Current Research

Development of mimosine-free L. leucocephala: We have been working on molecular biology and biochemistry of mimosine degradative pathway in root nodule bacteria. Recently, we have constructed a hybrid gene by combining the pydA and pydB of Rhizobium sp. strain TAL1145. pydA codes for a dioxygenase, while pydB encodes a hydrolase, and both these enzymes are essential for degradation of 3-hydroxy-4-pyridone (HP) which is an intermediate of mimosine degradation. HP is also a precursor for mimosine biosynthesis in leucaena. The pydA-pydB hybrid gene encodes a PydA-PydB fusion protein that has both the dioxygenase activity of PydA and the hydrolase activity of PydB. We are now transferring the hybrid gene into L. leucocephala. It is expected that the transgenic leucaena expressing the pydA-pydB hybrid gene will have reduced amount of mimosine.

Microsatellite markers for Acacia koa (koa): Koa is an important tree legume endemic to Hawaii. The koa forests are distributed in all major Hawaiian Islands. We are developing microsatellite markers for determining genetic diversity among the koa tree populations in different islands.

Development of recombinant vaccines against Mycobacerium tuberculosis: The aim of this project is to identify potential subunit protein vaccine candidates for immunization against Mycobacterium tuberculosis (Mtb). The focus is to produce an immune response that is MHC genotype specific and elicits elevated levels of interferon gamma (IFN-g), characteristic of a protective response. Bioinformatic, molecular and proteomic tools were employed to identify putative vaccine candidate peptides. In addition, hybrid peptides containing a number of immunogenic epitopes are being tested in mice to determine whether they might be more protective than the individual components. An in silico genomic subtraction of the tuberculosis vaccine strain of Mycobacterium bovis, BCG-Denmark from Mtb H37Rv, yielded 61 genes that are unique to the primary disease-causing agent, Mtb. Further, an in silico analysis platform is being developed to evaluate the potential genes for immune reactivity by mimicking proteasomal digestion, transport-associated antigen selection and H-2 antigen presentation. In addition to Mtb infections, this approach can be used to find host genotype-specific vaccine candidates for other related intracellular pathogens

Recent publications

Walton CB, Inos ABH, Andres OA, Jube S, de Couet HG, Douglas JT, Patek PQ, Borthakur D (2008) Immunization with hybrid recombinant Mycobacterium tuberculosis H37Rv proteins increases the TH1 cytokine response in mice following a pulmonary instillation of irradiated mycobacteria.  Vaccine 26 26,4396-4402.

Tittabutr P, Awaya JD, Li QX, Borthakur D (2008) The cloned 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene from Sinorhizobium sp. strain BL3 in Rhizobium sp. strain TAL1145 promotes nodulation and growth of Leucaena leucocephala. Systematic and Applied Microbiology 31:141-150.

Awaya JD, Tittabutr P, Li QX, Borthakur D (2008) Pyruvate carboxylase is involved in metabolism of mimosine by Rhizobium sp. strain TAL1145. Archives of Microbiology.  DOI:  10.1007/s00203-008-0384-4

Kutin RK, Jenkins DM, Borthakur D (2008) Characterization of a Corynebacterium strain that can reduce nitrate from high strength nitrate medium. Bioremediation Journal. 12(3):168-172.

Jube S, Borthakur D (2007) Expression of bacterial genes in transgenic tobacco: methods, applications and future prospects. Electronic J Biotechnol. 10 (3)452-467. Reprint PDF

Awaya JD, Walton C, Borthakur D (2007) The pydA-pydB gene produces an active dioxygenase-hydrolase that degrades 3-hydroxy-4-pyridone, an intermediate of mimosine metabolism. Appl. Microbiol. Biotechnol 75(3):583-588. DOI 10.1007/s00253-007-0858-3 Reprint PDF

Tittabutr P, Payakapong W, Teaumroong N, Boonkerd N, Singleton PW, Borthakur D (2006) The alternative sigma factor RpoH2 is required for salt tolerance in Sinorhizobium sp. strain BL3. Res Microbiol.157: 811-818 Reprint PDF

Leary JK, Singleton PW, Scowcroft PG, Borthakkur D (2006) Symbiotic diversity in the cosmopolitan genus Acacia. Symbiosis 41 (3): 107-117 Reprint PDF

Jube S, and Borthakur D (2006) Recent advances in food biotechnology research. In: Hui YH, Nip W-K, Nollet LML, Paliyath G, Sahlstrøm S, and Simpson BK (eds) Food Biochemistry and Food Processing. pp 35-70, Blackwell Publishing, Oxford, U.K. Reprint PDF

Payakapong W, Tittabutr P, Teaumroong N, Boonkerd N, Singleton PW, Borthakur D (2006) Identification of Two Clusters of Genes Involved in Salt Tolerance in Sinorhizobium sp. Strain BL3. Symbiosis 41: 47-51. Reprint PDF

Tittabutr P, Payakapong W, Teaumroong N, Boonkerd N, Singleton PW, Borthakur D (2006) A histidine kinase sensor protein gene is necessary for induction of low pH tolerance in Sinorhizobium sp. strain BL3. Antonie Van Leeuwenhoek 89 (1): 125-134 (Online: December 8, 2005; DOI : 10.1007/s10482-005-9015-0). Reprint PDF

Awaya JD, Fox PM, Borthakur D (2005) pyd genes of Rhizobium sp. strain TAL 1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism. J. Bacteriol. 187 (13): 4480-4487. Reprint PDF

Leary JK, Hue NV, Singleton PW, Borthakur D (2005) Soil acidification, nutrient depletion, and symbiotic nitrogen fixation are the major features of gorse (Ulex europaeus) infestation on volcanic soils in Hawaii. Biol. Fertility Soils. 42:215-223. Published online: 28 June 2005 Reprint PDF

Kaufusi PH, Forsberg LS, Tittabutr P, and Borthakur D (2004) Regulation of exopolysaccharide synthesis in Rhizobium sp. strain TAL1145 involves an alternative sigma factor gene, rpoH2. Micorobiology 150: 3473-3482. Reprint PDF

Leary J, Singleton PW and Borthakur D (2004) Canopy nodulation of the endemic tree legume Acacia koa in the mesic forests of Hawaii. Ecology 85:3151-3157. Reprint PDF

Jin H-J, Dunn MA, Borthakur D, and Kim YS (2004) Refolding and purification of unprocessed porcine myostatin. Protein Expression and Purification 35:1-10. Reprint PDF

Borthakur D, Soedarjo, Fox PM, and Webb DT (2003) The mid genes of Rhizobium sp. strain TAL1145 are required for degradation of mimosine into 3-hydroxy-4-pyridone and are inducible by mimosine. Microbiology 149: 537-546. Reprint PDF

Awaya J, Fox PM and Borthakur D (2003) Genes encoding a fructose-1,6-bisphosphate aldolase and a fructose-1,6-bisphosphatase are present within the gene cluster for mimosine degradation in Rhizobium sp. strain TAL1145. Plant Soil 257: 11-18. Reprint PDF

Saafi H and Borthakur D (2002) In vitro plantlet regeneration from cotyledon of the tree legume Leucaena leucocephala. Plant Growth Regulation 38:279-285. Reprint PDF

You S, Marutani M and Borthakur D (2002) Diversity among Bradyrhizobium isolates nodulating Yardlong Bean and Sunhemp in Guam. J. Appl. Microbiol. 93(4):577-84. Reprint PDF

Abaidoo RC, Keyser HH, Singleton PW and Borthakur D (2002) Comparison of molecular and antibiotic resistance profile methods for the population analysis of Bradyrhizobium spp. (TGx) isolates that nodulate the new TGx soybean cultivars in Africa. J. Appl. Microbiol. 92(1):109-17. Reprint PDF

Fox PM and Borthakur D. (2001) Selection of several classes of mimosine-degradation-defective Tn3Hogus-insertion mutants of Rhizobium sp. strain TAL1145 on the basis of mimosine-inducible GUS activity. Can J. Microbiol. 47: 488-494. Reprint PDF

Shigaki T, Gabriel DW, Patil SS, Borthakur D, Choi JH and Alvarez A. (2001) Blight-associated epitope and DNA fragment from Xanthomonas capestris pv campestris are not required for blight. Plant Biology 3: 106-112. Reprint PDF

Jin R-G., Liu Y-B, Tabashnik BE and Borthakur D. (2000) Development of transgenic cabbage (Brassica oleracea var. capitata) for insect resistance by Agrobacterium tumefaciens-mediated transformation. In Vitro Cellular Dev Biol Plant 36(4): 231-237. Reprint PDF

Abaidoo R, Keyser H, Singleton PW, and Borthakur D (2000) Bradyrhizobium spp. (TGx) Isolates nodulating the new soybean cultivars in Africa are diverse and distinct from bradyrhizobia that nodulate North American soybeans. Int. J. Syst. Evol. Microbiol. 50:225-234. Reprint PDF

Other academic activities

• Chairman, Graduate Program in Molecular Biosciences and Bioengineering, University of Hawaii (1996 - present).

• Member of the Editorial Board, Applied and Environmental Microbiology (2001-2009).

• Editorial Board Member (Editor), International Journal of Microbiology (2008 -present)

• Member of the Graduate Council, University of Hawaii (2007- present)

• Member of the Advisory Board, Faculty Mentoring Program, University of Hawaii (2002 - present)

• Member of the Organizing Committee, CTAHR Symposium (2001 -present)

Awards

• 2004 'North American Colleges and Teachers of Agriculture Teaching award of Merit'.

• 2004 'CTAHR Excellence in Teaching' Award.

• 2003 'Most Motivational CTAHR Faculty' award by the College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa.

Award received by my students:

• Sandro Jube: First prize for PhD poster presentation in the 2008 CTAHR symposium.

• Daniel Adamski: First prize for MS oral presentation in the 2008 CTAHR symposium.

• Rudolph Fredua-Agyeman: Best PhD poster presentation among MBBE students in the 2007 CTAHR symposium

• Sandro Jube: First prize in PhD oral presentation in the 2007 CTAHR symposium

• Rudolph Fredua-Agyeman: MBBE Best PhD student poster presentation in the 2007 CTAHR symposium

• Dan Adamski: First prize in MS poster presentation in the 2007 CTAHR symposium

• Chad Walton: Case Foundation Business Plan Award $16,000 (2006)

• Jon Awaya: National Science Foundation Postdoctoral Award (2006) at University of Notre Dame

• Sandro Jube: First prize in MS oral presentation in the 2005 CTAHR symposium.

• James Leary: Second prize in PhD oral presentation in the 2005 CTAHR symposium.

• Jon Awaya: Gamma Sigma Delta Doctoral Student Oral Presentation Award of Merit 2005.

• Jon Awaya: First prize for oral presentation, American Society of Microbiology, Hawaii 2005.

• Chad Walton: 2005 INBRE Research Award.

• Chad Walton: 2005 BRIN Research Award.

• Jon Awaya: ARC Foundation Excellence in Research Award 2004.

• Jon Awaya: Gamma Sigma Delta Doctoral Student Oral Presentation Award of Merit 2004.

• Jon Awaya: First prize for oral presentation, American Society of Microbiology, Hawaii 2004.

• Chad Walton: 2004 BRIN Research Award.

• Chad Walton: MBBE Departmental Award for oral presentation, CTAHR symposium 2004.

• James Leary: ARC Foundation Excellence in Research Award 2003.

• James Leary: First prize in PhD oral presentation in the 2003 CTAHR symposium.

• Jon Awaya: Gamma Sigma Delta Doctoral Student Oral Presentation Award of Merit 2003.

• Jon Awaya: Best in MBBE oral presentation in the 2003 CTAHR symposium

• Havila Saafi: Best in MBBE poster presentation in the 2003 CTAHR symposium.

• Jon Awaya: First prize in the research symposium organized by the American Society for Microbiology Hawaii Chapter on April 5, 2003.

• Chad Walton: First prize in the Biomedical Research Symposium organized by the John Burn Medical School on April 25, 2003.

• Ana Blossom Inos: First prize for oral presentation in the Annual Biomedical Research Conference for Minority Students held in San Diego, in October 15-18, 2003.

• Paul Fox: First prize in the Biomedical Research Symposium organized by the John Burn Medical School, 2002.

Teaching major courses:

• MBBE 304 Biotechnology Science and Ethical Issues (3 cr)

• MBBE 401 Molecular Biotechnology (3 cr) - Spring 09

• MBBE 461 Biotechnology for teachers (2 cr)

• MBBE 646 Bacteria-Plants Interactions (3 cr)

Current graduate students:

• Sandro Jube (2005- ) Ph.D. dissertation subject: Developing mimosine-free Leucaena leucocephala through metabolic pathway engineering.

• Rudolph Fredua-Agyeman (2005- ) Ph.D. Dissertation subject: Development and application of microsatellite markers for assessment of genetic diversity in Acacia koa.

• Vishal Negi (2007- ) Ph.D. dissertation subject: Genes for mimosine biosynthesis in Leucaena leucocephala.

Researcher:

Dr. Ricelle Agbayani (2007-08) Research project: Genes for Fusarium resistance in Acacia koa.

Previous students:

• PhD: Nikhat Parveen (1991-1995); Muchdar Soedarjo (1993-97), Ronguan Jin (1995-99), Pakieli Kaufusi (2000-05) Paul Fox (1999-02), Jon Awaya (2001-05), Chad Walton (2002-06), James Leary (2001-06)

• MS Plan-A (with thesis): Daniel Adamski(2006-2008)Shahriar Pooyan (1990-92), Xuefeng Gao (1992-95), Jyothirmai Gubili (1995-97), Zerong You (1996-98), Joy Anamizu (1999-03), Sandro Jube (2002-05), Havila Saafi (2000-01), Masaki Nasu (2003-06)

• MS Plan-B: Benjamin Tran (1997-98), Thomas Bui (1998-99), Carrie Tom (1999-2002), Asmahan Yussuf (2003-2005)
  * BS Honors (with thesis): Wendy Higashide (1999-2000), Ann Blossom Innos: (2002-200