Biology subjects

Ozawa, Y.

Publications and source records attributed to Ozawa, Y..

4 recordsLinked to original sources

bioRxiv2023

Downregulation and delayed induction of photosynthesis by coordinated transcriptomic changes induced by sink-source imbalance

Understanding comprehensive mechanisms of the downregulation of photosynthesis induced by accumulation of non-structural carbohydrates (NSCs) is essential for the future food security.x Despite numerous studies, whether NSCs accumulation directly affects steady-state maximum photosynthesis and photosynthetic induction, as well as underlying gene expression profiles, remains unknown so far. We evaluated the relationship between photosynthetic capacity and NSCs accumulation induced by cold-girdling, sucrose feeding, and low nitrogen treatment in Glycine max and Phaseolus vulgaris. In G. max, changes in transcriptome profiles were further investigated focusing on physiological processes of photosynthesis and NSCs accumulation. NSCs accumulation decreased maximum photosynthetic capacity and delayed photosynthetic induction in both species. In G. max, such photosynthetic downregulation was explained by coordinated downregulation of photosynthetic genes involved in Calvin cycle, Rubisco activase, photochemical reactions, and stomatal opening. Furthermore, sink-source imbalance may have triggered a change in the balance of sugar-phosphate translocators in chloroplast membranes, which may have promoted starch accumulation in chloroplasts. Our findings provided an overall picture of the photosynthetic downregulation and NSCs accumulation in G. max, demonstrating that the photosynthetic downregulation is triggered by NSCs accumulation and cannot be explained simply by N deficiency. One Sentence SummaryAccumulation of nonstructural carbohydrates directly induced both downregulation and delayed induction of photosynthesis by coordinated transcriptomic changes in photosynthetic genes in Glycine max.

plant biology↗

bioRxiv2022

Employing active learning in the optimization of culture medium for mammalian cells

Medium optimization is a crucial step of cell culture for biopharmaceutics and regeneration medicine. It remains challenging, as both media and cells are highly complex systems. To address the issue, we tried active learning to fine-tune the culture medium by combining the high-throughput assay and machine learning. As a pilot study, the cell line HeLa-S3 and the gradient-boosting decision tree algorithm were used. The regular and time-saving approaches were developed, and both successfully fine-tuned 29 components to achieve improved cell culture than the original medium. The fine-tuned media showed a significant decrease in fetal bovine serum and the differentiation in vitamins and amino acids. Unexpectedly, the medium optimization raised the cellular NAD(P)H abundance but not the cell concentration owing to the conventional method used for cell culture assay. Our study demonstrated the efficiency of active learning for medium optimization and provided valuable hints for employing machine learning in cell culture.

systems biology↗

bioRxiv2020

Robotic Search for Optimal Cell Culture in Regenerative Medicine

Induced differentiation is one of the most experience- and skill-dependent experimental processes in regenerative medicine, and establishing optimal conditions often takes years. We developed a robotic AI system with a batch Bayesian optimization algorithm that autonomously induces the differentiation of induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells. The system performed 216 forty-day cell culture experiments, with a total experimentation time of 8,640 days. From 200 million possible parameter combinations, the system performed cell culture in 143 different conditions in 111 days, resulting in 88% better iPSC-RPE production than that by the pre-optimized culture in terms of pigmented scores. Our work demonstrates that the use of autonomous robotic AI systems drastically accelerates systematic and unbiased exploration of experimental search space, suggesting immense use in medicine and research.

systems biology↗

bioRxiv2020

GSK3 activity is a cell fate switch that balances the ratio of vascular cell type

The phloem transports photosynthetic assimilates and signalling molecules. It mainly consists of sieve elements (SEs), which act as "highways" for transport, and companion cells (CCs), which serve as "gates" to load/unload cargos. Though SEs and CCs function together, it remains unknown what determines the ratio of SE/CC in the phloem. In this study, we develop a novel culture system for CC differentiation named VISUAL-CC, which reconstitutes the SE-CC complex formation. Comparative expression analysis in VISUAL-CC reveals that SE and CC differentiation tends to show negative correlation, while total phloem differentiation is unchanged. This varying SE/CC ratio is largely dependent on GSK3 kinase activity. Indeed, gsk3 hextuple mutants possess much more SEs and less CCs in planta. Conversely, gsk3 gain-of-function mutants induced by phloem-specific promoter partially increased the CC ratio. Taken together, GSK3 activity appears to function as a cell fate switch in the phloem, thereby balancing the SE/CC ratio.

plant biology↗