Biology subjects

Yamaguchi, Y.

Publications and source records attributed to Yamaguchi, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

Dual Impacts of a Glycan Shield on the Envelope Glycoprotein B of HSV-1: Evasion from Human Antibodies In Vivo and Neurovirulence

Identification of the mechanisms of viral evasion from human antibodies is crucial both for understanding viral pathogenesis and for designing effective vaccines. However, the in vivo efficacy of the mechanisms of viral evasion from human antibodies has not been well documented. Here we show in cell cultures that an N-glycan shield on the HSV-1 envelope glycoprotein B (gB) mediated evasion from neutralization and antibody-dependent cellular cytotoxicity due to pooled {gamma}-globulins derived from human blood. We also demonstrated that the presence of human {gamma}-globulins in mice and HSV-1 immunity induced by viral infection in mice significantly reduced the replication of a mutant virus lacking the glycosylation site in a peripheral organ but had little effect on the replication of its repaired virus. These results suggest that the glycan shield on the HSV-1 envelope gB mediated evasion from human antibodies in vivo and from HSV-1 immunity induced by viral infection in vivo. Notably, we also found that the glycan shield on HSV-1 gB was significant for HSV-1 neurovirulence and replication in the central nervous system (CNS) of naive mice. Thus, we have identified a critical glycan shield on HSV-1 gB that has dual impacts, namely evasion from human antibodies in vivo and viral neurovirulence. IMPORTANCEHSV-1 establishes lifelong latent and recurrent infections in humans. To produce recurrent infections that contribute to transmission of the virus to new human host(s), the virus must be able to evade the antibodies persisting in latently infected individuals. Here we show that an N-glycan shield on the envelope glycoprotein B of HSV-1 mediates evasion from pooled {gamma}-globulins derived from human blood both in cell cultures and mice. Notably, the N-glycan shield was also significant for HSV-1 neurovirulence in naive mice. Considering the clinical features of HSV-1 infection, these results suggest that the glycan shield not only facilitates recurrent HSV-1 infections in latently infected humans by evading antibodies, but is also important for HSV-1 pathogenesis during the initial infection.

microbiology↗

bioRxiv2022

Cold-induced Suspension and Resetting of Ca2+ and Transcriptional Rhythms in the Suprachiasmatic Nucleus Neurons

Mammalian circadian rhythms are coordinated by the master clock located in the hypothalamic suprachiasmatic nucleus (SCN). Under severe environmental conditions, such as during the harsh winter season for food, certain mammalian species reduce their basal metabolism and thermogenesis, thereby undergoing torpor, a controlled state of hypothermia, which naturally returns to the normothermic state. A long-lasting debate focused on whether the SCN with a temperature-compensated clock remains functional during hypothermia. However, so far, no direct and quantitative evidence has been reported of temperature sensitivity in living SCN neurons. In this study, we performed dual-color fluorescence imaging of clock gene transcriptions and intracellular Ca2+ in mouse SCN neurons, using slices at various temperatures. We demonstrated that the Bmal1 transcription and Ca2+ circadian rhythms persisted at 22{degrees}C-28{degrees}C, although the two rhythms underwent temporal dissociation at 22 {degrees}C. Notably, Ca2+, Bmal1, and Per2 rhythms were suspended at 15{degrees}C, coupled with a significant Ca2+ increase, and all rhythms were reset by rewarming to 35{degrees}C. Upon rewarming, the Ca2+ rhythm showed stable oscillations immediately, whereas the Bmal1 and Per2 rhythms took several days to reach stable oscillations and recover their phase relationship with the Ca2+ rhythm. Taken together, we concluded that SCN neurons remain functional under moderate hypothermic conditions at approximately 22{degrees}C-28{degrees}C but stop ticking time in deep hypothermia at 15{degrees}C and that the rhythms reset after deep hypothermia. These data also indicate that the stable Ca2+ oscillation precedes clock gene transcriptional rhythms in the SCN neurons.

neuroscience↗

bioRxiv2022

Non-classical glycosylation determines intracellular trafficking of APP and Aβ production

A primary pathology of Alzheimers disease (AD) is A{beta} deposition in brain parenchyma and blood vessels, the latter being called cerebral amyloid angiopathy (CAA). Parenchymal amyloid plaques presumably originate from neuronal A{beta} precursor protein (APP), but vascular amyloid deposits origins remain unclear. Endothelial APP expression in APP-knock-in mice was recently shown to expand CAA pathology, highlighting endothelial APPs importance. Furthermore, two types of endothelial APP--with and without O-glycans--have been biochemically identified, but only the former is cleaved for A{beta} production, indicating the critical relationship between APP O-glycosylation and processing. Here, we analyzed APP glycosylation and its intracellular trafficking in neurons and endothelial cells. Although protein glycosylation is generally believed to precede cell surface trafficking, which was true for neuronal APP, we unexpectedly observed that APP lacking O-glycans is externalized to the endothelial cell surface and transported back to the Golgi apparatus, where it then acquires O-glycans. Knockdown of genes encoding enzymes initiating APP O-glycosylation significantly reduced A{beta} production, suggesting this non-classical glycosylation pathway contributes to CAA pathology and is a novel therapeutic target.

neuroscience↗

bioRxiv2022

A FRET biosensor, SMART, monitors necroptosis in renal tubular epithelial cells in a cisplatin-induced kidney injury model

Necroptosis is a regulated form of cell death involved in various pathological conditions, including ischemic reperfusion injuries, virus infections, and drug-induced tissue injuries. However, it is not fully understood when and where necroptosis occurs in vivo. We previously generated a Forster resonance energy transfer (FRET) biosensor, termed SMART (the sensor for MLKL activation based on FRET), which specifically monitored necroptosis in human and murine cell lines in vitro. Here, we generated transgenic (Tg) mice that expressed the SMART biosensor in various tissues. SMART monitored necroptosis, but not apoptosis or pyroptosis, in primary cells, including peritoneal macrophages and embryonic fibroblasts. Moreover, the FRET signal was elevated in renal tubular cells of cisplatin-treated SMART Tg mice compared to untreated SMART Tg mice. Together, SMART Tg mice may provide a valuable tool for monitoring necroptosis in different types of cells in vitro and in vivo.

cell biology↗

bioRxiv2022

PD-L1 blockade restores CAR T cell activity through IFNγ-regulation of CD163+ macrophages

BackgroundThe immune suppressive tumor microenvironment (TME) that inhibits T cell infiltration, survival, and anti-tumor activity has posed a major challenge for developing effective immunotherapies for solid tumors. Chimeric antigen receptor (CAR)-engineered T cell therapy has shown unprecedented clinical response in treating patients with hematological malignancies, and intense investigation is underway to achieve similar responses with solid tumors. Immunologically cold tumors, including prostate cancers, are often infiltrated with abundant tumor-associated macrophages (TAMs), and infiltration of CD163+ M2 macrophages correlates with tumor progression and poor responses to immunotherapy. However, the impact of TAMs on CAR T cell activity alone and in combination with TME immunomodulators is unclear. MethodsTo model this in vitro, we utilized a novel co-culture system with tumor cells, CAR T cells, and polarized M1 or M2 macrophages from CD14+ PBMCs collected from healthy human donors. Tumor cell killing, T cell activation and proliferation, and macrophage phenotypes were evaluated by flow cytometry, cytokine production, RNA sequencing, and functional blockade of signaling pathways using antibodies and small molecule inhibitors. We also evaluated the TME in humanized mice following CAR T cell therapy for validation of our in vitro findings. ResultsWe observed inhibition of CAR T cell activity with the presence of M2 macrophages, but not M1 macrophages, coinciding with a robust induction of PD-L1 in M2 macrophages. We observed similar PD-L1 expression in TAMs following CAR T cell therapy in the TME of humanized mice. PD-L1, but not PD-1, blockade in combination with CAR T cell therapy altered phenotypes to more M1-like subsets and led to loss of CD163+ M2 macrophages via IFN{gamma} signaling, resulting in improved anti-tumor activity of CAR T cells. ConclusionThis study reveals an alternative mechanism by which the combination of CAR T cells and immune checkpoint blockade modulates the immune landscape of solid tumors to enhance therapeutic efficacy of CAR T cells.

immunology↗

bioRxiv2021

Generalized harmonic analysis reveals a frequency modulated timer regulates mammalian hibernation

Mammalian hibernators decrease basal metabolism and body temperature (Tb) to minimize energy expenditure in harsh seasons. During hibernation, Tb drops to low temperature (<10 {degrees}C) and remains constant for days, known as deep torpor in small mammalian hibernators. Spontaneous interbout arousals interrupt torpor bouts, when Tb recovers to euthermic state ~37 {degrees}C. Torpor-interbout arousal event repeats during several months of hibernation. However, little is known about mechanisms governing Tb fluctuation across torpor-interbout arousal cycles during hibernation. Recent improvement in data-logging techniques enables us to monitor Tb for more than hundred days with high precision, opening up new avenues for quantitative analysis to address the principle governing Tb fluctuation. Here, we analyzed Tb fluctuation across torpor-interbout arousal cycle of Syrian hamster, which can hibernate in response to chronic cold and short photoperiod under a laboratory condition, using generalized harmonic analysis and discovered a model with frequency modulation quantitatively reproducing Tb fluctuation. This analysis also identified an unexpectedly longer period of 120-430 days as the period that modulates another period of several days, generating Tb fluctuation for Syrian hamster. We propose that concerted action of two endogenous periods governs torpor-interbout arousal cycles during hibernation.

zoology↗

bioRxiv2021

Neural network embedding of functional microconnectome.

Our brain works as a complex network system. Experiential knowledge seems to be coded into the organisms network architecture rather than retaining only properties of individual neurons. In order to be better able to consider the high complexity of this network architecture, extracting simple rules through both automated as well as interpretable analysis of topological patterns will be necessary in order to allow more useful observations of interrelationships within the complex neural architecture. By combining these two types of analysis methods, we could automatically compress and naturally interpret topological patterns of functional connectivities, which produced electrical activities from many neurons simultaneously from acute slices of mice brain for 2.5 hours [Kajiwara et al. 2021]. As the first type of analysis, this study trained an artificial neural network system called Neural Network Embedding (NNE), and automatically compressed the functional connectivities into only small (25%) dimensions. As the second type of analysis, we widely compared the compressed features with ~15 representative network metrics, having clear interpretations, including > 5 centrality-type metrics and newly developed network metrics, that quantify degrees or ratio of hubs distanced by several-nodes from initially focused hubs. As the result, although we could give interpretations for only 55-60% of the extracted features, these new metrics, together with the commonly utilized network metrics, enabled interpretations for 80-100% features, using automated analysis. The result demonstrates not only the fact that the NNE method surpasses limitations of commonly used human-made variables, but also the possibility that acknowledgement of our own limitations drives us to extend interpretable possibilities by developing new analytic methodologies.

neuroscience↗

bioRxiv2021

The cell surface hyaluronidase TMEM2 plays an essential role in mouse neural crest cell development and survival

Neural crest cells (NCCs) are a migratory population that gives rise to a diverse cell lineage, including the craniofacial complex, the peripheral nervous system, and a part of the heart. Hyaluronan (HA) is a major component of the extracellular matrix, and its tissue levels are dynamically regulated in during development. Although the synthesis of HA has been shown to exert substantial influence on embryonic morphogenesis, the functional importance of the catabolic side of HA turnover is poorly understood. Here, we demonstrate that the transmembrane hyaluronidase TMEM2 plays an essential role in NCC development and the morphogenesis of their derivatives. Wnt1-Cre-mediated Tmem2 knockout (Tmem2CKO) mice exhibit severe craniofacial and cardiovascular abnormalities. Analysis of Tmem2 expression using Tmem2 knock-in reporter mice reveals that Tmem2 is expressed at the site of NCC delamination in the neural tube and in Sox9-positive emigrating NCCs, suggesting that Tmem2 is critical for NCC development. Consistent with this possibility, linage tracing analysis reveals that the contribution of Wnt1-Cre-labeled cells to NCC derivatives is significantly reduced in a Tmem2-deficient background. Moreover, the emigration of NCCs from the neural tube is greatly reduced in Tmem2CKO mice. In vitro assays demonstrate that Tmem2 expression is essential for the ability of mouse O9-1 NCCs to form focal adhesion on and migrate into HA-containing substrates. Tmem2CKO mice also exhibit increased apoptotic cell death in NCC-derived tissues. Collectively, our data demonstrate that Tmem2 is essential for normal development of NCC-derivatives, including the craniofacial complex, and that TMEM2-mediated HA degradation allows NCCs to generate a tissue environment suitable for efficient focal adhesion assembly and migration. This study reveals the hitherto unrecognized functional importance of the catabolic side of HA metabolism in embryonic development and highlights the pivotal role of Tmem2 in the process. Author SummaryThe functional significance of hyaluronan (HA) in embryonic developmental processes has been demonstrated by studies using genetic manipulation of HA synthesis. However, the expression of HA is regulated not only by its synthesis, but also by its degradation. This issue is of particular importance due to the extremely rapid metabolic turnover of HA. Curiously, mice with mutations/ablations of known hyaluronidase molecules, such as the lysosomal hyaluronidases HYAL1 and HYAL2, exhibit little embryonic phenotypes. This suggests the existence of yet another hyaluronidase molecule that plays a key role in regulating extracellular HA balance in developing tissues. In this context, transmembrane protein 2 (TMEM2) is a novel hyaluronidase that functions on the cell surface. Here, we demonstrate that TMEM2 is expressed at the site of neural crest development and in neural crest cell (NSC)-derived craniofacial tissue, and that NCC-targeted Tmem2 conditional knockout mice develop severe craniofacial defects, which attests to a requirement for TMEM2-mediated extracellular HA degradation in neural crest development. Our in vitro and in vivo analyses on the underlying mechanisms of the phenotype demonstrate that TMEM2 is essential for generating a tissue environment suitable for efficient focal adhesion formation by NCCs. This paper reveals for the first time that the catabolic machinery for HA exerts a specific regulatory role in embryonic morphogenesis, and that its dysregulation of HA degradation leads to severe developmental defects.

developmental biology↗

bioRxiv2021

Gpr19 is a circadian clock-controlled orphan GPCR with a role in modulating free-running period and light resetting capacity of the circadian clock

Background and PurposeGpr19 encodes an evolutionarily conserved orphan G-protein-coupled receptor (GPCR) with no established physiological function in vivo. The purpose of this study was to determine the role of Gpr19 in the circadian clock system. Experimental ApproachWe examined whether and how the master circadian clock neurons in the suprachiasmatic nucleus (SCN) express Gpr19. By analysing Gpr19-deficient (Gpr19-/-) mice, we asked whether Gpr19 has a role in modulating free-running period and light resetting capacity of the circadian clock. Key ResultsCompared with the known common core clock genes, Gpr19 was identified to show several distinct yet limited features related to the circadian clock. Gpr19 mRNA was mainly expressed in the middle-to-dorsal region of the SCN. A conserved cAMP-responsive element within the Gpr19 promoter drove the circadian expression of Gpr19. Gpr19-/- mice exhibited a prolonged circadian period and a delayed initiation of daily locomotor activity in a 12-h light/12-h dark cycle. Gpr19 deficiency caused the downregulation of several genes that normally peak during the night, including Bmal1 and Gpr176. Gpr19-/- mice had a reduced capacity for phase shift to early subjective night light. The defect was only observed for phase-delay, but not phase-advance, and accompanied by reduced response of c-Fos expression in the dorsal region of the SCN, while apparently normal in the ventral part of the SCN, in Gpr19-/- mice. Conclusion and ImplicationsGpr19 is an SCN-enriched orphan GPCR with a distinct role in circadian regulation and thus may be a potential target for alleviating circadian clock disorders. O_LIWhat is already known: Gpr19 is an evolutionarily conserved class-A orphan receptor with no established physiological role in vivo. The SCN is a light-entrainable master circadian pacemaker governing daily rhythms of behaviour and physiology. C_LIO_LIWhat this study adds: Gpr19 is an SCN-enriched orphan GPCR whose levels fluctuate in a circadian fashion. Gpr19 is a functional clock modulator involved in period determination and phase resetting. C_LIO_LIClinical significance: Targeting the orphan receptor Gpr19 may provide a therapeutic approach for alleviating circadian clock disorders. C_LI

neuroscience↗

bioRxiv2021

THz irradiation inhibits cell division by affecting actin dynamics

Biological phenomena induced by terahertz (THz) irradiation are described in recent reports, but underlying mechanisms, structural and dynamical change of specific molecules are still unclear. In this paper, we performed time-lapse morphological analysis of human cells and found that THz irradiation halts cell division at cytokinesis. At the end of cytokinesis, the contractile ring, which consists of filamentous actin (F-actin), needs to disappear; however, it remained for 1 hour under THz irradiation. Induction of the functional structures of F-actin was also observed in interphase cells. Similar phenomena were also observed under chemical treatment (jasplakinolide), indicating that THz irradiation assists actin polymerization. We previously reported that THz irradiation enhances the polymerization of purified actin in vitro; our current work shows that it increases cytoplasmic F-actin in vivo. Thus, we identified one of the key biomechanisms affected by THz waves.

cell biology↗

bioRxiv2020

High-dose pyruvate treatment alters skeletal muscle differentiation and expression of inflammation-related genes

Pyruvic acid therapy is used for various diseases, but the therapeutic effect decreases at high doses. The molecular mechanism of high-dose pyruvate is not well understood. The purpose of this study was to identify the effects of high dose pyruvate addition on skeletal muscle using C2C12. The gene expression profile for the GSE5497 dataset was taken from the Gene Expression Omnibus database. GEO2R was used to identify specifically expressed genes (DEGs). Functional analysis and pathway enrichment analysis of DEG were performed using the DAVID database. The protein-protein interaction (PPI) network was built in the STRING database and visualized using Cytoscape. GO analysis showed that up-regulated DEG was primarily involved in angiogenesis, cell adhesion, and inflammatory response. We also showed that down-regulated DEG is involved in the regulation of muscle contraction, skeletal muscle fiber development. In addition, the upregulated KEGG pathway of DEG included Rheumatoid arthritis, Chemokine signaling pathway, and Cytokine-cytokine receptor interaction. Downregulated DEG included Calcium signaling pathway, hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy, Neuroactive ligand-receptor interaction, and Cardiac muscle contraction. Further, analysis of two modules selected from the PPI network showed that high-dose pyruvate exposure to C2C12 was primarily associated with muscle contraction, muscle organ morphogenesis, leukocyte chemotaxis, and chemokine activity. In conclusion, High-dose pyruvate treatment of C2C12 was found to be associated with an increased inflammatory response and decreased skeletal muscle formation. However, further studies are still needed to verify the function of these molecules at high doses of pyruvate.

bioinformatics↗

bioRxiv2020

Lipopolysaccharide preconditioning augments phagocytosis of malaria-parasitized red blood cells through induced bone marrow-derived macrophages in the liver, thereby increasing the murine survival after Plasmodium yoelii infection

Malaria remains a grave concern for humans, as effective medical countermeasures for malaria infection have yet to be developed. Phagocytic clearance of parasitized red blood cells (pRBCs) by macrophages is an important front-line innate host defense against malaria infection. We previously showed that repeated injections of low-dose lipopolysaccharide (LPS) prior to bacterial infection, called LPS preconditioning, strongly augmented phagocytic/bactericidal activity in murine macrophages. However, how LPS preconditioning prevents murine malaria infection is unclear. We investigated the protective effects of LPS preconditioning against lethal murine malaria infection, focusing on CD11bhigh F4/80low liver macrophages, which are increased by LPS preconditioning. Mice were subjected to LPS preconditioning by intraperitoneal injections of low-dose LPS for 3 consecutive days, and 24 h later, they were intravenously infected with pRBCs of Plasmodium yoelii 17XL. LPS preconditioning markedly increased the murine survival and reduced parasitemia, while it did not reduce TNF secretions, only delaying the peak of plasma IFN-{gamma} after malaria infection in mice. An in vitro phagocytic clearance assay of pRBCs showed that the CD11bhigh F4/80low liver macrophages of the LPS-preconditioned mice had significantly augmented phagocytic activity against pRBCs. The adoptive transfer of CD11bhigh F4/80low liver macrophages from LPS-preconditioned mice to control mice significantly improved the survival after malaria infection. We conclude that LPS preconditioning stimulated CD11bhigh F4/80low liver macrophages to augment the phagocytic clearance of pRBCs, which may play a central role in resistance against malaria infection. LPS preconditioning may be an effective tool for preventing malaria infection.

immunology↗

bioRxiv2020

A new microcirculation culture method with a self-organized capillary network

A lack of microcirculation has been one of the most significant obstacles for three-dimensional culture systems of organoids and embryonic tissues. Here, we developed a simple and reliable method to implement a perfusable capillary network in vitro. The method employed the self-organization of endothelial cells to generate a capillary network and a static pressure difference for culture medium circulation, which can be easily introduced to standard biological laboratories and enables long-term cultivation of vascular structures. Using this culture system, we perfused the lumen of the self-organized capillary network and observed a flow-induced vascular remodeling process, cell shape changes, and collective cell migration. We also observed an increase in cell proliferation around the synthetic vasculature induced by flow, indicating functional perfusion of the culture medium. We also reconstructed extravasation of tumor and inflammatory cells, and circulation inside spheroids including endothelial cells and human lung fibroblasts. In conclusion, this system is a promising tool to elucidate the mechanisms of various biological processes related to vascular flow.

cell biology↗

bioRxiv2019

The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain

We describe our connectomics pipeline for processing tracer injection data for the brain of the common marmoset (Callithrix jacchus). Brain sections were imaged using a batch slide scanner (NanoZoomer 2.0-HT) and we used artificial intelligence to precisely segment the anterograde tracer signal from the background in the fluorescence images. The shape of each brain was reconstructed by reference to a block-face and all data was mapped into a common 3D brain space with atlas and 2D cortical flat map. To overcome the effect of using a single template atlas to specify cortical boundaries, each brain was cytoarchitectonically annotated and used for making an individual 3D atlas. Registration between the individual and common brain cortical boundaries in the flat map space was done to absorb the variation of each brain and precisely map all tracer injection data into one cortical brain space. We describe the methodology of our pipeline and analyze tracer segmentation and brain registration accuracy. Results show our pipeline can successfully process and normalize tracer injection experiments into a common space, making it suitable for large-scale connectomics studies with a focus on the cerebral cortex.

neuroscience↗

bioRxiv2019

Novel method to determine diagnosis-defining refraction points

Diagnosis of a certain disease generally relies on definitions established by professional medical societies and comprise the patients history, physical examination, and test results. These include physical compositions such as body mass index (BMI), and laboratory tests such as serum creatinine and albumin in urine samples. In general, laboratory tests are based on mathematical methods, e.g. defining critical values from the mean {+/-} k{sigma} of a population, where k is a natural number and the standard deviation is {sigma} (\"mean {+/-} k{sigma}-method\"). In most cases k is defined as 2, leading to reference ranges defining 95% of test results as normal. However, this method mostly depends on a normal distribution of values.\n\nHere we applied a novel method (\"SoFR-method\") based on data sorting to define refraction points, which carry informative value as diagnostic criteria. Applying the SoFR-method, standard measures such as critical BMI-values are categorized by equal robustness as by the mean {+/-} k{sigma}-method. However, the SoFR-method showed higher validity when analyzing non-normalized values such as creatinine and albumin, as well as hepatocyte growth factor (HGF) and hemoglobin in a novel Perioscreen assay in saliva of diabetic and non-diabetic patients.\n\nTaken together, we defined a novel method based on data sorting of test results from patients to effectively define refraction points which might guide more accurately clinical diagnoses and define relevant thresholds.

epidemiology↗

bioRxiv2018

Sufficient therapeutic effect of cryopreserved frozen adipose-derived regenerative cells on burn wounds

The purpose of this study was to evaluate whether cryopreserved (frozen) adipose-derived regenerative cells (ADRCs) have a therapeutic effect on burn wound healing as well as freshly isolated (fresh) ADRCs.\n\nFull thickness burns were created on dorsum of nude mice and burn wound was excised. The wound was covered by artificial dermis with; (i) fresh ADRCs, (ii) frozen ADRCs, and (iii) PBS (control). The assessment for wound healing was performed by morphological, histopathological and immunohistochemical analyses.\n\nIn vivo analyses exhibited the significant therapeutic effect of frozen ADRCs on burn wound healing up to the similar or higher level of fresh ADRCs. There were significant differences of wound closure, epithelized tissue thickness, and neovascularization between the treatment groups and control group. Although there was no significant difference of therapeutic efficacy between fresh ADRC group and frozen ADRC group, frozen ADRCs improved burn wound healing process in dermal regeneration with increased great type I collagen synthesis compared with fresh ADRCs.\n\nThese findings indicate that frozen ADRCs allow us to apply not only quickly but also for multiple times, and the cryopreserved ADRCs could therefore be useful for the treatment of burn wounds in clinical settings.

pathology↗

bioRxiv2018

Parallelized analysis of spatial gene expression patterns by database integration

We developed a computational framework for automated integration of a large number of two-dimensional (2D) images with three-dimensional (3D) image datasets located in the standard 3D coordinate. We applied the framework to 2,810 para-sagittal sectioned mouse brain 2D images of in situ hybridization (ISH), archived in the BrainTx database (http://www.cdtdb.neuroinf.jp). We registered the ISH images into the mouse standard coordinate space for MR images, Waxholm space (WHS, https://www.nitrc.org/projects/incfwhsmouse) by linearly transforming them into each of a series of para-sagittal MR image slices, and identifying the best-fit slice by calculating the similarity metric value ({delta}). Transformed 2D images were compared with 3D gene expression image datasets, which were made using a microtomy-based microarray assay system, Transcriptome Tomography, and archived in the ViBrism DB (http://vibrism.neuroinf.jp): the 3D images are located in the WHS.\n\nWe first transformed ISH images of 10 regionally expressed genes and compared them to signals of corresponding 3D expression images in ViBrism DB for evaluating the integration schema: two types of data, produced with different modalities and originally located in different dimensions, were successfully compared after enhancing ISH signals against background noise. Then, for the massive transformation of BrainTx database images, we parallelized our framework, using the IPython cluster package, and implemented it on the PC cluster provided for the Brain Atlasing Hackathon activity hosted by Neuroinformatics Japan Center in Japan. We could identify the best-fit positions for all of the ISH images. All programs were made available through the GitHub repository, at the web site of neuroinformatics/bah2016_registration (https://github.com/neuroinformatics/bah2016_registration).

neuroscience↗

bioRxiv2018

Identification of evolutionarily conserved virulence factor by selective pressure analysis of Streptococcus pneumoniae

Evolutionarily conserved virulence factors can be candidate therapeutic targets or vaccine antigens. Here, we investigated the evolutionary selective pressures on 16 pneumococcal choline-binding cell-surface proteins since Streptococcus pneumoniae is one of the pathogen posing the greatest threats to human health. Phylogenetic and molecular analyses revealed that cbpJ had the highest codon rates to total numbers of codons under significant negative selection among those examined. Our in vitro and in vivo assays indicated that CbpJ functions as a virulence factor in pneumococcal pneumonia by contributing to evasion of neutrophil killing. Deficiency of cbpL under relaxed selective pressure also caused a similar tendency but showed no significant difference in mouse intranasal infection. Thus, molecular evolutionary analysis is a powerful tool that reveals the importance of virulence factors in real-world infection and transmission, since calculations are performed based on bacterial genome diversity following transmission of infection in an uncontrolled population.

microbiology↗