Biology subjects

Kimura, R.

Publications and source records attributed to Kimura, R..

16 recordsLinked to original sources

bioRxiv2026

Genetic polymorphisms in a mate choice locus are maintained by balancing selection in a wild medaka population

Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii. Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

evolutionary biology↗

bioRxiv2026

Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations

Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700-900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to [~]6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of [~]2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred [~]1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

evolutionary biology↗

bioRxiv2025

Riluzole shifts glial responses to protect synapses and memory in Aβ oligomer-treated rats

Soluble A{beta}1-42 (amyloid beta) oligomers are potent neurotoxins that disrupt synaptic function, alter glial responses, and lead to memory impairment in Alzheimers disease (AD). Riluzole, a glutamate modulator approved for amyotrophic lateral sclerosis, reduces neuronal hyperexcitability, yet its in vivo effects on A{beta} oligomer-induced cognitive dysfunction and glial alterations remain incompletely understood. Here, we investigated whether riluzole ameliorates A{beta}1-42 oligomer-induced memory impairment and associated hippocampal pathology. A{beta}1-42 oligomers were bilaterally microinjected into the dorsal CA1 region of rats, followed by daily riluzole administration for seven days. Behavioral analyses revealed that riluzole significantly improved hippocampus-dependent memory, including contextual learning and spatial working memory, without affecting locomotor activity, anxiety-like behavior, or pain sensitivity. At the cellular level, riluzole reduced neuronal A{beta} accumulation and attenuated synaptic and dendritic pathology, while increasing A{beta} association with astrocytes and microglia in parallel with enhanced CD11b-related recognition and lysosomal processing. Notably, reductions in neuronal A{beta} burden were strongly associated with improved learning performance across individual animals. Riluzole also attenuated A{beta}-induced neuronal apoptosis, dendritic degeneration, and dendritic spine loss across the dorsal CA1 sublayers, and limited complement-dependent synaptic elimination by microglia. Although A{beta} oligomers induced robust recruitment of astrocytes and microglia, riluzole did not suppress glial activation; instead, it promoted morphological remodeling and shifted both astrocytes and microglia toward phenotypes associated with neuroprotection. Together, these findings indicate that coordinated remodeling of glial responses links glutamatergic modulation to enhanced amyloid handling, synaptic stability, and recovery of hippocampus-dependent memory under A{beta} oligomer challenge. Significance StatementSoluble A{beta} oligomers impair memory by disrupting synapses and altering glial responses in Alzheimers disease. Although glial activation is often viewed as detrimental, our findings demonstrate that the functional state of glia is a critical determinant of synaptic and cognitive outcomes. Using an A{beta} oligomer-based rat model, we show that the glutamate modulator riluzole restores hippocampus-dependent memory not by suppressing glial recruitment, but by promoting coordinated functional and morphological remodeling of astrocytes and microglia toward phenotypes associated with neuroprotection. These changes are accompanied by enhanced glia-mediated amyloid handling, reduced complement-dependent synaptic elimination, and preservation of dendritic spine integrity. Across individual animals, hippocampus-dependent learning performance was negatively associated with neuronal A{beta} burden, linking glial-mediated amyloid handling to behavioral recovery.

neuroscience↗

bioRxiv2025

Self-organized fingering instabilities drive the emergence of tissue morphogenesis in digit organoids.

The emergence of complex anatomical structures -such as the hands- from unstructured tissues remains a fundamental question in developmental biology. Turing-type reaction-diffusion models have provided a molecular explanation for the periodic pre-patterning of digits; however, the physical principles driving 3D morphogenesis remain incompletely understood. To identify the biophysical design principles leading to digit formation, we develop a limb-mesenchymal organoid system that spontaneously forms elongated, digit-like protrusions. Iterations between experiments and agent-based models at the cellular level identify sufficient microscopic mechanisms leading to morphogenesis of digit-like structures: symmetry-breaking and the elongation of digits result from a combination of differential cell adhesion and morphogen-induced chemotaxis and convergent-extension. Lastly, to describe tissue-scale deformations, we perform a coarse-graining analysis of the agent-based model and derive a continuum model that reveals a structural analogy to Cahn-Hilliard-type equations. These equations are typically used to describe fluid phase separation and so-called ''fingering instabilities'' in fluid physics. Here, we show that they also accurately describe organoid morphogenesis. These findings suggest that ''finger'' formation is driven by a mechanical fingering instability acting in concert with chemical patterning, shedding a new light on vertebrate limb morphogenesis.

developmental biology↗

bioRxiv2023

Hybridization and its impact on the ontogenetic allometry of skulls in macaques

The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, i.e., the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and non-additive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

evolutionary biology↗

bioRxiv2022

Long-term NAD+ supplementation prevents the progression of age-related hearing loss in mice

Age-related hearing loss (ARHL) is the most common sensory disability associated with human aging. Yet, there are no approved measures for preventing or treating this debilitating condition. With its slow progression, continuous and safe approaches are critical for ARHL treatment. Nicotinamide Riboside (NR), a NAD+ precursor, is well tolerated even for long-term use and is already shown effective in various disease models including Alzheimers and Parkinsons Disease. It has also been beneficial against noise induced hearing loss and in hearing loss associated with premature aging. However, its beneficial impact on ARHL is not known. Using two different wild-type mouse strains, we show that long-term NR administration prevents the progression of ARHL. Through transcriptomic and biochemical analysis, we find that NR administration restores age-associated reduction in cochlear NAD+ levels, upregulates biological pathways associated with synaptic transmission and PPAR signaling, and reduces the number of orphan ribbon synapses between afferent auditory neurons and inner hair cells. We also find that NR targets a novel pathway of lipid droplets in the cochlea by inducing the expression of CIDEC and PLIN1 proteins that are downstream of PPAR signaling and are key for lipid droplet growth. Taken together, our results demonstrate the therapeutic potential of NR treatment for ARHL and provide novel insights into its mechanism of action.

animal behavior and cognition↗

bioRxiv2021

Arf GTPase-Activating proteins SMAP1 and AGFG2 regulate the size of Weibel-Palade bodies and exocytosis of von Willebrand factor

Arf GTPase-Activating proteins (ArfGAPs) mediate the hydrolysis of GTP bound to ADP-ribosylation factors, which are important for intracellular transport. ArfGAPs have been shown to be critical for cargo sorting in the Golgi-to-ER and post-Golgi traffic. However, their roles in the sorting of secretory proteins remains unclear. Weibel-Palade bodies (WPBs) are cigar-shaped secretory granules in endothelial cells that contain von Willebrand factor (vWF) as their main cargo. WPBs are formed at the trans-Golgi Network, and this process is thought to be coupled with the sorting of vWF. WPB biogenesis was reported to be regulated by ADP-ribosylation factors and their regulators, but the role of ArfGAPs has been unknown. In this study, we performed siRNA screening of ArfGAPs to investigate the biogenesis of WPBs. We found two ArfGAPs, SMAP1 and AGFG2, to be involved in WPB size and vWF exocytosis, respectively. SMAP1 depletion resulted in small-sized WPBs, and the lysosomal inhibitor leupeptin recovered the size of WPBs. These results indicate that SMAP1 functions in preventing the degradation of cigar-shaped WPBs. However, AGFG2 downregulation resulted in the inhibition of vWF secretion upon Phorbol 12-myristate 13-acetate (PMA)-stimulation, suggesting that AGFG2 plays a role in vWF exocytosis. Our study revealed unexpected processes regulated by ArfGAPs for vWF transport. Summary StatementThe ArfGAP proteins SMAP1 and AGFG2 were identified as regulating WPB size and vWF exocytosis.

cell biology↗

bioRxiv2021

SPECT/CT imaging, biodistribution and radiation dosimetry of a 177Lu-DOTA-integrin αvβ6 cystine knot peptide in a pancreatic cancer xenograft model

IntroductionPancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignant neoplasms, as many cases go undetected until they reach an advanced stage. Integrin v{beta}6 is a cell surface receptor overexpressed in PDAC. Consequently, it may serve as a target for the development of probes for imaging diagnosis and radioligand therapy. Engineered cystine knottin peptides specific for integrin v{beta}6 have recently been developed showing high affinity and stability. This study aimed to evaluate an integrin v{beta}6-specific knottin molecular probe containing the therapeutic radionuclide 177Lu for targeting of PDAC. MethodsThe expression of integrin v{beta}6 in PDAC cell lines BxPC3 and Capan2 was analyzed using RT-qPCR and immunofluorescence. In vitro competition and saturation radioligand binding assays were performed to calculate the binding affinity of the DOTA-coupled tracer loaded with and without lutetium to BxPC3 and Capan2 cell lines. To evaluate tracer accumulation in the tumor and organs, SPECT/CT, biodistribution and dosimetry projections were carried out using a Capan2 xenograft tumor mouse model. ResultsRT-qPCR and immunofluorescence results showed high expression of integrin v{beta}6 in BxPC3 and Capan2 cells. A competition binding assay revealed high affinity of the tracer with IC50 values of 1.69 nM and 9.46 nM for BxPC3 and Capan2, respectively. SPECT/CT and biodistribution analysis of the conjugate 177Lu-DOTA-integrin v{beta}6 knottin demonstrated accumulation in Capan2 xenograft tumors (3.13 {+/-} 0.63 %IA/g at day 1 post injection) with kidney uptake at 19.2 {+/-} 2.5 %IA/g, declining much more rapidly than in tumors. Conclusion177Lu-DOTA-integrin v{beta}6 knottin was found to be a high-affinity tracer for PDAC tumors with considerable tumor accumulation and moderate, rapidly declining kidney uptake. These promising results warrant a preclinical treatment study to establish therapeutic efficacy.

cancer biology↗

bioRxiv2020

Programmable downsizing of CRISPR-Cas9 activity for precise and safe genome editing

CRSIPR-Cas9 system has opened up the avenue to efficient genome editing1-4. However, together with known off-target effects, several concerns of current CRISPR-Cas9 platform, including severe DNA damage, cytotoxicity, and large genomic alteration, have emerged in recent reports5-7 and establish a formidable obstacle to precisely model allele dosage effects of disease mutations and risk variants, especially mono-allelic effects, and correct them. Here, by developing an allele-specific indel monitor system (AIMS), we demonstrate that small and simple modification of conventional single-guide RNAs (sgRNAs) enable programmable tuning of CRISPR-Cas9 activities and alleviate such adverse effects. AIMS, which visualizes various indel events in two alleles separately in living cells, is convenient and accurate to determine the in vitro editing efficiency and revealed frequent mosaicism during genome editing. Using AIMS, we show that adding cytosine stretches to the 5 end of conventional sgRNA efficiently reduced Cas9 activity in a length dependent manner. By combining systematic experiments and computational modeling, we established the quantitative relationships between the length of cytosine extension and multiple aspects of CRISPR-Cas9 system. In general, short cytosine extension dramatically relieves p53-dependent cytotoxicity and suppression of homology-directed repair (HDR) while relatively maintaining on-target activity. Long cytosine extension further decreases on-target activity, thereby maximizing mono-allelic editing, while conventional system typically induces bi-allelic editing. Furthermore, such downregulation of on-target activity contributes to downregulation of relative off-target activity and protection of HDR-allele from second off-target editing. Therefore, cytosine extension method finally enables both single-step generation of heterozygous single-nucleotide disease mutations from homozygous states in mouse ES cells and correction of heterozygous disease mutations in human iPS cells. Taken together, our study proposes updates of standard CRISPR-Cas9 platform in mammalian cells toward precise and safe genome editing in diverse applications.

molecular biology↗

bioRxiv2020

Williams syndrome and autism: dissimilar socio-cognitive profiles with similar patterns of abnormal gene expression in the blood

Autism Spectrum Disorders (ASD) and Williams Syndrome (WS) exhibit quite opposite features in the social domain, but also share some common underlying behavioral and cognitive deficits. It is not clear, however, which genes account for the attested differences (and similarities) in the socio-cognitive domain. In this paper we adopted a comparative-molecular approach and looked for genes that might be differentially (or similarly) regulated in the blood of people with these two conditions. We found a significant overlap between differentially-expressed genes compared to neurotypical controls, with most of them exhibiting a similar trend in both conditions, but with genes being more dysregulated in WS than in ASD. These genes are involved in aspects of brain development and function (particularly, dendritogenesis) and are expressed in brain areas (particularly, the cerebellum, the thalamus and the striatum) of relevance for the ASD and the WS etiopathogenesis.

neuroscience↗

bioRxiv2019

Paternal aging affects the developmental patterns of ultrasonic vocalization induced by maternal separation in neonatal mice individually

Infant crying is an innate communicative behavior that is frequently impaired in certain neurodevelopmental disorders (NDDs). Since advanced paternal age is a reported risk factor for NDDs in offspring, we evaluated the impact of a fathers age on early vocal development in C57BL/6J mice. We recorded and applied a unique combination of computational analyses to ultrasonic vocalizations (USVs) emitted by mouse pups sired by young and aged fathers. Our data showed that advanced paternal age reduced the number and duration of USVs, and altered the syllable composition in pups. Moreover, pups born to young fathers showed convergent vocal characteristics with a rich repertoire during postnatal development, while those born to aged fathers exhibited more divergent vocal patterns with limited repertoire. Principal component analysis in conjunction with clustering analysis demonstrated that pups from aged fathers deviated from typical trajectories of vocal development, which were considered as atypical individuals. Thus, our study indicates that advanced paternal age has a significant effect on offsprings early vocal development. It is suggested that the trajectories of vocal development could be a useful marker of the NDD-like phenotype associated with the advanced paternal age. In addition, our comprehensive computational analysis described here is an effective approach to characterize the altered individual diversity relevant to neurodevelopmental disorders. One Sentence SummaryAdvanced paternal age affects vocal development in early postnatal mice, with more pups showing atypical developmental trajectories.

neuroscience↗

bioRxiv2019

Detailed profiles of histone modification in male germ line cells of the young and aged mice

Human epidemiological studies have shown paternal aging as one of the risks for neurodevelopmental disorders such as autism in offspring. A recent study has suggested that factors other than de novo mutations due to aging can influence biology of offspring. Here we are focusing on epigenetic alterations in sperm that can influence offspring developmental programs. In this study, we qualitatively and semi-quantitatively evaluated histone modification patterns in male germ line cells throughout spermatogenesis based on immunostaining of testes taken from young (3 months) and aged (12 months) old mice. Although localization patterns were not obviously changed between young and aged testes, some histone modification showed differences in their intensity. Among histone modifications that repress gene expression, H3K9me3 was decreased in the male germ line cells in the aged testis, while H3K27me2/3 was increased. The intensity of H3K27ac, an active mark, was relatively low in the aged testis. Interestingly, H3K27ac was detected in putative sex chromosomes of round spermatids, while other chromosomes were occupied by a repressive mark H3K27me3. Among other histone modifications that activate gene expression, H3K4me2 was drastically decreased in the male germ line cells in the aged testis. H3K79me3 was contrastingly increased and accumulated on the sex chromosomes at M-phase spermatocytes. Therefore, aging induced alterations in the amount of histone modifications, of which patterns were different in individual histone modifications. Moreover, histone modification seems to be differentially regulated by aging on the sex chromosomes and on others. These findings would help elucidate epigenetic mechanisms underlying influence of paternal aging on offsprings development.

developmental biology↗

bioRxiv2019

Jomon genome sheds light on East Asian population history

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

genomics↗

bioRxiv2019

Paternal age affects offspring's behavior possibly via an epigenetic mechanism recruiting a transcriptional repressor REST

Advanced paternal age has deleterious effects on mental health of next generation. Using a mouse model, we have confirmed that offspring derived from aged fathers showed impairments in behavior and abnormalities in the brain structure and activity. Comprehensive target DNA methylome analyses revealed in aged sperm more hypo-methylated genomic regions, in which REST/NRSF binding motif was enriched. Gene set enrichment analyses also identified enrichment of "REST/NRSF target genes", in addition to "Late-fetal genes" and autism spectrum disorder-related "SFARI genes", in up-regulated genes of developing brains from aged father. Indeed, gene sets near hypo-methylated genomic regions with REST/NRSF binding motif were also enriched in up-regulated genes of developing brains. Taken altogether, DNA hypo-methylation due to paternal aging in sperm will induce leaky expression of REST/NRSF target genes in the developing brain, thereby causing neuronal abnormalities and subsequent behavioral alteration in offspring.

neuroscience↗

bioRxiv2018

Robust candidates for language development and evolution are significantly dysregulated in the blood of people with Williams syndrome

Williams syndrome (WS) is a clinical condition entailing cognitive deficits and with an uneven language profile, which has been object of intense inquiry over the last decades. Although WS results from the hemideletion of around two dozens of genes in chromosome 7, no gene has been yet probed to account for, or contribute significantly to, the language problems exhibited by the affected people. In this paper we show that robust candidates for language disorder and for language evolution in the species, located outside the hemideleted region, are up- or downregulated in the blood of subjects with WS. Most of these genes play a role in the development and function of brain areas involved in language processing, which exhibit structural and functional anomalies in people with the condition. Overall, these genes emerge as robust candidates for language dysfunction in WS.

neuroscience↗

bioRxiv2017

Modest static pressure suppresses columnar epithelial cell proliferation in association with cell shape and cytoskeletal modifications

Intraluminal pressure elevation can cause degenerative disorders, such as ileus and hydronephrosis, and the threshold is fairly low and constant, 20-30 cm H2O. We previously devised a novel two-chamber culture system subjecting cells cultured on a semipermeable membrane to increased culture medium height (water pressure up to 60 cm H2O). Here, we cultured several different cell lines using the low static pressure-loadable two-chamber system, and examined cell growth, cell cycle, and cell morphology. Madin-Darby canine kidney (MDCK) columnar epithelial cells were growth-suppressed in a manner dependent on static water pressure ranging from 2-50 cm H2O, without cell cycle arrest at any specific phase. Two other types of columnar epithelial cells exhibited similar phenotypes. By contrast, spherical epithelial and mesenchymal cells were not growth-suppressed, even at 50 cm H2O. Phalloidin staining revealed that 50 cm H2O pressure load vertically flattened and laterally widened columnar epithelial cells and made actin fiber distribution sparse, without affecting total phalloidin intensity per cell. When the mucosal protectant irsogladine maleate (100 nM) was added to 50-cm-high culture medium, MDCK cells were reduced in volume and their doubling time shortened. Cell proliferation and morphology are known to be regulated by the Hippo signaling pathway, but a pressure load of 50 cm H2O did not alter the expression levels of Hippo signaling molecules in columnar epithelial cells, suggesting that this pathway was not involved in the pressure-induced phenotypes. RNA sequencing of MDCK cells showed that a 50 cm H2O pressure load upregulated keratin 14, an intermediate filament, 12-fold. This upregulation was confirmed at the protein level by immunofluorescence, suggesting a role in cytoskeletal reinforcement. These results provide evidence that cell morphology and the cytoskeleton are closely linked to cell growth. Pathological intraluminal pressure elevation may cause mucosal degeneration by acting directly on this linkage.\n\nSummaryWe provide evidence that columnar epithelial cells are growth-suppressed by pressure loads as low as 30 cm H2O, in association with cell-shape flattening and cytoskeletal alterations.

molecular biology↗