Plant Resources for Plant Biology Research

Resources for Plant Biology Research - Links to Plant Physiology Journals and Plant Pathology Journals

Toshiro Shigaki

My name is Toshiro Shigaki, and I am a plant molecular biologist currently doing my research work at Baylor College of Medicine in Houston, Texas. In 2007, I temporarily moved to Indian Institute of Advanced Research (IIAR) in Gandhinagar, Gujarat, India. For more details about IIAR, please read IIAR page in this website.

As a scientist, my interests are broad in scope and I tend to pursue any interesting subjects in biological sciences. However, I am on the following projects at present.

The cation/proton exchanger CAX

The well-characterized CAX exchanger proteins in plant cells are localized to the vacuolar membrane. The vacuole is the largest organelle in plant cell. Although many essential cell functions are attributed to the vacuole in recent studies, it has sometimes been considered a “waste basket” of the cell. It is true in the sense that once toxic substances are sequestered in the vacuole, the cell is protected from their toxic effects. CAXs transfer metal ions, including toxic heavy metals, into the vacuole. They are therefore ideal for engineering metal-tolerant plants, or metal-accumulating plants for the removal of toxic metals from soil (phytoremediation). The same principle can be applied to make vegetables and fruits fortified with nutrient minerals such as calcium. Some calcium-enriched crops have been developed using CAX genes. For more detailed information, please look at the CAX page.

DNA barcoding

Species identification has been the domain of specially-trained taxonomists, but recent advancement in genome sequencing made it possible to identify a specific DNA region that is variable enough to allow correct species identification, and is present in all species. By sequencing this piece of DNA (DNA barcode), we should be able to identify any organism on earth fast and accurately. For more details, please read the DNA barcoding page.

Bioinformatics

Bioinformatics, or computational analysis of biological information, is fast becoming an indispensable tool for all branches of modern biology. Most of my projects are heavily dependent on bioinformatics, and fortunately, many tools are found on the net free of charge. But sometimes the exact program that I need for my work is not available anywhere. So, I’m trying to find time to learn computer languages so that I can write the programs by myself.

Here are examples of useful programs written in JavaScript by Dr. Stothard (University of Alberta), and made available on this web site with his kind permission. I’m hoping that I will be able to make my own programs in the near future.

Reference:
Stothard P (2000) The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102-1104.

I have published a number of peer-reviewed papers in plant molecular biology and plant pathology. Occasionally, I develop new methods, tools, and vectors, and make them available to interested people. Some methods, such as the class II-S restriction enzyme based site-directed mutagenesis, are used by many labs in the world. Here is my brief introduction about me:

Education
B.S. (Physics) The University of Toyama
M.S. (Plant Pathology) The University of Wyoming
Ph.D. (Plant Pathology) The University of Hawaii at Manoa

Employment
The Samuel Roberts Noble Foundation (1996-1999)
Baylor College of Medicine (1999-present)
Indian Institute of Advanced Research (2007-present)

Publications
(31) 2008. C. Edmond, T. Shigaki, S. Ewert, M. Nelson, J. Connorton, V. Chalova, Z. Noordally, and J. K. Pittman. Comparative analysis of CAX2-like cation transporters indicates functional and regulatory diversity. Biochemical Journal (in press).

(30) 2006. T. Shigaki, I. Rees, L. Nakhleh, and K. D. Hirschi. Identification of three distinct phylogenetic groups of CAX cation/proton antiporters. Journal of Molecular Evolution 63:815-825.

(29) 2006. C. K. Kim, J. -S. Han, H. S. Lee, J. Y. Oh, T. Shigaki, S. H. Park, and K. D. Hirschi. Expression of an Arabidopsis CAX2 variant in potato tubers increases calcium levels with no accumulation of manganese. Plant Cell Reports 25:1226-1232.

(28) 2006. T. Shigaki and K. D. Hirschi. Diverse functions and molecular properties emerging for CAX cation/H⁺ exchangers in plants. Plant Biology 8:419-429.

(27) 2006. F. A. Gray, T. Shigaki, D. W. Koch, R. D. Delaney, F. Hruby, A. M. Gray, M. E. Majerus, D. Cash, R. L. Ditterline, and D. M. Wichman. Registration of ‘Shoshone’ sainfoin. Crop Science 46:988.

(26) 2005. T. Shigaki, M. Kole, J. M. Ward, H. Sze, and K. D. Hirschi. Cre-loxP recombination vectors for the expression of Riken Arabidopsis full-length cDNAs in plants. BioTechniques 39:301-304.

(25) 2005. T. Shigaki, B. J. Barkla, M. C. M. Vergara, J. Zhao, O. Pantoja, and K. D. Hirschi. Identification of a crucial histidine involved in metal transport activity in the Arabidopsis cation/proton exchanger CAX1. Journal of Biological Chemistry 280:30136-30142.

(24) 2005. N. -H. Cheng, J. K. Pittman, T. Shigaki, J. Lachmansingh, S. LeClere, B. Lahner, D. E. Salt, and K. D. Hirschi. Mutations of multiple CAX transporters alter plant growth, H⁺-ATPase activity and the ionome. Plant Physiology 138:2048-2060.

(23) 2005. T. Shigaki, R. R. Vyzasatya, A. B. Sivitz, J. M. Ward, H. Sze, and K. D. Hirschi. The Cre-loxP recombination-based reporter system for plant transcriptional expression studies. Plant Molecular Biology 58:65-73.

(22) 2005. J. K. Pittman, T. Shigaki, and K. D. Hirschi. Evidence of differential pH regulation of the Arabidopsis vacuolar Ca²⁺/H⁺ antiporters CAX1 and CAX2. FEBS Letters 579:2648-2656.

(21) 2004. J. K. Pittman, T. Shigaki, J. L. Marshall, J. L. Morris, N. -H. Cheng, and K. D. Hirschi. Functionaland regulatory analysis of the Arabidopsis thaliana CAX2 cation transporter. Plant Molecular Biology 56:959-971.

(20) 2004. W. -M. Chou*, T. Shigaki*, C. Dammann, Y. -Q. Liu, and M. K. Bhattacharyya. Inhibition of phosphoinositide-specific phospholipase C results in the induction of pathogenesis-related genes in soybean. Plant Biology 6:664-672. (*co-first authors).

(19) 2004. J. K. Pittman, N. -H. Cheng, T. Shigaki, M. Kunta, and K. D. Hirschi. Functional dependence on calcineurin by variants of the Saccharomyces cerevisiae vacuolar Ca²⁺/H⁺ exchanger Vcx1p. Molecular Microbiology 54:1104-1116.

(18) 2003. T. Shigaki, J. K. Pittman, and K. D. Hirschi. Manganese specificity determinants in the Arabidopsis metal/H⁺ antiporter CAX2. Journal of Biological Chemistry 278:6610-6617.

(17) 2003. N. -H. Cheng, J. K. Pittman, B. J. Barkla, T. Shigaki, and K. D. Hirschi. The Arabidopsis cax1 mutant exhibits impaired ion homeostasis, development, and hormonal responses, and reveals interplay among vacuolar transporters. Plant Cell 15:347-364.

(16) 2002. J. K. Pittman, C. S. Sreevidya, T. Shigaki, H. Ueoka-Nakanishi, and K. D. Hirschi. Distinct N-terminal regulatory domains of Ca²⁺/H⁺ antiporters. Plant Physiology 130:1054-1062.

(15) 2002. T. Shigaki, C. Sreevidya, and K. Hirschi. Analysis of the Ca²⁺ domain in the Arabidopsis H⁺/Ca²⁺ antiporters CAX1 and CAX3. Plant Molecular Biology 50:475-483.

(14) 2002. J. K. Pittman, T. Shigaki, N. -H. Cheng, and K. D. Hirschi. Mechanism of N-terminal autoinhibition in the Arabidopsis Ca²⁺/H⁺ antiporter CAX1. Journal of Biological Chemistry 277:26452-26459.

(13) 2002. T. Shigaki and K. D. Hirschi. Chimeric gene construction without reference to restriction sites. BioTechniques 32:736-740.

(12) 2002. N. -H. Cheng, J. K. Pittman, T. Shigaki, and K. D. Hirschi. Characterization of CAX4, an Arabidopsis H⁺/cation antiporter. Plant Physiology 128:1245-1254.

(11) 2002. T. Shigaki and M. K. Bhattacharrya. Nutrients induce an increase in inositol 1,4,5-trisphosphate in soybean cells: implication for the involvement of phosphoinositide-specific phospholipase C in DNA synthesis. Plant Biology 4:53-61.

(10) 2001. T. Shigaki, N. -H. Cheng, J. K. Pittman, and K. Hirschi. Structural determinants of Ca²⁺ transport in the Arabidopsis H⁺/Ca²⁺ antiporter CAX1. Journal of Biological Chemistry 276:43152-43159.

(9) 2001. T. Shigaki and K. D. Hirschi. Use of Class IIS restriction enzymes for site-directed mutagenesis: variations on phoenix mutagenesis. Analytical Biochemistry 298:118-120.

(8) 2001. T. Shigaki, D. W. Gabriel, S. S. Patil, D. Borthakur, J. H. Choi, and A. M. Alvarez. The blight-associated epitope and DNA fragment from Xanthomonas campestris pv. campestris are not required for blight. Plant Biology 3:106-112.

(7) 2000. T. Shigaki and K. D. Hirschi. Characterization of CAX-like genes in plants: implications for functional diversity. Gene 257:291-298.

(6) 2000. T. Shigaki, S. C. Nelson, and A. M. Alvarez. Symptomless spread of blight-inducing strains of Xanthomonas campestris pv. campestris on cabbage seedlings in misted seedbeds. European Journal of Plant Pathology 106:339-346.

(5) 2000. T. Shigaki and M. K. Bhattacharyya. Decreased inositol 1,4,5-trisphosphate content in pathogen-challenged soybean cells. Molecular Plant-Microbe Interactions 13:563-567.

(4) 2000. T. Shigaki and M. K. Bhattacharyya. Phosphate induces rapid H2O2 accumulation in soybean suspension cells. Plant Biology 2:149-151.

(3) 1999. T. Shigaki and M. K. Bhattacharyya. Color coding the cell death status of plant suspension cells. BioTechniques 26:1060-1062.

(2) 1998. T. Shigaki, F. A. Gray, R. H. Delaney, and D. W. Koch. Evaluation of host resistance and intercropping for management of the northern root-knot nematode in common sainfoin, Onobrychis viciifolia. Journal of Sustainable Agriculture 12:23-39.

(1) 1994. S. S. Gnanamanickam, T. Shigaki, E. S. Medalla, T. W. Mew, and A. M. Alvarez. Problems in detection of Xanthomonas oryzae pv. oryzae in rice seed and potential for improvement using monoclonal antibodies. Plant Disease 78:173-178.