[Environments and Biotechnology] Year Started : 2020

Ayumi Agata

Elucidation of environmental plasticity of inflorescence morphology in wild Oryza

Researcher
Ayumi Agata

NIG Postdoctoral Research Fellow
National Institute of Genetics
Research Organization of Information and Systems

Outline

Plant inflorescence morphology is the most important factor affecting crop productivity. However, the mechanism of the plasticity of inflorescence morphology under environmental stress condition is largely unknown. In this project, I will elucidate the molecular basis of the diversity of inflorescence morphology and the plasticity of inflorescence morphology which changes in response to environmental stress by molecular genetic techniques using wild Oryza collections. Understanding these mechanisms will help us to design the inflorescence architecture that shows resilience to environmental changes for food stability.

Nobuyuki Okahashi

Development of an omics-data integratation platform for estimating novel metabolites and their enzyme genes

Researcher
Nobuyuki Okahashi

Associate Professor
Graduate School of Information Science and Technology
Osaka University

Outline

In order to realize a sustainable society, there is a growing need to discover and utilize functional metabolites and their producing enzyme genes from unused microorganisms. In this study, we will develop an information analysis platform for estimating the structure of unidentified compounds and the function of unknown genes by integrating untargeted metabolome and whole genome data of microorganisms.

Zen-ichiro Kimura

Establishment of specific isolation methods for environmental microorganisms using target gene mutation

Researcher
Zen-ichiro Kimura

Associate Professor
Civil and Environmental Engineering
National Institute of Technology (Kosen), Kure College

Outline

The vast majority of microorganisms in the environment cannot be isolated. There are many factors that prevent isolation. One thing is certain, human technology has not even established a tactic for “acquiring targeted bacteria from the environment” yet. The proposed research aims to establish a gene-targeted, arbitrary microbial isolation technology (i.e., a technology to isolate targeted bacteria) based on genome editing.

Naoyoshi Kumakura

Elucidation of infection mechanism using a multiplex gene disruption method

Researcher
Naoyoshi Kumakura

Researcher
Center for Sustainable Resource Science
Riken

Outline

Plant pathogenic fungi complete their infection utilizing virulence factors that suppress plant immunity. However, it has been difficult to identify virulence factors by conventional methods likely due to the redundancy of virulence factors. In this study, I will identify virulence factors of plant pathogenic fungi and their target factors in host plants using a newly developed experimental system that allows multiple gene disruptions both in a pathogenic fungus and its host plant. The expected findings of this study will contribute to disease-resistance breeding of crops and the development of pesticides with low environmental impact.

Yasunori Saitoh

Structural analysis of a crop silicic acid transporter.

Researcher
Yasunori Saitoh

Assistant Professor (Specially appointed)
Research Institute for Interdisciplinary Science
Okayama University

Outline

Crops acquire tolerance to various environmental stresses such as insect damage, strong winds, and soil mineral deficiencies etc. by taking up silicon from soil. Therefore, the function of silicic acid transporter, which are responsible for silicon uptake, is directly related to grain yield, but the transport mechanism is poorly understood. In this project, I will elucidate the structure of crop silicic acid transporter at the atomic level. Based on the obtained structural information, I will analyze the function of the mutants to elucidate the silicic acid transport mechanism.

Atsushi Shibai

Developing a feedback control system for cellular states by an automatic culture system and machine learning techniques

Researcher
Atsushi Shibai

Research Scientist
Center for Biosystems Dynamics Research
RIKEN

Outline

Living cells are dynamical systems with even their spontaneous internal dynamics. Therefore, the realization and control of arbitrary cellular states essentially require feedback controls. In this study, I will attempt to realize new feedback control systems for the cell state of bacteria, yeast, and cultured cells, respectively, using an automatic culture system. These contribute to the creation of innovative automated technologies that dynamically control and stabilize the cell state through external manipulation.

Haruhiko Jimbo

External control of photosynthetic activity by using fatty acids

Researcher
Haruhiko Jimbo

Assistant Professor
Graduate School of Arts and Sciences
The University of Tokyo

Outline

Free fatty acids (FFA), essential substrates for membrane lipids and cellular storage compounds, differ broadly in terms of lengths, unsaturations, and the cis/trans moieties. I have discovered that different FFA compounds have different effects on the repair and damage of photosystem II (PSII). My research aims to design advanced FFA to externally control photosynthetic activity by changing its sensitivity to photoinhibition. I will model the effects of FFA on the photoinhibition of PSII by taking advantage of the diversity of FFA and the proteomic analysis of lipid-modified proteins.

Hirobumi Sunayama

Development of nano-interfaces with highly integrated molecular recognition-based functional molecules for ultra-sensitive detection of virus

Researcher
Hirobumi Sunayama

Associate Professor
Graduate School of Engineering
Kobe University

Outline

Technological developments for achieving highly sensitive and selective detection of analytes such as hormones, lipids, amino acids, proteins, virus and cells, are of great importance in the field of life sciences. The aim of this project is to develop synthetic polymer-based nano-interfaces in which both molecular recognition elements for capturing virus and fluorescent signaling molecules for readout of the binding events are integrated for ultra-sensitively detecting virus. This technology could diagnose viral infections more precisely, facilitating the understanding on virus-related phenomena.

Toshiyuki Takagi

Ecoprobiotics: increasing coral adaptability to climate change through microbiome engineering

Researcher
Toshiyuki Takagi

Assistant Professor
Atmosphere and Ocean Research Institute
The University of Tokyo

Outline

Coral reefs only occupy 0.1% of the area of the sea but harbor approximately 25% of all marine species. Therefore, they are extremely important ecosystems for the conservation of biodiversity. However, many species of corals are on the verge of extinction because of increasing anthropogenic disturbances, including global warming. The mass bleaching events of coral reefs triggered by rising ocean temperature have been increasing over the last few decades, causing reef degradation on a global scale. In this project, I propose the concept of ecoprobiotics that preserves the coral reef ecosystems by the abilities of microorganisms, and aim to create innovative breeding methods using microbiome engineering that save coral reefs of the world.

Ryoma Takeshima

Genetic analysis of inbreeding depression in plants

Researcher
Ryoma Takeshima

Researcher
Institute of Crop Science (NICS)
National Agriculture and Food Research Organization (NARO)

Outline

This project aims to reveal the molecular genetic mechanisms of inbreeding depression using common buckwheat, an outcrossing crop. Using the inbred lines of buckwheat, I will attempt to develop a quantitative evaluation system of inbreeding depression traits, identify the genetic loci, and reveal the molecular mechanism by methylome/transcriptome analysis. These research results could contribute to creating new, environmentally adapted crops that avoid inbreeding weaknesses.

Yoko CHIBA

Revisiting the Km values of enzymes: The search for factors that determine optimal values

Researcher
Yoko CHIBA

Senior Scientist
Center for Sustainable Resource Science
RIKEN

Outline

Why is it that different organisms may have enzymes that catalyze the same reaction but have different genetic backgrounds and/or kinetic parameters? This study focuses on the Km value, a kinetic parameter that indicates the affinity between the enzyme and the substrate and will answer this question by applying an evaluation method used in catalytic chemistry. Furthermore, we aim to apply the findings to provide guidelines for designing enzymes suitable for chemical production systems.

Teppei Niide

Computational design of metabolic pathways guided by structure-based enzyme engineering

Researcher
Teppei Niide

Assistant Professor
Graduate School of Information Science and Technology
Osaka University

Outline

Redesign of the metabolic network in cells is essential to developing useful cells for the eco-friendly production of numerous compounds, including fuels and drugs. However, cells’ metabolic systems are complicated and elusive since several thousands of proteins that have each role in maintaining life are involved in cells. Besides, the proteins’ activities are strictly regulated by other proteins, metabolites, and external factors. By pursuing this project, we will apply protein engineering and genome-scale modeling to rational metabolic pathway design for the potential practical use of cell factories for our society in the future. Additionally, we aim to add an artificial cell metabolic pathway by the proteins from different organisms and viruses and de novo proteins to expand bioproduction capability.

Tomoki Nishioka

Basic research on artificial control of microbial communities for environmentally friendly managements of plant diseases

Researcher
Tomoki Nishioka

Collaborating Visitor
Bioproduction Research Institute
Advanced Industrial Science and Technology

Outline

In order to achieve sustainable agricultural production, it is urgent to establish an environmentally friendly control method of plant diseases. This project will conduct research that will lead to the establishment of a new environment friendly control measure of soil borne diseases based on microbiota control, which was suggested by focusing on the mode of soil borne diseases development. ‚ÄčIn particular, this study aims to obtain basic knowledge on artificial control of soil microbiota using microbial isolates, which is necessary for the establishment of a new environment friendly control method of soil borne diseases.

Yohei Nishikawa

Single-cell and Single-virus genomics for exploring host-phage interactions in aquatic environment

Researcher
Yohei Nishikawa

Junior Researcher
Research Organization for Nano & Life Innovation
Waseda University

Outline

Viruses are biologically classified as non-living organisms but are the most prevalent on Earth in terms of populations. Our understanding of phage diversity and classification is still limited although the importance of the bacteriophages has been advocated in a variety of environments, including the aquatic environment. Hence, this project aims to develop a technology for single-virus genome sequencing with droplet microfluidics. This project will expand the virus genome database by obtaining high-throughput and high-accuracy genome sequences on virus particles in the aquatic environment. Furthermore, this project will reveal “how often” “what kinds of viruses” infect “what kinds of bacteria” by acquiring the draft genomes of the host microbiomes as well.

Akihiro Ninomiya

Development of fungal secondary metabolism using viral genome

Researcher
Akihiro Ninomiya

Research Associate
Graduate School of Agricultural and Life Sciences
The University of Tokyo

Outline

As is often with bacteria, fungi are infected with viruses called mycoviruses. The aim of this study is to establish methods for development of fungal secondary metabolism using viral genome. I will search for viruses or their genes, which promote fungal secondary metabolism, using a model fungus Aspergillus fumigatus. Then, I will utilize such viral factors for search for new natural products, and for efficient production of industrially important fungal secondary metabolites.

Kaisei Maeda

Functions of sulfated polysaccharides in cyanobacterial biofilms

Researcher
Kaisei Maeda

Research Fellow
Faculty of Life Sciences
Tokyo University of Agriculture

Outline

Cyanobacteria, the oxygen-generating photosynthetic bacteria, uniquely contains sulfated extracellular polysaccharides among bacteria. In a model cyanobacterium, I have revealed the sulfated polysaccharide-dependent biofilm formation and biosynthesis and regulation genes of the sulfated polysaccharide synthesis and regulation in a model cyanobacteria specie. Based on this finding and other reports, I hypothesized that sulfated polysaccharides probably play important roles in the formation and function of various cyanobacterial biofilms in nature. In this study, I will establish transformation systems and analysis methods for some cyanobacterial species including non-model ones, that accumulate polysaccharide sulfate, to reveal the functions of the polysaccharides in cyanobacterial biofilm.

Keisuke Miyazawa

Super-resolution AFM for visualizing surface and inside of biological samples

Researcher
Keisuke Miyazawa

Assistant Professor
College of Science and Engineering
Kanazawa University

Outline

In the research field of biotechnology, an analysis technique for visualizing biological samples in liquid with molecular-scale resolution has been strongly demanded to understand the structures and functions of biological samples at the molecular level for development of new biological functions and expansion of applied technologies using biotechnology. In this research, I develop a super-resolution atomic force microscopy in liquid with an atomically controlled AFM tip with a diameter of 0.4 nm to establish the measurement technique for visualizing surface and inside of unstained biological samples in liquid with subnanometer-scale resolution.

Yuta Miyoshi

Research for the control of photosynthate translocation

Researcher
Yuta Miyoshi

Researcher
Takasaki Advanced Radiation Research Institute
National Institutes for Quantum and Radiological Science and Technology

Outline

We aim to establish the efficient cultivation system that can recover the input energy for crop cultivation as a harvest by controlling the photosynthate translocation inside the plant and concentrating the translocation to edible parts. In this study, to obtain the fundamental knowledge, we will use positron emitting tracer imaging system to visualize the movement of nutrient elements inside the plant and challenge to clarify how genes expressed in specific tissues and organs function to regulate translocation throughout the plant.

Yuri Yoshida

Elucidation of the Molecular Basis of Plant-Microbe Interaction in Seeds via Secondary Metabolites produced by Wild Oryza.

Researcher
Yuri Yoshida

Project Researcher
National Institute of Genetics
Research Organization of Information and Systems

Outline

The seeds of many wild plant species exhibit deep seed dormancy. Despite the presence of harmful microorganisms in the soil, the dormant seeds can survive for a long time without decay. However, the defense mechanism against microbial attack in seeds is still unclear. In this study, I will clarify the genetic factors and plant molecules involved in the suppression of microbial invasion and infection of seeds, using wild Oryza as a model. The findings of this research can be applied to improve the quality and long-term storage of crop seeds by taking advantage of the potential of wild plant genetic resources.

Masahiko Yoshimura

Control of biosynthesis by protein polymerization technology

Researcher
Masahiko Yoshimura

Designated Assistant Professor
Institute for Advanced Study
Kyoto University

Outline

Plant-derived small molecules are used for medicinal drugs and building blocks of chemical synthesis. Therefore, controlling complex plant biosynthesis would be an innovative technology for a sustainable materials production. In this project, we develop a novel chemical-based technology that induces in vivo protein polymerization leading to control of biosynthesis.

Shogo Yoshimoto

Molecular design of enzyme complexes for degrading solid substrates

Researcher
Shogo Yoshimoto

Project Assistant Professor
Graduate School of Engineering
Nagoya University

Outline

Polymeric wastes such as plastics and rubber accumulate in the natural environment for long periods. Biocatalytic (enzymatic) decomposition has been the focus of attention as an environmentally friendly way to recycle polymeric materials, but the degradation is extremely low. This study aims to improve the rate of degradation of polymeric materials that are solid substrates, by assembling enzymes.

Takatoshi Wakabayashi

Tailor-made creation of crops resistant to root parasitic weeds

Researcher
Takatoshi Wakabayashi

Research Associate
Graduate School of Agricultural Science
Kobe University

Outline

Root parasitic weeds, which are causing devastating damage to agricultural production all over the world, germinate by sensing strigolactones (SLs) produced by and released from roots of host plants. The structures of SLs are diverse, and the germination inducing activity of SLs against each root parasitic weed differs depending on its structure. This project aims to create root parasitic weed resistant crops by modifying SLs originally produced by a particular crop to SLs with low germination inducing activity against root parasitic weeds that are infested to that crop through elucidating the SL biosynthesis mechanism in host crops.

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