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Intro to the P3 Center concept Management and logistics in Year 2 Strategic Goals – Highlights of Year 2 accomplishments

The Arkansas Center for Plant-Powered Production (The P3 Center) . Intro to the P3 Center concept Management and logistics in Year 2 Strategic Goals – Highlights of Year 2 accomplishments. What is the P3 Center?. UAF. ASU. UALR. UCA. NCTR.

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Intro to the P3 Center concept Management and logistics in Year 2 Strategic Goals – Highlights of Year 2 accomplishments

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  1. The Arkansas Center for Plant-Powered Production (The P3 Center) Intro to the P3 Center concept Management and logistics in Year 2 Strategic Goals – Highlights of Year 2 accomplishments

  2. What is the P3 Center? UAF ASU UALR UCA NCTR • NSF EPSCoR-supported research consortium targeting cross-disciplinary approaches to plant biology and plant products • 5 Universities • Arkansas State University • University of AR, Fayetteville • University of AR, Little Rock • University of AR, Pine Bluff • University Central Arkansas • > 45 faculty (plant biologists, chemists, molecular biologists, environmental scientists, plant pathologists, entomologists, food scientists, computer scientists, biochemical engineers)

  3. P3 Center Mission Our research is focused on understanding the underlying mechanisms that drive the amazing biosynthetic capacity of plants To take advantage of the unique biosynthetic capacity of plants as scalable biofactories for proteins, chemicals, and biomaterials to address global challenges in energy, human health, climate change, and food security.

  4. Some Year 2 Logistics • Our Technical Advisory Committee • Rotation structure established • New chair : Kent Chapman (and many thanks to Joe Chappell!) • New members: Industry - John Howard (Adv. Biotech. Institute, CA) and Bioinformatics - Robin Buell (Michigan State University) • Gary Thompson and Celia MacIntosh “retired” – Many thanks!!! • Management team • Comprised of campus leads, cluster leads, outreach coordinator • And our program managers, Emily Devereux and Lacy Nelson • Meet every 2 weeks by phone • Campus visits - faculty and administrators • P3 Lead change at UCA (now Ben Cash, David Dussourd)

  5. P3 Center Strategic Plan • Build instrumentation infrastructure and capabilities • Enhance research competitiveness of P3 focal areas • Build intellectual infrastructure thru professional and workforce development • Build national reputation • Build sustainability of the program Some highlights……

  6. I. Instrumentation • Collecting exceptional data! • Training session at ACMAP mtg • Initiated collaboration with Nebraska EPSCoR (joint proposal to NSF pending) Web database “live” by end of year Campuses tasked with sustainability plan for multi-user items Highlight – the Scanalyzer - truly enabling technology for high-thru-put phenotyping (ArgeliaLorence)

  7. II. Research Competitiveness Research clusters • Plant interactions with other organisms • Ken Korth (UAF) • 3. Productivity “set-points” • Beth Hood (ASU) • 4. Next-GenSeq and bioinformatics • Xiuzhen Huang (ASU) • Comparative metabolomics: • Steve Grace (UALR); Julie Carrier (UAF)

  8. Comparative metabolomics: • Gene, pathway enzyme, discovery • Metabolite engineering • HTP metabolite data management Metabolic Profiling Genetic Phenotyping Gene Discovery Student Involvement Expression Profiling Ryne Ramaker Destiny Davis (INBRE) Delice Kayeshgiue (INBRE) Chen Chen Marissa de La Paz • Presented at Phytochemical Society of North America and P3/ACMAP • See poster by Marissa de La Paz Revealed Novel Aspects of Light Regulation of Plant Metabolism

  9. NeedleFinder: a New Bioinformatics Tool for Mining Metabolomic Datasets 3D Barcode • What is it? • A versatile software tool designed to parse, filter, and mine LCMS datasets Export LCMS data in CDF format NeedleFinder Object Loader() MySql Tables runs, scan_number, and point_number • What is it good for? • Produces rapid unbiased “barcode” of LCMS data for statistical analysis • Class assignment, detection of outliers, etc. • Data mining for important variables, biomarkers, etc. NeedleFinder Object BucketFiller() NeedleFinder Object Parser() Class Assignment Output files in csv format MySql Tables bin and bucket_analysis MVA MetaboAnalyst Statistica • Presented at MCBIOS 2012 and P3/ACMAP 2012 • See poster by Stephen Embry

  10. Plant interactions– plant proteins and metabolites serve as signals in host pathways, in defense against pests, and to promote health and nutrition in animals Applying tools of genomics, plant culture, and metabolomics to fungal pathogenesis, insect herbivory, food science, neurobiology, mammalian cell culture, and immunology

  11. Biological “set-points” -- addressing mechanisms that limit protein and biomass accumulation • Key Activities and Accomplishments • Held campus brainstorming meetings • Visited NSF ‘plant genome’; USDA ‘plant biology’ (plan collab. grant) • Initiated interactions with iPlant Collaborative • Submitting BMC Plant Biology/ Biotechnology “special issue” (review and 4 research articles) • Nature has selected for metabolic efficiency • Plants make what they need – • but have tremendous untapped capacity • INPUTS • Genes • Genotypes • Nutrients • Conditions • OUTPUTS • Proteins • Phytochemicals • Biomass • Biomaterials

  12. Research Highlight • Determined factors affecting high-level protein accumulation in transgenic maize seed—P3 seed grant • Xiuzhen Huang, Thomas Teoh, Elizabeth Hood • Moved from Microarray to Next Gen Sequencing to compare high and low protein accumulation in embryos; First Next Gen project at ASU • One manuscript submitted, one in preparation • Network proposal submitted to NSF 2010 • Set Points proposal planned for USDA 2012

  13. Next-Gen and BioInformatics • iPlant Workshop • May 17-18 at UALR • ~45 participants; > 20 P3 • State Breakdown : AR: 34, MS: 7 (EPSCoR link), LA: 1, KY:1 ~17 P3 projects (Just received last data sets) Secure data storage on P3 servers (ASU) Xiuzhen Huang’s students are performing initial alignment, assembly, and expression counts NSF-EPSCoRBioInformatics Conference (Huang & McClure)

  14. Faculty successes and reputation building III. Professional and Workforce Development • Invited book editors • Argelia Lorence, Recombinant Gene Expression, Reviews and Protocols, 3rd Edition • Burt Bluhm, Fungal Genomics: Methods and Protocols (co-ed) • Julie Carrier, BiorefineryCo-Products: Phytochemicals, Primary Metabolites and Value-Added Biomass Processing (co-ed) • Increased participation on grant review panels • DOE, NSF, USDA

  15. Faculty successes and reputation building III. Professional and Workforce Development • Leadership in national organizations • e.g., Fabricio Medina-Bolivar, VP for ACMAP • EPSCoR reviewer (6 P3 members on Missouri Review) • Entrepreneurship recognition • Cramer, Radin (BioStrategies-LC) win 2012 Tibbetts Award for innovation from SBA (awarded in White House)

  16. P3 Student updates • 85 UG, Grad Student, PD • Current student support • Graduate student: 10 in Yr2; 13 in Yr3 • Undergrads : 16 in Yr2; 16 in Yr3 • 7 successful SURF awards (1 UCA; 2 UAF; 4 ASU) • 4 LSAMP students (1 UCA; 3 ASU) • Accomplishments • John Ridenour (UAF) was awarded NSF Graduate Student Research Fellowship • Walter Acosta (ASU) took 1st prize in his poster category, National EPSCoR conference

  17. Educational outreach & diversity BTNB: ELECTROPHORESIS BTNB: BIOFUELS BioTech-iN-a-Box Program Comprehensive teaching module ($6000 equipment) Two-week loan period; Lesson plans provided 50+ AR Teachers certified for use

  18. Expanding Throughout AR – UAPB • Spring 2012 UG Biofuels Class: • 10 UAPB UG Students trained as “teacher mentors” for BioTech-iN-a-Box: Biofuels (BTNB). • Professional Development Workshop, May 31st- June 1st • 8 regional (South AR) science teachers trained/certified • Participation by UG teacher mentors

  19. IV. National Reputation P3 website is live! www.plantpoweredproduction.org

  20. P3 Annual Research Symposium – joint with ACMAP • Great science: 250 scientists, 19 countries, 22 states • P3 Participation: 28 Faculty; 61 Students/Postdocs; 12 Oral Presentations; 41 Poster Presentations. • Awards: Best Oral: Debbie Vicuna; Best Graduate Poster: Tianhong Yang; Best Undergraduate Poster: Zach Marsh • National Agricultural Biotechnology Council (NABC) Meeting hosted in Fayetteville, May 2012; co-organized by Ken Korth 2013 P3 Research Symposium will be held in conjunction with the Southern Section – American Society of Plant Biology Little Rock, April 6-9, 2013 MariyaKhodakovskaya (UALR), host

  21. V. Sustainability • More than $3 M in new grants funded • Examples of major federal award • QingfangHe (UALR) - NSF ($451,460), Functional analysis of the high-light-inducible proteins (HLIP) in Synechocystis PCC 6803.  • EstenMason (UAF) – USDA AFRI ($331,310), Development of physiological & genetic markers for waterlogging tolerance in wheat • LirongZeng (UALR) – USDA-NIFA ($149,979) Genome-wide identification & characterization of tomato E2 ubiqutin-conjugating enzymes in plants • Correll, Burt Bluhm(UAF), et al. – USDA-NIFA-SCRI ($827,745), Managing Downy Mildew of spinach, a genomics-based approach to the host and the pathogen • IoannisTzanetakis(UAF) – United Soybean Board ($115,000), Epidemiology and identification of resistance to Soybean Vein Necrosis virus • Carole Cramer (ASU) – NIH-R21 ($374,000), RTB-mediated delivery: Orchestrating antigen trafficking to enhance cell immunity

  22. Entrepreneurship and Industry Awards • Industry Awards • Fabricio Medina-Bolivar (ASU) – Infiniti Pharmaceuticals ($215,695), Root cultures of Veratrumcalifornicum as a sustainable source of cyclopamine and related steroidal alkaloids • SBIRs to P3-associated start-ups • Hood & Hood (ASU) USDA SBIR phase II to Infinite Enzymes ($450,000), Formulating new cellulases for diverse markets: Defining QA parameters • Radin, Cramer (ASU), Medrano (ASU), USDA SBIR phase II ($460,000) to BioStrategies LC, Plant-based production of porcine IL-12

  23. P3 - Continuing to build Thank you! Questions? Iterative strategic planning to ensure that the more dispersed investment in a “research network” Builds transformational infrastructure Empowers research in Arkansas Brings value to its members

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