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Patent
National Institutes Of Natural Science | Date: 2017-01-25

A kinematic support structure of a groove - groove - groove type that reduces friction between a first base and a second base is provided. In a kinematic support structure (100), a first base (110) comprises three grooves (111, 112, 113) and a second base (120) comprises three other grooves (121, 122, 123). Balls (130, 140, 150) are all movable with respect to the first base (110) and the second base (120). Two grooves corresponding in the two bases face each other across respective one of the balls.


Kimura Y.,National Institutes of Natural science | Hisano Y.,RIKEN | Kawahara A.,RIKEN | Kawahara A.,Yamanashi University | Higashijima S.-I.,National Institutes of Natural science
Scientific Reports | Year: 2014

The type II bacterial CRISPR/Cas9 system is rapidly becoming popular for genome-engineering due to its simplicity, flexibility, and high efficiency. Recently, targeted knock-in of a long DNA fragment via homology-independent DNA repair has been achieved in zebrafish using CRISPR/Cas9 system. This raised the possibility that knock-in transgenic zebrafish could be efficiently generated using CRISPR/Cas9. However, how widely this method can be applied for the targeting integration of foreign genes into endogenous genomic loci is unclear. Here, we report efficient generation of knock-in transgenic zebrafish that have cell-type specific Gal4 or reporter gene expression. A donor plasmid containing a heat-shock promoter was co-injected with a short guide RNA (sgRNA) targeted for genome digestion, a sgRNA targeted for donor plasmid digestion, and Cas9 mRNA. We have succeeded in establishing stable knock-in transgenic fish with several different constructs for 4 genetic loci at a frequency being exceeding 25%. Due to its simplicity, design flexibility, and high efficiency, we propose that CRISPR/Cas9-mediated knock-in will become a standard method for the generation transgenic zebrafish.


Uchiyama I.,National Institutes of Natural science | Uchiyama I.,Japan National Institute for Basic Biology | Mihara M.,Dynacom Co. | Nishide H.,Japan National Institute for Basic Biology | Chiba H.,National Institutes of Natural science
Nucleic Acids Research | Year: 2013

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire mi-crobial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity. © The Author(s) 2012.


Kimura Y.,National Institutes of Natural science | Satou C.,National Institutes of Natural science | Fujioka S.,Kyoto University | Shoji W.,Tohoku University | And 4 more authors.
Current Biology | Year: 2013

Background: During locomotion in vertebrates, reticulospinal neurons in the hindbrain play critical roles in providing descending excitation to the spinal cord locomotor systems. However, despite the fact that many genes that are used to classify the neuronal identities of neurons in the hindbrain have been identified, the molecular identity of the reticulospinal neurons that are critically involved in locomotor drive is not well understood. Chx10-expressing neurons (V2a neurons) are ipsilaterally projecting glutamatergic neurons in the spinal cord and the hindbrain. Many of the V2a neurons in the hindbrain are known to project to the spinal cord in zebrafish, making hindbrain V2a neurons a prime candidate in descending locomotor drive. Results: We investigated the roles of hindbrain V2a neurons using optogenetic and electrophysiological approaches. The forced activation of hindbrain V2a neurons using channelrhodopsin efficiently evoked swimming, whereas the forced inactivation of them using Archearhodopsin3 or Halorhodpsin reliably stopped ongoing swimming. Electrophysiological recordings of two populations of hindbrain reticulospinal V2a neurons showed that they were active during swimming. One population of neurons, small V2a neurons in the caudal hindbrain, fired with low rhythmicity, whereas the other population of neurons, large reticulospinal V2a neurons, called MiV1 neurons, fired more rhythmically. Conclusions: These results indicated that hindbrain reticulospinal V2a neurons play critical roles in providing excitation to the spinal locomotor circuits during swimming by providing both tonic and phasic inputs to the circuits. © 2013 Elsevier Ltd.


Patent
Canon Kabushiki Kaisha and National Institutes Of Natural Science | Date: 2014-10-29

A shape calculation apparatus obtains measurement data of a first shape of a first partial region on a surface to be measured, and obtains measurement data of a second shape of a second partial region partially overlapping the first partial region on the surface to be measured. The apparatus determines a first shape correction parameter and a second correction parameter so that the value of an evaluation function for evaluating shape data obtained by correcting the measurement data of the first and second shapes by the first shape correction parameter and the second correction parameter falls within a tolerance range. The apparatus generates shape data of an entire region including the first and second partial regions by respectively correcting the measurement data of the first and second shapes using the first shape correction parameter and the second correction parameter, and combining the corrected shape data.


Kimori Y.,National Institutes of Natural science
Journal of Clinical Bioinformatics | Year: 2011

Background: Medical image processing is essential in many fields of medical research and clinical practice because it greatly facilitates early and accurate detection and diagnosis of diseases. In particular, contrast enhancement is important for optimal image quality and visibility. This paper proposes a new image processing method for enhancing morphological features of masses and other abnormalities in medical images.Method: The proposed method involves two steps: (1) selective extraction of target features by mathematical morphology and (2) enhancement of the extracted features by two contrast modification techniques.Results: The goal of the proposed method is to enable enhancement of fine morphological features of a lesion region with high suppression of surrounding tissues. The effectiveness of the method was evaluated in quantitative terms of the contrast improvement ratio. The results clearly show that the method outperforms five conventional contrast enhancement methods. The effectiveness and usefulness of the proposed method were further demonstrated by application to three types of medical images: a mammographic image, a chest radiographic image, and a retinal image.Conclusion: The proposed method enables specific extraction and enhancement of mass lesions, which is essential for clinical diagnosis based on medical image analysis. Thus, the method can be expected to achieve automatic recognition of lesion location and quantitative analysis of legion morphology. © 2011 Kimori; licensee BioMed Central Ltd.


Kimori Y.,National Institutes of Natural science
Journal of Synchrotron Radiation | Year: 2013

Image processing methods significantly contribute to visualization of images captured by biomedical modalities (such as mammography, X-ray computed tomography, magnetic resonance imaging, and light and electron microscopy). Quantitative interpretation of the deluge of complicated biomedical images, however, poses many research challenges, one of which is to enhance structural features that are scarcely perceptible to the human eye. This study introduces a contrast enhancement approach based on a new type of mathematical morphology called rotational morphological processing. The proposed method is applied to medical images for the enhancement of structural features. The effectiveness of the method is evaluated quantitatively by the contrast improvement ratio (CIR). The CIR of the proposed method is 12.1, versus 4.7 and 0.1 for two conventional contrast enhancement methods, clearly indicating the high contrasting capability of the method.


Kimura T.,National Institutes of Natural science
Journal of Cutaneous Medicine and Surgery | Year: 2011

Background/Objective: In previous studies, the author noticed hypertrophic scar formation in hairless dogs. The purpose of this study was to evaluate both grossly and histopathologically hypertrophic scars in hairless dogs to explore any similarities with hypertrophic scars in humans and to introduce these dogs as an appropriate model for further investigation on hypertrophic scarring. Methods: Full-thickness wounds were made on the dorsolumbar skin of hairless dogs. Hypertrophic scarring was examined with three methods: clinical observations, dihydroxyphenylalanine (DOPA)-positive melanocytes, and skin histopathology. Results: Hairless dogs clinically developed the formation of hyperpigmented and hypertrophic scars that did not extend beyond the original wound margins. In hypertrophic scars of hairless dogs, the split epidermal sheet showed an increased number of DOPA-positive melanocytes with well-developed dendrites exhibiting activated melanocytes. There were very few DOPA-positive melanocytes in the repaired skin of haired dogs. Histopathologic examinations demonstrated that hypertrophic scars were fully reepithelialized and granulation tissue formation was accompanied by inflammatory cell infiltration. There was remodeling of thick collagens and fine elastic fibers in the course of hypertrophic scar formation. Conclusion: Experimental hypertrophic scars produced in hairless dogs have morphologic properties similar to those of human hypertrophic scars. © 2011 Canadian Dermatology Association.


Patent
National Institutes Of Natural Science | Date: 2015-06-01

A kinematic support structure of a groove-groove-groove type that reduces friction between a first base and a second base is provided. In the kinematic support structure, a first base comprises three grooves and a second base comprises three other grooves. Balls are all movable with respect to the first base and the second base. Two grooves corresponding in the two bases face each other across respective one of the balls.


Patent
National Institutes Of Natural Science | Date: 2015-12-30

A kinematic support structure of a groove - groove - groove type that reduces friction between a first base and a second base is provided. In a kinematic support structure (100), a first base (110) comprises three grooves (111, 112, 113) and a second base (120) comprises three other grooves (121, 122, 123). Balls (130, 140, 150) are all movable with respect to the first base (110) and the second base (120). Two grooves corresponding in the two bases face each other across respective one of the balls.

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