Biology subjects

Kasuga, Y.

Publications and source records attributed to Kasuga, Y..

3 recordsLinked to original sources

bioRxiv2026

A genomic and proteomic characterization of mannan-degradable Bacillus sp. TTS1, isolated from Tomakomai Forest in Hokkaido

A challenge in using plant biomass is its highly recalcitrant nature, which makes it economically infeasible to utilize. In natural environments, various microbes, including bacteria and fungi, are reported to decompose plant cell wall materials such as cellulose and hemicellulose, and there may be undescribed microbes that contribute to the degradation of plant biomass. We focused on isolating novel plant biomass-degrading bacteria and screened more than 100 isolates from the Tomakomai experimental forest in Hokkaido, Japan. Among them, one novel Bacillus species was chosen for whole-genome sequencing. Comparative genomics and a carbon source utilization assay indicated that the isolate belongs to a subspecies of Bacillus subtilis, which we named B. sp. TTS1. Glucose, cellobiose, xylose, xylan, mannose, or mannan was used as the sole carbon source in the minimum medium, and the growth of this bacterium was determined. Furthermore, a proteomic analysis of B. sp. TTS1 was performed using culture supernatants from various polysaccharide-containing media. In the present study, several key enzymes involved in plant biomass degradation were identified, namely {beta}-1,4-mannanase and xylanase, and they were highly enriched in all tested polysaccharides.

microbiology↗

bioRxiv2025

A neural circuit targeting technique for investigating functional input-output organization in the nervous system

Neurons communicate information across circuits and the function of cells in these circuits is determined by both the afferent inputs they receive and the efferent outputs they send to other brain regions1,2. To study the activity and function of specific neuronal populations, transneuronal anterograde3 and retrograde4-6 viral approaches have been employed to define neural circuit elements by inputs or outputs, respectively. However, what is missing is a way to study the function of neurons based on both their inputs and outputs. Applying a combination of multiple recombinases and transneuronal anterograde/retrograde viruses, we developed a technique called input-output Projection-based INtersectional Circuit-tagging Enabled by Recombinases (PINCER) to target specific neuronal cell types and investigate functional input-output organization in neural circuits. We show the logic and application of this technique with in vivo calcium imaging and optogenetic approaches to reveal the distinct functions and neural dynamics of connectivity defined neuronal populations in the amygdala for emotional processing. Specifically, PINCER allowed the parsing of valence and salience functions of the amygdala to reveal an input-output cell type selectively mediating aversive memory formation. This technique allows neuroscientists to identify novel subclasses of cells based on their combinatorial input-output anatomical connectivity, providing a tool for fine dissection of the functional properties of neural circuits.

neuroscience↗

bioRxiv2025

Identification of novel cis-acting elements, E-box and ISRE, regulating IFNγ-IRF1 axis-mediated NLRC5 expression

NLRC5 and CIITA are the primary transcriptional regulators of MHC class I and MHC class II, respectively, and play essential roles in adaptive immunity. While the regulatory mechanisms of CIITA have been extensively characterized, the transcriptional control of NLRC5 remains incompletely understood. In this study, we identified two novel conserved cis-regulatory elements within the NLRC5 promoter, an E-box and an ISRE. Furthermore, we revealed IRF1 as a novel transcriptional regulator of NLRC5, binding directly to the ISRE within the NLRC5 promoter. Using the newly identified NLRC5 ISRE, we established a screening platform to identify modulators of the IFN{gamma}-IRF1-NLRC5 axis. This system corroborated the inhibitory effects of known viral antagonists and led to the identification of novel SARS-CoV-2 viral factors that suppress IFN{gamma}- mediated IRF1 nuclear translocation, thereby inhibiting the MHC class I pathway. By elucidating the previously unproven molecular mechanism underlying IFN{gamma}-mediated NLRC5 regulation, our study provides critical insights into viral immune evasion strategies and the modulation of antigen presentation. These findings may facilitate the development of MHC class I-targeted therapeutics by modulating the IRF1-NLRC5 axis.

immunology↗