Selected Publications



Abe, S., H. Motai, H. Tanaka, M. Shibata, Y. Kominami & T. Nakasahizuka, Population maintenance of the short-lived shrub Sambucus in a decedious forest. Ecology 89: 1155-1167 (2008).

Kurokawa, H. & T. Nakashizuka, Leaf herbivory and decomposability in a Malaysian tropical rain forest, Ecology 89: 2645-2656 (2008).

Tanaka, H.,Shibata, M., Masaki, T., Iida, S., Niiyama, K., Abe, S., Kominami, Y. & Nakashizuka, T., Comparative demography of three coexisting Acer species in gaps and under closed canopy, Journal of Vegetation Science 19: 127-138 (2008).

Aiba, M. & Nakashizuka, T., Architectural differences associated with adult stature and wood density in 30 temperate tree species, Functional Ecology 23: 265-273 (2009).

Shibata, M., Masaki, T.,Tanaka, H.,Niiyama, K., Iida, S., Abe, S. and Nakashizuka, T., Effects of abiotic and biotic factors and stochasticity on tree regeneration in a temperate forest community, EcoScience, (in press) (2010).



Ohtsuki, H., J. Yokoyama, N. Ohba, Y. Ohmiya & M. Kawata, Nitric Oxide Synthase (NOS) in the Japanese fireflies, Luciola lateralis and Luciola cruciata, Archives of Insect Biochemistry and Physiology 69:176-188 (2008).

Yoshino, H., K. Armstrong, M. Izawa, J. Yokoyama, & M. Kawata. Genetic and acoustic population structuring in the Okinawa Least Horsehoe bat: inter-colony acoustic differnces maintained by vertical maternal transmission?, Molecular Ecology 17: 4978-4991 (2008).

Mizuno, N. A &M. Kawata, The effects of the evolution of stoichiometry-related traits on population dynamics in plankton communities, Journal of Theoretical Biology 259: 209-218 (2009).

Bridle, J. R., J. Polechova, M. Kawata, & R. K. Butlin, Why is adaptation prevented at ecological margins? New insights from individual-based simulations, Ecology Letters,13:485-494 (2010).



Urabe, J. and N. Waki, Mitigation of adverse effects of rising CO2 on a planktonic herbivore by mixed algal diets, Global Change Biology 15:523-531 (2009).

Shimizu, Y. and J. Urabe, Regulation of phosphorus stoichiometry and growth rate of consumers: theoretical and experimental analyses with Daphnia, Oecologia 155: 21-31 (2008).

Togashi,H., T. Suzuki and J.Urabe, Spatial variation in chironomid larvae and dragonfly predation in pools on a Japanese high mountain moor, Verhandlungen Internal. Verein. Limnol 30(9): 1357-1362 (2009).

Tsugeki, N. K., S. Ishida and J. Urabe, Sedimentary records of reduction in resting egg production of Daphnia galeata in Lake Biwa during the 20th century: A possible effect of winter warming, Journal of Paleolimnology 42: 155-165 (2009).

Iwabuchi, T. and Urabe, J., Phosphorus acquisition and competitive abilities of two herbivorous zooplankton, Daphnia pulex and Ceriodaphnia quadrangular, Ecological Research, (in press) (2010).



Oikawa S, K. Hikosaka and T. Hirose, Does leaf shedding increase the whole-plant carbon gain despite some nitrogen being lost with shedding? New Phytologist 178: 617-624 (2008).

Onoda Y, Hirose T, Hikosaka K, Does leaf photosynthesis adapt to CO2-enriched environments? An experiment on plants originating from three natural CO2 springs, New Phytologist 182: 698-709 (2009).

Hikosaka K, Shigeno A, The role of Rubisco and cell walls in the interspecific variation in photosynthetic capacity, Oecologia 160: 443-451 (2009).

Nagano S, Nakano T, Hikosaka K, Maruta E, Needle traits of evergreen coniferous shrub growing at wind-exposed and protected sites in a mountain region: Does Pinus pumila produce needles with greater mass per area under wind-stress conditions? Plant Biology 11: 94-100.(2009).

Yamori W, Noguchi K, Hikosaka K, Terashima I, Phenotypic plasticity in photosynthetic temperature acclimation among crop species with different cold tolerance, Plant Physiology 152: 388-399 (2010).



Chiba, S. Invasive non-native species’ provision of refugia for endangered native species, Conservation Biology (DOI: 10.1111/j.1523-1739.2010.01457)

Okajima, R. and Chiba, S., Cause of bimodal distribution in the shape of a terrestrial gastropod, Evolution 63: 2877-2887 (2009).

Chiba, S., Okochi, I., Obayashi, T., Miura, D., Mori, H., Kimura, K., and Wada, S. , Effect of habitat history and extinction selectivity on species richness pattern of an island snail fauna, Journal of Biogeography 36: 1913-1922 (2009)

Chiba, S., Invasive rats alter assemblage characteristics of land snails in the Ogasawara Islands, Biological Conservation (in press) (2010).

Kimura, K. and Chiba, S., Interspecific interference competition alters habitat use patterns in two species of land snails. Evolutionary Ecology (DOI: 10.1007/s10682-009-9339-8)

Davison, A. and Chiba, S. Contrasting response to Pleistocene climate change by ground living and arboreal Mandarina snails from the oceanic Hahajima archipelago. Phil. Trans. R. Soc. Lond. B 363:3391-3400 (2008).



Yuhara,S., H. Komatsu, H.Goto, Y.Ohtsubo, Y.Nagata, and M.Tsuda, Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans, Microbiology 154: 1763-1774 (2008).

Miyazaki,R., Y. Ohtsubo, Y. Nagata and M. Tsuda, Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer, Journal of Bacteriology 190: 6281-6289 (2008).

Pavlova,M., M. Klvana, Z. Prokop, R. Chaloupkova, P. Banas, M. Otyepka, R. C. Wade, M. Tsuda, Y. Nagata, and J. Damborsky, Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate, Nature Chemical Biology 5: 727-733 (2009).

Nishiyama,E., Y.Ohtsubo, Y.Nagata, and M.Tsuda, Identification of Burkholderia multivorans ATCC 17616 genes induced in soil environment by in vivo expression technology, Environmental Microbiology (in press) (2010).



Miyazawa Y, Takahashi A, Kobayashi A, Kaneyasu T, Fujii N, Takahashi H., GNOM-mediated vesicular trafficking plays an essential role in hydrotropism of Arabidopsis roots, Plant Physiology 149: 835-840 (2009).

Takahashi H, Miyazawa Y, Fujii N., Hormonal interactions during root tropic growth: hydrotropism versus gravitropism, Plant Molecular Biology 69: 489-502 (2009).

Kitazawa D, Miyazawa Y, Fujii N, Hoshino A, Iida S, Nitasaka E, Takahashi H., The gravity-regulated growth of axillary bud is mediated by a mechanism different from decapitation-induced release, Plant and Cell Physiology 49: 891-900 (2008).



Yamazaki, S., S. Matsuo, T. Muta, M. Yamamoto, S. Akira, K. Takeshige, Gene-specific Requirement of A Nuclear Protein, IkB-z, for Promoter Association of Inflammatory Transcription Regulators, J. Biol. Chem. 283(47): 32404-32411 (2008) .

Okamoto, K., Iwai, Y., Oh-hora, M., Yamamoto, M., Morio, T., Aoki, K., Ohya, K., Jetten, A. M., Akira, S., Muta, T., and Takayanagi, H., IκBζ Regulates TH17 Development by Cooperating with ROR Nuclear Receptors. Nature (in press) (2010).



Noro, M., A. Uejima, G. Abe, M. Manabe and K. Tamura, Normal developmental stages of the Madagascar ground gecko Paroedura pictus with special reference to limb morphogenesis, Developmental Dynamics 238: 100-109 (2009).

Kidokoro, H., M. Okabe and K. Tamura. Time-lapse analysis reveals local asymmetrical changes in C-looping heart tube, Developmental Dynamics 237: 3545-3556 (2008).

Yonei-Tamura, S., G. Abe, Y. Tanaka, H. Anno, M. Noro, H. Ide, H. Aono, R. Kuraishi, N. Osumi, S. Kuratani and K. Tamura, Competent stripes for diverse positions of limbs/fins in gnathostome embryos, Evolution & Development 10: 737-745 (2008).

Kuraku, S., Y. Takio, K. Tamura, H. Aono, A. Meyer and S. Kuratani, Non-canonical Role of Hox14 revealed by its expression patterns in lamprey and shark, PNAS 105: 6679-6683 (2008).

Ohgo, S., Itoh, A., Suzuki, M., Satoh, A., Yokoyama, H., and Tamura, K., Analysis of hoxa11 and hoxa13 expression during patternless limb regeneration in Xenopus, Developmental Biology 338: 148-157 (2010).



Sekiya, M., K. Ueda, K. Okazaki, H. Kikuchi, S. Kurata, and Y. Oshima, A cyclopentanediol analogue selectively suppresses the conserved innate immunity pathways, Drosophila IMD and TNF-a pathways, Biochem. Pharm. 75: 2165-2174 (2008).

Prince, F., T. Katsuyama, S. Plaza, D. Resendez-Perez, M. Berry, S. Kurata, and W. J. Gehring, The YPWM-motif links Antennapedia to the basal transcriptional machinery, Development 135:1669-1679 (2008) .

Yano, T., S. Mita, H. Ohmori, Y. Oshima, Y. Fujimoto, R. Ueda, H. Takada, W. E. Goldman, K. Fukase, N. Silverman, T. Yoshimori, and S. Kurata, Autophagic control of Listeria through intracellular innate immune recognition in Drosophila, Nature Immunology 9: 908-916 (2008).

Yano, T., and Kurata, S.,An unexpected twist for autophagy in Crohn's desease, Nature Immunology 10: 134-136 (2009).



Kijima, A., M. Ikeda and M. Kanno. Recent research topics in genetic approaches for sustainable yield and conservation of marine organisms. Tohoku Journal of Agricultural Research 59(3-4): 93-95 (2009).

Kefeng Xu, Manami Kanno, Hong . Yu, Qi Li and Akihiro Kijima, Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys ferreri (Bivalva: Pectinidae), Molecular Biology Report, DOI 10. 1007/s 11033-010-9974-8 (2009).



Endo,Y., F. Yamano and K. Taki, How does molting affect reproductive activities of Euphausia pacifica (Crustacea, Euphausiacea)? Plankt. Benthos Res. 3:46-49 (2008).


Agatsuma, Y., H. Endo, K. Taniguchi, Inhibitory effect of 2,4-dibromophenol and 2,4,6-tribromophenol on larval survival and metamorphosis of the sea urchin Strongylocentrotus nudus, Fish. Sci. 74 (4): 837-841 (2008).

Matsui,T., Y. Agatsuma, M. Ogasawara and K. Taniguchi, Coincidence in reproduction of the sea urchin Strongylocentrotus intermedius in Hirota Bay, J. Shellfish Res. 27 (5): 1283-1289 (2008).

Li, J-Y., Y. Agatsuma, T. Nagai, Y. Sato and K. Taniguchi, Difference in resource storage pattern between Laminaria longissima and L. diabolica (Laminariaceae; Phaeophyta) reflecting their morphological characteristics, J. Appl. Phycol. 21 (2): 215-224 (2009).


Suyama, Y., U. Gunnarsson and L. Parducci. Analysis of short DNA fragments from Holocene peatmoss samples, The Holocene 18 (6): 1003-1006 (2008).

Tomita, M., H. Saito and Y. Suyama, Effect of local stand density on reproductive processes of the sub-boreal conifer Picea jezoensis Carr. (Pinaceae), Forest Ecology and Management 256 (6): 1350-1355 (2008).

Hasegawa, Y., Y. Suyama and K. Seiwa, Pollen donor composition during the early phases of reproduction revealed by DNA genotyping of pollen grains and seeds of Castanea crenata, New phytologist, (in press) (2009).

Honma,H., R.Asano, M.Obara, K.Otawa, Y.Suyama, and Y.Nakai , Bacterial populations in epilithic biofilms along two oligotrophic rivers in the Tohoku region in Japan, The Journal of General and Applied Microbiology 55 (5): 359-371 (2009).


Song,H.-L., K. Nakano, T. Taniguchi, M. Nomura, O. Nishimura. Estrogen removal from treated municipal effluent in small-scale constructed wetland with different depth, Bioresource Technology 100: 2945-2951 (2009).

Southichak, B., K.Nakano, M.Nomura, N.Chiba, O.Nishimura, Differences in adsorption mechanisms of heavy metal by two different plant biomass: reed and brown seaweed, Water Science and Technology 59(2): 339-346 (2009).

Taniguchi, T., K.Nakano, N.Chiba, M.Nomura, O.Nishimura. Evaluation of extremely shallow vertical subsurface flow constructed wetland for nutrient removal, Water Science and Technology 59(2): 295-301 (2009).


Fukumoto, J., Investigation of the Roles of Proposal-Based Systems ofRegional Policy, Social Capital and Development Trends in Rural Areas,MARG, 4: 249-263(2009).

Fukumoto, J. and Okamoto, Y., Social Network Analysis of Japanese Special Zones System, Proceedings of 11th International Conference on Computers in Urban Planning and Urban Management, CD-Rom (2009).


Pu,Z., S.Mei, Y.Hayashiyama and W.Zhong: Determinants of Regional University-Industry Cooperation Technical Innovation in China, Proceedings of the International Conference on China and World Economy in Post Crisis Era, CD-ROM, (2009).

Hayashiyama,Y. and K.Nohara: Evaluation of Recreation Benefit by Household Production Function Approach, Economics Bulletin 29(2): 703-711 (2009).


Konoshima, M., C. McKetta, and A. Yoshimoto, Combining Market and Traditional Values in Tribal Forestry using Interactive Forest Decision Synthesis (INFODS), Journal of Forest Research 13(6), 331-337 (2008).

Yoshimoto, A., H. Yanagihara and A. Kato. Economic analysis of snow damage on sugi (Cryptomeria japonica) forest stands in Japan within the forest stand optimization framework, Journal of Forest Science 24: 141-147 (2008).

Yoshimoto, A. Threshold price as an economic indicator for sustainable forest management under stochastic log price, Journal of Forest Research 14:193- 202 (2009).