ARKANSAS CENTER FOR PLANT-POWERED PRODUCTION EPSCoR ASSET II Annual Meeting, 2012 Intro to the P3...

ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012

• 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)

http://www.asta.arkansas.gov/asset/Pages/default.aspx


What is the P3 Center?

• 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)

NCTR

UCA


P3 Center Mission

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.

Our research is focused on understanding the underlying mechanisms that drive the amazing biosynthetic capacity of plants


Some Year 2 Logistics

• 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)

• 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!!!


I. Build instrumentation infrastructure and capabilities

II. Enhance research competitiveness of P3 focal areas

III. Build intellectual infrastructure thru professional and workforce development

IV. Build national reputation

V. Build sustainability of the program

P3 Center Strategic Plan

Some highlights……


I. Instrumentation• 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 (Argelia Lorence)

– Collecting exceptional data!– Training session at ACMAP mtg– Initiated collaboration with Nebraska

EPSCoR (joint proposal to NSF pending)


II. Research Competitiveness Research clusters

1. Comparative metabolomics:– Steve Grace (UALR); Julie Carrier (UAF)

3. Productivity “set-points”– Beth Hood (ASU)

2. Plant interactions with other organisms

– Ken Korth (UAF)

4. Next-Gen Seq and bioinformatics– Xiuzhen Huang (ASU)


Metabolic Profiling

Expression Profiling

Presented at Phytochemical Society of North America and P3/ACMAP

See poster by Marissa de La Paz

Student InvolvementRyne RamakerDestiny Davis (INBRE)Delice Kayeshgiue (INBRE)Chen ChenMarissa de La Paz

Comparative metabolomics:• Gene, pathway enzyme, discovery• Metabolite engineering• HTP metabolite data management

Genetic Phenotyping

Gene Discovery

Revealed Novel Aspects of Light

Regulation of Plant Metabolism


Presented at MCBIOS 2012 and P3/ACMAP 2012 See poster by Stephen Embry

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.

What is it? A versatile software tool designed to parse,

filter, and mine LCMS datasets

MySql Tables runs, scan_number, and point_number

NeedleFinder Object BucketFiller()

MySql Tables bin and bucket_analysis

Export LCMS data in CDF format

MVA MetaboAnalystStatistica

Output files in csv format

NeedleFinderObject Loader()

NeedleFinder Object Parser()

Class Assignment

3D Barcode

NeedleFinder: a New Bioinformatics Tool for Mining Metabolomic Datasets


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


Biological “set-points” -- addressing mechanisms that limit protein and biomass accumulation

INPUTS• Genes• Genotypes• Nutrients• Conditions

OUTPUTS• Proteins• Phytochemicals• Biomass• Biomaterials

Nature has selected for metabolic efficiency

Plants make what they need – but have tremendous untapped capacity

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)


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

Stage Total # of genes expressed

S15 17,107

S21 18,177

S27 16,122

Avg. 17,105

Research Highlight


Next-Gen and BioInformatics• ~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-EPSCoR BioInformatics Conference (Huang & McClure)

• iPlant Workshop– May 17-18 at UALR– ~45 participants; > 20 P3– State Breakdown : AR:

34, MS: 7 (EPSCoR link), LA: 1, KY:1


Faculty successes and reputation building

• Invited book editors– Argelia Lorence, Recombinant Gene Expression,

Reviews and Protocols, 3rd Edition

– Burt Bluhm, Fungal Genomics: Methods and Protocols (co-ed)

– Julie Carrier, Biorefinery Co-Products: Phytochemicals, Primary Metabolites and Value-Added Biomass Processing (co-ed)

• Increased participation on grant review panels– DOE, NSF, USDA

III. Professional and Workforce Development


Faculty successes and reputation building

• 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)

III. Professional and Workforce Development


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


Educational outreach & diversityBioTech-iN-a-Box Program• Comprehensive teaching module ($6000 equipment)• Two-week loan period; Lesson plans provided• 50+ AR Teachers certified for use

BTNB: BIOFUELSBTNB: ELECTROPHORESIS


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


IV. National Reputation

P3 website is live!www.plantpoweredproduction.org

http://www.plantpoweredproduction.org/


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 BiologyLittle Rock, April 6-9, 2013

Mariya Khodakovskaya (UALR), host


V. Sustainability• More than $3 M in new grants funded• Examples of major federal award

– Qingfang He (UALR) - NSF ($451,460), Functional analysis of the high-light-inducible proteins (HLIP) in Synechocystis PCC 6803.

– Esten Mason (UAF) – USDA AFRI ($331,310), Development of physiological & genetic markers for waterlogging tolerance in wheat

– Lirong Zeng (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

– Ioannis Tzanetakis (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


Entrepreneurship and Industry Awards• Industry Awards

– Fabricio Medina-Bolivar (ASU) – Infiniti Pharmaceuticals ($215,695), Root cultures of Veratrum californicum 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


P3 - Continuing to build

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

Thank you! Questions?

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