Biology subjects

Onda, Y.

Publications and source records attributed to Onda, Y..

4 recordsLinked to original sources

bioRxiv2025

PhenoDEL as a Novel Screening Strategy Based on Intracellular Protein Degradation Activity

Targeted protein degradation (TPD), including proteolysis targeting chimeras (PROTACs) and molecular glue degraders (MGDs), is a promising therapeutic approach. However, systematic discovery of such small molecules remains a major challenge. Here, we present PhenoDEL, a novel phenotypic DNA-encoded library (DEL) screening platform that integrates one-bead one-compound DEL (OBOC-DEL) with the Beacon(R) optofluidic system for high-throughput, single-cell analysis. By co-culturing individual OBOC-DEL beads and engineered reporter cells in nanoliter-scale chambers, PhenoDEL enables direct observation of compound-induced protein degradation at single-cell resolution. We demonstrate this approach by identifying compounds that induce degradation of FKBP12F36V-EGFP fusion proteins in PC-3 cells. The workflow allows precise linkage between compound identity and cellular phenotype via DNA barcoding and next-generation sequencing. PhenoDEL overcomes limitations of conventional screening methods, offering high sensitivity, spatial control, and scalability. This platform holds significant potential for mechanism-driven drug discovery, including identification of novel PROTACs and MGDs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/690606v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fe27bforg.highwire.dtl.DTLVardef@1e38ef5org.highwire.dtl.DTLVardef@be958aorg.highwire.dtl.DTLVardef@4bc48a_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2023

Label-free ghost cytometry for manufacturing of cell therapy products

Automation and quality control (QC) are critical in manufacturing safe and effective cell and gene therapy products. However, current QC methods, reliant on molecular staining, pose difficulty in in-line testing and can increase manufacturing costs. Here we demonstrate the potential of using label-free ghost cytometry (LF-GC), a machine learning-driven, multidimensional, high-content, and high-throughput flow cytometry approach, in various stages of the cell therapy manufacturing processes. LF-GC accurately quantified cell count and viability of human peripheral blood mononuclear cells (PBMCs) and identified non-apoptotic live cells and early apoptotic/dead cells in PBMCs, T cells and non-T cells in white blood cells (WBCs), activated T cells and quiescent T cells in PBMCs, and particulate impurities in PBMCs. The data support that LF-GC is a non-destructive label-free cell analytical method that can be used to monitor cell numbers, assess viability, identify specific cell subsets or phenotypic states, and remove impurities during cell therapy manufacturing. Thus, LF-GC holds the potential to enable full automation in the manufacturing of cell therapy products with reduced cost and increased efficiency.

cell biology↗

bioRxiv2019

Experimental and field data support habitat expansion of the allopolyploid Arabidopsis kamchatica owing to parental legacy of heavy metal hyperaccumulation

Little empirical evidence is available whether allopolyploid species combine or merge adaptations of parental species. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the diploid parents A. halleri, a heavy metal hyperaccumulator, and A. lyrata, a non-hyperaccumulating species. Zinc and cadmium were measured in native soils and leaf tissues in natural populations, and in hydroponic cultures of A. kamchatica and A. halleri. Pyrosequencing was used to estimate homeolog expression ratios. Soils from human modified sites showed significantly higher Zn concentrations than non-modified sites. Leaf samples of A. kamchatica collected from 40 field localities had > 1,000 {micro}g g-1 Zn in over half of the populations, with significantly higher amounts of Zn concentrations in plants from human modified sites. In addition, serpentine soils were found in two populations. Most genotypes accumulated >3000 {micro}g g-1 of Zn in hydroponic culture with high variability among them. Genes involved in hyperaccumulation showed a bias in the halleri-derived homeolog. A. kamchatica has retained constitutive hyperaccumulation ability inherited from A. halleri. Our field and experimental data provides a compelling example in which the inheritance of genetic toolkits for soil adaptations likely contributed to the habitat expansion of an allopolyploid species.

evolutionary biology↗

bioRxiv2017

Multiple strategies for heat adaptation in rice endosperms revealed by on-site cell-specific analysis

Plant cells have multiple strategies to adapt to environmental stresses. Rice endosperms form chalkiness in a part of the tissue under heat conditions during the grain-filling stage, although nitrogen supply reduces chalky rice. Air spaces formed in the cells cause an irregular light reflection and create chalkiness, yet what exactly occurs remains unclear at cell level. Through on-site cell-specific analysis, we show that heat-treated cells adjust osmotically and retard protein synthesis to preserve protein storage vacuoles in the cytosol, resulting in air space formation. Application of nitrogen enhances heat tolerance to sustain protein body and amyloplast development during strong osmotic adjustment, which diminishes air spaces to avoid chalkiness. Hence, we conclude that rice endosperm cells could alter organelle compartments spatially during the heat adaptation, depending on the available nitrogen level. Our findings provide new insight into the cellular mechanism of rice chalky formation as a strategy for heat acclimation.

plant biology↗