Sylvain Agostini
Ecophysiology of hermatypic corals
agostini.sylvain@shimoda.tsukuba.ac.jp
http://coralecophy.agoremix.com
Hermatypic corals are on the fore front of climate change. Rising temperature has
resulted in increased mass bleaching and disease occurrence in the tropics, but it has alsofavor a poleward shift/expansion of corals in Japan and other parts of the world. In order tounderstand the future extent of this expansion and the possibility that high latitudes provides afuture refuge for corals, a better understanding of the effect of environmental parameters oncoral ecology and physiology is required.
Monitoring and diverse surveys including citizen surveys of coral communities
around Izu and the Izu Islands were established to study the competition with macroalgae, thebleaching occurrence and the growth and diversity of high latitude corals under different pH
conditions. The effects of pH on natural coral communities is studied at the recently
discovered CO2 seep in Shikine Island. Laboratory experiments complement the investigationof the stress response of corals. The physiological mechanisms of the effects of high and low
temperature stresses and of ocean acidification are studied under controlled conditions in thelaboratory.

Porites heronensis is a dominant species of hermatypic corals inhigh latitude of Japan. It forms dense patchy communities
around Shimoda and Izu. It cohabit and compete with a diverse
community of macroalgae. Low temperature often cause
important bleaching and mortality during winter.

Publications
1. Agostini, S., Fujimura, H., Higuchi, T., Yuyama, I., Casareto, B.E., Suzuki, Y., andNakano, Y. (2013). The effects of thermal and high-CO2 stresses on the metabolism andsurrounding microenvironment of the coral Galaxea fascicularis. Comptes Rendus
Biologies 336, 384–391.
2. Agostini, S., Wada, S., Kon, K., Omori, A., Kohtsuka, H., Fujimura, H., Tsuchiya, Y.,
Sato, T., Shinagawa, H., Yamada, Y., et al. (2015). Geochemistry of two shallow CO2
seeps in Shikine Island (Japan) and their potential for ocean acidification research.
Regional Studies in Marine Science.
3. Agostini, S., Fujimura, H., Hayashi, H., and Fujita, K. (2016). Mitochondrial electrontransport activity and metabolism of experimentally bleached hermatypic corals.
Journal of Experimental Marine Biology and Ecology 475, 100–107.
4. Higuchi, T., Agostini, S., Casareto, B.E., Suzuki, Y., and Yuyama, I. (2015). The
northern limit of corals of the genus Acropora in temperate zones is determined by theirresilience to cold bleaching. Scientific Reports 5, 18467.

Casco Martin
Regenerative Physiology
e-mail：casco.miguel.gm@u.tsukuba.ac.jp
Room：⽣物農林学系棟 D604
Keywords: newt, tissue, regeneration, patterning

Urodele amphibians such as the newt are the only known
adult vertebrates to carry out scar less tissue regeneration in
multiple tissues (heart, jaw, brain, limb, retina, and lens)following a traumatic event. Humanson the other hand undergo scarformation. Scar formation (or fibrosis)
in humans is a serious medical setback
that can have health consequences topatients. Multiple human diseases areassociated with scar formation invarious tissue types. Therefore, understanding the newt’s scar less regeneration provides hopethat medical applications can be developed for human patients. Great advancements have been
made in this field using a transgenic approach to study the underlying mechanisms of newt tissue
regeneration. To understand scar less tissue regeneration we use multidisciplinary approach.
Selected Publications
1. Roman Casco-Robles, Akihiko Watanabe, Ko Eto, Kazuhito Takeshima, Shuichi Obata, Tsutomu
Kinoshita, Takashi Ariizumi, Kei Nakatani, Tomoaki Nakada, Panagiotis Tsonis, Casco-Robles MM,
Keisuke Sakurai, Kensuke Yahata, Fumiaki Maruo, Fubito Toyama, and Chikafumi Chiba. (2018) Novelerythrocyte clumps revealed by an orphan gene Newtic1 in circulating blood and regenerating limbs of
the adult newt. Scientific Reports, 8 (1):7455.
2. Casco-Robles MM, Islam MR, Inami W, Tanaka Hibiki, Kunahong A, Yasumuro H, Hanzawa S, CascoRobles RM, Toyama F, Maruo F, and Chiba C. (2016) Turning the fate of reprogramming cells fromretinal disorder to regeneration by Pax6 in newts. Scientific Reports, 6:1-9.
3. Tanaka HT, Yin Ng NC, Yu ZY, Casco-Robles MM, Maruo F, Tsonis PA, and Chiba C. (2016) A
developmentally-regulated switch from stem cells to dedifferentiation for limb skeletal muscle
regeneration in newts. Nature Communications, 7: 1-8.
4. Casco-Robles MM, Miura T, and Chiba C. (2014). The newt (Cynops pyrrhogaster) RPE65 promoter:molecular cloning, characterization and functional analysis. Transgenic Research, 24:463-473.
5. Casco-Robles MM, Yamada S, Miura T, Nakamura K, Haynes T, Maki N, Del Rio-Tsonis K, Tsonis, PA
and Chiba, C. (2011). Expressing exogenous genes in newts by transgenesis. Nature Protocols, 6:600608. Selected for the Journal cover.

Google Scholar: https://scholar.google.com/citations?user=_pJkOsEAAAAJ&hl=en

Chikafumi Chiba
Regenerative Physiology
chichiba@biol.tsukuba.ac.jp
https://www.biol.tsukuba.ac.jp/~chichiba/english01.html
Keywords: regeneration, scar formation, reprogramming, stem cell, newt------------------------------------------------------------------------------------------------My research purpose is to save the lives of people who suffer traumatic injuries, through theapplication of newts’ strategy for regeneration of body-parts in medical treatments. Thus, I am
now trying to uncover the cellular and molecular mechanisms of newt body-parts regeneration(a biological mystery over two centuries) while comparing them with mammalian woundhealing and tissue repair mechanisms as well as with their pathogenic or oncogenic processes
after traumatic injuries.
The newt is the master of regeneration.
No other animal can parallel its regenerative
abilities in body-parts such as the limbs, thetail and spinal cord, parts of the eye (such as
the retina and the lens), the brain, the heart
and the jaws. This regeneration is mediatedby dedifferentiation or transdifferentiation of
fully matured somatic cells at the site of
injury, making this process relevant to anumber of important issues, such as theinvolvement of stem cells in wound healing,
reprogramming, differentiation, patterning, and the restoration of physiological function.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.
6.

Casco-Robles, R. M. et al. (2018) Novel erythrocyte clumps revealed by an orphan gene
Newtic1 in circulating blood and regenerating limbs of the adult newt. Scientific Reports
8:7455.
Casco-Robles, M. M. et al. (2016) Turning the fate of reprogramming cells from retinal
disorder to regeneration by Pax6 in newts. Scientific Reports 6:33761.
Tanaka, H. V. et al. (2016) A developmentally regulated switch from stem cells to
dedifferentiation for limb muscle regeneration in newts. Nature Communications
7:11069.
Chiba, C. (2014) The retinal pigment epithelium: An important player of retinal disorders
and regeneration. Experimental Eye Resarch 123:107-114.
Casco-Robles, M. M. et al. (2011) Expressing exogenous genes in newts by transgenesis.
Nature Protocols 6:600-608.
Tsonis, P. A. et al. (2011) Controlling gene loss of function in newts with emphasis onlens regeneration. Nature Protocols 6:593-599.

Tomoki Chiba, Ph. D.
Molecular Biology
tchiba@biol.tsukuba.ac.jp
http://tchibalab.org/
In our body, proteins are in a dynamic state, and the speed of protein synthesis anddegradation is tightly regulated. The degradation of protein is individually regulated by the“Ubiquitin and the Proteasome System” which plays critical roles in many biological aspects
such as embryogenesis, immune system, and memory.
The major goal of our laboratory is to understand;(1) The component and regulation of intracellular protein degradation at molecular level.
(2) The physiological roles of selective protein degradation in our body.
E2s$
E1$

Ub$

E3s$

Th e U b iq uitin System(E1 , E2 s, E3 s)

Ub$
Ub$Ub$Ub$

Sub strate

PA 7 0 0

ユビ
修飾酵素
PA
2 8キチンPA
200

Ecm 2 9The Ubiquitin System.
Ubiquitin acts as a degradation signal and its attachment to thesubstrate is tightly catalyzed by a cascade reaction composed of E1,E2s and E3s enzymes.
(Keywords; Cullin, NEDD8, signalosome)Proteasome Activators
Proteasome is a barrel-shaped multisubunit protease complex that
captures and degrades ubiquitinated proteins. The activitiy of theproteasome is regulated by multiple proteasome activators.
(Keywords; Proteasome, PA28, PA200, Ecm29)

Proteasom e A ctivators

My lab is focusing on;(1) The regulation and function of Cullin-RING-type Ubiquitin ligases.
(2) The regulation and function of proteasome activators using multiple knockout mice.
Publications
1. Huang L, et al. Proteasome activators, PA28γ and PA200, play indispensable roles inmale fertility. Sci. Rep. 2016, 6: 23171.
2. Kigoshi Y, et al. CACUL1/CAC1 regulates the antioxidant response by stabilizing Nrf2.
Sci. Rep. 2015, 5: 12857.
3. Ebina M, et al. Myeloma overexpressed 2 (Myeov2) regulates L11 subnuclear
localization through Nedd8 modification. PLoS ONE 2013, 8: e65285.
4. Qian MX, et al. Acetylation-Mediated Proteasomal Degradation of Core Histones during
DNA Repair and Spermatogenesis. Cell 2013, 153: 1012-1024.
5. Takashima O, et al. Brap2 regulates temporal control of NF-kB localization mediated byinflammatory response. PLoS ONE 2013, 8: e58911.
6. Kigoshi Y, et al. Ubiquitin Ligase Activity of Cul3-KLHL7 Protein Is Attenuated by
Autosomal Dominant Retinitis Pigmentosa Causative Mutation. J. Biol. Chem. 2011
286: 33613-33621.

Yoko Chiba
Metabolic Biochemistry and Evolution
chiba.yoko.gp@u.tsukuba.ac.jp
http://rnakamura-lab.riken.jp/member.html
Keywords: Microorganism, Thermophile, Enzymology, Origin of Life------------------------------------------------------------------------------------------------Our scientific goal is to understand the diversity of metabolism and evolutionary principles
of existing organisms in order to clarify the nature of primitive life and "to what" and "how"the metabolism of each organism has adapted. Specifically, we will identify novel central
metabolic pathways and enzymes, and conduct comparative analysis of enzymes andmetabolism by integrating biology and physicochemistry.
Elucidation of metabolic evolution by identifying novel amino acid biosynthetic pathways
The emergence of an autotroph and CO2 fixation pathway is essential for the creation of asustainable biosphere. However, the oldest CO22 fixation pathway remains unidentified.
The biosynthetic pathways of glycine and serine (amino acids) are interesting in that they
are closely related to CO2 fixation pathway. Furthermore, the glycine and serine synthetic
pathways in existing organisms are diverse, are some of them remain unidentified. Therefore,
we will identify the novel amino biosynthetic pathways, and use the knowledge to estimate
the evolution of CO2 fixation pathways.
Identification of enzyme optimizing factors by integrating biochemistry and catalysis
Enzymes that catalyze the same reaction but have different origins (functional homolog)
suggest that each organism selects a suitable type of enzyme in the process of evolution,
however, the selective pressure is unknown. We are developing a new methodology tocompare the physicochemical parameters of the enzymes to discuss how and to what they
have adapted to explain the diversity of enzymes and evolutionary principles.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.

Chiba Y., Miyakawa T., Shimane Y., Takai K., Tanokura M., Nozaki T. (2019) Structuralcomparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectoriesof these phosphodiester energy-conversion enzymes. J Biol Chem 294:19269-19278.
Chiba Y., Yoshida A., Shimamura S., Kameya M., Tomita T., Nishiyama M., Takai K.
(2019) Discovery and analysis of a novel type of the serine biosynthetic enzyme
phosphoserine phosphatase in Thermus thermophilus. FEBS J 286:726-736.
Kim K., Chiba Y., Kobayashi A., Arai H., Ishii M. (2017) Phosphoserine phosphatase isrequired for serine and one-carbon unit synthesis in Hydrogenobacter thermophilus. J
Bact 199:e00409-e00417.
Chiba Y., Oshima K., Arai H., Ishii M., Igarashi Y. (2012) Discovery and analysis ofcofactor-dependent phosphoglycerate mutase homologs as novel phosphoserine
phosphatases in Hydrogenobacter thermophilus. J Biol Chem 287:11934-11941.

Yousuke Degawa
Mycology
degawa@sugadaira.tsukuba.ac.jp,
http:/ https://dgw-sugadaira.jimdofree.com/
Keywords: fungi, biodivesity, natural history, phylogeny, yeast, slime mold-------------------------------------------------------------------------------------------------The Kingdom Fungi is one of the most important on
Earth. At present there are 100,000 known species, but
the total number is estimated to be over 5 million. Our
Laboratory of Mycology is situated in the Japan Alpsin the Sugadaira Highland, at an elevation of about
1300 m. It has 30 ha of well-preserved natural fields,
including grasslands and Pinus–Quercus forests. The
lab has been managed by the late Emer. Prof. H. Indoh Biodiversity of the Kingdom Fungi. Top row, left to
Chytridiomycota (zoospores discharged from(1908–2003), the late Emer. Prof. K. Tubaki (1924– right:
zoosporangium of Chytriomyces), Mucoromycota
2005), and Emer. Prof. S Tokumasu (1945–).
(sporangiophores of Pilobolus), and Zooagomycota(zygospores of Basidiobolus). Bottom row, left to
The Kingdom Fungi is regarded a sister group ofright: Ascomycota (conidiophores of theanamorphic hyphomycete Kumanasamuha),
the Kingdom Animalia in the supergroup
Ascomycota (apothecium of Trichaleurina),
Basidiomycota (basidiocarp of Pluteus).
Opisthokonta. But how did fungi originate anddiversify? In our laboratory, we are studying the natural history (taxonomy, phylogeny, andecology) of a wide range of fungal taxa and its relatives (slime molds and pseudofungi), using
living natural materials. Our focus is 1) the biodiversity of the Chytridiomycota and basal
lineages of fungi, in order to elucidate the origin of fungi; 2) the biodiversity of the
Zygomycota (Mucoromycota, Zoopagomycota), to examine the terrestrialization of fungi
considered based on the interactions between fungi and other organisms; 3) the biodiversity
and life histories (teleomorph–anamorph connections) of the Ascomycota and Basidiomycota.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Matsuzaki, R., Takashima, Y., Suzuki, I., Kawachi, M., Nozaki, H., Nohara, S., and Degawa, Y.
(2021). The enigmatic snow Microorganism, Chionaster nivalis, is closely related to Bartheletia
paradoxa (Agaricomycotina, Basidiomycota). Microbes and environments 36:ME21011.
Hashimoto, A., Masumoto, H., Endoh, R., Degawa, Y., and Ohkuma, M. (2021) Revision of
Xylonaceae (Xylonales, Xylonomycetes) to include Sarea and Tromera. Mycoscience 62:47-63
Masumoto, H. and Degawa, Y. (2020). Bryoclavula phycophila gen. et sp. nov. belonging
to a novel lichenized lineage in Cantharellales (Basidiomycota). Mycological Progress
19:705-714. https://doi.org/10.1007/s11557-020-01588-2
Takashima, Y., Degawa, Y., Nishizawa, T., Ohta, H. and Narisawa, K. (2020).
Aposymbiosis of a Burkholderiaceae-related endobacterium impacts on sexual
reproduction of its fungal host. Microbes and environments 35:ME19167.
Seto. K., Van den Wyngaert, S., Degawa, Y., Kagami, M. (2020). Taxonomic revision of
the genus Zygorhizidium: Zygorhizidiales and Zygophlyctidales ord. nov.
(Chytridiomycetes, Chytridiomycota). Fungal Systematics and Evolution 5:17-38.

Sumire Fujiwara
Plant Molecular Biology and Biotechnology
fujiwara-s@aist.go.jp
https://unit.aist.go.jp/bpri/bpri-pgrr/index_e.html
Plant growth and functions are controlled by the dynamic regulation of gene
expression by transcription factors. We work on functional analyses and utilization of suchtranscription factors that are promising to solve many problems we are facing, such as foodshortage, energy issues, and global warming. Our current projects include: 1) basic studies oftranscriptional regulation mechanisms, 2) identifications and analyses of transcription factorsthat can be utilized for the development of useful plants, and 3) research and development of
useful plants by modifications of transcription factors.
VP16‐fusion lines under the normal growth condition
Screening underenvironmental stressconditions
Control

VP16 line

Freezing tolerant

Control
Partially reported in Fujiwara et al (2014) FEBS Lett.
and Fujiwara et al (2014) Plant Biotechnol.

VP16 line

Drought tolerant

To understand the functions of transcriptional
repressors and isolate candidates for the targetsof super-plant production, we generated approx.
300 Arabidopsis transgenic lines in which atranscriptional repressor fused with anactivation domain (VP16) is constitutively
expressed. In these lines, the genes whosetranscription is usually repressed by thetranscriptional repressor are expected to behighly transcribed which could result in causing
strong phenotypes. We grew all of them andfound many lines showing unique phenotypes
or useful traits such as stress tolerance or higher
yield.

Select Publications
1.

2.
3.
4.

5.

Fujiwara, S., Sakamoto, S., Kigoshi, K., Mitsuda, N., Suzuki, K., and Ohme-Takagi, M.
(2014) VP16 fusion induces the multiple-knockout phenotype of redundanttranscriptional repressors partly by Med25-independent mechanisms in Arabidopsis.
FEBS Lett. 588, 3665-3672
Fujiwara, S., Kigoshi, K., Mitsuda, N., Ohme-Takagi, M., and Suzuki, K. (2014) VP16
fusion efficiently reveals the function of transcriptional repressors in Arabidopsis. Plant
Biotechnol. 31, 123-132
Wang, L., Fujiwara, S., and Somers, D.E. (2010) PRR5 regulates nuclear import andsubnuclear localization of TOC1 in the Arabidopsis circadian clock. EMBO J., 29,
1903-1915
Fujiwara, S., Oda, A., Yoshida, R., Niinuma, K., Miyata, K., Tomozoe, Y., Tajima, T.,
Nakagawa, M., Hayashi, K., Coupland, G., and Mizoguchi, T. (2008) Circadian Clock
Proteins LHY and CCA1 Regulate SVP Protein Accumulation to Control Flowering in
Arabidopsis. Plant Cell 20, 2960-2971
Kim, W.Y.*, Fujiwara, S.*, Suh, S.S., Kim, J., Kim, Y., Han, L., David, K., Putterill, J.,
Nam, H.G., and Somers, D.E. (2007) ZEITLUPE is a circadian photoreceptor stabilized
by GIGANTEA in blue light. Nature 449, 356-360 (*: equal contribution)

Ben Harvey
Global Change Marine Ecology
ben.harvey@shimoda.tsukuba.ac.jp
http://benjamin-harvey.co.uk
Keywords: ocean acidification, climate change, community structure, ecosystem functioning

Oceans help regulate the global climate system, and support the environmental, economic, andsocial needs of the global population. Over three billion people are dependent on the marine
and coastal biodiversity of our oceans for their livelihood. However, continued exploitation
over many years has led to the increasing degradation of marine ecosystems at an oftenalarming rate. Any loss or deterioration of coastal ecosystems can compromise their ability toprovision functioning, goods, and services; thereby affecting human wellbeing. The decline ofcoastal ecosystems has already begun but is expected to greatly accelerate with future ocean
acidification and climate change.
Our research group seeks to understand how changes in environmental conditions (focussing
on ocean acidification, ocean warming, and marine heatwaves) will change our oceans, withparticular focus on marine communities and ecosystems.
Our research is multidisciplinary,combining field-based surveys andexperiments using CO2 seeps,
aquarium-based manipulative
experiments, and modelling
approaches. Taken together, thiswill allow us to better understandthe impacts of global climatechange on coastal ecosystems
worldwide.

Selected publications
1.
2.
3.
4.
5.

Harvey, B. P. et al. 2021a. Feedback mechanisms stabilise degraded turf algal systems at a CO2 seep site.
Communications Biology 4:219.
Harvey, B. P. et al. 2021b. Ocean acidification locks algal communities in a species‐poor early
successional stage. Global Change Biology 27:2174–2187.
Harvey, B. P. et al. 2021c. Predicting responses to marine heatwaves using functional traits. Trends in
Ecology & Evolution. https://doi.org/10.1016/j.tree.2021.09.003
Agostini, S., Harvey, B. P. et al. 2021. Simplification, not “tropicalization”, of temperate marine
ecosystems under ocean warming and acidification. Global Change Biology.
https://doi.org/10.1111/gcb.15749
Cornwall, C. E., Harvey, B. P., et al. (2021). Understanding coralline algal responses to ocean
acidification: Meta-analysis and synthesis. Global Change Biology. https://doi.org/10.1111/gcb.15899

Tetsuo Hashimoto
Molecular Evolution of Microbes
hashi@biol.tsukuba.ac.jp
https://sites.google.com/site/memicrobes/

The central focus of our research is to gain insight into the origin and early
evolution of eukaryotes. This is currently the most important open problem in evolutionary
biology. We are using molecular and cellular biological methods, including comparative‘omics’ analyses and molecular phylogeny, to approach the evolutionarily interesting issues
presented by diverse eukaryotic microorganisms.
One of the goals of our research is to reconstruct a reliable eukaryotic tree. We arecontinuing to perform phylogenomic analyses using high-performance computing to elucidate
the early phase of eukaryotic evolution. By using a refined tree of the organisms of interest,
we compare genomic, transcriptomic, and proteomic data so as to trace the evolutionary
history of the divergence of cellular functions and molecular mechanisms. Our recent focus iselucidation of the reductive evolution of mitochondria in a diverse anaerobic organismalgroup, the Fornicata, all of which contain no typical mitochondria but havemitochondrion-related, reduced organelles.
Giardia intestinalis is a flagellated organism belonging to adiverse anaerobic group, the Fornicata. It is a mammalianparasite that colonizes and reproduces in the small intestine,causing giardiasis. Tiny double membrane–bound organelles
called mitosomes are present in the cell; these are considered
to be reduced mitochondria.
(Photo by N. Yubuki)

Select Publications
1.

2.

3.

Arisue, N., Hashimoto, T., Mitsui, H., Palacpac, N.M.Q., Kaneko, A., Kawai, S.,
Hasegawa, M., Tanabe, K., and Horii, T. (2012). The Plasmodium apicoplast genome:
conserved structure and close relationship of P. ovale to rodent malaria parasites. Mol
Biol Evol, in press.
Takishita, K., Kolisko, M., Komatsuzaki, H., Yabuki, A., Inagaki, Y., Cepicka, I.,
Smejkalová, P., Silberman, J.D., Hashimoto, T., Roger, A.J., and Simpson, A.G.B. (2012).
Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest
relatives of ‘amitochondriate’ diplomonads and retortamonads. Protist 163, 344-355.
Kamikawa, R., Inagaki, Y., Tokoro, M., Roger, A.J., and Hashimoto, T. (2011). Split
introns in the genome of a divergent eukaryote Giardia intestinalis are excised byspliceosome-mediated trans-splicing. Curr Biol 21, 311-315.

Yoshiki Hayashi
Developmental Genetics
yoshikih@tara.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/researcher/0000003771
Keywords: Tissue stem cells, Germline, Aging, Metabolism,
Extra-Cellular-Matrix-------------------------------------------------------------------------------------------------

Understanding of development & aging of tissue stem cells andprimordial-germ-cells.
The research focus of our group is to understand the development and aging processes oftissue stem cells that is crucial for tissue maintenance. We also intensively study thedevelopmental process of primordial-germ-cells that have unique cellular characteristics
having potential multipotency. Recently we are focusing on the role of cellular metabolism inabove processes. Since cellular metabolism plays important role in regulation of cancer
development and animal’s life span, we hope we could shed the light to those fields from ourbasic life science. Drosophilamelanogaster, our favorite
生殖幹細胞/ Germline stem cell
animal is easy to be used and to
卵産生have the advantage for genetic/ Egg production
experiments and aging analysis,
and we have good techniques for
Aged
Young
gene expression, epigenome,Met
SAM
Met SAMandcellularmetabolism
analysis. We are tackling theabove research aims bycombining our advantages.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Hayashi* et al. (2021). The heparan sulfate proteoglycan molecules, syndevan andperlecan have distinct role in the maintenance of germline stem cell in Drosophilamelanogasiter. Dev. Growth Differ. 63:295-305.
Hayashi* et al (2020). The regulation of Drosophila ovarian stem cell niches by signaling
cross talk. Curr. Opin. Insect Sci. 37:23-29.
Hayashi et al. (2012). Glypicans regulate JAK/ STAT signaling and distribution of
Unpaired morphogen. Development 139:4162-4171. # Evaluated by Faculty of 1000
Hayashi et al. (2009). Drosophila glypicans regulate the germline stem cell niche.
J. Cell Biol. 187:473-480. # Cited in the “Molecular Biology of the Cell”
Hayashi et al. (2004). Nanos suppresses somatic cell fate in Drosophila germline.
Proc. Natl. Acad. Sci. USA 101:10338-10342.
# Cited in the “Gilbert, Developmental Biology”

Yoshihisa Hirakawa
Molecular Biology and Evolution
hirakawa.yoshi.fp@u.tsukuba.ac.jp
https://yhirakawa.weebly.com/research.html
Keywords: endosymbiosis, microalgae, organelle, plastid, pyrenoid------------------------------------------------------------------------------------------------Photosynthetic organelles, plastids (chloroplasts), were evolved through endosymbioses. In thelong history, endosymbiotic events have occurred many times between a photosyntheticorganism and a phagotrophic eukaryote host. In mylab, we use the marine unicellular algae“chlorarachniophytes” that obtained their complex
plastids by the uptake of green algae.
We are currently investigating about plastid
targeting proteins, plastid division machinery, andplastid carbon concentration mechanism inchlorarachniophytes. My major research interest is
to understand the diversity and evolution of plastid
functions.
Current research topics: “Study on the pyrenoid construction in algal plastids”, “Study on thealgal plastid division mechanism”, “Study on the development of genetic transformation
system”.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Hirakawa Y. Senda M., Fukuda K., Yu H. Y., Ishida M., Taira M., Kinbara K., Senda T.
(2021) Characterization of a novel type of carbonic anhydrase thta acts without metal
cofactors. BMC Biology 19: 105
Fukuda K., Cooney E.C., Irwin N.A.T., Keeling P.J., Hirakawa Y. (2020) High-efficiency
transformation of the chlorarachniophyte Amorphochlora amoebiformis byelectroporation. Algal Research 48:101903
Hirakawa Y. (2017) Secondary endosymbioses. Advance in Botanical Research volume
84, Academic press.
Hirakawa Y., Ishida K. (2015) Prospective function of FtsZ proteins in the secondary
plastid of chlorarachniophyte algae. BMC Plant Biology 15: 276
Hirakawa Y., Burki F., Keeling P.J. (2012). Dual targeting of aminoacyl-tRNA synthetases
to the mitochondrion and plastid in chlorarachniophytes. Journal of Cell Science 125:6176-6184

Mitsuru Hirota
Terrestrial Ecosystem Ecology
hirota@biol.tsukuba.ac.jp
http://kankyo.envr.tsukuba.ac.jp/~terraeco/

We are seeking to improve process-based understanding of carbon dynamics interrestrial ecosystems by investigating carbon fluxes and pools. By demonstrating suchparameters and their relationships with various environmental factors, we will be able not
only to estimate carbon sink capacity with high accuracy, but also to demonstrate the featuresof individual ecosystems. Current projects include
 Responses of alpine grassland carbon dynamics to recent environmental changes
 Relationship between biodiversity and ecosystem functioning in a highly diverse Tibetan
grassland ecosystem
 Island ecosystem restoration focused on decomposition processes after the 2000 eruption
on Miyake Island, Japan Reevaluation of the carbon sink capacity of old-growth forest ecosystems.

Select publications
1.

2.

3.

4.

5.

6.

Hirota M., Zhang P., Gu S., Shen H., Kuriyama T., Li Y., and Tang, Y. (2010).
Small-scale variation in ecosystem CO2 flux in an alpine meadow depends on plantbiomass and species richness. Journal of Plant Research 123, 531-541.
Hirota M., Zhang P., Gu S., Du M., Shimono A., Shen H., Li Y., and Tang. Y. (2009).
Altitudinal variation of ecosystem CO2 fluxes in an alpine grassland from 3600 to 4200
m. Journal Plant Ecology 2, 197-205.
Hirota, M., Senga, Y., Seike, Y., Nohara, S., and Kunii, H. (2007). Fluxes of carbon
dioxide, methane and nitrous oxide in two contrastive fringing zones of coastal lagoon,
Lake Nakaumi, Japan. Chemosphere 68, 597-603.
Hirota, M., Tang, Y., Hu, Q., Kato, T., Hirata, S., Mo, W., Cao, G., and Mariko, S. (2006).
Carbon dioxide dynamics and controls in a deep-water wetland on the Qinghai-Tibetan
Plateau. Ecosystems 9, 673-688.
Hirota, M., Tang, Y., Hu, Q., Kato, T., Hirata, S., Mo, W., Cao, G., and Mariko, S. (2005).
The potential importance of grazing to the fluxes of carbon dioxide and methane in an
alpine wetland on the Qinghai-Tibetan Plateau. Atmospheric Environment 39,
5255-5259.
Hirota, M., Tang, Y., Hu, Q., Hirata, S., Kato, T., Mo, W., Cao, G., and Mariko, S. (2004).
Methane emissions from different vegetation zones in a Qinghai-Tibetan Plateau wetland.
Soil Biology and Biochemistry 36, 737-748.

Masanao Honda
Taxonomy, Phylogeny and Conservation Biology
honda.masanao.ge@u.tsukuba.ac.jp
https://www.biol.tsukuba.ac.jp/~hwada/index.html
Keywords: reptiles, amphibians, birds, alien species, Ryukyu Archipelago------------------------------------------------------------------------------------------------Our researches focus on molecular phylogenetics and conservation genetics of reptiles. As to
researches on the Kuroiwa’s ground gecko distributed in the Central Ryukyus, we found thenorthern and southern populations of Okinawa Island, which were classified as the same
subspecies, were genetically highly differentiated than the recognized subspecies. This points
out that the current classification and conservation
based on morphology underestimates the true
diversity of species. Each population should berecognized as a unit to be conserved. Other interests
include amphibians and birds. In the study ofAnderson’s crocodile newt in the Central Ryukyus, wefound populations in the southern part of Okinawa
Island lacked genetic diversity and were more
vulnerable to environmental changes than would be
expected from their population size.

------------------------------------------------------------------------------------------------Selected publications
1.

2.

3.
4.

5.

Igawa, T., Sugawara, H., Honda, M., Tominaga, A., Oumi, S., Katsuren, S., Ota, H., Matsui,
M. and Sumida, M. （2019）. Detecting inter- and intra-island genetic diversity: population
structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus.
Conservation Genetics 21: 13-26.
Honda, M. and Ota, H. (2017). On the live coloration and partial mitochondrial DNA
sequences in the topotypic population of Goniurosaurus kuroiwae orientalis (Squamata:
Eublepharidae), with description of a new subspecies from Tokashikijima Island, Ryukyu
Archipelago, Japan. Asian Herpetological Research 8: 96-107.
Karasawa, S., Nagata S., Aoki J., Yahata K. and Honda, M. (2015). Phylogeographic studyof whip scorpions (Chelicerata: Arachnida: Thelyphonida) in Japan and Taiwan.
Zoological Science 32: 352-363.
Honda, M., Kurita, T., Toda, M. and Ota, H. (2014). Phylogenetic relationships, genetic
divergence, historical biogeography and conservation of an endangered gecko,
Goniurosaurus kuroiwae (Squamata: Eublepharidae), from the Central Ryukyus, Japan.
Zoological Science 31: 309-320.
Honda, M., Matsui, M., Tominaga, A., Ota, H. and Tanaka, S. (2012). Phylogeny andbiogeography of the Anderson’s crocodile newt, Echinotriton andersoni (Amphibia:
Caudata), as revealed by mitochondrial DNA sequences. Molecular Phylogenetics andEvolution 65: 642-653.

Horie Takeo
Neural Circuit Development and Functionin Ascidian Larvae
horie@shimoda.tsukuba.ac.jp
https://cionaneuron.wixsite.com/labhomepage-english
Keywords: ascidian, neural circuit, single cell transcriptomics. optogenetics------------------------------------------------------------------------------------------------Animal behavior results fundamentally from the coordinated activity of neural circuits. Ourlaboratory is studying the relationships among neurons, neural circuits, and behavior in ascidian
larvae. These larvae have a very simple central nervous system (CNS) consisting of only about
100 neurons. Despite its simplicity, the CNS of ascidian larvae shares several properties withthose of vertebrates. The small number of neurons in these larvae enables us to describe neuralcircuits at the single-cell level. Our ability to manipulate the activity of individual neurons
makes it possible to elucidate how neural circuits function. We are using a combination of
optogenetics, in vivo Ca2+ imaging, proteomics, and behavioral genetics in the ascidian Ciona
intestinalis to gain an understanding of the operating principles of the neural circuits underlying
animal behavior. Cilia are microtubule-based organelles that extend from basal bodies and formon the apical surfaces of cells. We are also studying the developmental role and physiological
functions of the cilia present in the nervous system of ascidian larvae.
The CNS of the ascidian larva.
Green: neurons Magenta: nuclei------------------------------------------------------------------------------------------------Selected publications

1. Zhao, D+., Chen, S+., Horie, T+., Gao, Y., Bao, H and Liu, X. (2020). Comparison ofdifferentiation gene batteries for migratory mechanosensory neurons across bilaterians.
Evolution & Development 54: 438-450.
2. Horie, T+*., Horie, R+., Chen, K+., Cao C+., Nakagawa, M., Kusakabe, TG., Satoh, N.,
Sasakura, Y* ann Levine, M*. (2018) . Regulatory cocktail for dopaminergic neurons in a
proto-vertebrate identified by whole embryo single cell transcriptomics. Genes &Development 32: 1297-1302.
3. Horie, R., Hazbun, A., Chen, K., Cao, C., Levine, M and Horie, T*. (2018). Sharedevolutionary origin of vertebrate neural crest and cranial placodes. Nature 560: 228-232.
4. Li, Y+., Zhao, D+., Horie, T+., Chen, G+., Bao, H., Chen, S., Liu, W., Horie, R., Liang, T.,
Dong, B., Feng, Q., Tao, Q and Liu, X. (2017). Conserved gene regulatory module specifies
lateral neural borders across bilaterians. Proceedings of the National Academy of Sciencesof the United States of America 114: E6352-6360.
5. Horie, T*., Shinki, R., Ogura, Y., Kusakabe, TG., Satoh, N and Sasakura Y (2011).
Ependymal cells of chordate larvae are stem-like cells that form the adult nervous system.
Nature 469: 525-528.

Tsuyoshi Hosoya
Biodiversity of Fungi
hosoya@kahaku.go.jp
http://www.kahaku.go.jp/research/researcher/researcher.php?d=hosoya
My research is focused on the biodiversity of the order Helotiales, phylum
Ascomycota, Kingdom of Fungi. Fungi is one of the largest group of organisms in the world, estimated toconsisted of more than 1.5 millions of species. Ascomycota is the largest group of fungi, and Helotiales is
one of the most diverse group in Ascomycota. The members of Helotiales produces small saucer tonail-shaped mushroom, called apothecia. The majority of the members of Helotiales were thought to be
weak saprophytes occurring on decaying plant substrates. Recently, however, the majority of plant root
endophytes (fungi that live in plant symbiotically or without showing any symptoms) turned out to be
Helotiales. Helotiales were more versatile than we imagined! Then which species are there? Actually, we
cannot tell which species by names, because the taxonomy of Helotiales is so poor, and we are not sure
how many species exactly are there in Japan, either.
We use molecular barcoding technique andconventional taxonomic technique (morphology
and isolation) to evaluate the biodiversity of
species. Enumeration of all the Helotiales inJapan is one of the goal. Another issue is thecomparisons with previously known European
species.

Ourpredecessors

haveidentified

Japanese species based on European literature.
However, the present knowledge suggests thatJapanese species may be different from that in Europe. We have to critically examine the identity using
molecular technique. Finally, we also use isolates to help understanding the lifecycles.
[Selected Publications]1.

Zhao YJ, Hosaka K, Hosoya T (2016) Taxonomic re-evaluation of the genus Lambertella
Rutstroemiaceae, Helotiales) and allied stroma-forming fungi. Mycological Progress 15:1215-1228.

2.

Hosoya T, Jinbo U, Tanney J (2015) "MolliBase", a new sequence database including unidentified
Mollisia and its allied genera. Ascomycete.org 7:311-314.

3.

Gross A, Hosoya T, Zhao, Y.-J., Baral, H.-O. (2015) Hymenoscyphus linearis sp. nov.: another close
relative of the ash dieback pathogen H. fraxineus. Mycological Progress 14:1-15.

4.

Han JG, Hosoya T, Sung GH, Shin HD (2014) Phylogenetic reassessment of Hyaloscyphaceae sensu
lato (Helotiales, Leotiomycetes) based on multigene analysses. Fungal Biology 118:150-167.

5.

Hosoya T, Hosaka K, Saito Y, Degawa Y, Suzuki R (2013) Naemacyclus culmigenus, a newly reported
potential pathogen to Miscanthus sinensis, new to Japan. Mycoscience 54:433-443.

Kazuo Inaba
Cell Biology of Sperm, Cilia and Flagellakinaba@shimoda.tsukuba.ac.jp
http://www.shimoda.tsukuba.ac.jp/~inaba/index.html
Our research goal is to explore the biological significance of sperm and eukaryotic cilia andflagella by using several marine organisms, including tunicates, sea urchins, sea snails, comb
jellies, spiny lobsters, flounder and marine algae. The main projects in my lab are as follows:
Biology of sperm: Molecular characterization of sperm flagella; molecular mechanism andregulation of flagellar motility; sperm activation and chemotaxis by egg-derived substances;
genomics and proteomics analyses of testis-expressed genes and proteins; ocean acidificationand sperm function; molecular mechanisms of spermatogenesis; the structure and function ofgastropod parasperm; and the molecular diversity of sperm protein.
Biology of cilia and flagella: Structure and function of dynein motors; regulation of flagellar
motility by protein kinases and protein phosphatases; molecular architecture of the axoneme
and comb plate; cDNA and proteomics analysis of axonemal proteins; novel Ca2+-binding
protein and photoreceptor protein; in vitro assembly of the axoneme; phylogenetic analysis ofciliary and flagellar proteins; and eukaryotic evolution and diversity of cilia and flagella.

Select Publications
1. Miyata H et al. (2015). Sperm calcineurin inhibition prevents mouse fertility with implications formale contraceptive. Science 350 442-445.
2. Inaba K. (2015). Calcium sensors of ciliary outer arm dynein: functions and phylogenetic
considerations for eukaryotic evolution. Cilia. 4:6.
3. Mizuno K et al. (2012). Calaxin drives sperm chemotaxis by Ca²⁺-mediated direct modulation of adynein motor. Proc Natl Acad Sci U S A. 109:20497-20502.
4. Inaba K. (2011). Sperm flagella: comparative and phylogenetic perspectives of protein
components. Mol Hum Reprod. 17, 524-538.
5. Konno A et al. (2010). Distribution and structural diversity of cilia in tadpole larvae of the ascidian
Ciona intestinalis. Dev Biol. 337, 42-62.
6. Satouh Y et al. (2005). Molecular characterization of radial spoke subcomplex containing radial
spoke protein 3 and heat shock protein 40 in sperm flagella of the ascidian Ciona intestinalis.
Mol Biol Cell 16, 626-636.
7. Murata Y et al. (2005) Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor.
Nature 435, 1239-1243.

Yuji Inagaki
Molecular Evolution of Microbes
yuji@ccs.tsukuba.ac.jp
https://sites.google.com/site/yujiswebsite/Home
Keywords: eukaryotic phylogeny, genomes, transcriptomes, phylogenomics,
organelles, endosymbiosis------------------------------------------------------------------------------------------------We endeavor to understand the evolutionary
path of eukaryotes by inferring their
phylogenetic relationships and performing
comparative genomic analyses based on
nucleotide and amino acid sequences ofexisting species. We are investigating “novel”
organisms in the natural environment, which
are evolutionarily important but have not yet
been investigated, to search for the key tosolving various problems in eukaryotic
evolution. We are also interested in the origin
and evolution of organelles established throughendosymbioses
andobligate
bacterialendosymbionts in eukaryotes.
Molecular phylogenetic analysis requires statistical processing using the maximum likelihood
method, and computers are used for this purpose. To accurately infer the relationship between
major eukaryotic phylogenetic groups that may have diverged in the distant past, it is necessary
to analyze large amounts of sequence data. We are obtaining transcriptome and genome data
and using supercomputers to handle large-scale sequence data.

Selected publications
1.
2.
3.
4.
5.

Yazaki, E et al. (2020). Barthelonids represent a deep-branching matamonad clade withmitochondrion-related organelles predicted to generate no ATP. Proc Royal Soc B 287:20201538.
Sarai, C et al. (2020). Dinoflagellates with relic endosymbiont nuclei as models for elucidatingorganellogenesis.. Proc Nat Acad Sci USA 117:5364-5375.
Brown, MW et al. (2018). Phylogenomics places orphan protistan lineages in a novel candidate
super-group. Genome Biol Evol 10:427-433.
Leger, MM et al. (2017). Organelles that illuminate the origins of Trichomonas hydrogenosomes
and Giardia mitosomes.. Nat Ecol Evol 1:00092.
Nakayama, T et al. (2014). Complete genome of a nonphotosynthetic cyanobacterium in a diatom
reveals recent adaptations to an intercellular lifestyle. Proc Nat Acad Sci USA 111:11407-11412.

You can find the list of my publications at Google Scholar.
https://scholar.google.ca/citations?hl=en&user=ZjRo4uMAAAAJ&view_op=list_works

Louis J Irving
Plant Ecophysiology
irving.louis.fb@u.tsukuba.ac.jp
https://www.global.tsukuba.ac.jp/bio/irving
Keywords: parasitic plant, nutrient uptake, biomass allocation, growth-------------------------------------------------------------------------------------------------

Parasitic plant ecophysiology
Parasitic plants cause millions of dollars of damage to agriculture annually. However, themechanisms by which this damage is caused are not well understood.
Our group aims to investigate the influence of environmental factors (particularly nutrition) on
the host / parasite relationship, focusing on methods to suppress the negative impacts ofparasitism on the host plant. We use a range of techniques focusing on photosynthesis, isotope
labelling, nutrient measurements, and biomass allocation to understand how the parasite
damages the host, and how the host can resist the parasite.
Plant competition for resources
Plants compete for resources both above andbelowground. Root proliferation in nutrient—rich patches is thought to help them competewith other plants, while aboveground plants
compete for light, mainly by changing leaf
area and thickness. However, the mechanisms
by which plants “decide” whether to invest
resources in new leaves or roots are not clear.
Our goal is to understand how plants makedecisions, and the influence of these decisions
on plant competition.
A maize plant parasitized by P. japonicum------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Irving, LJ. and Mori, S. (2021). Effect of light, N and defoliation on biomass allocation in
Poa annua. Plants 10(9):1783.
Irving, LJ. and Zhang, HX. (2021). Modelling the effect of salt and PEG on water uptake
in wheat seeds. Agronomy 11(8):1660.
Irving, LJ. et al. (2019). Host nutrient supply affects the interaction between thehemiparasite Phtheirospermum japonicum and its host, Medicago sativa. Environmental
and Experimental Botany 162:125-132.
Irving, LJ. et al. (2019). Differential carbon allocation to nitrogen-rich patches in Poaannua precedes root proliferation but has no immediate benefit to N uptake. Journal of
Plant Physiology 234:54-59.
Jokinen, JI. and Irving, LJ. (2019). Effects of light level and nitrogen supply on the red
clover – Orobanche minor host – parasite interaction. Plants 8(6):146.

Ken-ichiro Ishida
Plant Systematics and Evolution
ishida.kenichiro.gm@u.tsukuba.ac.jp
https://www.biol.tsukuba.ac.jp/~ken/
Keywords: algae, protists, endosymbiosis, evolution, algal biomass------------------------------------------------------------------------------------------------Research interest in my lab is to elucidate the diversity and evolution of photosynthetic
protists (algae) and their non-photosynthetic relatives. Following three major subjects are thecurrent focuses in my research.
1. Cellular evolution in the endosymbiotic acquisition of plastids: Plastids were born by aprimary endosymbiosis and transferred to the different eukaryotic lineages by several
secondary endosymbioses. We are interested in how a photosynthetic endosymbiont was
integrated into a host cell as an organelle. This mystery is being uncovered by various
approaches, such as genomics, cell biology, electron microscopy and molecularphylogenetics.
2. Classification and evolution of protists: We lookfor new protist species, especially the ones that canconnect missing links in the tree of life. We collectprotists from the nature, establish clonal cultures,
observe them under light and electron microscopes
and perform molecular phylogenetic analyses. We are
the protist hunters.
3. Search for useful protists for bio-fuel production:
We are studying how to look for oil-producing algae
and protists in the nature and establish cultures ofhigh-performance strains.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Shiratori, T., Yabuki, A. and Ishida, K. (2020). Morphology, ultrastructure and phylogenyof two novel species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp., Thecofilosea
Cercozoa). Protist 171:125731.
Nomura, M., Kamikawa, R. and Ishida, K. (2020). Fine structure observation of feeding
behavior, Nephroselmis spp.-derived chloroplast engulfment and mitotic process in the
katablepharid Hatena arenicola. Protist 171:125714.
Shiratori, T., Suzuki, S., Kakizawa, Y. and Ishida, K. (2019). Phagocytosis-like cell
engulfment by a planctomycete bacterium. Nature Commun. 10:5529.
Thakur, R., Shiratori, T. and Ishida, K. (2019). Taxon-rich multigene ohylogenetic
analyses resolve the phylogenetic relationship among deep-branching Stramenopiles.
Protist 170:125682.
Yabuki, A. and Ishida, K. (2018). An orphan protist Quadricilia rotundata finally finds its
phylogenetic home in Cercozoa. J. Euk. Microbiol. 65:729-732.

Kaori Ishikawa
Mitochondrial Biology
k_ishikawa@biol.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000003578
Keywords: mitochondria, mtDNA (mitochondrial DNA), model mice, diseasephenotype, mitochondrial dynamics------------------------------------------------------------------------------------------------Mitochondria are dynamic organelles which fuse and divide continuously, and they have
evolved with eukaryotic cells, developing a symbiotic relationship and complementing eachother. Understanding "normal" and "abnormal" mitochondrial functions is very important touncover the mechanisms of human diseases.
We are studying the impact of mitochondrial DNA (mtDNA) mutations on cellular or tissue
functions using in vitro and in vivo models.

◀

Mitochondria in human cells are visualized by green
dye. Blue dye indicates nuclei. Mitochondria construct
dynamic networks in cytosols.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.

4.

Ishikawa K, Yamamoto S, Hattori S, Nishimura N, Matsumoto H, Miyakawa T, Nakada
K. (2021). Neuronal degeneration and cognitive impairment can be prevented via thenormalization of mitochondrial dynamics. Pharmacol Res 163:105246.
Ishikawa K, Yamamoto S, Hattori S, Nishimura N, Tani H, Mito T, Matsumoto H,
Miyakawa T, Nakada K. (2019). Acquired Expression of Mutant Mitofusin 2 Causes
Progressive Neurodegeneration and Abnormal Behavior. J Neurosci 39:1588-1604.
Ishikawa K, Toyama-Sorimachi N, Nakada K, Morimoto M, Imanishi H, Yoshizaki M,
Sasawatari S, Niikura M, Takenaga K, Yonekawa H, Hayashi J. (2010). The innate immune
system in host mice targets cells with allogenic mitochondrial DNA. J Exp Med 207:22972305.
Ishikawa K, Takenaga K, Akimoto M, Koshikawa N, Yamaguchi A, Imanishi H, Nakada
K, Honma Y, Hayashi J. (2008). ROS-generating mitochondrial DNA mutations canregulate tumor cell metastasis. Science 320:661-664.

Yuzuru Ito
Stem Cell Engineeringfor Regenerative Medicine
ito yuzuru.fe@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000004473
Keywords: mesenchymal stem cell, iPS cell, process, quality control,
regenerative medicine
Human pluripotent stem cells (ES/iPS cells) and mesenchymal stem cell are expected as
powerful tool for regenerative medicine in the world. However, those cells are likely to lose theuseful ability for cell therapy during preparation (establishment, culture, cryopreservation etc.)
Moreover, method for preparation of some organ cells is insufficient so safe and effective
method of treatment isn’t realized yet.
To establish the facile, economical and safe regenerative medicine, we should develop several
supporting technology for quality control, safety administration and so on. We will promote thedevelopment of technology for supporting regenerative medicine.
Fluoresceinated rBC2LCN directly stains human iPS cellcolonies. This new probe that we developed can detect good
iPS/ES cells accurately, nondestructively and quickly. We
can use this probe as “high-sensitive” and “low-toxic”
technology for human ES/iPS cells to facilitate of quality
control.

------------------------------------------------------------------------------------------------Selected publications

1.
2.
3.

4.
5.

Oyane, A., Araki, H., Nakamura, M., Aiki, Y. and Ito Y. (2021). Storable bFGF-releasing
membrane allowing continuous human iPSC culture. Materials 14:651.
Haramoto, Y., Onuma, Y., Mawaribuchi, S., Nakajima, Y., Aiki, Y., Higuchi, K., Shimizu,
M., Tateno, H., Hirabayashi, J. and Ito, Y. (2020). A technique for removing tumourigenic
pluripotent stem cells using rBC2LCN lectin. Regen. Ther. 14:306-314.
Oyane, A., Araki, H., Nakamura, M., Aiki, Y., Higuchi, K., Pyatenko, A., Adachi, M. and
Ito Y. (2020). Controlled release of basic fibroblast growth factor from a water-floatablepolyethylene nonwoven fabric sheet for maintenance culture of iPSCs. Rsc Advances
10:95-104.
Mawaribuchi, S., Aiki, Y., Ikeda, N. and Ito, Y. (2019). mRNA and miRNA expression
profiles in an ectoderm-biased substate of human pluripotent stem cells. Sci. Rep.
9(1):11910.
Mawaribuchi, S., Onuma, Y., Aiki, Y., Kuriyama, Y., Mutoh, M., Fujii, G. and Ito, Y.
(2019). The rBC2LCN-positive subpopulation of PC-3 cells exhibits cancer stem-like
properties. BBRC 515(1):176-182.

Hiroaki Iwai
Plant Cell Wall Biology
iwai.hiroaki.gb@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000001213
Keywords: Cell wall, Pectin, Fruit ripening, Seed germination, Salinity
response, Heavy metal response------------------------------------------------------------------------------------------------We are interested in understanding plants development and environmental responses.
We focus on the cell wall because it is themost characteristic feature of vascularplants. The cell wall plays multiple roles,
including determining cell shape and size,
cell-cell adhesion, controlling celldifferentiation and growth, and promoting
abiotic and biotic stress tolerance. We are
studying the function of the cell wall
matrix and its regulation in plant growthand environmental responses.

Selected publications
1.

2.
3.

4.
5.
6.

Hasegawa K, Kamada S, Takehara S, Takeuchi H, Nakamura A, Satoh S, Iwai H. (2021).
Rice Putative Pectin Methyltransferase Gene OsPMT10 is Required for Maintaining the
Cell Wall Properties of Pistil Transmitting Tissues via Pectin Modification. Plant Cell
Physiol (in press)
Iwai H. (2021). Cell Wall Functions in Plant Growth and Environmental Responses. J
Plant Res. 134(6):1155-1158
Ohara T, Takeuchi H, Sato J, Nakamura A, Ichikawa H, Yokoyama R, Nishitani K, Minami
E, Satoh S, Iwai H. (2021). Structural Alternation of Rice Pectin Affects Cell Wall
Mechanical Strength and Pathogenicity for the Rice Blast Fungus under Weak Light
Conditions. Plant Cell Physiol. 62: 641-649
Takebe N, Nakamura A, Watanabe T, Miyashita A, Satoh S, Iwai H. (2020). Cell wall
Glycine-rich Protein2 is involved in tapetal differentiation and pollen maturation. J Plant
Res. 133(6):883-895.
Hasegawa K, Kamada S, Takehara S, Takeuchi H, Nakamura A, Satoh S, Iwai H. (2020).
Rice Putative Methyltransferase Gene OsPMT16 Is Required for Pistil Development
Involving Pectin Modification. Front Plant Sci. 11:475
Nagayama T., Nakamura A., Yamaji N., Satoh S., Furukawa J., Iwai H. (2019). Changes
in the Distribution of Pectin in Root Border Cells Under Aluminum Stress. Frontiers in
Plant Science, 10: 1216

Akira Kikuchi
Stress Physiology in Higher Plants
kikuike@gene.tsukuba.ac.jp
http://www.gene.tsukuba.ac.jp/Plant/GeneticDiversity/
Keywords: abiotic stresses, somatic embryo, carrot, potato------------------------------------------------------------------------------------------------

Stress tolerance in higher plants is an interesting phenomenon. Plants are immobile and must
evolve defense systems that are uniquely suited to their ambient environmental stresses.
Several genes associated with these defense systems have been identified. Our aim here is togenerate genetic lines conferring abiotic stress tolerance and to verify their performance. We
are also studying the impacts of transgenic plants on biological diversity so as to establish anenvironmental biosafety risk-assessment system for transgenic plants. In addition, we aretrying to elucidate the mechanisms of abiotic stress tolerance in higher plants by using GM(genetically modified) techniques, and we are studying the induction of somatic
embryogenesis by abiotic stress. In this way, while elucidating the mechanism of abiotic
stress in higher plants, we are also working on the development of abiotic stress–tolerant GM
plants that can be used for crop production.
Somatic embryogenesis induced in carrots by abiotic
stressIn carrots, somatic embryo production can be induced
from apical tip segments by application and removal ofstress treatment. The somatic cells are converted toembryogenic cells by the stress treatment. After removalof the stress, the embryogenic cell begins to develop
into a somatic embryo.

-----------------------------------------------------------------------------------------------Select Publications
1.
2.
3.
4.
5.

Shimazaki T., Endo T., Kazsuga M., Yamaguchi-Shinozaki K., Watanabe K., Kikuchi A.
(2016) Evaluation of the yield of abiotic-stress-tolerant AtDREB1A transgenic potato
under saline conditions in advance of field traials. Breeding science. 66:703-710.
Kikuchi A., Huynh D., Endo T., Watanabe K. (2015) Review of recent transgenic studies
on abiotic stress tolerance and future molecular breeding in potato. Breeding science.
65:85-102.
Kikuchi A., Asahina M., Tanaka M., Satoh S., Kamada H. (2013) Acquisition ofembryogenic competency does not require cell division in carrot somatic cell. J Plant
Res, 126:243-250.
Shibukawa T., Yazawa K., Kikuchi A., Kamada H. (2009) Possible involvement of DNA
methylation on expression regulation of Carrot LEC1 gene in its 5'-upstream region.
Gene 437, 22-31.
Tanaka M., Kikuchi A., Kamada H. (2008) The Arabidopsis histone deacetylases HDA6
and HDA19 contribute to the repression of embryonic properties after germination. Plant
Physiol 146, 149-161.

Satoru Kobayashi
Molecular Mechanisms Regulating
Germline Development
skob@tara.tsukuba.ac.jp

Germ cells are specialized cells that can transmit genetic
materials from one generation to the next through sexual reproduction.
All other cells of the body are somatic cells. This separation of germand somatic cells is one of the oldest problems in developmental
biology. In many animal groups, a specialized portion of egg
cytoplasm, or germ plasm, is inherited by the cell lineage which gives
rise to germ cells. This cell lineage is called germline. The germline
progenitors eventually migrate into the gonads, where theydifferentiate as germline stem cells (GSC) to form eggs and sperm
when the organisms are physically matured. Our laboratory aims tofind the molecular mechanisms regulating germline segregation,
germline sex determination, and GSC niche function in Drosophila.

Publications
1. Ohhara, Y., Shimada-Niwa, Y., Niwa, R., Kayashima, Y., Hayashi, Y., Akagi, K., Ueda, H.,
Yamakawa-Kobayashi, K. and Kobayashi, S. (2015) Autocrine regulation of ecdysone
synthesis by 3-octopamine receptor in the prothoracic gland is essential for Drosophila
metamorphosis. Proc. Natl. Acad. Sci., USA., 112, 1452-1457.
2. Hashiyama, K., Hayashi, Y. and Kobayashi, S. (2011). Drosophila Sex lethal gene initiates
female development in germline progenitors. Science 333, 885-888.
3. Kitadate, Y. and Kobayashi, S. (2010). Notch and Egfr signaling act antagonistically toregulate germline stem cell niche formation in Drosophila male embryonic gonads. Proc.
Natl. Acad. Sci. USA 107, 14241-14246.
4. Kitadate, Y., Shigenobu, S., Arita, K. and Kobayashi, S. (2007). Boss/Sev signaling from
germline to soma restricts germlinestem-cell-niche formation in the anterior region of
Drosophila male gonad. Dev. Cell 13, 151-159.
5. Hayashi, Y., Hayashi, M. and Kobayashi, S. (2004). Nanos suppresses somatic cell fate in
Drosophila germline. Proc. Natl. Acad. Sci. USA. 101, 10338-10342.
6. Asaoka-Taguchi, M., Yamada, M., Nakamura, A., Hanyu, K. and Kobayashi, S. (1999)
Maternal Pumilio acts together with Nanos in germline development in Drosophila
embryos. Nature Cell Biol. 1, 431-437.
7. Kobayashi, S., Yamada, M., Asaoka, M., and Kitamura, T. (1996). Essential role of theposterior morphogen nanos for germline development in Drosophila. Nature 380, 708-711.

Hidekazu Kuwayama
Molecular Mechanisms and Dynamics ofBiological Self-organization
Kuwayama.hidekazu.fu@u.tsukuba.ac.jp

https://trios.tsukuba.ac.jp/en/researcher/0000001199
Self-reproduction or Self-organization is a characteristic observed in all biologicalorganisms. In my Lab, we research self-organization using a cellular slime mold,
Dictyostelium discoideum, as a model system, by a combination of experimental andtheoretical methods. Our aim is to clarify the molecular systems that regulate cell orientationand to simulate its dynamics.
Dictyostelium discoideum is a solitary amoeboid microorganism that grows as asingle cell, but during starvation it initiates chemotaxis towards a cAMP signal secreted byneighboring cells and constructs a multicellular “slug”. This feature is simple but very usefulfor investigating how cells interact to construct multi-cellular organisms. At present, we arefocusing on biological soliton phenomenon which was firstly discovered in my Lab, andchemotaxis which involves questions about how cells recognize their environment using
molecular techniques. We are also interested in disease-causing genes related tobiological self-organization.
Biological soliton phenomena in multi-cellular
movement observed in Dictyostelium mutant.

Selected Publications
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.

Kuwayama, H. (2021) Peptide nucleic acid as a template for Taq DNA polymerase. Biochemical andbiophysical research communications, 579, 76-80
Kuwayama, H, Higashinakagawa, T. (2019) The Life Cycle of Dictyostelium discoideum Is
Accelerated via MAP Kinase Cascade by a Culture Extract Produced by a Synthetic Microbial
Consortium. Jounal of Molecular Biology and Biotechnology, 29, 35-42
Kida, Y., Pan, K. and Kuwayama, H. (2019) Some chemotactic mutants can be progress throughdevelopment in chimeric populations.
Differentiation., 105, 71-79.
Kuwayama, H., Kikuchi, H., Oshima, Y. and Kubohara, Y. (2016) Glutathione S-transferase 4 is aputative DIF-binding protein that regulates the size of fruiting bodies in Dictyostelium discoideum.
Bioch., and Biophy., Reports, 8, 219-226.
Kuwayama, H. and Kubohara, Y. (2016) Differentiation-inducing factor 2 modulates chemotaxis via
the histidine kinase DhkC-dependent pathway in Dictyostelium discoideum. FEBS Lett. 590,760-768.
Kuwayama, H. et al. (2014) Cross-species functional complementation of cellulose synthase during
the development of cellular slime molds. Dev. Growth and Diff., 56, 526–533.
Kuwayama, H. et al. (2013) A RabGAP Regulates Life-Cycle Duration via Trimeric G-protein
Cascades in Dictyostelium discoideum. PLoS One 8, e81811.
Kuwayama, H. and Ishida, S. (2013) Biological soliton in multicellular movement. Scientific Reports,
3, Article number: 2272.
Kuwayama, H. (2012). Arachidonic Acid Enhances Caffeine-Induced Cell Death via
Caspase-Independent Cell Death. Scientfic Reports 2, Article number: 577.
Kuwayama, H., Kikuchi, H., Oshima, Y. and Kubohara, Y. (2011). Artificial compounds differentiallycontrol Dictyostelium chemotaxis and cell differentiation. Cell Struct Funct 36, 21-26.

Fumiaki Maruo
Developmental Biology of Stem Cells
maru@biol.tsukuba.ac.jp
http://www.biol.tsukuba.ac.jp/~maru/
http://imori-net.org/

Stem cells and regeneration are currently hot research subjects in the life sciences
and provide many possibilities for future treatments for major diseases, including organ
damage and degenerative conditions. We are studying the mechanisms regulating stem cellmaintenance, proliferation, and differentiation. Our experimental system uses the germline
stem cells in Drosophila oogenesis. We also use neuronal stem cells in the regenerating newt
retina and undifferentiated germline cells in developing newt gonads. Our approaches involve
genetic, immunological, and molecular biological techniques.
Keywords on our research are “cell differentiation”, “regeneration”, “Drosophila”,“newt”, “germ cell”, and “stem cell”.

Steps in developmental potency (left), and a model mechanism of stem cell maintenance (right).

Select Publications
1.

2.

Chiba, C., Hoshino, A., Nakamura, K., Susaki, K., Yamano, Y., Kaneko, Y., Kuwata, O.,
Maruo, F., and Saito, T. (2006). Visual cycle protein RPE65 persists in new retinal cells
during retinal regeneration of adult newt. The Journal of Comparative Neurology 495,
391-407.
Maruo, F. (1996). Developmental genetics of oogenesis. In Developmental Genetics (ed.
Okada, M.), pp. 35-68. SHOKABO, Tokyo. (in Japanese)Hisanori Matsui
Translational Science in Drug Discovery
hisanori.matsui@takeda.com
https://www.takeda.com
Keywords: Drug Discovery, Translational, Open Science-------------------------------------------------------------------------------------------------

Functional analysis of orphan GPCR was my first research area as a biologist in drug discovery
research. Kisspeptin was one of the most impactful research topics for me, starting from thediscovery of its physiological functions in relation to reproductive neuroendocrinology and its
therapeutic application for prostate cancer. Through this program I gained experience andknowledge ranging from the drug target discovery to drug development as clinical studies. I
then changed my research field from oncology to drug repurposing, expanded my researchtherapeutic areas and strengthened translational science. I am now leading External
Neuroscience Research to deliver breakthrough medicine through innovative partnership. My
experience of therapeutic area includes oncology, reproductive neuroendocrinology,
inflammation, and neuroscience.
Drug discovery and development is a teamwork-oriented process where very diverse multifunctional professionals are working together. In addition, drug discovery and development
cannot be achieved without external professional partners as well. I really like thismultidisciplinary research approach because we can overcome hurdle after hurdle to eventuallyachieve our goals. Let's work together to make innovation happen.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.

4.

5.

6.

Kimura M., Ishii N.M., Seki N., Sakai Y., Yamashita T., Awatsuji H., Kanda K., Matsumoto K., andMatsui, H. (2019). Reduction of Kiss1 expression in the anteroventral periventricular nucleus isassociated with atrazine-induced attenuation of the luteinizing hormone surge in female rats. Biol
Reprod. 100, 41-48.
Muller, S, Ackloo S, Arrowsmith C, Bauser M, Baryza J, et al. (2018). Donated chemical probes foropen science. eLife 7:e34311
Ishikawa K., Tanaka A., Kogame A., Watanabe T., Tagawa Y., and Matsui H. (2018). Usefulness ofpharmacokinetic/efficacy analysis of an investigational kisspeptin analog, TAK-448, in quantitatively
evaluating anti-tumor growth effect in the rat VCaP androgen-sensitive prostate cancer model. Eur. J.
Pharmacol. 828, 126-134.
Tanaka A., Nakata D., Masaki T., Kusaka M., Watanabe T., and Matsui H. (2018). Evaluation ofpharmacokinetics/pharmacodynamics and efficacy of one-month depots of TAK-448 and TAK-683,
investigational kisspeptin analogs, in male rats and an androgen-dependent prostate cancer model.
Eur. J. Pharmacol. 822, 138-146.
MacLean D.B., Matsui H., Suri A., Neuwirth R., and Colombel M. (2014). Sustained exposure to theinvestigational Kisspeptin analog, TAK-448, down-regulates testosterone into the castration range inhealthy males and in patients with prostate cancer: results from two phase 1 studies. J Clin Endocrinol
Metab 99, E1445-1453.
Matsui H., Takatsu Y., Kumano S., Matsumoto H., and Ohtaki T. (2004). Peripheral administration ofmetastin induces marked gonadotropin release and ovulation in the rat. Biochem. Biophys. Res.
Commun. 320, 383-388.

Ayumi Minoda
Plant Molecular Physiology
minoda.ayumi.gb@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/researcher/0000003189
Keywords: photosynthesis, environmental response, carbon metabolism,
metal metabolism, green technology, algae, microorganisms------------------------------------------------------------------------------------------------Regulation of photosynthesis and metabolism under extreme environment
A unicellular red alga, Galdieria sulphuraria is found in nature in acidic hot springs and soils
where other organisms cannot live. In order to survive these environments, they have strong
environmental tolerance to strong acids, high osmotic pressure, and high concentrations ofmetals. In addition, they are the only alga that can grow photoautotrophically under pure CO2.
However, little is known about how they are able to adapt to such extreme environments. To
elucidate the mechanisms, we have found new regulatory mechanisms for photosynthesis andmetal tolerance, and have identified unique factors such as multi-metal tolerance factors.
Green technology for sustainability
Microorganisms
environment

adapt

throughandcreatethebiological

and

non-

biological phenomena. By examining theseG. sulphuraria (right panel)
SEM images(lower panel, from left):
Living cell, Lyophilized cell,Au-adsorbed lyophilized
cell of G. sulphuraria,

phenomena with the latest technology, we are
exploring sustainable green technology.

----------------------------------------------Selected publications
1.
2.
3.
4.
5.

Miyashita S, Ogura T, Fujii S, Inagaki K, Takahashi Y and Minoda A Recovery of Au from dilute aquaregia solutions via adsorption on the lyophilized cells of a unicellular red alga Galdieria sulphuraria:
A mechanism study. 2021 J Hazard Mater in press
Miyashita S, Ogura T, Fujii S, Inagaki K, Takahashi Y and Minoda A Effect of lyophilization on theacid resistance of a unicellular red alga Galdieria sulphuraria during platinum recovery. 2021 J Hazard
Mater Advances
Sakurai T , Aoki M, Ju X, Ueda T, Nakamura Y, Fujiwara S, Umemura T, Tsuzuki, M and Minoda A
Profiling of lipid and glycogen accumulations under different growth conditions in thesulfothermophilic red alga Galdieria sulphuraria. 2016 Bioresource Technol. 200, 861-866.
Minoda A, Weber APM, Tanaka K and Miyagishima SY Nuclear independent control of Rubisco
operon by the plastid-encoded transcription factor Ycf30 in the red alga Cyanidioschyzon merolae 2010
Plant Physiol, 154, 1532-1540.
Minoda A, Sonoike K, Okada K, Sato N and Tsuzuki M. Decrease in the efficiency of the electron
donation to tyrosine Z of photosystem II in an SQDG-deficient mutant of Chlamydomonas. 2003 FEBS
Lett., 553, 109-112

Kenji Miura
Plant Molecular Biology
miura.kenji.ga@u.tsukuba.ac.jp
https://sites.google.com/view/tsukubapmcben
Keywords: transient expression, genome editing, plant abiotic stressresponses, plant biotechnology-------------------------------------------------------------------------------------------------(1) “Tsukuba System” for high amount of protein production system in plants
We established high amount of protein
production system in plants, termed “Tsukuba
System”. The yield of protein production iscompatible to other expression systems, such as
E. coli and yeast. By using this system, we arenow establishing the following application
methodology;
1. High amount of pharmaceutical protein
production in plants for cost effectiveness. The
targets are proteins for regenerative medicine,veterinary medicine, etc.
2. High amount of production of plant secondary metabolites by expression of enzymes.
3. Transient expression of Cas9 and sgRNA in plants to achieve plant genome editing withouttransformation.
(2) Elucidation of molecular mechanisms of abiotic stress signaling and sugar
accumulation
Because sugar accumulation and abiotic stress responses arecorrelated, e.g. cold stress enhances sugar accumulation inplants, we are elucidating molecular mechanism of abiotic
stress signaling and sugar accumulation. We are to identify
interacting factors to control abiotic stress signaling. Several
factors have already isolated, thus, we are checking
functional role of these factors.
For sugar accumulation, we
have already isolated high sugar tomato mutant (Brix: 12-15). The
level of Brix is similar to that of grape. We are now identifying
the mutation in this mutant and characterizing functional role ofthis mutation.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.

Nosaki, S. et al. (2021). Prevention of necrosis caused by transient expression in Nicotiana
benthamiana by application of ascorbic acid. Plant Physiology 186: 832-835.
Miura, K. et al. (2020). The PHD finger of Arabidopsis SIZ1 recognizes trimethylated
histone H3K4 mediating SIZ1 function and abiotic stress response. Commun. Biol. 3: 23.
Shimatani, Z. et al. (2017). Targeted base editing in rice and tomato using CRISPR-Cas9
cytidine deaminase fusion. Nature Biotechnology 35: 441-443.

Shinichi Miyamura
Cell Biology of Sexual Dimorphism inGreen Plants
miyamura.shinichi.fw@u.tsukuba.ac.jp

My lab is working on two projects: 1) the cellular and molecular mechanisms ofsexual dimorphism of gametes in isogamous, anisogamous, and oogamous green algae; and 2)
sexual reproduction in green algae, mosses, ferns, and gymnosperms. Marine green algae
belonging to the Ulvophyceae, as well as the unicellular green alga Chlamydomonas and land
plant sperm, are used mainly as our experimental systems.
Sexual dimorphism of green algal gametes
We have been focusing on asymmetric placement of the mating structure(cell-fusion apparatus) in gametes as a feature of sexual dimorphism ingreen algae. The gamete of green algae belonging to the Chlorophyta has
two flagella elongated from the cell apex and a mating structure that is a
specialized plasma membrane near the flagellar apparatus. The spatial
position of the mating structure differs between the sexes. In the malegamete, the mating structure is located on the opposite side to the eyespot(E), whereas it is located on the same side as the eyespot in the female
gamete. As a result of this difference, the two eyespots align on the sameside of the planozygote after fertilization. Our lab is trying to elucidate thecellular and molecular mechanisms of mating structure development andplacement in green algal gametes. We also aim to elucidate themachanisms of gamete-type differentiation according to mating-type
locus by using Chlamydomonas and ulvophycean green algae.

Select Publications
1.
2.

3.

4.

5.

Miyamura, S. (2010). Cytoplasmic inheritance in green algae: patterns, mechanisms andrelation to sex type. J Plant Res 123, 171-184.
Miyamura, S., Sakaushi, S., Hori, T., and Nagumo, T. (2010). Behavior of flagella andflagellar root systems in the planozygotes and settled zygotes of the green alga Bryopsis
maxima Okamura (Ulvophyceae, Chlorophyta) with reference to spatial arrangement ofeyespot and cell fusion site. Phycol Res 58, 258-269.
Miyamura, S., Mogi, Y., Mitsuhashi, F., Kawano, S., and Nagumo, T. (2009). Visualizing
the spatial arrangement of flagella-eyespot-cell fusion sites in gametes and planozygotes
of Chlamydomonas reinhardtii (Chlorophyceae, Chlorophyta) with high-resolution
FE-SEM. Cytologia 74, 409-415.
Mogi, Y., Kagami, Y., Kuwano, K., Miyamura, S., Nagumo, T., and Kawano, S. (2008).
Asymmetry of eyespot and mating structure positiobs in Ulva compressa (Ulvales,
Chlorophyta) revealed by a new field emission scanning electron microscopy method. J
Phycol 44, 1290-1299.
Miyamura, S. (2007). Inheritance pattern of chloroplast DNA is correlated with gamete
types based on sex-specific arrangement of the cell fusion site in Caulerpa(Ullvophyceae, Chlorophyta). Phycol Res 55, 47-57.

Yoshiaki Morino
Evolution and Development
morino.yoshiaki.ge@u.tsukuba.ac.jp
https://sites.google.com/view/wada-lab-univ-tsukuba/home
Keywords: spiralian, EvoDevo, transcriptome, transcription factor, NGS------------------------------------------------------------------------------------------------Ourresearch

focuses

on

the

early

development of marine invertebrates, particularly
spiralian (higher taxa including molluscs, andannelids and platyhelminthes), to reveal how
animal development evolves. In order to get abetter picture of the evolution of development,
information from non-model animal is important. We use bidirectional approachesof bioinformatics and experimental embryology to extract as much evolutionary
information as possible from non-model animals.
Examples of current research projects: "Role of lineage-specifictranscription factors in spiralian development", "Search for genes controllingspiralian development", "Developmental system drift in spiralian development".

------------------------------------------------------------------------------------------------Selected publications *corresponding author
1.

2.
3.
4.

5.

*Supanat Phuangphong, Jumpei Tsunoda, Hiroshi Wada, *Yoshiaki Morino (2021)"Duplication of spiralian-specific TALE genes and evolution of the blastomere
specification mechanism in the bivalve lineage" EvoDevo 12:1, 1-16
*Yoshiaki Morino, Naoki Hashimoto, Hiroshi Wada (2017) “Expansion of TALE
homeobox genes and the evolution of spiralian development” Nature Ecology and
Evolution 1, 1942–1949
Yoshiaki Morino, Hiroyuki Koga, Hiroshi Wada. (2016) “The conserved genetic
background for pluteus arm development in brittle stars and sea urchin” Evolution &Development 18, 2, 89-95.
Yoshiaki Morino, Kazunori Okada, Miyuki Niikura, Masanao Honda, Nori Satoh,*Hiroshi Wada (2013) “A genome-wide survey of genes encoding transcription factors in
the Japanese pearl oyster, Pinctada fucata: I. Homeobox Genes” Zoological Science 30,
851-857.
*Yoshiaki Morino1, Hiroyuki Koga1, Kazunori Tachibana, Eiichi Shoguchi, Masato
Kiyomoto, Hiroshi Wada (2012) “Heterochronic activation of VEGF signaling and theevolution of the skeleton in echinoderm pluteus larvae” Evolution & Development 14, 5,
1428-436.
:Equal Contribution

Kisaburo Nagamune
How to Become a Parasite andSurvive as One
nagamune@nih.go.jp
http://www.kisanagamune.com
Apicomplexan parasites, including Toxoplasma gondii and malarial parasites, havean organelle called the apicoplast, which a kind of plastid and developed from a secondary
symbiont of the ancestor of red algae. Apicomplexan parasites have lost their photosynthetic
activity because they gained a new, parasitic ability during evolution. However, they still
possess the apicoplast, which is essential for their survival. The biology of T. gondii andmalarial parasites is therefore similar in some ways to that of plant systems because they still
have a plant inside the cell. We are investigating the plant-like nature of apicomplexanparasites as a target for the development of anti-parasitic drugs. We are also focusing on theparasitic ability that replaced their photosynthetic ability, and studying how they highjack
host functions for their survival.

Toxoplasma gondii produces plant
hormones and regulates the
progression of the cell cycle anddivision of plastids. It also secretes
rhoptry proteins and highjacks gene
expression and organelles in the hostcell. Through this highjacking, T.
gondii can escape the host immune
response and take up essential
molecules.

Select Publications
1.

2.
3.
4.
5.

Toyama, T. et al. (2011). Gibberellin Biosynthetic Inhibitors Make Human Malaria
Parasite Plasmodium falciparum Cells Swell and Rupture to Death. PLoS ONE 7,
e32246.
Nakatani, F. et al. (2011). Identification of a second catalytically active trans-sialidase in
Trypanosoma brucei. Biochem Biophysic Res Comm 415, 421-425.
Yamamoto, M. et al. (2011). ATF6β is a host cellular target of the Toxoplasma virulence
factor ROP18. J Exp Med 208, 1533-1546.
Hirakawa, Y. et al. (2009). Protein targeting into secondary plastids ofchlorarachniophytes. PNAS 106, 12820-12825.
Nagamune, K. et al. (2008). Abscisic acid controls calcium-dependent egress anddevelopment in Toxoplasma gondii. Nature 451, 207-210.

Kazuto Nakada

Mitochondrial Biology and Medicine

knakada@biol.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/1193
Keywords: mitochondrial DNA, mitochondria-based diseases, model mice-------------------------------------------------------------------------------------------------

・ Studies on biological and medical significance of mitochondrial fission, fusion, and quality
control・ Studies on inheritance and gene expression of mitochondrial genome
・ Generation of model mice for mitochondria-related diseases
・ Studies on pathogeneses of mitochondria-related diseases using model cells and mice・ Studies on mitochondrial diabetes mellitus
・ Studies on the mitochondrial theory of aging
・ Therapeutic strategies for mitochondria-related diseases------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.
6.
7.
8.
9.

Ishikawa K et al. Neuronal degeneration and cognitive impairment can be prevented via
normalization of mitochondrial dynamics. Pharmacol Res, 63: 105246.(2021).
Ogasawara E et al. Distal control of mitochondrial biogenesis and respiratory activity by
extracellular lactate caused by large-scale deletion of mitochondrial DNA. Pharmacol
Res, 160: 05204 (2020).
Ishikawa K et al. Acquired Expression of Mutant Mitofusin 2 Causes Progressive
Neurodegeneration and Abnormal Behavior. J Neurosci, 39: 1588-1604 (2019).
Ishihara T et al. Dynamics of mtDNA nucleoids regulated by mitochondrial fission isessential for maintenance of homogeneously active mitochondria during neonatal heartdevelopment. Mol Cell Biol, 35: 211–223 (2015).
Shimizu A et al. Transmitochondrial mice as models for primary prevention of diseases
caused by mutation in the tRNALys gene. PNAS, 111: 3104-3109 (2014).
Hashizume O et al. A specific mitochondrial DNA mutation in mice regulates diabetes andlymphoma development. PNAS, 109: 10528-10533 (2012).
Ishikawa K et al. ROS-generating mitochondrial DNA mutations can regulate tumor cell
metastasis. Science, 320: 661-664 (2008).
Nakada K et al. Mitochondria-related male infertility. PNAS, 103, 15148-15153 (2006).
Nakada K et al. Inter-mitochondrial complementation: mitochondria-specific systempreventing mice from expression of disease phenotypes by mutant mtDNA. Nature Med,
7: 934-939 (2001).

Kouji Nakamura
It’s a Small RNA World
nakamura.kouji@biol.tsukuba.ac.jp

Until recently, gene expression was thought to be controlled mainly at the level oftranscription initiation by repressor or activator proteins. It has now been revealed that othermechanisms can regulate gene expression and involve RNAs that might act as antisense
RNAs, sequestering molecules, or thermosensors. Bacterial pathogens sense theirenvironments, and in response, virulence genes are induced or repressed through spatial andtemporal regulation. These pathogens are also subjected to stress conditions, which requireappropriate responses. Recent research has revealed that RNAs are key regulators inpathogens. Small RNAs regulate the translation or stability of mRNAs that encode virulenceproteins, namely proteins that are triggered by environmental cues and stresses. In most cases,
these small RNAs act directly on target RNAs by an antisense mechanism.
Molecular recognition of RNA by distal site of
Hfq. (A) Left panel: surface representation ofhexameric BsHfq (gray) with stick representationof A (cyan) and G (magenta) residues of AGr.
Right panel: surface representation of hexameric
EcHfq (gray) with stick representation of poly(A)(cyan). Subunit boundaries are indicated bydashed lines. (B) Stereo view of BsHfq–AGr andEcHfq–poly(A) (left and right panel, respectively).
R is a purine nucleotide and N is any nucleotide[6).

Select Publications
1.

2.

3.

4.

5.

6.

Someya, T., Baba, S., Fujimoto, M., Kawai, G., Kumasaka, T., and Nakamura, K. (2012).
Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA
aptamer: insight into RNA-binding properties of bacterial Hfq. Nucleic Acids Research40, 1856-1867.
Kakeshita, H., Kageyama, Y., Endo, K., Tohata, M., Ara, K., Ozaki, K., and Nakamura,K.
(2011b). Secretion of biologically-active interferon- by Bacillus subtilis. Biotechnology
letters 33, 1847-1852.
Obana, N., and Nakamura, K. (2011a). A novel regulator, the CPE1446-1447 protein
heterodimeric complex, controls toxin genes in Clostridium perfringens. J. Bacteriology
193, 4417-4424.
Obana, N., Shirahama, Y., Abe, K., and Nakamura, K. (2010b). Stabilization of
Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5’
leader sequence. Molecular Microbiology 77, 1416-1428.
Abe, K., Obana, N., and Nakamura, K. (2010a). Effects of depletion of RNA-binding
protein Tex on the expression of toxin genes in Clostridium perfringens. Bioscience,
Biotechnology and Biochemistry 74, 1564-1571.
Saito, S., Kakeshita, H., and Nakamura, K. (2009). Novel small RNA-encoding genes in
the intergenenic regions of Bacillus subtilis. Gene 428, 2-8.

Hiroaki Nakano
Evolutionary Zoology
h.nakano@shimoda.tsukuba.ac.jp
https://sites.google.com/site/hiroakinakanolaben/home
Keywords: marine invertebrates, placozoa, Xenoturbella, acoel, diversity-------------------------------------------------------------------------------------------------We are performing zoological studies on less studied marine invertebrates, currently
focusing on placozoans, Xenoturbella, acoels, and sea slugs. Our laboratory is situated at
Shimoda Marine Research Center, and the research animals are mostly collected at or aroundShimoda. By studying the morphology, taxonomy, development, and ecology of theseanimals, we aim to gain new information on the evolution and diversity of metazoans andbilaterians.
Placozoa is an amoebae-like marine flat animal about 1mm in diameter, possessing one of
the simplest body plans within the metazoans. It lacks tissues or organs, and even neurons ormuscle cells. There are still no reports of their complete development.
Xenoturbella is a marine animal about 1 cm long lacking typical bilaterian traits such asanus, gonads, and coelomic cavities. We made the first report of its development, anddescribed a new species, X. japonica, from Japanese waters.
Acoels share a similar body plan with Xenoturbella, and the two groups form the phylum
Xenacoelomorpha. Although the phylum is widely believed to be important when considering
the origins of bilaterians, the phylogenetic position of this phylum still remains unresolved.
from left
・placozoa
・Xenoturbella・acoel------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Miyazawa H., et al. (2021). Mitochondrial Genome Evolution of Placozoans: Gene
Rearrangements and Repeat Expansions. Genome Biology and Evolution 13, evaa213
Philippe H., et al. (2019) Mitigating anticipated effects of systematic errors supports sistergroup relationship between Xenacoelomorpha and Ambulacraria. Current Biology 29,
1818-1826.
Nakano, H., et al. (2017). A new species of Xenoturbella from the western Pacific Ocean
and the evolution of Xenoturbella. BMC Evolutionary Biology 17, 245.
Nakano, H. (2014). Survey of the Japanese coast reveals abundant placozoan populationsin the northern Pacific Ocean. Scientific Reports 4, 5356.
Nakano, H., et al. (2013). Xenoturbella bocki exhibits direct development withsimilarities to Acoelomorpha. Nature Communications 4, 1537.

Kentaro Nakano
Molecular Dynamics and Cellular Function ofCytoskeletons and membranes
nakano.kentaro.fw@u.tsukuba.ac.jp
https://www.biol.tsukuba.ac.jp/organelle/nakano.html
Keywords: actin, cytokinesis, fission yeast, phagocytosis, Tetrahymena-------------------------------------------------------------------------------------------------My goal is to understand the molecular mechanisms that control cell behavior, such as cell
division, cell morphogenesis, and intracellular trafficking, from the perspective of thecytoskeletons and membranes. These processes are fundamental to life. In my lab, unicellularorganisms, including fission yeast and ciliate Tetrahymena, are used as models for this purpose.
We try to achieve the goal by combining several methodologies, including genetics, cell biology,
and biochemical approaches.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.

5.

Morita, R., K. Nakano, Y. Shigeta, & R. Harada. 2020. Molecular Mechanism for the
Actin-Binding Domain of α-Actinin Ain1 Elucidated by Molecular Dynamics
Simulations and Mutagenesis Experiments. J. Phys. Chem. B 124, 8495–8503.
Morita, R., M. Takaine, O. Numata, & K. Nakano. 2017. Molecular dissection of theactin-binding ability of the fission yeast α-actinin, Ain1, in vitro and in vivo. J. Biochem.
162, 93-102.
Yasuda, T., M. Takaine, O. Numata, & K. Nakano. 2016. Anillin-related protein Mid1
regulates timely formation of the contractile ring in the fission yeast
Schizosaccharomyces japonicus. Genes Cells 21, 594-607.
Shiozaki, N.,Nakano, K., Kushida, Y., Noguchi, T.Q., Uyeda, T.Q., Wloga, D., Dave,D.,
Vasudevan, K.K., Gaertig, J. & Numata, O. (2013) ADF/cofilin is not essential but
critically important for actin activities during phagocytosis in Tetrahymena thermophila.
Eukaryot. Cell., 12, 1080-1086.
Nakano, K., M. Toya, A. Yoneda, Y. Asami, A. Yamashita, N. Kamasaki, M. Osumi, &M. Yamamoto. 2011. Pob1 ensures cylindrical cell shape by coupling two distinct Rho
signaling events during secretory vesicle targeting. Traffic 12, 726-739.

Takuro Nakayama
Molecular Evolution of Unicellular Organisms
ntakuro@ccs.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000004542
Keywords: evolution, symbiosis, genome, cyanobacteria, protists-------------------------------------------------------------------------------------------------

Symbiogenesis and Diversity of Unicellular Organisms
Looking over the diversity of life, with only some exceptions of a few lineages (animals andplants), most organisms are unicellular. We are researching on the evolution and diversity ofunicellular organisms, as an essential factor for a better understanding of life on Earth.
Particularly, we focus on symbiotic phenomena among unicellular organisms, and aim toelucidate the evolution of intracellular symbiosis and its ecological role through various nucleic
acid sequence analysis methods.

Protists with symbiotic cyanobacteria (arrowheads)------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Kawachi M, Nakayama T, Kayama M, Nomura M, Miyashita H, et al. (2021)
Rappemonads are haptophyte phytoplankton. Curr Biol 31: 2395-2403.
Sarai C, Tanifuji G, Nakayama T, Kamikawa R, Takahashi K, et al. (2020) Dinoflagellateswith relic endosymbiont nuclei as models for elucidating organellogenesis. Proc Natl Acad
Sci USA 117: 5364–5375.
Nakayama T, Nomura M, Takano Y, Tanifuji G, Shiba K, et al. (2019) Single-cellgenomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden
by a dinoflagellate host. Proc Natl Acad Sci 116: 15973–15978.
Nakayama T, Kamikawa R, Tanifuji G, Kashiyama Y, Ohkouchi N, et al. (2014) Complete
genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations toan intracellular lifestyle. Proc Natl Acad Sci 111: 11407–11412.
Nakayama T, Ishida K (2009) Another acquisition of a primary photosynthetic organelle
is underway in Paulinella chromatophora. Curr Biol 19: R284–R285.

Ryusuke Niwa
Molecular and Physiological Genetics of Insects
ryusuke-niwa@umin.ac.jp
https://sites.google.com/view/niwa-lab-tsukuba
Keywords: interorgan communication, stem cell, homeostasis, developmental
timing, Drosophila melanogaster-------------------------------------------------------------------------------------------------My research interests are in the areas of developmental biology,
cell biology, neuroendocrinology, and molecular genetics in
insects, particularly the fruit fly Drosophila melanogaster.
Currently I am interested in understanding how interorgan
communication is adaptively involved in regulations of nutrientdependent developmental plasticity, mating-induced female
germline stem cell proliferation, reproductive dormancy, and thehost-parasitoid wasp interactions.

------------------------------------------------------------------------------------------------Selected Publications
1.

2.

Yoshinari Y, Kosakamoto H, Kamiyama T, Hoshino R, Matsuoka R, Kondo S, Tanimoto H,
Nakamura A, Obata F, Niwa R (2021) The sugar-responsive enteroendocrine neuropeptide F
regulates lipid metabolism through glucagon-like and insulin-like hormones in Drosophilamelanogaster. Nature Communications 12: 4818.
Yoshinari Y, Ameku T, Kondo S, Tanimoto H, Kuraishi T, Shimada-Niwa Y, Niwa R (2020)
Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female
Drosophila melanogaster. eLife 9: e57101.

3.

Imura E, Shimada-Niwa Y, Nishimura T, Hückesfeld S, Schlegel P, Ohhara Y, Kondo S, Tanimoto
H, Cardona A, Pankratz MJ, Niwa R (2020) The Corazonin-PTTH neuronal axis controls systemic
body growth by regulating basal ecdysteroid biosynthesis in Drosophila melanogaster. Current
Biology 30: 1–10.

4.

Koiwai K, Inaba K, Morohashi K, Enya S, Arai R, Kojima H, Okabe T, Fujikawa Y, Inoue H,
Yoshino R, Hirokawa T, Kato K, Fukuzawa K, Shimada-Niwa Y, Nakamura A, Yumoto F, Senda
T, Niwa R (2020) An integrated approach unravels a crucial structural property required for thefunction of the insect steroidogenic Halloween protein Noppera-bo. Journal of Biological
Chemistry 295: 7154-7167.

5.

Ameku T, Yoshinari Y, Texada MJ, Kondo S, Amezawa K, Yoshizaki G, Shimada-Niwa Y, Niwa
R (2018) Midgut-derived neuropeptide F controls germline stem cell proliferation in a matingdependent manner. PLOS Biology 16: e2005004.

6.

Komura-Kawa K, Hirota K, Shimada-Niwa Y, Yamauchi R, Shimell M, Shinoda T, Fukamizu A,
O’Connor MB, Niwa R (2015) The Drosophila zinc finger transcription factor Ouija board
controls ecdysteroid biosynthesis through specific regulation of spookier. PLOS Genetics 11:
e1005712.

7.

Shimada-Niwa Y, Niwa R (2014) Serotonergic neurons respond to nutrients and regulate thetiming of steroid hormone biosynthesis in Drosophila. Nature Communications 5: 5778

Kazuharu Ohashi
Pollinator-mediated evolution of flowers
kohashi@biol.tsukuba.ac.jp
https://www.ohashilab.com/
Keywords: floral ecology, foraging, plant-animal interactions, pollination------------------------------------------------------------------------------------------------Research in our lab covers a wide rangeof topics, with the common theme thattheyallinvolveplant-animal
interactions. We use field, indoor
experimental,
andcomputational
approaches to elucidate how plants have
evolved various floral traits andcombinations to maximize fitness,mediated through interactions withdiverse organisms. We often focus on
how flower visitors such as bumble bees
and other insects respond to variation in
a set of floral traits at different spatial
scales, based on foraging economics that has been neglected in the past studies of floral
evolution. We have learned from our research that one could effectively predict and test what
behavioral responses floral traits have evolved to elicit from animals by incorporatingknowledge from behavioral ecology, animal physiology, and animal psychology. To promote
such interdisciplinary research in evolutionary ecology, we have collaborated with researchers
from diverse fields, such as behavioral ecologists and animal physiologists/psycologists.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Ohashi, K., A. Jürgens, and J. D. Thomson (2021) Trade-off mitigation: a conceptual
framework for understanding floral adaptation in multispecies interactions. Biological
Reviews 96(5): 2258-2280.
Ohashi, K. and A. Jürgens (2021) Three options are better than two: compensatory natureof different pollination modes in Salix caprea L. Journal of Pollination Ecology (SCAPE
Special Issue) 28(2021): 75-90.
Ohashi, K., T. T. Makino, and K. Arikawa (2015) Floral colour change in the eyes ofpollinators: testing possible constraints and correlated evolution. Functional Ecology
29(9): 1144-1155.
Ohashi, K. and J. D. Thomson (2009) Trapline foraging by pollinators: its ontogeny,
economics and possible consequences for plants. Annals of Botany 103(9): 1365-1378.
Ohashi, K. and T. Yahara (2002) Visit larger displays but probe proportionally fewer
flowers: counterintuitive behaviour of nectar-collecting bumble bees achieves an ideal free
distribution. Functional Ecology 16(4): 492-503.

Naoki Okamoto
Neuroendocrine mechanisms regulating
development and behavior in insects
naoki-okamoto@tara.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000004423
Keywords: Comparative endocrinology, Insect physiology, Developmental
biology, Hormones, Neuropeptides, Drosophila melanogaster------------------------------------------------------------------------------------------------We are interested in understanding neuroendocrine mechanisms that control importantbiological phenomena such as growth, metamorphosis, and behavior during insect development.
Mainly by using powerful fruit fly genetic tools, we aim to understand what kind of hormonesand receptors are involved in these regulatory mechanisms and how they function at themolecular level.
Genetic regulation of the function of hormones in the fruit fly
Drosophila melanogaster induces changes in the body size andshape of individuals during development.
(A) Suppression of the neuropeptide that controls bodycontraction during puparium formation results in elongatedpupae.
(B) Suppression of the function of insulin-like peptides
significantly suppresses systemic body growth and results insmall pupae.
(C) Inhibition of steroid hormone production delays pupation
and results in large pupae.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.
6.

Okamoto, N. and Yamanaka, N. (2020). Steroid hormone entry into the brain requires amembrane transporter in Drosophila. Curr. Biol. 30:359-366.
Okamoto, N. et al. (2018). A membrane transporter is required for steroid hormone uptake
in Drosophila. Dev. Cell 47: 294-305.
Okamoto, N. and Nishimura, T. (2015). Signaling from glia and cholinergic neurons
controls nutrient-dependent production of an insulin-like peptide for Drosophila body
growth. Dev. Cell 35: 295-310.
Okamoto, N. et al. (2013). A secreted decoy of InR antagonizes insulin/IGF signaling to
restrict body growth in Drosophila. Genes Dev. 27: 87-97.
Okamoto, N. et al. (2012). Conserved role for the Dachshund protein with Drosophila
Pax6 homolog Eyeless in insulin expression. PNAS 109: 2406-2411.
Okamoto, N. et al. (2009). A fat body-derived IGF-like peptide regulates post-feeding
growth in Drosophila. Dev. Cell 17: 885-891.

Michiyuki Ono
Plant Developmental Physiology
ono.michiyuki.fm@u.tsukuba.ac.jp
http://gm-edu.sakura.ne.jp/english
Keywords: photoperiodism, flowering, making new flower, edible vaccine------------------------------------------------------------------------------------------------Japanese morning glory (Ipomoea nil, formally Pharbitis nil) is one of the plants
selected for the national bio-resource project (NBRP) of MEXT Japan. I. nil has
long been studied as the model plant of the shortday induction of flowering and the garden plantwith significant variation. Using CRISPRed
mutant lines and wild strains, we are uncovering
the mechanisms in photoperiodic regulation of
flower-induction and flower-opening.
We are developing a new self-illuminating systemfor plant that allows the non-invasive detection ofchanges in gene expression for observing
circadian rhythm etc. This system also can beapplied to make self-illuminating plants that may
CRISPRed Early Flowering
facilitate understanding GM crop through"Science Arts", like as our GM Yellow flower etc.
We have been also collaborating with medical
researchers on the developing edible vaccine
CRISPRed White GM Yellow
against to viruses and food poisonings.
------------------------------------------------------------------------------------------------Selected publications

1.

2.
3.
4.

Watanaba, K., Oda-Yamamizo, C., Sage-Ono, K., Ohmiya, A. and Ono, M. (2018)
Alteration of flower colour in Ipomoea nil through CRISPR/Cas9-mediated mutagenesisof carotenoid cleavage dioxygenese 4. Transgenic Research 27: 25-38.
Watanabe, K., Kobayashi, A., Endo, M., Sage-Ono, K., Toki, S. and Ono, M. (2017)
CRISPR/Cas9-mediated mutagenesis of the dihydroflavonol-4-reductase-B (DFR-B)
locus in the Japanese mornig glory Ipomoea (Pharbitis) nil. Scientific Reports 7: 10028.
Watanabe, K., Oda-Yamamizo, C., Sage-Ono, K., Ohmiya, A. and Ono, M. (2017)
Overexpression of carotenogenic genes in the Japanese morning glory Ipomoea(Pharbitis) nil. Plant Biotechnology 34: 177-185.
Ono, M., Kataoka, M., Yokoyama, M., Ifuku, O., Ohta, M., Arai, S., Kamada, H. andSage-Ono, K. (2013) Effects of 9,10-ketol-octadecadienoic acid (KODA) application on
single and marginal short-day induction of flowering in Pharbitis nil cv. Violet. Plant
Biotechnology 30: 1-8.

Kazuichi Sakamoto
Molecular Biology of Health and Nutrition
sakamoto@biol.tsukuba.ac.jp
http://www.biol.tsukuba.ac.jp./~sakamoto/We have developed a new bioassay system to find and evaluate natural bioactive
compounds (e.g. phytochemicals, plant extracts, fermented foods, and animal tissues) that
influence health and aging; this novel bioassay system uses nematodes to characterize thebioactivity of natural substances. Because of its biological characteristics (easy culture, shortlifespan, and availability of mutants), the nematode is a suitable and well-characterized model
for investigating the physiology and mechanisms of human aging and disease. We are using
this animal to screen for biomaterials with potential benefits for human health.
To promote health (prevention and amelioration of lifestyle-related diseases) andyouth (anti-aging and vitality), we are searching for natural bioactive compounds. We arescientifically evaluating the bioactivity of these substances and developing novel bioactive
materials. We are also conducting applied studies to develop functional foods, functional
feeds, cosmetics, and medicines.

Phytochemicals such as catechin from tea,
resveratrol from red grapes, and hydroxytyrosol
from olives are famous bioactive compounds that
can act against aging and help protect against
lifestyle-related diseases. We are using thesematerials in functional foods, cosmetics,
medicines, and other materials to promote healthand slow aging.

Select Publications
1) Drira, R., Chen, S., and Sakamoto, K. (2011). Oleuropein and hydroxytyrosol inhibited adipocyte
differentiation in 3T3-L1 cells. Life Sciences, 89, 708-716.
2) Kim, H., and Sakamoto, K. (2011). (-)-Epigallocatechin gallate suppresses adipocyte differentiation throughthe MEK/ERK and PI3K/AKT pathways. Cell Biology International, 36, 147-153.
3) Shintani, H., Furuhashi, T., Hano, H., Matsunaga, M., Usumi, K., Shudo, N., and Sakamoto, K. (2011).
Physiological Effects of Salmon Milt Nucleoprotein on Movement, Stress Tolerance and Lifespan of C.
elegans. Food and Nutrition Sciences, 3, 48-54.
4) Nomura, T., Horikawa, M., Shimamura, S., Hashimoto, T., and Sakamoto, K. (2010). Fat accumulation in
Caenorhabditis elegans is mediated by SREBP homolog SBP-1. Genes and Nutrition, 5, 17-27.
5) Kamon, M., Zhao, R., and Sakamoto, K. (2010). Green tea polyphenol (-)-epigallocatechin gallate suppressed
the differentiation of murine osteoblast MC3T3-E1. Cell Biology International, 34, 109-116.

Keisuke Sakurai
Neurophysiology
sakurai@biol.tsukuba.ac.jp
https://sakuraik.bitbucket.io/index.html
Keywords: photoreceptor, retina, mouse, electrophysiology, opsin------------------------------------------------------------------------------------------------In vertebrate species, most ambient information is derived through photoreceptors where light
is absorbed and signaled to the nervous system. Visual perception initiates with light absorption
by rod and cone photoreceptors in the retina, which mediate dim light vision and bright lightvision, respectively. In addition to the vision, light reception by inner retinal neurons or
extraocular photoreceptors is thought to be of great importance to animal behaviors such as
circadian phase shift and body colour change. Our research aims to elucidate the underlying
light perception mechanism by which absorbed photons are converted into an electricalresponse and signaled to the brain. To achieve this goal, we primarily use electrophysiological
techniques in combination with genetically manipulated animals, which is powerful to elucidate
molecular mechanisms in neurons.

Rod and cone photoreceptors employ homologous or sometimes even identical proteins in theirphototransduction cascades, indicating that the same principles of phototransduction are likely to exist.
Despite these similarities, rods and cones exhibit important functional differences, with still largely unknown
origins.

------------------------------------------------------------------------------------------------Selected publications
1.
2.

3.
4.

Sakurai, K. : Physiological characteristics of photoreceptors in the lamprey, Lethenteron Japonicum"
Zoological Science, 34(4), 326~330, 2017
Kojima, K., Y. Matsutani , T. Yamashita , M. Yanagawa , Y. Imamoto , Y. Yamano , A. Wada , O.
Hisatomi , K. Nishikawa , K. Sakurai , & Y. Shichida: Adaptation of cone pigments found in green
rods for scotopic vision through a single amino acid mutation. Proceedings of the National Academyof Sciences,114(21), 5437~5442, 2017
Sakurai, K., F. Vinberg, T. Wang, J. Chen, & V. J. Kefalov:The Na(+)/Ca(2+), K(+) exchanger 2
modulates mammalian cone phototransduction.Scientific Reports. 6:32521, 2016
Sakurai, K., Chen, J., Khani, S. C., & V. J. Kefalov: Regulation of mammalian cone phototransduction
by recoverin and rhodopsin kinase.Journal of Biological Chemistry, 290(14), 9239~9250, 2015

Yasunori Sasakura
Developmental Genetics
sasakura@shimoda.tsukuba.ac.jp
https://www.shimoda.tsukuba.ac.jp/~sasakura/index.html
Keywords: chordate, Ciona, metamorphosis, neuron, evolution-------------------------------------------------------------------------------------------------

Our group is interested in developmental mechanismsof the marine invertebrate chordate Ciona intestinalis.
Ciona is the model species of tunicate ascidians.
Among invertebrates, tunicate is the closest living
relative of vertebrate. Studies of tunicates are thus
necessary for elucidating evolution of vertebrates. In
Ciona, tools for investigating molecular mechanisms
have been established, such as well-annotated genome
sequence and embryological techniques. We haveestablished the methods for manipulating genomes
and genes in Ciona, as exemplified by transposonbased transgenesis and genome editing. Using thesetechniques, we are addressing mechanisms underlying
development of Ciona.
We currently focus on metamorphosis.
Swimming tadpole larvae of Ciona complete
metamorphosis within a few days, and they start sessile adult life. Ciona larvae possess only
177 neurons. The simple nervous system regulates complicated metamorphic processes. We areinterested in the molecular and cellular mechanisms underlying metamorphosis; how signaling
molecules and neurotransmitters regulate destruction of larval organs and construction of adultorgans to complete this event. By comparing mechanisms of metamorphosis between animals,
we aim to understand the evolution of metamorphic events among animals.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Yamaji, S. et al. (2020). Orchestration of the distinct morphogenetic movements indifferent tissues drives tail regression during ascidian metamorphosis. Developmental
Biology 465:66-78.
Hozumi, A. et al. (2020). GABA-Induced GnRH Release Triggers Chordate
Metamorphosis. Current Biology 30:1555-1561.
Yoshida, K. et al. (2017). Hox-mediated endodermal identity patterns pharyngeal muscle
formation in the chordate pharynx. Development 144:1629-1634.
Matsunobu, S. and Sasakura, Y. (2015). Time course for tail regression duringmetamorphosis of the ascidian Ciona intestinalis. Developmental Biology 405:71-81.
Treen, N. et al. (2014). Tissue-specific and ubiquitous gene knockouts by TALEN
electroporation provide new approaches to investigating gene function in Ciona.
Development 141:481-487.

Yukie Sato
Behavioural & Evolutionary Ecology
sato.yukie.gn @u.tsukuba.ac.jp
http:// /www.u.tsukuba.ac.jp/~sato.yukie.gn/
Keywords: sexual selection, social behaviour, speciation, conservation biology,
biological control, Acarology------------------------------------------------------------------------------------------------The general aim of my research is to reveal the mechanisms of ecological diversification at thelevel of species and populations, as well as speciation mechanisms. Furthermore, I deal withbehavioral variations in different individuals of the same population. In particular, I focus onsocial behavior and mating behavior in spider mites. Spider mites are small arthropod
herbivores less than 1 mm in length. They are good model organisms because they complete
their development (egg to adult) in a short period (ca. 5- 20 days under optimal conditions) and they can be
mass-reared in small spaces. These advantages allow
investigation of the following projects:






Alternative reproductive tactics in spider mitemales
Speciation in haplodiploid spider mites
Kin selection and lethal male fights
Reproductive interference between invasive andnative spider mites
Biological control for invasive bamboo mites in Europe------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.

4.
5.

Sato, Y., Fujiwara, S., Egas, M., Matsuda, T. and Gotoh, T. (2021). Patterns of reproductive
isolation in a haplodiploid mite, Amphitetranychus viennensis: prezygotic isolation, hybrid
inviability and hybrid sterility. BMC Ecology and Evolution 21: 177.
Sato, Y., Tsuda, Y., Sakamoto, H., Egas, M., Gotoh, T., Saito, Y., Zhang, Y.-X., Lin, J.-Z.,
Chao, J.-T. and Mochizuki, A. (2019). Phylogeography of lethal male fighting in a social
spider mite. Ecology and Evolution 9: 1590-1602.
Sato, Y., Sakamoto, H., Gotoh, T., H., Saito, Y., Chao, J.-T., Egas, M. and Mochizuki, A.
(2018). Patterns of reproductive isolation in a haplodiploid – strong post-mating,prezygotic barriers among three forms of a social spider mite. Journal of Evolutionary
Biology 31: 866-881.
Sato, Y., Sabelis, M.W. and Egas, M. (2014). Alternative male mating behaviour in the
two-spotted spider mite: dependence on age and density. Animal Behaviour 92: 125-131.
Sato, Y., Egas, M., Sabelis, M.W., and Mochizuki, A. (2013) Male-male aggression peaks
at intermediate relatedness in a social spider mite. Ecology and Evolution 3: 2661-2669.

Kyoichi Sawamura
Mechanisms of Speciation in Drosophilasawamura@biol.tsukuba.ac.jp
https://www.biol.tsukuba.ac.jp/~sawamura/english.html

Keywords: reproductive isolation, hybrid incompatibility, interspecificintrogression, natural population, courtship/copulatory behavior------------------------------------------------------------------------------------------------Do you know what an interspecific hybrid is?
Mules from mares and donkeys, leopons fromlionesses and leopards… Interspecific hybrids arerare in nature; most of them are sterile and therefore
cannot produce descendants. If these hybrids were
not rare, then biological species would become
fused and lost from the world. In other words,
species exist because of reproductive isolation: theorigin of new species is completed by acquiring
reproductive isolation between populations.
Therefore, speciation is a major driving force ofevolution. The purpose of our research is toelucidate the genetic mechanisms of speciation.
Our model organism is Drosophila. Genomic sequencing has been completed in ~50 Drosophila
species. The biodiversity of this genus is spectacular: 3950 extant species (and 12 fossil species)
have been described in the Drosophilidae (Brake & Bächli, 2008). Furthermore, Drosophila has
many crossable sibling species pairs and can be used to provide useful experimental systems
for investigating the genetic mechanisms of speciation.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Onuma, M. et al. (2021) Genital coupling and copulatory wounding in the Drosophila
auraria species copmlex (Diptera: Drosophilidae). Biol J Linnean Soc in press
Hama, Y. et al. (2020) Long-term coexistence of a hybridization-derived population of
Drosophila parapallidosa with closely related Drosophila ananassae (Diptera:
Drosophilidae). Entomol Sci 23: 405-415.
Hirai, K. et al. (2018) Genetic analysis of Elys mutations in Drosophila show maternaleffect lethality and interactions with Nucleoporin genes. G3 8: 2421-2431.
Shirata, M. et al. (2014) Allelic asymmetry of the Lethal hybrid rescue (Lhr) gene
expression in the hybrid between Drosophila melanogaster and D. simulans: confirmationby using genetic variations of D. melanogaster. Genetica 142: 43-48.
Maehara, K. et al. (2012) Genetic dissection of Nucleoporin 160 (Nup160), a gene
involved in multiple phenotypes of reproductive isolation in Drosophila. Jpn J Genet 87:
99-106.

Kogiku Shiba
Cell Biology
kogiku@shimoda.tsukuba.ac.jp
https://inaba-lab-shimoda.jimdofree.com/english/
Keywords: sperm, flagella, cilia, fertilization, cell motility------------------------------------------------------------------------------------------------The structures of cilia and flagella have been highly conserved through evolution and play
important roles in sperm motility, embryonic locomotion, current generation in epidermal
tissues such as the oviduct and trachea, and cell signal reception. We are using the embryos orsperm of marine invertebrates such as tunicates, sea urchins, fishes and snails to study theregulatory mechanism of ciliary and flagellar movement. Research topics are a signaling
pathway in sperm motility activation and chemotaxis to egg, and a regulatory mechanism offlagellar and ciliary waveforms. To analyze motility and waveforms in cilia and flagella we areusing a high-speed camera, a stroboscopic lighting system, auto-tracking software, and a Ca2+imaging system.

------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.
5.

Sasaki K†, Shiba K†, Nakamura A†, Kawano N, Satouh Y, Yamaguchi H, Morikawa M,
Shibata D, Yanase R, Jokura K, Nomura M, Miyado M, Takada S, Ueno H, Nonaka S,
Baba T, Ikawa M, Kikkawa M, Miyado K, Inaba K. Calaxin is required for cilia-driven
determination of vertebrate laterality. Commun Biol 2:226. (2019) †equal contribution.
Shiba K, Inaba K. Inverse relationship of Ca2+-dependent flagellar response between
animal sperm and prasinophyte algae. J Plant Res 130(3):465-473. (2017)
Miyata H, Satouh Y, Mashiko D, Muto M, Nozawa K, Shiba K, Fujihara Y, Isotani A,
Inaba K, Ikawa M. Sperm calcineurin inhibition prevents mouse fertility with implications
for male contraceptive. Science, 350(6259):442-5. (2015)
Shiba K, Inaba K. Distinct roles of soluble and transmembrane adenylyl cyclases in theregulation of flagellar motility in Ciona sperm. Int J Mol Sci 15(8):13192-208. (2014)
Shiba K, Shibata D, Inaba K. Autonomous changes in the swimming direction of sperm in
the gastropod Strombus luhuanus. J Exp Biol 217(Pt 6):986-96. (2014)

Yasuteru Shigeta
Theoretical biophysics
shigeta@ccs.tsukuba.ac.jp
https://www.ccs.tsukuba.ac.jp/eng/research-divisions/division-of-life-sciences/bi
ological-function-and-information-group/
Keywords: Theoretical calculations, Drug Discovery, Bioenergetics------------------------------------------------------------------------------------------------

Phenomena expressing in life are dominated by a series of chemical reactions driven bymacromolecules such as proteins, nucleic acids, lipids, and sugars. To understand the life, thefundamental molecular mechanisms of biological phenomena should be clarified byinvestigating the electronic structure changes and the spatial rearrangements of atoms
accompanied by the chemical reactions. In our group, dynamic structure-function correlationsof biomolecules are explored by using theoretical calculations such as quantum chemical andclassical molecular dynamics simulations.
Using these methods, we have investigated catalytic chemical reaction mechanisms inbioenergy conversion processes such as electron transport chain, photosystems, andhydrogenase at microscopic level. In particular, the stability of X-ray and/or neutron
crystallographic structures was examined byusing quantum chemical calculations, andthen electron transport pathways in a given
protein were estimated to specify the detailed
mechanism. We have also conducted the drug
discovery researches on antiviral candidates
towards Dengi, Zika, and SARS-Cov-2
viruses. The use of supercomputers enables
us to examine protein-drug interaction more
precisely and screen the potential drugs frommany candidates.

Selected publications
1.

2.

3.

A. Kimura, H. Kitoh-Nishioka, Y. Shigeta, S. Ito, (2021) Comparison of Light
Harvesting Mechanisms of Photosynthetic Type-I Reaction Centers of Heliobacteria with
Photosystem I. Pigments Site Energy Distribution and Exciton States", J. Phys. Chem. B,
125(15), 3727-3738.
T. Murakawa, K. Kurihara, M. Shoji, C. Shibazaki, T. Sunami, T. Tamada, N. Yano, T.
Yamada, K. Kusaka, M. Suzuki, Y. Shigeta, R. Kuroki, H. Hayashi, T. Yano, K. Tanizawa,
M. Adachi, T. Okajima (2020), Neutron crystallography of copper amine oxidase reveals
a keto form cofactor and proton sharing, Proc. Nat. Acad. Sci. U.S.A. 117, 10818-10824.
B. Nutho, P. Mahalapbutr, K. Hengphasatporn, N.C. Pattaranggoon, N. Simanon, Y.
Shigeta, S. Hannongbua, T. Rungrotmongkol (2020) Why are lopinavir and ritonavir
effective against the newly emerged Coronavirus 2019?: Atomistic insights into theinhibitory mechanisms, Biochemistry, 59(18), 1769-1779.

Yuko Shimada
Developmental Biology and Genetics
shimada.yuko.gn@u.tsukuba.ac.jp
https://www.researchgate.net/profile/Yuko-ShimadaNiwa
https://researchmap.jp/yukoshimada
Keywords: Drosophila melanogaster, ecdysteroid biosynthesis, neuroendocrine system,
steroid hormone-------------------------------------------------------------------------------------------------

Nutrient-Neuro-endocrine Mechanisms of Maturation
in Drosophila melanogasterHow do the organisms know their appropriate timing of maturation from the juvenile
to the adult? One of the key regulatory mechanisms is steroid hormone biosynthesis
in response to various environmental conditions. We have been studying the neuronal
regulatory mechanism of steroid hormone
biosynthesis in the fruit fly Drosophilamelanogaster. By using molecular genetics,
cell biological analysis, and live-imaging
system, we are trying to understand how thegenetic program of organisms is flexibly
coordinated to accomplish the development
from

eggs

to

individuals.

Anyoneandeveryone are welcome to share our scientificinterests in the lab!

Selected publications:
1.

The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)
Seong KH, Matsumura T, Shimada-Niwa Y, Niwa R, Kang Siu.
eLife 9:e58630, Nov, 2020

2.

The Corazonin-PTTH Neuronal Axis Controls Systemic Body Growth by Regulating Basal
Ecdysteroid Biosynthesis in Drosophila melanogaster.
Imura E, Shimada-Niwa Y, Nishimura T, Hückesfeld S, Schlegel P, Ohhara Y, Kondo S, Tanimoto
H, Cardona A, Pankratz MJ, Niwa R.
Current biology 30(11) 2156-2165, Jun 8, 2020

3.

Protocols for Visualizing Steroidogenic Organs and Their Interactive Organs with
Immunostaining in the Fruit Fly Drosophila melanogaster.
Imura E, Yoshinari Y, Shimada-Niwa Y, Niwa R.
Journal of visualized experiments 122, e55519, Apr, 2017

Takashi Shiratori
Phylogeny and evolution of microbes
shiratori.takashi.gm@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/researcher/0000004374
Keywords: protist, molecular phylogeny, evolution, prokaryote, microbiology-------------------------------------------------------------------------------------------------

Most of the phylogenetic diversity is dominated by prokaryotes and unicellular eukaryotes.
However, most of them have not been adequately studied due to the lack of culture strains. To
clarify the whole picture of the tree of life and the process of the evolution, it is necessary to
discover unknown microorganisms from the environment and study them.
We screen novel unicellular organisms from various environments, isolate and cultivate them,and analyze their fine structures using electron and fluorescence microscopy and genome andtranscriptome data to clarify the early evolution, diversity, and phylogenetic relationships oflife on the earth.

XXX X XXXX.

Light and electron micrographs of Candidatus
Uab amorphum. We discovered this bacteriumin the Republic of Palau in 2015 and showed it
performs cell uptake like a eukaryote. Becauseof this unusual feature, this bacterium isimportant for revealing the early evolution of
eukaryotes.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Shiratori, T. Yabuki, A. Ishida, K. (2020) Morphology, Ultrastructure, and Phylogeny of
Two Novel Species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp., Thecofilosea,
Cercozoa). Protist, 171:125731.
Shiratori, T. Shigekatsu, S. Kakizawa, Y. Ishida, K (2019) Phagocytosis-like cell
engulfment by a novel planctomycete bacterium. Nature Communicarions, 10:5529.
Shiratori, T. Fujita, S. Shimizu, T. Nakayama, T. Ishida, K. (2017) Viridiuvalis adhaerens
gen. et sp. nov., a novel colony-forming chlorarachniophyte. Journal of Plant Research,
130:999-1012.
Shiratori, T. Thakur, R. Ishida, K. (2017) Pseudophyllomitus vesiculosus (Larsen and
Patterson 1990) Lee, 2002, a poorly studied phagotrophic biflagellate is the firstcharacterized member of stramenopile environmental clade MAST-6. Protist, 168:439-451.
Shiratori, T. Ishida, K. (2016) A new heterotrophic cryptomonad: Hemiarma marina n. g.,
n. sp. The Journal of Eukaryotic Microbiology, 63:804-812.

Hiroshi Shitara
Molecular Genetics of Mitochondrial DNA
in Mammals
shitara-hr@igakuken.or.jp
http://www.igakuken.or.jp/

Mitochondria play important roles in cell functions such as ATP production andapoptosis. Mammalian mitochondria contain multiple copies of approximately 16-kbp
double-stranded DNA with a closed circular conformation. Two genetic characteristics thatare major specific phenomena observed during the inheritance of mitochondrial DNA(mtDNA) are maternal inheritance and rapid segregation. We have been investigating themode of mtDNA transmission in a mouse model.
Our particular focus is the genetic machinery of rapid segregation. Usually, 1000 to
10,000 copies of mtDNA molecules exist in a single somatic cell, and the mutation rate of
mtDNA is higher than that of nuclear DNA. Thus, mtDNA is thought to show heteroplasmy:in other words, more than one type of mtDNA exists in a cell. However, rapid shifts in
mtDNA variants between generations have been observed in several species, and mtDNA
homoplasmy is maintained in mostindividuals. Our group previously
proposed models for the mitochondrial
Confocal image of mitochondria
bottleneck effect, which is a concept forin kidney from mtGFP-Tg mice.
the genetic machinery of rapid
Mitochondria were visualized bysegregation. We are currently
using green fluorescent protein.
Nuclei are counterstained withinvestigating mtDNA and mitochondrial
DAPI (blue).
segregation by using transgenic mousestrains.

Select Publications
1.
2.
3.
4.

Yamaguchi, J., Nishiyama, S., Shimanuki, M., Ono, T., Sato, A., Nakada, K., Hayashi, J.,
Yonekawa, H., and Shitara, H. (2012). Comprehensive application of an mtDsRed2-Tg mousestrain for mitochondrial imaging. Transgenic Res 21, 439-447.
Nishiyama, S., Shitara, H., Nakada, K., Ono, T., Sato, A., Suzuki, H., Ogawa, T., Masaki, H.,
Hayashi, J., and Yonekawa, H. (2010). Over-expression of Tfam improves the mitochondrial
disease phenotypes in a mouse model system. Biochem Biophys Res Commun 401, 26-31.
Cao, L., Shitara, H., Sugimoto, M., Hayashi, J., Abe, K., and Yonekawa, H. (2009). New
evidence confirms that the mitochondrial bottleneck is generated without reduction of
mitochondrial DNA content in early primordial germ cells of mice. PLoS Genet 5, e1000756.
Cao, L., Shitara, H., Horii, T., Nagao, Y., Imai, H., Abe, K., Hara, T., Hayashi, J., and Yonekawa,
H. (2007). The mitochondrial bottleneck occurs without reduction of mtDNA content in female
mouse germ cells. Nat Genet 39, 386-390.

Akiko Shoji
Behavioural Ecology
shoji.akiko.gw@u.tsukuba.ac.jp
https://cpnc.conservation.tsukuba.ac.jp/shoji/home-en/
Keywords: life-history, foraging, migration, toxicology, biologging------------------------------------------------------------------------------------------------My research focuses on many facets of behavioural ecology, dealing with spatial ecology,
life-history, individuality, ecotoxicology and population dynamics. I study the interactions
between prey and predator as well as individuality and fitness mainly on top avian predatorssuch as colonial seabirds and raptors, addressing a range of questions from understanding theconsequences of migratory strategies on individual fitness and population dynamics, toinvestigating foraging strategies in sympatric species and incubation strategies from an
ecophysiology point of view, the mechanism of carry-overeffects in migratory species. I recently expanded myresearch interest to include understanding the mechanismof biotransport through behaviour and the extent of theconsequences on trans-ecosystems. I am currently leading
projects on seabirds and raptors breeding in the Pacific
Ocean. I am collaborating with various researchers andNGOs which lead some of my research results to help
making conservation policies in the Atlantic Ocean.
Tufted puffins breeding at Middleton Island, Alaska, USA
where we are currently studying wintering movements andbehaviour with bio-logging techniques. Throughcollaboration with Dr. Kyle Elliott at McGill University inMontréal, Dr. Stéphane Aris-Brosou at University ofOttawa in Canada, and Dr. Anntte Fayet at Oxford
University, and many more cannot be listed all here, we aretagging several seabirds in the Pacific Ocean.

------------------------------------------------------------Selected publications
1. Shoji et al. (2021) Geolocators link marine mercury with levels in wild seabirds
throughout their annual cycle: consequences for trans-ecosystem biotransport.
Environmental Pollution 284: 117035
2. Shoji, A.et al.(2019) Biotransport of metallic trace elements from marine to terrestrial
ecosystems by seabirds. Environmental Toxicology & Chemistry 38: 106-114.
3. Van-Tatenhove, A. et al. (2018) Streaked shearwater Calonectris leucomelas moonlightavoidance in response to low aerial predation and effects of wind speed and direction oncolony attendance. Marine Ornithology 46: 177-185
4. Shoji, A.et al.(2016) Physiological constraints scale with body mass during dives in auks:
a comparative analysis. Comparative Biochemistry and Physiology 196:54-60
5. Shoji, A.et al.(2015) Breeding phenology and winter activity predict subsequent breeding
success in a trans-global migratory seabird. Biology Letters 11: 20150671

Takuya Suzaki
Plant Molecular Biology,
Plant-microbe symbiosis
suzaki.takuya.fn@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000003814
Keywords: root nodule symbiosis, legume, environmental response,transcription factor, organ-to-organ communication------------------------------------------------------------------------------------------------Using genetic and molecular biological approaches, weare trying to elucidate molecular mechanisms underlying
plant-microbe symbiosis with a model legume Lotus
japonicus and nitrogen-fixing bacteria called rhizobia.
We are particularly interested in to reveal the molecularmechanisms by which plants control root nodule
symbiosis in response to the change of environmental
factors. Examples of research projects: "Studies on transcription factors that regulate root
nodule symbiosis", "Organ-to-organ communication to regulate root nodule symbiosis","Control of root nodule symbiosis in response to nutritional environment",etc.

------------------------------------------------------------------------------------------------Selected publications
1.

2.

3.
4.

5.

Nishida, H., Nosaki, S., Suzuki, T., Ito, M., Miyakawa, T., Nomoto, M., Tada, Y., Miura, K.,
Tanokura, M., Kawaguchi, M. and *Suzaki, T. (2021) Different DNA-binding specificities of NLP
and NIN transcription factors underlie nitrate-induced control of root nodulation. Plant Cell
33:2340-2359.
*Suzaki, T., Takeda, N., Nishida, H., Hoshino, M., Ito, M., Misawa, F., Handa, Y., Miura, K. and
Kawaguchi, M. (2019) LACK OF SYMBIONT ACCOMODATION controls intracellular symbiont
accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus. PLOS
Genet. 15:e1007865.
Nishida, H., Tanaka, S., Handa, Y., Ito, M., Sakamoto, Y., Matsunaga, S., Betsuyaku, S., Miura,
K., Soyano, T., Kawaguchi, M. and *Suzaki, T. (2018) A NIN-LIKE PROTEIN mediates nitrateinduced control of root nodule symbiosis in Lotus japonicus. Nat. Commun. 9:499.
*Suzaki, T., Ito, M., Yoro, E., Sato, S., Hirakawa, H. Takeda, N. and Kawaguchi, M. (2014)
Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus.
Development 141:2441-2445.
*Suzaki, T., Yano, K., Ito, M., Umehara, Y., Suganuma, N. and Kawaguchi, M. (2012) Positive
and negative regulation of cortical cell division during root nodule development in Lotus japonicus
is accompanied by auxin response. Development 139:3997-4006.

Daichi G. Suzuki
Evolutionary Behavioral Neurobiology
suzuki.daichi.gp@u.tsukuba.ac.jp
https://researchmap.jp/suz_dg?lang=en
Keywords: cyclostomes, hagfish, lamprey, brain, evolution

Evolution of neural circuits, behavior, and mind of basal vertebrates

Cyclostomes (lampreys and hagfish) are the only surviving jawless fishes, the earliest
vertebrates. As being basal-most group of vertebrates, they provide crucial information forunderstanding early evolution of the vertebrates. To elucidate the evolutionary origin ofvertebrate brain, behavior, and mind, we take an integrative approach combining molecularbiology, neuroscience, bioinformatics, and so on.
Although lampreys and hagfish form a monophyletic group, they show different
lifestyles and lineage-specific adaptations. As lampreys transform from riverbed-burrowing
larvae to actively swimming adults, their visual system shows stepwise development fromimmature photoreception to matured image-forming vision. In contrast, hagfish live in the deepsea and thus show a degenerate visual system. Instead, they have a sophisticated olfactory
system and an enlarged pallium, the brain region homologous to the mammalian cortex. We
focus on these peculiarities to reconstruct ancestral conditions.

-----------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.
5.

Suzuki, D. G., Wada, H., and Higashijima, S. (2021). Generation of knock-in lampreys by
CRISPR-Cas9-mediated genome engineering. Scientific Reports 11:19836.
Suzuki, D. G. (2021). Consciousness in jawless fishes. Frontiers in Systems Neuroscience
15:751876.
Suzuki, D. G., Pérez-Fernández, J., Wibble, T., Kardamakis, A. A., and Grillner, S. (2019).
The role of the optic tectum for visually evoked orientating and evasive movements. Proc.
Natl. Acad. Sci. USA 116(30):15272–15281.
Suzuki, D. G. and Grillner, S. (2018). The stepwise development of the lamprey visualsystem and its evolutionary implications. Biological Reviews 93:1461–1477.
Suzuki, D. G., Murakami, Y., Escriva, H., and Wada, H. (2015). A comparative
examination of neural circuit and brain patterning between the lamprey and amphioxus
reveals the evolutionary origin of the vertebrate visual center. Journal of Comparative
Neurology 523(2):251–261.

Iwane Suzuki
Mechanisms of signal perception by sensory
kinases in photosynthetic organisms
iwane.suzuki.fw@u.tsukuba.ac.jp
http://www.sakura.cc.tsukuba.ac.jp/~plmet302/index.html
Living organisms recognize changes in their environmental conditions and regulate
their gene expression to acclimate to such changes. However, the molecular mechanisms ofsignal perception by cellular sensors are not yet well characterized. We developed a way toconstruct chimeric sensors, which contain a signal-recognition domain from an unknown
sensory kinase and a kinase domain from the well-studied phosphate-deficient sensor, SphS,
from the cyanobacterium Synechocystis sp. PCC 6803. This system is a powerful tool forstudying the functions of sensory kinases and the molecular mechanisms of signal perception,
as well as for developing artificial switches to regulate gene expression in systems biology.
Chimera sensor for character izat ion of hist idine kinases
Uncharacter ized hist idine kinase
X

SphS (Hik7)

Hik

Condit ion A
Condit ion B
・
・
・

PAS

X

Screening for cult ure condit ionsfor expressing AP act ivit y
Deter minat ion of st imuli
perceived by Hik

Hik

Hik

Expression of t he phoA gene
Hik: hisit idine kinase domain
PAS: Per -Ar nt-Sim domain
AP: alkaline phosphatase

Construction of a chimeric sensory kinase in
Synechocystis. A phosphate sensor, SphS, regulates
expression of the phoA gene encoding alkaline
phosphatase (AP). The chimeric sensory kinase
containing the signal-recognition domain of an
uncharacterized kinase and the kinase domain of
SphS regulate the expression of the phoA gene
under the conditions perceived by theuncharacterized sensory kinase.

Select Publications
1.
2.
3.
4.
5.

Y. Shimura, Y. Shiraiwa, I. Suzuki (2012) Characterization of the subdomains in theamino-terminal region of histidine kinase Hik33 in the cyanobacterium Synechocystis sp.
PCC 6803, Plant Cell Physiol., 53, 1255–1266
J.G. Rowland, X. Pang, I. Suzuki, N. Murata, W.J. Simon, A.R. Slabas (2010)
Identification of components associated with thermal acclimation of photosystem II in
Synechocystis sp. PCC6803, PLoS One 5, e10511
S. Kimura, Y. Shiraiwa, I. Suzuki (2009) Function of the N-terminal region of thephosphatesensing histidine kinase, SphS, in Synechocystis sp. PCC 6803, Microbiol. 155,
2256-2264
T. Sakayori, Y. Shiraiwa, I. Suzuki (2009) A Synechocystis homolog of SipA protein,
Ssl3451, enhances the activity of the histidine kinase Hik33, Plant Cell Physiol. 50,
1439-1448
Y. Kanesaki, H. Yamamoto, K. Paithoonrangsarid, M. Shoumskaya, I. Suzuki, H.
Hayashi, N. Murata (2007) Histidine kinases play important roles in the perception andsignal transduction of H2O2 in the cyanobacterium, Synechocystis. Plant J. 49, 313-324

Kenta Tanaka
Evolutionary & Conservation Ecology
kenta@sugadaira.tsukuba.ac.jp
http://www.sugadaira.tsukuba.ac.jp/kenta/
Keywords: plant, plants-related interaction, mountain, grassland, forest-------------------------------------------------------------------------------------------------How has biodiversity in front of us evolved and how could it be conserved? To answer thisquestion, we conduct evolutionary & conservation ecology of plants and interacting organisms
at the genetic- to community- levels in mountains, grasslands and forests.
In various model organisms, more than half of genes have noknown function, and interest has focused on the role of thosegenes in field ecosystems. Arabidopsis kamchatica, closely
related to the plant model A. thaliana, adapts to an elevationof 0 ~ 3000 m, and its life span evolved to vary greatly
depending on elevation. We are identifying the "life spangene" and related environmental adaptation.
Grasslands that have been for > 300 years remain in ski
resorts, reservoirs and mountain castles. Their legacy effects
maintain high biodiversity in plants, butterflies, moths,
beetles and fungi. In the Sugadaira grasslands, genetic
resources over ¥ 10,000,000,000 are being lost, unknown andunused. The results of this research are being used to conserve
biodiversity through regional cooperation.

------------------------------------------------------------------------------------------------Selected publications
1.
2.
3.
4.

5.

Inoue, T., Yaida, Y. A., …., Ushimaru, A. & Kenta, T. (2021). The effects of temporalcontinuities of grasslands on the diversity and species composition of plants. EcologicalResearch, 36:24-31.
Toju, H., Kurokawa, H., & Kenta, T. (2019). Factors influencing leaf-and root-associatedcommunities of bacteria and fungi across 33 plant orders in a grassland. Frontiers in
Microbiology 10:241
Timothy Paape, …., Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese, Kentaro
K. Shimizu (2018) Patterns of polymorphism and selection in the subgenomes of theallopolyploid Arabidopsis kamchatica. Nature communication 9(1): 3909
T. Kenta, A. Yamada & Y. Onda. 2011. Clinal variation in flowering time and vernalisation
requirement across a 3000-m altitudinal range in perennial Arabidopsis kamchatica ssp.
kamchatica and annual lowland subspecies kawasakiana. Journal of Ecosystem and
Ecography S6:1-10. doi:10.4172/2157-7625.S6-001
T. Kenta, N. Inari, T. Nagamitsu, K. Goka, & T. Hiura. 2007. Commercialized European
bumblebee can cause pollination disturbance: an experiment on seven native plant species
in Japan. Biological Conservation 134:298-309

Yukihiko Toquenaga
Population Biology
toque@biol.tsukuba.ac.jp
http://www.biol.tsukuba.ac.jp/~toqueI am an associate professor in the Doctoral Program in Biological Sciences at the Universityof Tsukuba, where I teach ecology, theoretical biology, biometry, and computer programming.
I specialize in population biology using a wide range of materials, including naturalcommunities of egrets and herons in the eastern region of the Kanto Plain; laboratory
populations of bean weevils collected from all over the world; natural populations of bumble
bees in urban and rural regions, and the in silico digital bugs that occupy gigabytes on thehard disks attached to my computers. I am using these materials to question, in an
evolutionary sense, why some organisms live in groups but others tend to live solitarily. My
speciation philosophy was converted to Wrightian from Fisherian when I studied evolution
and ecology under Prof. Michael Wade in 1995–1996. I believe that Wright’s shifting balance
scheme is realistic. I’m often described as a theoretician, but I consider myself primarily to bean ecological field worker. Somehow I have become good at capturing wild egrets and herons
by hand!
The photographs (clockwise from the top left panel)show a larva of Callosobruchus maculatus, a notorious
bean-weevil pest of legume seeds, constructing a roughwall inside a bean when it happened to break into thecavity of another larva. The larva has used feces and asecreted substance to form the wall. The C. maculatus
larvae are of the scramble type, so multiple adults canemerge from a bean, but if the wall structure is
artificially removed the larva will fight with the otherlarva in the cavity and one or both of them will die as aresult. The rough wall acts as a kind of language thatprevents fights between inherently quarrelsome larvae.

Select Publications
1.

2.

3.

4.
5.
6.

Mashiko, M., Fujioka, M., Moriya, K., Hagimoto, T., Yamaguchi, M., and Toquenaga, Y. (2012).
Natural hybridization between a Little Egret (Egretta garzetta) and a Chinese Pond Heron(Ardeola bacchus) in Japan. Waterbirds 35, 160-163.
Kondo, N., Tuda, M., Toquenaga, Y., Lan, Y-C., Buranapanichpan, S., Horng, S-B., Shimada, M.,
and Fukatsu, T. (2011). Wolbachia infections in world populations of bean beetles (Coleoptera:
Chrysomelidae: Bruchinae) infesting cultivated and wild legumes. Zool Sci 14, 166-172.
Suzuki-Ohno, Y., Kawaguchi, L., Munidasa, D., and Toquenaga, Y. (2010). Do bumble bee
queens choose nest sites to maximize foraging rate? -Testing models of nest site selection- Behav.
Ecol Sociol 63, 1353-1362.
Toquenaga, Y., and Kokuvo, N. (2010). Full-sib reconstruction in haplodiploid populations. Appl
Entomol Zool 45, 59-64.
Otsuka, Y. , and Toquenaga, Y. (2009). The Patch Distribute Producer-Scrounger Game, J Theor
Biol, 260, 261-266.
Mano, H., and Toquenaga, Y. (2008). Wall-making Behavior in Callosobruchus maculatus(Coleoptera: Bruchidae). Ann Entomol Soc Am 101, 449-455.

Fuminori Tsuruta
Molecular and cellular neurobiology
tsuruta.fuminori.fn@u.tsukuba.ac.jp
https://ftsuruta.wixsite.com/fuminori-tsuruta
Keywords: microglia, astrocytes, neurons, neuroinflammation,
synaptogenesis, developmental disorders, neurodegenerationneurogenesis,-------------------------------------------------------------------------------------------------

Our laboratory is interested in understanding the mechanisms of how glial cells contribute toneurogenesis, synaptogenesis, and neural circuits formations. Also, we have been investigating
mechanisms by which glial dysfunctions cause an increased risk of neuronal disorders.
Currently, we implement several projects, such as (1) microglial diversity regulated byextracellular micronuclei, (2) microglial maturation and purine metabolism, (3) atypicalsecretory pathway in neurons and astrocytes, (4) hypothermia control mediated by neuronastrocyte interaction. Moreover, we have been developing tools and screening systems to
elucidate abnormal post-translational modifications that induce neuroinflammation. We aim toclarify some of the principles of neuron-glia interactions in the developing brain through thesechallenging projects. We welcome highly motivated students interested in molecular
neuroscience to investigate the mechanisms underlying glial functions.

------------------------------------------------------------------------------------------------Selected publications

Yano S, Akiyama K, Tsuchiya R, Kubotani H, Chiba T, Nagata T, Tsuruta F
A MATLAB-based program for three-dimensional quantitative analysis of micronuclei reveals thatneuroinflammation induces micronuclei formation in the brain
Sci Rep 11, 18360 (2021)
Okajima T, Tsuruta F
Exploring genes that control microglial heterogeneity and transition.
Neural Regen Res. 16:2397-2398 (2021)
Okajima T, Gu Y, Teruya R, Yano S, Taketomi T, Sato B, Chiba T, Tsuruta F
Atypical cadherin FAT3 is a novel mediator for morphological changes of microglia
eNeuro. ENEURO.0056-20.2020 (2020)
Kim J, Nakamura J, Hamada C, Taketomi T, Yano S, Okajima T, Kashiwabara SI, Baba T, Sato B,
Chiba T, Tsuruta F
USP15 deubiquitinates TUT1 associated with RNA metabolism and maintains cerebellar homeostasis
Mol. Cell Biol. 40:e00098-20 (2020)

Hiroshi Wada
Evolutionary Developmental Biology
hwada@biol.tsukuba.ac.jp
http://www.biol.tsukuba.ac.jp/~hwada/index.html
Our interest is in the evolutionary processes of various animal body plans. We are especiallyinterested in the following issues.
1) Establishment and evolution of the chordate body plan. Chordates acquired several novel
characters such as notochord, dorsal central nervous system, vertebrae, and pharyngeal arches.
We explore how these novel organs evolved by comparing developmental genetics inamphioxus and lampreys.
2) Evolution of echinoderm larval morphology. Echinoderms show two types of larvae,
pluteus and auricularia. We asked how these discrete larval morphologies evolved bycomparing developmental genetics in sea urchins and starfish.
3) Evolution of bivalve shell plate in bivalve mollusks. Bivalve mollusks acquired bilaterally
separated shell plates, and this unique morphology is visible as early as the gastrula stage,
showing that the separated shell plates are established by modifying their early
embryogenesis.
4) Establishment of the unique body plan of caprellids. The unique body plan of the caprellids
was established from a gammarid-like body plan through the loss of some thoracic limbs andabdominal segments. We are seeking the genetic modification response for this loss. We areinterested in this phenomenon because some caprellid species re-acquired the limbs.
Expression of pax3/7 and soxE, whose
homologues
areinvolvedinthedifferentiation of the dorsal neural tube invertebrates, mark dorsal part of the acorn
worm nerve cord, showing that acorn worms
possess similar DV patterning mechanism intheir nerve cord. (Miyamoto and Wada,
Nature Comm. (2013).

Publications
1.

2.
3.

Suzuki, D. G., Murakami, Y., Escriva, H. and Wada. H. (2015) A comparative
examination of neural circuit and brain patterning between the lamprey andamphioxus reveals the evolutionary origin of the vertebrate visual center. J. Comp.
Neurol. 523, 251-261.
Miyamoto, N. and Wada. H. (2013) Hemichordate neurulation and the origin of theneural tube. Nat. Comm. 4, 2713
Morino, Y., Koga, H., Tachibana, K., Shoguchi, E., Kiyomoto, M. and Wada. H. (2012).
Heterochronic Activation of VEGF Signaling and the Evolution of the Skeleton in
Echinoderm Pluteus Larvae. Evol. Dev. 14, 428-436.

Shigeki Wada
Biological Oceanographyswadasbm@shimoda.tsukuba.ac.jp
https://sites.google.com/site/wadasbm/home
Keywords: biogeochemistry, carbon sequestration, ocean acidification------------------------------------------------------------------------------------------------Marine ecosystems have face serious threat from environmental change. To mitigate and adapt
against those issues, we have to understand the mechanisms of ecosystems and thereby predictthe response to environmental stressors. Our laboratory has mainly focused on three topics; 1)
Ecosystem response to ocean acidification, 2) Estimation of Blue Carbon, and 3) Mechanismsof marine snow formation.
1) Ecosystem response to ocean acidification: Ocean acidification is caused by anthropogenic
CO2 emission. A part of CO2 released by human activity is absorbed to surface ocean, anddisturbance of carbonate chemistry leads serious effects on marine organisms. Using natural
analogues of ocean acidification; volcanic CO2 seeps, we have assessed the response ofmarine ecosystems to ocean acidification.
2) Blue Carbon: Coastal vegetation such as macroalgae and seagrass has been recently focusedas carbon sink termed as Blue Carbon, because a part of organic carbon derived from theirphotosynthetic products is sequestrated into sediment and deep sea. We trace the fate ofphotosynthetic products to understand their contribution to Blue Carbon
3) Marine snow, particles settling to deep sea, has a role as a carrier of organic carbon, and its
contribution to carbon sequestration buffers climate change. Combination of biological andphysical process would be important in the mechanism of marine snow formation, but it has
been largely unknown. We have assessed the effect of physical disturbance to dynamics ofmarine snow to understand the mechanisms of carbon sequestration in pelagic ecosystems.
1231) Normal (upper) and highCO2 (lower) sites,2) Survey in marine forest of
macroalgae
3) Marine snow formed byphysical disturbance------------------------------------------------------------------------------------------------Selected publications
1.

2.
3.
4.

Wada, S. et al. (2021). Ocean acidification increases phytobenthic carbon fixation andexport in a warm-temperate system. Estuarine, Coastal and Shelf Science 250:107113.
Wada, S. et al. (2020). Seasonal dynamics of seawater CO2 system at a coastal site near
the southern tip of Izu Peninsula, Japan. Journal of Oceanography 76:227-242.
Wada, S. et al. (2020). Aggregation of marine organic matter by bubbling. Journal of
Oceanography 76:317-326.
Wada, S. & Hama, T. (2013). Conttribution of macroalgae to coastal dissolved organic
matter pool. Estuarine, Coastal and Shelf Science 129:77-85.

Matthew Wood
Science Communication
mattwood@biol.tsukuba.ac.jp

Carefully considered public communication of science and related issues is vital fora healthy relationship between science and the society that both depends on and supports it. It
is becoming increasingly apparent that this communication is multifaceted, highly complex,
and must be better understood to face the challenges of our progressively science-reliant
society.
I have broad academic interests in the areas of public perceptions of science andscientists; the portrayal of science in news and the media; risk perception; and the use ofvisual media to communicate science concepts and issues in informal education settings.
I develop and conduct undergraduate and postgraduate courses in communication
skills and introductory science communication. These courses are designed to equip students
to effectively communicate their future research. In a previous life I trained in marine biology
and environmental chemistry, and worked on projects searching for potential new drugs frommarine invertebrates.

Shunsuke Yaguchi
Developmental Biology(Shimoda Marine Research Center)yag@shimoda.tsukuba.ac.jp
https://sites.google.com/site/yaguchisea/english
Keywords: sea urchin, nervous system, neural function, axis specification------------------------------------------------------------------------------------------------The primary research goal of our lab is to understand the molecularmechanisms of embryonic axis specification and formation in thesea urchin. It has been suggested that this embryo has two
independent, maternally specified axes, primary (anterior–posterior) and secondary (dorsal–ventral). My previous work
showed that specification of these two axes is linked by a single
transcription factor, FoxQ2, during early embryogenesis. My goal is
to try to understand how FoxQ2 isrelated to, or interacts with, signaling
pathways like the Wnt/ß-catenin, Nodal,
and BMP2/4, which are responsible foraxis specification and formation.
Another research goal is to understandthe molecular mechanisms ofneurogenesis and neural functions,
including the specification andpatterning of the neurogenic ectoderm
that develops at the anterior end of
the sea urchin embryo.

Recently we have succeeded
to make genetically modified
sea urchins like albino by
applying CRISPR/Cas9.

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Yaguchi J, Yaguchi S. Sea urchin larvae utilize light for regulating the pyloric opening.
BMC Biology. 2021; 19:64
Yaguchi S, Yaguchi J, Suzuki H, Kinjo S, Kiyomoto M, Ikeo K, Yamamoto T.
Establishment of homozygous knock-out sea urchins. Current Biology. 2020; 30:R427429.
Yaguchi J, Yaguchi S. Evolution of nitric oxide regulation of gut function. Proc Natl
Acad Sci USA (PNAS). 2019; 116:5607-5612. DOI: 10.1073/pnas.1816973116
Yaguchi J, Yamazaki A, Yaguchi S. Meis transcription factor maintains the neurogenic
ectoderm and regulates the anterior-posteriot patterning in embryos of a sea urchin,
Hemicentrotus pulcherrimus. Dev . Biol. 2018;444:1-8.
Suzuki H, Yaguchi S. Transforming growth factor-ß signal regulates gut bending in thesea urchin embryo. Dev Growth Differ. 2018;60:216-225.

Kensuke Yahata
Arthropod phylogeny and systematics
yahata.kensuke.gf@u.tsukuba.ac.jp
https://trios.tsukuba.ac.jp/en/researcher/0000001154
Keywords: Arthropoda, comparative morphology, phylogeny, systematics------------------------------------------------------------------------------------------------The Phylum Arthropoda is known to have a huge species diversity. And there is also great
diversity in the morphology of various organs and tissues. Although morphological features ofmany organs and tissues have been investigated in the past centuries, there will be many
structures that we do not know well yet. Some of these unknown structures may have importantphylogenetic significance. In my laboratory, we are clarifying the phylogenetic significance ofthe characteristics newly discovered in the arthropods from the viewpoint of comparative
morphology. The following are two examples of our research.
In one project, we identified distinctive structure in ovaries of myriapods. Although the
Myriapoda has been known to have few new traits that characterize the taxon, this ovarian
structure is considered to have important phylogenetic significance as an undoubted
synapomorphy of the Myriapoda. In another project, we newly found some structures forappendage autotomy in centipedes. And we clearly suggested that the difference in the degreeof development of the autotomic structures is related to the frequency of their autotomic
behaviors and that the difference also corresponds to their order level phylogeny. Our researches
will not only add new insights to arthropod morphology but also contribute to a better
understanding of arthropod phylogeny and evolution.

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Chikami, Y. and K. Yahata (2019) Comparative morphology of ovarian follicle in two
polydesmid millipedes: evolutionary implication on folded structure of follicle epitheliumin Polydesmida (Myriapoda: Diplopoda). Proc. Arthropod. Embryol. Soc. Jpn., 52, 1–9.
Yahata, K., E. Umetani and Y. Chikami (2018) Morphological study of the ovary in
Hanseniella caldaria (Myriapoda; Symphyla): The position of oocyte-growth andevolution of ovarian structure in Arthropoda. Arthropod Structure and Development, 47,
655–661.
Niikura, M., M. Honda and K. Yahata (2015) Phylogeography of Semiterrestrial Isopod,
Tylos granuliferus, on East Asian Coasts. Zool. Sci., 32, 105–113.
Suguro, T. and K. Yahata (2014) Taxonomic notes on Japanese species of the genera
Pseudicius and Tasa (Araneae: Salticidae). Acta Arachnol., 63, 87–97.
Miyachi, Y. and K. Yahata (2012) Morphological study of ovarian structures inscolopendromorph centipedes (Myriapoda: Chilopoda) with special reference to theposition of oocyte growth. Proc. Arthropod. Embryol. Soc. Jpn., 47, 21–28.
Matsui, A. and K. Yahata (2012) Study of autotomic structure in centipedes (Arthropoda:
Chilopoda). Proc. Arthropod. Embryol. Soc. Jpn., 47, 11–19.