Biology subjects

Kaneko, Y.

Publications and source records attributed to Kaneko, Y..

14 recordsLinked to original sources

bioRxiv2025

Benefits and costs of a hypercapsule and the mechanism of its loss in a clinical isolate of Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen in which capsule production is closely linked to immune evasion and environmental persistence. Recent studies have described two seemingly contradictory phenomena--increasing prevalence of capsule-overproducing clinical isolates and frequent isolation of capsule-deficient variants. The biological significance of these phenomena remains unclear. In this study, we analyzed a clinical isolate, OCU_Ac16b, which spontaneously gives rise to two phenotypically distinct variants: the L type forming large colonies with an extremely thick capsule, and the S type forming small colonies with a substantially reduced or absent capsule. When L-type cells were cultured in test tubes under low-shaking conditions, S-type variants reproducibly emerged, constituting 45-80% of the population within 24 hours. Whole-genome sequencing revealed that this conversion is driven by distinct mutations in the capsular polysaccharide synthesis cluster, including insertion sequence (IS) insertions and a single-nucleotide deletion. PCR analysis confirmed that IS insertions in wzy (polysaccharide polymerase) occur within individual L-type colonies prior to liquid culture, providing a likely explanation for the rapid and reproducible emergence of S-type variants. Phenotypic characterization demonstrated a biological trade-off, with L-type cells exhibiting enhanced resistance to serum killing, desiccation, and certain {beta}-lactam antibiotics, whereas S-type cells showed superior surface attachment, increased biofilm formation, and a growth advantage under oxygen-limited conditions. Our findings uncover a highly reproducible, mutation-driven capsule switching mechanism that enables rapid phenotypic adaptation to changing environments. This phenotypic heterogeneity has significant implications for pathogenesis, persistence, diagnostic evaluation, and clinical management. ImportanceAcinetobacter baumannii is a clinically important opportunistic pathogen that exhibits striking phenotypic diversity. In particular, some clinical isolates produce unusually thick capsules, which are thought to contribute to immune evasion and persistence, while others lack capsule altogether. However, the biological significance of these contrasting phenotypes has remained unclear. In this study, we analyzed a clinical isolate that spontaneously gives rise to capsule-deficient variants from a hypercapsulated form. We found that the conversion is driven by spontaneous mutations in capsule biosynthesis genes that arise naturally within colonies, while the expansion of capsule-deficient cells is promoted under oxygen-limited conditions. The two variants differed in serum resistance, desiccation tolerance, growth characteristics, and antibiotic responses, revealing a trade-off between protective barriers and environmental adaptability. These findings provide new insights into how A. baumannii balances survival strategies through genetic and phenotypic heterogeneity, with important implications for diagnosis, treatment, and bacterial persistence in clinical settings.

microbiology↗

bioRxiv2025

Pleasure in groove is associated with neuromelanin levels in the substantia nigra of younger healthy individuals: A neuromelanin-sensitive MRI study

The pleasurable urge to move in response to music is called groove. Prior research has suggested a potential link between groove and dopamine function. However, no studies to date have directly investigated the relationship between the two. Here, we aimed to assess individual dopamine function in the substantia nigra of healthy individuals using neuromelanin-sensitive magnetic resonance imaging (NM-MRI), a non-invasive method associated with dopamine function, and to investigate the relationship between the individual dopamine proxy index and sensitivity to the groove experience. In this study, 15 younger (< 48 years) and 16 older ([greater double equals]48 years) healthy individuals participated. Participants listened to ten musical excerpts and rated the groove experience based on "pleasure" and "wanting to move." To assess whether the groove experience is related to NM levels, type of musical excerpts, and sex, we analyzed with linear mixed-effects regression models. The results showed that higher NM levels (p = 0.032) and male sex (p = 0.034) were associated with higher pleasure ratings in the younger group. For the "urge to move" ratings, type of musical excerpts was associated with ratings in both groups (ps < 0.001), where high-groove music (Janata et al., 2012) receiving higher ratings. Taken together, these results suggest that the "pleasure" aspect of the groove experience in younger individuals was related to dopamine levels in the substantia nigra, but may not be associated with the "urge to move." Thus, pleasure and the urge to move are likely to involve distinct dopaminergic pathways and mechanisms, warranting further investigation.

neuroscience↗

bioRxiv2025

Longitudinal analysis of antibody titers after primary and booster mRNA COVID-19 vaccination can identify individuals at risk for breakthrough infection

A key issue in the post-COVID-19 era is the ongoing administration of COVID-19 vaccines. Repeated vaccination is essential for preparing against currently circulating and newly emerging SARS-CoV-2 variants while enabling people to continue with daily life. Optimizing vaccination strategies is crucial to efficiently manage medical resources and establish an effective vaccination framework. Therefore, it is important to quantitatively understand vaccine-induced immunity dynamics and to be able to identify poor responders with lower sustained antibody titers as potential priorities for revaccination. We investigated longitudinal antibody titer data in a cohort of 2,526 people in Fukushima, Japan, from April 2021 to November 2022 for whom basic demographic and health information was available. Using mathematical modeling and machine learning, we stratified the time-course patterns of antibody titers after 2 primary doses and 1 booster dose of mRNA COVID-19 vaccines. We identified 3 notable populations, which we refer to as the durable, the vulnerable, and the rapid-decliner populations, approximately half of which remained in the same population after the booster dose. Notably, the rapid-decliner population experienced earlier infections than the others. Furthermore, when comparing IgG(S) titers, IgA(S) titers, and T-spot counts between participants who experienced breakthrough infections after booster vaccination and those who did not, we found that IgA(S) titers were significantly lower in breakthrough infected participants during the early stage after booster vaccination. Our computational approach is adaptable to various types of vaccinations. This flexibility can inform policy decisions on vaccine distribution to enhance immunity both in future pandemics and in the post-COVID-19 era.

immunology↗

bioRxiv2025

Atypical endo-β-1,4-mannannases are necessary for normal glucomannan synthesis in Arabidopsis

The molecular mechanisms underlying the synthesis of large cell wall polysaccharides in plant cells are not fully understood. Here we report that two atypical endo-{beta}-1,4-mannanases (MANs), which are not secreted and do not degrade glucomannan in the cell wall, play a novel role in glucomannan synthesis. Among the six MANs in Arabidopsis, AtMAN2 and AtMAN5 contain a transmembrane domain at their N-terminal region instead of a signal peptide. Subcellular localization using MAN protein fused with fluorescent protein demonstrated that AtMAN2 localizes to the endomembrane system including the Golgi apparatus in xylem and interfascicular fiber cells. We found that an Arabidopsis man2 man5 double mutant lost 65% of glucomannan in the cell walls of the inflorescence stem. Immunostaining and immunoelectron microscopic observation also revealed that the man2 man5 double mutant lost glucomannan in the cell walls to about the same extent as the csla2 csla9 double mutant, which lacks major glucomannan synthases. Gene complementation experiments showed that the enzymatic activities of AtMAN2 and AtMAN5 are important for the function in synthesis of glucomannan for the cell wall. Arabidopsis possesses another atypical MAN, AtMAN6, with an HDEL retention signal at its C-terminus. However, mutation of AtMAN6 did not affect glucomannan content in the cell walls, suggesting distinct functions for these MANs. This study has identified AtMAN2 and AtMAN5 as novel factors necessary for the normal glucomannan synthesis in Arabidopsis, along with GDP-mannose generating enzymes and CslAs, and suggests that the glucomannan hydrolysis by these MANs contributes to the maintenance of glucomannan synthesis.

plant biology↗

bioRxiv2024

LATE MERISTEM IDENTITY2 regulates cuticle formation on the seed surface and influences seed longevity

The seed coat protects the embryo from severe external environment. Like the aerial plant parts, the exterior surface of the seed coat is surrounded by a cuticle consisting of lipid polyesters and wax. However, the protective role of the cuticle in mature seeds has not been characterized. We herein study the transcriptional regulation of cuticle formation on the seed surface, which influences seed longevity. A chimeric repressor of Arabidopsis thaliana R2R3 MYB transcription factor gene LATE MERISTEM IDENTITY2 (LMI2) and a Torenia fournieri ortholog (TfMYBML3) was expressed in A. thaliana and T. fournieri, respectively. These lines and A. thaliana LMI2 T-DNA insertion lines were analyzed for cuticle deficiencies. A. thaliana LMI2 mutants and chimeric repressor lines exhibited a similar cuticle deficiency in immature seeds. Transmission electron microscopy observations, polyester composition analyses, and gene expression investigations revealed that LMI2 plays an essential role in cuticle development in the seed coat epidermis by regulating cutin biosynthesis. The lmi2-2 mutant exhibited shorter seed longevity than the wild-type controls in an accelerated aging test. These results indicate that LMI2 is a key regulator of cuticle formation in the seed coat, and is important for maintaining seed longevity. Significance statementCuticle is well known to have multiple important roles for surviving in the terrestrial environment, but their specific role on the seed coat and transcriptional regulation have not yet been elucidated. Here we show that LATE MERISTEM IDENTITY 2, encoding a transcription factor regulating floral meristem transition, is required for seed cuticle formation and maintaining seed longevity, providing evidence for a link between surface cuticle and seed longevity.

plant biology↗

bioRxiv2024

Targeting fatty acid synthase suppresses tumor development in NF2/CDKN2A-deficient malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is an uncommon yet deadly cancer linked to asbestos exposure. The lack of effective early diagnosis and treatment leads to reduced life expectancy among patients with MPM. This study is aimed to identify a novel molecular target inhibitor to develop more effective therapeutics for MPM. Our drug screening assay showed that the fatty acid synthase (FASN) inhibitor cerulenin demonstrates strong and selective anti-proliferative properties against NF2/CDKN2A(p16)-deficient MPM cells, surpassing the effects of cisplatin or pemetrexed. FASN protein is frequently detected in NF2/p16-deficient MPM tumor-derived tissues (15/15, 100%), but rarely in NF2/p16-intact MPM tumors (8/25, 32%). Notably, cerulenin administration successfully reduced the growth of NF2/p16-deficient MPM tumors in xenografted mice. Cerulenin inhibits mitochondrial fission by targeting dynamin-related protein 1 (DRP1) in NF2/p16-deficient cells. Moreover, the disruption of the FASN gene leads to increased ubiquitination of DRP1. These findings suggest that FASN might play a role in the tumorigenesis of MPM cells through the regulation of mitochondrial dynamics. This research offers a novel perspective on the potential development of precision medicine for MPM.

cancer biology↗

bioRxiv2024

Excitation Spillover from PSII to PSI Measured in Leaves at 77K

Heterogeneous distribution of PSI and PSII in thick grana in shade chloroplasts is argued to hinder spillover of chlorophyll excitations from PSII to PSI. To examine this dogma, we measured fluorescence induction at 77K at 690 nm (PSII) and 760 nm (mainly PSI) in the leaf discs of Spinacia oleracea, Cucumis sativus and shade tolerant Alocasia odora, grown at high and low light, and quantified their spillover capacities. PSI fluorescence (FI) consists of the intrinsic PSI fluorescence (FI) and fluorescence caused by excitations spilt over from PSII (FI{beta}). When FI and FII parameters between State 1 and State 2, induced by weak far-red and blue light, were compared, PSII maximum fluorescence (FIIm) and FI{beta} were greater, and FI was smaller in State 1 and thereby the spillover ratio, FI{beta}/(FI +FI{beta}) or FI{beta}/FIm, was greater in State 1. Since the leftover FIIm was found to be about 10% of total Fm at 760 nm, all the data were corrected. Even after the correction, the spillover ratio in FIm in State 1 ranged from 21 to 32%, and the spillover ratios were comparable irrespective of growth light conditions. Although extensive grana in low light grown plants would suggest that PSII and PSI are too separated for spillover, in A. odora chloroplasts, the ratio of non-appressed thylakoid membranes/total thylakoid membranes was little affected by growth light and more than 40%. Abundant non-appressed thylakoids would contribute to efficient spillover.

plant biology↗

bioRxiv2023

Conserved use of the sodium/bile acid cotransporter (NTCP) as an entry receptor by hepatitis B virus and domestic cat hepadnavirus

The Orthohepadnavirus genus includes hepatitis B virus (HBV) that can cause chronic hepatitis and hepatocarcinoma in humans. Recently, a novel hepadnavirus in cats, domestic cat hepadnavirus (DCH), was identified that is genetically close to HBV. DCH infection is associated with chronic hepatitis in cats, suggesting a similarity with HBV pathogenesis and the potential to use DCH as a novel animal model for HBV research. HBV is shown to use the sodium/bile acid cotransporter (NTCP) as a major cell entry receptor, but the equivalent receptor for DCH remains unknown. Here we sought to identify the entry receptor for DCH. HBV- and DCH-derived preS1 peptides efficiently bound to both human and cat NTCPs, and residue 158 of NTCP proteins determined the species-specific binding of the DCH preS1 peptide. Myrcludex B, an HBV entry inhibitor, blocked binding of the DCH preS1 peptide. Thus, DCH and HBV may share cell entry molecules, suggesting a possibility of inter-species transmission. Furthermore, our study suggests that DHC can be useful as a novel model for HBV research.

microbiology↗

bioRxiv2022

Immune Isoform Atlas: Landscape of alternative splicing in human immune cells

Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generated a comprehensive full-length isoform annotation of human immune cells, Immune Isoform Atlas, by long-read sequencing for 29 cell subsets. Our atlas contained a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE. We profiled functional characteristics of isoforms including encoded domains, inserted repetitive elements, and translational efficiency, and we showed that repetitive elements significantly explained the diversity of unannotated isoforms. Some of the isoforms are expressed in a cell-type specific manner, whose alternative 3-UTRs usage contributed to their specificity. Further, we identified a number of disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the pathomechanism of diseases via alternative splicing.

genetics↗

bioRxiv2022

Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.

The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from COVID-19-convalescent patients, and identified antibodies that exhibited comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced, and showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.

microbiology↗

bioRxiv2022

Liver lipophagy ameliorates nonalcoholic steatohepatitis through lysosomal lipid exocytosis

Nonalcoholic steatohepatitis (NASH) is a progressive disorder with aberrant lipid accumulation and subsequent inflammatory and profibrotic response. Therapeutic efforts at lipid reduction via increasing cytoplasmic lipolysis unfortunately worsens hepatitis due to toxicity of liberated fatty acid. An alternative approach could be lipid reduction through autophagic disposal, i.e., lipophagy. We engineered a synthetic adaptor protein to induce lipophagy, combining a lipid droplet-targeting signal with optimized LC3-interacting domain. Activating hepatocyte lipophagy in vivo strongly mitigated both steatosis and hepatitis in a diet-induced mouse NASH model. Mechanistically, activated lipophagy promoted the excretion of lipid from hepatocytes via lysosomal exocytosis, thereby suppressing harmful intracellular accumulation of nonesterified fatty acid. A high-content compound screen identified alpelisib and digoxin, clinically-approved compounds, as effective activators of lipophagy. Administration of alpelisib or digoxin in vivo strongly inhibited the transition to steatohepatitis. These data thus identify lipophagy as a promising therapeutic approach to prevent NASH progression.

cell biology↗

bioRxiv2022

Identification of domestic cat hepadnavirus from a cat blood sample in Japan

The hepatitis B virus (Hepadnaviridae) induces chronic hepatitis and hepatic cancer in humans. A novel domestic cat hepadnavirus (DCH) was recently identified in several countries, however, the DCH infection status of cats in Japan is unknown. Therefore, we investigated the DCH infection rate of 139 cat samples collected in Japan. We identified one positive blood sample (0.78%) from a 17-year-old female cat with chronically elevated alanine aminotransferase. Phylogenetic analysis demonstrated that the DCH strain identified in this study is genetically distinct from strains in other countries. Further investigations are required to elucidate the evolution of DCH and the impact of DCH infection on hepatic diseases in domestic cats.

microbiology↗

bioRxiv2021

Uterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quail

The precursor of heme, protoporphyrin IX (PPIX), accumulates abundantly in the uterus of birds, such as Japanese quail, Coturnix japonica, resulting in brown-speckled eggshells. The molecular basis of PPIX production in the uterus remains largely unknown. Here, we investigated the cause of low PPIX production in a classical Japanese quail mutant exhibiting white eggshells by comparing its gene expression in the uterus with that of the wild type using transcriptome analysis and performed genetic linkage mapping to identify the causative genomic region of the white eggshell phenotype. We showed that 11 genes, including the 5-aminolevulinic acid synthase 1 (ALAS1) and ferroxidase hephaestin-like 1 (HEPHL1) genes, were specifically upregulated in the wild-type uterus and downregulated in the mutant. We mapped the 172 kb candidate genomic region on chromosome 6, which contains several genes, including a part of the paired-like homeodomain 3 (PITX3), which encodes a transcription factor. ALAS1, HEPHL1, and PITX3 were expressed in the apical cells of the luminal epithelium and lamina propria cells of the uterine mucosa of the wild-type quail, and their expression was downregulated in these cells of the mutant quail. Biochemical analysis using uterine homogenates indicated that the restricted availability of 5-aminolevulinic acid is the main cause of low PPIX production. These results suggest that uterus-specific transcriptional regulation of heme-biosynthesis-related genes is an evolutionarily acquired mechanism of eggshell pigment production in Japanese quail.

genetics↗

bioRxiv2020

A comprehensive framework for handling location error in animal tracking data

Animal tracking data are being collected more frequently, in greater detail, and on smaller taxa than ever before. These data hold the promise to increase the relevance of animal movement for understanding ecological processes, but this potential will only be fully realized if their accompanying location error is properly addressed. Historically, coarsely-sampled movement data have proved invaluable for understanding large scale processes (e.g., home range, habitat selection, etc.), but modern fine-scale data promise to unlock far more ecological information. While GPS location error can often be ignored in coarsely sampled data, fine-scale data require more care, and tools to do this have not kept pace. Current approaches to dealing with location error largely fall into two categories--either discarding the least accurate location estimates prior to analysis or simultaneously fitting movement and error parameters in a hidden-state model. In some cases these approaches can provide a level of correction, but they have known limitations, and in some cases they can be worse than doing nothing. Here, we provide a general framework to account for location error in the analysis of triangulated and trilatcralizcd animal tracking data, which includes GPS, Argos Doppler-shift, triangulated VHF, trilatcralized acoustic and cellular location data. We apply our error-modelselection framework to 190 GPS, cellular, and acoustic devices representing 27 models from 14 manufacturers. Collectively, these devices were used to track a wide range of taxa comprising birds, fish, reptiles, and mammals of different sizes and with different behaviors, in urban, suburban, and wild settings. In almost half of the tested device models, error-model selection was necessary to obtain the best performing error model, and in almost a quarter of tested device models, the reported DOP values were actually misinformative. Then, using empirical tracking data from multiple species, we provide an overview of modern, error-informed movement analyses, including continuous-time path reconstruction, home-range distribution, home-range overlap, speed, and distance estimation. Adding to these techniques, we introduce new error-informed estimators for outlier detection and autocorrelation visualization. Because error-induced biases depend on many factors--sampling schedule, movement characteristics, tracking device, habitat, etc.--differential bias can easily confound biological inference and lead researchers to draw false conclusions. We demonstrate how error-informed analyses on calibrated tracking data can provide more accurate estimates are that are insensitive to location error, and allow researchers to use all of their data.

ecology↗