Biology subjects

Kaneko, A.

Publications and source records attributed to Kaneko, A..

9 recordsLinked to original sources

bioRxiv2026

Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques

The relative roles of genetic drift, inbreeding, and natural selection in island evolution have been fundamental themes in evolutionary biology for nearly a century. However, empirical studies have yet to reach a consensus, and research integrating both genotypes and phenotypes in primates remains limited. The present study aims to estimate the demographic history of an island primate population, the Yakushima macaque (Macaca fuscata yakui), and evaluate the genomic and morphological consequences of its isolation. To this end, we conducted population genetic analyses based on whole-genome sequencing and geometric morphometric analyses of cranial shape. Our results indicate that M. f. yakui has been isolated with an effective population size of several thousand individuals for over 100,000 years. Although we detected signatures of purifying selection, deleterious alleles have not been sufficiently purged. The degree of fluctuating asymmetry in males was slightly, yet significantly, higher in M. f. yakui than in mainland populations, whereas this trend was not observed in females. Marginal evidence of directional selection was found for cranial size, but not for shape. Overall, our findings suggest that due to long-term isolation, genetic drift and inbreeding have exerted a substantial influence on shaping genotypic and phenotypic variation in this island population.

evolutionary biology↗

bioRxiv2026

Single-Molecule Activity Profiling of Glycosidase Proteoforms Using Water-Soluble Fluorogenic Probes

In this study, we report a series of highly water-soluble fluorogenic probes for glycosidases useful for microdevice-based single-molecule enzyme activity profiling (SEAP). The assay was able to detect trace glycosidase activities in blood with high sensitivity and with proteoform resolution. This platform revealed the potential of -mannosidase as sensitive blood-based liquid-biopsy biomarkers for liver injury, highlighting the potential of this approach for activity-based diagnostics.

biochemistry↗

bioRxiv2024

Ca2+-evoked sperm cessation determines embryo number in mammals.

In mammals, fertilization takes place followed by fetus development in the maternal body, so the number of fetuses that exceeds the mothers capacity increases the frequency of stunted growth and stillbirths, while an excessive number of pups increases postnatal stunting and maternal child-rearing stress, which is detrimental to offspring procreation and species maintenance. Therefore, various control mechanisms are thought to be at work to ensure that fertilization occurs in appropriate numbers. Sperm are not capable of fertilization immediately after they are produced in the testis, and must undergo a stepwise activation process including capacitation, hyper motility activation or acrosome reaction before they meet the egg in the oviduct, where fertilization takes place, contributing positively on fertilization, which in turn ensures the number of fetuses for the maintenance of species. In contrast, in this study, we found that a subpopulation of sperm is derived in a Ca2+-dependent manner during the process for sperm to acquire fertility, which may regulate the number of fetuses. When sperm were harvested from the epididymis of mice and activated in vitro, a subpopulation of sperm emerged from the sperm population in which Lypd4 was expressed on the sperm surface at a ratio up to 30%. The sperm in this subpopulation were rather small in size, more permeable to dyes, and had already ceased motility. We further characterized this sperm population by surface antigen screening using various monoclonal antibodies and found the expression of several proteins, such as CD55, ICOS or Ccr3, specific to this population. The emergence of this sperm population was induced at a concentration of about 4% of Ca2+ in body fluids and was independent of capacitation or acrosome reaction, and also apoptotic process. This subpopulation also appeared over time in sperm ejaculated into the female body, accounting for about 50% of the sperm that reached the oviduct in an hour. When this sperm subpopulation was then removed from the entire population using anti-Lypd4 antibody followed by in utero insemination, the fertilization rate of the oocytes collected from the oviducts doubled. Such a sperm subpopulation was also observed in macaque monkeys, and removal of this subpopulation increased the egg penetration rate of sperm, suggesting that this sperm subpopulation exists commonly in mammals and that the mothers acceptable fetal number is adjusted by systematically sterilizing a certain number of sperm.

developmental biology↗

bioRxiv2024

Investigating EMT-mediated resistance to EGFR tyrosine kinase inhibitors in NSCLC using innovative organoid models

BackgroundEpithelial-mesenchymal transition (EMT) has emerged as a key mechanism underlying resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in EGFR-mutant non-small cell lung cancer (NSCLC). However, the intricacies of EMT-mediated resistance, driven by tumor microenvironment (TME) interactions, remain enigmatic. This study aimed to probe EMT-induced resistance in NSCLC using innovative in vitro organoid models. MethodsWe generated organoids by co-culturing EGFR-mutant NSCLC cells (HCC827, H1975), mesenchymal stem cells and endothelial cells. Drug susceptibility was compared between organoids and spheroids (cancer cells only) using EGFR TKIs - Gefitinib, Afatinib, Osimertinib. EMT marker (E-cadherin, ZEB1) expression was analyzed via immunofluorescence and western blotting. The effects of Bevacizumab and miR200c on overcoming resistance were also investigated. ResultsThe study identified a significant link between EMT and EGFR-TKI resistance. Notable findings included the decrease of E-cadherin and an increase in ZEB1, both of which influenced EMT and resistance to treatment. Bevacizumab showed promise in improving drug resistance and mitigating EMT, suggesting an involvement of the VEGF cascade. Transfection with miR200c was associated with improved EMT and drug resistance, further highlighting the role of EMT in TKI resistance. ConclusionsThis study offered vital insights into EMT-driven EGFR TKI resistance, highlighting the utility of organoid models in evaluating resistance modulated by TME interactions. Our findings reveal promising directions for overcoming EMT-mediated resistance involving Bevacizumab and miR200c, warranting further in vivo validation.

cancer biology↗

bioRxiv2023

Three-dimensional markerless motion capture of multiple freely behaving monkeys for automated characterization of social behavior

Given their high sociality and close evolutionary distance to humans, monkeys are an essential animal model for unraveling the biological mechanisms underlying human social behavior and elucidating the pathogenesis of diseases exhibiting abnormal social behavior. However, behavioral analysis of naturally behaving monkeys requires manual counting of various behaviors, which has been a bottleneck due to problems in throughput and objectivity. Here, we developed a three-dimensional markerless motion capture system that utilized multi-view data for robust tracking of individual monkeys and accurate reconstruction of the three-dimensional poses of multiple monkeys living in groups. Validation analysis in two monkey groups revealed that the system enabled the characterization of individual social dispositions and relationships through automated detection of various social events. Analyses of social looking facilitated the investigation of adaptive behaviors in a social group. These results suggest that this motion capture system will significantly enhance our ability to analyze primate social behavior.

animal behavior and cognition↗

bioRxiv2021

Effects of short-term isolation on social animals' behavior: an experimental case study of Japanese macaque

One of the goals in animal socioecology is to understand the functions and dynamics of group living. While observations of free-ranging animals are a crucial source of information, an experimental investigation that manipulates the size or composition, or both, of animal groups in captivity can also bring complementary contributions to the research inquiry. When paired with an automatic data collection by biologging technology, experimental studies on captive animals also allow for big data analyses based on recent machine learning techniques. As an initial exploration of this research paradigm, the present study inquired to what extent isolation of captive Japanese macaques (Macaca fuscata) changed their movement patterns. Using three-dimensional location trajectories of the macaques that were systematically collected via Bluetooth Low Energy beacons and a deep neural network, we estimated the identifiability of whether a macaque was behaving in isolation or in group. We found that the neural network identified the isolation vs. in-group conditions with more than 90% accuracy from a five-minute location trajectory, suggesting that the isolation caused notable changes from the canonical group-living behaviors. In addition, the isolation made each individual more identifiable from one another based on their location trajectories.

animal behavior and cognition↗

bioRxiv2020

Non-Parametric Analysis of Inter-Individual Relations Using an Attention-Based Neural Network

O_LISocial network analysis, which has been widely adopted in animal studies over the past decade, enables the revelation of global characteristic patterns of animal social systems from pairwise inter-individual relations. Animal social networks are typically drawn based on geometric proximity and/or frequency of social behaviors (e.g., grooming), but the appropriate metric for inter-individual relationship is not clear, especially when prior knowledge on the species/data is limited. C_LIO_LIIn this study, researchers explored a non-parametric analysis of inter-individual relations using a neural network with the attention mechanism, which plays a central role in natural language processing. The high interpretability of the attention mechanism and flexibility of the entire neural network allow for automatic detection of inter-individual relations included in the raw data, without requiring prior knowledge/assumptions about what modes/types of relations are included in the data. For these case studies, three-dimensional location data collected from simulated agents and real Japanese macaques were analyzed. C_LIO_LIThe proposed method successfully recovered the latent relations behind the simulated data and discovered female-oriented relations in the real data, which are in accordance with previous generalizations about the macaque social structure. C_LIO_LIThe proposed method does not exploit any behavioral patterns that are particular to Japanese macaques, and researchers can use it for location data of other animals. The exibility of the neural network would also allow for its application to a wide variety of data with interacting components, such as vocal communication. C_LI

animal behavior and cognition↗

bioRxiv2020

Intron retention as a new marker of the pre-disease state and its recovery to the normal state by a traditional Japanese multi-herbal medicine

Intron retention (IR) is an important regulatory mechanism that affects gene expression and protein functions. Using klotho mice at the pre-symptomatic state, we discovered that retained-introns accumulated in several organs including the liver and that among these retained introns in the liver a subset was recovered to the normal state by a Japanese traditional herbal medicine. This is the first report of IR recovery by a medicine. IR-recovered genes fell into two categories: those involved in liver-specific metabolism and in splicing. Metabolome analysis of the liver showed that the klotho mice were under starvation stress. In addition, our differentially expressed gene analysis showed that liver metabolism was actually recovered by the herbal medicine at the transcriptional level. By analogy with the widespread accumulation of intron-retained pre-mRNAs induced by heat shock stress, we propose a model in which retained-introns in klotho mice were induced by an aging stress and in which this medicine-related IR recovery is indicative of the actual recovery of liver-specific metabolic function to the healthy state. Accumulation of retained-introns was also observed at the pre-symptomatic state of aging in wild-type mice and may be an excellent marker for this state in general.

molecular biology↗

bioRxiv2019

Animals exhibit personality traits in their movement: a case study on location trajectories of primates

Researching individual recognition (IR) is essential to understand the life history and adaptive behavior of social animals. Investigation of personality traits may also provide insights into how social animals distinguish between different individuals. This study investigates IR behavior in Japanese macaques (Macaca fuscata), focusing on one specific trait, which is movement. Using a recently developed tracking system based on Bluetooth(R) Low Energy beacons, we collected three-dimensional (3D) location data from five Japanese macaques living in a group cage. A non-parametric, neural network-based analysis of the data revealed the existence of personality traits in extremely limited aspects of the movement data (2-min trajectory of 3D location). Our results support the validity of multimodal approaches in studying IR, beyond the typical single-frame face recognition method, both for researchers and animal agents.

animal behavior and cognition↗