Research concept

Jump to Research projects, Using microorganisms, Techniqus, Equipments

Microbial research to date has often involved direct analysis or modification of specific microorganisms. Although much infomation and knowledge has been obtained in this way, the unique functions and mechanisms of a particular microorganism can only be utilized in the cells of that microorganism. However, advances in genetic engineering have enabled heterologously expression of many genes and large-scale genome modification in several model microorganisms, making it possible to reproduce the functions (principles) of specific microorganisms by introducing them as genes. In this laboratory, we aim to understand and apply the specific function of a particular microorganism, and then to reproduce that function in a different microorganism. However, some genes are difficult to functionally express in phylogenetically different microorganisms. Until now, such genes whose functions are difficult to reproduce have been left untouched, and no progress has been made in accumulating knowledge on why these genes do not function in the microorganisms they are expressed in. Therefore, we aim to accumulate such knowledge and techniques.

The functions to be analyzed are mainly those related to catabolism. We are also interested in the relationship between catabolic metabolism and cell robustness.

Research projects

• Research on the unique metabolic mechanisms of microorganisms
  Propionate oxidation under anaerobic conditions requires a syntrophic relationship between propionate-oxidizing bacteria and hydrogenotrophic methanogens, but the oxidation of propionate involves unique metabolic mechanisms of each microorganism. Our research focuses on the mechanism by which propionate oxidizing bacteria produce hydrogen and formic acid from propionate. On the other hand, genes of microorganisms living in extreme environments may be able to confer their unique metabolism to other microorganisms. Currently, we are attempting to express genes unique to archaea living in highly alkaline environments in Escherichia coli.

• Research on metabolism and robustness of microorganisms
  We are studying the robustness of microorganisms, especially their response to heat and its relationship to metabolism. We are investigating which pathways are required by E. coli for growth at high temperatures and how the intermediate metabolites synthesized by these pathways are required for growth at high temperatures. On the other hand, we are studying how to optimally construct metabolic pathways in E. coli that produce specific substances.

• Research on visualization of gene function using microbial cells
  Genome modification is able to be carried out process, and fluorescent proteins and tags are helpful to monitor the expression of target genes. Using these techniques, we are investigating methods to visualize internal metabolism and protein expression, especially in E. coli.

Using microorganisms

• Escherichia coli
• Pelotomaculum thermopropionicum
• Methanothermobacter sp.
• Bacillus subtilis
• Corynebacterium glutamicum
• Cupriavidus necator
• Shewanella oneidensis

Techniqus

• Microorganism Culture
  • Culture medium
  • Culture with Oxygen
  • Culture without Oxygen
  • Culture with hydrogen
• Ultra-low temperature preservation of microorganisms
• Observation of bacteria
  • Fluorescence microscopy
  • Fluorescence observation on plates
• DNA extraction
  • Genome extraction
  • Plasmid extraction
  • Agarose gel electrophoresis
• DNA processing
  • PCR
  • Gibson assembly
  • iVec3
• Microbial transformation
  • Heat shock
  • Electroporation
  • Joining
  • P1 transduction
  • lambda RED recombination
• Protein extraction and analysis
  • Bacterial disruption
  • Ultracentrifugation
  • SDS-PAGE
  • Western blotting
  • Protein purification
• Substance analysis
  • Spectroscopic analysis
  • Fluorescence analysis
  • Gas chromatography
  • Liquid chromatography
  • Mass spectrometry
• Bioinformatics
  • Database Search
  • PCR Primer Design
  • Gene analysis
  • Genome Information Analysis
  • Transcriptome analysis
  • Other Omics Analysis
• Metabolism Simulation
  • Flax Balance Analysis
• Programming languages and programs
  • Ruby
    • Bioruby
  • R
    • Bioconductor
  • Python
    • cobrapy
  • Julia
  • SQL
    • SQLite3
  • Commandline tools
    • Homebrew
    • Primer3

Equipments

• Balances
• pH Meter
• Pure Water Production Equipment
  • ADVANTEC
• Sterilizer
• Clean bench
• Constant temperature machine
• Shaking temperature controller
  • TAITEC
  • Eppendorf ThermoMixer C
• Anaerobic chamber
  • Bacbasic
• Cell disruption system
  • MPB FastPrep 24
  • French press (common)
• Centrifuge
  • KUBOTA 3740
  • KUBOTA PlateSpin3
  • Hitachi Ultracentrifuge (common)
• Thermal Cycler
  • Applied Biosystems GeneAmp PCR System 2700
  • Bio-rad T100
  • Takara
• Electrophoresis system
  • Takara Mupid-exU
• Transilluminator
  • UV
  • LED 470 530
• Image Analyzers
  • ATTO PrintGraph
• Spectrophotometer
  • Shimadzu UV-1850
  • Berthold biochrom Libra S12
• Fluorescence Spectrometer
  • JASCO FP-6200
• Fluorescence microscope
  • Nikon type 120
• Bioanalyzer
  • Agilent 2100
• Deep freezer
• Freezer
• Refrigerator
• Refrigeration Chamber
• Gas Chromatography
  • Shimadzu GC-8A TCD
• Liquid Chromatography
  • Waters Alliance (common)
  • Shimadzu LDx (common)
• Protein Chromatography
  • Cytiva AKTAprime plus (loaner)