Biology subjects

Uchida, Y.

Publications and source records attributed to Uchida, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-nucleus multiome profiling reveals osteocyte-centered remodeling of human subchondral bone across osteoarthritis severity

Objective: Subchondral bone remodeling is a hallmark of osteoarthritis (OA), but osteocytes, the principal regulators of bone homeostasis, have been inaccessible to single-cell studies because they are embedded in mineralized matrix. We aimed to define the cellular, transcriptional and chromatin changes of human subchondral bone across OA severity, osteocytes included, and to identify candidate signals between cartilage and bone. Design: Subchondral bone from the medial femoral condyle of human knees graded by the Outerbridge system was analyzed by bulk RNA sequencing (89 knees) and by single-nucleus multiome sequencing of gene expression and chromatin accessibility after mechanical nuclear isolation (16 donors). Three hypotheses were prespecified: with increasing OA severity, (1) the osteoprogenitor fraction increases, (2) the osteocyte fraction increases, and (3) osteocyte SMAD2/3 motif activity increases. Results: With OA severity, bulk expression shifted toward extracellular matrix and ossification programs. The atlas resolved 26 cell states among 61,570 nuclei, including 906 osteocytes. Osteoprogenitors (p = 0.003) and osteocytes (p = 0.036) increased in share along an osteogenic continuum that starts from CXCL12-abundant reticular cells. Chondrocytes at the osteochondral junction upregulated FN1, FGF1, FGF2 and TNFSF11 without increased hypertrophic gene expression, and their share of the inferred FN1 signal received by osteocytes rose from 4% in normal knees to 33% in severe OA. Osteocyte SMAD2/3 motif activity increased with severity (rho = 0.70, p = 0.003), and all three hypotheses remained significant after Holm correction. Across the osteogenic lineage, SMAD2/3 activity correlated with junction chondrocyte FN1 (rho = 0.63, p = 0.017), and in osteocytes it was accompanied by TGF-{beta}-responsive matrix genes and perilacunar-remodeling genes. Conclusions: This osteocyte-inclusive atlas of human OA subchondral bone shows expansion of the osteogenic compartment and a rise of osteocyte SMAD2/3-linked matrix remodeling with disease, and identifies chondrocyte-derived FN1 as a candidate contributor to cartilage-bone communication associated with osteocyte TGF-{beta}/SMAD2/3 signaling.

molecular biology↗

bioRxiv2026

Spatial Patterns of White Matter Hyperintensities and Cognitive Function in Older Adults: A Community-Based Study

Abstract Objectives White matter hyperintensities (WMH) are associated with cognitive decline in older adults. We examined whether anatomically defined spatial WMH patterns are associated with cognitive performance and subsequent decline in a large community-based cohort with approximately six years of follow-up. Methods We analyzed 1,667 participants (mean age 76 years) from the Atherosclerosis Risk in Communities Neurocognitive Study. WMH were segmented from FLAIR images and mapped to 112 white matter regions using deep-learning-based parcellation. Principal component analysis identified dominant WMH distribution patterns; candidate components were selected by Horn's parallel analysis and retained if stable across resampled split samples. Linear mixed-effects models examined associations between WMH patterns and cognitive performance at baseline and follow-up, adjusting for demographic, genomic, and vascular risk factors. Robustness was assessed using analyses accounting for total WMH burden, study center, and selective attrition. Results Of 14 candidate principal components (PCs) identified by parallel analysis, eight met the resampling stability criterion and were retained, together explaining 42% of the variance. Three components were associated with cross-sectional or future cognition. PC3, characterized by deep white matter burden in the corpus callosum and anterior corona radiata with relative preservation of superficial white matter, showed no cross-sectional association at baseline but was associated with accelerated decline across multiple domains. Interpretation A deep spatial pattern of WMH loading on the corpus callosum and anterior corona radiata was associated with subsequent cognitive decline in the absence of a cross-sectional association at baseline, independent of total lesion burden.

neuroscience↗

bioRxiv2026

NAT10 supports CAG repeat-associated mRNA stabilization and is associated with hepatic metabolic reprogramming during spaceflight

The regulatory factors underlying posttranscriptional adaptation to spaceflight are incompletely understood. We identified NAT10, an RNA acetyltransferase, among RNA modification enzymes significantly upregulated in spaceflight-exposed mouse liver. Transcriptome-wide correlation analysis linked NAT10 expression to an RNA-metabolism module enriched for CAG repeat density in coding sequences. Actinomycin D chase assays showed that NAT10 knockdown destabilized CAG repeat-containing transcripts, with DDX17 serving as the primary validated target; DCP1A showed a directionally consistent pattern. Wild-type NAT10 re-expression fully rescued DDX17 mRNA stability, the acetyltransferase-dead G641E mutant rescued mRNA stability to a comparable extent, and the K290A helicase-domain mutant failed to rescue, consistent with a requirement for helicase domain integrity, whereas acetyltransferase activity was not strictly required under these experimental conditions. RNA immunoprecipitation further supported preferential NAT10 association with CAG repeat-containing mRNAs, with reduced association after single-site CAGCAG deletion in DDX17 and DCP1A reporters. Gene set enrichment analysis associated NAT10 upregulation in spaceflight liver with suppressed fatty acid beta-oxidation and induced cholesterol biosynthesis; NAT10 depletion in hepatocellular carcinoma cells selectively opposed the cholesterol-associated, but not the broader metabolic, component of this signature. These findings support a model linking NAT10 to CAG repeat-associated mRNA stabilization in the context of hepatic metabolic and posttranscriptional adaptation to spaceflight.

molecular biology↗

bioRxiv2025

VCAP-102 Achieves Exceptional BBB Penetration in Marmosets After Ten Years of AAV Capsid Evaluation

Efficient passage of adenoassociated virus (AAV) vectors across the blood-brain barrier (BBB) is essential for achieving broad central nervous system transduction following systemic delivery. Since PHP.B was reported in 2016 to exhibit high BBB permeability in C57BL/6J mice, many BBB-penetrant capsids have been developed, yet their performance often varies substantially across species. From 2016 to 2025, we produced each newly reported BBB-penetrant capsid as its sequence became available and evaluated it under standardized intravenous administration conditions in marmosets. This included PHP.B, PHP.eB, AAV-F, CAP-B22, CAP-B10, CPP.16, CAP-Mac, and BR1N. Although several of these capsids have been reported to penetrate the marmoset BBB, none reproduced these effects under our unified evaluation conditions. We also pursued several directed-evolution approaches to engineer AAV9-based variants with improved BBB permeability; however, none surpassed AAV9. In 2025, VCAP-102 was reported as an AAV9-derived capsid with BBB permeability in mice and non-human primates. When evaluated using our standardized framework, VCAP-102 consistently mediated markedly stronger and more widespread whole-brain transduction than AAV9 across all three animals tested. These findings provide a decade-long, systematic assessment of BBB-penetrant AAV capsids in marmosets and identify VCAP-102 as a highly promising candidate for future systemically delivered AAV-based gene therapies.

neuroscience↗

bioRxiv2025

In vivo chemical reprogramming is associated with a toxic accumulation of lipid droplets hindering rejuvenation

Partial reprogramming has emerged as a promising strategy to reset the epigenetic landscape of aged cells towards more youthful profiles. Recent advancements have included the development of chemical reprogramming cocktails that can lower the epigenetic and transcriptomic age of cells and upregulate mitochondrial biogenesis and oxidative phosphorylation. However, the ability for these cocktails to affect biological age in a mammalian aging model has yet to be tested. Here, we have analyzed the effects of partial chemical reprogramming on mitochondrial structure in aged mouse fibroblasts and tested its in vivo efficacy in genetically diverse male UM-HET3 mice. This approach increases the size of mitochondria, alters cristae morphology, causes an increased fusing of mitochondrial networks, and speeds up movement velocity. We also discover that partial chemical reprogramming upregulates the formation of intracellular lipid droplets. At lower doses, the chemical reprogramming cocktail can be safely administered to middle-aged mice using implantable osmotic pumps, albeit with no effect on the transcriptomic age of kidney or liver tissues, and only a modest effect on the expression of OXPHOS complexes. However, at higher doses, the cocktail causes a drastic reduction in body weight and body condition scores. In the livers and kidneys of these animals, we observe significant increases in oil red o staining indicative of excessive lipid droplet accumulation in these organs. Thus, the upregulation of lipid droplet formation during partial chemical reprogramming may cause toxicity hindering the rejuvenation of cells and tissues in aged mammals.

cell biology↗

bioRxiv2025

Flexible value coding in the mesolimbic dopamine system depending on internal water and sodium balance

Homeostatic imbalances elicit strong cravings, such as thirst and salt appetite, to restore equilibrium. Although midbrain dopaminergic neurons are known to encode the value of foods, their nutritional state-dependency remains unknown. Here, we show that the activity of the dopaminergic mesolimbic pathway flexibly expresses the positive and negative values of water and salt depending on the internal state in mice. Mice showed behavioral preference and aversion to water and salt depending on their internal water and sodium balance. Fiber photometry recordings revealed that dopamine neurons in the ventral tegmental area and dopamine release in the nucleus accumbens flexibly showed bidirectional excitatory and inhibitory responses to water and salt intake in a state-dependent manner. Furthermore, these dopaminergic and behavioral responses could be simulated by a homeostatic reinforcement learning model. Our results demonstrate the nutritional state-dependency of value coding in mesolimbic dopamine systems, providing new insights into neural circuits underlying homeostatic regulation of appetitive and avoidance behaviors.

neuroscience↗

bioRxiv2025

Agricultural land use induces broader homogenization of soil microbial functional composition than taxonomic composition

Land-use changes from natural ecosystems to farmlands significantly alter soil functioning worldwide, especially challenging sub-Saharan Africa with rapid population growth and intensive agriculture. Soil microbial diversity is vital in supporting ecosystem multifunctionality and preventing pathogen growth. Recent studies have revealed that farming activities homogenize microbial communities across distant sites, which may lead to functional homogenization on that scale. However, given the redundancy of microbial functions, functional homogenization driven by farming may occur on a broader scale than taxonomic homogenization. We compared the taxonomic and functional compositions of soil prokaryotic and fungal communities between natural lands and farmlands at scales ranging from within-site ([~]200 m) to across-site ([~]1500 km) in Kenya and Malawi, using amplicon sequencing of 16S rRNA and ITS genes and the prediction of microbial functions. Soil microbial functional compositions were homogenized more broadly than taxonomic compositions in farmlands compared to natural lands, suggesting that similar functional responses to farming occur across scales where different taxa thrive. Furthermore, environmental factors predominantly influenced within-site homogeneity, whereas farming itself was a significant contributor to across-site homogeneity, indicating an overriding influence of farming compared to environmental variations. Additionally, pathogenic fungi were relatively more abundant in farmlands, likely due to reduced species competition and farming-induced environmental changes such as low soil pH. Our findings highlight the need to investigate microbial functional diversity alongside taxonomic diversity when assessing the impacts of land-use changes on soil health to develop sustainable land management strategies.

ecology↗

bioRxiv2024

Heterogeneous Appetite Patterns in Depression: Computational Modeling of Nutritional Interoception, Reward Processing, and Decision-Making

Accurate interoceptive processing in decision-making is essential to maintain homeostasis and overall health. Disruptions in this process have been associated with various psychiatric conditions, including depression. Recent studies have focused on nutrient homeostatic dysregulation in depression for effective subtype classification and treatment. Neurophysiological studies have associated changes in appetite in depression with altered activation of the mesolimbic dopamine system and interoceptive regions, such as the insular cortex, suggesting that disruptions in reward processing and interoception drive changes in nutrient homeostasis and appetite. This study aimed to explore the potential of computational psychiatry in addressing these issues. Using a homeostatic reinforcement learning model formalizing the link between internal states and behavioral control, we investigated the mechanisms by which altered interoception affects homeostatic behavior and reward system activity via simulation experiments. Simulations of altered interoception demonstrated behaviors similar to those of depression subtypes, such as appetite dysregulation. Specifically, reduced interoception led to decreased reward system activity and increased punishment, mirroring the neuroimaging study findings of decreased appetite in depression. Conversely, increased interoception was associated with heightened reward activity and impaired goal-directed behavior, reflecting an increased appetite. Furthermore, effects of interoception manipulation were compared with traditional reinforcement learning parameters (e.g., inverse temperature {beta} and delay discount{gamma} ), which represent cognitive-behavioral features of depression. The results suggest that disruptions in these parameters contribute to depressive symptoms by affecting the underlying homeostatic regulation. Overall, this study findings emphasize the importance of integrating interoception and homeostasis into decision-making frameworks to enhance subtype classification and facilitate the development of effective therapeutic strategies.

systems biology↗

bioRxiv2024

Hair follicles modulate skin barrier function

Our skin provides a protective barrier that shields us from our environment. Barrier function is typically associated with interfollicular epidermis; however, whether hair follicles influence this process remains unclear. Here, we utilize a potent genetic tool to probe barrier function by conditionally ablating a quintessential epidermal barrier gene, Abca12, which is mutated in the most severe skin barrier disease, harlequin ichthyosis. With this tool, we deduced 4 ways by which hair follicles modulate skin barrier function. First, the upper hair follicle (uHF) forms a functioning barrier. Second, barrier disruption in the uHF elicits non-cell autonomous responses in the epidermis. Third, deleting Abca12 in the uHF impairs desquamation and blocks sebum release. Finally, barrier perturbation causes uHF cells to move into the epidermis. Neutralizing Il17a, whose expression is enriched in the uHF, partially alleviated some disease phenotypes. Altogether, our findings implicate hair follicles as multi-faceted regulators of skin barrier function.

developmental biology↗

bioRxiv2024

Unveiling the dominant role of soil pH in shaping nitrogen cycling microbial gene abundances: Insights from 65-years of chemical fertilizer selection in acidic grassland meadow

Understanding the microbial processes driving the nitrogen (N) cycle is crucial for enhancing plant productivity and mitigating environmental pollution. The long-term application of synthetic fertilizers induces significant alterations in the microbial community functions. Microbes inhabiting acidic soils may exhibit distinct responses to chemical fertilizer application compared to soils with neutral pH. However, the chronic or occasional changes resulting from repeated nutrient flushes due to fertilizer application remain insufficiently elucidated, especially in acidic grasslands. Therefore, our study was on an acidic semi-natural grassland, where the soil was subjected to chemical fertilizer P (superphosphate), K (potassium sulfate), PK, N (ammonium nitrate), NPK, PK+N (PK applied in spring and N applied once in summer) over a span of 65 years. Gene abundances associated with the N-cycle (amoA, nifH, nirK, nirS, and nosZ) were quantified at seven different time points throughout the year considering the temporal effect caused by fertilizer application. Our findings reveal that in the long term, soil pH emerged as the predominant factor influencing the gene abundance related to N-fixation and denitrification outweighing the impact of nutrient availability. Notably, the application of N fertilizer had a positive effect on the abundance of nitrifiers, while the abundance of denitrifiers decreased due to soil acidification induced by fertilizer application. In summary, our study highlights that the microbial community involved in N cycling is more sensitive to the difference in soil pH shaped by long-term fertilizer application rather than to the direct impact of fertilizer application. HighlightO_LISeasonal sampling confirmed the long-term effect of fertilizer on microbial N-cycling genes C_LIO_LIFertilizer types shaped soil pH, consequently impacted on diazotrophs and denitrifies abundances C_LIO_LIAbundance of denitrifying microbe did not explain the increase of N2O emission by N fertilizer C_LIO_LIN2O emission was positively correlated with AOA abundance C_LI

microbiology↗

bioRxiv2024

Liming enhances the abundance and stability of nitrogen-cycling microbes: The buffering effect of long-term lime application

Lime application (liming) has historically been used to ameliorate soil acidity in grasslands. Liming effectively improves soil pH, plant productivity, and soil physicochemical properties, but the long-term impact of acidity control by liming on key microbial nitrogen (N)-cycling genes in semi-natural grasslands is unknown. We investigated the effect of 65 years of liming on N-cycling processes in the limed and control plots of the Ossekampen long-term grassland experiment in the Netherlands. These plots have not received any other fertilizers for 65 years. Soil sampling and nitrous oxide (N2O) emission measurements were conducted three times in spring and four times in summer, and quantitative real-time PCR was performed to determine the abundances of N-cycling genes, including ammonia-oxidation (amoA), denitrification (nirS, nirK, nosZ), and N-fixation (nifH) genes. Long-term liming increased the abundances of nitrifiers and denitrifiers but did not increase N2O emissions. Additionally, liming had a buffering effect that stabilized the population of N-cycling microbes against seasonal variations in abundance. Our results indicate that improving soil acidity through liming facilitates microbial N-cycling processes without increasing N2O emissions. HighlightsO_LI65 years of liming increased bacterial but not archaeal and fungal community abundance. C_LIO_LILiming increased the abundance of microbial N-cycling genes. C_LIO_LIThe buffering effect of liming reduced seasonal variations in the abundance of N microbes. C_LI

microbiology↗

bioRxiv2024

Ribonanza: deep learning of RNA structure through dual crowdsourcing

Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.

biophysics↗

bioRxiv2023

A non-toxic equinatoxin-II reveals the dynamics of sphingomyelin in the cytosolic leaflet of the plasma membrane

Super-resolution microscopic observation of a novel non-toxic sphingomyelin probe revealed the formation of dynamic small domains including sphingomyelin and cholesterol in the cytosolic leaflet of living cell plasma membranes. AbstractSphingomyelin (SM) is a major sphingolipid in mammalian cells. SM is enriched in the extracellular leaflet of the plasma membrane (PM). Besides this localization, recent electron microscopic and biochemical studies suggest the presence of SM in the cytosolic leaflet of the PM. In the present study, we generated a non-toxic SM-binding variant (NT-EqtII) based on equinatoxin-II (EqtII) from the sea anemone Actinia equina, and examined the dynamics of SM in the cytosolic leaflet of living cell PMs. NT-EqtII with two point mutations (Leu26Ala and Pro81Ala) had essentially the same specificity and affinity to SM as wild-type EqtII. NT-EqtII expressed in the cytosol was recruited to the PM in various cell lines. Super-resolution microscopic observation revealed that NT-EqtII formed tiny domains that were significantly colocalized with cholesterol and N-terminal Lyn. Meanwhile, all the examined lipid probes including NT-EqtII underwent apparent fast simple Brownian diffusion, exhibiting that SM and other lipids in the cytosolic leaflet rapidly moved in and out of domains. Thus, the novel SM-binding probe demonstrated the presence of the raft-like domain in the cytosolic leaflet of living cell PMs.

cell biology↗

bioRxiv2023

Activation of prefrontal parvalbumin interneurons ameliorates treatment-resistant working memory deficit even under continuous antipsychotic treatment in a mouse model of schizophrenia

BACKGROUNDOne of the critical unmet medical needs in schizophrenia is a remedy for cognitive deficits. However, the neural circuit mechanisms of them remain unresolved. In addition, despite the patients with schizophrenia cannot stop taking antipsychotics due to a high rate of discontinuation-induced relapse, previous studies using animal models of schizophrenia have not considered these clinical situations. METHODSHere, we employ multi-dimensional approaches, including histological analysis in the prelimbic cortex, LC-MS/MS-based in vivo dopamine D2 receptor occupancy analysis for antipsychotic drugs, in vivo calcium imaging and behavioral analyses of mice using chemogenetic manipulation, to investigate neural mechanisms and potential therapeutic interventions for working memory deficit in a mouse model with chronic phencyclidine (PCP) administration that resembles the schizophrenia symptomatology. RESULTSChronic PCP administration led to abnormalities in excitatory and inhibitory synapses, including dendritic spines of pyramidal neurons, vesicular glutamate transporter 1 (VGLUT1) positive terminals, and parvalbumin (PV) positive GABAergic interneurons, in layer 2-3 of the prelimbic cortex. Continuous olanzapine, which achieved a sustained therapeutic window of dopamine D2 receptor occupancy (60-80%) in the striatum, did not affect these synaptic abnormalities and working memory deficit in the PCP-treated mice. We found that the selective prelimbic PV activation, using hM3D(Gq)-DREADD system confirmed by in vivo calcium imaging, restored working memory deficit, even under continuous olanzapine treatment. CONCLUSIONSOur study raises a possibility that intervention in prefrontal PV neurons leads to an add-on therapy to antipsychotics targeting amelioration of treatment-resistant cognitive deficits in schizophrenia.

neuroscience↗

bioRxiv2022

Long-term recoveries of forest ecosystem components after shallow landslides were asynchronized among slope positions

Landslides are a common disturbance in mountainous areas of the world. Transporting and accumulating landslide debris, i.e., disturbance legacies, such as coarse woody debris (CWD), vegetation patches, and surface soils, generate a heterogeneous environment along slopes (zones), which are suggested to affect forest recovery. However, the long-term changes in forest ecosystems after landslides remain unknown, particularly zone-dependent change patterns. We aimed to reveal the differences in the changes in live trees, understory vegetation, CWD, and soils among zones by surveying forests with landslide ages (years since the landslide) ranging from 3 to 74 years and reference stands. The increase in live tree aboveground biomass occurred at a faster rate at the lower part of the slopes where the disturbance legacies were rich and surface soils were stabilized due to the smaller slope angle. Chronological patterns of understory vegetation amounts were determined by the differences in disturbance legacy richness and the timing of subsequent canopy closure. The amounts and decay-class diversity of CWD were determined by the differences in legacy richness and mortality through stand development. These zone-dependent chronological changes influenced litter production and determined the recovery rates of surface soil carbon stocks and nitrogen contents. The increase in the dominance rates of forest herbaceous species was faster in the lower part of the slopes due to the faster surface soil development and canopy closure. Our results illustrate that long-term forest ecosystem succession and recovery after landslides occurs more rapidly at the lower parts than at the upper parts of slopes. HighlightsO_LIRich landslide legacies and low slope angles promoted vegetation and soil recovery C_LIO_LILegacy richness and timing of canopy closure determined changes in the understory C_LIO_LILandslide mortality and stand development mortality determined changes in dead wood C_LI

ecology↗

bioRxiv2021

Computational mechanisms of osmoregulation: a reinforcement learning model for sodium appetite

Homeostatic control with oral nutrient intake is a vital complex system involving the orderly interactions between the external and internal senses, behavioral control, and reward learning. Sodium appetite is a representative system and has been intensively investigated in animal models of homeostatic systems and oral nutrient intake. However, the system-level mechanisms for regulating sodium intake behavior and homeostatic control remain unclear. In the current study, we attempted to provide a mechanistic understanding of sodium appetite behavior by using a computational model, the homeostatic reinforcement learning model, in which homeostatic behaviors are interpreted as reinforcement learning processes. Through simulation experiments, we confirmed that our homeostatic reinforcement learning model successfully reproduced homeostatic behaviors by regulating sodium appetite. These behaviors include the approach and avoidance behaviors to sodium according to the internal states of individuals. In addition, based on the assumption that the sense of taste is a predictor of changes in the internal state, the homeostatic reinforcement learning model successfully reproduced the previous paradoxical observations of the intragastric infusion test, which cannot be explained by the classical drive reduction theory. Moreover, we extended the homeostatic reinforcement learning model to multi-modal data, and successfully reproduced the behavioral tests in which water and sodium appetite were mediated by each other. Finally, through an experimental simulation of chemical manipulation in a specific neural population in the brain stem, we proposed a testable hypothesis for the function of neural circuits involving sodium appetite behavior. The study results support the idea that osmoregulation via sodium appetitive behavior can be understood as a reinforcement learning process and provide a mechanistic explanation for the underlying neural mechanisms of sodium appetite and homeostatic behavior. Author SummaryThe taste of high-concentration saltwater is rewarding during sodium depletion, while it is aversive in a sodium sufficient state. This "sodium appetite" is a clear manifestation of homeostasis maintenance and proper action selection in animals, reflecting the internal environment. To reveal the computational mechanism of this property, we applied a machine learning model, in which homeostatic stability is a reward and the goal is to maximize the sum of the reward, and simulated animal behavioral experiments. The results suggest that the mechanism of sodium-appetite behavior is based on the machine learning model. Specifically, by replicating the results of neural circuit manipulation, which controls sodium appetite, an algorithm in which the function of a neural population affects sodium appetite behaviors was proposed. Our results provide a fundamental computational model for a mechanism by a function of a neural cell type to regulate animal behavior. More generally, this study can be fundamental to understanding the computational process of decision making reflecting the internal environment.

neuroscience↗

bioRxiv2020

Evaluation of microbial diversification mechanisms in legume-based mixed cropping systems with different legume species and types of fertilizer management

Biodiversity loss is becoming a global concern due to its negative impact on services associated with the ecosystem. For agricultural soil to maintain these multi-services, the conservation of soil microbial diversity is of utmost importance. Mixed cropping systems involve the utilisation of multiple crop species on the field as well as the diversification of aboveground plants, although several contradicting results have been reported regarding their impacts on soil microbial diversity. Therefore, for the evaluation of the impact of different leguminous species used in mixed cropping systems as well as types of fertilizer on the diversity of soil microbes, a pot study was performed under maize/legume mixed cropping systems with one of three legumes, including cowpea (Vigna unguiculate (L.) Walp.), velvet bean (Mucuna pruriens (L.) DC.), and common bean (Phaseolus vulgaris L.) as well as one of three types of fertilizer treatments, namely chemical fertilizer (CF), carbonised chicken manure (CM), or the lack of fertilizer (Ctr). 16S rRNA analyses were conducted using the soils sampled from each pot for soil bacterial diversity assessment. Concerning the results, a decrease in the microbial diversity after CM application was shown by the soil with velvet bean + maize (MM) when compared to the Ctr treatment, while an increase in the microbial diversity was shown by the soil with common bean + maize (PM) under the same condition. In case of the CM application, the abundance of treatment-unique bacteria increased in the PM treatment, although their decrease was observed for the MM treatment. In contrast, the abundance of dominant microbes, including Thaumarchaeota was significantly lower in PM but higher in MM when the CM was applied. Legume species-dependent factors, including nutrient absorption and root exudate composition might be important concerning soil bacterial diversities. For the conservation of soil microbial diversity with mixed cropping, the interaction effect of legume species and fertilizer type should be considered in future studies.

microbiology↗

bioRxiv2020

Integrated Analysis of Cell Shape and Movement in Moving Frame

The cell movement and morphological change are two interrelated cellular processes. The integrated analysis is needed to explore the relationship between them. However, it has been challenging to investigate them as a whole. The cell trajectory can be described by its speed, curvature, and torsion. On the other hand, the 3-Dimensional (3D) cell shape can be studied by using a shape descriptor such as Spherical harmonic (SH) descriptor which is an extension of Fourier transform in 3D space. To integrate these shape-movement data, we propose a method to use a parallel-transport (PT) moving frame as the 3D-shape coordinate system. This moving frame is purely determined by the velocity vector. On this moving frame, the movement change will influence the coordinate system for shape analysis. By analyzing the change of the SH coefficients over time in the moving frame, we can observe the relationship between shape and movement. We illustrate the application of our approach using simulational and real datasets in this paper.

bioinformatics↗