Biology subjects

Yoshikawa, N.

Publications and source records attributed to Yoshikawa, N..

4 recordsLinked to original sources

bioRxiv2025

Multi-objective optimization for designing structurally similar proteins with diverse sequences

Recent advances in artificial intelligence technologies have accelerated the development of computational protein design techniques. Although the structure of the designed proteins has been the primary focus, diversity of designed amino acid sequences is another important aspect of protein design. To address the trade-off between reducing sequence similarity and improving structural similarity, simultaneous optimization of these two objectives can be effective. We present a method that integrates ProteinMPNN with the multi-objective optimization algorithm NSGA-II to design proteins that retain high structural similarity to a target while exhibiting low sequence similarity. Using Top7 as a reference protein, we demonstrate that our approach improves sequence diversity compared to the original ProteinMPNN while maintaining comparable structural similarity.

bioinformatics↗

bioRxiv2025

Proteomic profiling of bacterial extracellular vesicles for exploring ovarian cancer biomarkers

Extracellular vesicles (EVs) are present in body fluids and act as disease biomarkers. Emerging evidence has proven that EVs are released not only from mammalian cells but also from bacteria. Ovarian cancer has a dismal prognosis because of difficulties in early detection. This study aimed to identify bacterial EV (BEV) proteins associated with ovarian cancer. Fifteen patients with ovarian cancer or benign tumors were recruited, and EVs were isolated from the ascites. BEVs were recovered from seven in vitro-cultured strains of bacteria present in the vaginal microbiota, and LC-MS/MS analysis was performed. The detected peptide data were annotated to both human and bacterial references, and the human data showed that the profiles of cancer EVs were distinct from those of patients with benign tumors. As analyzed by bacterial proteins, P15636_Protease1 was found as the BEV-associated protein highly expressed in patients with cancer. To distinguish patients with cancer, the area under the curve was 0.88 (95% CI, 0.64-1.00). In addition, homology analysis showed that P15636_Protease1 is a unique protein only detected in bacteria. In this study, ovarian cancer-specific bacterial proteins were identified on EVs, and BEVs in bodily fluids are promising in the discovery of disease biomarkers.

cancer biology↗

bioRxiv2024

Environmental Impacts of Serum-free Food-grade and Complex Culture Medium Production for Cultivated Meat

Culture medium accounts for most of the environmental impact of cultivated meat production. This study quantitatively evaluated and analyzed the environmental impact of producing a culture medium consisting of serum-free, food and complex ingredients for cultivated meat by performing a life cycle assessment (LCA) based on activity data at the laboratory scale. In addition, specific measures were proposed to reduce the environmental impact further. LCAs were performed at current and future production scales. This study also evaluated the impact of multiple electricity sources on the environmental impact of culture medium production. Energy, animal-derived materials, and expendables at the current scale, and energy, animal-derived materials, amino acids, and glucose at future scale are hotspots in the environmental impact of this culture medium production. The production of serum substitutes accounts for most of the environmental impact. As the scale shifts, the environmental impacts are expected to decrease by more than 70% in all impact categories. As the composition of electricity sources changed, the impact on certain categories decreased. However, as the share of renewable energy increased, the impact on land use also increased significantly. This study promotes the practical application of new culture-media for low-cost and low-environment-impact cultivated meat. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/611339v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@ac6daorg.highwire.dtl.DTLVardef@1852ef4org.highwire.dtl.DTLVardef@cdbbe8org.highwire.dtl.DTLVardef@eb8703_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO SYNOPSIS. This study evaluated the environmental impact of culture-medium production for cultivated meat and reports that energy, animal-derived materials, expendables, amino acids and glucose are hotspots of this impact. C_FIG

ecology↗

bioRxiv2020

Reduced intra- and inter-individual diversity of semantic representations in the brains of schizophrenia patients

Schizophrenia patients often manifest semantic processing deficits. It has been proposed that these deficits stem from disorganized semantic representations in the brain. However, no study has yet examined the neural correlates of semantic disorganization by directly evaluating semantic representations in the brain. We used voxelwise modeling on functional magnetic resonance imaging signals to evaluate the semantic representations associated with several thousand words in individual patient brains. We then compared the structural properties of semantic representations to those in healthy controls. The variability of semantic representations was smaller both within individual patients and across patients compared to controls. Surrogate data analysis suggests that the observed reduction in representational variability is associated with disorganization of categorical information. To our knowledge, these findings provide the first evidence for sematic disorganization in schizophrenia at the level of brain representations.

neuroscience↗