Biology subjects

Ito, Y.

Publications and source records attributed to Ito, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Comparative analysis based on shared amplicon sequence variants reveals that cohabitation influences gut microbiota sharing between humans and dogs

IntroductionThe One Health concept is a comprehensive understanding of the interaction between humans, animals, and the environment. The cohabitation of humans and dogs positively affects their physical, mental, and social well-being. It is recognized as an essential factor from the One Health perspective. Furthermore, a healthy balance in the gut microbiome is essential for good health, and the sharing of gut microbes between humans and dogs may positively impact the health of both hosts. Therefore, elucidating the sharing of gut bacteria between humans and dogs is important for understanding One Health. However, most studies have examined sharing at the taxonomic level, and it remains unclear whether the same bacteria are transferred between humans and dogs, and whether they mutually influence each other. MethodsHere, microbiome analysis and 16S rRNA gene amplicon sequence variant (ASV) analysis was performed to address this question. Results16S rRNA gene ASVs analysis indicated that gut microbes have been transferred between humans and dogs. The overall structure of the gut microbiota within human-dog pairs remained unchanged after three months of adaptation. However, some ASVs were shared within human-dog pairs. Many shared ASVs were highly abundant within each host, and this high abundance may be considered a factor that influences bacterial transfer between hosts. DiscussionOur results demonstrate the possibility of the direct transfer of gut bacteria between humans and dogs, providing an important insight for achieving good health through human-dog cohabitation.

microbiology↗

bioRxiv2023

ER-to-Golgi trafficking via a dynamic intermediate cis-Golgi tubular network in Arabidopsis

Endoplasmic Reticulum (ER)-to-Golgi trafficking is a central process of the secretory system of eukaryotic cells that ensures proper spatiotemporal sorting of proteins and lipids1-5. However, the nature of the ER-Golgi Intermediate Compartments (ERGIC) and the molecular mechanisms mediating the transition between the ERGIC and the Golgi, as well as the universality of these processes amongst Eukaryotes, remain undiscovered. Here, we took advantage of the plant cell system in which the Golgi is highly dynamic and in close vicinity to the ER6-9. We discovered that the ERGIC is composed from at least two distinct subpopulations of cis-Golgi. A subpopulation is a reticulated tubulo-vesicular network mostly independent from the Golgi, highly dynamic at the ER-Golgi interface and crossed by ER-induced release of luminal cargos at early stage. Another subpopulation is more stable, cisterna-like and mostly associated to the Golgi. Our results identified that the generation and dynamics of the ER-Golgi intermediate tubulo-vesicular network is regulated by the acyl-chain length of sphingolipids as well as the contacts it establishes with existing Golgi cisternae. Our study is a major twist in the understanding of the Golgi by identifying that the ERGIC in plants is a Golgi-independent highly dynamic tubular network from which arise more stable cisternae-like Golgi structures. This novel model presents a mechanism for early secretory trafficking adapted to respond to developmental and environmental stimuli, including susceptibility or resistance to diseases, autophagy or cell-reprograming.

cell biology↗

bioRxiv2023

Analysis of chronic host-aspergilloma interactions using a novel mouse model

An aspergilloma is a fungus ball caused by chronic infection of Aspergillus species in a pre- existing cavity, such as a destroyed lung or the sinuses. Patients with pulmonary aspergilloma are at risk of sudden life-threatening hemoptysis. Antifungal therapy is administered to aspergilloma patients who are ineligible for surgery, but its efficacy is limited. Understanding the pathophysiology of aspergilloma is crucial for developing further treatment strategies. The mechanism behind the long-term host response to aspergilloma is poorly understood. We created a novel mouse model to analyze the host response to aspergilloma by implanting a fungus ball of Aspergillus fumigatus into an air-filled subcutaneous cavity. Our findings indicate that a live fungus ball led to tissue invasion, even in immunized mice. When a fungus ball consisting of dead hyphae was implanted, it persisted for over three months and induced pathological findings simulating human aspergilloma, including an inflammatory cell infiltration into the fungus ball and angiogenesis in the cavity wall. Dead fungus ball induced Th1 and Th17 inflammatory cytokines and vascular endothelial growth factor. Neutrophils infiltrated the inside of the fungus ball immediately after implantation, and macrophages surrounded it after a one-week delay. The macrophages around the fungus ball were swollen with phagocytosed fragments of dead hyphae and transformed into foam cells containing fat droplets. We also confirmed in vitro that macrophages were damaged and transformed into foam cells by direct contact with dead hyphae. This model holds promise to provide new insights into the fungal-host interaction during aspergillomas. NOTATION OF PRIOR ABSTRACT PUBLICATION/PRESENTATIONNone IMPORTANCEChronic aspergillosis, which affects over 3 million people worldwide with a 5-year survival rate of 50%, is understudied compared to other forms. Our study focuses on aspergilloma, a key aspect of chronic aspergillosis, using a groundbreaking mouse model that mirrors clinical features over three months. By studying host-fungal interactions within aspergillomas, we discovered Th1 and Th17 inflammatory responses to dead fungal hyphae. Initially, neutrophils dominate, later giving way to macrophages with a lipid-accumulating foamy phenotype. This transition may impede aspergilloma clearance. In addition, even dead hyphae induce vascular endothelial growth factor and promote angiogenesis. Our findings, which are critical for the prevention of fatal hemoptysis, highlight the need for innovative treatments that target fungal clearance and challenge the limited efficacy of antifungal agents against dead fungal bodies. This research represents a significant step forward in the understanding of chronic aspergillosis.

microbiology↗

bioRxiv2023

The reciprocal regulation between mitochondrial-associated membranes and Notch signaling in skeletal muscle atrophy

Skeletal muscle atrophy and the inhibition of muscle regeneration are known to occur as a natural consequence of aging, yet the underlying mechanisms that lead to these processes in atrophic myofibers remain largely unclear. Our research has revealed that the maintenance of proper mitochondrial-associated endoplasmic reticulum membranes (MAM) is vital for preventing skeletal muscle atrophy in microgravity environments. We discovered that the deletion of the mitochondrial fusion protein Mitofusin2 (MFN2), which serves as a tether for MAM, in human iPS cells or the reduction of MAM in differentiated myotubes caused by microgravity interfered with myogenic differentiation process and an increased susceptibility to muscle atrophy, as well as the activation of the Notch signaling pathway. The atrophic phenotype of differentiated myotubes in microgravity and the regenerative capacity of Mfn2-deficient muscle stem cells in dystrophic mice were both ameliorated by treatment with the gamma-secretase inhibitor DAPT. Our findings demonstrate how the orchestration of mitochondrial morphology in differentiated myotubes and regenerating muscle stem cells plays a crucial role in regulating Notch signaling through the interaction of MAM. digestThis study investigated the link between Mfn2 and Notch signaling in skeletal muscle atrophy. We used a microgravity system to induce muscle atrophy and found that the loss of Mfn2 leads to decreased numbers of MAM and activation of Notch signaling and that treating MFN2-deficient human iPS cells with a gamma-secretase inhibitor DAPT improved their mitochondrial morphology and function. Additionally, Mfn2-deficient muscle stem cells in mice have a lower capacity to regenerate dystrophic muscles and DAPT treatment improves the regeneration of these cells. The study suggests that targeting the Notch signaling pathway with a gamma-secretase inhibitor could be a therapeutic option for skeletal muscle atrophy caused by defects in Mfn2.

developmental biology↗

bioRxiv2023

Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system

In order to investigate SARS-CoV-2 mutations and their impact on immune evasion and infectivity, we developed a Deep Mutational Scanning (DMS) platform utilizing an inverted infection assay to measure spike expression, ACE2 affinity, and viral infectivity in human cells. Surprisingly, our analysis reveals that spike protein expression, rather than ACE2 affinity, is the primary factor affecting viral infectivity and correlated with SARS-CoV-2 evolution. Notably, within the N-terminal domain (NTD), spike expression and infectivity-enhancing mutations are concentrated in flexible loops. We also observed that Omicron variants BA.1 and BA.2 exhibit immune evasion through receptor binding domain (RBD) mutations, although these mutations reduce structural stability. Interestingly, the NTD has evolved to increase stability, compensating for the RBD instability and resulting in heightened overall infectivity. Our findings, available in SpikeScanDB, emphasize the importance of spike expression levels and compensatory mutations in both the NTD and RBD domains for shaping Omicron variant infectivity.

microbiology↗

bioRxiv2023

Laser-induced auditory perception: transtympanic laser irradiation of the cochlea from the outer ear evokes an auditory-related neural and behavioral response

Brain-machine interfaces are emerging devices that act as a medium for communication between the neural system and external software and hardware. Over the last decade, there has been a discussion on applying infrared laser stimulation to the brain-machine interfaces, including cochlear implants. Infrared lasers can selectively activate neural populations without introducing exogenous agents to tissues. This study presents the first demonstration that laser irradiation of the cochlea, a peripheral sensory organ, can elicit a clear behavioral auditory response. Mongolian gerbils (Meriones unguiculatus) were divided into two groups, each subjected to classical conditioning where a reward water delivery was predicted by either cochlear laser stimulation or sound stimulus. Laser-conditioned animals successfully learned licking behavior, with conditioned responses and behavioral properties comparable to auditory-conditioned animals. The laser-evoked response was significantly inhibited by auditory masking, and auditory-conditioned animals demonstrated stimulus generalization to laser stimulation. In a subsequent experiment, simultaneous presentation of auditory and laser stimulation induced nonlinear amplification in both auditory cortical and behavioral responses, suggesting that combining auditory and laser stimulation can enhance auditory perception beyond the effects of each stimulus alone. These findings indicate that infrared laser irradiation of the cochlea can potentially evoke and enhance auditory perception, making it a promising candidate for implementation in auditory prostheses.

neuroscience↗

bioRxiv2023

Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression

Tumors acquire an increased ability to obtain and metabolize nutrients. Here, we engineered and implanted adipocytes to outcompete tumors for nutrients and show that they can substantially reduce cancer progression. Growing cells or xenografts from several cancers (breast, colon, pancreas, prostate) alongside engineered human adipocytes or adipose organoids significantly suppresses cancer progression and reduces hypoxia and angiogenesis. Transplanting modulated adipocyte organoids in pancreatic or breast cancer mouse models nearby or distal from the tumor significantly suppresses its growth. To further showcase therapeutic potential, we demonstrate that co-culturing tumor organoids derived from human breast cancers with engineered patient-derived adipocytes significantly reduces cancer growth. Combined, our results introduce a novel cancer therapeutic approach, termed adipose modulation transplantation (AMT), that can be utilized for a broad range of cancers.

cancer biology↗

bioRxiv2023

Slitflow: a Python framework for single-molecule dynamics and localization analysis

Single-molecule imaging is a promising method for direct quantification of the dynamics and distribution of biomolecules in living cells. Although numerous methods have been developed to gain biological insights into molecular behavior, the high diversity of microscopes and single-molecule dynamics can result in incomplete reproducibility of analyses. Here, we present Slitflow, an open-source framework for a single-molecule analysis workflow that includes image processing, dynamics analysis, and figure creation. We demonstrated the integrity and flexibility of the workflow using 1) a cherry-picked tracking method combining popular tools and 2) various state-of-the-art analyses in a single pipeline. The software accommodates a large variety of data and methods, paving the way for integrative analyses. Code metadata O_TBL View this table: org.highwire.dtl.DTLVardef@1923125org.highwire.dtl.DTLVardef@d8790borg.highwire.dtl.DTLVardef@1f2f0ccorg.highwire.dtl.DTLVardef@9ee527org.highwire.dtl.DTLVardef@1d693f9_HPS_FORMAT_FIGEXP M_TBL C_TBL

biophysics↗

bioRxiv2022

Horizontal transmission of penicillin binding protein 1A caused a nationwide spread of β-lactam resistance in pneumococci

The emergence and spread of drug-resistant bacteria continue to be a global crisis. The mechanism of the resistance spread via mobile genetic elements such as plasmids is well known, however, the impact of the natural transformation on the spread remains unclear. Streptococcus pneumoniae is well known to be a transformable pathogen by natural competence and they become {beta}-lactam resistance by the acquisition of chromosomal genetic elements including mutated PBPs by natural transformation. To trace the transmission of pneumococcal PBPs among nationwide pediatric population and analyze the impact of transformed PBPs to {beta}-lactam resistance, we collected and analyzed more than 1300 isolates of S. pneumoniae through nationwide surveillance study for pediatric pneumococcal diseases between 2012-2017 in Japan. We discovered a high prevalence of a specific PBP1A type (pbp1a-13) in {beta}-lactam resistant pneumococci that had a 370SSMK substitution in their {beta}-lactam binding SXXK motif, suggesting that this pbp1a-13 transferred horizontally between different clones resulting in emergence and spread of {beta}-lactam resistant pneumococcal clones. Divergence dating analysis suggested that pbp1a-13 was inserted into major resistant lineages in the early 1990s through the 2000s, before introduction of pneumococcal conjugate vaccines in Japan. Our additional analysis for pneumococcal isolates that were recovered in the 90s in Japan suggested that pbp1a-13 in GPSC1 (serotype 19F-CC236) and GPSC14 (serotype 23F-CC242) isolates were the origin of the currently spread pbp1a-13. We provide evidence of pbp1a horizontal transmission at a nationwide scale and highlight the importance of PBP profile monitoring for identifying the emergence and spread of resistant pneumococci lineages.

microbiology↗

bioRxiv2022

Safety margin evaluations for transtympanic laser stimulation of the cochlea from the outer ear in Mongolian gerbils (Meriones unguiculatus)

Infrared laser cochlear stimulation has been suggested as an alternative to traditional auditory prostheses. Previous research has mainly examined the short-term effects of laser stimulation, but to effectively use this technique, it is necessary to study whether prolonged laser exposure can safely and sustainably induce cochlear responses. This study assessed the effect of laser-induced cochlear damage using classically-conditioned Mongolian gerbils. The white noise was presented as a conditioned stimulus, and reward licking was recorded as a conditioned response. After training, the subjects cochlea was exposed to a continuous pulsed laser for 15 h. The licking rate drastically decreased after the exposure of 26.4 W/cm2, while it did not change after 6.6 W/cm2 or weaker. These findings showed, for the first time, that the safety margin of long-term, at least several hours, cochlear laser stimulation exists and will contribute to the safe and effective delimitation of laser parameters in future research.

bioengineering↗

bioRxiv2022

Structural and biochemical insights into heterotetramer formation between human oncogenic K-Ras4BG12V and Rgl2, a RalA/B activator

About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA. The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the Switch I and Switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs, and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.

biochemistry↗

bioRxiv2022

Subjective Audibility Modulates the Susceptibility to Sound-Induced Flash Illusion

When a brief flash is presented along with two brief sounds, the single flash is often perceived as two flashes. This phenomenon is called a sound-induced flash illusion, in which the auditory sense, with its relatively higher reliability in providing temporal information, modifies the visual perception. Decline of audibility due to hearing impairment is known to make subjects less susceptible to the flash illusion. However, the effect of decline of audibility on susceptibility to the illusion has not been directly investigated in subjects with normal hearing. The present study investigates the relationship between audibility and susceptibility to the illusion by varying the sound pressure level of the stimulus. In the task for reporting the number of auditory stimuli, the lowering of the sound pressure level caused the rate of perceiving two sounds to decrease on account of forward masking. The occurrence of the illusory flash was reduced as the intensity of the second auditory stimuli decreased, and was significantly correlated with the rate of perceiving the two auditory stimuli. These results suggest that the susceptibility to sound-induced flash illusion depends on the subjective audibility of each sound.

animal behavior and cognition↗

bioRxiv2022

Characteristics of intestinal microflora and dysbiosis in relation to the disease duration in patients with Meniere's disease

HypothesisDysbiosis of the intestinal microflora has been reported in stress-induced depression and irritable colitis, a similar abnormality may also occur in stress-triggered Menieres disease. BackgroundMenieres disease is an intractable disease characterized by paroxysms of intense rotatory dizziness, hearing loss, and other auditory symptoms. It is believed to be caused by endolymphatic hydrops of the vestibule and cochlea. The diagnosis of Menieres disease is based on the diagnostic criteria established by the Barany Society and AAO-HNS and Journal of Vestibular Research as definite or probable cases. Endolymphatic hydrops identification using cochlear contrast-enhanced MRI (hybrid of reversed image of positive endolymph signal and native image of positive perilymph signal [HYDROPS]) is an objective test for Menieres disease, enabling reliable diagnosis of this disease. MethodsWe investigated the gut microbiota of 10 patients (6 males and 4 females, mean age 49.6 {+/-} 8.1 years) who met the diagnostic criteria for a unilateral definite case of Menieres disease using the diagnostic criteria of the Journal of Vestibular Research, and who also had significant endolymphatic hydrops on the affected side on HYDROPS. Intestinal microbiota tests were performed on these 10 patients and the results were evaluated in relation to the duration of disease, results of audiometry of the affected side, and DHI (Dizziness Handicap Inventory) score. ResultsA significant negative correlation was found between the disease duration and Shannon diversity index and Faiths phylogenetic diversity, which indicated dysbiosis of the intestinal microflora. No correlation was found between the indicators of microbial diversity and the results of audiometry or the DHI on the affected side. Dysbiosis of the intestinal microbiota worsened with increasing duration of Menieres disease. Moreover, Akkermansia muciniphila was not detected in any patient with Menieres disease. Conclusions.Despite the small number of cases in this study (n = 10), the findings indicate the possibility of abnormalities of the intestinal microflora in Menieres disease.

microbiology↗

bioRxiv2022

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Metabolic regulation in skeletal muscle is essential for blood glucose homeostasis. Obesity causes insulin resistance in skeletal muscle, leading to hyperglycemia and type 2 diabetes. In this study, we performed multiomic analysis of the skeletal muscle of wild-type (WT) and genetically obese (ob/ob) mice, and constructed regulatory transomic networks for metabolism after oral glucose administration. Our network revealed that metabolic regulation by glucose-responsive metabolites had a major effect on WT mice, especially carbohydrate metabolic pathways. By contrast, in ob/ob mice, much of the metabolic regulation by glucose-responsive metabolites was lost and metabolic regulation by glucose-responsive genes was largely increased, especially in carbohydrate and lipid metabolic pathways. We present some characteristic metabolic regulatory pathways found in central carbon, branched amino acids, and ketone body metabolism. Our transomic analysis will provide insights into how skeletal muscle responds to changes in blood glucose and how it fails to respond in obesity.

systems biology↗

bioRxiv2022

Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes

Robust translation elongation of any given amino acid sequence is a prerequisite to shape proteomes. Nevertheless, nascent peptides could destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains stochastically can induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in the N-terminal regions could prematurely terminate translation, producing premature products as peptidyl-tRNA species. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we found many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk. Indeed, a bioinformatics analysis revealed that the N-terminal regions of ORFs avoid D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.

biochemistry↗

bioRxiv2021

Highly efficient Runx1 enhancer eR1-mediated genetic engineering for fetal, child and adult hematopoietic stem cells

A cis-regulatory genetic element which targets gene expression to stem cells, termed stem cell enhancer, serves as a molecular handle for stem cell-specific genetic engineering. Here we show the generation and characterization of a tamoxifen-inducible CreERT2 transgenic (Tg) mouse employing previously identified hematopoietic stem cell (HSC) enhancer for Runx1, eR1 (+24m). Kinetic analysis of labeled cells after tamoxifen injection and transplantation assays revealed that eR1-driven CreERT2 activity marks dormant adult HSCs which slowly but steadily contribute to unperturbed hematopoiesis. Fetal and child HSCs which are uniformly or intermediately active were also efficiently targeted. Notably, a gene ablation at distinct developmental stages, enabled by this system, resulted in different phenotypes. Similarly, an oncogenic Kras induction at distinct ages caused different spectrums of malignant diseases. These results demonstrate that the eR1-CreERT2 Tg mouse serves as a powerful resource for the analyses of both normal and malignant HSCs at all developmental stages.

developmental biology↗

bioRxiv2021

MTCL2 promotes asymmetric microtubule organizationby crosslinking microtubules on the Golgi membrane

The Golgi complex plays an active role in organizing asymmetric microtubule arrays essential for polarized vesicle transport. The coiled-coil protein MTCL1 stabilizes microtubules nucleated from the Golgi membrane. Here, we report an MTCL1 paralog, MTCL2, which preferentially acts on the perinuclear microtubules accumulated around the Golgi. MTCL2 associates with the Golgi membrane through the N-terminal coiled-coil region and directly binds microtubules through the conserved C-terminal domain without promoting microtubule stabilization. Knockdown of MTCL2 significantly impaired microtubule accumulation around the Golgi as well as the compactness of the Golgi ribbon assembly structure. Given that MTCL2 forms parallel oligomers through homo-interaction of the central coiled-coil motifs, our results indicate that MTCL2 promotes asymmetric microtubule organization by crosslinking microtubules on the Golgi membrane. Results of in vitro wound healing assays further suggest that this function of MTCL2 enables integration of the centrosomal and Golgi-associated microtubules on the Golgi membrane, supporting directional migration. Additionally, the results demonstrated the involvement of CLASPs and giantin in mediating the Golgi association of MTCL2.

cell biology↗

bioRxiv2021

Distinct repertoire expansion patterns during affinity maturation of antigen responding camelid-derived single-domain VHH antibody

Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that precise observation of this process by high-throughput sequencing along time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additional in vitro screening. An alpaca was immunized by IgG fragments using multiple antigen injections and antibody repertoire development was traced via high-throughput sequencing periodically for months. The sequences were processed into clusters and the antibodies in the 16 most abundant clusters were generated to determine whether the clusters included antigen-binding antibodies. The sequences of most antigen-responsive clusters resembled those of germline cells in the early stages. These sequences were observed to accumulate significant mutations and also showed continuous sequence turnover throughout the experimental period. The foregoing characteristics gave us 75% successful prediction of clusters composed of antigen-responding VHHs against IgG fragment. In addition, the prediction method was applied to the data from other alpaca immunized by epidermal growth factor receptor and 77% successful prediction confirmed the generality of the prediction method. Superior to previous studies, we identified the immune responsive but very rare clusters or sequences from the immunized alpaca without any empirical screening data. Significance StatementWe have developed a method for selecting VHH antibody sequences that react to antigens without in vitro screening by performing a large-scale sequence analysis of VHH along the immunization time course, clustering the sequences, and tracking the evolution of the sequences in the clusters. This method enables the identification of antibodies with low frequencies of occurrence, which has been difficult with existing in silico antibody identification methods.

immunology↗