User:Ai Oikawa

Ai Oikawa - Genetic Engineering & Computational System Biology

Managing Director :
AFINGEN, Inc.
Biologist Affiliate Scientist :
Lawrence Berkeley National Laboratory & Joint BioEnergy Institute

Physical address :
Joint BioEnergy Institute
5885 Hollis street, Emery Station East 4th Floor
Emeryville, CA 94608 USA

AFINGEN, Inc: www.AFINGEN.org
E-mail: AOikawa@lbl.gov
E-mail: AOikawa@afingen.org

A biologist specializing in the field of molecular biology and computational system biology. I am interested in engineering regulatory gene networks to make sustainable agricultural systems better.

Experience

Principal Investigator

• STTR FY2017 program at the National Aeronautics and Space Administration
• 2017 – Current

• SBIR FY2016 program at U.S. Department of Agriculture
• 2016 – Current

• SBIR FY2014 & FY2015 programs at U.S. Department of Energy
• 2014 – Current

• Emeryville, CA, USA

R&D Director & co-founder

• Afingen, Inc.
• 2014 – Current
• Emeryville, CA, USA

Biologist Affiliate Scientist

• Lawrence Berkeley National Laboratory & Joint BioEnergy Institute
• 2014 – Current
• Berkeley, CA, USA

Biologist Project Scientist

• Lawrence Berkeley National Laboratory & Joint BioEnergy Institute
• 2013 – 2014
• Berkeley, CA, USA
• My molecular biology and bioinformatics analysis have revealed functions of several transcription factors important for woody tissue cell differentiation and cell wall deposition/accumulation in plants. This study is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research.

Postdoctoral Research Fellow

• UC Berkeley
• 2008 – 2013
• Berkeley, CA, USA
• My molecular biology, biochemistry and bioinformatics analysis have revealed functions of several Golgi-localized carbohydrate active enzymes, which are important for understanding mechanism of cell wall components, deposition, and accumulation. This study was funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research.

21st Century COE Program Graduate Research Assistant

• The United Graduate School of Agricultural Sciences (UGAS), Iwate University
• 2004 – 2008
• Morioka, Iwate, Japan
• My subcellular localization analysis and protein-protein interaction analysis have revealed that a novel grass protein is localized on Golgi apparatus membrane and is involved in synthesis of grass unique cell wall polysaccharide. This study was funded by funded by the 21st Century Center of Excellence Program - Establishment of Thermobiosystem Research Program from the Japan Society for the Promotion of Science (JSPS).

Graduate Research Associate

• Cryobiofrontier Research Center (CRC), Iwate University
• 2003 – 2008
• Morioka, Iwate, Japan
• I developed new molecular biology technique, namely “Virus-Induced Gene Silencing (VIGS)” applied to cell-wall-related genes in cereal crops. This study was funded by a grant-in-aid from Iwate University, Japan.

Visiting Research Scholar

• Yale University
• 2007 – 2007
• New Haven, CT, USA
• I performed a study entitled -“Unraveling the gene network involved in the barley seed development by LCM (Laser-captured Microdissection)") with Professor Timothy Nelson at department of Molecular, Cellular and Developmental Biology of Yale University This study was funded by a Young Overseas Joint Research Fellowship granted by the Japanese Society of Plant Physiologists (JSPP).

Undergraduate Research Assistant

• Iwate University
• 2001 – 2003
• Morioka, Iwate, Japan
• I performed expression analysis and peptidase activity assay of a major urinary protein of the domestic cat which regulates the production of Felinine, a putative pheromone precursor. This study was funded by a grant-in-aid from Iwate University, Japan.

Publications

2015

• Silvia M. Velasquez, Martiniano M. Ricardi*, Christian Peter Poulsen*, Ai Oikawa*, Adiphol Dilokpimoladil*, Adnan Halim, Silvina Mangano, Silvina Paola Denita Juarez, Eliana Marzol, Juan D. Salgado Salter, Javier Gloazzo Dorosz, Cecilia Borassi, Svenning Rune Möller, Rafael Buono, Yukiko Ohsawa, Ken Matsuoka, Marisa S. Otegui, Henrik V. Scheller, Naomi Geshi, Bent Larsen Petersen, Norberto D. Iusem and José M. Estevez. Complex regulation of Prolyl-4-hydroxylases impacts root hair expansion. Molecular Plant, 8:734-746 Article * Equal contributions

2014

• Jeemeng Lao, Ai Oikawa, Jennifer Bromley, Peter McInerney, Anongpat Suttangkakul, Andreia Smith-Moritz, Hector Plahar, Tsan-Yu Chiu, Susana González Fernández-Niño, Berit Ebert, Fan Yang, Katy Christiansen, Sara Hansen, Solomon Stonebloom, Paul Adams, Pamela Ronald, Nathan Hillson, Masood Hadi, Miguel Vega-Sanchez, Dominique Loque, Henrik Scheller & Joshua Heazlewood. The Plant Glycosyltransferase Clone Collection for Functional Genomics. The Plant Journal, 79:517-529 Article

2013

• Ai Oikawa, Christian Have Lund, Yumiko Sakuragi, Henrik Vibe Scheller. Golgi-localized enzyme complexes for plant cell wall biosynthesis. Trend in Plant Science, 18:49-58 Article
• Xuewei Chen, Miguel E Vega-Sánchez, Yves Verhertbruggen, Dawn Chiniquy, Patrick E Canlas, Alexandra Fagerström, Lina Prak, Ulla Christensen, Ai Oikawa, Mawsheng Chern, Shimin Zuo, Lin Fan, Manfred Auer, William GT Willats, Laura Bartley, Jesper Harholt, Henrik V Scheller, Pamela C Ronald. Inactivation of OsIRX10 leads to decreased xylan content in rice stem cell walls and improved biomass saccharification. Molecular Plant, 6:570-573 Article

2012

• April J. M. Liwanag, Berit Ebert, Yves Verhertbruggen, Emilie A. Rennie, Carsten Rautengarten, Ai Oikawa, Mathias C. F. Andersen, Mads H. Clausen, and Henrik Vibe Scheller. Pectin Biosynthesis: GALS1 in Arabidopsis thaliana Is a β-1,4-Galactan β-1,4-Galactosyltransferase. Plant Cell, 24:5024-5036 Article
• Sara Fasmer Hansen, Jesper Harholt, Ai Oikawa, Henrik Vibe Scheller. Plant glycosyltransferases beyond CAZy: a perspective on DUF families. Frontier in plant science, 3:59 Article

2011

• Yves Verhertbruggen, Lan Yin, Ai Oikawa, Henrik Vibe Scheller. Mannan synthase activity in the CSLD family. Plant Signaling & Behavior, 6:1620-1623 PDF
• Lan Yin, Yves Verhertbruggen, Ai Oikawa, Chithra Manisseri, Bernhard Knierim, Lina Prak, Jacob Krüger Jensena, J. Paul Knox, Manfred Auer, William G. T. Willats, Henrik Vibe Scheller. The Cooperative Activities of CSLD2, CSLD3 and CSLD5 are Required for Normal Arabidopsis Development. Molecular Plant, 4:1024-1037 PDF

2010

• Ai Oikawa, Hiren J. Joshi, Emilie A. Rennie, Berit Ebert, Chithra Manisseri, Joshua L. Heazlewood and Henrik Vibe Scheller. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One, 5:e15481 Article

2009

• Ai Oikawa, Kazuya Nagai, Kiyoaki Kato, Shin-ichiro Kidou. Gene silencing of barley P23k involved in secondary wall formation causes abnormal tiller formation and intercalary elongation. Breeding Science, 59: 664-670 PDF

2007

• Ai Oikawa, Abidur Rahman, Tetsuro Yamashita, Hideharu Taira and Shin-ichiro　Kidou. Virus-induced gene silencing of P23k in barley leaf reveals morphological changes involved in secondary wall formation. Journal of Experimental Botany, 58:2617-2625 PDF
• Ai Oikawa, Tetsuro Yamashita, Hideharu Taira, Shin-ichiro Ejiri and Shin-ichiro Kidou. Jasmonate-induced 23kD protein (JIP-23) is involved in seed development of barley. Plant Biotechnology, 24:217-220 PDF

2006

• Shin-ichiro Kidou, Ai Oikawa, Naoko Sasaki, Hiroshi Yasuda, Tetsuro Yamashita, Hiroyuki Koiwa, Kiyoaki Kato, Shin-ichiro Ejiri. Identification of a 23 KD protein (P23k) related to the sugar supply in germinating seed. Plant Biotechnology, 23:357-364 PDF

Awards and Grants

Small Business Innovation Research (SBIR) Phase I Grant 2015

• By U.S. Department of Energy (DOE) Office of Science
• The SBIR program was established to support scientific excellence and technological innovation through the investment of Federal research funds in critical American priorities to build a strong national economy. As a principal investigator at AFINGEN, Inc, FY 2015 SBIR Phase I grant was awarded by the DOE Office of Science Biological and Environmental Research Program, to conduct a study on "Engineering robust yeasts for biorefinery applications". Scientific and business advisers: Dr. Dominique Loque, Dr. Miguel Vega-Sánchez, Dr. Henrik Scheller, and Mr. William Shelander at Lawrence Berkeley National Laboratory.

Small Business Innovation Research (SBIR) Fast-track Grant 2014

• By U.S. Department of Energy (DOE) Office of Science
• As a principal investigator at AFINGEN, Inc, FY 2014 SBIR Fast-Track grant $1.72M was awarded by the DOE Office of Science Biological and Environmental Research Program, to conduct a study on "Generation of feedstocks with optimized biomass composition for biofuel production". Scientific and business advisers: Dr. Dominique Loque, Dr. Miguel Vega-Sánchez, Dr. Henrik Scheller, and Mr. William Shelander at Lawrence Berkeley National Laboratory.

National Interest Waver (NIW) for Permanent Residency 2013

• By U.S. Citizenship and Immigration Service
• As an alien who has exceptional ability and whose employment in the United States would greatly benefit the national, the NIW was granted by U.S. Citizenship and Immigration Service (USCIS).

Yamada Science Foundation (YSF) Abroad Research Grant 2008

• By Yamada Science Foundation
• The YSF was established to promote basic natural science by providing funding complementary to that of the Japanese government. The YSF extends financial support to five Japanese researchers (selected amongst a pool of applicants) for abroad research projects. I was awarded the 2008 abroad research grant in order to conduct a study on “Unraveling the gene network involved in the construction of plant cell wall” with Dr. Henrik Vibe Scheller at DOE Joint BioEnergy Institute (CA, USA).

Japan Student Services Organization (JASSO) - Scholarship Programs for Japanese Students 2008

• By Japan Student Services Organization
• I was granted a scholarship by JASSO in consideration of my outstanding achievements and of the results I obtained during the course of my Ph.D. studies.

Japanese Society of Plant Physiologists (JSPP) Fellow 2008

• By Japanese Society of Plant Physiologists
• The JSPP is one of the largest societies with 6000 members in Japan. I was awarded, by the Japanese Society of Plant Physiologists (JSPP), the Young Overseas Joint Research Fellowship for conducting a collaborative research (the subject of which was “Unraveling the gene network involved in the barley seed development by LCM (Laser-captured Microdissection)") with Professor Timothy Nelson at Department of Molecular, Cellular and Developmental Biology of Yale University.

Life Science Foundation Travel Grant 2007

• By Life Science Foundation Japan
• I was awarded a Life Science Travel Grant in order to cover the costs of (i) travelling abroad in order to conduct a collaborative research with Professor Timothy Nelson at Yale University, and (ii) attending the Annual meeting of American Society of Plant Biologists (ASPB) held in Chicago, USA.

Education

Doctor of Biology (Ph.D.)

• Bioprocess Engineering, 2005 - 2008
• The United Graduate School of Agricultural Sciences (UGAS), Iwate University, Japan

Master of Science (MS)

• Bioscience and Technology, 2003 - 2005
• Graduate School of Agricultural Sciences, Iwate University, Japan

Bachelor of Science (BS)

• Bioscience and Technology, 1999 – 2003
• Faculty of Agriculture, Iwate University, Japan

Professional Affiliations

• [American Society of Plant Biologists]
• [Japanese Society of Plant Physiologist]
• [Scandinavian Plant Physiology Society]