Biology subjects

Kasahara, K.

Publications and source records attributed to Kasahara, K..

15 recordsLinked to original sources

bioRxiv2026

Gut microbial phenylalanine metabolism contributes to MASLD in a dietary protein-dependent manner

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly a third of adults worldwide, yet how diet shapes the microbiota's contribution remains unclear. In a diet-induced mouse model varying protein content independently of caloric intake, microbiota depletion ameliorated hepatic steatosis and liver injury under protein- sufficient but not protein-restricted conditions. Caecal and plasma metabolomics implicated microbial phenylalanine catabolism and its host conjugates phenylacetylglutamine (PAGln) and phenylacetylglycine (PAGly). PAGln supplementation exacerbated steatosis and liver injury without altering body weight, adiposity or glucose homeostasis. Individual-antibiotic perturbation with metagenomics linked bacterial phenylalanine catabolic capacity to disease severity, and in gnotobiotic mice, genetic disruption of bacterial phenylalanine-to-phenylacetic acid conversion lowered circulating conjugates and attenuated steatosis and fibrosis. In a human cohort, circulating PAGln was selectively elevated in cardiometabolic MASLD. These findings identify dietary protein availability as a modifier of the contribution of microbial phenylalanine metabolism to MASLD and highlight PAGln as a microbiota-derived metabolite that exacerbates hepatic disease.

microbiology↗

bioRxiv2026

Structural basis for the intestinal protocadherin-based intermicrovillar adhesion complex

The intestinal brush border (BB), composed of densely packed microvilli on enterocytes, is essential for nutrient absorption and host defense. Its organization relies on the intermicrovillar adhesion complex (IMAC), mediated by protocadherins CDHR2 and CDHR5. Despite their clinical relevance in inflammatory bowel disease and several carcinomas, structural details of IMAC assemblies have remained elusive. Herein, we report the Cryo-EM structure of the adhesive complex at 3.4 [A] resolution, revealing a heterotetrameric ensemble composed of a dimer of CDHR2 and a dimer of CDHR5. This assembly ensures uniform adhesive strength between neighboring microvilli, and facilitates hexagonal packing of microvilli. Biophysical analyses and molecular dynamics simulations revealed a kinked, Ca{superscript 2}-free linker between domains EC3 and EC4 of CDHR5 conferring the necessary flexibility to withstand the shear stress caused during intestinal peristalsis. Collectively, these findings provide a structural framework for understanding BB organization and suggest strategies for therapeutics targeting IMAC in intestinal disorders.

biophysics↗

bioRxiv2024

Effects of foam rolling intervention on lactate clearance and cognitive function after high-intensity exercise with incremental load

PurposeThe effects foam rolling (FR) intervention on lactate clearance and the impaired executive function associated with fatigue after high-intensity exercise remain unclear. This study examined whether FR is an effective tool for fatigue recovery. MethodsEighteen healthy adults (10 males, 8 females; 21.8{+/-}1.7 years) without consistent exercise habits participated. The participants performed high-intensity exercises using an ergometer with a progressive load. Post-exercise FR intervention was compared with the control condition. Measurements included lactate, vigor/fatigue by the Profile of Mood States 2nd edition, cognitive function (cognitive task performance), and leg and body rating of perceived exertion (RPE) pre-and post-exercise, and post-intervention (5 min post-exercise). ResultsThe blood lactate concentration post-FR intervention (-7.3{+/-}3.0 mmol/L) was significantly reduced. Increased lactate clearance by FR correlated with faster recovery of executive function for those with greater lactate clearance, although cognitive fatigue was not observed after high-intensity exercise (P = .086, r = 0.41). Lactate clearance was not significantly correlated with RPE in the FR condition, whereas RPE decreased with increased lactate clearance for those with greater lactate clearance in the control condition (leg; r = 0.778, body; r = 0.669). ConclusionsThese results indicated FR intervention may be an effective recovery tool for exhausting exercises.

physiology↗

bioRxiv2023

A whole-brain analysis of functional connectivity and immediate early gene expression revealed functional network shifts after operant learning

Previous studies of operant learning have addressed neuronal activities and network changes in specific brain areas, such as the striatum, sensorimotor cortex, prefrontal/orbitofrontal cortices, and hippocampus. However, how changes in the whole-brain network are caused by cellular-level changes remains unclear. We combine resting-state functional magnetic resonance imaging (rsfMRI) and whole-brain immunohistochemical analysis of early growth response 1 (EGR1), a marker of neural plasticity, to elucidate the spatiotemporal functional network changes and underlying cellular processes during operant learning. We used an 11.7 Tesla scanner and whole-brain immunohistochemical analysis of EGR1 in mice during the early and late stages of operant learning. In the operant training, mice received a reward when they pressed the left and right buttons alternately and were punished with a bright light when they made a mistake. Control mice spent the same time and received the same amount of reward in the same operant box. A group of mice (n = 22) underwent the first rsfMRI before behavioral sessions, the second after 3 days of sessions (early stage), and the third after 21 days of sessions (late stage). Another group of mice (n = 40) was subjected to histological analysis 15 min after the early or late stages of behavioral sessions. After the early stage of training, functional connectivity was increased between the limbic areas and thalamus or auditory cortex, and the correlations of the number of EGR1-immunopositive cells between the limbic area and auditory cortex were also increased. After the late stage of training, the increases in functional connectivity and correlations of EGR1-immunopositive cells primarily occurred between the motor cortex, somatosensory cortex, and striatum. The subcortical networks centered around the limbic areas that emerged in the early stage have been implicated in rewards, pleasures, and fears. The connectivity between the motor cortex, somatosensory cortex, and striatum that consolidated in the late stage have been implicated in motor learning. Our multimodal longitudinal study successfully revealed the temporal shifts of brain regions involved in behavioral learning together with the underlying cellular-level plasticity between these regions for the first time. Our study represents a first step toward establishing a new experimental paradigm that combines rsfMRI and immunohistochemistry for linking macroscopic and microscopic mechanisms of learning.

neuroscience↗

bioRxiv2023

Increased interhemispheric functional connectivity during non-dominant hand movement in right-handed subjects

Hand preference is one of the behavioral expressions of lateralization in the brain. Previous fMRI studies, using conventional task-based functional MRI (fMRI), investigated the lateralization of brain function, and several regions including the motor cortex, putamen, thalamus, and cerebellum were activated during the single-hand movement. However, lateralization of functional connectivity related to hand preference has not been investigated. Here, we used the generalized psychophysiological interaction (gPPI) approach to investigate the alteration of functional connectivity during single-hand movement from the resting state in right-hand subjects. The functional connectivity in interhemispheric motor-related regions including the supplementary motor area, putamen, precentral gyrus, and cerebellum was significantly increased during non-dominant hand movement, while functional connectivity was not increased during dominant hand movement. The general linear model (GLM) showed activation in the left supplementary motor area, left precentral gyrus, and right cerebellum during right hand movement and activation in the right supplementary motor area, right precentral gyrus, and left cerebellum during left hand movement. These results indicate that a combination of GLM and gPPI analysis can detect the lateralization of hand preference more clearly in right-handed subjects.

neuroscience↗

bioRxiv2022

Gut bacteria impact host uric acid burden and its association with atherosclerosis

Humans with metabolic and inflammatory diseases, including atherosclerosis harbor dysbiotic gut communities. However, the microbes and microbial pathways that influence disease progression remain largely undefined. Here, we show that variation in atherosclerosis burden is in part driven by the gut microbiota and it is associated with circulating levels of the proinflammatory molecule uric acid both in mice and humans. We identify bacterial taxa present in the gut spanning multiple phyla, including Bacillota (Firmicutes), Fusobacteriota and Pseudomonadota (Proteobacteria), that use uric acid and adenine- a key precursor of nucleic acids in intestinal cells, as carbon and energy sources anaerobically, and uncover a gene cluster encoding key steps of purine degradation that is widely distributed among gut dwelling bacteria. Furthermore, we demonstrate that colonization of germ-free mice with purine-degrading bacteria modulates levels of uric acid and other purines in the gut and systemically. Altogether this work demonstrates that gut microbes are important drivers of host global purine homeostasis and uric acid levels, and suggests that gut bacterial catabolism of purines may represent a novel mechanism by which the gut microbiome influences host health.

microbiology↗

bioRxiv2022

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

To elucidate computationally a binding mechanism of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB), a GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was performed. This method is one of generalized ensemble methods and produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions accompanied with stably keeping the fragile cell-membrane structure. All molecular components (bosentan, hETB, membrane, and solvent) were represented with an all-atom model, and sampling was carried out from conformations where bosentan was distant from the binding site in the hETBs binding pocket. The deepest basin in the resultant free-energy landscape was assigned to the native-like complex conformation. The obtained binding mechanism is as follows. First, bosentan fluctuating randomly in solution is captured by a tip region of the flexible N-terminal tail of hETB via nonspecific attractive interactions (fly-casting). Bosentan then occasionally slides from the tip to root of the N-terminal tail (ligand-sliding). In this sliding, bosentan passes the gate of the binding pocket from outside to inside of the pocket with accompanying a quick reduction of the molecular orientational variety of bosentan (orientational selection). Last, in the pocket, ligand-receptor attractive native contacts are formed, and eventually the native-like complex is completed. The bosentan-captured conformations by the tip- and root-regions of the N-terminal tail correspond to two basins in the free-energy landscape, and the ligand-sliding corresponds to overcoming a free-energy barrier between the basins.

biophysics↗

bioRxiv2021

Systems genetics uncovers microbe-lipid-host connections in the murine gut

The molecular bases of how host genetic variation impact gut microbiome remain largely unknown. Here, we used a genetically diverse mouse population and systems genetics strategies to identify interactions between molecular phenotypes, including microbial functions, intestinal transcripts and cecal lipids that influence microbe-host dynamics. Quantitative trait loci (QTL) analysis identified genomic regions associated with variations in bacterial taxa, bacterial functions, including motility, sporulation and lipopolysaccharide production, and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and cecal levels of ornithine lipids (OL). Follow-up studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that OL have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits. Collectively, these results suggest that OL are key players in A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.

genetics↗

bioRxiv2021

Don't think, feel: basal ganglia-cortical connectivity underlies self-regulation of brain oscillations in humans

Brain-computer interfaces (BCIs) provide an artificial link by which the brain can directly interact with the environment. To achieve fine BCI control, participants must modulate the patterns of the cortical oscillations generated from the motor and somatosensory cortices. However, it remains unclear how humans regulate cortical oscillations, the controllability of which substantially varies across individuals. Here, we performed simultaneous electroencephalography (to assess BCI control) and functional magnetic resonance imaging (to measure brain activity) in healthy participants. Self-regulation of cortical oscillations induced activity in the basal ganglia-cortical network (BgCN) and the neurofeedback control network (NfCN). Successful self-regulation correlated with striatal activity in the BgCN, through which patterns of cortical oscillations were likely modulated. Moreover, BgCN and NfCN connectivity correlated with strong and weak self-regulation, respectively. The findings indicate that the BgCN is important for self-regulation, the understanding of which should help advance BCI technology.

neuroscience↗

bioRxiv2021

Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides

Preparation of stable isotope-labeled internal standard peptides is crucial for mass spectrometry (MS)-based targeted proteomics. Herein, we developed versatile and multiplexed absolute protein quantification method using MS. A previously developed method based on the cell-free peptide synthesis system, termed MS-based quantification by isotope-labeled cell-free products (MS-QBiC), was improved for multiple peptide synthesis in one-pot reaction. We pluralized the quantification tags used for the quantification of synthesized peptides and thus, made it possible to use cell-free synthesized isotope-labeled peptides as mixtures for the absolute quantification. The improved multiplexed MS-QBiC method was proved to be applied to clarify ribosomal proteins stoichiometry in the ribosomal subunit, one of the largest cellular complexes. The study demonstrates that the developed method enables the preparation of several dozens and even several hundreds of internal standard peptides within a few days for quantification of multiple proteins with only a single-run of MS analysis.

synthetic biology↗

bioRxiv2021

Modeling SARS-CoV-2 nsp1-5'-UTR complex via the extended ensemble simulations

Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2s own RNA evades nsp1s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of the SARS-CoV-2 RNA 5-untranslated region (SL1) is recognized by both nsp1s globular region and intrinsically disordered region. The recognition presumably enables selective translation of viral RNAs. Cluster analysis of the binding mode and detailed analysis of the binding poses revealed several residues involved in the SL1 recognition mechanism. The simulation results imply that the nsp1 C-terminal helices are lifted from the 40S ribosome upon the binding of SL1 to nsp1, unblocking translation of the viral RNA.

biophysics↗

bioRxiv2020

Molecular interaction mechanism of 14-3-3ε protein with phosphorylated Myeloid leukemia factor 1 revealed by an enhanced conformational sampling

Enhanced conformational sampling, a genetic-algorithm-guided multi-dimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semi-stable complex structures, and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3{varepsilon}, and a flexible peptide, phosphorylated Myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3{varepsilon}. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3{varepsilon} surface, and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spots are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding-constant changes resultant from alanine-mutation experiment for the residues. We performed a simulation of non-phosphorylated peptide and 14-3-3{varepsilon}, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3{varepsilon}.

biophysics↗

bioRxiv2019

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.

genomics↗

bioRxiv2019

Inoculum size effects in blaIMP-6 and plasmid-mediated quinolone resistance gene-positive Enterobacteriaceae in Japan

The aim of this study was to examine the resistance genes in clinical isolates which produced IMP-6 type metallo-{beta}-lactamase lactamase (MBL) and had mildly reduced susceptibilities to levofloxacin and/or amikacin. The inoculum size effect was also assessed. A total of 14 Enterobacteriaceae isolates (2 Escherichia coli and 12 Klebsiella pneumoniae) which produced IMP-6 MBL, and had mild increases in their MICs for levofloxacin and amikacin were examined. Thirteen out of 14 isolates harbored CTX-M-2, with the remaining isolate co-harboring CTX-M-2 and CTX-M-1 as ESBLs. All isolates carried one or more PMQRs; aac(6')-Ib-cr was the most prevalent (92.8%), followed by oqxA (64.3%), qnrS (42.9%), oqxAB (21.4%), and qnrB (14.3%). The inoculum size effects were significant in all strains for meropenem, 13 for imipenem, 7 for levofloxacin, and 3 for amikacin. Conjugation was successfully performed with 8 isolates and 11 strains were obtained. Eleven of the experimental strains (100%), and 8 strains (72.7%) showed inoculum size effects for meropenem and imipenem, respectively. No inoculum size effect was seen for levofloxacin. Four strains harbored qnr genes and 2 strains harbored qnr genes and QRDR mutations concurrently. blaIMP-6 positive Enterobacteriaceae with mildly reduced susceptibilities to levofloxacin and/or amikacin also harbored at least one plasmid-mediated drug resistance gene. These represent an unrecognized threat, capable of compromising the in vitro activity of many classes of antimicrobial agents. We conclude that IMP-6 MBL plays an important role in decreasing the MIC for carbapenems, whereas qnr does not for levofloxacin.

microbiology↗

bioRxiv2018

Characteristics of Interactions at Protein Segments External to Globular Domains in the Protein Data Bank

The principle of three-dimensional protein structure formation is a long-standing conundrum in structural biology. A globular domain of a soluble protein is formed by a network of atomic contacts among amino acid residues, but regions external to globular domains, like loop and linker, often do not have intramolecular contacts with globular domains. Although these regions can play key roles for protein function as interfaces for intermolecular interactions, their nature remains unclear. Here, we termed protein segments external to globular domains as floating segments and sought for them in tens of thousands of entries in the Protein Data Bank. As a result, we found that 0.72 % of residues are in floating segments. Regarding secondary structural elements, coil structures are enriched in floating segments, especially for long segments. Interactions with polypeptides and polynucleotides, but not small compounds, are enriched in floating segments. The amino acid preferences of floating segments are similar to those of surface residues, with exceptions; the small side chain amino acids, Gly and Ala, are preferred, and some charged side chains, Arg and His, are disfavored for floating segments compared to surface residues. Our comprehensive characterization of floating segments may provide insights into understanding protein sequence-structure-function relationships.

bioinformatics↗