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Biology

Research

The Department of Biology is engaged in various fields of biology including molecular, cellular and population biology. Diverse aspects of modern biological sciences are studied employing a wide range of innovative methods. Advanced research is carried out in close cooperation with the Department of Molecular Biology of the Faculty of Medical Science.

Education

Undergraduate School

The Department of Biology offers basic lecture courses and experimental training focused on basic and modern biology areas; both of which have seen dramatic developments in recent years. The department is mostly concerned with educating students as professionals for the life sciences and related fields. Lectures and experimental training encompass animal physiology, developmental biology, plant physiology, ecology, genetics, molecular genetics, biophysics, biochemistry, mathematical biology, cell biology, and marine biology.

Graduate School

Our Graduate School of System Life Science has two courses; the “Division of Molecular Life Sciences” and “Division of Biological Sciences”.

Division of Molecular Life Sciences

he eukaryotic cell is a core structural unit that constitutes the bodies of higher organisms, and operates various activities of life with highly sophisticated membrane structures. The Division of Molecular Life Sciences conducts research into the integrated biology of animals and plants from basic structures of genes to high-order functions of bodies by focusing on the following aspects; mechanisms of chromosomal DNA replication for maintaining genome structures, molecular dynamics of high-ordered structures from protein complexes to organelles managing cellular functions, for example, signaling mechanisms of cell-cell communication for cell proliferation, cell formations and metabolism regulation mechanistic features of functions in individual bodies including development and differentiation, and formation of neural networks and immune systems. We also provide basic lectures to students concerning other divisions aiming to understand molecular biology of life from molecular, cellular and individual aspects. The lectures include basic structures and functions of the cell, developmental mechanisms of individual bodies from fertilization to highly organized cell societies, and the coordination of nerve systems to manage high-ordered biological activities.

Division of Biological Sciences

Recent developments in ecology and evolutionary biology provide us with better tools to investigate interactions among individuals and the coexistence of species within ecosystems. Similar advances in other branches of biology have likewise led to improved knowledge and techniques. At the individual level of cell developments in physiology we have refined our methodologies of analyzing biological phenomena. Comparable advances in molecular biology have enhanced our knowledge of genomes and clarified the details of mechanisms underlying physiological processes.

The current requirement is to integrate all such developments to investigate interactions between organisms and their environments, and to deepen our understanding of the mechanisms underlying various biological attributes found between individuals and populations.

With this in mind, our study areas include 1) perceptions of, and responses to, environmental stimuli in animals, 2) reception of, and responses to, light in plants, 3) adaptive strategies in reproduction and social structures in organisms, 4) establishment and maintenance of community structures in marine organisms, 5) molecular evolution and the maintenance of genetic diversity, and 6) mathematical aspects of complex biological phenomena.

With this focus we aim to integrate biological knowledge from the molecular, cellular, individual and population levels. By participating in research in our division, students can learn how to conduct cutting-edge research on mechanisms of animal and plant responses to environmental stimuli, ecological interactions between organisms and environments, and the generation and maintenance of biodiversity.

Research Groups

Division of Molecular Life Sciences

Molecular and Developmental Cell Biology
  • Kazuya Nomura, Associate Professor
  • Nobushige Nakajyo, Lecturer
The nematode Caenorhabditis elegans is an ideal model organism for functional genomics. The human genome and the nematode genome have many glycome-related genes in common. In our laboratory, we select human glycome-related genes systematically and study the functions of genes by using the nematode. RNAi and deletion mutagenesis are systematically used for this purpose, aiming toward the complete functional analysis of glycome-related genes and associated gene networks. Special attention is paid to the roles of molecules present in the outer most layers of cell membranes that control cell surface molecules or mediating infection.
Plant Molecular Biology
  • Koh Iba, Professor
  • Jyuntaro Negi, Associate Professor
  • Kensuke Kusumi, Assistant Professor
  • Osamu Matsuda, Assistant Professor
At the Laboratory of Plant Molecular Biology, the functions of plant cells related to environmental adaptability are studied using genetic engineering approaches. Our efforts focus on the model plants Arabidopsis and rice. The objective is to characterize the key genes involved in the adaptation of plants to stress factors such as temperature, CO2, and pathogen invasion. By analyzing the functions of these genes in detail, we gain an understanding of the molecular mechanisms by which plants adapt to their environments.
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Molecular Cell Biology
  • Shigehiko Tamura, Professor
  • † Faculty of Arts and Science
Peroxisomes are present in a wide variety of eukaryotic cells, from yeast to humans, and function in various metabolic pathways, including the β-oxidation of very long chain fatty acids and the synthesis of ether-lipids. The functional consequence of human peroxisomes is highlighted by fatal genetic peroxisome biogenesis disorders (PBD), including Zellweger syndrome, all of which are linked to a failure of peroxisome assembly. In our studies we aim to elucidate the molecular mechanism of peroxisome biogenesis and protein trafficking in eukaryotes
Membrance Cell Biology
  • Junichi Ikenouchi, Professor
  • Kanji Okumoto, Assistant Professor
  • Kenji Matsuzawa, Assistant Professor
Epithelial cells are constitutively polarized to play fundamental functions such as vectorial transport. There are two membrane domains of epithelial cells, the apical membrane and separated by cell adhesion apparatus. To understand the molecular mechanisms of epithelial polarity and cell adhesion, our lab has identified important proteins involved in these processes. In addition to the researches focused on proteins, we are now trying to clarify the roles of membrane lipids in epithelial cells. The aim of our study from the viewpoint of basic science is to clarify the roles of individual lipid species by using epithelial polarity and cell adhesion as experimental systems. The research purpose for clinical science is to find novel therapeutic targets in diseases correlated with epithelial-polarity disorders and epithelial-mesenchymal transition, such as cancer, polycystic kidney disease and pulmonary fibrosis.
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Molecular Genetics
  • Takeshi IshiharaI, Professor
  • Makoto KogaII, Associate Professor
  • Takayuki TeramotoI, Associate Professor
  • Manabi FujiwaraI, Assistant Professor
  • Takaaki HirotsuI, Assistant Professor
  1. Animals process various kinds of sensory information in their nervous systems to regulate their behavior. To elucidate those mechanisms at molecular and neural network levels, we study the behavioral regulation of C. elegans as a model system, by using molecular genetics, behavioral analyses, and imaging studies on the neural network. Among many kinds of information processing, we focus on the behavioral plasticity, sensory integration, olfaction, and behavioral regulation by internal environments. We also analyze the effects in C. elegans of medical drugs that target manic depression. These studies will provide fundamental insight into the function of central nervous systems in animals.
  2. The most significant thing for organisms, and the primary function of their behavior, is to maintain their populations and produce offspring for the next generation. Efficient foraging, strategic utilization of food resources, and successful sexual reproduction are among the most important activities for organisms. The healthy functioning of the cerebral nervous system is necessary for all organisms to achieve these behaviors, from mammals with a complex nervous system to creatures with relatively simple nervous systems such as the a wooly aphid. Our research centers on molecular genetic analysis, using C. elegans as a model, to study the behavioral changes and control mechanisms relating to eating behavior.
Molecular Neuroscience
  • Isao Ito, Professor
  • Hiroshi Udo, Assistant Professor
  • Tsuneyuki Koga, Assistant Professor
Left-right (L-R) asymmetry is a fundamental feature of higher-order neural function. Conventional laterality research dealt with asymmetries in higher-order functions and macroscopic structures of the brain. However, the molecular basis of brain asymmetry remains unclear. We found functional and structural asymmetry of hippocampal circuitry caused by differential allocation of N-methyl-D-aspartate receptor (NMDAR) subunit GluRε2 (NR2B) in hippocampal synapses. The synaptic distribution of ε2 subunits and the NMDAR-mediated synaptic functions provide sensitive and quantitative indices for detecting abnormalities in the L-R asymmetry of the brain. Using these indices in combination with multidisciplinary research, we explore the molecular basis of brain asymmetry.
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Chromosomal Functions
  • Toshiki Tsurimoto, Professor
  • Tatsuro Takahashi, Associate Professor
  • Eiji Nitasaka, Lecturer
  • Eiji Ohashi, Assistant Professor
Precise DNA replication in eukaryotic cells is essential for the maintenance of genome integrity during cell proliferation. This step is also crucial for the coordination of various cellular signals with cell proliferation through regulation of DNA damage responses, reorganization of chromosomal structures and segregation of sister chromatids, and thus tightly involved in differentiation, cancer-development, and the aging of eukaryotic cells. Our major interest is in understanding the molecular dynamics of the replication fork complex in human cells, focusing on functions of its major components, clamp and loader complexes. We have taken molecular biological and biochemical approaches to study their molecular interaction networks and structure-function relevance.
Protein Science and Cellular Biochemistry
  • Shun-ichiro KawabataI, Professor
  • Takumi KoshibaII, Associate Professor
  • Yasuhiro ImafukuI, Assistant Professor
  • Toshio ShibataI, Assistant Professor
  1. Our laboratory specializes in protein science and cellular biochemistry, which include biochemical and biophysical characterization of native or recombinant proteins involved in innate immunity. We have been conducting studies on molecular mechanisms of invertebrate innate immunity using the horseshoe crab Tachypleus tridentatus and Drosophila melanogaster. Interactions between protein and other biomolecules including lipids and carbohydrates are measured by surface plasmon resonance and quartz crystal microbalance analyses. Physiological functions of the identified proteins are also characterized in vivo by RNAi in the Drosophila system. Three dimensional structures of proteins and peptides are determined in collaboration with other laboratories through X-ray crystal and NMR analysis.
  2. Mitochondria are dynamic organelles that undergo cycles of homotypic fusion and fission events, which are believed to play an important role in controlling organelle numbers, subcellular distribution, morphology, and ATP production. In some cells, fusion of numerous mitochondria into a well-organized reticulum is thought to enable transmission of the mitochondrial membrane potential, thereby facilitating ATP generation to active regions of the cells. However, the reality of the mitochondrial dynamics and their functional significance still has plenty of room for further understanding. Our lab is trying to decipher the relationship between mitochondrial dynamics and its physiological relevancy, especially for the human metabolism and immune response system. To address this issue, we use a wide range of approaches, including cell biology, biochemistry, and biophysics.

Division of Biological Sciences

Ecology
  • Tetsukazu YaharaI, Professor
  • Eiichi KasuyaII, Associate Professor
  • Akiko SatakeI, Associate Professor
  • Natsuko HamamuraI, Associate Professor
  • Takahiro HosokawaI, Assistant Professor
  1. I am interested in understanding the evolution of various reproductive strategies of vascular plants (asexual reproduction, sexual reproduction, selfing, pollination etc) by combining techniques of molecular and genome biology with empirical studies in the field. I am also working in some conservation projects in local and regional scales (Ito campus, Yaku Island, Cambodia, whole tropical Asia).
  2. In our laboratory we are currently carrying out evolutionary ecological research on animal behavior and plant reproduction. Field observations, experiments in a common garden and laboratory and DNA-based analyses of relatedness and phylogeny are employed to test hypotheses on adaptive significance of animal and plant behavior. Feral cats, water striders, social bees and wasps, grey-crowned Babbler, daylilies, and stevias are among the various organisms we are studying. We are also active in ecological conservation research. Projects on biodiversity conservation and ecosystem managements are being conducted in the biodiversity reserve of Kyushu University Ito Campus, World Natural Heritage area on Yaku Island, freshwater ecosystems in Lake Tai in China, and tropical forests in Cambodia.
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Theoretical Biology
  • Yoh IwasaI, Professor
  • Shingo IwamiII, Associate Professor
  • Hiroshi HaenoI, Assistant Professor
  1. We analyze biological phenomena by developing mathematical and computational models. The targets of study in our group cover the whole gamut of biology and life sciences. Examples of our study areas include: pattern formation in the cone mosaic of fish retina; leaf vein formation; circadian rhythm; somatic evolution of cancer; genomic imprinting; mate preference evolution; forest dynamics both in temperate and tropical climates; species coexistence and diversity in coral reef environments, and population extinction risk of animals and plants.
  2. Along with the rapid development of experimental techniques in molecular and cell biology, important results have been achieved in the field of virological and immunological disease. In many studies, however, these experimental techniques have focused on elucidating only one aspect of the disease. Mathematical modeling, in tandem with rigorous experimental work, offers an opportunity to analyze disease progression more comprehensively. At one time, modeling work was essentially ignored by the experimental immunology and virology communities, but in the last 15 years it has become an important tool to aid biology. In fact, almost all modern experimental biology groups are now collaborating with a theoretical scientist, although Japan has lagged behind in this type of cooperation. The strength of mathematical modeling comes from its ability to provide quantitative insights which cannot be obtained by experimental and clinical studies alone, particularly in the fields of human-specific infectious disease such as HIV, HCV and influenza infection. I am currently working to establish a new field in Japan called “Computational virology and immunology” which combines experimental analyses, mathematical modeling and analysis, and computational simulation to understand the dynamical systems of disease.
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Cell Function
  • Yoshitaka Kobayakawa, Professor
  • † Faculty of Arts and Science
In our laboratory, we study Hydra, class Hydrozoa phylum Cnidaria, in the many fields of biology. In the fields of developmental biology, we study pattern formation, cell differentiation, and gametogenesis of Hydra. We are also studying symbiosis between hydra and green algae. Molecular phylogeny in genus Hydra is also a subject of our research.
Evolutionary Genetics
  • Hidenori TachidaI, Professor
  • Alfred Edward SzmidtII, Associate Professor
  • Toshiyuki HayakawaIII, Associate Professor
  • Kousuke TeshimaI, Assistant Professor
  • † Faculty of Arts and Science
  1. We study biological evolution using empirical and theoretical approaches of population genetics. Evolutionary changes of organisms occur through the processes of mutation, selection, genetic drift and migration. Population genetics provides us with tools to infer the roles and nature of those processes from the data of genetic diversity. We are currently using trees in temperate and tropical forests, cichlid fishes and Drosophila as research materials to understand how genetic diversity in those organisms is shaped through the evolutionary processes mentioned above.
  2. Our main interest is to understand the maintenance mechanisms of naturally occurring genetic variation within and between species. Analysis of the levels of polymorphism and patterns of nucleotide substitutions enable us to infer what evolutionary forces have acted on nucleotide sequences. Population genetic surveys provide information about fitness-related genes upon which natural selection acts. Current studies focus on:
    1) the molecular evolution of duplicated genes.
    2) the molecular genetic basis of adaptation by gene duplication following functional diversification.
    and 3) the detection of epistatic selection and characterization of responsible genetic factors.
  3. Sialic acids are components of cell-surface glycans, and play important roles in cell-cell communication and host-pathogen interaction. Over 55 genes, encoding receptors, enzymes and transporters are known to be involved in sialic acid biology. Interestingly, several of these genes show human-specific changes in genome structure, expression, and/or function. What makes us human? This is a popular question for mankind. An unusually large number of human-specific changes have been found in genomic loci involved in sialic acid biology. Exploration of human uniqueness in sialic acid biology is one of scientific approaches to answer this question. Phenotypes expressed by human-specific changes in sialic acid biology can be guessed from relationships between these changes and diseases. Based on a viewpoint of evolutionary medicine, we are studying human-specific changes in sialic acid biology to know their roles in the human evolution.
Marine and Freshwater Biology
  • Mutsunori Tokeshi, Professor
  • Seiji Arakaki, Assistant Professor
  • Win Ni Ni, Assistant Professor
Located on the western coast of Kyushu facing the East China Sea, the AMBL specializes in studies of marine and coastal ecosystems including estuaries and streams. Our research involves field and laboratory work on the population and community ecology of various invertebrate, fish and plant/algal species, focusing in particular on various facets of intra- and inter-specific relationships. Our research includes comparative studies of coral reef ecosystems in Amakusa, Okinawa and South-East Asia, particularly Indonesia. We aim to gain a better understanding of the biodiversity and functioning of aquatic ecosystems which are seriously threatened by climate change and various anthropogenic factors.
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