A multi-state alliance of regional INBRE Networks.

RAIN

Shared Resources

Proteomics, Metabolomics, and Mass Spectrometry Facility at Montana State University

Overview

RAIN is a novel approach intended to share and capitalize on participant states’ complementary expertise and resources in order to reduce redundancy and improve outcomes. The alliance intends to increase the biomedical research capacity in participating states by sharing insight and resources pertaining to each states’ strongest areas of expertise. An overview of those strengths and opportunities include:

Idaho

Idaho INBRE provides RAIN member states with access to Bioinformatics Education through four degree programs and extensive online training modules. Modules include training students and faculty in bioinformatics, biostatistics, computer science, and statistics. An online Bioinformatics Education Repository housing a vetted, community-curated resource for learning or teaching bioinformatics is also available with updated material organized in three categories:

  1. Bioinformatics Background with topics in molecular biology, computer science, statistics and probability
  2. Basic Bioinformatics with topics in database content and retrieval, bioinformatics tools and data interpretation
  3. Specialized Bioinformatics with topics in omics, macromolecules, and pathways

The University of Idaho in Moscow, Idaho, offers both M.S. and Ph.D. degrees in Bioinformatics and Computational Biology (BCB). BCB is a research-intensive interdisciplinary graduate program established with INBRE support in 2003 that trains graduate students with an interdisciplinary core curriculum, a required rotation/internship outside their area of expertise, in-depth training in one area, and opportunities for cutting edge research. The program’s main focus areas include computer sciences, biological sciences, and mathematical and statistical sciences to prepare students for solving complex problems in health sciences, biotechnology, engineering, and other industries. Students have access to state of the art core facilities, including Idaho’s Computational and Genomics Resources Core facilities.

Boise State University offers an M.S. degree in Bioinformatics. This interdisciplinary program prepares students in analysis and interpretation of large-scale biological datasets and incorporates biology, biochemistry, mathematics, statistics, computing, and engineering. Students receiving the M.S. in Bioinformatics will typically complete a research thesis but a “non-thesis” option will be available for students who complete a project or research article.

Lewis-Clark State College (LC State) in Lewiston, Idaho, offers a B.S. degree in Bioinformatics. The prevailing challenges to sustainable life on earth include pioneering novel sources of renewable energy, feeding a growing human population, endangered species conservation, improving forest health and emerging infectious disease mitigation. Current innovations in biotechnology such as precise genome editing, phenomics and ultra-high throughput DNA sequencing technologies have a tremendous potential to address these challenges and have indeed contributed to new findings in cancer genomics, genetic disorders, biofuels, C4 photosynthesis, and drug discovery. The rapid ascendency of the 21st century bioeconomy had created career opportunities in cancer genomics, personal genomics, precision agriculture, paleogenomics, pharmacogenomics, gene function discovery and next-generation biofuels. These emerging fields require specialized skillsets in bioinformatics to generate key insights from large-scale DNA sequencing datasets.

The Lewis-Clark State College undergraduate program in Bioinformatics provides a cost-effective opportunity for studying cutting-edge bioinformatics skills in small classroom settings. The on-campus facilities include high-performance computing clusters dedicated to bioinformatics research and large-scale data analysis. Topics of focus include whole genome assemblies and analysis, transcriptomics, metagenomics, mutation detection, small silencing RNAs, digital image classification, machine learning, and biostatistics.

Bioinformatics faculty actively pursue biomedical research funding opportunities and are currently investigators in various ongoing NIH and NSF funded research projects. As a result, students have opportunities for undergraduate research mentoring, summer research assistantships, internships, research conference presentations and scientific publications.

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Degree requirements

Transfer/articulation agreements are planned with Lewis-Clark State College so students from Montana, Nevada, New Mexico, and Wyoming can finish a B.S. in Bioinformatics in a timely manner.

LC State offers four out-of-state tuition waivers for motivated students from RAIN states (Montana, Nevada, New Mexico, and Wyoming), who enroll in the bioinformatics program.

Montana

Statistical Consulting and Research Services (SCRS) at Montana State University is a Montana INBRE-supported resource that investigators can use to improve research design, implementation and outcomes. SCRS makes available a team of statistical experts to guide research planning, design, evaluation, and communication with the overall goal of building better research projects through statistics. SCRS is a shared user facility that works with investigators to design experiments maximizing experimental outcomes in terms of data quality and quantity. SCRS works with students and research professionals from a wide variety of disciplines, including the life sciences, physical sciences, social sciences, and clinical sciences. Clients include public health professionals, medical professionals, bench or laboratory scientists in a variety of fields, epidemiologists, community and tribal leaders, computer scientists and information systems experts, engineers, statisticians, social scientists and behavioral health professionals. RAIN researchers will be able to take immediate advantage of the expertise built up over years through support by Montana INBRE.

In addition, MSU is one of the few academic institutions in the US that has both NMR and Mass Spectrometry integrated for metabolomics projects. Metabolomics is the newest of the functional-omics trilogy and provides a direct read out of biological activity. Mass spectrometry coupled to liquid (or gas) chromatography (LCMS) and nuclear magnetic resonance (NMR) are the most powerful analytical tools currently available to investigate the metabolome. Leading edge instrumentation is available for conducting NMR, LCMS, GCMS and coupled LC-NMR-MS. Example RAIN projects thus far include studies from Idaho on the stress response of bacteria in a consortia and the use of metabolomics to predict dual risks of stress and toxins in mammals from urine. For RAIN collaborators, the Metabolomics Facility is able to help analyze samples, and train users of all levels in experimental design, sample prep, data collection, and analysis. RAIN researchers and students will be able to apply for pilot funds to take advantage of the unique and powerful research capabilities of these facilities.

The Montana IDeA Community Engagement Core fosters and enhances tribal and rural community-academic partnerships aimed at mitigating health disparities.  This core is a shared resource among MSU-based IDeA programs abd draws on the expertise of a team of community-academic partners who highly value the mutual goal of improved community health through engagement, dialogue, and collective problem solving. To establish and maintain sustainable community collaborations, the Core’s methodological approach is grounded in community-based participatory research (CBPR) practices, fostering a partnership where communities are equitable collaborators in the research and an environment for producing mutually beneficial goals.

Key components of the CEC, which are intended to be part of RAIN Community Engagement shared resource, include access to expertise and training opportunities focusing on innovative health communications that consider relevant cultural, linguistic, and literacy needs; CBPR practices; best practices in developing respectful community-academic research partnerships; developing agreements regarding data ownership and plans for disseminating study results; sustaining relationships with community partners; identifying potential barriers to collaborative research and approaches to addressing them; designing collaborative research protocols (including IRB approvals); establishing Community Advisory Boards, and incorporating qualitative and quantitative methods to identify health issues of particular concern to communities. Community Research Associates (CRAs) within the Core serve as liaisons to tribal and rural communities and facilitate connections between these groups and investigators who have the scientific research expertise to help address the health issues and priorities identified by tribal and rural communities. CRAs provide training and mentoring to both investigators and community members to facilitate effective research partnerships following CBPR practices. RAIN partners will have the opportunity to tap into the Core’s trainings in culturally appropriate research practices and CBPR as well as methods for developing their own CRAs within their statewide networks

Nevada

Data Science Core for Biomedical Research (UNR) The experienced staff offer services and consulting to meet your research needs. We have a broad range of expertise including, but not limited to, biochemistry, biomedical sciences, cellular and molecular biology, computational science, computer science, network modeling, proteomic bioinformatics, and statistical and quantitative analysis. 

Mick Hitchcock PhD Nevada Proteomics Center (UNR) offers high quality mass spectral proteomic analysis using state-of-the-art technologies.  Our goal is to assist investigators with qualitative and quantitative characterization of proteins to gain a greater understanding of physiological pathways, molecular interactions and regulatory signaling.

Nevada Genomics Center (UNR) serves academic and industry researchers in their studies on the function and structure of genomes.  Services offered can support a range of options and sequencing yield, from intensive, data-rich projects to pilot projects.  We offer services for next-generation Illumina sequencing, Sanger sequencing, fragment analysis and nucleic acid quantification and sizing.

Genomics Core Facility (UNLV) provides a full range of structural and functional genomics services to investigators in Nevada and beyond. The state-of-the-art facility provides a wide range of genomics instrumentation and offers training for the use of equipment. Staff may also be contracted to perform selected services.

National Supercomputing Institute (UNLV) is a full-service supercomputing facility with on-site and off-site user training, national network accessibility and a mission for excellence in education and research in supercomputing and its applications.  NSI provides supercomputing training and services to academic
and research institutions, government and private industry for research and development related to energy, the environment, medical informatics, and health care delivery.

Zetaview Nanoparticle Microscope Tracking System (UNLV) This instrument supports identification and characterization of nanoparticles like exosomes; this will include determining the concentration, size, fluorescence, and Zeta Potential of nanoparticles.

New Mexico

The New Mexico IDeA Networks of Biomedical Research Excellence Bioinformatics Core at the National Center for Genome Resources (NCGR) in Santa Fe prescribes sequencing experiments, provides advanced bioinformatics, and delivers bioinformatics education through workshops and training under the experienced scientific research umbrella of NCGR to the Regional Alliance of INBRE Networks. The NCGR is a world-renowned bioinformatics, research, and service facility that touts a Human Genome Project pedigree. In 1994, NCGR was spun out of Los Alamos National Laboratory, where staffers provided the bioinformatics support for some of the earliest human genome sequence data ever generated and developed the first relational human genome sequence database (GSDB). By leveraging NCGR’s 20+ years of experience in the genomic and bioinformatics field and institutional commitment of approximately $7 million in equipment, facilities and infrastructure, RAIN researchers are provided turnkey access to top-notch NGS, bioinformatics and technical staff enabling high-impact research in -omics and molecular biology.

Wyoming

The Wyoming Bioinformatics Core will offer informatics support to other RAIN members when needed, will offer curriculum development expertise to educators, and will provide workshop support. The Core will also assist RAIN member states developing relationships and projects with local, state and federal public health agencies.

Currently under construction, Wyoming will provide RAIN investigators and students access to the University of Wyoming Center for Advanced Scientific Imaging (CASI). In the new Science Initiative Building CASI will co-locate UW’s elite imaging scientists, their student teams, and unique instrumentation in a state-of-the-art staffed laboratory, allowing them to achieve unprecedented sensitivities and efficiencies in probing the fundamental interactions among atoms, molecules, and cells that underlie all next-generation technologies. The center will rank among the world’s best, attracting faculty and students from across the globe as it spotlights Wyoming’s commitment to the sciences that serve state and national needs.