Biology subjects

Ito, K.

Publications and source records attributed to Ito, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Genomic prediction models based on a large-scale recombinant population allow quick breeding of high-yield rice

Rapid development of cultivars with optimal genome-wide allele combinations is essential for addressing agricultural challenges. However, constructing desired genotypes through conventional cross-breeding requires many generations, calling for a more efficient methodology. Here, we present a rapid breeding strategy that combines a large-scale recombinant population as starting material with interpretable genomic prediction models trained on that population. This approach enables efficient construction of target genotypes optimized for multiple traits in cultivars. To validate our strategy in rice (Oryza sativa), we established a nested association mapping population of 2,787 recombinant inbred lines derived from an elite cultivar 'Hitomebore' and 19 diverse donors. We built highly accurate genomic prediction models using this population. We then used the models to estimate haplotype-specific effects and account for trade-offs among yield-related traits, and selected optimal lines and designed breeding schemes. Crossbreeding based on these schemes produced rice lines with the target genotypes for multiple yield-related traits, supporting the predicted effects and validating the effectiveness of our strategy. This genomic breeding approach provides a general framework for rapidly breeding cultivars able to meet the challenges posed by a changing environment.

genetics↗

bioRxiv2025

Visualization of the microstructure and distribution of follicles in deep human ovaries using speckle-modulated optical coherence microscopy

Ovarian tissue cryopreservation (OTC) and transplantation (OTT) are the only fertility preservation (FP) options for children, adolescents, and young adults (CAYA) who dont enough time until treatment of primary disease. OTC is still unestablished FP options, but it is expected that selective preservation of ovarian tissue with high follicle density will enhance pregnancy efficiency. Despite its value as a noninvasive follicle visualization method, optical coherence microscopy (OCM) lacks sufficient spatial resolution, imaging depth, and noise suppression capabilities to resolve fine follicular structures in deep ovarian tissue. In this study, we applied speckle modulation to a wavelength-swept OCM optical system in the near-infrared region to visualize the fine structure of follicles distributed in deep tissues. OCM images of 4-day-old mice revealed dense superficial-layer distributions of primordial follicles. These follicles were distinguishable from primary follicles, which were surrounded by a single layer of granulosa cells. In 14-day-old ovarian tissue, secondary follicles exhibited spatial dominance, and the fine structures constituting the follicles were successfully visualized. In ovarian tissues extracted from a patient diagnosed with acute myeloid leukemia (AML), the fine structures of primordial follicles were visualized to a depth of 300 m, and a comparison with HE staining revealed that follicle density varied significantly depending on the ovarian regions. Speckle modulation-assisted OCM visualized the microstructure of follicles with varying degrees of maturation in human ovaries at the depth necessary for clinical application. Overall, this technology enables quantitative ovarian reserve assessment and selective cryopreservation of ovarian tissue rich in immature follicles, supporting FP in CAYA diagnosed with cancer.

bioengineering↗

bioRxiv2025

Comparative genomics and transcriptomics on salt tolerance of Vigna luteola

Vigna luteola, a wild legume species, shows remarkable variation in salinity tolerance across its natural habitats, with coastal populations exhibiting high tolerance and riverbank populations being sensitive. This intraspecific variation provides a valuable system for investigating the genetic basis of salt tolerance. A major QTL for salt tolerance was previously identified by crossing salt-tolerant and salt-sensitive accessions, but the responsible genes remain unknown. In this study, grafting experiments between the two accessions revealed that the root plays a primary role in salt tolerance by suppressing Na transport to the shoot. We then conducted root transcriptome analysis and identified four candidate genes located within the QTL and highly expressed under salt stress in the tolerant accession: CBL-INTERACTING PROTEIN KINASE 6 (CIPK6), CAFFEOYL SHIKIMATE ESTERASE (CSE), FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13), and DROUGHT-INDUCED 21 (DI21). Promoter analysis revealed that the CIPK6 promoter contains transcription factor binding motifs unique to the salt-tolerant accession, which may contribute to its high expression under salt stress. These findings suggest that CIPK6 is regulated by cis-regulatory differences and is the most promising candidate for the salt-tolerance QTL. The identified genes in this study provide a foundation for developing salt-tolerant crops in the future.

genomics↗

bioRxiv2025

Fine-tuning quantitative agronomic traits by manipulating gene copy number in rice

Although recent plant pan-genome studies have revealed extensive copy number variations, there are limited studies addressing the phenotypic consequences of these variations. Here, we manipulated the copy number of OsMADS18 in rice (Oryza sativa) through gene editing and evaluated the effects. OsMADS18, which encodes a MADS-box transcription factor known to regulate plant development, is tandemly duplicated in the elite rice cultivar Hitomebore as a natural variant. We therefore edited the OsMADS18 copy number using a basic CRISPR/Cas9 system and established rice lines harboring one to three tandem copies of OsMADS18, as identified through high throughput qPCR screening. The presence of one to three OsMADS18 tandem copies was reflected in stepwise increases in transcript levels and concomitant trait values for leaf blade length and culm length. These results demonstrate that manipulating gene copy number can fine-tune important agronomic traits, providing a novel breeding strategy for crop improvement.

plant biology↗

bioRxiv2025

Class I myosins direct circumferential F-actin flows to define cell chirality

Eukaryotic cells possess intrinsic chirality in their structure, motility, and intracellular dynamics, which are designated cell chirality. Cell chirality participates in the left-right asymmetric morphogenesis and tissue integrity. However, the mechanisms of cell chirality formation remain elusive. In Drosophila, two evolutionarily conserved myosin I genes, Myosin 1D (Myo1D) and Myosin 1C (Myo1C), respectively, dictate the dextral and sinistral chirality of the cells and body. Here, we reported that Myo1D and Myo1C respectively directed the clockwise and counterclockwise circumferential flow of F-actin in Drosophila macrophages. Both induced the corresponding circular cytoplasm flows and depended on Myosin2 (Myo2). In a modified in vitro motility assay using near-physiological actin concentrations, Myo1D triggered the self-organization of the F-actin ring (chiral F-actin ring) that rotated clockwise; conversely, Myo1C induced the random flow of F-actin. The chiral F-actin ring implied that the F-actin bundle was parallelly and annularly polarized concerning its barbed pointed end. Considering that Myo1D and Myo1C are localized to the dorsal plasma membrane of macrophages, Myo1D and Myo1C might organize the parallelly polarized F-actin in macrophages. Our results suggest that Myo2 might drive the clockwise circumferential flow of F-actin along its parallel and annular polarity induced by Myo1D, which may be a molecular basis of cell and organ chirality.

cell biology↗

bioRxiv2025

MARK4 enhances stress granule formation and increases tau accumulation

Stress granules (SGs) are membrane-less organelles that are formed in response to cellular stress. SG formation protects cells against stress; however, their dysregulation and longer persistence may disrupt proteostasis. Abnormal activity of Microtubule-affinity regulating kinase 4 (MARK4) has been linked to cancer and Alzheimers disease. Here, we report that MARK4 is a component of SGs and enhances SG formation. MARK4 is found in SGs in mammalian cultured cells and primary neurons with T-cell intracellular antigen 1 (TIA1). MARK4 expression enhances SG formation induced by hydrogen peroxide. The spacer domain of MARK4 mediates its localization to SGs, and its kinase activity is required for the enhancement of SG formation. MARK4 suppresses TIA1 dimerization induced by hydrogen peroxide. Furthermore, we found that MARK4 and TIA1 synergistically promoted tau accumulation in cultured cells, and knockdown of a fly TIA1 homolog suppressed tau toxicity in a Drosophila model. These results indicate that MARK4 regulates TIA1 and SG formation and suggest that MARK4 and TIA1 synergistically contribute to tau toxicity.

cell biology↗

bioRxiv2025

Elucidating Chiral Myosin-Induced Actin Dynamics: From Single Filament Behavior to Collective Structures

The myosin superfamily comprises over 70 classes, each with multiple subclasses, and shows substantial diversity in properties such as velocity, ATPase activity, duty ratio, and directionality. This functional diversity enables the specialized roles of each myosin in various organisms, organs, and cell types. Recent studies have revealed that certain myosins induce chiral curved motions of actin filaments. However, this newly identified property remains largely unexplored. Here, we investigated this chiral motion in vitro using Chara corallina myosin XI (CcXI), which drives fast counterclockwise (CCW) movement of actin filaments. This chiral motion arises from asymmetric displacement at the filaments leading tip, and its curvature depends on the surface density of myosin. Surprisingly, at near-physiological actin concentrations, actin filaments exhibiting chiral curved motion undergo collective motion, spontaneously forming a novel structure--termed the actin chiral ring (ACR)--that exhibits persistent CCW rotation. ACRs display remarkable stability, continuing to rotate at their formation site until ATP is depleted, while maintaining their structure even after rotation ceases. This stability is unprecedented among reported collective motions of cytoskeletal proteins driven by various motors. Our findings demonstrate that myosins with chiral activity can autonomously organize actin filaments into stable, chiral structures through collective motion, providing new insights into actin self-organization by unconventional myosins. This study advances our understanding of the diverse functional roles of unconventional myosins and introduces a new paradigm for cytoskeletal organization. Significance StatementMyosins are motor proteins that move along actin filaments and support various intracellular functions. Recently, some myosins have been found to drive actin filaments along chiral curved paths, but the mechanisms and significance of this behavior remain poorly understood. Here, we analyzed this activity and discovered that it not only drives chiral curved motion of single actin filaments, but also organizes them into stable, unidirectionally rotating ring structures through collective motion. These rings, termed actin chiral rings (ACRs), spontaneously emerge at near-physiological actin concentrations. Our findings uncover a previously unrecognized organizing principle of actin self-assembly driven by myosin with chiral activity and provide a new framework for understanding how cytoskeletal chirality is made.

cell biology↗

bioRxiv2025

Lactate dehydrogenase A-coupled NAD+ regeneration is critical for acute myeloid leukemia cell survival

BackgroundEnhanced glycolysis plays a pivotal role in fueling the aberrant proliferation, survival and therapy resistance of acute myeloid leukemia (AML) cells. Here, we aimed to elucidate the extent of glycolysis dependence in AML by focusing on the role of lactate dehydrogenase A (LDHA), a key glycolytic enzyme converting pyruvate to lactate coupled with the recycling of NAD+. MethodsWe compared the glycolytic activity of primary AML patient samples to protein levels of metabolic enzymes involved in central carbon metabolism including glycolysis, glutaminolysis and the tricarboxylic acid cycle. To evaluate the therapeutic potential of targeting glycolysis in AML, we treated AML primary patient samples and cell lines with pharmacological inhibitors of LDHA and monitored cell viability. Glycolytic activity and mitochondrial oxygen consumption were analyzed in AML patient samples and cell lines post-LDHA inhibition. Perturbations in global metabolite levels and redox balance upon LDHA inhibition in AML cells were determined by mass spectrometry, and ROS levels were measured by flow cytometry. ResultsAmong metabolic enzymes, we found that LDHA protein levels had the strongest positive correlation with glycolysis in AML patient cells. Blocking LDHA activity resulted in a strong growth inhibition and cell death induction in AML cell lines and primary patient samples, while healthy hematopoietic stem and progenitor cells remained unaffected. Investigation of the underlying mechanisms showed that LDHA inhibition reduces glycolytic activity, lowers levels of glycolytic intermediates, decreases the cellular NAD+ pool, boosts OXPHOS activity and increases ROS levels. This increase in ROS levels was however not linked to the observed AML cell death. Instead, we found that LDHA is essential to maintain a correct NAD+/NADH ratio in AML cells. Continuous intracellular NAD+ supplementation via overexpression of water-forming NADH oxidase from Lactobacillus brevis in AML cells effectively increased viable cell counts and prevented cell death upon LDHA inhibition. ConclusionsCollectively, our results demonstrate that AML cells critically depend on LDHA to maintain an adequate NAD+/NADH balance in support of their abnormal glycolytic activity and biosynthetic demands, which cannot be compensated for by other cellular NAD+ recycling systems. These findings also highlight LDHA inhibition as a promising metabolic strategy to eradicate leukemic cells.

cancer biology↗

bioRxiv2025

The Translation Termination Factor eRF3 Interacts Sequentially with eRF1 and ABCE1 on the Ribosome

To elucidate the molecular mechanisms connecting translation termination and ribosome recycling, interactions among eRF1, eRF3, and ABCE1, were genetically investigated in Saccharomyces cerevisiae. Heterologous factors from Pneumocystis carinii and humans, along with their mutants were successfully used for co-functional studies in conditional double knockout, double tetOFF strains. Combination of P. carinii eRF3 mutants with S. cerevisiae eRF1 and ABCE1 revealed that all the eRF3 mutants co-functioned with eRF1, but exhibited varying interactions with ABCE1 depending on the mutants. These findings provide evidence that eRF3 remains bound to the GTPase center of the ribosome, awaiting ABCE1. Thus, eRF3 sequentially interacts with eRF1 and ABCE1 during the final steps of translation.

genetics↗

bioRxiv2025

Cell-cultured PDMS vascular model to allow placement of implant devices

BackgroundA stent maintains normal blood flow by expanding a stenotic artery from the inside. Stents currently in clinical use are mechanically sub-optimized and, therefore, exert excessive mechanical stimuli on the vascular wall. This can lead to arterial inflammation and potentially in-stent restenosis. To optimize the force exerted by a stent on the vascular wall, we should understand, reproduce, and analyze in detail the mechanical field to which the stented vessel is exposed. However, to date, no in vitro model has been established that can adequately evaluate the mechanical effects of a stent on the vascular wall and be constructed without relying on a laboratorys know-how. This study aims to develop a three-dimensional in vitro vascular model that allows stent placement and to provide the details of its construction method. MethodsPolydimethylsiloxane (PDMS) was used to mimic the adventitial structure of arteries. Human carotid artery endothelial cells (HCtAECs) were then seeded on the luminal surface and cultured for 24 h to form a confluent monolayer (intima). The constructed model was installed in the flow-exposure culturing system, and hemodynamic stimulation (two types of shear stress (SS); 0.5 Pa and 2.3 Pa) was applied to the HCtAECs inside to reproduce the physiological state of blood vessels. In addition, a self-expanding stent was placed in the model during perfusion culture. ResultsWe examined the performance of the developed model based on quantitative evaluations of endothelial morphology in response to SS and in-stent endothelialization. Exposure to SS for 24 and 48 h caused endothelial orientation and elongation in the direction of flow, confirming the physiological responses of blood vessels. We were also able to quantitatively evaluate endothelial migration (endothelialization) to the stent. DiscussionOur model can reproduce the mechanical field inside the stented blood vessel, including hemodynamic stimuli. Based on the results obtained, the developed cell-cultured vascular model has sufficient performance to be used not only for quantitative evaluation of in-stent endothelialization but also for optimization of the mechanical fields in the stented vessel.

bioengineering↗

bioRxiv2025

Inhibition of EMT driver PTK6 enhances anti-tumor immune responses against triple-negative breast cancer

The non-receptor tyrosine kinase PTK6 is expressed in 70% of triple negative breast cancers (TNBC) and is an oncogenic driver of epithelial-mesenchymal transition (EMT). EMT promotes metastasis and immune evasion of TNBC. Therefore, targeting EMT drivers could reverse these properties and lead to more favorable outcomes. Treatment of TNBC tumors with a small molecule inhibitor of PTK6 kinase (P21d) suppressed their growth in vivo. Tumor inhibition by P21d is dependent on an induced immune response because: 1) inhibition is observed in immunocompetent, but not immunodeficient, mice; 2) P21d increases tumor-infiltrating CD8+ T and NK cells and decreases immunosuppressive myeloid-derived suppressor cells; and 3) tumor inhibition by P21d is abrogated by co-treatment with NK or CD8+ T cell-depleting antibodies. These effects on tumor growth and cytotoxic TILs are phenocopied by the knockdown of tumoral PTK6 or SNAIL, which supports EMT inhibition as a mechanism for enhanced anti-tumor immune response. RNA sequencing (RNA-seq) profiling of P21d-treated tumors also revealed changes consistent with activation of the immune response and identified CXCL10 as a critical chemokine induced intratumorally by P21d that promotes recruitment of NK/CD8+ T cells to the tumor site, leading to tumor growth inhibition. Our study highlights the novel tumor immune microenvironmental functions of PTK6 with important consequences for tumor growth that could lead to new immunotherapeutic approaches for TNBC.

cancer biology↗

bioRxiv2025

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zone are largely clustered to form complex porous structural unit called aggregates where highly diverse microbes coexist and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microbes exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. Yet, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus adequate cell extraction method from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) isolated from a topsoil of cultivated Acrisol. Using the same six individual aggregates, we performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion methods improved the extractability of bacterial cells compared to previous studies, the latter yielded higher number and more diverse microbes compared to the former. The analyses of nitrogen-cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to greater recovery of microbes strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microbes having the genes (i.e., potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. In addition, all six aggregates studied showed overall similarity in pore characteristics, phylum-level composition, and the microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggest that conventional methods employed for the extraction of cell and DNA may not be optimal. The current findings underscore the necessity to advance extraction methodologies, thereby facilitating a more comprehensive understanding of the microbial diversity and functioning within soil environments.

microbiology↗

bioRxiv2024

Biochemical state in tissue can be detected through ultrasound signal

Three-dimensional (3D) cell cultures, such as spheroids, are indispensable models for investigating cellular behaviors and responses under conditions that closely resemble in vivo environments. Conventional imaging techniques, including optical microscopy, are often limited by penetration depth and phototoxicity, complicating the analysis of structural and biochemical changes within dense 3D systems. This study demonstrates the application of ultrasound imaging for the non-invasive evaluation of internal dynamics in cancer spheroids over a 15-day period. Scattering-based acoustic parameters revealed spatial variations in brightness and density, correlating with cellular proliferation, apoptosis, and necrosis. Brightness values in central regions progressively decreased after Day 3, approaching near-zero by Day 15, reflecting necrotic core formation. Artificial inhibition of myosin contractility significantly influenced these patterns, providing insights into biomechanical contributions to spheroid organization. The findings establish ultrasound imaging as a label-free, high-penetration technique capable of addressing critical challenges in 3D culture analysis, offering new opportunities for studying cellular dynamics and therapeutic responses in spheroids and organoid models.

bioengineering↗

bioRxiv2024

Xolography for Biomedical Applications: Dual-color Light-sheet Printing of Hydrogels with Local Control over Shape and Stiffness

AbstractCurrent challenges in tissue engineering include creation of extracellular environments that support and interact with cells using biochemical, mechanical, and structural cues. Spatial control over these cues is currently limited due to a lack of suitable fabrication techniques. This study introduces Xolography, an emerging dual-color light-sheet volumetric printing technology, to achieve control over structural and mechanical features for hydrogel-based photoresins at micro-to macroscale while printing within minutes. We propose a water-soluble photoswitch photoinitiator system and are the first to demonstrate Xolography with a library of naturally-derived, synthetic, and thermoresponsive hydrogels. Centimeter-scale, three-dimensional constructs with positive features of 20 {micro}m and negative features of [~] 100 {micro}m are fabricated with control over mechanical properties (compressive moduli 0.2 kPa - 6.5 MPa). Notably, switching from binary to grayscaled light projection enables spatial control over stiffness (0.2 - 16 kPa). As a proof of concept, grayscaled Xolography is leveraged with thermoresponsive hydrogels to introduce reversible anisotropic shape changes beyond isometric shrinkage. We finally demonstrate Xolography of viable cell aggregates, laying the foundation for cell-laden printing of dynamic, cell-instructive environments with tunable structural and mechanical cues in a fast one-step process. Overall, these innovations unlock unique possibilities of Xolography across multiple biomedical applications.

bioengineering↗

bioRxiv2024

Mother-to-infant plasmid transmission in early postpartum and its association with dominant gut bacteria

BackgroundThe gut microbiome plays a crucial role in human health, and it is known that the microbiome is transmitted from mother to infant at birth and has profound effects on an individuals health. Although extensive research has been conducted on mother-to-infant microbiome transmission, little is known about plasmid transmission and its effects on the infant microbiome. Plasmids are considered important contributors to early development of the gut microbiome due to their functions, such as antibiotic resistance, and their ability to be transferred between a wide range of host bacteria. MethodsIn this study, we assembled plasmid sequences from longitudinal fecal data of 65 mother-infant pairs and analyzed plasmid sharing between mothers and infants during the first year of life. After identifying shared plasmids, we investigated the relationship between plasmid sharing and delivery mode. We also characterized the functions and host range of shared plasmids. ResultsWe found that the number of plasmids was lower in infants than in mothers, probably reflecting the lower overall diversity of the infant microbiome. Additionally, we detected shared plasmids between mothers and infants, marking the first discovery of mother-to-infant plasmid transmission. Our findings revealed that plasmids are more likely to be transmitted from mother to infant immediately after birth, with the likelihood of transmission decreasing as infants age. This underscores the critical role of the maternal microbiome in shaping early development of the gut microbiome. Moreover, plasmids from dominant bacteria in mother-to-infant microbiome transmission, such as Bacteroides, were frequently transmitted to infants and carried specific functional traits. In particular, plasmid genes such as mbpA, mbpB, and mbpC were frequently shared between mothers and infants. Each of these genes encodes a protein of a specific size and plays an important role in plasmid mobilization, or the transfer of plasmids to other bacteria. Plasmids improve the fitness and environmental adaptability of host bacteria, which may contribute to the development of a healthy gut microbiome in infants. ConclusionsThis study revealed that mother-to-infant plasmid transmission likely occurs during the early postpartum period and is influenced by dominant gut bacteria. These findings provide new insights into the mothers role in shaping the infants gut microbiome development.

microbiology↗

bioRxiv2024

Odor sensory tests vs. In-silico prediction for the high-definition quantification of olfaction dynamics

The intricate dynamics of volatile organic compounds (VOCs) in the human respiratory system remain poorly understood. In the present study, we integrate odor sensory tests (OSTs) coupled with computational fluid dynamics and a physiologically based pharmacokinetic (CFD-PBPK) model to elucidate various aspects of the olfaction process. Safe yogurt-derived substances were incorporated in OSTs to prevent harmful exposure. Acetaldehyde was identified as a key active component in determining odor intensity, prompting further analysis of acetone and other four constituents of yogurt. Logarithmic correlations were established between the perceived odor intensity from the OSTs and both time-averaged absorption flux and equilibrium concentration within the olfactory mucus layer. These parameters were numerically captured, enabling the logarithmic approximation of odor intensity for different breathing profiles and the development of reliable prediction models for odor sensation based on quantifiable physiological parameters. The CFD-PBPK model captured detailed spatial and temporal variations of these parameters, which offers potential for future integrated/in-silico applications. Minor peaks of odor concentration were observed in the posterior olfactory regions during exhalation, revealing a retro-nasal phenomenon. Location-specific analysis revealed the nostrils and olfactory regions as the most accurate indicators of perceived odor intensity, proving the limitations of rough sensory assessments in the indoor/breathing zone scales. Acetone exhibited distinct absorption and desorption trends during the transitional phase between inhalation and exhalation, owing to the physical properties (diffusion and partition coefficients) that strongly characterize the olfaction dynamics. Author SummaryWe developed an integrated method using odor sensory tests (OSTs) coupled with computational fluid dynamics and physiologically based pharmacokinetic models (CFD-PBPK) to assess the temporal and spatial transport of yogurt odorants to the human olfactory region. Multiple phenomena were observed, including ortho-nasal and retro-nasal olfaction, temporal changes in the perceived odor intensity associated with breathing/sniffing profiles, absorption and desorption curves of acetone in the mucus epithelium, and regional-based olfaction distribution. The perceived odor intensity from OSTs can be predicted logarithmically in correlation with both the time-averaged absorption flux and the equilibrium concentration in the olfactory mucus layer, offering a reliable in-silico prediction model for odor sensation based on numerically quantifiable parameters. This model offers potential implications for multiple computational, biomedical, and industrial applications, such as the electric noses, smart odor sensors, food assessments, and fragrance development, particularly for long-term exposure in the industries that emit odorous compounds. It can open the door for more accurate predictions of the complex micro-fluid dynamics in the microbial ciliated tissues in the olfactory receptors.

bioengineering↗

bioRxiv2024

Raw materials and manufacturing environment as determinants of miso microbial community.

Miso is a Japanese traditional fermented food with soybeans, salt and koji, and has gained attention among people for its sophisticated flavor and preservability. Koshu miso is a unique miso made by mixing two types of koji (rice and barley), and is produced primarily in Yamanashi Prefecture, Japan. We characterized the microbiota of Koshu miso at three distinct fermentation stages. Our analysis revealed that the genus Staphylococcus dominated across all miso samples. Notably, Staphylococcus sequences in the miso matched those found in rice and barley koji, indicating the influence of raw ingredients on the initial microbial community. Additionally, analysis of the manufacturing environment suggested similarities between the environmental surfaces and miso, highlighting the importance of the manufacturing environment in serving as a medium for microbial transfer. These findings underscore the critical importance of both raw ingredients and manufacturing equipment in shaping the microbial composition and evolution of miso throughout the fermentation process.

microbiology↗

bioRxiv2024

Deep Learning-Based Inference of Uterine Contractions from Maternal ECG

BackgroundPreterm birth and stillbirth have multifaceted causes, many of which remain unknown. Factors such as maternal age, sexually transmitted infections, and genetic abnormalities are notably implicated. Globally, there has been minimal improvement in preterm birth rates, leading to substantial economic losses and underscoring the need for innovative approaches. ObjectiveThis study aims to analyze and detect uterine contractions by applying deep learning techniques to physiological data derived from maternal electrocardiograms (ECGs). Leveraging ECGs, which are easily obtainable from wearable devices, allows for effective and convenient monitoring of uterine contractions outside clinical settings. Since uterine contractions are a critical indicator for assessing the risk of preterm birth, our algorithm has the potential to facilitate early identification of high-risk individuals, thereby contributing to timely interventions and improved maternal-fetal outcomes. MethodsParticipants meeting all inclusion criteria and none of the exclusion criteria were recruited from patients admitted to or attending outpatient services at Saintpaulia Misao Ladies Hospital in Gifu, Japan, between December 6, 2023, and July 31, 2024. Our deep learning model was developed using maternal ECG data, uterine contraction waveforms obtained from cardiotocograms (CTGs). The collected data were divided into training and evaluation datasets. The AI-generated uterine contraction waveforms from the developed model were compared with ground truth labels obtained from the fetal monitoring devices. This study was reviewed and approved by the Ethics Committee of the Graduate School of Medicine at Gifu University and was conducted as a collaborative research effort with nonat Inc. (the lead research institution) and Saintpaulia Misao Ladies Hospital (joint research institution). ResultsFinally, 73 participants took part in this study, and 57 datasets were used for algorithm development and evaluation. Multiple measurements were taken on the same subjects on different days only with their consent. Our analysis demonstrated a strong correlation between the uterine contraction waveforms estimated by the developed model and the ground truth waveforms from CTGs, achieving an average correlation across all evaluation data (Pearson correlation coefficient = 0.53). ConclusionThis is the worlds first trial to detect uterine contractions from maternal ECGs using deep learning algorithms. In this study, we successfully developed a deep learning algorithm capable of accurately inferring uterine contraction waveforms from maternal ECGs. Given that ECGs can be easily obtained using wearable devices, this approach may provide healthcare professionals with objective and precise information on uterine contractions--a crucial indicator of preterm labor--even in resource-limited settings outside hospital environments.

physiology↗