1. The Nebraska Center for Rapid Bioanalysis An Overview of the NIH COBRE Program David S. Hage COBRE Retreat - January 16, 2009

2. Overview of Presentation  An Introduction to the NIH COBRE Program  Rationale for a COBRE Proposal in Rapid Bioanalysis  Details behind the COBRE Proposal to create a Center for Rapid Bioanalysis

3. What is the NIH COBRE Program? (Centers of Biomedical Research Excellence) Program Objectives:  To strengthen an institution’s biomedical research infrastructure through the establishment of a thematic multi- disciplinary center  To enhance the ability of investigator’s to compete independently for complementary NIH individual research grants

4. Details of the NIH COBRE Program  Program supports initiation and development of unique, state-of-the-art biomedical and behavior research in the full spectrum of basic and clinical sciences  Application must have a thematic focus  COBRE awards are supported through the IDeA Program, aimed at states with historically low aggregate success rates for grants from NIH  A substantial commitment on the part of the institution is required to provide additional faculty lines in the thematic area  Awards are made for 5 years, renewable, with up to 1.5 million (direct costs) being awarded per year; an additional 500 K may be requested in year 1 for facility renovations

5. Structure of a COBRE Grant  Description of PI Qualifications – Background, Funding History, Mentoring, etc. Qualifications – Background, Funding History, Mentoring, etc.  Overall Research Descriptions of 3-5 projects to be performed by junior facultyDescriptions of 3-5 projects to be performed by junior faculty  Administrative Core Organization, plans for development of Center and junior facultyOrganization, plans for development of Center and junior faculty  Research Core Facilities  Alteration & Renovation (if applicable)

6. Rationale for Creation of Nebraska Center for Rapid Bioanalysis  Many areas of research in biotechnology, medical research and pharmaceutical science are turning to more rapid screening or analysis methods  Examples include: Proteomics Glycomics Metabolomics DNA Sequencing High-throughput Screening of Drugs Identification & Analysis of Biomarkers Clinical Assays Combinatorial Chemistry

7. Rationale for Creation of Nebraska Center for Rapid Bioanalysis (Cont’d)  Need for improved and more rapid bioanalytical methods is recognized in several parts of NIH Roadmap for Medical Research Building Blocks, Biological Pathways, and Networks Building Blocks, Biological Pathways, and Networks Molecular Libraries and Imaging Molecular Libraries and Imaging Human Microbiome Project Human Microbiome Project  Among the more than 70 COBRE programs in existence, none deals primarily with bioanalysis

8. Current Research Interests/Strengths at UNL & UNMC in Rapid Bioanalysis  Mass Spectrometry  NMR  Chemical Separations  Electrochemistry  Optical Spectroscopy o Although instrumentation and facilities are available in these areas, UNL and UNMC currently lack a critical mass of researchers and the infrastructure needed to achieve national leadership in bioanalysis  Rapid PCR/DNA Sequencing  Microfluidics/Nanofabrication  Combinatorial Chemistry  Single Molecule Imaging & Manipulation

9. Complementary Nature of Center for Rapid Bioanalysis with Other COBRE Programs/Efforts in Nebraska  Center for Virology (UNL)  Center for Redox Biology (UNL)  Cell signaling (UNMC)  Neurosensory systems (UNMC)  Nanomedicine (UNMC)

10. Fit of Proposed Center with Other Research at UNL & UNMC  Proposed Center would be complementary to current research in the areas of pharmaceutical science, combinatorial chemistry, chemical engineering, biochemistry, molecular biology, and environmental toxicology  A similar fit can be made with efforts in biotechnology, food science, bioinformatics, & general medical research or cancer research  Program would also have a good fit with several local industries (LICOR, MDS Pharma, etc.)

11. History of Current COBRE Proposal from UNL  Up to three COBRE Awards allowed per institution (e.g., UNL has two – Virology & Redox Biology)  Only one full proposal can be submitted per institution  Current proposal was selected by UNL for development in 2007 and was submitted Oct. 24, 2007  Reviews of current proposal were received in June 2008, with an Overall rating of “Excellent”. Final announcement of funding will be made in Spring 2009.  If not funded this round, a revision of this proposal is planned for the next call for COBRE proposals, which is expected to be made in Jan/Feb 2009

12. Specific Proposal Submitted by UNL: Nebraska Center for Rapid Bioanalysis (NCRB) Overall Objectives  Creation of a Center at UNL and in cooperation with UNMC focusing on the development of methods for the rapid analysis and high-throughput screening of biological agents  Support and mentoring of junior faculty in the field of rapid bioanalysis and related areas  Development and expansion of the infrastructure at UNL, UNMC and in the state of Nebraska to support research in the field of rapid bioanalysis  Center would be housed in Dept. Chemistry at UNL but directly involve faculty from the Depts. of Chemical & Biomolecular Engineering and Biological Systems Engineering at UNL, as well as faculty in Depts. of Pharmaceutical Science and Biochemistry & Molecular Biology at UNMC (among many others)

13. Specific Aims of the NCRB  Specific Aim 1: Mobilize and expand the collective expertise at UNL and UNMC in the areas of chemistry, biochemistry, engineering, pharmaceutical science and basic medical research to develop, optimize, validate and apply new technologies for rapid bioanalysis  Specific Aim 2: Establish a critical mass of experienced researchers in the area of rapid bioanalysis through the mentoring and training of junior investigators, and through the targeted recruitment of additional faculty members in this area

14. Specific Aims of the NCRB (Cont’d)  Specific Aim 3: Develop/maintain an infrastructure of support and facilities in areas such as bioinformatics and computational chemistry, instrument development and microfabrication, structural and functional analysis, protein and cell production, and nanoimaging to enhance the research capability for new and existing investigators in the area of rapid bioanalysis

15. Primary Elements for Meeting the Specific Aims of the NCRB

16. Administrative Core of the NCRB  PI/Program Director (D.S. Hage, UNL)  Assistant Director (Y. Lyubchenko, UNMC)  Junior Project Leaders  Mentors & Mentoring Council  External Advisory Board (EAB)  Industrial & Clinical Advisory Board (ICAB)  Core Facilities

17. Overall Structure of the Nebraska Center for Rapid Bioanalysis (NCRB)

18. Initial Research Focus of NCRB: Bioanalytical Tools for Drug Discovery & Biomarker Detection  Drug Discovery Use of proteomics, glycomics or metabolomics for drug discovery Use of proteomics, glycomics or metabolomics for drug discovery Development of bioanalytical methods for rapidly identifying and characterizing new drugs to target a given protein or biological pathway Development of bioanalytical methods for rapidly identifying and characterizing new drugs to target a given protein or biological pathway Creation of high-throughput screening (HTS) methods for examining potential drugs and for characterizing their properties Creation of high-throughput screening (HTS) methods for examining potential drugs and for characterizing their properties  Biomarker Detection Creation of improved methods for biomarker detection/identification Creation of improved methods for biomarker detection/identification Improved analysis of biomarkers for disease treatment and detection Improved analysis of biomarkers for disease treatment and detection Creation of improved methods for the study of biological pathways for biomarker identification Creation of improved methods for the study of biological pathways for biomarker identification  Related Topics Development of miniaturized or nanofabricated analytical systems for drug discovery & biomarker detection Development of miniaturized or nanofabricated analytical systems for drug discovery & biomarker detection

19. Projects by Junior Faculty  Project 1: High-Throughput Screening of Drug Candidates by NMR (Dr. Robert Powers – Dept. Chemistry, UNL)  Project 2: Single Molecule Tracking & Imaging for High-Throughput Screening (Dr. Greg Bashford – Dept. Biological Systems Engineering, UNL)  Project 3: Cell Array Chips Based on Patterned Nanostructures (Dr. Barry Cheung – Dept. Chemistry, UNL)  Project 4: Folding-Based Electrochemical Biosensors (Dr. Rebecca Lai – Dept. Chemistry, UNL)  Project 5: Proteomic & Metabolomic Studies of a Microbial Community (Dr. Laurey Steinke – Dept. Biochem. & Mol. Biology, UNMC)

20. General relationship between Junior Projects & Theme of High-Throughput Screening of Drugs and Biomarker Detection

21. Mentoring of Junior Faculty: The Mentoring Council  Mentoring of junior project leaders is an important part of the COBRE program  Each Junior Project Leader is assigned three mentors A lead mentor in an area closely related to the project A lead mentor in an area closely related to the project A second mentor in an area complementary to the project A second mentor in an area complementary to the project Center Director or Assistant Director Center Director or Assistant Director  Rationale behind mentor selection One mentor for the method used in the project + one mentor for the area of biomedical applications One mentor for the method used in the project + one mentor for the area of biomedical applications At least one mentor from UNL and at least one from UNMC At least one mentor from UNL and at least one from UNMC Center Director or Assistant Director will be assigned based on the location of the project and/or the area of research Center Director or Assistant Director will be assigned based on the location of the project and/or the area of research

22. Mentoring Council: Initial Members from UNL Dr. Ronald Cerny - mass spectrometry and applications in proteomics and the study of small molecules (L. Steinke) Dr. Ronald Cerny - mass spectrometry and applications in proteomics and the study of small molecules (L. Steinke) Dr. Liangcheng Du - use of mol. biology and mass spectrometry to investigate pathways in microorganisms and create new products (L. Steinke) Dr. Liangcheng Du - use of mol. biology and mass spectrometry to investigate pathways in microorganisms and create new products (L. Steinke) Dr. Gerard Harbison - NMR spectroscopy (R. Powers) Dr. Gerard Harbison - NMR spectroscopy (R. Powers) Dr. Natale (Ned) J. Ianno - Materials research & thin film deposition; pulsed laser deposition and sputter deposition of various materials (B. Cheung) Dr. Natale (Ned) J. Ianno - Materials research & thin film deposition; pulsed laser deposition and sputter deposition of various materials (B. Cheung) Dr. Larry Parkhurst - Application of fluorescence spectroscopy in the study of biomolecular structure and function (G. Bashford) Dr. Larry Parkhurst - Application of fluorescence spectroscopy in the study of biomolecular structure and function (G. Bashford) Dr. Jody Redepenning - Electrochemistry and in the microfabrication of novel devices such as chemical-modified nanoelectrodes (R. Lai) Dr. Jody Redepenning - Electrochemistry and in the microfabrication of novel devices such as chemical-modified nanoelectrodes (R. Lai) Dr. David S. Hage – Bioanalytical separations, affinity-based methods, miniaturized analytical systems (R. Lai, R. Powers, L. Steinke) Dr. David S. Hage – Bioanalytical separations, affinity-based methods, miniaturized analytical systems (R. Lai, R. Powers, L. Steinke)

23. Mentoring Council: Initial UNMC Members Dr. Kenneth W. Bayles – M icrobiologist; cellular biology of S. aureus and Bacillus anthracis as related to biofilm formation & the development of antibiotics. (R. Powers) Dr. Kenneth W. Bayles – M icrobiologist; cellular biology of S. aureus and Bacillus anthracis as related to biofilm formation & the development of antibiotics. (R. Powers) Dr. Steven H. Hinrichs – Microbiologist; interests in new antibiotics, molecular microbiology, and use of methods such as mass spectrometry (L. Steinke) Dr. Steven H. Hinrichs – Microbiologist; interests in new antibiotics, molecular microbiology, and use of methods such as mass spectrometry (L. Steinke) Dr. Michael Hollingsworth - M icrobiologist and immunologist; pancreatic cancer and biomarkers for its detection (R. Lai) Dr. Michael Hollingsworth - M icrobiologist and immunologist; pancreatic cancer and biomarkers for its detection (R. Lai) Dr. Ming-Fong Lin - Biochemist and pathologist; interests in prostate cancer, cell growth regulation by tyrosine phosphorylation signal transduction and androgen regulation of cell proliferation (B. Cheung) Dr. Ming-Fong Lin - Biochemist and pathologist; interests in prostate cancer, cell growth regulation by tyrosine phosphorylation signal transduction and androgen regulation of cell proliferation (B. Cheung) Dr. Yuri Lybuchenko – Pharmaceutical science, single molecule imaging, fluorescence spectroscopy (G. Bashford, B. Cheung) Dr. Yuri Lybuchenko – Pharmaceutical science, single molecule imaging, fluorescence spectroscopy (G. Bashford, B. Cheung)

24. Evaluation & Advising of the NCRB: The External Advisory Committee (EAC)  The EAC will consist of outstanding scientists representing the NCRB’s key research areas will provide an independent mechanism for evaluation of the research projects, core facilities and activities  The EAC will also give advice on strategic planning, including allocation of resources and the targeting of emerging funding opportunities  The EAC meet annually on site with the Director and Mentoring Council and provide an annual written critique of the Center as part of the formative evaluation process

25. External Advisory Council (EAC) Dr. Susan Lunte (Univ. Kansas) – Creation of new tools for bioanalysis based on electrochemistry, chemical separations, electrochemical sensors, and microfabricated devices Dr. Susan Lunte (Univ. Kansas) – Creation of new tools for bioanalysis based on electrochemistry, chemical separations, electrochemical sensors, and microfabricated devices Dr. Fred W. McLafferty (Cornell Univ.) – Mass spectrometry & its applications in various systems Dr. Fred W. McLafferty (Cornell Univ.) – Mass spectrometry & its applications in various systems Dr. John L. Markley (Univ. Wisconsin) - Use of NMR spectroscopy in the study of structural genomics, metabolomics and structure-function relationships in proteins; multi-dimensional NMR Dr. John L. Markley (Univ. Wisconsin) - Use of NMR spectroscopy in the study of structural genomics, metabolomics and structure-function relationships in proteins; multi-dimensional NMR Dr. Irving Wainer (NIH) - Bioanalytical chemistry, use of mass spectrometry and chromatography in the study of biological samples Dr. Irving Wainer (NIH) - Bioanalytical chemistry, use of mass spectrometry and chromatography in the study of biological samples Dr. Edward Yeung (Iowa State Univ.) - Nonlinear spectroscopy, laser- based detectors for liquid chromatography, capillary electrophoresis, single-cell and single-molecule analysis, DNA sequencing Dr. Edward Yeung (Iowa State Univ.) - Nonlinear spectroscopy, laser- based detectors for liquid chromatography, capillary electrophoresis, single-cell and single-molecule analysis, DNA sequencing

26. A Clinical & Industrial Perspective: The Industrial & Clinical Advisory Board (ICAB)  ICAB will provide feedback regarding the NCRB’s research portfolio, programmatic activities and center direction from the perspective of clinical laboratories and the pharmaceutical/biotechnology industries  This feedback will be used by the NCRB to develop contacts for the transition of methods to the biomedical community and provide an industrial/clinical perspective on critical needs for drug discovery & biomarker detection  The ICAB will meet with the Center Director and Mentoring Council annually in the spring, or six months prior to/following the meeting of the EAC

27. Industrial & Clinical Advisory Board (ICAB) Dr. Michael Grace (Director of Bioanalytical Sciences, Bristol-Myers Squibb) - P rotein characterization, process analytical technology, biological interaction studies and the characterization of glycoconjugates. Dr. Michael Grace (Director of Bioanalytical Sciences, Bristol-Myers Squibb) - P rotein characterization, process analytical technology, biological interaction studies and the characterization of glycoconjugates. Dr. James E. McClurg (Senior Vice President and Chief Scientific Officer, MDS Pharma Services) – Pharmaceutical analysis & related instrumentation Dr. James E. McClurg (Senior Vice President and Chief Scientific Officer, MDS Pharma Services) – Pharmaceutical analysis & related instrumentation Dr. John Masters (Head of Discovery Chemistry in Research & Technology, Eli Lilly and Company) - Medicinal chemistry, development of new analytical methods for screening of drugs and their metabolites Dr. John Masters (Head of Discovery Chemistry in Research & Technology, Eli Lilly and Company) - Medicinal chemistry, development of new analytical methods for screening of drugs and their metabolites Mr. Larry Middendorf (Senior Vice President of Marketing/Sales, LI- COR Biosciences).- Development and marketing of new tools and instruments for bioanalysis Mr. Larry Middendorf (Senior Vice President of Marketing/Sales, LI- COR Biosciences).- Development and marketing of new tools and instruments for bioanalysis Dr. Thomas Moyer (Mayo Clinic;) - Clinical chemist ry, toxicology and drug analysis Dr. Thomas Moyer (Mayo Clinic;) - Clinical chemist ry, toxicology and drug analysis

28. Facilities at UNL/UNMC in Area of Rapid Bioanalysis  Bioinformatics & Computational Facilities. Methods and tools for traditional are available through existing facilities at UNL and UNMC (in collaboration with UNO) Methods and tools for traditional are available through existing facilities at UNL and UNMC (in collaboration with UNO) More advanced computations and a cyberinfrastructure will be available through a new Computational Core More advanced computations and a cyberinfrastructure will be available through a new Computational Core  Instrument Development/Microfabrication Machine shop, and electronics shop are available at UNL Machine shop, and electronics shop are available at UNL Microfabrication can be conducted in the Nanofabrication Facility that is part of UNL’s Center for Materials Research and Analysis Microfabrication can be conducted in the Nanofabrication Facility that is part of UNL’s Center for Materials Research and Analysis  Nanoimaging Facility available now at UNMC Facility available now at UNMC

29. Facilities at UNL/UNMC in Area of Rapid Bioanalysis (Cont’d)  Structural & Functional Analysis Mass spectrometry - Nebraska Center for Mass Spectrometry (UNL) & proteomics facility at UNMC Mass spectrometry - Nebraska Center for Mass Spectrometry (UNL) & proteomics facility at UNMC NMR spectroscopy – UNL (Dept. Chemistry) & UNMC NMR spectroscopy – UNL (Dept. Chemistry) & UNMC Functional analysis – Biacore & DNA arrays at both UNL & UNMC Functional analysis – Biacore & DNA arrays at both UNL & UNMC Rapid structural analysis will be enhanced through the creation of a new Robotics & Automated Sample Preparatio nCore Rapid structural analysis will be enhanced through the creation of a new Robotics & Automated Sample Preparatio nCore  Protein & Cell Production Facilties for protein expression, cell culturing & protein purification in UNL, Dept. Chemical & Biomolecular Engineering Facilties for protein expression, cell culturing & protein purification in UNL, Dept. Chemical & Biomolecular Engineering Monoconal antibody production facility at UNMC Monoconal antibody production facility at UNMC

30. New Core Facilities Created by NCRB  Computational Core (Hui Li - Director, UNL) Core will provide advanced computations and training involving simulations and quantum chemical calculations will be needed by some Center members (e.g., electronic structure calculations of protein active sites, estimation of pK a values, redox potentials, binding energies, solvation energies, NMR chemical shifts) Core will provide advanced computations and training involving simulations and quantum chemical calculations will be needed by some Center members (e.g., electronic structure calculations of protein active sites, estimation of pK a values, redox potentials, binding energies, solvation energies, NMR chemical shifts) Core also will provide a cyberinfrastructure for the NCRB, where researchers can readily exchange their data and link into programs and data generated by other Center facilities Core also will provide a cyberinfrastructure for the NCRB, where researchers can readily exchange their data and link into programs and data generated by other Center facilities

31. New Core Facilities Created by NCRB (Cont’d)  Robotics & Automated Sample Preparation Core (Joseph Dumais & Kurt Wulser - Directors, UNL) Core will provide stations that will allow the automated preparation of samples for analysis by mass spectrometry and/or NMR spectroscopy Core will provide stations that will allow the automated preparation of samples for analysis by mass spectrometry and/or NMR spectroscopy Core will be housed near the MS and NMR facilities at UNL Core will be housed near the MS and NMR facilities at UNL Automated sample injection systems for the high- throughput analysis of samples by NMR and mass spectrometry will also be available through this Core Automated sample injection systems for the high- throughput analysis of samples by NMR and mass spectrometry will also be available through this Core

32. Other Components of Infrastructure for the NCRB Small grants programSmall grants program Annual conferenceAnnual conference Monthly seminar programMonthly seminar program Center membershipsCenter memberships WebsiteWebsite

33. Proposed Future Hires under NCRB Junior level mass spectrometrist (proteomics, metabolomics or associated areas) - Currently planned in Dept. Chemistry, UNL, under PoE in Functional Genomics Junior level mass spectrometrist (proteomics, metabolomics or associated areas) - Currently planned in Dept. Chemistry, UNL, under PoE in Functional Genomics Junior level chemical engineer (biomolecular materials) - Planned by UNL Dept. Chemical & Biomolecular Engineering, UNL Junior level chemical engineer (biomolecular materials) - Planned by UNL Dept. Chemical & Biomolecular Engineering, UNL Junior level analytical chemist (single molecule spectroscopy/ bioanalytical spectroscopy) - Planned by Dept. Chemistry, UNL Junior level analytical chemist (single molecule spectroscopy/ bioanalytical spectroscopy) - Planned by Dept. Chemistry, UNL Junior level pharmaceutical chemist (drug analysis/proteomics) - Planned by Dept. Pharmaceutical Science, UNMC Junior level pharmaceutical chemist (drug analysis/proteomics) - Planned by Dept. Pharmaceutical Science, UNMC Junior level chemist/biochemist (glycomics, protein-protein interactions or DNA-protein interactions) - Planned by Dept. Chemistry, UNL Junior level chemist/biochemist (glycomics, protein-protein interactions or DNA-protein interactions) - Planned by Dept. Chemistry, UNL

34. Task Quarter 1Quarter 2Quarter 3Quarter 4 Administrator X Mentoring Council Meetings XXXX Internal Coordinating Committee Meetings XX Website Development XXX Monthly Seminar Series (X)XXX Internal Coordinating Committee Meetings XX External Advisory Committee Meeting c X (Year 2) Industrial & Clinical Advisory Board Meeting X Symposium X (Year 2) Center Reviews XX Formative Evaluation X (Year 2) What will Occur During the Early Formation of NCRB? (Year 1 - Quarter 1/Year 2)

35. Benchmark Year 1Year 2Year 3Year 4Year 5 Hire #1 (Mass Spectrometrist) XX Hire #2 (Chemical Engineer) XX Hire #3 (Analytical Chemist) XX Hire #4 (Pharmaceutical Chemist) XX Hire # 5 (Chemist/Biochemist) XX Seed Grants XXXX R01 Submission (Projects 1-5) (X) b XX Project Turnover (Projects 1-5) (X) c XX First P01 Submission (resubmission in Year 2, if needed) X Summative Evaluation (4th Quarter, Year 5) X What will Occur after the Foundation of the NCRB? (Years 1 – 5)

36. What is Next for the NCRB COBRE Proposal?  A final decision on funding of the current proposal is pending and expected in Spring 2009.  Preparations are underway to help address comments in review of previous proposal in preparation for resubmission later in 2009, if needed  Seed funds have been obtained from UNL & UNMC for Junior Project Leader to conduct preliminary studies to address comments of their individual proposals  Efforts to promote work and collaborations between UNL and UNMC in the area of rapid bioanalysis, as evidenced by this retreat