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  1. Article ; Online: O-Linked N-Acetylglucosamine Transferase Ensures Survival of Mouse Fetal Liver Hematopoietic Progenitors Partly by Regulating Bcl-xL and Oxidative Phosphorylation.

    Soma, Shunsuke / Murakami, Koichi / Fukuchi, Yumi / Kunimoto, Hiroyoshi / Nakajima, Hideaki

    Stem cells (Dayton, Ohio)

    2024  Volume 42, Issue 1, Page(s) 55–63

    Abstract: O-linked N-acetylglucosamine transferase (OGT) critically regulates wide variety of biological processes such as gene expression, metabolism, stress response, signaling and proteostasis. In adult hematopoiesis, OGT is crucial for differentiation of B and ...

    Abstract O-linked N-acetylglucosamine transferase (OGT) critically regulates wide variety of biological processes such as gene expression, metabolism, stress response, signaling and proteostasis. In adult hematopoiesis, OGT is crucial for differentiation of B and T cells and the maintenance of hematopoietic stem cells (HSCs). However, a role for OGT in fetal liver (FL) hematopoiesis remains unknown. To investigate a role for OGT in FL hematopoiesis, we conditionally disrupted OGT in hematopoietic cells in developing FLs. Hematopoietic specific disruption of OGT resulted in embryonic lethality in late stage of gestation due to severe anemia and growth retardation. OGT loss led to profound reduction of differentiating erythroid cells and erythroid progenitors in FLs due to massive apoptosis. In addition, clonogenic capacity of FL cells was severely impaired by OGT loss. Interestingly, expression of BCL-XL, a well-known inhibitor of apoptosis in FL cells, dramatically decreased, and the levels of reactive oxygen species (ROS) were increased in OGT-deficient FL cells. Overexpression of Bcl-xL and reduction of ROS significantly restored the colony formation of OGT-deficient FL cells. This study revealed a novel role for OGT during embryogenesis, which ensures survival of FL hematopoietic cells partly by regulating Bcl-xL and oxidative phosphorylation.
    MeSH term(s) Mice ; Animals ; Oxidative Phosphorylation ; Reactive Oxygen Species/metabolism ; Cell Differentiation ; N-Acetylglucosaminyltransferases/genetics ; Liver/metabolism
    Chemical Substances UDP-N-acetylglucosamine-peptide beta-N-acetylglucosaminyltransferase (EC 2.4.1.-) ; Reactive Oxygen Species ; N-Acetylglucosaminyltransferases (EC 2.4.1.-)
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1143556-2
    ISSN 1549-4918 ; 1066-5099
    ISSN (online) 1549-4918
    ISSN 1066-5099
    DOI 10.1093/stmcls/sxad076
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: O-GlcNAcylation: Implications in normal and malignant hematopoiesis.

    Nakajima, Hideaki / Murakami, Koichi

    Experimental hematology

    2021  Volume 101-102, Page(s) 16–24

    Abstract: Posttranslational protein modification through addition of the O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) moiety to serine or threonine residues, termed O-GlcNAcylation, is a highly dynamic process conserved throughout eukaryotes. O-GlcNAcylation is ... ...

    Abstract Posttranslational protein modification through addition of the O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) moiety to serine or threonine residues, termed O-GlcNAcylation, is a highly dynamic process conserved throughout eukaryotes. O-GlcNAcylation is reversibly catalyzed by a single pair of enzymes, O-GlcNAc transferase and O-GlcNAcase, and it acts as a fundamental regulator for a wide variety of biological processes including gene expression, cell cycle regulation, metabolism, stress response, cellular signaling, epigenetics, and proteostasis. O-GlcNAcylation is regulated by various intracellular or extracellular cues such as metabolic status, nutrient availability, and stress. Studies over decades have unveiled the profound biological significance of this unique protein modification in normal physiology and pathologic processes of diverse cell types or tissues. In hematopoiesis, recent studies have indicated the essential and pleiotropic roles of O-GlcNAcylation in differentiation, proliferation, and function of hematopoietic cells including T cells, B cells, myeloid progenitors, and hematopoietic stem and progenitor cells. Moreover, aberrant O-GlcNAcylation is implicated in the development of hematologic malignancies with dysregulated epigenetics, metabolism, and gene transcription. Thus, it is now recognized that O-GlcNAcylation is one of the key regulators of normal and malignant hematopoiesis.
    MeSH term(s) Acetylglucosamine/genetics ; Acetylglucosamine/metabolism ; Animals ; Epigenesis, Genetic ; Hematologic Neoplasms/genetics ; Hematologic Neoplasms/metabolism ; Hematologic Neoplasms/pathology ; Hematopoiesis ; Hematopoietic Stem Cells/metabolism ; Hematopoietic Stem Cells/pathology ; Humans ; Protein Processing, Post-Translational
    Chemical Substances Acetylglucosamine (V956696549)
    Language English
    Publishing date 2021-07-22
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 185107-x
    ISSN 1873-2399 ; 0531-5573 ; 0301-472X
    ISSN (online) 1873-2399
    ISSN 0531-5573 ; 0301-472X
    DOI 10.1016/j.exphem.2021.07.003
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  3. Article: High-power laser irradiation for high-temperature in situ transmission electron microscopy

    Uemura, Naoki / Egoshi, Tomoya / Murakami, Koichi / Kizuka, Tokushi

    Micron. 2022 June, v. 157

    2022  

    Abstract: We developed high temperature in situ transmission electron microscopy using a high-density laser irradiation device (nominal maximum laser density ~9.4 GW/m²) and a corresponding heat shielding sample mount device. The spatial line resolution of the ... ...

    Abstract We developed high temperature in situ transmission electron microscopy using a high-density laser irradiation device (nominal maximum laser density ~9.4 GW/m²) and a corresponding heat shielding sample mount device. The spatial line resolution of the microscope was maintained to be 0.14 nm at ambient temperatures after the installation of the laser irradiation device. The system was applied to the investigation of high temperature structural variation in tungsten plates. When the laser power was increased up to irradiation densities of approximately 61–280 MW/m² (laser source output: 130–590 mW) to degrade tungsten plates, the microscope was undamaged. The surface dynamics was observed in situ by lattice imaging at irradiation densities of approximately 61–75 MW/m² (laser source output: 130–160 mW); the spatial line resolution of the microscope was maintained to be 0.23 nm at high temperatures. It was expected that high temperature observation is realized using this heating system, which can be applied to the investigation of various advanced heat-resistant materials. We found using this heating system that degradation in tungsten plates started from surfaces and progressed through the preferential generation of characteristic defects, such as atomistic and nanometer holes and rods, and their subsequent evolution in thinner regions during the heating. It was demonstrated that the holes and rod were truncated with {110} sidewalls, i.e., these surfaces were stable in tungsten at high temperatures.
    Keywords heat ; irradiation ; transmission electron microscopy ; tungsten
    Language English
    Dates of publication 2022-06
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 207808-9
    ISSN 1878-4291 ; 0047-7206 ; 0968-4328
    ISSN (online) 1878-4291
    ISSN 0047-7206 ; 0968-4328
    DOI 10.1016/j.micron.2022.103244
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: High-power laser irradiation for high-temperature in situ transmission electron microscopy.

    Uemura, Naoki / Egoshi, Tomoya / Murakami, Koichi / Kizuka, Tokushi

    Micron (Oxford, England : 1993)

    2022  Volume 157, Page(s) 103244

    Abstract: We developed high temperature in situ transmission electron microscopy using a high-density laser irradiation device (nominal maximum laser density ~9.4 GW/ ... ...

    Abstract We developed high temperature in situ transmission electron microscopy using a high-density laser irradiation device (nominal maximum laser density ~9.4 GW/m
    Language English
    Publishing date 2022-03-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 207808-9
    ISSN 1878-4291 ; 0047-7206 ; 0968-4328
    ISSN (online) 1878-4291
    ISSN 0047-7206 ; 0968-4328
    DOI 10.1016/j.micron.2022.103244
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Acute peritonitis caused by the acute pancreatitis of an ectopic pancreas in a jejunal duplication, in an adult with intestinal malrotation: a case report.

    Yoshikawa, Chihiro / Migita, Kazuhiro / Yamato, Ichiro / Ueno, Masato / Kashizuka, Hisanori / Murakami, Koichi / Ishikawa, Hirofumi

    Surgical case reports

    2023  Volume 9, Issue 1, Page(s) 150

    Abstract: Background: Intestinal duplication and ectopic pancreas are two rare independent congenital anomalies. Few reports describe cases of patients with ectopic pancreas in an intestinal duplication causing acute peritonitis.: Case presentation: A 31-year- ... ...

    Abstract Background: Intestinal duplication and ectopic pancreas are two rare independent congenital anomalies. Few reports describe cases of patients with ectopic pancreas in an intestinal duplication causing acute peritonitis.
    Case presentation: A 31-year-old man was admitted to the hospital for epigastric pain. The patient was diagnosed with acute peritonitis caused by the acute pancreatitis of an ectopic pancreas in a jejunal duplication, with intestinal malrotation. The patient underwent the partial resection of the jejunum and Ladd's procedure. The histopathological findings indicated ectopic pancreatitis in the jejunal duplication.
    Conclusions: We presented the case of acute peritonitis caused by the acute pancreatitis of an ectopic pancreas in a jejunal duplication in an adult with intestinal malrotation. Surgery is the primary treatment and is necessary for a definitive diagnosis.
    Language English
    Publishing date 2023-08-28
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2809613-7
    ISSN 2198-7793
    ISSN 2198-7793
    DOI 10.1186/s40792-023-01736-2
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  6. Article ; Online: ABCG2, CD44 and SOX9 are increased with the acquisition of drug resistance and involved in cancer stem cell activities in head and neck squamous cell carcinoma cells.

    Murakami, Koichi / Umemura, Naoki / Adachi, Makoto / Motoki, Masahiro / Ohkoshi, Emika

    Experimental and therapeutic medicine

    2022  Volume 24, Issue 6, Page(s) 722

    Abstract: Cancer stem cells are a sub-population of cancer cells with self-renewal activity that play key roles in tumor resistance to chemotherapy and radiation. Several cancer stem cell markers have been identified to correlate with clinical prognosis. However, ... ...

    Abstract Cancer stem cells are a sub-population of cancer cells with self-renewal activity that play key roles in tumor resistance to chemotherapy and radiation. Several cancer stem cell markers have been identified to correlate with clinical prognosis. However, which marker is associated with which cancer stem cell characteristic is unclear. The present study aimed to clarify the relationship between cancer stem cell markers associated with drug resistance acquisition and the characteristics of cancer stem cells. We generated cisplatin-resistant head and neck squamous cell carcinoma cells by culturing cells in increasing concentrations of cisplatin. The cisplatin-resistant head and neck squamous cell carcinoma cells also acquired multidrug resistance and were named resistant HSC-3 (R HSC-3) cells. R HSC-3 showed no differences in cell proliferation or cell cycle distributions compared with parental cells. R HSC-3 cells showed increased drug excretion ability and elevated expression of ATP-binding cassette subfamily G member 2 (ABCG2), a drug excretion pump. R HSC-3 cells also highly expressed CD44, a cancer stem cell marker, and exhibited enhanced cell invasion and spheroid formation abilities. Furthermore, the stem cell-related factor SRY-box transcription factor 9 (SOX9) was identified as increased in R HSC-3 cells by microarray analysis. Knockdown experiments showed that SOX9 and ABCG2 were involved in the drug excretion ability of R HSC3 cells and ABCG2 was involved in the spheroid formation ability of R HSC-3 cells. These results indicate that CD44, SOX9 and ABCG2 expression levels were enhanced in head and neck squamous cell carcinoma cells that acquired multidrug resistance and that these molecules are important for maintaining cancer stem cell characteristics. Overall, regulating CD44, SOX9 and ABCG2 may be a strategy to inhibit cancer stem cells.
    Language English
    Publishing date 2022-10-18
    Publishing country Greece
    Document type Journal Article
    ZDB-ID 2683844-8
    ISSN 1792-1015 ; 1792-0981
    ISSN (online) 1792-1015
    ISSN 1792-0981
    DOI 10.3892/etm.2022.11658
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  7. Article ; Online: Pan-Cancer Comparative and Integrative Analyses of Driver Alterations Using Japanese and International Genomic Databases.

    Horie, Sara / Saito, Yuki / Kogure, Yasunori / Mizuno, Kota / Ito, Yuta / Tabata, Mariko / Kanai, Takanori / Murakami, Koichi / Koya, Junji / Kataoka, Keisuke

    Cancer discovery

    2024  Volume 14, Issue 5, Page(s) 786–803

    Abstract: Using 48,627 samples from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), we present a pan-cancer landscape of driver alterations and their clinical actionability in Japanese patients. Comparison with White patients in Genomics Evidence ...

    Abstract Using 48,627 samples from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), we present a pan-cancer landscape of driver alterations and their clinical actionability in Japanese patients. Comparison with White patients in Genomics Evidence Neoplasia Information Exchange (GENIE) demonstrates high TP53 mutation frequencies in Asian patients across multiple cancer types. Integration of C-CAT, GENIE, and The Cancer Genome Atlas data reveals many cooccurring and mutually exclusive relationships between driver mutations. At pathway level, mutations in epigenetic regulators frequently cooccur with PI3K pathway molecules. Furthermore, we found significant cooccurring mutations within the epigenetic pathway. Accumulation of mutations in epigenetic regulators causes increased proliferation-related transcriptomic signatures. Loss-of-function of many epigenetic drivers inhibits cell proliferation in their wild-type cell lines, but this effect is attenuated in those harboring mutations of not only the same but also different epigenetic drivers. Our analyses dissect various genetic properties and provide valuable resources for precision medicine in cancer.
    Significance: We present a genetic landscape of 26 principal cancer types/subtypes, including Asian-prevalent ones, in Japanese patients. Multicohort data integration unveils numerous cooccurring and exclusive relationships between driver mutations, identifying cooccurrence of multiple mutations in epigenetic regulators, which coordinately cause transcriptional and phenotypic changes. These findings provide insights into epigenetic regulator-driven oncogenesis. This article is featured in Selected Articles from This Issue, p. 695.
    MeSH term(s) Humans ; Neoplasms/genetics ; Genomics/methods ; Mutation ; Databases, Genetic ; Japan ; Epigenesis, Genetic ; Asian People/genetics ; East Asian People
    Language English
    Publishing date 2024-01-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comparative Study
    ZDB-ID 2625242-9
    ISSN 2159-8290 ; 2159-8274
    ISSN (online) 2159-8290
    ISSN 2159-8274
    DOI 10.1158/2159-8290.CD-23-0902
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  8. Article: Honeycomb liver abscess.

    Mori, Nobuaki / Murakami, Koichi

    IDCases

    2017  Volume 8, Page(s) 66–67

    Language English
    Publishing date 2017-03-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2745454-X
    ISSN 2214-2509
    ISSN 2214-2509
    DOI 10.1016/j.idcr.2017.03.009
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  9. Article: Development of a Flexible MEMS Sensor for Subsonic Flow.

    Murakami, Koichi / Shiraishi, Daiki / Mizumi, Shunsuke / Oya, Yoshiko / Omura, Naoto / Shibata, Takanori / Ichikawa, Yoshiyasu / Motosuke, Masahiro

    Micromachines

    2022  Volume 13, Issue 8

    Abstract: Detection and control of flow separation is a key to improving the efficiency of fluid machinery. In this study, we developed a flexible MEMS (microelectromechanical systems) sensor for measuring the wall shear stress and flow angle in subsonic airflow. ... ...

    Abstract Detection and control of flow separation is a key to improving the efficiency of fluid machinery. In this study, we developed a flexible MEMS (microelectromechanical systems) sensor for measuring the wall shear stress and flow angle in subsonic airflow. The developed sensor is made of a flexible polyimide film and a microheater surrounded by three temperature sensor pairs. The sensor measures the wall shear stress from the heater output and the flow angle from the temperature gradient around the heater. The geometry and design of the heater and temperature sensors were determined based on numerical simulations. To evaluate the validity of the sensor, we conducted an experiment to measure the wall shear stress and the flow angle in a wind tunnel in different velocities ranging from 30 m/s to 170 m/s, equivalent to Mach numbers from 0.1 to 0.5. The heater output was proportional to one-third power of the wall shear stress. Additionally, the bridge output correlating the temperature difference between two opposing temperature sensors showed sinusoidal variation depending on the flow angle. Consequently, we have clarified that the developed sensor can measure both the wall shear stress and flow direction in subsonic flow.
    Language English
    Publishing date 2022-08-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2620864-7
    ISSN 2072-666X
    ISSN 2072-666X
    DOI 10.3390/mi13081299
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  10. Article ; Online: MPEXS-DNA, a new GPU-based Monte Carlo simulator for track structures and radiation chemistry at subcellular scale.

    Okada, Shogo / Murakami, Koichi / Incerti, Sebastien / Amako, Katsuya / Sasaki, Takashi

    Medical physics

    2019  Volume 46, Issue 3, Page(s) 1483–1500

    Abstract: Purpose: Track structure simulation codes can accurately reproduce the stochastic nature of particle-matter interactions in order to evaluate quantitatively radiation damage in biological cells such as DNA strand breaks and base damage. Such simulations ...

    Abstract Purpose: Track structure simulation codes can accurately reproduce the stochastic nature of particle-matter interactions in order to evaluate quantitatively radiation damage in biological cells such as DNA strand breaks and base damage. Such simulations handle large numbers of secondary charged particles and molecular species created in the irradiated medium. Every particle and molecular species are tracked step-by-step using a Monte Carlo method to calculate energy loss patterns and spatial distributions of molecular species inside a cell nucleus with high spatial accuracy. The Geant4-DNA extension of the Geant4 general-purpose Monte Carlo simulation toolkit allows for such track structure simulations and can be run on CPUs. However, long execution times have been observed for the simulation of DNA damage in cells. We present in this work an improvement of the computing performance of such simulations using ultraparallel processing on a graphical processing unit (GPU).
    Methods: A new Monte Carlo simulator named MPEXS-DNA, allowing high computing performance by using a GPU, has been developed for track structure and radiolysis simulations at the subcellular scale. MPEXS-DNA physics and chemical processes are based on Geant4-DNA processes available in Geant4 version 10.02 p03. We have reimplemented the Geant4-DNA process codes of the physics stage (electromagnetic processes of charged particles) and the chemical stage (diffusion and chemical reactions for molecular species) for microdosimetry simulation by using the CUDA language. MPEXS-DNA can calculate a distribution of energy loss in the irradiated medium caused by charged particles and also simulate production, diffusion, and chemical interactions of molecular species from water radiolysis to quantitatively assess initial damage to DNA. The validation of MPEXS-DNA physics and chemical simulations was performed by comparing various types of distributions, namely the radial dose distributions for the physics stage, and the G-value profiles for each chemical product and their linear energy transfer dependency for the chemical stage, to existing experimental data and simulation results obtained by other simulation codes, including PARTRAC.
    Results: For physics validation, radial dose distributions calculated by MPEXS-DNA are consistent with experimental data and numerical simulations. For chemistry validation, MPEXS-DNA can also reproduce G-value profiles for each molecular species with the same tendency as existing experimental data. MPEXS-DNA also agrees with simulations by PARTRAC reasonably well. However, we have confirmed that there are slight discrepancies in G-value profiles calculated by MPEXS-DNA for molecular species such as H
    Conclusion: The MPEXS-DNA Monte Carlo simulation achieves similar accuracy to Monte Carlo simulations performed using other codes such as Geant4-DNA and PARTRAC, and its predictions are consistent with experimental data. Notably, MPEXS-DNA allows calculations that are, at maximum, 2900 times faster than conventional simulations using a CPU.
    MeSH term(s) Computer Simulation ; DNA/chemistry ; DNA/radiation effects ; DNA Damage ; Electrons ; Humans ; Linear Energy Transfer ; Models, Chemical ; Monte Carlo Method ; Pulse Radiolysis ; Radiochemistry ; User-Computer Interface ; Water/chemistry
    Chemical Substances Water (059QF0KO0R) ; DNA (9007-49-2)
    Language English
    Publishing date 2019-01-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 188780-4
    ISSN 2473-4209 ; 0094-2405
    ISSN (online) 2473-4209
    ISSN 0094-2405
    DOI 10.1002/mp.13370
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