Soichiro Tsuda
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View article: From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance
From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance Open
How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were discovered for their role in antibiotic resistance. These rudimentary enzymes are evolutionarily di…
View article: A Combination of Two‐Enzyme System and Enzyme Engineering Improved the Activity of a New PET Hydrolase Identified from Soil Bacterial Genome
A Combination of Two‐Enzyme System and Enzyme Engineering Improved the Activity of a New PET Hydrolase Identified from Soil Bacterial Genome Open
We here report a novel PET hydrolase originating from a soil microbial genome sequence. This enzyme, bbPET0069, exhibits characteristics resembling a cutinase‐like Type I PET‐degrading enzyme but lacks disulfide bonds. Notably, bbPET0069 d…
View article: Performance Evaluation of High-performance Liquid Chromatography Instrument in Determining the Serum Concentration of Linezolid
Performance Evaluation of High-performance Liquid Chromatography Instrument in Determining the Serum Concentration of Linezolid Open
LM1010, a high-performance liquid chromatography system for therapeutic drug monitoring (TDM) of various agents in clinical practice, is currently approved in Japan. Unlike conventional systems, LM1010 can rapidly measure clinical samples,…
View article: Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism
Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism Open
Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA …
View article: Development of Chimera AMP–Endolysin with Wider Spectra Against Gram-Negative Bacteria Using High-Throughput Assay
Development of Chimera AMP–Endolysin with Wider Spectra Against Gram-Negative Bacteria Using High-Throughput Assay Open
Bacteriophage-derived endolysins are being developed as an alternative to antimicrobials. The development of endolysins against Gram-negative bacteria requires the discovery of effective endolysins against the target species and the capabi…
View article: A combination of two-enzyme system and enzyme engineering improved the activity of a new PET hydrolase identified from soil bacterial genome
A combination of two-enzyme system and enzyme engineering improved the activity of a new PET hydrolase identified from soil bacterial genome Open
We here report a novel PET hydrolase originating from a soil microbial genome sequence. This enzyme, bbPET0069, exhibits characteristics resembling a cutinase-like Type I PET-degrading enzyme but lacks disulfide bonds. Notably, bbPET0069 d…
View article: Uncovering novel endolysins against methicillin-resistant<i>Staphylococcus aureus</i>using microbial single-cell genome sequencing
Uncovering novel endolysins against methicillin-resistant<i>Staphylococcus aureus</i>using microbial single-cell genome sequencing Open
Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of endolysins is vital. We here pr…
View article: Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process Open
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under de…
View article: Author response: Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
Author response: Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Crustacean aquaculture is expected to be a…
View article: Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process Open
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under de…
View article: The Effect of Minimum Medical Conditions and Community Pharmacy Practice on Outcome in Hospital Pharmaceutical Practice
The Effect of Minimum Medical Conditions and Community Pharmacy Practice on Outcome in Hospital Pharmaceutical Practice Open
The Model Core Curriculum for Pharmacy Education (2013 version) presents eight disease areas as the minimum medical conditions that require student trainees to be continuously engaged in pharmacotherapy, during practical training at a comm…
View article: Establishment of a novel method for the production of chimeric mouse embryos using water-in-oil droplets
Establishment of a novel method for the production of chimeric mouse embryos using water-in-oil droplets Open
Production of chimeric animals is often a necessity for the generation of genetically modified animals and has gained popularity in recent years in regenerative medicine for the reconstruction of xenogeneic organs. Aggregation and injectio…
View article: A programmable chemical computer with memory and pattern recognition
A programmable chemical computer with memory and pattern recognition Open
View article: Establishment of a novel method for the production of chimeric mouse embryos using oil droplets
Establishment of a novel method for the production of chimeric mouse embryos using oil droplets Open
The production of chimeric animals is frequently necessary for the constructing genetically modified animals, and has gained popularity in regenerative medicine in the recent years for the reconstruction of xenogeneic organs. The aggregati…
View article: High-throughput screening of high protein producer budding yeast using gel microdrop technology
High-throughput screening of high protein producer budding yeast using gel microdrop technology Open
The need for protein production has been growing over the years in various industries. We here present a high-throughput screening strategy to isolate high producer budding yeast clones from a mutagenized cell population using gel microdro…
View article: Effects of Co-administration of Proton Pump Inhibitors on Methotrexate Elimination and Adverse Events
Effects of Co-administration of Proton Pump Inhibitors on Methotrexate Elimination and Adverse Events Open
Co-administration of methotrexate (MTX) and proton pump inhibitors (PPIs) is reported to increase serum MTX concentrations in patients receiving high-dose MTX therapy. However, the range of MTX high dosage is wide. We attempted to clarify …
View article: A programmable chemical computer with memory and pattern recognition
A programmable chemical computer with memory and pattern recognition Open
A programmable chemical computer with memory that can perform pattern recognition using a reaction-diffusion reaction is demonstrated
View article: A programmable chemical computer with memory and pattern recognition
A programmable chemical computer with memory and pattern recognition Open
A programmable chemical computer with memory that can perform pattern recognition using a reaction-diffusion reaction is demonstrated
View article: A Portable 3D-Printed Platform for Point-of-Care Diagnosis of Clostridium Difficile Infection and Malaria
A Portable 3D-Printed Platform for Point-of-Care Diagnosis of Clostridium Difficile Infection and Malaria Open
Here, we integrate 3D-printing technology with low-cost open source electronics to develop a portable diagnostic platform suitable for a wide variety of diagnostic and sensing assays. We demonstrate two different clinical applications in t…
View article: A Portable 3D-Printed Platform for Point-of-Care Diagnosis of Clostridium Difficile Infection and Malaria
A Portable 3D-Printed Platform for Point-of-Care Diagnosis of Clostridium Difficile Infection and Malaria Open
Here, we integrate 3D-printing technology with low-cost open source electronics to develop a portable diagnostic platform suitable for a wide variety of diagnostic and sensing assays. We demonstrate two different clinical applications in t…
View article: Using Evolutionary Algorithms and Machine Learning to Explore Sequence Space for the Discovery of Antimicrobial Peptides
Using Evolutionary Algorithms and Machine Learning to Explore Sequence Space for the Discovery of Antimicrobial Peptides Open
View article: Exploring Peptide Sequence Space Using Artificial Intelligence for Antimicrobial Peptides
Exploring Peptide Sequence Space Using Artificial Intelligence for Antimicrobial Peptides Open
View article: Uncovering cell-free protein expression dynamics by a promoter library with diverse strengths
Uncovering cell-free protein expression dynamics by a promoter library with diverse strengths Open
Cell-free protein expression systems have been widely used for synthetic biology and metabolic engineering applications in recent years. Yet little is known about protein expression in the cell-free systems. Here we take a systems approach…
View article: Adaptive artificial evolution of droplet protocells in a 3D-printed fluidic chemorobotic platform with configurable environments
Adaptive artificial evolution of droplet protocells in a 3D-printed fluidic chemorobotic platform with configurable environments Open
View article: Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro
Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro Open
View article: Population–reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems
Population–reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems Open
Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often re…
View article: Customizable 3D Printed ‘Plug and Play’ Millifluidic Devices for Programmable Fluidics
Customizable 3D Printed ‘Plug and Play’ Millifluidic Devices for Programmable Fluidics Open
Three dimensional (3D) printing is actively sought after in recent years as a promising novel technology to construct complex objects, which scope spans from nano- to over millimeter scale. Previously we utilized Fused deposition modeling …
View article: Shape Transformations of Lipid Vesicles by Insertion of Bulky-Head Lipids
Shape Transformations of Lipid Vesicles by Insertion of Bulky-Head Lipids Open
Lipid vesicles, in particular Giant Unilamellar Vesicles (GUVs), have been increasingly important as compartments of artificial cells to reconstruct living cell-like systems in a bottom-up fashion. Here, we report shape transformations of …
View article: Towards heterotic computing with droplets in a fully automated droplet-maker platform
Towards heterotic computing with droplets in a fully automated droplet-maker platform Open
The control and prediction of complex chemical systems is a difficult problem due to the nature of the interactions, transformations and processes occurring. From self-assembly to catalysis and self-organization, complex chemical systems a…