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  1. Article ; Online: Landscape of semi-extractable RNAs across five human cell lines.

    Zeng, Chao / Chujo, Takeshi / Hirose, Tetsuro / Hamada, Michiaki

    Nucleic acids research

    2023  Volume 51, Issue 15, Page(s) 7820–7831

    Abstract: Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability using the conventional RNA extraction method, and can be efficiently retrieved by needle shearing or heating during RNA extraction. Semi-extractable RNAs ... ...

    Abstract Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability using the conventional RNA extraction method, and can be efficiently retrieved by needle shearing or heating during RNA extraction. Semi-extractable RNAs are promising resources for understanding RNA-centric phase separation. However, limited assessments have been performed to systematically identify and characterize semi-extractable RNAs. In this study, 1074 semi-extractable RNAs, including ASAP1, DANT2, EXT1, FTX, IGF1R, LIMS1, NEAT1, PHF21A, PVT1, SCMH1, STRG.3024.1, TBL1X, TCF7L2, TVP23C-CDRT4, UBE2E2, ZCCHC7, ZFAND3 and ZSWIM6, which exhibited consistent semi-extractability were identified across five human cell lines. By integrating publicly available datasets, we found that semi-extractable RNAs tend to be distributed in the nuclear compartments but are dissociated from the chromatin. Long and repeat-containing semi-extractable RNAs act as hubs to provide global RNA-RNA interactions. Semi-extractable RNAs were divided into four groups based on their k-mer content. The NEAT1 group preferred to interact with paraspeckle proteins, such as FUS and NONO, implying that RNAs in this group are potential candidates of architectural RNAs that constitute nuclear bodies.
    MeSH term(s) Humans ; Cell Line ; Cell Nucleus/metabolism ; Chromatin/metabolism ; DNA-Binding Proteins/genetics ; RNA/isolation & purification ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism
    Chemical Substances Chromatin ; DNA-Binding Proteins ; RNA (63231-63-0) ; RNA, Long Noncoding
    Language English
    Publishing date 2023-07-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad567
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Optimization of body configuration and joint-driven attitude stabilization for transformable spacecrafts under solar radiation pressure

    Kubo, Yuki / Chujo, Toshihiro

    2023  

    Abstract: A solar sail is one of the most promising space exploration system because of its theoretically infinite specific impulse using solar radiation pressure (SRP). Recently, some researchers proposed "transformable spacecrafts" that can actively reconfigure ... ...

    Abstract A solar sail is one of the most promising space exploration system because of its theoretically infinite specific impulse using solar radiation pressure (SRP). Recently, some researchers proposed "transformable spacecrafts" that can actively reconfigure their body configurations with actuatable joints. The transformable spacecrafts are expected to greatly enhance orbit and attitude control capability due to its high redundancy in control degree of freedom if they are used like solar sails. However, its large number of input poses difficulties in control, and therefore, previous researchers imposed strong constraints to limit its potential control capabilities. This paper addresses novel attitude control techniques for the transformable spacecrafts under SRP. The authors have constructed two proposed methods; one of those is a joint angle optimization to acquire arbitrary SRP force and torque, and the other is a momentum damping control driven by joint angle actuation. Our proposed methods are formulated in general forms and applicable to any transformable spacecraft that has front faces that can dominantly receive SRP on each body. Validity of the proposed methods are confirmed by numerical simulations. This paper contributes to making most of the high control redundancy of transformable spacecrafts without consuming any expendable propellants, which is expected to greatly enhance orbit and attitude control capability.

    Comment: 16 pages, 11 figures, submitted to Astrodynamics published by Tsinghua University Press and Springer
    Keywords Computer Science - Machine Learning ; Computer Science - Robotics ; Mathematics - Optimization and Control
    Subject code 629
    Publishing date 2023-01-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications.

    Chujo, Takeshi / Tomizawa, Kazuhito

    The FEBS journal

    2021  Volume 288, Issue 24, Page(s) 7096–7122

    Abstract: tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability ...

    Abstract tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as 'tRNA modopathies'. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
    MeSH term(s) Brain Diseases/metabolism ; Brain Diseases/pathology ; Humans ; Kidney Diseases/metabolism ; Kidney Diseases/pathology ; Mitochondrial Diseases/metabolism ; Mitochondrial Diseases/pathology ; RNA Processing, Post-Transcriptional/genetics ; RNA, Transfer/genetics ; RNA, Transfer/metabolism
    Chemical Substances RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2021-02-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15736
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications

    Chujo, Takeshi / Tomizawa, Kazuhito

    FEBS journal. 2021 Dec., v. 288, no. 24

    2021  

    Abstract: tRNA molecules are post‐transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability ...

    Abstract tRNA molecules are post‐transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life‐threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as ‘tRNA modopathies’. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
    Keywords brain ; enzymes ; humans ; kidneys ; mitochondria ; pathogenesis ; protein synthesis ; transfer RNA
    Language English
    Dates of publication 2021-12
    Size p. 7096-7122.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note REVIEW
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15736
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Talonavicular Arthrodesis Using a Screw and Compression Staple in a Patient With Bipartite Navicular Bone: A Case Report.

    Chujo, Taro / Nakasa, Tomoyuki / Ikuta, Yasunari / Kawabata, Shingo / Adachi, Nobuo

    Cureus

    2023  Volume 15, Issue 8, Page(s) e43122

    Abstract: The bipartite navicular bone is a relatively rare pathological condition in which the navicular bone is segmented. As a high nonunion rate in talonavicular arthrodesis of the foot has been reported, an effective fixation method is required to achieve ... ...

    Abstract The bipartite navicular bone is a relatively rare pathological condition in which the navicular bone is segmented. As a high nonunion rate in talonavicular arthrodesis of the foot has been reported, an effective fixation method is required to achieve bone union. A compression staple can provide a persistent strong compressive force on the bone surface, which is advantageous for arthrodesis, especially for the joints with a high incidence of nonunion. A 13-year-old boy presenting with left foot pain was diagnosed with bipartite navicular. Imaging of the left foot showed that the navicular bone was divided into two parts and flatfoot deformity. After the failure of conservative treatment, talonavicular arthrodesis was performed. The lateral fragment was removed, and the talar and medial fragments were fixed using a cannulated cancellous screw (CCS) (Ace Medical, El Segundo, CA, USA) and compression staple (DynaNite, 15 mm × 12 mm, Arthrex, Inc., Naples, USA) to correct the flatfoot. Bone union was achieved, and flatfoot improved. Thirteen months postoperatively, his symptoms disappeared, and all categories of the Self-Administered Foot Evaluation Questionnaire scored 100 points. Although the bipartite navicular bone has no established treatment due to its rareness, talonavicular arthrodesis using a combination of CCS and compression staple yields good short-term clinical outcomes including good alignment.
    Language English
    Publishing date 2023-08-08
    Publishing country United States
    Document type Case Reports
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.43122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Paediatric case of group A streptococcal pharyngitis, arthritis and osteomyelitis associated with dental neglect.

    Hiraoka, Tomohiro / Chujo, Taro / Tsuge, Mitsuru / Kondo, Yoichi

    BMJ case reports

    2021  Volume 14, Issue 1

    Abstract: Group A streptococcus (GAS) causes a wide variety of infections in the paediatric population, ranging from pharyngitis to rare but severe invasive diseases, such as bacterial arthritis and osteomyelitis. Dental neglect is a type of child neglect in which ...

    Abstract Group A streptococcus (GAS) causes a wide variety of infections in the paediatric population, ranging from pharyngitis to rare but severe invasive diseases, such as bacterial arthritis and osteomyelitis. Dental neglect is a type of child neglect in which caregivers fail to provide adequate care and treatment for dental diseases. This results in poor oral hygiene and can lead to complications including sepsis. We report the case of a 4-year-old boy, suffering from child neglect, presenting with GAS pharyngitis and subsequent bacterial arthritis in the right ankle, osteomyelitis in the right talus and abscess in the right calcaneus. He was first treated with penicillin, which was changed to clindamycin because of a suspected drug-induced rash. He was discharged after 6 weeks of intravenous therapy when symptoms had resolved and inflammatory markers were within the normal range. The case highlights that dental neglect may present a risk for subsequent invasive infections.
    MeSH term(s) Arthritis, Infectious/diagnosis ; Arthritis, Infectious/microbiology ; Child, Preschool ; Humans ; Male ; Oral Hygiene ; Osteomyelitis/diagnosis ; Osteomyelitis/microbiology ; Pharyngitis/diagnosis ; Pharyngitis/microbiology ; Streptococcal Infections/diagnosis ; Streptococcus pyogenes/isolation & purification
    Language English
    Publishing date 2021-01-18
    Publishing country England
    Document type Case Reports ; Journal Article
    ISSN 1757-790X
    ISSN (online) 1757-790X
    DOI 10.1136/bcr-2020-239196
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Genetic Study of

    Kokubun, Katsutoshi / Yamamoto, Kei / Akashi, Yoshihiko / Chujo, Takatoshi / Nakajima, Kei / Matsuzaka, Kenichi

    International journal of surgical pathology

    2022  Volume 30, Issue 4, Page(s) 378–384

    Abstract: Background and ... ...

    Abstract Background and aim
    MeSH term(s) Ameloblastoma/genetics ; Humans ; Japan ; Mutation ; Odontogenic Tumors/genetics ; Proto-Oncogene Proteins B-raf/genetics ; Smoothened Receptor/genetics
    Chemical Substances SMO protein, human ; Smoothened Receptor ; BRAF protein, human (EC 2.7.11.1) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1)
    Language English
    Publishing date 2022-01-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1336393-1
    ISSN 1940-2465 ; 1066-8969
    ISSN (online) 1940-2465
    ISSN 1066-8969
    DOI 10.1177/10668969211064203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Nuclear Bodies Built on Architectural Long Noncoding RNAs: Unifying Principles of Their Construction and Function.

    Chujo, Takeshi / Hirose, Tetsuro

    Molecules and cells

    2017  Volume 40, Issue 12, Page(s) 889–896

    Abstract: Nuclear bodies are subnuclear, spheroidal, and membraneless compartments that concentrate specific proteins and/or RNAs. They serve as sites of biogenesis, storage, and sequestration of specific RNAs, proteins, or ribonucleoprotein complexes. Recent ... ...

    Abstract Nuclear bodies are subnuclear, spheroidal, and membraneless compartments that concentrate specific proteins and/or RNAs. They serve as sites of biogenesis, storage, and sequestration of specific RNAs, proteins, or ribonucleoprotein complexes. Recent studies reveal that a subset of nuclear bodies in various eukaryotic organisms is constructed using architectural long noncoding RNAs (arcRNAs). Here, we describe the unifying mechanistic principles of the construction and function of these bodies, especially focusing on liquid-liquid phase separation induced by architectural molecules that form multiple weakly adhesive interactions. We also discuss three possible advantages of using arcRNAs rather than architectural proteins to build the bodies: position-specificity, rapidity, and economy in sequestering nucleic acid-binding proteins. Moreover, we introduce two recently devised methods to discover novel arcRNA-constructed bodies; one that focuses on the RNase-sensitivity of these bodies, and another that focuses on "semi-extractability" of arcRNAs.
    MeSH term(s) Cell Nucleus/metabolism ; Humans ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2017-12-20
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1148964-9
    ISSN 0219-1032 ; 1016-8478
    ISSN (online) 0219-1032
    ISSN 1016-8478
    DOI 10.14348/molcells.2017.0263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Intraoral Minor Salivary Gland Tumors: A Retrospective, Clinicopathologic, Single-Center Study of 432 Cases in Japan and a Comparison with Epidemiological Data.

    Kokubun, Katsutoshi / Chujo, Takatoshi / Yamamoto, Kei / Akashi, Yoshihiko / Nakajima, Kei / Takano, Masayuki / Katakura, Akira / Matsuzaka, Kenichi

    Head and neck pathology

    2023  Volume 17, Issue 3, Page(s) 739–750

    Abstract: Background: Intraoral minor salivary gland tumors are relatively rare lesions with histological subtypes not commonly found in major salivary glands. This study aimed to retrospectively evaluate the clinicopathologic features of intraoral minor salivary ...

    Abstract Background: Intraoral minor salivary gland tumors are relatively rare lesions with histological subtypes not commonly found in major salivary glands. This study aimed to retrospectively evaluate the clinicopathologic features of intraoral minor salivary gland tumors from the Tokyo Dental College Hospital, Japan, and compare them with findings from other epidemiological studies.
    Methods: We conducted a retrospective clinicopathologic evaluation of 432 cases of intraoral minor salivary gland tumors [161 male (37.3%) and 271 female (62.7%) patients; mean age: 52.5 and 48.6 years for males and females, respectively; age at diagnosis: 7-87 (mean: 50.1) years] from the Tokyo Dental College Hospital between 1975 and 2022, including 283 benign tumors (65.5%) and 149 malignant tumors (34.5%).
    Results: The most common benign tumor was pleomorphic adenoma (n = 239), whereas mucoepidermoid carcinoma was the most common malignant tumor (n = 74). The mean age of patients with benign and malignant tumors was 48.4 and 53.2 years, respectively, with patients with malignant tumors being significantly older (P = 0.0042). The mean age of patients with malignant tumors was significantly higher in males (56.7 years) than in females (50.9 years) (P = 0.0376), although the mean age of patients with benign tumors did not differ by sex. Tumors were commonly located in the palate [250 cases (57.9%)]. Benign tumors were more frequent in the palate, upper lip, and buccal mucosa, whereas malignant tumors were more frequent in the palate, floor of the mouth, buccal mucosa, and retromolar area.
    Conclusions: Understanding the features of intraoral minor salivary gland tumors is useful for diagnosis. Our study provides important epidemiological data (patient differences in age at occurrence, sex, and site of origin) that will inform clinicians and researchers.
    MeSH term(s) Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Salivary Glands, Minor/pathology ; Japan/epidemiology ; Salivary Gland Neoplasms/epidemiology ; Salivary Gland Neoplasms/pathology ; Adenoma, Pleomorphic/epidemiology ; Adenoma, Pleomorphic/pathology ; Carcinoma, Mucoepidermoid/epidemiology ; Carcinoma, Mucoepidermoid/pathology ; Carcinoma, Adenoid Cystic/pathology
    Language English
    Publishing date 2023-04-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2407834-7
    ISSN 1936-0568 ; 1936-055X
    ISSN (online) 1936-0568
    ISSN 1936-055X
    DOI 10.1007/s12105-023-01551-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing.

    Iwakiri, Junichi / Tanaka, Kumiko / Chujo, Takeshi / Takakuwa, Hiro / Yamazaki, Tomohiro / Terai, Goro / Asai, Kiyoshi / Hirose, Tetsuro

    RNA (New York, N.Y.)

    2022  Volume 29, Issue 2, Page(s) 170–177

    Abstract: The mammalian cell nucleus contains dozens of membrane-less nuclear bodies that play significant roles in various aspects of gene expression. Several nuclear bodies are nucleated by specific architectural noncoding RNAs (arcRNAs) acting as structural ... ...

    Abstract The mammalian cell nucleus contains dozens of membrane-less nuclear bodies that play significant roles in various aspects of gene expression. Several nuclear bodies are nucleated by specific architectural noncoding RNAs (arcRNAs) acting as structural scaffolds. We have reported that a minor population of cellular RNAs exhibits an unusual semi-extractable feature upon using the conventional procedure of RNA preparation and that needle shearing or heating of cell lysates remarkably improves extraction of dozens of RNAs. Because semi-extractable RNAs, including known arcRNAs, commonly localize in nuclear bodies, this feature may be a hallmark of arcRNAs. Using the semi-extractability of RNA, we performed genome-wide screening of semi-extractable long noncoding RNAs to identify new candidate arcRNAs for arcRNA under hyperosmotic and heat stress conditions. After screening stress-inducible and semi-extractable RNAs, hundreds of readthrough downstream-of-gene (DoG) transcripts over several hundreds of kilobases, many of which were not detected among RNAs prepared by the conventional extraction procedure, were found to be stress-inducible and semi-extractable. We further characterized some of the abundant DoGs and found that stress-inducible transient extension of the 3'-UTR made DoGs semi-extractable. Furthermore, they were localized in distinct nuclear foci that were sensitive to 1,6-hexanediol. These data suggest that semi-extractable DoGs exhibit arcRNA-like features and our semi-extractable RNA-seq is a powerful tool to extensively monitor DoGs that are induced under specific physiological conditions.
    MeSH term(s) Animals ; Base Sequence ; Cell Nucleus/metabolism ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Mammals/genetics
    Chemical Substances RNA, Untranslated ; RNA, Long Noncoding
    Language English
    Publishing date 2022-11-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079469.122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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