Biology subjects

Mochizuki, M.

Publications and source records attributed to Mochizuki, M..

6 recordsLinked to original sources

bioRxiv2025

Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature

Inflammageing is a hallmark of ageing. Commensal microbiota plays crucial roles in maintaining tissue homeostasis, yet its impact on cellular ageing and inflammageing remains poorly understood. Here we present a comprehensive single-cell epigenomic and transcriptomic atlas of tissues from mice aged under specific pathogen-free (SPF) or germ-free (GF) conditions. Microbiota conferred beneficial effects in young mice but accelerated various ageing features in old, such as age-related AP-1 pathway upregulation, senescence and transcriptomic alterations, likely due to age-associated dysbiosis. Strikingly, inflammatory signatures persisted across cell types in aged GF mouse tissues, establishing sterile inflammation as an intrinsic feature of ageing. Age-associated B cells expanded equally under GF and SPF conditions, raising the possibility that they function as intrinsic, microbiota-independent drivers of inflammageing and potential therapeutic targets. The atlas provides a resource for distinguishing intrinsic ageing features from those modulated by the microbiota, illuminating mechanisms of cellular ageing and potential anti-ageing interventions. HighlightsSterile inflammation and age-associated B cell expansion are prominent intrinsic ageing features The upregulation of age-associated AP-1 pathways and senescence of alveolar macrophages are attenuated in germ-free condition Germ-free condition induces premature ageing-like features in young mouse tissues but delays ageing features in old mice across multiple cell types

genomics↗

bioRxiv2025

Domoic acid biosynthesis and genome expansion in Nitzschia navis-varingica

Production of the neurotoxin domoic acid (DA) by benthic diatom Nitzschia navis-varingica poses considerable health and economic concerns. In this study, we employed whole genome sequencing and transcriptomic analyses of regionally distinct N. navis-varingica strains to unravel the genomic underpinnings of DA biosynthesis. Our analyses revealed sizable genomes--characterized by an abundance of repetitive elements and noncoding DNA--that exceed the size of any other pennate diatoms. Central to our findings is the discovery of an expanded domoic acid biosynthesis (dab) gene cluster, spanning over 60 kb and marked by a unique organization that includes core genes interspersed with additional genetic elements. Phylogenetic and syntenic comparisons indicate that transposition events may have driven the expansion and reorganization of this cluster. Biochemical assays validated that the kainoid synthase encoded by dabC catalyzes the formation of isodomoic acid B, thereby establishing a distinct chemotype in contrast to the DA profiles of planktonic diatoms. These results highlight the evolutionary trajectory of DA biosynthesis in diatoms and potential advantages conferred by genome expansion and enzyme diversification in dynamic marine environments. IMPORTANCEDomoic acid (DA) is a potent neurotoxin produced by marine micro- and macroalgae problematic to fisheries and toxic to humans and animals. Our study elucidates the molecular mechanisms underlying DA production in the widespread Western Pacific benthic diatom, Nitzschia navis-varingica. Genomic and biochemical insights add information to our understanding of the evolution of toxin production across diverse phyla and also fill a gap in the knowledge of secondary metabolism in marine diatoms. These findings provide a genetic framework for identifying toxin production and its impacts in the benthos of vulnerable, coastal ecosystems.

genomics↗

bioRxiv2025

Miniaturized Workflow for Transcriptomic Profiling of Urinary Extracellular RNA during Pregnancy

Urine contains extracellular RNA (exRNA) carried by extracellular vesicles (EVs) and other biomolecular complexes. There is currently a need for studies focused on female cohorts to develop new methods for non-invasive analysis of biofluids to create reference profiles and for identification of biomarkers of reproductive and pregnancy disorders. The objective of this study was therefore to identify optimal methods for transcriptomic profiling of urine by testing different exRNA isolation and scalable library preparation methods that enable detection of biomarkers that reflect pregnancy-associated changes in the placenta and maternal tissues. RNA was extracted from pooled and individual urine samples obtained from normal non-pregnant and pregnant females, as well as males, using input volumes of either 0.6 mL, 1 mL, or 4 mL. Samples were extracted using methods that focused either on isolating vesicular (EV-associated) or total (EV-associated and non EV-associated) exRNA. Small RNA libraries (n=208) were prepared using the NEBNext Small RNA Library Prep kit and long RNA libraries (n=97) were prepared using the SMART-Seq v4 Ultra Low Input RNA or the SMARTer Stranded Total RNA-Seq Kit v2 Pico Input kits (Takara). Principal component analysis showed that the greatest source of variance amongst technical replicates of small RNA libraries (n=176 which passed quality control) was exRNA isolation method, and amongst long RNA libraries (n=97 which passed quality control) was library preparation method. Long RNA libraries prepared from exRNA extracted using miRCURY showed that the SMART-Seq v4 method yielded significantly more uniquely mapped reads compared to the Pico v2 method (p<0.05). We have established a scalable pipeline for small and long RNA-Seq profiling of exRNA in urine in a reproducible manner, which we used to identify differentially expressed urinary exRNAs in pregnancy, and will enable transcriptomic profiling of urinary exRNA in disorders of pregnancy, including preeclampsia.

genetics↗

bioRxiv2024

Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions

Mass-based fingerprinting can characterize unknown strains, however expansion of these methods to predict specific gene functions is lacking. Therefore, rapid mass fingerprinting was developed to functionally profile a comprehensive yeast knockout library. Matrix assisted laser desorption ionization (MALDI)-time of flight (TOF) mass fingerprints of 3,238 Saccharomyces cerevisiae knockouts were digitized for correlation with gene ontology (GO) annotations. Random forests and support vector machine (SVM) algorithms precisely assigned GO accessions with AUC scores all above 0.83. SVM was the best predictor with average true positive and true negative rates of 0.975 and 0.991, respectively. The SVM model suggested new functions for 28 uncharacterized yeast genes. Metabolomics analysis of two knockouts (YDR215C and YLR122C) of uncharacterized genes predicted to be involved in methylation-related metabolism, showed altered intracellular contents of methionine-related metabolites. Increased S-adenosylmethionine in YDR215C highlights potential for enhancement of methylation pathways. These results demonstrate that MALDI-TOF fingerprints can be rapidly digitized, resulting in datasets that enable prediction of microbial genotypes and even the function of specific genes. This fingerprinting method can inform optimal bioproduction chassis selection.

systems biology↗

bioRxiv2024

Split RNA switch: Programmable and precise control of gene expression by ensemble of pre- and post-translational regulation

Regulating gene expression in response to biomolecules is a powerful strategy for monitoring intracellular environments and controlling cellular programs. RNA switch is a synthetic mRNA-based technology that controls gene expression at the translational level in response to cellular RNA and protein molecules, thus enabling cell type-specific gene regulation and showing promise for gene therapy, regenerative medicine, and cell therapy. However, single RNA switches often lack the specificity required for practical applications due to low ON/OFF ratios and difficulty in finding distinct and single biomolecule targets. To address these issues, we developed "split RNA switches" that integrate outputs from multiple RNA switches by exploiting protein splicing, a post-translational modification mechanism. We demonstrated that split RNA switches significantly improve the ON/OFF ratio of microRNA (miRNA)-responsive ON switch systems by canceling undesirable leaky OFF level. We achieved efficient and robust target cell purification based on endogenous miRNA profiles, which was impossible with an ON switch alone. Additionally, we constructed multi-output and multi-input RNA-based synthetic circuits using split RNA switches to enable the detection of multiple miRNAs for precise gene control with logical operations. Split RNA switches illustrate a novel application of protein splicing and demonstrate the potential of post-translational processing as a comprehensive solution for advancing translational control technologies toward widespread mRNA therapies.

synthetic biology↗

bioRxiv2020

First and broad detection of three typical carbapenemase genes on the surfaces of commercially available spices worldwide and isolation of complete NDM-1 genes from black pepper, cumin, and clove

The spread of multidrug-resistant bacteria, particularly those producing carbapenemases, has become a major public health concern. The presence of carbapenemase genes has primarily been reported in clinical samples, whereas the presence of these genes in commercially available foods has insufficiently been studied despite its growing importance. The present study aimed to detect and characterize carbapenemase genes (blaNDM, blaIMP, blaKPC, and blaOXA-48-like) on the surfaces of commercially available spices using PCR to amplify conserved regions of these genes. It was revealed that DNAs of these genes are commonly present (13 genes/29 samples) on spices derived from at least 9 different countries. This is the first detection of any carbapenemase gene on eight spices (black pepper, cumin, clove, cardamom, mustard, caraway, parsley, and rosemary) among these. This is also the first detection of the blaIMP and blaNDM as well as the broad detection of the blaOXA-48-like on spices. We also isolated complete, functional blaNDM-1 genes from three spices (black pepper, cumin, and clove) up to the present.

microbiology↗