Biology subjects

Nagai, S.

Publications and source records attributed to Nagai, S..

6 recordsLinked to original sources

bioRxiv2026

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

The +1 nucleosome has emerged as a key regulator of eukaryotic transcription, but how it controls transcription initiation remains poorly understood. Here we reconstitute transcription through the +1 nucleosome using eleven purified yeast factors: RNA polymerase II (Pol II), the six general transcription factors (GTFs), TFIIS, the activator Pho4, and the SAGA and Mediator complexes. The system recapitulates key features of regulation observed in vivo. SAGA, acting with Pho4, directs pre-initiation complex (PIC) assembly to the correct position through its TBP-loading activity. Mediator stimulates transcription when the +1 nucleosome imposes a barrier to PIC formation, consistent with stabilization of productive TFIIH-DNA engagement. Contrary to the prevailing model, SAGA remains bound to the PIC after TBP loading and acetylates the +1 nucleosome within the assembled complex. The isolated PIC-Mediator-SAGA-nucleosome complex is transcriptionally active, and the repressive effect of the nucleosome is relieved by the DNA translocase activity of Ssl2, the TFIIH subunit that opens promoter DNA. TFIIH thus couples promoter melting to remodeling of the +1 nucleosome.

biochemistry↗

bioRxiv2026

Omitting end preparation reduces index misassignment in Nanopore-based DNA metabarcoding: application to a decadal coastal time series in the Sea of Okhotsk

Environmental DNA (eDNA) metabarcoding enables sensitive, non-invasive assessment of fish communities, but highly multiplexed analyses using Oxford Nanopore Technologies (ONT) platforms require stringent control of sample-index misassignment and sequencing errors. We developed a MiFish experimental workflow combining unique dual indexes, a library protocol that omitted end preparation and used 5'-phosphorylated primers, BLAST-based demultiplexing, quality-dependent clustering, consensus generation, and haplotype partitioning by SNP/INDEL patterns. Omitting pooled end-prep reduced the mean index-chimera rate from 0.0674% to 0.000420%, a 160-fold reduction. We applied the workflow to an archive of seawater samples collected weekly off Monbetsu, Hokkaido, Japan, from 2012 to 2022. Relative read abundance (RRA) data were obtained for 274 samples, and eight taxa showed significant seasonality. For six of these taxa, the three-year mean RRA peaks coincided with reported spawning periods in Hokkaido. The workflow substantially reduced index misassignment and enabled cost-efficient, highly multiplexed analysis of a decadal fish eDNA time series.

ecology↗

bioRxiv2026

Spatiotemporal Patterns of Active Deformation Reveal Downregulation of Cell-Cell Adhesion in Patient-Derived Colorectal Cancer Organoids with BRAF Mutation

Colorectal cancer (CRC) is the second most common cause of cancer-related mortality. At the molecular level, CRC is associated with genetic mutations and epigenetic modifications that dysregulate various signaling networks. From the biophysical viewpoint, invasive and metastatic cell migration need to be empowered by mechanical forces. In this study, we analyze the dynamic deformation of patient-derived CRC organoids in Fourier space and demonstrate how organoids with protooncogene BRAF mutation exhibit deformation phenotypes at an early stage. The organoids with BRAFmut have significantly lower elasticity and higher viscosity than those with BRAFWT, which mathematically indicated as the weakening of cell-cell adhesion. Immunohistochemical images, qRT-PCR, and TCGA data analysis confirm the downregulation of E-cadherin (CDH1) in BRAFmut organoids as well as in BRAFmut CRC, suggesting that the decrease in cell-cell adhesion in BRAFmut CRC facilitates invasive and metastatic migration. Notably, the recovery of CDH1 expression by pharmacological inhibition of DNA methylation can quantitatively be detected as the change in mechanical properties, suggesting that the complementary combination of dynamic phenotyping, mathematical modelling, and molecular-level analyses has a potential to unravel the mechanistic causality of the critical gene mutation and CRCs prognosis and the response to therapeutic interventions.

biophysics↗

bioRxiv2025

Modulation of gluconic acid metabolism enhances nanofibrillated bacterial cellulose production from agro-industrial by-products

Efficient and robust bacterial cellulose production is essential for advancing the sustainable bioeconomy. In this study, we investigated the impacts of metabolism of organic acids, mainly gluconic acid (GA), on nanofibrillated bacterial cellulose (NFBC) production by Komagataeibacter intermedius NEDO-01 under various culture conditions in aerated stirred-tank reactors. In cultures of the wild-type strain in a standard medium, rapid GA production decreased the medium pH and depleted glucose, inhibiting cell growth and reducing the NFBC yield. However, proper pH control and continuous feeding reversed these effects, resulting in a 3-fold increase in NFBC yield (from 2.45 to 7.59 g/L). In cultures of a glucose dehydrogenase gene-deficient ({Delta}gcd) strain, lack of a pH drop and glucose depletion facilitated better cell growth, yielding 1.85-times more NFBC than that in wild-type cultures under pH-uncontrolled no-feed conditions (4.53 g/L). Notably, GA supplementation accelerated cell growth but significantly inhibited NFBC synthesis, suggesting that GA uptake redirects the carbon flux toward central metabolism. In the corn steep liquor (Csl)-based medium, cell growth was significantly enhanced, and NFBC yield was equivalent to or higher than that obtained with the Hestrin-Shramm medium. GA accumulation was markedly reduced, suppressing pH fluctuation. Under these optimized conditions, three molasses types were tested with Csl, yielding relatively high NFBC. Structural analysis of NFBC produced using these alternative media revealed slight differences in the fiber width distribution, with crystallinity and fiber width remaining constant. Overall, NFBC of consistent quality can be produced in stirred-tank reactors using Komagataeibacter spp. from various agricultural by-products. ImportanceIn this study, we investigated the interplay between organic acid metabolism and nanofibrillated bacterial cellulose (NFBC) production in stirred-tank reactor (STR) cultures of Komagataeibacter intermedius NEDO-01. While it is well known that gluconic acid production competes with cellulose biosynthesis in Komagataeibacter, the quantitative relationship between these pathways under varying culture conditions has not been fully elucidated. By applying optimized feeding strategies and employing a glucose dehydrogenase knockout mutant, we demonstrated that suppressing gluconic acid accumulation significantly enhances NFBC yield. Furthermore, we explored the use of agro-industrial by-products, including molasses and corn steep liquor, as alternative, low-cost feedstocks. Structural characterization confirmed that NFBCs produced under these conditions maintained consistent quality. These findings contribute to the development of scalable, cost-effective microbial production processes for nanocellulose, which is essential for advancing the sustainable bioeconomy. Key PointsO_LIGA accumulation inhibited growth and cellulose production by Komagataeibacter C_LIO_LIEnhanced central metabolism elevated NFBC yield but reduced its production rate C_LIO_LIConsistent NFBC properties were achieved in STRs using various by-product sources C_LI

bioengineering↗

bioRxiv2022

Seasonal movement of royal chambers: where are the kings and queens of temperate termites in winter?

Overwintering is a critical part of the annual cycle for species that live in temperate, polar, and alpine regions. As a result, low-temperature biology is a key determinant of temperate species distribution. Termites distribute predominantly in tropical regions, and only a few species are found in the temperate zone. As with other social insects, termites are characterized by the division of labor between reproductive and non-reproductive castes in which the survival of reproductives is crucial to maintaining their society. Here, in the termite Reticulitermes speratus, we report the discovery of an underground royal chamber that kings and queens use to survive the winter, which is separate from the one they use during the warmer breeding season. Our investigation of field colonies indicates that in the spring the royals are localized in decayed logs on the ground, then move to their underground royal chamber located in the roots of stumps in the fall. The winter minimum temperature measured in the royal chamber was higher than the ground surface temperature. In overwintering termites, the kings and queens had higher cold tolerance than workers and soldiers. The kings and queens were at risk of mortality from -8 {degrees}C, compared to the workers and soldiers at -4 {degrees}C. Air temperatures dropped below this critical temperature of -8 {degrees}C multiple times, as evidenced from the past 140 years of weather records in Kyoto. This suggests that the underground movement of the royal chamber may contribute to avoiding the risk of overwintering mortality. These results demonstrate the social strategies implemented to overcome the environment met while living at the latitudinal limits. This study sheds light on one of the most important aspects of the biology of termites in terms of predicting their geographic distribution and spread by climate change. This work also helps further the understanding of the termites social system, seasonal phenology, long-term survivorship, and life cycle, and contributes to the development of pest control strategies.

ecology↗

bioRxiv2021

New markers for qPCR detection of the dinoflagellate Alexandrium catenella in Chile

Alexandrium catenella (Whedon & Kofoid) is a dinoflagellate known as a primary source of paralytic shellfish poisoning in Chile. The distribution range of harmful algal blooms generated by this species has extended during the last decades, and the frequency of these events has increased. In this work, we developed TaqMan markers from Chilean strains that can be used to identify and quantify through qPCR, which can be implemented in monitoring programs for the early detection of this species.

genetics↗