Doctoral Program in Biological Sciences
The Institute of Biological Sciences is one of the Graduate Schools of the University
of Tsukuba offering a Ph.D. degree [Doctor of Philosophy, (in Science or Biological
Sciences)]. The course extends over five years generally, but for excellent students,
the course can be completed after three years. The degree of Ph.D. is awarded
to a student who has completed the required course work, presented an acceptable
dissertation, published papers in international journals, and passed the final
examination.
The field of Biological Sciences is one of the most attractive and progressive
sciences in the world, including modern molecular biology, biotechnology, chemistry
and physics. Research in this field is essential for continued advance in science
and technology and for the survival of the earth. Research in the Graduate School
is broadly representative of classical and modern biology, and covers research
on a wide range of biological problems that can be approached at the molecular,
cytological, physiological, and population levels. It includes systematics, morphology,
physiology, genetics, developmental biology, dynamic biochemistry, molecular biology,
biotechnology and ecology. Specific research topics are indicated in the research
specialities as listed below for the faculty members.
The Graduate School of Biological Sciences has two courses, the Biology course
and the Biophysics-Biochemistry course. Each student applies for one of the two
broad programs. The names of the courses are rather historical and do not always
represent the specific research fields. Applicants are advised to study the list
of faculty members to decide their senior professor, and to get in contact with
the professor of their choice in advance. Approximately 20 students are admitted
to this Graduate School every year after the entrance examination of Biological
Sciences, or that of the Interfaculty Biotechnology curriculum (Seibutsu-Kougaku
gakusai curriculum).
Graduate students are required to take courses to obtain a minimum of 30 credits.
They must also make a satisfactory oral presentation of their research at the
end of their second year of studies.
The Cooperative Graduate School System of the Doctoral Program
In spring 1992, at the initiative of the doctoral degree program, the University
of Tsukuba started a "Cooperative Graduate School System" (Renkei Daigakuin
Hoshiki), with a view to promoting collaboration with various national research
laboratories and other institutes in Tsukuba Science City. This further enriches
the existing graduate programs, and improves students' competence and capabilities.
Competent research scholars working at other institutes can become adjunct
professors of this university. Students can receive research supervision from
these adjunct professors at their institutes, which broadens the range of research
topics and research facilities and equipment that are available. In this system
there are also two courses, a Biology course and a Biophysics-Biochemistry course.
The applicant must take the same entrance examination as the Biological Sciences
Doctoral Program. Students in this system can be awarded the degree of Ph.D.
under the same conditions as students belonging to the Doctoral Program in Biological
Sciences of the University of Tsukuba.
Professors
FUJII, Koichi
Research on ecology, and in particular on the dynamics and structure of the biotic
populations and communities. One focus is on the regulation mechanisms of animal
populations. Approaches used involve laboratory experiments with bean-bean weevils-parasitic
wasps systems, and their mathematical modeling. Another research project involves
the mechanisms of colony formation by egrets.
HAYASHI, Ichiroku
I have studied on mechanism of successional changes of plant communities. According
to the information on the plant succession, we are able to predict the vegetation
dynamics under various conditions of human perturbation. Based on the results,
I have attempted to restore the degraded stands by human impacts with vegetation
recovery in drought deciduous woodlands in Brazil, Kenya and Inner Mongolia, China.
HAYASHI, Jun-Ichi
1. Somatic cell genetical and molecular biological approaches to understand dynamics of the mitochondrial genetic system and of organelle biogenesis in living human and rodent cells. 2. Molecular biological approaches for analyzing the inheritance and expression of mtDNA mutations in mammals. 3. Diagnosis of mitochondrial diseases and diabetes using intercellular transfer of the patient mtDNA to mtDNA-less human cells. 4. Isolation and characterization of transgenic mice possessing pathogenic mtDNA mutations for screening the drugs and for understanding the mechanisms of phenotypic expression of mitochondrial diseases.
HIRABAYASHI, Tamio
Research on muscle differentiation, muscle cell lineage establishment, expression
and accumulation of muscle proteins, isoform transition mechanism of troponin
T during chicken development, and gene structure analysis of fast- and slow-skeletal
muscle troponin Ts. Techniques used include protein chemistry, gene cloning, immunohistochemistry,
cell and tissue culture.
HORI, Terumitsu
Research on fertilization of green plants, especially green algae and gymnosperms.
Forcus is on ultrastructural and cell biological analyses of gametogenesis and
gamete fusion, and on the mechanism of cytoplasmic inheritance of chloroplasts
mediated concomitantly with sexual reproduction. Another projects are comparative
studies of ultrastructure of the flagellar apparatus, cell division, cell organell
multiplication of green and haptophyte algae from the viewpoint of evolution,
and functional and structural studies of chloroplast nucleoid- and pyramidal-DNA.
INOUE, Isao
Systematics and phylogeny of phytoflagellates which form many distinct lineages
in the eukaryotic world. For obtaining better framework of ph otosynthetic organisms
and understanding of their early divergence, microalg ae exhibiting primitive
features and non-pigmented flagellates, probably the descendants of ancestors
of photosynthetic lineages, are focused. Major techniques presently employed are
electron microscopy of cellular components, especially of the flagellar apparatus,
and DNA sequencing. Description and classification of new taxa are also important
part of work.
KAMADA, Hiroshi
Main subject is to elucidate the mechanisms of morphogenesis in higher plants,
especially embryogenesis and flower formation. On embryogenesis, we are analysing
the molecular mechanisms for induction of embryogenic competence (totipotency)
and for development of somatic and zygotic embryos. On flower formation, we are
characterizing various genes of which the expression is correlated to induction
of flowering and to determine the flower structure. We are also working on molecular
mechanisms of biological clock in higher plants. Approaches used involve gene
cloning, plant transformation and cell engineering as well as plant tissue culture.
KURAMOTO, Taketeru
Research on physiological function of the central nervous system(CNS) using marine invertebrates, especially lobsters. A main target has been functional coupling of CNS and cardio-vascular system. Recent targets are cool-sensitive neurons in crustacean CNS. This research suggests that some cold neurons in the thoracic ganglia play an important role to control neurosecretory activity of the pericardial organs. Our goal is to understand generally how CNS controls or regulates the cellular function and finally, animal behavior.
MAKIOKA, Toshiki
Research on animal phylogeny, and in particular on the origin and evolution of the arthropod subphyla, the Pycnogonida, Chelicerata, Crustacea, Myriapoda, and Hexapoda, and on their systematic relationships. Approaches used involve comparative histological analyses on structure of the ovaries and on the modes of oogenesis at the intra- and inter-subphyletic levels. Another research project involves thelytokous parthenogenesis in the viviparous scorpion, Liocheles australasiae, to analyse its process andmechanism, and to elucidate the biological, evolutional, and systematical meaning.
OGUMA, Yuzuru
Research on insect speciation, particularly in genetic aspect of sexual isolation.
Genetic control of courtship behavior based on acoustic, olfactory and visual
signals in Drosophila. Identification of the genes controlling sexual isolation
between sibling species. Another research project is to elucidate relationship
between resistance for coldness or desiccation and speciation.
OIKAWA, Takehisa
Research on plant ecology, and in particular on the physiological ecology of terrestrial
plants. As part of IGBP (International Geosphere-Biosphere Programme) in Japan,
productivity of a plant community is analyzed in relation to global change in
environmental conditions such as temperature, CO2 concentration and heat balance
through field measurements and model simulation. Another research project is to
study decomposition of soil organic material from the viewpoint of global carbon
cycling.
SAITO, Takehiko
Research on cellular and molecular mechanisms regulating development and regeneration
in the vertebrate retina; How do retinal neurons differentiate? How do they make
specific synaptic connections? Generally, developmental work involves fish and
chick, and studies of retinal regeneration are carried out with newt and chick.
Techiniques include electrophysiology, immunohistochemistry, and cell and tissue
culture. Another line of research concerns retinal neuro-circuitry.
SAKAI, Shingo
Research on physiological functions and the mode of action of plant hormones.
One research project involves the regulation of gene expression by plant hormones
in sexual modification, cut injury and immortal cell induction. Another research
project involves the characterization of putative plant hormone receptors. A new
project is the purification and gene cloning of telomerase of higher plants.
SEKI, Humitake
Research on microbiology, in particular on the ecological role of microorganisms
in the biosphere. The major research subject is on microbial intervention to the
cycling of biological elements in the hydrosphere. This looks at the microbial
role not only in the production and decomposition processes of organic materials
but also in the food webs of the aquatic environments. Another major subject is
on the function of environmental factors affecting aquatic microbial communities.
This research field is closely connected with environmental sciences and space
biology, as well as the basic biological sciences.
SHIRAIWA, Yoshihiro
Regulatory mechanisms for the photosynthetic fixation of CO2 by microalgae, such as unicellular green algae and coccolithophorids, and for the changes in the photosynthetic properties during acclimation to high or low CO2 conditions are our main interests for research. Mechanism of intracellular calcification by marine coccolithophorids is also actively studied. Research themes in detail are as follows: mechanisms for the efficient utilization and transport of inorganic carbons, the regulatory mechanisms of carbon metabolisms in photosynthesis and photorespiration, the CO2-concentrating mechanism by microalgae, and the induction mechanisms and the physiological functions of high- and low-CO2-inducible proteins.
TAKAHASHI, Mihoko
Research on genetic control of locomotive and mating behavior in ciliates,mainly
in Paramecium caudatum and Tetrahymena thermophila. Isolation of
mutants, genetic analysis, characterization of gene products and genetic relationships
among mutants, especially among voltage-sensitive Ca2+ channel mutants. Cloning
of the genes controlling function of Ca2+ channels is now looked for. Identification
of mating type specific molecules relating to sexual recognition by mating-type
specific monoclonal antibodies. Elucidation of the determination factor(s) of
germinal and somatic nuclei.
TANAKA, Yoshimasa
Studies on development and differentiation of the cellular slime molds using reverse
genetics. One project is to clone and determine the sequence of total cDNAs and
to elucidate the function of each gene and the genetic network in Dictyostelium
discoideum. Another project is to clone and analyze genes for morphogenesis in
Polysphondylium pallidum using insertinal mutagenesis. A novel mitochondrial small
RNA is also being studied to address the function.
YAMANE, Kunio
(1) Research on molecular mechanism of the targeting and membrane translocation
of secretory proteins, and on the molecular relationships between protein localization
and morphogenesis in Bacillus subtilis. (2) protein engineering and structural/functional
analyses of cyclodextrin glucanotransferase. (3) Participating in the International
project on the Bacillus subtilis genome DNA sequencing and functional analyses.
Associate Professors
FURUKUBO-TOKUNAGA, Katsuo
Molecular Genetics of Brain Development: understanding the molecular and genetic mechanisms of brain development is a central issue in neuroscience. Using Drosophila melanogaster as a model system, I focus on the molecular mechanisms of brain patterning and neural network formation that set up the computational basis for higher order functions such as learning, memory and perception. Recent studies have revealed a conserved genetic program of brain development between flies and mammals. Studies on the Drosophila brain will have general impact to the understanding of the human brain.
KUWABARA, Tomohiko
Studying security systems of photosynthesis, which are the defense system against
environmental stresses that is expressed before the occurrence of the stress.
The security system located in the thylakoid lumen involves violaxanthin de-epoxidase
(VDE) and polyphenol oxidase (PPO). These are not directly involved in the photosynthetic
assimilation of light energy, but necessary for the protection of phototsynthetic
machinery against environmental stresses.
MACER, Darryl
Researches especially on environmental, ethical, social, economic and legal issues
of biotechnology in medicine and agriculture. International comparisons of perceptions
of bioethics, life and nature. Promotion of bioethics education at schools and
university. Developing international bioethics networks, particularly in poorer
countries. Students should be willing to try to use English to become international
in focus. Papers are on-line on this site. He is Director of Eubios Ethics Institute
and the International Union of Biological Sciences (IUBS) Bioethics Program (details
on-line); editor of EJAIB; publications include 7 authored books, 10 edited books
in English or Japanese, 100+ academic papers.
MACHIDA, Ryuichiro
Research on the phylogeny of Atelocerata, especially on the origin, evolution
and ground plan of Insecta, based on the comparative embryological and morphological
approaches. Another field of study concerns the classification of thysanurans
(Archaeognatha and Zygentoma).
NAKATANI, Kei
My research is concerned with the molecular mechanisms of signal transduction
and its modulation in sensory receptor neurons. The techniques we use include
electrophysiology (e.g. patch-clamp recording), computer simulation, and immunocytochemistry.
We are currently working on olfactory transduction, using isolated olfactory neurons
from the newt. Recently, we observed inhibitory responses induced by odorant stimuli.
We are now focusing on these inhibitory responses, in order to understand the
underlying mechanism and the physiological significance of the phenomenon.
NAKAYAMA, Kazuhisa
Most secretory and membrane proteins are synthesized in the endoplasmic reticulum
and transported to the cell surface through the Golgi complex. The protein transport
between these organelles is mediated by carrier vesicles. The formation of carrier
vesicles is regulated by many cytosolic proteins, including coat proteins and
small GTPases. We have isolated many novel coat proteins and small GTPases that
appear to regulate the vesicle formation. The final goal of our study is to understand
the vesicle formation at the molecular level by revealing the function of these
novel cytosolic proteins.
NUMATA, Osamu
Research on molecular mechanism of cytokinesis using ciliated protozoan Tetrahymena.
One project is to study the mechanism of division plane determination using cell
division arrest mutant cdaA1. A second project is to elucidate functions of actin-binding
proteins and myosin in contractile ring formation. Techniques used include immunohistochemistry,
protein chemistry, electronmicroscopy and gene engineering.
SAKAMOTO, Kazuichi
Research on molecular mechanisms of prostaglandin induced luteral cell apoptosis,
cell differentiation, and cell proliferation in mammalian ovary. Currently we
focused on gene expression of PG receptor in the bovine estrous cycle, and the
regulatory mechanisms of signal transduction by receptor associated proteins.
As our second project, we focused on telomerase actions in cell differentiation
of tumor cell lines, and the telomerase associated regulatory RNA and proteins,
to understand the molecular interaction between telomerase and tumorgenesis.
SATOH, Shinobu
Research on physiology and molecular biology of plant development and function.
Main focus is on the molecular functions of apoplast in cell-to-cell, tissue-to-tissue
and organ-to-organ interactions of higher plants. 1. Functions of root and organic
substances including proteins in xylem sap in the development and functions of
above-ground organs. 2. Functions of proteins and pectic polysaccharides of cell
wall in morphogenesis, development and functions of plant cells and seeds.
SUGITA, Hiroaki
Research on evolution and phylogeny of Chelicerata (horseshoe crabs, spiders,
scorpion, etc). Approaches used involve comparative studies, between horseshoe
crabs, of amino acid sequences and antigenicity of hemocyanin subunits, nucleotide
sequences of two mitochondrial genes, and developmental capacity of artificial
hybrids. Current focus is on molecular evolution of hemocyanin subunits and species
evolution of horseshoe crabs and spiders based on amino acid sequence analyses.
TOKUMASU, Seiji
Research on ecology of fungi, and in particular on the fungal successions associated
with the decay of plant debris. One focus is on the floristic descriptions of
the development of fungal communities on various substrata, and another is on
the effects of climate on the geographic ranges of saprophytic microfungi involving
the successions. Other research project involves the infra-specific structures
of some zygomycetous fungi related to their geographic ranges.
URUSHIHARA, Hideko
Studying the mechanism of genetic control of sexual cell interactions using the
cellular slime mold Dictyostelium discoideum as a model organism. In addition
to conventional approaches such as use of inhibitory antibodies and generation
of defective insertional mutants, random and massive analysis of clones in the
gamete cDNA library is being performed. Novel genes are subjected to homology
searches, determination of expression pattern, and gene targeting by antisense
RNA and disruption to identify their functions. Construction and management of
databases is also my subject.
WASHITANI, Izumi
Eco-physiological and evolutionary-ecological studies on plant strategies related
to 'reproduction by seeds'. Main concerns are the evolution and ecological significance
of seasonal schedules for reproduction and breeding systems such as heterostyly.
Conservation-oriented studies on population dynamics of red-data and alien-invader
plants, dynamics of soil seed banks, and utilization of soil seed banks for habitat
restoration.
Assistant Professors
KANZAKI, Ryouhei
Insects have rather a small number of constituent neurons of the brain, and eventually
display simple patterned movements, a so-called 'instinctive behavior'. The behavioral
strategies employed by insects must be efficient and adaptive to circumstances
which change every moment. Insects will become an excellent model for understanding
adaptive control in biological system which will inspire the control and communication
in engineered system. We are interested in the following two topics. 1) Releasing
mechanisms of the adaptive behavior by the processing of the insect brain. 2)
Bio-micromachine based on the behavioral and neural mechanisms of the insect.
KOBAYASHI, Satoru
Research on molecular mechanism underlying germ-line establishment in Drosophila
melanogaster. I have previously reported that both mitochondrial large ribosomal
RNA and Nanos protein are essential for germ-line development. One focus is to
understand how these molecules regulate the pathway leading to germ-line establishment.
Approaches used involve molecular biology, histology at light and electron microscopic
level, genetics and microinjection technique.
MIYAMURA, Shinichi
Research on plant morphology, and in particular on the cell biology of the reproduction
of green plants, especially green algae, liverworts, ferns and gymnosperms. One
focus is on the mechanism of gametogenesis of siphonous green algae and ferns.
Approaches used involve fluorescence microscopy, electronmicroscopy and biochemical
analysis of flagellar apparatus of gamete. Another research project involves the
structure and function of pyrenoids.
MIYAZAKI, Jun-ichi
1. Developmental biology and comparative biochemistry on muscle, especially study
on 1)determination, differentiation, and maturation of muscle development and
2)structures and transcriptional control of muscle-specific genes, and 3)biological
significance of developmentally and tissue-specifically regulated isoforms of
muscle regulatory proteins. 2. Systematics for resolving phylogenetic relationships
of organisms such as freshwater and Antarctic fishes and deep-sea animals and
understanding evolutionary events mainly by means of molecular approaches.
NAKAMURA, Kouji
Research on the biological function of the signal recognition particle (SRP) RNA-related
RNA in eubacteria, including Escherichia coli and Bacillus subtilis. How they
concern with transcription, translation and secretion? What protein(s) bind to
them? Another research project to identify new small cytoplasmic RNAs (~300 nucleotides)
is undergoing.
SAITO, Yasunori
Research on the self-nonself recognition mechanisms in colonial marine invertebrates,
sponges, bryozoans and compound ascidians. The focus is on the relationship between
the allorecognition in those animals and transplantation immunity controlled by
the major histocompatibility gene complex (MHC) in vertebrates. Another research
projects are on the mechanisms of periodical degeneration of zooids in botryllid
ascidians and on the taxonomic and phylogenetic study of botryllid ascidians.
SAITOU, Takashi
Research on social organization of the Great Tit and breeding biology of the Grey
Starling. The focus is on lifetime reproductive strategy related to individual
history in the former and on intraspecific brood parasitism in the latter.
TOQUENAGA, Yukihiko
Researches on ecology, and in particular on theoretical studies of populations, communities, and ecosystems in virtual as well as real worlds. Materials are laboratory/natural bean weevil populations, egrets and herons living around Tsukuba City, and computer bugs occupying several giga bites of hard disks and Jazz media.
YAMAGISHI, Hiroshi
Research on physiology and development of the cardio-vasucular system in invertebrates.
Main focus is to explore ontogenic and phylogenic diversity in heartbeat pacemaker
mechanisms and in its regulatory systems in crustaceans using morphological, imunohistochemical
and electrophysiological methods.
Gooperative Graduate Doctoral Program System
Professors
AMANUMA , Hiroshi
Research on development of cell type (tissue)-specific retrovirus vectors for
human gene therapy and pathogenesis of mouse retroviruses. Cell type (tissue)-specific
retrovirus vectors will be made by genetical modification of the env gene or by
placing an internal transcriptional promoter in the vector genome. How dose the
Friend spleen focus-forming virus (F-SFFV) cause acute erythroleukemia in mice?
ISOGAI, Takao
Research on genetics of metabolisms and the disease related genes based on a functional genomics of mammalian cDNAs. Full-length enriched cDNA libraries from cultured cells and tissues are constructed using an oligo-capping method and a mammalian expression vector for an efficient system for a high-throughput functional analysis of novel genes, which will be principally associated with human diseases.
JIGAMI, Yoshifumi
Research on yeast molecular glycobiology. One focus is on the protein glycosylation
and its regulation in relation to the cell wall mannoprotein function in budding
yeast and fission yeast. Approaches used involve yeast genetics to isolate mutants,
cloning of the corresponding genes, contstruction of gene disruptants, and analysis
of gene product. Another research project involves the application of above tools
and knowledges to glycotechnology, namely, re-modeling of sugat chain to produce
various mammalian oligosaccharides by manipulating yeast and mammalian sugar chain
biosynthetic genes in yeast.
OMASA, Kenji
ONDA, Haruo
Research on bioactive peptides and their receptors.
SHINOZAKI, Kazuo
Research on gene expression and signal transduction in higher plants under environmental
stress conditions and by plant hormones. Research on the molecular mechnism of
environmental stress tolerance in higher plants. Analysis of genome structure
and gene function of a model plant, Arabidopsis thaliana.
WATANABE, Makoto M.
Research on biosystematics of microalgae; How species should be recognized in
cyanobacteria and sexual microalgae? Chemo- and molecular-taxonomy of cyanobacteria
and study on reproductive isolations of green algae are carried out based on axenic
culture. Another research projects involve the fate of toxins produced by water-blooms
of cyanobacteria in a eutrophic lake and the conservation of the endangered algae,
charophytes.
YAMADA, Masahiro
Information science and technology of neural network. Special interests in 1)
neurophysiology of retinal neural circuits, 2) visual signal processing and synaptic
mechanisms and 3) plasticity of chemical and electrical synapses in the retinal
circuitry and its pharmacological basis.
Associate Professor
AIDA, Yohko
1) Bovine leukemia virus (BLV) and the human T-cell leukemia viruses-I and -II belong to the same subfamily of retroviruses. To investigate the mechanisms of BLV-induced leukemogenesis, the following subjects are in progress: a relationship between polymorphism of the bovine MHC classII gene and resisitance and susceptibility to BLV-induced lymphosarcoma, and biological roles for the YXXL motifs of the BLV transmembrane envelop glycoprotein, gp30 and for the BLV transactivator Tax. 2) human immunodeficiency virus type 1 (HIV-1), the causative agent of acquired immunodeficiency syndrome (AIDS), is a member of the lentivirus subfamily of retroviruses; it encodes for the structural, regulatory and accessary genes (vpr, vpu, vif, and nef). The characterization and analysis of the function of viral protein R, Vpr, are in progress.
NOJIRI, Yukihiro
Global biogeochemical cycles of greenhouse gases. Monitoring study of partial
pressure of carbon dioxide in the North Pacific. Oceanic uptake of carbon dioxide
in the North Pacific with relationship of primary production. Isotopic study of
carbon dioxide exchange in the forest. Global distributions of carbon dioxide,
methane and nitrous oxide, and the analysis of their sources and sinks. Methane
emission from the aquatic environment, including lakes and wetlands, related to
the microbial activity.