Biology subjects

Takahashi, K.

Publications and source records attributed to Takahashi, K..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Trichomes on female reproductive tract: rapid diversification and underlying gene regulatory network in Drosophila suzukii and its related species

BackgroundThe ovipositors of some insects are external female genitalia, which have their primary function to deliver eggs. Drosophila suzukii and its sibling species D. subpulchrella are known to have acquired highly sclerotized and enlarged ovipositors upon their shifts in oviposition sites from rotting to ripening fruits. Inside the ovipositor plates, there are scale-like polarized protrusions termed "oviprovector scales" that are likely to aid the mechanical movement of the eggs. The size and spatial distribution of the scales need to be rearranged following the divergence of the ovipositors. In this study, we examined the features of the oviprovector scales in D. suzukii and its closely related species. We also investigated whether the scales are single-cell protrusions comprised of F-actin under the same conserved gene regulatory network as the well-characterized trichomes on the larval cuticular surface. ResultsThe oviprovector scales of D. suzukii and D. subpulchrella were distinct in size and spatial arrangement compared to those of a closely related species D. biarmipes and D. melanogaster. The comparisons of the size of the scales suggested that the apical cell area of the oviprovector has expanded upon the elongation of the ovipositor plates in these species. Our transcriptome analysis revealed that 43 out of the 46 genes known to be involved in the trichome gene regulatory network are expressed in the developing female genitalia of D. suzukii and D. subpulchrella. An antibody staining depicted the presence of Shavenbaby (Svb) in the inner cavity of the developing ovipositors of D. melanogaster at 44-48 h after puparium formation (APF). Also, shavenoid (sha) was expressed in the corresponding patterns in the developing ovipositors and showed differential expression levels between D. suzukii and D. subpulchrella at 48 h APF. ConclusionsThe oviprovector scales have divergent size and spatial arrangements among species. Therefore, these scales may represent a rapidly diversifying morphological trait of the female reproductive tract reflecting ecological contexts. Furthermore, our results showed that the gene regulatory network underlying trichome formation is adopted to develop the rapidly evolving trichomes on the oviprovectors of these flies.

developmental 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↗

bioRxiv2022

Joint copy number and mutation phylogeny reconstruction fromsingle-cell amplicon sequencing data

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.

bioinformatics↗

bioRxiv2021

Morphological variation and phylogeny of Karenia selliformis (Gymnodiniales, Dinophyceae) in an intensive cold-water algal bloom in eastern Hokkaido, Japan in September-November 2021

Harmful algal blooms responsible for mass mortalities of marine organisms have so far been rare in Hokkaido, northern Japan, although fish killing blooms have been frequently reported from western Japanese coasts. In September-November 2021, a huge and prolonged cold-water bloom occurred along the Pacific coast of eastern Hokkaido, Japan, and was associated with intensive mortalities of sea urchin, fish, octopus, shellfish, etc. In this study, morphology and phylogeny of the dominant and co-occurred unarmored dinoflagellates of the Kareniaceae in the bloom were examined by using light microscopy, scanning electron microscopy and molecular phylogeny inferred from ITS and LSU rDNA (D1-D3) sequences. Morphological observation and molecular phylogeny showed that the dominant species was Karenia selliformis, with co-occurrences of other kareniacean dinoflagellates, Kr. longicanalis, Kr. mikimotoi, Karlodinium sp., Takayama cf. acrotrocha, Takayama tuberculata and Takayama sp. The typical cell forms of K. selliformis in the bloom were discoid, dorsoventrally flattened, and larger than the cell sizes in previous reports, 35.3-43.6 (39.4{+/-}2.1) m in length. Transparent cells of Kr. selliformis lacking or having several shrunken chloroplasts and oil droplets were also found. Cells of Kr. selliformis had morphological variation, but the species could be distinguished from other co-occurred Karenia species by its numerous (46-105) and small granular (2.9-4.6 m in diameter) chloroplasts and the nucleus positioned in the hypocone. Cell density of Kr. selliformis exceeding 100 cells/mL was recorded in the range of temperature 9.8-17.6{degrees}C. The rDNA sequences determined from Kr. selliformis in the blooms of Hokkaido, Japan in 2021 were identical to those from another bloom in Kamchatka, Russia in 2020. HighlightsO_LIA marine fauna-destructive harmful algal bloom in the Pacific coast of eastern Hokkaido, Japan in September-November 2021 was dominated by Karenia selliformis. C_LIO_LICells of Karenia selliformis typical in the bloom were discoid and possessing numerous small chloroplasts, approximately 70 in number. C_LIO_LICells of Karenia selliformis showed morphological variation in size and shape, and transparent motile cells lacking or having degraded chloroplasts were also present. C_LIO_LICo-occurred kareniaceans in the bloom were Karenia longicanalis, Karenia mikimotoi, Karlodinium sp. and Takayama spp. C_LIO_LIrDNA sequences of Karenia selliformis in the blooms of Hokkaido in 2021 and Kamchatka in 2020 were identical, which belong to the group I of Kr. selliformis. C_LI

ecology↗

bioRxiv2021

Post-transcriptionally regulated genes are essential for pluripotent stem cell survival

The effects of transcription factors on the maintenance and differentiation of pluripotent stem cells (PSCs) have been well studied. However, the importance of post-transcriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 post-transcriptionally regulated genes with strict upregulation of the protein level in PSCs. Among them, we found that 84 genes were vital for the survival of PSCs and HDFs, including 20 genes that were specifically necessary for the survival of PSCs. These 20 proteins were upregulated only in PSCs and not in differentiated cells derived from the three germ layers. Subcellular fractionation of the mRNA showed that the expression of most of the 20 proteins was regulated at the mRNA localization stage from the nucleus to the cytoplasm, but their translation efficiency was constant. Together, these results revealed that post-transcriptionally regulated genes have a crucial role in PSC survival.

molecular biology↗

bioRxiv2021

A stress-reduced passaging technique improves the viability of human pluripotent cells

Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, yet some problems, such as the reproducibility among the experiments, remain. Here we describe an improved method for the subculture of human PSCs. The revised method significantly enhanced the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing, gene delivery, and directed differentiation. Furthermore, the method did not alter PSC characteristics after long-term culture and attenuated the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application. HighlightsO_LIThe revised passaging method significantly increases the viability of human PSCs. C_LIO_LIThe method triggers less DNA damage and apoptosis signals compared to the conventional method. C_LIO_LIThe stress-reduced method improves the results of downstream applications. C_LIO_LIThe method does not alter PSC characters and attenuates the overgrowth of abnormal subpopulations. C_LI

cell biology↗

bioRxiv2021

Clonal hematopoiesis is associated with increased toxicity in large B-cell lymphoma patients treated with chimeric antigen receptor T cell therapy

To explore the role of clonal hematopoiesis (CH) on chimeric antigen receptor (CAR) T-cell therapy outcomes, we performed targeted deep-sequencing on 114 large B-cell lymphoma patients treated with anti-CD19 CAR T-cells. We detected CH in 42 (36.8%) pre-treatment patient samples, most frequently in PPM1D (19/114) and TP53 (13/114) genes. The incidence of grade [≥]3 immune-effector cell-associated neurotoxicity syndrome (ICANS) was higher in CH-positive patients compared to CH-negative patients (45.2% vs. 25.0%, p=0.038). Higher toxicities with CH were primarily driven by three CH genes, DNMT3A, TET2 and ASXL1 (DTA mutations). The incidence of grade [≥]3 ICANS [58.9% vs. 25%, p=0.02] and grade [≥]3 cytokine release syndrome [17.7% vs. 4.2%, p=0.08] were higher in patients with DTA mutations than those without CH. The estimated 24-month cumulative incidence of therapy-related myeloid neoplasms after CAR-T therapy was higher in patients with CH than those without CH (19% [95%CI: 5.5-38.7] vs. 4.2% [95%CI: 0.3-18.4], p=0.028). Statement of SignificanceOur study reveals that clonal hematopoiesis mutations, especially those associated with inflammation (DNMT3A, TET2, ASXL1), are associated with severe grade toxicities in lymphoma patients receiving anti-CD19 chimeric antigen receptor therapy. Further studies to investigate the mechanisms and interventions to improve toxicities in the context of CH are warranted.

genetics↗

bioRxiv2021

Characterizing brain state-dependent pupil dynamics based on lateral hypothalamic activity

Pupil dynamics presents varied correlation features with brain activity under different vigilant levels. The modulation of brain state changes can arise from the lateral hypothalamus (LH), where diverse neuronal cell types contribute to arousal regulation in opposite directions via the anterior cingulate cortex (ACC). However, the relationship of the LH and pupil dynamics has seldom been investigated. Here, we performed local field potential (LFP) recordings at the LH and ACC, and the whole brain fMRI with simultaneous fiber photometry Ca2+ recording in the ACC, to evaluate their correlation with brain state-dependent pupil dynamics. Both LFP and functional MRI (fMRI) data showed opposite correlation features to pupil dynamics, demonstrating an LH activity-dependent manner. Our results demonstrate that the correlation of pupil dynamics with ACC LFP and whole-brain fMRI signals depends on LH activity, indicating a role of the latter in brain state regulation.

neuroscience↗

bioRxiv2021

Aboveground biomass increments over 26 years (1993-2019) in an old-growth cool-temperate forest in northern Japan

Assessing long-term changes in biomass of old-growth forests is critical in evaluating forest ecosystem functions under a changing climate. Long-term biomass changes are the result of accumulated short-term changes, which can be affected by endogenous processes such as gap filling in small-scale canopy openings. Here, we used 26 years (1993-2019) of repeated tree census data in an old-growth, cool-temperate, deciduous mixed forest that contains three topographic units (riparian, denuded slope, and terrace) in northern Japan to document decadal changes in aboveground biomass (AGB) and their processes in relation to endogenous processes and climatic factors. AGB increased steadily over the 26 years in all topographic units, but different tree species contributed to the increase among the topographic units. AGB gain within each topographic unit exceeded AGB loss via tree mortality in most of the measurement periods despite substantial temporal variation in AGB loss. At the local scale, variations in AGB gain were partially explained by compensating growth of trees around canopy gaps. Climate affected the local-scale AGB gain: the gain was larger in the measurement periods with higher mean temperature during the current summer but smaller in those with higher mean temperature during the previous autumn, synchronously in all topographic units. The decadal climate trends of warming are likely to have contributed to the steady increase in AGB in this old-growth forest.

ecology↗

bioRxiv2021

A statistical test for clonal exclusivity in tumour evolution

Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Pairs of mutations that are overrepresented in a clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical test, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our test for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 6 clonally exclusive and 2 clonally co-occurring gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways.

cancer biology↗

bioRxiv2021

Focal fMRI signal enhancement with implantable inductively coupled detectors

Despite extensive efforts to increase the signal-to-noise ratio (SNR) of fMRI images for brain-wide mapping, technical advances of focal brain signal enhancement are lacking, in particular, for animal brain imaging. Emerging studies have combined fMRI with fiber optic-based optogenetics to decipher circuit-specific neuromodulation from meso to macroscales. Acquiring fMRI signal with high spatiotemporal resolution is needed to bridge cross-scale functional dynamics, but SNR of targeted cortical regions is a limiting factor. We have developed a multi-modal fMRI imaging platform with an implanted inductive coil detector. This detector boosts the tSNR of MRI images, showing a 2-3 fold sensitivity gain over conventional coil configuration. In contrast to the cryoprobe or array coils with limited spaces for implanted brain interface, this setup offers a unique advantage to study brain circuit connectivity with optogenetic stimulation and can be further extended to other multi-modal fMRI mapping schemes.

neuroscience↗

bioRxiv2021

A meta-analysis of Microarray Data is Effective for Identifying Gravity-Sensitive Genes

Gravity affects the function and maintenance of organs, such as bones, muscles, and the heart. Several studies have used DNA microarrays to identify genes with altered expressions in response to gravity. However, it is technically challenging to combine the results from various microarray datasets because of their different data structures. We hypothesized it is possible to identify common changes in gene expression from the DNA microarray datasets obtained under various conditions and methods. In this study, we grouped homologous genes to perform a meta-analysis of multiple vascular endothelial cell and skeletal muscle datasets. According to the t-distributed stochastic neighbor embedding (t-SNE) analysis, the changes in the gene expression pattern in vascular endothelial cells formed specific clusters. We also identified candidate genes in endothelial cells that responded to gravity. Further, we exposed human umbilical vein endothelial cells to simulated microgravity using a clinostat and measured the expression levels of the candidate genes. Gene expression analysis using qRT-PCR revealed that the expression level of the prostaglandin transporter gene SLCO2A1 decreased in response to microgravity, consistent with the meta-analysis of microarray datasets. Furthermore, the direction of gravity affected the expression level of SLCO2A1, buttressing the finding that its expression was affected by gravity. These results suggest that a meta-analysis of DNA microarray datasets may help identify new target genes previously overlooked in individual microarray analyses.

cell biology↗

bioRxiv2021

Implications of cholesterol and sphingomyelin in STING phosphorylation by TBK1

Stimulator of interferon genes (STING) is essential for the type I interferon response induced by microbial DNA from virus or self-DNA from mitochondria/nuclei. In response to emergence of such DNAs in the cytosol, STING translocates from the endoplasmic reticulum (ER) to the Golgi, and activates TANK-binding kinase 1 (TBK1) at the trans-Golgi network (TGN). Activated TBK1 then phosphorylates STING at Ser365, generating an interferon regulatory factor 3 (IRF3)-docking site on STING. How this reaction proceeds specifically at the TGN remains poorly understood. Here we report a cell-free reaction in which endogenous STING is phosphorylated by TBK1. The reaction utilizes microsomal membrane fraction prepared from TBK1-knockout (KO) cells and recombinant TBK1. We observed agonist-, TBK1-, "ER-to-Golgi" traffic-, and palmitoylation-dependent phosphorylation of STING at Ser365, mirroring the nature of STING phosphorylation in vivo. Treating the microsomal membrane fraction with sphingomyelinase or methyl-{beta}-cyclodextrin, an agent to extract cholesterol from membranes, suppressed the phosphorylation of STING by TBK1. Given the enrichment of sphingomyelin and cholesterol in the TGN, these results may provide the molecular basis underlying the specific phosphorylation reaction of STING at the TGN.

cell biology↗

bioRxiv2021

Exponentiating pixel values for data augmentation to improve deep learning image classification in chest X-rays

A previous study reported that exponentiating pixel values of a medical can be used for DA through enhancing contrast of the image. However, it is still unclear whether exponentiating pixel values of CXR images can be used for DA with CNN. The aim of this study is to evaluate the effectiveness of exponentiating pixel values for DA using CNN in the task of classifying normal and abnormal CXR images. In constructing an image for DA, each pixel value of the original images was exponentiated by the exponent ranging from 1 to 10, incrementing by 0.5. We call this image as exponentiated image (EI). For each exponent (1.0, 1.5, 1.5, 2.0,..., 10.0), the CNN model was trained using the original training dataset and EI for 40 epochs. Test accuracy was calculated at the end of each epoch using the test dataset. The maximum test accuracy (MTA) among the 40 test accuracies was saved for statistical analysis. This process was repeated 50 times for each exponent (1.0, 1.5, 1.5, 2.0,..., 10.0). The mean MTA for each exponent (1.5, 1.5, 2.0,..., 10.0) was compared using Students t-test, to that of 1.0. The mean MTA when the exponent was 1.0 was 0.749 (reference). The mean MTA was higher than the reference at exponent values 4.5(MTA=0.762, p-value=0.014), 5.0(0.762, 0.019), 5.5(0.772, 2.9 x 10-5), and 6.5(0.763, 0.010). Exponentiating pixel values can be used for DA with CNN to classify normal and abnormal CXR images.

bioinformatics↗

bioRxiv2021

Decoding the brain state-dependent relationship between pupil dynamics and resting state fMRI signal fluctuation

Pupil dynamics serve as a physiological indicator of cognitive processes and arousal states of the brain across a diverse range of behavioral experiments. Pupil diameter changes reflect brain state fluctuations driven by neuromodulatory systems. Resting state fMRI (rs-fMRI) has been used to identify global patterns of neuronal correlation with pupil diameter changes, however, the linkage between distinct brain state-dependent activation patterns of neuromodulatory nuclei with pupil dynamics remains to be explored. Here, we identified four clusters of trials with unique activity patterns related to pupil diameter changes in anesthetized rat brains. Going beyond the typical rs-fMRI correlation analysis with pupil dynamics, we decomposed spatiotemporal patterns of rs-fMRI with principal components analysis (PCA) and characterized the cluster-specific pupil-fMRI relationships by optimizing the PCA component weighting via decoding methods. This work shows that pupil dynamics are tightly coupled with different neuromodulatory centers in different trials, presenting a novel PCA-based decoding method to study the brain state-dependent pupil-fMRI relationship.

neuroscience↗

bioRxiv2021

Elevation-related climate trends dominate fungal co-occurrence patterns on Mt. Norikura, Japan

Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, the trends of co-occurrence networks across similar gradients remain elusive. Here, we constructed co-occurrence networks for fungal community along a 2300 m elevation gradient on Mt Norikura, Japan, hypothesizing a progressive decline in network connectivity with elevation due to reduced niche differentiation caused by declining temperature and ecosystem productivity. Results agreed broadly with predictions, with an overall decline in network connectivity with elevation for all fungi and the high abundance phyla. However, trends were not uniform with elevation, most decline in connectivity occurred between 700 m and 1500 m elevation, remaining relatively stable above this. Temperature and precipitation dominated variation in network properties, with lower mean annual temperature (MAT) and higher mean annual precipitation (MAP) at higher elevations giving less network connectivity, largely through indirect effects on soil properties. Among keystone taxa that played crucial roles in network structure, the variation in abundance along the elevation gradient was also controlled by climate and also pH. Our findings point to a major role of climate gradients in mid-latitude mountain areas in controlling network connectivity. Given the importance of the orographic precipitation effect, microbial community trends seen along elevation gradients might not be mirrored by those seen along latitudinal temperature gradients. ImportanceAlthough many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts across environmental gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation, and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Assemblages of keystone taxa playing crucial roles in network structure varied along the elevation gradient and were also largely controlled by climate. Our results provide insight into the shift of soil fungal community co-occurrence structure along elevational gradients, and possible driving mechanisms behind this. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/428196v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@12e555aorg.highwire.dtl.DTLVardef@e5c4d7org.highwire.dtl.DTLVardef@de00bdorg.highwire.dtl.DTLVardef@102967c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Swallowing-related neural oscillation: An intracranial EEG study

Swallowing is a unique movement due to the indispensable orchestration of voluntary and involuntary movement. The transition from voluntary to involuntary swallowing is executed on the order of milliseconds. We hypothesized that its neural mechanism is revealed by high frequency cortical activities. Eight epileptic participants fitted with intracranial electrodes over the orofacial cortex were asked to swallow a water bolus, and cortical oscillatory changes, including high {gamma} band (75-150 Hz) and {beta} band (13-30 Hz) were investigated at the time of mouth-opening, water-injection, and swallowing. High {gamma} power increases associated with mouth-opening were observed in the ventrolateral prefrontal cortex with water-injection in the lateral central sulcus and with swallowing in the region along the Sylvian fissure. Mouth-opening induced a {beta} power decrease, which continued until the completion of swallowing. The high {gamma} burst activity was focal and specific to swallowing, however, the {beta} activities were extensive and not specific to swallowing. At the boundary time between voluntary and involuntary swallowing, swallowing-related high {gamma} power achieved the peak, and subsequently, the power decreased. We demonstrated three distinct activities related to mouth-opening, water-injection, and swallowing induced at different timings, using high {gamma} activities. The peak of high {gamma} power related to swallowing suggests that during voluntary swallowing phases, the cortex is the main driving force for swallowing rather than the brain stem.

neuroscience↗

bioRxiv2020

Robotic Search for Optimal Cell Culture in Regenerative Medicine

Induced differentiation is one of the most experience- and skill-dependent experimental processes in regenerative medicine, and establishing optimal conditions often takes years. We developed a robotic AI system with a batch Bayesian optimization algorithm that autonomously induces the differentiation of induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells. The system performed 216 forty-day cell culture experiments, with a total experimentation time of 8,640 days. From 200 million possible parameter combinations, the system performed cell culture in 143 different conditions in 111 days, resulting in 88% better iPSC-RPE production than that by the pre-optimized culture in terms of pigmented scores. Our work demonstrates that the use of autonomous robotic AI systems drastically accelerates systematic and unbiased exploration of experimental search space, suggesting immense use in medicine and research.

systems biology↗