Biology subjects

Kimura, K.

Publications and source records attributed to Kimura, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris (Stylommatophora: Camaenidae)

While terrestrial land snails have long been subjected to evolutionary research, a lack of high-quality genomic resources has impeded recent progress. Bradybaena snails in particular have numerous intriguing traits that make them a good model for studying evolution, including shell pattern polymorphism and convergent evolution. They are also introduced and invasive across the world. In this study, we present a chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris utilizing 88-fold Illumina short-read sequences, 125-fold Nanopore long-read sequences, 63-fold PacBio HiFi sequences, and 47-fold Hi-C sequences. The assembled genome of 2.18 Gb is anchored to 28 chromosomes, and exhibits high completeness (98.8% metazoan BUSCO completeness) and contiguity (N50 of 75.6 Mb). Additionally, we also obtained a high-quality transcriptome for annotation. This resource represents the first chromosome-level assembly for snails in the superfamily Helicoidea, which includes more than 5,000 species of terrestrial snails, and will facilitate genomic study in Bradybaena and, more broadly, in the superfamily Helicoidea. SIGNIFICANCE STATEMENTWhile the Helicoidea is the largest land snail superfamily, consisting of more than 5,000 species, many of interest to evolutionary studies, no chromosome-level assembly has been available for any species. Previously, the genus Bradybaena in the Helicoidea has been studied in the context of speciation, adaptation and invasive biology, and thereby has high potential for further research. In this study, we present a chromosome-level assembly and transcriptome of the Asian tramp snail Bradybaena similaris. These high-quality genomic resources will facilitate research on related species, and eventually enhance our understanding of many areas of evolutionary biology.

genomics↗

bioRxiv2024

Comprehensive expression data for two honey bee species, Apis mellifera and Apis cerana japonica

Comprehensive expression datasets were constructed for Apis mellifera and Apis cerana japonica. Post-oviposition day 6 to day 58 samples of A. mellifera workers (larva to adult); day 9, 10, 12, and 13 samples of A. mellifera queen (larva to pupa); and day 9 to day 18 samples of A. cerana japonica workers (larva to adult) were prepared, and RNA-Seq data were obtained. For A. cerana japonica, reference transcript sequence data, predicted amino acid sequence data, and functional annotation data were generated based on the genome sequence and RNA-Seq data. Using the transcript sequence and RNA-Seq data, comprehensive expression data for all transcripts of A. mellifera and A. cerana japonica were prepared. Hierarchical clustering analyses and the used sample preparation method ensured that both sets of expression data were reliable for use as comprehensive reference expression datasets. Therefore, these data are applicable for honey bee research or for comparative or evolutionary studies on insect species or social insect species at the genetic and molecular levels.

genetics↗

bioRxiv2024

Deep learning-based detector of invasive alien frogs, Polypedates leucomystax and Rhinella marina, on an island at invasion front

This study aimed to develop and evaluate a deep learning-based detector for Southeast Asian treefrog (Polypedates leucomystax) and cane toad (Rhinella marina) on Iriomote Island, a Natural World Heritage Site located 30 km from established populations of these alien species on the nearby Ishigaki Island. Although a deep learning model typically requires local training data to be most accurate, the alien frogs have been eradicated from Iriomote Island, making such data unavailable. To address the data gap, we first trained the BirdNET model with acoustic data collected on Ishigaki Island, where these species were common, as well as native frog calls from Iriomote Island. Next, we evaluated model performance using (1) wild sounds on Ishigaki Island, and (2) sounds obtained by playing back the calls of the alien species on Iriomote Island. Model precision and recall for wild sounds were both 0.987 for P. leucomystax and 1 for R. marina. For playback sounds, model recall values decreased (0.629 for P. leucomystax and 0.906 for R. marina), while precisions remained nearly identical (1 for both P. leucomystax and R. marina). Despite the lower recall particularly for P. leucomystax, playback survey dates were mostly identifiable from the high number of detections. These results suggest that data from Ishigaki Island enabled training a model with adequate, though not complete, generalization across invasion front.

ecology↗

bioRxiv2024

A novel genetic mouse model of fatal aortic dissection reveals massive inflammatory cell infiltration in the thoracic aorta

BackgroundAortic dissection (AD) is the separation of medial layers of the aorta and is a major cause of death in patients with connective tissue disorders such as Marfan syndrome. However, molecular triggers instigating AD, its temporospatial progression, and how vascular cells in each vessel layer interact and participate in the pathological process remain incompletely understood. To unravel the underlying molecular mechanism of AD, we generated a spontaneous AD mouse model. MethodsWe incorporated a novel missense variant (p.G234D) in FBN1, the gene for fibrillin-1, identified in a non-syndromic familial AD patient into mice using CRISPR/Cas9 system. We performed histopathological analyses of the aortic lesions by histology, immunofluorescence staining, electron microscopy, synchrotron-based imaging and single-cell (sc)RNA-sequencing. Biochemical analysis was performed to examine the binding capacity of mutant human FBN1G234D protein to latent Tgf{beta} binding proteins (LTBPs), and signaling pathways in the mutant aortic wall were examined by western blot analysis. Results50% of the Fbn1G234D/G234D mutant mice died within 5 weeks of age from multiple intimomedial tears that expanded longitudinally and progressed to aortic rupture accompanied by massive immune cell infiltration. scRNA-sequencing, validated by immunostaining, revealed a significant increase in MHC class II-positive pro-inflammatory macrophages and monocytes at the site of intima tears with upregulation of MMP2/9 and marked disruption of elastic lamina. Subendothelial matrices, such as type IV collagen and laminin, expanded into the medial layer, where fibronectin expression was highly upregulated. Fbn1G234D/G234D endothelial cells exhibited altered mechanosensing with loss of parallel alignment to blood flow and upregulation of VCAM-1 and ICAM-1, all of which likely contributed to the infiltration of immune cells. Biochemically, FBN1G234D lost the ability to bind to latent TGF{beta} binding protein (LTBP)-1, -2, and -4, resulting in the downregulation of TGF{beta} signaling in the aortic wall. ConclusionsWe show that dynamic interactions involving endothelial cells (ECs) and macrophages/monocytes in the intima, where the ECM microenvironment is altered with the reduced TGF{beta} signaling, contributes to the initiation of AD. Our novel AD mouse model provides a unique opportunity to identify target molecules involved in the intimomedial tears that can be utilized for development of therapeutic strategies.

pathology↗

bioRxiv2024

A novel VCP modulator, KUS121, attenuates atherosclerosis progression by maintaining intracellular ATP and mitigating ER stress in endothelial cells

BackgroundEndoplasmic reticulum (ER) stress signaling pathways have pivotal roles in atherosclerosis progression. Recently, we have developed Kyoto University Substance (KUS) 121, which selectively inhibits ATPase activities of valosin-containing protein (VCP) and consequently saves intracellular ATP consumption and mitigates ER stress. Methods and ResultsWe assessed the efficacy of KUS121 against atherosclerosis by its daily injection into Apoe-/- mice fed with Western Diet (WD) for 8 weeks. Consequently, KUS121 treatment reduced atherosclerosis progression by approximately 40% in atherosclerotic plaques. Interestingly, we found that C/EBP homologous protein (CHOP), an established ER stress marker, was mainly expressed in plaque endothelium. Therefore, we assessed the action of KUS121 in endothelial cells using the human endothelial cell line (EA.hy926 cells). As a result, KUS121 prevented ER stress-induced apoptosis and downregulated the IRE1 (Inositol-requiring enzyme) -associated inflammatory pathways. Consistent with these in vitro findings, KUS121 treatment also significantly reduced endothelial apoptosis assessed by TUNEL staining and inflammation examined by immunostaining of Nuclear factor kappa B (NF-{kappa}B) and Intercellular adhesion molecule (ICAM) 1 at plaque endothelium. We also demonstrated that KUS121 maintained ATP levels in EA.hy926 cells and atherosclerotic plaque lesions using the single-wavelength or the FRET-based fluorescent ATP sensor. Supplementation of intracellular ATP by Methyl pyruvate (MePyr) attenuated ER stress-induced apoptotic and inflammatory pathways in endothelial cells, which could be the main mechanism how KUS121 reduces ER stress. ConclusionsKUS121 can be a new therapeutic option for atherosclerotic diseases by maintaining intracellular ATP levels and attenuating ER stress-induced apoptosis and inflammation in plaque endothelium.

pathology↗

bioRxiv2024

Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans

We develop a data harmonization approach for C. elegans volumetric microscopy data, still or video, consisting of a standardized format, data pre-processing techniques, and a set of human-in-the-loop machine learning based analysis software tools. We unify a diverse collection of 118 whole-brain neural activity imaging datasets from 5 labs, storing these and accompanying tools in an online repository called WormID (wormid.org). We use this repository to train three existing automated cell identification algorithms to, for the first time, enable accuracy in neural identification that generalizes across labs, approaching human performance in some cases. We mine this repository to identify factors that influence the developmental positioning of neurons. To facilitate communal use of this repository, we created open-source software, code, web-based tools, and tutorials to explore and curate datasets for contribution to the scientific community. This repository provides a growing resource for experimentalists, theorists, and toolmakers to (a) study neuroanatomical organization and neural activity across diverse experimental paradigms, (b) develop and benchmark algorithms for automated neuron detection, segmentation, cell identification, tracking, and activity extraction, and (c) inform models of neurobiological development and function.

neuroscience↗

bioRxiv2023

Establishing an AI-based evaluation system that quantifies social/pathophysiological behaviors of common marmosets

Nonhuman primates (NHPs) are indispensable animal models by virtue of the continuity of behavioral repertoires across primates, including humans. However, behavioral assessment at the laboratory level has so far been limited. By applying multiple deep neural networks trained with large-scale datasets, we established an evaluation system that could reconstruct and estimate three-dimensional (3D) poses of common marmosets, a small NHP that is suitable for analyzing complex natural behaviors in laboratory setups. We further developed downstream analytic methodologies to quantify a variety of behavioral parameters beyond simple motion kinematics, such as social interactions and the internal state behind actions, obtained solely from 3D pose data. Moreover, a fully unsupervised approach enabled us to detect progressively-appearing symptomatic behaviors over a year in a Parkinsons disease model. The high-throughput and versatile nature of our analytic pipeline will open a new avenue for neuroscience research dealing with big-data analyses of social/pathophysiological behaviors in NHPs.

neuroscience↗

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↗

bioRxiv2023

Genome assembly reconstruction of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae), using homology-based assembly and nanopore long-reads

Honey bees are important for agriculture (e.g., pollination and honey production). Additionally, honey bees are an important insect model species, especially as model social insects. The Japanese honey bee, Apis cerana japonica (a subspecies of the Asian honey bee, Apis cerana), is a Japanese domestic honey bee, which has several subspecies-specific traits. We previously constructed the draft genome sequence data of A. cerana japonica, but it needed to be improved considering the use of the genome sequence data for genome structural analysis and repetitive region analysis, as well as the availability of chromosome-level genome data of A. mellifera and A. cerana. In this study, we constructed the improved A. cerana japonica genome data and new gene set data with functional annotations. The constructed genome data, including 16 pseudochromosomes, was found to be highly contiguous and complete, and the gene set data covered most of the core genes in the BUSCO database. Thus, the constructed genome and gene set data have become more suitable as the reference data of A. cerana japonica.

genomics↗

bioRxiv2023

Δ246p53 is a new p53 isoform that responds to DNA damage and regulates tumour growth

p53 is with little doubt one of the most powerful genes in our genome, as it makes growth vs arrest, repair vs replacement, catabolism vs anabolism, life vs death decisions in the cell. An alteration or malfunction in p53 may lead to cancer, degeneration or premature ageing. So, it is not surprising that p53 is also one of the most complex and tightly regulated genes, encoding for at least 10 RNA variants and 12 widely accepted protein forms. Here we identify one new p53 protein isoform of approximately 18 kDa that we termed {Delta}246p53. {Delta}246p53 is translated from an alternative translation initiation site (TIS) in codon 246. TIS-246 is preceded by a strong Kozak sequence and appears conserved in vertebrates, from sea lamprey to humans. {Delta}246p53s origin and expression in cells were confirmed by frameshift and start codon mutations; five different antibodies against several epitopes from its N-terminus down to its C-terminus and one against the DNA binding domain region just upstream of its initiator methionine working as negative control; as well as siRNAs and an antisense oligo targeting TIS-246, which knocked-down {Delta}246p53 with little or no effect on full-length (FL) p53 protein levels. {Delta}246p53 was induced by DNA damage and triggered senescence and impaired tumour formation/growth in colony formation assays. Mechanistically, {Delta}246p53 interacted with FLp53, leading to a decrease in the expression of downstream target genes HDM2 and p21. Concurrently, it also interacted with {Delta}Np63, leading to p53-independent p63-mediated activation of p21, a known senescence activator. Our results unveil a new naturally occurring and tightly controlled factor with specific functions in p21 regulation and senescence. Future studies on {Delta}246p53 are likely to help us better understand and control the processes of tumour suppression and ageing.

cancer biology↗

bioRxiv2023

Molecular Weight-dependent Diffusion, Biodistribution, and Clearance Behavior of Tetra-armed Poly(ethylene glycol) Subcutaneously Injected into the Back of Mice

Four-armed poly(ethylene glycol) (PEG)s are essential hydrophilic polymers extensively utilized to prepare PEG hydrogels, which are valuable tissue scaffolds. When hydrogels are used in vivo, they eventually dissociate due to the cleavage of the backbone structure. When the cleavage occurs at the cross-linking point, the hydrogel elutes as an original polymer unit, i.e., four-armed PEG. Although four-armed PEGs have been utilized as subcutaneously implanted biomaterials, the diffusion, biodistribution, and clearance behavior of four-armed PEG from the skin are essential. This paper investigates time-wise diffusion from the skin, biodistribution to distant organs, and clearance of fluorescence-labeled four-armed PEGs with molecular weight (Mw) ranging from 5-40 kg/mol subcutaneously injected into the back of mice. Changes over time indicated that the fate of subcutaneously injected PEGs is Mw-dependent. Four-armed PEGs with Mw [≤] 10 kg/mol gradually diffused to deep adipose tissue beneath the injection site and distributed dominantly to distant organs, such as the kidney. PEGs with Mw [≥] 20 kg/mol stagnated in the skin and deep adipose tissue, and were mainly delivered to the heart, lung, and liver. The fundamental understanding of the Mw-dependent behavior of four-armed PEGs is beneficial for preparing biomaterials using PEGs, providing a reference in the field of tissue engineering.

bioengineering↗

bioRxiv2022

A Novel Bacterial Speciation Process Observed in a Symbiotic Marine Population

Incomplete lineage sorting (ILS), where ancestral polymorphisms persist through rapid speciation, is a hallmark of eukaryotic radiations but undocumented in prokaryotes. We report ILS associated speciation in the globally distributed marine bacterium Sulfitobacter, analyzing 74 strains from 16 oceanic regions and 15 ecosystem types. Genomic analysis resolved over ten genetically monomorphic clades sharing near uniform whole genome divergence (average nucleotide identity {approx}95%). However, individual genes and even adjacent nucleotide sites support conflicting phylogenetic relationships among clades. The median length of nearly identical sequence blocks supporting alternative topologies is less than 50 base pairs, far shorter than typical adaptive cassettes. This within gene, site level discordance provides a diagnostic signature of ancestral polymorphism retention following rapid fragmentation, ruling out adaptive gene sweeps. Demographic inference places this radiation on a timescale of tens of millennia, 100 to 1,000 fold faster than eukaryotic ILS, and traces the clades to a hyper polymorphic, highly recombining ancestor. Neutral simulations show that transient mutation surges or population bottlenecks alone can generate this pattern, without adaptive selection or ecological partitioning. By bridging eukaryotic and prokaryotic speciation paradigms, our findings demonstrate that ILS, previously considered exclusive to sexual eukaryotes, can drive rapid, neutral diversification in bacteria, expanding the mechanisms known to generate prokaryotic biodiversity.

microbiology↗

bioRxiv2022

Cardiac cycle affects the asymmetric value updating in instrumental reward learning

This study aimed to investigate whether instrumental reward learning is affected by the cardiac cycle. To this end, we examined the effects of the cardiac cycle (systole or diastole) on the computational processes underlying the participants choices in the instrumental learning task. In the instrumental learning task, participants were required to select one of two discriminative stimuli (neutral visual stimuli) and immediately receive reward/punishment feedback depending on the probability assigned to the chosen stimuli. To manipulate the cardiac cycle, the presentation of discriminative stimuli was timed to coincide with either cardiac systole or diastole. We fitted the participants choices in the task with reinforcement learning (RL) models and estimated parameters involving instrumental learning (i.e., learning rate and inverse temperature) separately in the systole and diastole trials. Model-based analysis revealed that the learning rate for positive prediction errors was higher than that for negative prediction errors in the systole trials; however, learning rates did not differ between positive and negative prediction errors in the diastole trials. These results demonstrate that the natural fluctuation of cardiac afferent signals can affect asymmetric value updating in instrumental reward learning.

neuroscience↗

bioRxiv2022

Diversity in DNA sequence, structure, and heterozygosity of nuclear rRNA gene region in Neopyropia yezoensis

DNA sequence reads of Neopyropia yezoensis (susabi-nori), its relative N. tenera (asakusa-nori), and their hybrids available in the sequence read archive produced assembled sequences of the nuclear rRNA gene region for 82 samples. Analysis of the assembled sequences revealed structural differences in the region of nuclear rRNA genes, with 17 forms depending on the presence or absence of introns and their lengths. The samples were divided into three groups based on differences in DNA sequences: Japanese N. yezoensis, Chinese N. yezoensis, and N. tenera/hybrids of N. tenera and N. yezoensis that exist in both countries. Despite genetic differentiation, the Japanese and Chinese N. yezoensis exhibit common structural forms. One sample of Chinese N. yezoensis presented almost 1:1 heterozygosity, whereas five other samples of Chinese N. yezoensis showed non-1:1 heterozygosity. In the latter case, neither the ratio of alleles nor the ratio of the number of introns was 1:1, suggesting the existence of an ongoing mechanism to eliminate the nuclear rRNA gene region on one of the homologous chromosomes in N. yezoensis.

plant biology↗

bioRxiv2022

Expectation for sweet taste changes peripheral glucose metabolism via basolateral amygdala

Anticipatory physiological responses to food were first reported by Ivan Pavlov a century ago but the associated neural mechanism is still ill-defined. Here, we identified two types of neurons in the basolateral amygdala (BLA), which are activated by sweetener (saccharin) or water after sucrose conditioning, representing expected sweet taste and unmet expectation, respectively. Saccharin-induced met-expectation of sweet taste enhances, while H2O-induced unmet-expectation deteriorates, glucose metabolism in peripheral tissues. Deletion of saccharin-responsive neurons in BLA impaired saccharin-induced increase in insulin sensitivity. Deletion of H2O-responsive neurons in BLA improved glucose intolerance by unmet-expectation. Saccharin- and H2O-responsive neurons had different gene expressions. Our data suggest that the gap between the expected incoming sugar and sweet taste is evaluated by distinct BLA neurons to control peripheral glucose metabolism. One-Sentence SummaryNeurons in the basolateral amygdala control blood glucose levels by comparing anticipated sugar intake and sweet taste

physiology↗

bioRxiv2021

Change in the bladder function of rats with focal cerebral infarction induced by photochemically-induced thrombosis

The photochemically-induced thrombosis(photothrombosis) method can create focal cerebral infarcts anywhere in the relatively superficial layers of the cerebrum; it is easy to implement and minimally invasive. Taking advantage of this versatility, we aimed to establish a new rat model of urinary frequency with focal cerebral infarction, which was characterized by its simplicity, nonlethal nature, and high reproducibility. The prefrontal cortex and the anterior cingulate cortex, which are urinary centers, were targeted for focal cerebral infarction, and urinary parameters were measured by cystometrogram. Cystometric analysis indicated that micturition intervals significantly shortened in photothrombosis-treated rats compared with those in the sham operative group on Days 1 and 7 (P < 0.01), but prolonged after 14 days, with no difference between the two groups. Immunopathological evaluation showed an accumulation of activated microglia, followed by an increase in reactive astrocytes at the peri-infarct zone after photothrombotic stroke. Throughout this study, all postphotothrombosis rats showed cerebral infarction in the prefrontal cortex and anterior cingulate cortex; there were no cases of rats with fatal cerebral infarction. This model corresponded to the clinical presentation, in that the micturition status changed after stroke. In conclusion, this novel model combining nonlethality and high reproducibility may be a suitable model of urinary frequency after focal cerebral infarction.

physiology↗

bioRxiv2021

A mosaic adeno-associated virus vector as a versatile tool that exhibits high levels of transgene expression and neuron specificity in primate brain

Recent emphasis has been placed on gene transduction mediated through recombinant adeno-associated virus (AAV) vector to manipulate activity of neurons and their circuitry in the primate brain. In the present study, we created a novel AAV vector of which capsid was composed of capsid proteins derived from the serotypes 1 and 2 (AAV1 and AAV2). Following the injection into the frontal cortex of macaque monkeys, this mosaic vector, termed AAV2.1 vector, was found to exhibit the excellence in transgene expression (for the AAV1 vector) and neuron specificity (for the AAV2 vector) simultaneously. To explore its applicability to chemogenetic manipulation and in vivo calcium imaging, the AAV2.1 vector expressing excitatory DREADDs or GCaMP was injected into the striatum or the visual cortex of macaque monkeys, respectively. Our results have defined that such vectors secure intense and stable expression of the target proteins and yield conspicuous modulation and imaging of neuronal activity.

neuroscience↗

bioRxiv2021

Dissecting the clonality of I1 plasmids using ORF-based binarized structure network analysis of plasmids (OSNAp)

Phylogenetic relationship of 97 I1 plasmids harboring blaCTX-M genes encoding extended-spectrum beta-lactamase (ESBL) was analyzed using the ORF-based binarized structure network analysis of plasmids (OSNAp). The majority of plasmids carrying blaCTX-M-1 or blaCTX-M-8, ESBL genes primarily associated with domestic animals, were clonal. On the other hand, plasmids carrying blaCTX-M-14 or blaCTX-M-15, identified from both humans and domestic animals, were diverse in their contents. The findings suggest that circulation of I1 plasmids among humans and animals may contribute to their diversity.

microbiology↗