[Environments and Biotechnology] Year Started : 2021

Ryota Akiyama

Elucidation of the biosynthesis of hatching factor for cyst nematode and its application to novel control method 

Researcher
Ryota Akiyama

Researcher
Graduate School of Agricultural Science
Kobe University

Outline

Cyst nematodes are highly evolved sedentary endoparasites that are considered as harmful pests worldwide. The hatching of the dormant eggs of cyst nematodes occurs in response to hatching factors, which are compounds that are secreted from the roots of host plants. Therefore, understanding of hatching factors is essential for effective control of cyst nematodes. The purpose of this project is to elucidate the biosynthetic pathway for hatching factors, which was completely unknown until now. Furthermore, the goal is to develop a novel cyst nematode control method using the information about hatching factors biosynthesis.

Naoki Azuma

Single molecule analysis of DNA using plasmonic nanochannels

Researcher
Naoki Azuma

Assistant Professor
Engineering
Nagoya University

Outline

DNA size analyses have been utilized for epidemiological analyses of infectious bacterium and viruses. In the conventional methods such as gel electrophoresis, a large number of DNA fragments are required for the analysis. However, the amplification process of the DNA fragments hinders the realization of the DNA analysis with high speed. The objective of this project is to realize a single molecule analysis of DNAs using plasmonic nanochannels. The method enables DNA size analysis with high speed and high accuracy because the method can eliminate the amplification process by a single molecule analysis.

Ryo Iwama

Roles of extracellular aliphatic compounds acting on biomembrane composition

Researcher
Ryo Iwama

Assistant Professor
Graduate School of Agricultural and Life Sciences
The University of Tokyo

Outline

A wide variety of aliphatic compounds exist in natural environment and are thought to act on the biological membranes of various organisms due to their hydrophobic nature, but their effects on the entire biological membrane are not comprehensively understood. In this study, I will quantify the effects of extracellular aliphatic compounds on the biomembrane composition of eukaryotic microorganisms, and analyze how cellular functions are altered in the presence of the compounds. I will develop the field for exploring microbial functions using aliphatic compounds altering biomembrane properties.

Ryo Kato

Nanoscale hybrid vibrational spectroscopy for biomolecular functional analysis

Researcher
Ryo Kato

Designated Assistant Professor
Institute of Post-LED Photonics
Tokushima University

Outline

Chemical characterization and analysis of biomolecules at the single molecule level is essential for development of biotechnology since chemical properties of biomolecules dominate their biomolecular functions. In this project, I develop a nanoscale hybrid vibrational spectroscopic technique to analyze any vibrational signatures of a single molecule based on both Raman scattering and infrared absorption, and to reveal chemical dynamics of a single biomolecule and influence of molecular interactions on biomolecular functions of biomolecules.

Keiichiro Koiwai

Interaction analysis between immune cells and bacterial flora in hemolymph of shrimp and it’s utilization in aquaculture

Researcher
Keiichiro Koiwai

Assistant Professor
Faculty of Marine Science
Tokyo University of Marine Science and Technology

Outline

Although shrimps are actively cultivated, how their immune function is controlled is still unknown. I will reveal how shrimp overcome pathogen by analyzing the interactions of the immune cells and bacterial flora in the hemolymph of shrimp during pathogen infection. This research will lead to the establishment of a screening method for new immunostimulants, and will contribute to environment-friendly aquaculture technology that does not use antibiotics.

Shizuka Koshimizu

Micro structures producing structural color in flowers -creating the foundation to realize photonics agriculture-

Researcher
Shizuka Koshimizu

Assistant Professor
School of Agriculture
Meiji University

Outline

Structural color is coloration produced as results of optical interference caused by micro structures. Some plant flowers have the structural color. To create crops, which do not need pesticides and agents promoting fruit set, becomes possible by using visual effects of the flower’s structural color against insects. In addition, to create multicolored materials harmless to human body also becomes possible because flower’s structural color is by micro structures in cell wall. ​In this study, I will analyze the mechanisms to form micro structures producing structural color in flowers aimed at development of new technology in agriculture and industry.

Yuki Sakamoto

A novel environmental response system based on organelle attachment

Researcher
Yuki Sakamoto

Assistant Professor
Graduate School of Science
Osaka University

Outline

Organelles in plant cells respond to various environmental stimuli by communicating closely with each other. In this project, I focus on the physical attachment of organelles, which is direct communication between organelles. I will use proteomics-based methods to elucidate the molecular mechanisms that regulate the attachment of organelles. This research will contribute to the creation of crops that are adapted to environmental changes.

Michitaro Shibata

A gene regulatory network of root hairs as a mechanism of environmental response

Researcher
Michitaro Shibata

Visiting Scientist
Center for Sustainable Resource Science
RIKEN

Outline

Plants control their own “growth” in response to the surrounding environments. The growth of root hairs, for example, is well regulated depending on soil conditions in order to increase insufficient nutrients. Thus, this study aims to reveal the molecular mechanisms behind the plasticity of plant growth by using Arabidopsis root hairs in the context of gene regulatory networks. Furthermore, based on this achievement, I aim to establish a technology to freely control plant growth.

Taisuke Seike

Phenotypic evaluation of wild yeasts isolated from Drosophila and construction of industrial yeast strains

Researcher
Taisuke Seike

Assistant Professor
Graduate School of Information Science and Technology
Osaka University

Outline

In microbial cell factories for production of chemicals, fuels, and materials, non-model yeasts have been increasingly expected to be used due to their unique physiology and metabolic capabilities, in addition to the budding yeast Saccharomyces cerevisiae. In this study, I will evaluate the characteristics of many wild yeasts isolated from fruit flies, Drosophila, and attempt to construct useful industrial yeast strains by using evolutionary engineering such as horizontal gene transfer and mating. I aim to organize the genetic information of isolated wild yeasts by finding their potential functions (e.g., genes and metabolites) toward the realization of a sustainable society.

Daisuke Takagi

Elucidation of phytic acid-dependent mechanisms for regulating mRNA transport through nuclear pore in land plants

Researcher
Daisuke Takagi

Assistant Professor
Faculty of Agriculture
Setsunan University

Outline

Preliminary results suggest that the increase in phytic acid concentration negatively regulates mRNA transport activity through the nuclear pores and dynamically changes transcriptome in plant cells. In this project, I will quantitatively evaluate the effects of phytic acid concentration on mRNA transport activity using rice plants. Subsequently, I will elucidate a common sequence structure of genes that receive feedback control of phytic acid-dependent mRNA transport, and the molecular entity responsible for the feedback control.

Haruka Takagi

Identification of genes associated with photosymbiosis, the key process in marine biological deserts

Researcher
Haruka Takagi

Assistant Professor
Faculty of Science
Chiba University

Outline

In the warm and oligotrophic ocean, known as the marine biological desert, organisms that carry out “photosymbiosis,” or the intracellular symbiosis with algae, form minute photosynthetic hotspots. However, the molecular mechanism underlying photosymbiosis is still unknown. In this study, I will try to identify genes associated with photosymbiosis in a single-celled plankton called planktonic foraminifera. I aim to elucidate the molecular basis of photosymbiosis and to identify marker genes that can be used to evaluate the contribution of photosymbiosis to marine material cycling.

Hiraku Takada

Taking lessons from history ~novel facets of mechanism and regulation in bacterial translation ~

Researcher
Hiraku Takada

Postdoctoral Fellow
Faculty of Life Sciences
Kyoto Sangyo University

Outline

With the development of innovative technologies such as Cryo-electron microscopy, there has been a growing momentum to re-evaluate the work of our predecessors, especially in the field of translation research. I have recently revealed the existence of a novel quality control mechanism for abnormal translation (RQC: Ribosome-associated Quality Control) in B. subtilis. In this project, I aim to understand the full picture of the RQC pathway and to elucidate the novel environmental response mechanisms inherent in the translation machinery, which have been revealed in the course of the analysis.

Michiko Takahashi

Salvage of damaged viruses from the environment

Researcher
Michiko Takahashi

Project Assistant Professor
Medical School
Kochi University

Outline

Although it has been reported that viruses are abundant in aquatic environments by sequencing analysis, there are few reports regarding the isolation and/or cultivation of viruses from the environment. The reason for this may be that the viral capsid is damaged by various environmental stresses. This project aims to develop a virus-salvage method to obtain a variety of viruses including damaged viruses, as infectious particles by electroporation of virus genome into candidate host cells.

Jun Takeuchi

Study on the mechanism of high-temperature induced germination inhibition

Researcher
Jun Takeuchi

Associate Professor
Faculty of Agriculture
Shizuoka University

Outline

As global warming progresses, seed germination inhibition caused by high-temperature stress (thermoinhibition) has become a serious problem that affects crop productivity. Recent studies have suggested that KARRIKIN INSENSITIVE 2 (KAI2), a karrikin-binding protein, is involved in the regulation of thermoinhibition. However, plant endogenous ligands for KAI2 remains unclear. In this project, I aim to identify the endogenous KAI2 ligand that may function as a KAI2 antagonist by focusing on germination inhibitors and to thoroughly elucidate the mechanism of germination inhibition by high-temperature stress.

Kazutaka Takeshita

Molecular basis for adaptation of a bacterial symbiont to different host organisms

Researcher
Kazutaka Takeshita

Assistant Professor
Faculty of Bioresource Sciences
Akita Prefectural University

Outline

I have found that a beneficial bacterial symbiont of a plant can also establish another symbiotic interaction with an insect and function as an obligate symbiont of this insect. I supposed a common molecular basis for adaptation of this symbiont to these completely different host organisms. In this project, I explore such a common molecular basis by performing comparative transcriptome analysis of the symbiont within the insect and plant hosts, constructing genetically modified symbionts through genetic manipulation, and conducting infection experiments of the modified symbionts to both the insect and plant hosts.

Xiao Deng

Development of termite sensor based on electrochemical characteristics of termite gut cellulolytic bacteria

Researcher
Xiao Deng

Researcher
International Center for Materials Nanoarchitectonics (MANA)
National Institute for Materials Science

Outline

Detection of termite activities has been difficult because termites reside in underground soil or inside of wood. This project aims to develop a novel type of electrochemical biosensor for termites using soil and water samples collected at target sites and the surroundings. This project will also study the metabolic activities of termite gut bacteria from a view point of electrochemistry.

Takashi Nakanishi

Development of acid tolerant industrial Bacillus strains for enzyme production by artificial laboratory evolution.

Researcher
Takashi Nakanishi

Senior Scientist
R&D
Novozymes Japan Ltd.

Outline

Industrial enzymes are widely used to improve production efficiency in many industrial fields. They are mostly produced by microbial fermentation in bioreactors, however, available microbes for enzyme production are limited, which also limits the producibility of enzymes due to host dependent factors. To accelerate the production and application of new enzymes, this project employs laboratory evolution approach to develop an acid tolerant bacterial strain for enzyme production, which has never been found in the nature.

Tomoya Nakayama

Elucidation of the molecular basis of flexible and robust seasonal temperature adaptability

Researcher
Tomoya Nakayama

Designated Assistant Professor
Institute for Advanced Research
Nagoya University

Outline

Changes in seawater temperature due to global warming are seriously affecting ectothermic animals, including fish, in marine ecosystems. However, the mechanisms of temperature adaptation in ectothermic animals remain unclear. In this study, I aim to elucidate the molecular basis of the flexible and robust seasonal temperature adaptability of Japanese medaka (Oryzias latipes), a species inhabiting temperate regions. The study findings will provide fundamental knowledge for the conservation of marine ecosystems and for the development of countermeasures and adaptation technologies to address climate change in the fisheries industry.

Akifumi Nishida

Cell-free protein synthesis system of non-model bacteria developed by transfer learning

Researcher
Akifumi Nishida

Assistant Professor
Faculty of Life Sciences
Tokyo University of Agriculture

Outline

The cell-free protein synthesis (CFPS) system, used as a breadboard for genetic parts, have recently been developed from non-model bacteria. One of the bottleneck for developing the system of non-model bacteria is buffer composition. Therefore, in this study, utilizing machine learning model optimizing buffer composition of E. coli CFPS system as transfer learning, I establish a method for efficiently developing CFPS systems derived from other non-model bacteria.

Yosuke Nishimura

Elucidation of key factors for microbial adaptation through metagenomic big data analysis

Researcher
Yosuke Nishimura

Project Researcher
Research Institute for Marine Resources Utilization
Japan Agency for Marine-Earth Science and Technology (JAMSTEC)

Outline

How microbes have been adapted to various environments in the planet is a fundamental question in evolutionary biology and ecology. This study aims to establish a comprehensive information platform that characterizes environment-specific gene distribution through a development of bioinformatics approaches for cross-environment meta-analysis of a large-scale metagenome dataset. Utilizing the platform, I will elucidate key factors for microbial adaptation and discover prominent genetic resources within a huge pool of ‘function unknown’ genes derived from metagenomic big data.

Shohei Nosaki

Study on the pivotal transcription factor for the generation of the next Green Revolution

Researcher
Shohei Nosaki

Assistant Professor
Faculty of Life and Environmental Sciences
University of Tsukuba

Outline

The Green Revolution plants, which have led to increased food production around the world, exhibit the useful trait of being short and thus hard to fall, but have the disadvantage of reduced nitrogen absorption and the need for vast amounts of fertilizer. In this study, I focus on a pivotal transcription factor that has the potential in the generation of the next Green Revolution plant that overcomes the disadvantages of the current Green Revolution plants and elucidate the structural basis of its molecular function. In the next step, based on the obtained structure information, I will design a functional variant of the transcription factor that will lead to the next Green Revolution.

Akiko Hida

Elucidation of boric-acid-mediated infection mechanism in plant pathogenic bacteria

Researcher
Akiko Hida

Assistant Professor
Graduate School of Integrated Sciences for Life
Hiroshima University

Outline

Several plant pathogenic bacteria are attracted by boric acid. However, the meaning of this behavior is unclear. Based on some knowledge, I made a hypothesis that “boric acid leaks from a plant wound, which serves as a maker for pathogenic bacteria to invade the plant”. In this study, I will analyze a role of boric acid in infection by pathogens and the possibility of boric acid leakage from plants, and aim to elucidate the mechanism of boric-acid-mediated infection in plant pathogenic bacteria.

Chihaya Yamada

Analysis of the relationship between intestinal bacterial species using 13C-labeled human milk oligosaccharides

Researcher
Chihaya Yamada

Assistant Professor
Graduate School of Agricultural and Life Sciences
The University of Tokyo

Outline

During infant and weaning periods, forming what kinds of human gut microbiota is important, and affects subsequent health. Human milk oligosaccharides increase growth of bifidobacteria that produce acetate in the intestines of infants, but it has recently been discovered that the oligosaccharides also increase butyrate-producing bacteria. Therefore, I aim to understand the more accurate function of human milk oligosaccharides by clarifying the interspecies relationships of intestinal bacteria, mainly bifidobacteria, using 13C-labeled human milk oligosaccharides.

Toshiyuki Waki

Exploring intracellular dynamics of flavonoid biosynthesis

Researcher
Toshiyuki Waki

Assistant Professor
Graduate School of Engineering
Tohoku University

Outline

Intracellular metabolism is believed to be spatiotemporally controlled by a sequential metabolic enzymes complex, called a metabolon. In this project, I aim at elucidating the molecular dynamics of flavonoid metabolons by analyzing regulatory mechanisms of promiscuous enzyme specificity and substrate channeling via protein-protein interactions. The results obtained through this project will open the way to the Green Biotechnology for efficient production of high value added compounds.

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