)

• One Synergy 2 (luminescence)

• Both operated using Gen5 2.0 software

路CRB Room 19:

• One Synergy HT (fluorescence and absorbance)

搂Operated using Gen5 2.0 software

路CRB Room 31:

• One ThermoMax (absorbance)

• One SpectroMax Gemini EM (luminescence)

• Both are operated using SoftMax Pro software

Two Real-Time PCR Systems are located in WB Hall room 2017:听

路Stratagene Mx3000P

路Stratagene Mx3005P

路Both systems are operated using MXPro software

路Two Eppendorf thermocyclers are also available within the same space

3. Chromatography听

One HPLC is in WB Hall room 2025:

路Operated using Karat 32 software

4. Cell Culture听

Two cell culture facilities are also available:

路One is located in WB Hall room 2023

路One is located in CRB room 27

Animal Facility & Pathology Services:

The College has a modern animal facility capable of accommodating from rodents to large animals and well-organized Comparative Medicine Resource Center (CMRC) for research involving laboratory animals and small ruminants. The facility provides all services to researchers who have projects approved for animal use. The animal facility serves the biomedical research community in the university and is fully equipped with, among others, offices, garment changing areas, animal isolation/quarantine, housing rooms (for both conventional and special accommodations), and rooms for feed storage, cold holding and necropsy. A designated attending veterinarian, a facility manager, a center director and adequate non-technical support personnel are available.

听 Pathology services are provided to the clinical and research community on a fee-for-service basis. Fully equipped and man-powered tissue processing service facility is located in Williams-Bowie building. One board-certified veterinary pathologist and three faculty (with a Doctorate degree in Anatomical Pathology) are available for consultation.听

Core 2

Infrastructure Development in Computational Biology and Bioinformatics (CBB)

The goal of Core II: Computational Biology and Bioinformatics (CBB) 听is to continue strengthening the optimal use of computational resources and Information Technology (IT) by Research Centers in 听Minority Institutions (RCMI) researchers at 快活视频 (TU) to address health disparities in听under served听communities. The CBB's multidisciplinary faculty and staff at 快活视频's Center for Computational Epidemiology, Bioinformatics & Risk Analysis (CCEBRA) and its' counterpart, Biomedical Information Management Systems (BIMS) provide services and training in computational biology, bioinformatics, experimental design and statistical analysis etc. to the RCMI researchers and the biomedical research community at TU. Of central importance is the fact that the CCEBRA research team works in conjunction with BIMS' strong IT team. The BIMS team provides all IT needs of the College of听Veterinary听Medicine, Nursing and Allied Health including the RCMI web page at TU, development of online application forms and different database management. The team also provides technical support and training for both hardware and software as well as troubleshooting.

Overarching Aims:

1.Sponsor Computational Biology and Bioinformatics and related workshops to train scientists, graduate-students and undergraduate-students听to become competent听in the use听of听computational biology and听bioinformatics听resources that are available at the CBB at TU. This includes accessing, searching and extracting data from national and international bioinformatics databases, genomics facilities and sequencing facilities.

2.Increase the CBB resources selectively to create sustainable research capacity and听 state-of-the-art听 professional development support for RCMI scientists and other researchers;

3.Promote collaborative research among RCMI scientists at TU as well as at other institutions. Active collaboration with the RCMI-Translational Research Network (RTRN) is most important in this arena. This includes providing a common data management and application development framework, with a robust services-oriented-infrastructure that standardizes听 and听 streamlines听 the听 RCMI's听 researcher听 community听 collaborations;听 and

4.Create听a Telehealth/ Telemedicine infrastructure at CBR to address health disparities in the BBC of Alabama. 听听

厂别谤惫颈肠别蝉:听

CBB has been providing services in four major areas:听

1. Bioinformatics service delivery capacity;
2. Computational biology support;听
3. Statistical analysis support; and
4. IT support

Specifically, services being provided by CBB to TU researchers include:

• Software related
  • Data Modeling
  • Development environment (Test, Develop, production environment)
  • DNA and RNA Sequence Analysis

• Provide Biostatistics consultation to RCMI researchers:
  • Develop and provide high-level bioinformatics capabilities and services, including the storage, management, curation, integration and collaborative annotation of -omic data, generated by TU researchers;
  • Ensure best practice in bioinformatics and statistical analysis of all research data, and the transfer of technology and skills into the application of research in the area of health disparities;
  • Establish听 and听 consolidate听 links听 with听 RTRN/RCMI听 institutions听 and听 with听 other听 major bioinformatics centers and programs; and
  • Leverage TeraGrid resources: This team will train faculty and staff so they can tap into the ample resources of TeraGrid. TeraGrid is an open scientific discovery infrastructure that combines leadership and enterprise-class resources at eight partner sites to create an integrated, persistent computational resource. TeraGrid integrates high-performance computers, data resources and tools for high-end experimental facilities around the country.听听 These integrated resources include more than 102 Teraflops (i.e., 1012 or trillions) of computing capabilities and more than 15 petabytes (quadrillions of bytes) of online and archival data storage, with rapid access and retrieval over high-performance networks. Through the TeraGrid, researchers can access over 100 discipline-specific databases.听 With this combination of resources, the TeraGrid is the world's largest, most comprehensive distributed cyber-infrastructure for open scientific research.

• Database Development:
  • Outcome听 assessments听 tool听 development听 from听 the听 database development to the analysis
  • Back-end interfacing to data processing systems and displays
  • Privacy protection and security assessment

• Web based software tools: 听
  • 听Web interface
  • Website development, hosting and maintenance
  • Search engine development and management
  • Webpage student statistics

• Workflow technology:
  • Network security and monitoring
  • Systems design and development
  • Testing and deployment of collaborative technologies

• Training and Workshops:
  • Seminar and Workshop Series
  • Participate in Bioinformatics webinar series in collaboration with RCMI Translational Research Network (RTRN) Bioinformatics working group
  • Consultant epidemiological services to investigators in the areas of Cancer, HIV/AIDS, and other infectious diseases

• Videoconferencing:
  • Two pilot Internet Telemedicine/Telehealth centers have been set up
  • The first center is with Medical Aids Outreach where two Apple laptop computers were provided for use in providing services to their clients (like: education, counseling) and to facilitate remote meetings connecting their main office to their branch offices which are located in different counties听 and are apart more than 45 minutes. The second center is based in Macon County and we have provided one Apple laptop computer听

• Other Basic Services:
  • Consultation regarding software, hardware and accessories
  • Quality control of the core lab computers
  • Troubleshooting of networks, PC's, Mac's, and servers

• Facilitate advice, lead, coordinate and manage bioinformatics capabilities at TU in the area of听 the Genomics, Proteomics and Metabolomics (-omics) platforms;
  • Genomics Processes Include:
    • Assembly
    • Annotation
    • Mapping
    • Searching Non-Coding RNA
    • Disease Association
    • Comparative Genomics
    • New Tools for Alignment
    • Phylogenetic
    • Visualization
  • Transcriptomics Processes Includes:
    • Similarity Searching and Clustering
    • Alternative Splicing
    • Annotation
    • Gene Expression and Statistical Analysis
    • Small RNA Gene Identification
    • Visualization
  • Proteomics Processes Include:
    • Peptide Mass Fingerprinting Analyses
    • Custom Protein Data sets
    • Visualization

Equipment

听