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Article ; Online: Autophosphorylation and Self-Activation of DNA-Dependent Protein Kinase.

Kurosawa, Aya

2021 Volume 12, Issue 7

Abstract: The DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related kinase family, phosphorylates serine and threonine residues of substrate proteins in the presence of the Ku complex and double-stranded ... ...

Abstract	The DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related kinase family, phosphorylates serine and threonine residues of substrate proteins in the presence of the Ku complex and double-stranded DNA. Although it has been established that DNA-PKcs is involved in non-homologous end-joining, a DNA double-strand break repair pathway, the mechanisms underlying DNA-PKcs activation are not fully understood. Nevertheless, the findings of numerous in vitro and in vivo studies have indicated that DNA-PKcs contains two autophosphorylation clusters, PQR and ABCDE, as well as several autophosphorylation sites and conformational changes associated with autophosphorylation of DNA-PKcs are important for self-activation. Consistent with these features, an analysis of transgenic mice has shown that the phenotypes of DNA-PKcs autophosphorylation mutations are significantly different from those of DNA-PKcs kinase-dead mutations, thereby indicating the importance of DNA-PKcs autophosphorylation in differentiation and development. Furthermore, there has been notable progress in the high-resolution analysis of the conformation of DNA-PKcs, which has enabled us to gain a visual insight into the steps leading to DNA-PKcs activation. This review summarizes the current progress in the activation of DNA-PKcs, focusing in particular on autophosphorylation of this kinase.
MeSH term(s)	Animals ; Cell Differentiation/genetics ; DNA/metabolism ; DNA Damage/genetics ; DNA End-Joining Repair/physiology ; DNA Repair/genetics ; DNA-Activated Protein Kinase/genetics ; DNA-Activated Protein Kinase/metabolism ; DNA-Activated Protein Kinase/physiology ; DNA-Binding Proteins/genetics ; Humans ; Mice ; Mice, Transgenic ; Phosphorylation/genetics ; Phosphorylation/physiology
Chemical Substances	DNA-Binding Proteins ; DNA (9007-49-2) ; DNA-Activated Protein Kinase (EC 2.7.11.1) ; PRKDC protein, human (EC 2.7.11.1)
Language	English
Publishing date	2021-07-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12071091
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Autophosphorylation and Self-Activation of DNA-Dependent Protein Kinase

Kurosawa, Aya

Genes. 2021 July 19, v. 12, no. 7

2021

Abstract	The DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related kinase family, phosphorylates serine and threonine residues of substrate proteins in the presence of the Ku complex and double-stranded DNA. Although it has been established that DNA-PKcs is involved in non-homologous end-joining, a DNA double-strand break repair pathway, the mechanisms underlying DNA-PKcs activation are not fully understood. Nevertheless, the findings of numerous in vitro and in vivo studies have indicated that DNA-PKcs contains two autophosphorylation clusters, PQR and ABCDE, as well as several autophosphorylation sites and conformational changes associated with autophosphorylation of DNA-PKcs are important for self-activation. Consistent with these features, an analysis of transgenic mice has shown that the phenotypes of DNA-PKcs autophosphorylation mutations are significantly different from those of DNA-PKcs kinase-dead mutations, thereby indicating the importance of DNA-PKcs autophosphorylation in differentiation and development. Furthermore, there has been notable progress in the high-resolution analysis of the conformation of DNA-PKcs, which has enabled us to gain a visual insight into the steps leading to DNA-PKcs activation. This review summarizes the current progress in the activation of DNA-PKcs, focusing in particular on autophosphorylation of this kinase.
Keywords	DNA ; DNA repair ; protein kinases ; protein phosphorylation ; protein subunits ; serine ; threonine
Language	English
Dates of publication	2021-0719
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12071091
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Article ; Online: The respiratory elastance ratio in thanatophoric dysplasia: A case report.

Aoki, Kazunori / Kurosawa, Hiroshi / Shirasawa, Aya / Shiomi, Yuki / Seino, Yusuke

Pediatrics international : official journal of the Japan Pediatric Society

2023 Volume 65, Issue 1, Page(s) e15534

MeSH term(s)	Humans ; Thanatophoric Dysplasia/diagnosis ; Thanatophoric Dysplasia/genetics ; Respiration, Artificial ; Respiratory Function Tests ; Receptor, Fibroblast Growth Factor, Type 3
Chemical Substances	Receptor, Fibroblast Growth Factor, Type 3 (EC 2.7.10.1)
Language	English
Publishing date	2023-03-23
Publishing country	Australia
Document type	Case Reports ; Journal Article
ZDB-ID	1470376-2
ISSN	1442-200X ; 1328-8067
ISSN (online)	1442-200X
ISSN	1328-8067
DOI	10.1111/ped.15534
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Article ; Online: Arsenic affects homologous recombination and single-strand annealing but not end-joining pathways during DNA double-strand break repair.

Kurosawa, Aya / Saito, Shinta / Sakurai, Mikiko / Shinozuka, Mizuki / Someya, Yuduki / Adachi, Noritaka

The FEBS journal

2023 Volume 290, Issue 22, Page(s) 5313–5321

Abstract: Arsenic is a carcinogen that can cause skin, lung, and bladder cancer. While DNA double-strand breaks (DSBs) have been implicated in arsenic-induced carcinogenesis, the exact mechanism remains unclear. In this study, we performed genetic analysis to ... ...

Abstract	Arsenic is a carcinogen that can cause skin, lung, and bladder cancer. While DNA double-strand breaks (DSBs) have been implicated in arsenic-induced carcinogenesis, the exact mechanism remains unclear. In this study, we performed genetic analysis to examine the impact of arsenic trioxide (As
MeSH term(s)	Humans ; DNA Breaks, Double-Stranded ; Arsenic ; DNA Repair ; Homologous Recombination ; DNA End-Joining Repair ; DNA ; Carcinogenesis
Chemical Substances	Arsenic (N712M78A8G) ; DNA (9007-49-2)
Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16922
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Article ; Online: Effect of Lithium Compound Addition on the Dehydration and Hydration of Calcium Hydroxide as a Chemical Heat Storage Material.

Maruyama, Aya / Kurosawa, Ryo / Ryu, Junichi

ACS omega

2020 Volume 5, Issue 17, Page(s) 9820–9829

Abstract: Many studies on calcium hydroxide [Ca(OH) ...

Abstract	Many studies on calcium hydroxide [Ca(OH)
Language	English
Publishing date	2020-04-21
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.9b04444
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Article ; Online: The transcription factor NF-YA is crucial for neural progenitor maintenance during brain development.

Yamanaka, Tomoyuki / Kurosawa, Masaru / Yoshida, Aya / Shimogori, Tomomi / Hiyama, Akiko / Maity, Sankar N / Hattori, Nobutaka / Matsui, Hideaki / Nukina, Nobuyuki

The Journal of biological chemistry

2024 Volume 300, Issue 2, Page(s) 105629

Abstract: In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance ... ...

Abstract	In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.
MeSH term(s)	Animals ; Mice ; CCAAT-Binding Factor/genetics ; CCAAT-Binding Factor/metabolism ; Cerebral Cortex/cytology ; Cerebral Cortex/growth & development ; Cerebral Cortex/metabolism ; Gene Expression Regulation ; Neurogenesis ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Transcription Factors/metabolism
Chemical Substances	CCAAT-Binding Factor ; Protein Isoforms ; Transcription Factors ; Nfya protein, mouse
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.105629
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Article ; Online: A Cell System-Assisted Strategy for Evaluating the Natural Antioxidant-Induced Double-Stranded DNA Break (DSB) Style.

Someya, Yuduki / Kobayashi, Sakine / Toriumi, Kazuya / Takeda, Shigeki / Adachi, Noritaka / Kurosawa, Aya

Genes

2023 Volume 14, Issue 2

Abstract: Natural antioxidants derived from plants exert various physiological effects, including antitumor effects. However, the molecular mechanisms of each natural antioxidant have not yet been fully elucidated. Identifying the targets of natural antioxidants ... ...

Abstract	Natural antioxidants derived from plants exert various physiological effects, including antitumor effects. However, the molecular mechanisms of each natural antioxidant have not yet been fully elucidated. Identifying the targets of natural antioxidants with antitumor properties in vitro is costly and time-consuming, and the results thus obtained may not reliably reflect in vivo conditions. Therefore, to enhance understanding regarding the antitumor effects of natural antioxidants, we focused on DNA, one of the targets of anticancer drugs, and evaluated whether antioxidants, e.g., sulforaphane, resveratrol, quercetin, kaempferol, and genistein, which exert antitumor effects, induce DNA damage using gene-knockout cell lines derived from human Nalm-6 and HeLa cells pretreated with the DNA-dependent protein kinase inhibitor NU7026. Our results suggested that sulforaphane induces single-strand breaks or DNA strand crosslinks and that quercetin induces double-strand breaks. In contrast, resveratrol showed the ability to exert cytotoxic effects other than DNA damage. Our results also suggested that kaempferol and genistein induce DNA damage via unknown mechanisms. Taken together, the use of this evaluation system facilitates the analysis of the cytotoxic mechanisms of natural antioxidants.
MeSH term(s)	Humans ; DNA Breaks, Double-Stranded ; Antioxidants/pharmacology ; Kaempferols ; Resveratrol ; Quercetin ; HeLa Cells ; Genistein ; DNA
Chemical Substances	Antioxidants ; sulforaphane (GA49J4310U) ; Kaempferols ; Resveratrol (Q369O8926L) ; Quercetin (9IKM0I5T1E) ; Genistein (DH2M523P0H) ; DNA (9007-49-2)
Language	English
Publishing date	2023-02-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14020420
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effect of Lithium Compound Addition on the Dehydration and Hydration of Calcium Hydroxide as a Chemical Heat Storage Material

Aya Maruyama / Ryo Kurosawa / Junichi Ryu

ACS Omega, Vol 5, Iss 17, Pp 9820-

2020 Volume 9829

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	American Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Cell System-Assisted Strategy for Evaluating the Natural Antioxidant-Induced Double-Stranded DNA Break (DSB) Style

Someya, Yuduki / Kobayashi, Sakine / Toriumi, Kazuya / Takeda, Shigeki / Adachi, Noritaka / Kurosawa, Aya

Genes (Basel). 2023 Feb. 06, v. 14, no. 2

2023

Abstract	Natural antioxidants derived from plants exert various physiological effects, including antitumor effects. However, the molecular mechanisms of each natural antioxidant have not yet been fully elucidated. Identifying the targets of natural antioxidants with antitumor properties in vitro is costly and time-consuming, and the results thus obtained may not reliably reflect in vivo conditions. Therefore, to enhance understanding regarding the antitumor effects of natural antioxidants, we focused on DNA, one of the targets of anticancer drugs, and evaluated whether antioxidants, e.g., sulforaphane, resveratrol, quercetin, kaempferol, and genistein, which exert antitumor effects, induce DNA damage using gene-knockout cell lines derived from human Nalm-6 and HeLa cells pretreated with the DNA-dependent protein kinase inhibitor NU7026. Our results suggested that sulforaphane induces single-strand breaks or DNA strand crosslinks and that quercetin induces double-strand breaks. In contrast, resveratrol showed the ability to exert cytotoxic effects other than DNA damage. Our results also suggested that kaempferol and genistein induce DNA damage via unknown mechanisms. Taken together, the use of this evaluation system facilitates the analysis of the cytotoxic mechanisms of natural antioxidants.
Keywords	DNA ; DNA damage ; antioxidants ; crosslinking ; cytotoxicity ; genistein ; humans ; kaempferol ; protein kinases ; quercetin ; resveratrol ; sulforaphane
Language	English
Dates of publication	2023-0206
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14020420
Database	NAL-Catalogue (AGRICOLA)

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Article: Complex genetic interactions between DNA polymerase β and the NHEJ ligase

Kurosawa, Aya / Kuboshima, Hiroyuki / Adachi, Noritaka

FEBS journal. 2020 Jan., v. 287, no. 2

2020

Abstract: Mammalian cells possess multiple pathways for repairing various types of DNA damage. Although the molecular mechanisms of each DNA repair pathway have been analyzed by biochemical analysis and cell biological analysis, interplay between different ... ...

Abstract	Mammalian cells possess multiple pathways for repairing various types of DNA damage. Although the molecular mechanisms of each DNA repair pathway have been analyzed by biochemical analysis and cell biological analysis, interplay between different pathways has not been fully elucidated. In this study, using human Nalm‐6–mutant cell lines, we analyzed the relationship between the base excision repair factor DNA polymerase β (POLβ) and DNA ligase IV (LIG4), which is essential for DNA double‐strand break (DSB) repair by non‐homologous end‐joining (NHEJ). We found that cells lacking both POLβ and LIG4 grew significantly more slowly than either single mutant, indicating cooperative functions of the two proteins in normal cell growth. To further investigate the genetic interaction between POLβ and LIG4, we examined DNA damage sensitivity of the mutant cell lines. Our results suggested that NHEJ acts as a backup pathway for repairing alkylation damage (when converted into DSBs) in the absence of POLβ. Surprisingly, despite the critical role of POLβ in alkylation damage repair, cells lacking POLβ exhibited increased resistance to camptothecin (a topoisomerase I inhibitor that induces DNA single‐strand breaks), irrespective of the presence or absence of LIG4. A LIG4‐independent increased resistance associated with POLβ loss was also observed with ionizing radiation; however, cells lacking both POLβ and LIG4 were more radiosensitive than either single mutant. Taken together, our findings provide novel insight into the complex interplay between different DNA repair pathways.
Keywords	DNA ; DNA damage ; DNA repair ; DNA-directed DNA polymerase ; alkylation ; cell growth ; humans ; ligases ; mutants
Language	English
Dates of publication	2020-01
Size	p. 377-385.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15012
Database	NAL-Catalogue (AGRICOLA)

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