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Biology subjects

Kumano, S.

Publications and source records attributed to Kumano, S..

3 recordsLinked to original sources

EMPAC: A Multimodal Dataset for Bridging Affective and Cognitive Empathy

Empathy, a key element of social interaction, involves both cognitive and affective processes and is commonly investigated through measures such as empathic accuracy and affective physiological synchrony. While physiological synchrony offers a continuous measure of affective processes, empathic accuracy typically relies on discrete self-reports, leaving their temporal relationship largely unexplored. Advancing this line of research requires datasets that integrate time-continuous self-reports with physiological signals, yet such datasets--particularly those focusing on the empathizee--remain limited. To fill this gap, we present EMPAC (Empathy Measurement: Physiological, Affective, and Cognitive), a multimodal dataset constructed. To create empathy-eliciting stimuli, professional actors performed emotionally intense, pseudo-autobiographical narratives while their physiological signals (e.g., ECG, EDA) and continuous self-reported emotional states were recorded. We then conducted two observer experiments using these video recordings. In Experiment 1, to validate the stimuli as empathy-eliciting materials, observers continuously rated emotional intensity without being informed of the specific emotion portrayed, following the protocol of previous studies on time-series empathic accuracy. Yet this approach sometimes revealed a gap between the emotion category portrayed by the target and that perceived by the observers. In Experiment 2, we introduced a revised procedure in which the target emotion category was disclosed prior to viewing, revealing that specifying the target emotion led to a different relationship between individual empathy traits and empathic accuracy than observed in Experiment 1. EMPAC thus provides a rich, temporally aligned resource for investigating empathy dynamics in naturalistic settings and for evaluating methodological variations in empathic accuracy paradigms.

neuroscience↗

A beta-Galactosidase acting on unique galactosides: the structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of {beta}-galactosidases in degrading these carbohydrates is important. In particular, identifying {beta}-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identified a {beta}-galactosidase with novel substrate specificity from Bacteroides xylanisolvens, an intestinal bacterium. The enzyme did not show hydrolytic activity toward natural {beta}-galactosides during the first screening. However, when -D-galactosyl fluoride (-GalF) as a donor substrate and galactose or D-fucose as an acceptor substrate were incubated with a nucleophile mutant, reaction products were detected. The galactobiose produced from the -GalF and galactose was identified as {beta}-1,2-galactobiose using NMR. Kinetic analysis revealed that this enzyme effectively hydrolyzed {beta}-1,2-galactobiose and {beta}-1,2-galactotriose. In the complex structure with methyl {beta}-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl {beta}-galactopyranose faces in the direction of subsite -1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we concluded that the enzyme is a {beta}-galactosidase acting on {beta}-1,2-galactooligosaccharides. SynopsisThe structural and functional analysis of {beta}-galactosidase from an intestinal bacterium led to the discovery of a new {beta}-galactosidase hydrolyzing unique {beta}-1,2-galactooligosaccharides.

biochemistry↗

Epoxidized graphene grid for high-throughput high-resolution cryoEM structural analysis

Many specimens suffer from low particle density and/or preferred orientation in cryoEM specimen grid preparation, making data collection and structure determination time consuming. We developed an epoxidized graphene grid (EG-grid) that effectively immobilizes protein particles by applying an oxidation reaction using photoactivated ClO2* and further chemical modification. The particle density and orientation distribution are both dramatically improved, having enabled us to reconstruct the density map of GroEL and glyceraldehyde 3-phosphate dehydrogenase (GAPDH), at 1.99 and 2.16 [A] resolution from only 504 and 241 micrographs, respectively. A low concentration sample solution of 0.1 mg ml-1 was sufficient to reconstruct a 3.10 [A] resolution density map of SARS-CoV-2 spike protein from 1,163 micrographs. The density maps of V1-ATPase, {beta}-galactosidase, and apoferritin were also reconstructed at 3.03, 1.81, and 1.29 [A] resolution, respectively. These results indicate that the EG-grid will be a powerful tool for high-throughput cryoEM data collection to accelerate high-resolution structural analysis of biological macromolecules.

molecular biology↗