Biology subjects

Horinouchi, T.

Publications and source records attributed to Horinouchi, T..

3 recordsLinked to original sources

bioRxiv2024

Evaluation of Microplate Handling Accuracy for Applying Robotic Arms in Laboratory Automation

An inexpensive single-arm robot is widely utilized for recent laboratory automation solutions. The integration of a single-arm robot as a transfer system into a semi-automatic liquid dispenser without a transfer system can be realized as an inexpensive alternative to a fully automated liquid handling system. However, there has been no quantitative investigation of the positional accuracy of robot arms required to transfer microplates. In this study, we constructed a platform comprising aluminum frames and digital gauges to facilitate such measurements. We measured the position repeatability of a robot arm equipped with a custom-made finger by repeatedly transferring microplates. Further, the acceptable misalignment of plate transfer was evaluated by adding an artificial offset to the microplate position using this platform. The results of these experiments are expected to serve as benchmarks for the selection of robot arms for laboratory automation in biology. Furthermore, all information for replicating this device will be made publicly available, thereby allowing many researchers to collaborate and accumulate knowledge, hopefully contributing to advances in this field.

systems biology↗

bioRxiv2020

High-throughput laboratory evolution and evolutionary constraints in Escherichia coli

Understanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation for evolutionary constraints is lacking. Here, we performed a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Using interpretable machine learning techniques, we analyzed the phenotype-genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis revealed the underlying biological processes responsible for these distinct states, leading to the identification of novel trade-off relationships associated with drug resistance. We also report a novel constraint that leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space and lead to a better understanding of evolutionary constraints for antibiotic resistance.

evolutionary biology↗

bioRxiv2017

High-Throughput Laboratory Evolution Of Escherichia coli Under Multiple Stress Environments

Bacterial cells have a remarkable capacity to adapt and to evolve to environmental changes. Although many mutations contributing to adaptive evolution have been identified, the relationship between the mutations and the phenotypic changes responsible for fitness gain has yet to be fully elucidated. For a better understanding of phenotype-genotype relationship in evolutionary dynamics, we performed high-throughput laboratory evolution of Escherichia coli under various stress conditions using an automated culture system. One measure of phenotype, transcriptome analysis, revealed that the expression changes which occurred during the evolution were generally similar among the strains evolved in the same stress environment. We also found several genes and gene functions for which mutations were commonly fixed in the strains resistant to the same stress, and whose effects on resistance were verified experimentally. We demonstrated that the integration of transcriptome and genome data enables us to extract the mechanisms for stress resistance.\n\nAuthor summaryUnderstanding the relationship between phenotypic and genetic changes is a fundamental goal in evolutionary biology, which can provide insights into the past and future evolutionary trajectories. Evolution of microorganisms in a laboratory has been the primary approach to clarify the mappings of phenotypic and genotypic changes. Here, we performed high-throughput laboratory evolution with bacteria using an automated culture system, to quantify phenotypic and genotypic changes occurred under various stress conditions. We identified various stress-specific gene expression changes and mutations, and contributions of them to fitness gain were validated. These results demonstrated that the integration of phenotypic and genotypic changes makes it possible to extract the mechanisms for stress resistance evolution, which will contribute to bioengineering applications.

evolutionary biology↗