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Kim S, Kim HS, Yoo J. Sarcopenia classification model for musculoskeletal patients using smart insole and artificial intelligence gait analysis. J Cachexia Sarcopenia Muscle 2023; 14:2793-2803. [PMID: 37884824 PMCID: PMC10751435 DOI: 10.1002/jcsm.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/23/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND The relationship between physical function, musculoskeletal disorders and sarcopenia is intricate. Current physical function tests, such as the gait speed test and the chair stand test, have limitations in eliminating subjective influences. To overcome this, smart devices utilizing inertial measurement unit sensors and artificial intelligence (AI)-based methods are being developed. METHODS We employed cutting-edge technologies, including the smart insole device and pose estimation based on AI, along with three classification models: random forest (RF), support vector machine and artificial neural network, to classify control and sarcopenia groups. Patient data of 83 individuals were divided into train and test sets, with approximately 67% allocated for training. Classification models were implemented using RStudio, considering individual and combined variables obtained through pose estimation and smart insole measurements. RESULTS Performance evaluation of the classification models utilized accuracy, precision, recall and F1-score indicators. Using only pose estimation variables, accuracy ranged from 0.92 to 0.96, with F1-scores of 0.94-0.97. Key variables identified by the RF model were 'Hip_dif', 'Ankle_dif' and 'Hipankle_dif'. Combining variables from both methods increased accuracy to 0.80-1.00, with F1-scores of 0.73-1.00. CONCLUSIONS In our study, a classification model that integrates smart insole and pose estimation technology was assessed. The RF model showed impressive results, particularly in the case of the Hip and Ankle variables. The growth of advanced measurement technologies suggests a promising avenue for identifying and utilizing additional digital biomarkers in the management of various disorders. The convergence of AI technologies with diagnostics and treatment approaches a promising future for enhanced interventions in conditions like sarcopenia.
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Affiliation(s)
- Shinjune Kim
- Department of Biomedical Research InstituteInha University HospitalIncheonSouth Korea
| | - Hyeon Su Kim
- Department of Biomedical Research InstituteInha University HospitalIncheonSouth Korea
| | - Jun‐Il Yoo
- Department of Orthopaedic SurgeryInha University HospitalIncheonSouth Korea
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2
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Lee DH, Jo I, Lee HS, Kang J. Combined impact of myosteatosis and liver steatosis on prognosis in stage I-III colorectal cancer patients. J Cachexia Sarcopenia Muscle 2023; 14:2908-2915. [PMID: 37964719 PMCID: PMC10751431 DOI: 10.1002/jcsm.13369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Myosteatosis and liver steatosis (LS) have been recognized as patient-derived image biomarkers that correlate with prognosis in colorectal cancer (CRC) patients. However, the significance of considering fat deposition in multiple body areas simultaneously has been underestimated. This study aimed to investigate the combined effect of myosteatosis and LS in stage I-III CRC patients. METHODS A total of 616 stage I-III CRC patients were included in the study. Myosteatosis was assessed using skeletal muscle radiodensity (SMD), and LS was estimated by calculating the Hounsfield unit of the liver and spleen ratio (LSR). Cox proportional hazard models were utilized to evaluate disease-free survival (DFS). A combination of myosteatosis and LS was proposed, and its discriminatory performance was compared using the C-index. RESULTS Among the 616 participants, the median (interquartile) age was 64 (55-72) years, and 240 (38.9%) were female. The median and interquartile range of LSR were determined as 1.106 (0.967-1.225). The optimal cutoff value for LSR was identified as 1.181, leading to the classification of patients into low (410, 66.5%) and high LSR (206, 33.4%) groups. Among the patients, 200 were categorized into the low SMD group, while 416 were allocated to the high SMD group. Both myosteatosis and LS were identified as independent prognostic factors in the multivariable analysis. The combination of these two variables resulted in a three-group classification: high SMD with low LSR group, high SMD with high LSR group, and low SMD group. When comparing the C-index values, the three-group classification exhibited superior discriminatory performance compared with considering myosteatosis and LS separately. CONCLUSIONS Myosteatosis was associated with poorer survival, while the presence of LS was linked to a better prognosis in non-metastatic CRC patients. Simultaneously considering fat infiltration can serve as a more effective prognosticator in non-metastatic CRC patients.
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Affiliation(s)
- Dong Hee Lee
- Department of Surgery, Gangnam Severance HospitalYonsei University College of MedicineSeoulRepublic of Korea
| | - Il Jo
- Department of Surgery, Gangnam Severance HospitalYonsei University College of MedicineSeoulRepublic of Korea
| | - Hye Sun Lee
- Biostatistics Collaboration UnitYonsei University College of MedicineSeoulRepublic of Korea
| | - Jeonghyun Kang
- Department of Surgery, Gangnam Severance HospitalYonsei University College of MedicineSeoulRepublic of Korea
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3
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Park K, Kim S, Jung J. Analysis of temperature effects on the protein accumulation of the FT-FD module using newly generated Arabidopsis transgenic plants. Plant Direct 2023; 7:e552. [PMID: 38116182 PMCID: PMC10727963 DOI: 10.1002/pld3.552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 12/21/2023]
Abstract
Arabidopsis flowering is dependent on interactions between a component of the florigens FLOWERING LOCUS T (FT) and the basic leucine zipper (bZIP) transcription factor FD. These proteins form a complex that activates the genes required for flowering competence and integrates environmental cues, such as photoperiod and temperature. However, it remains largely unknown how FT and FD are regulated at the protein level. To address this, we created FT transgenic plants that express the N-terminal FLAG-tagged FT fusion protein under the control of its own promoter in ft mutant backgrounds. FT transgenic plants complemented the delayed flowering of the ft mutant and exhibited similar FT expression patterns to wild-type Col-0 plants in response to changes in photoperiod and temperature. Similarly, we generated FD transgenic plants in fd mutant backgrounds that express the N-terminal MYC-tagged FD fusion protein under the FD promoter, rescuing the late flowering phenotypes in the fd mutant. Using these transgenic plants, we investigated how temperature regulates the expression of FT and FD proteins. Temperature-dependent changes in FT and FD protein levels are primarily regulated at the transcript level, but protein-level temperature effects have also been observed to some extent. In addition, our examination of the expression patterns of FT and FD in different tissues revealed that similar to the spatial expression pattern of FT, FD mRNA was expressed in both the leaf and shoot apex, but FD protein was only detected in the apex, suggesting a regulatory mechanism that restricts FD protein expression in the leaf during the vegetative growth phase. These transgenic plants provided a valuable platform for investigating the role of the FT-FD module in flowering time regulation.
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Affiliation(s)
- Kyung‐Ho Park
- Department of Biological SciencesSungkyunkwan UniversitySuwonSouth Korea
| | - Sol‐Bi Kim
- Department of Biological SciencesSungkyunkwan UniversitySuwonSouth Korea
| | - Jae‐Hoon Jung
- Department of Biological SciencesSungkyunkwan UniversitySuwonSouth Korea
- Research Centre for Plant PlasticitySeoul National UniversitySeoulSouth Korea
- Biotherapeutics Translational Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonSouth Korea
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Moon SW, Zhao L, Matloff W, Hobel S, Berger R, Kwon D, Kim J, Toga AW, Dinov ID. Brain structure and allelic associations in Alzheimer's disease. CNS Neurosci Ther 2023; 29:1034-1048. [PMID: 36575854 PMCID: PMC10018103 DOI: 10.1111/cns.14073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD), the most prevalent form of dementia, affects 6.5 million Americans and over 50 million people globally. Clinical, genetic, and phenotypic studies of dementia provide some insights of the observed progressive neurodegenerative processes, however, the mechanisms underlying AD onset remain enigmatic. AIMS This paper examines late-onset dementia-related cognitive impairment utilizing neuroimaging-genetics biomarker associations. MATERIALS AND METHODS The participants, ages 65-85, included 266 healthy controls (HC), 572 volunteers with mild cognitive impairment (MCI), and 188 Alzheimer's disease (AD) patients. Genotype dosage data for AD-associated single nucleotide polymorphisms (SNPs) were extracted from the imputed ADNI genetics archive using sample-major additive coding. Such 29 SNPs were selected, representing a subset of independent SNPs reported to be highly associated with AD in a recent AD meta-GWAS study by Jansen and colleagues. RESULTS We identified the significant correlations between the 29 genomic markers (GMs) and the 200 neuroimaging markers (NIMs). The odds ratios and relative risks for AD and MCI (relative to HC) were predicted using multinomial linear models. DISCUSSION In the HC and MCI cohorts, mainly cortical thickness measures were associated with GMs, whereas the AD cohort exhibited different GM-NIM relations. Network patterns within the HC and AD groups were distinct in cortical thickness, volume, and proportion of White to Gray Matter (pct), but not in the MCI cohort. Multinomial linear models of clinical diagnosis showed precisely the specific NIMs and GMs that were most impactful in discriminating between AD and HC, and between MCI and HC. CONCLUSION This study suggests that advanced analytics provide mechanisms for exploring the interrelations between morphometric indicators and GMs. The findings may facilitate further clinical investigations of phenotypic associations that support deep systematic understanding of AD pathogenesis.
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Affiliation(s)
- Seok Woo Moon
- Department of Neuropsychiatry, Research Institute of Medical ScienceKonkuk University School of MedicineSeoulKorea
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Lu Zhao
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - William Matloff
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Sam Hobel
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Ryan Berger
- Microbiology & ImmunologyUniversity of MichiganAnn ArborMichiganUSA
| | - Daehong Kwon
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulKorea
| | - Jaebum Kim
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulKorea
| | - Arthur W. Toga
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
| | - Ivo D. Dinov
- USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USCCaliforniaLos AngelesUSA
- Department of Health Behavior and Biological Sciences, Statistics Online Computational Resource (SOCR), Michigan Institute for Data Science (MIDAS)University of MichiganAnn ArborMichiganUSA
- Department of StatisticsUniversity of CaliforniaLos AngelesCaliforniaUSA
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5
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Kwon M, Lee JH, Yoon Y, Pleasure SJ, Yoon K. The CRHR1/CREB/REST signaling cascade regulates mammalian embryonic neural stem cell properties. EMBO Rep 2023; 24:e55313. [PMID: 36413000 PMCID: PMC9900344 DOI: 10.15252/embr.202255313] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Growing evidence suggests that the corticotropin-releasing hormone (CRH) signaling pathway, mainly known as a critical initiator of humoral stress responses, has a role in normal neuronal physiology. However, despite the evidence of CRH receptor (CRHR) expression in the embryonic ventricular zone, the exact functions of CRH signaling in embryonic brain development have not yet been fully determined. In this study, we show that CRHR1 is required for the maintenance of neural stem cell properties, as assessed by in vitro neurosphere assays and cell distribution in the embryonic cortical layers following in utero electroporation. Identifying the underlying molecular mechanisms of CRHR1 action, we find that CRHR1 functions are accomplished through the increasing expression of the master transcription factor REST. Furthermore, luciferase reporter and chromatin immunoprecipitation assays reveal that CRHR1-induced CREB activity is responsible for increased REST expression at the transcriptional level. Taken together, these findings indicate that the CRHR1/CREB/REST signaling cascade plays an important role downstream of CRH in the regulation of neural stem cells during embryonic brain development.
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Affiliation(s)
- Mookwang Kwon
- Department of Integrative Biotechnology, College of Biotechnology and BioengineeringSungkyunkwan UniversitySuwonSouth Korea
| | - Ju Hyun Lee
- Department of Biopharmaceutical ConvergenceSungkyunkwan UniversitySuwonSouth Korea
| | - Youngik Yoon
- Department of Biopharmaceutical ConvergenceSungkyunkwan UniversitySuwonSouth Korea
| | - Samuel J Pleasure
- Department of NeurologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Keejung Yoon
- Department of Integrative Biotechnology, College of Biotechnology and BioengineeringSungkyunkwan UniversitySuwonSouth Korea
- Department of Biopharmaceutical ConvergenceSungkyunkwan UniversitySuwonSouth Korea
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6
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Kim JY, Lee SJ, Min WK, Cha S, Song JT, Seo HS. COP1 mutation causes low leaf temperature under various abiotic stresses in Arabidopsis thaliana. Plant Direct 2022; 6:e473. [PMID: 36545005 PMCID: PMC9763638 DOI: 10.1002/pld3.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Stomata are microscopic pores on epidermal cells of leaves and stems that regulate water loss and gas exchange between the plant and its environment. Constitutive photomorphogenic 1 (COP1) is an E3 ubiquitin ligase that is involved in plant growth and development and multiple abiotic stress responses by regulating the stability of various target proteins. However, little is known about how COP1 controls stomatal aperture and leaf temperature under various environmental conditions. Here, we show that COP1 participates in leaf temperature and stomatal closure regulation under normal and stress conditions in Arabidopsis. Leaf temperature of cop1 mutants was relatively lower than that of wild type (WT) under drought, salt, and heat stress and after abscisic acid (ABA), CaCl2, and H2O2 treatments. However, leaf temperature was generally higher in both WT and cop1 mutants after abiotic stress and chemical treatment than that of untreated WT and cop1 mutants. Stomatal aperture was wider in cop1 mutants than that in WT under all conditions tested, although the extent of stomatal closure varied between WT and cop1 mutants. Under dark conditions, leaf temperature was also lower in cop1 mutants than that in WT. Expression of the genes encoding ABA receptors, ABA biosynthesis proteins, positive regulators of stomatal closure and heat tolerance, and ABA-responsive proteins was lower in cop1 mutants that that in WT. In addition, expression of respiration-related genes was lower in cop1 mutants that that in WT. Taken together, the data provide evidence that mutations in COP1 lead to wider stomatal aperture and higher leaf temperature under normal and stress conditions, indicating that leaf temperature is highly correlated with stomatal aperture.
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Affiliation(s)
- Joo Yong Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - Seung Ju Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - Wang Ki Min
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - Seoyeon Cha
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - Jong Tae Song
- Department of Applied BiosciencesKyungpook National UniversityDaeguSouth Korea
| | - Hak Soo Seo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
- Bio‐MAX InstituteSeoul National UniversitySeoulSouth Korea
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7
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Kwon YS, Lee J, Lee S(S. The impact of background music on film audience's attentional processes: Electroencephalography alpha-rhythm and event-related potential analyses. Front Psychol 2022; 13:933497. [PMID: 36467199 PMCID: PMC9713244 DOI: 10.3389/fpsyg.2022.933497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/27/2022] [Indexed: 08/17/2023] Open
Abstract
Background music is an indispensable part of films and plays an important role in enhancing audiences' attention to scenes. However, few studies have examined the cognitive effect of background music at the neurophysiological level. Using electroencephalography (EEG), the present study examines the effect of background music tempo on the viewer's attentional processes. Participants' (N = 24) EEG responses were recorded while the participants watched segments of action films in three conditions with variations on the presence and tempo of background music (i.e., no background music vs. slow-tempo music vs. fast-tempo music). These responses were analyzed using the alpha-rhythm suppression and event-related potential (ERP) P300, a brainwave indicator of attentional processes. The results suggest that participants' attention levels increased when background music was present (compared to when background music was absent), but there was no difference in participants' attention levels based on tempo. The theoretical and practical implications of these findings are discussed.
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Affiliation(s)
- Young-Sung Kwon
- Department of Media and Communication, Dong-A University, Busan, South Korea
| | - Jonghyun Lee
- Department of English Language and Literature, College of Humanities, Seoul National University, Seoul, South Korea
| | - Slgi (Sage) Lee
- Department of Media and Communication, Pusan National University, Busan, South Korea
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8
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Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J 2022; 41:e111338. [PMID: 36121125 PMCID: PMC9627674 DOI: 10.15252/embj.2022111338] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
The balance between self-renewal and differentiation in human foetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID, we place SOX9 at the centre of a transcriptional network, which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new workflow for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease.
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Affiliation(s)
- Dawei Sun
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Oriol Llora Batlle
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Jelle van den Ameele
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Present address:
Department of Clinical Neurosciences and MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - John C Thomas
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Peng He
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Walfred Tang
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Chufan Xu
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Department of Anaesthesiology and Surgical Intensive Care Unit, Xinhua HospitalShanghai Jiaotong University School of MedicineShanghaiChina
| | | | - Sarah A Teichmann
- Wellcome Sanger InstituteCambridgeUK
- Department of Physics/Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Andrea H Brand
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
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9
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Kim J, Park J, Kim H, Son N, Kim E, Kim J, Byun D, Lee Y, Park YM, Nageswaran DC, Kuo P, Rose T, Dang TVT, Hwang I, Lambing C, Henderson IR, Choi K. Arabidopsis HEAT SHOCK FACTOR BINDING PROTEIN is required to limit meiotic crossovers and HEI10 transcription. EMBO J 2022; 41:e109958. [PMID: 35670129 PMCID: PMC9289711 DOI: 10.15252/embj.2021109958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
The number of meiotic crossovers is tightly controlled and most depend on pro-crossover ZMM proteins, such as the E3 ligase HEI10. Despite the importance of HEI10 dosage for crossover formation, how HEI10 transcription is controlled remains unexplored. In a forward genetic screen using a fluorescent crossover reporter in Arabidopsis thaliana, we identify heat shock factor binding protein (HSBP) as a repressor of HEI10 transcription and crossover numbers. Using genome-wide crossover mapping and cytogenetics, we show that hsbp mutations or meiotic HSBP knockdowns increase ZMM-dependent crossovers toward the telomeres, mirroring the effects of HEI10 overexpression. Through RNA sequencing, DNA methylome, and chromatin immunoprecipitation analysis, we reveal that HSBP is required to repress HEI10 transcription by binding with heat shock factors (HSFs) at the HEI10 promoter and maintaining DNA methylation over the HEI10 5' untranslated region. Our findings provide insights into how the temperature response regulator HSBP restricts meiotic HEI10 transcription and crossover number by attenuating HSF activity.
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Affiliation(s)
- Juhyun Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jihye Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Heejin Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Namil Son
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Eun‐Jung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jaeil Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Dohwan Byun
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Youngkyung Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Yeong Mi Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | | | - Pallas Kuo
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Teresa Rose
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Tuong Vi T Dang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Ildoo Hwang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Christophe Lambing
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Ian R Henderson
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Kyuha Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
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10
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Ju MK, Lee JR, Choi Y, Park SY, Sul HJ, Chung HJ, An S, Lee S, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y, Kim H, Zang DY. PWWP2B promotes DNA end resection and homologous recombination. EMBO Rep 2022; 23:e53492. [PMID: 35582821 PMCID: PMC9253748 DOI: 10.15252/embr.202153492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2023] Open
Abstract
Genome instability is one of the leading causes of gastric cancers. However, the mutational landscape of driver genes in gastric cancer is poorly understood. Here, we investigate somatic mutations in 25 Korean gastric adenocarcinoma patients using whole-exome sequencing and show that PWWP2B is one of the most frequently mutated genes. PWWP2B mutation correlates with lower cancer patient survival. We find that PWWP2B has a role in DNA double-strand break repair. As a nuclear protein, PWWP2B moves to sites of DNA damage through its interaction with UHRF1. Depletion of PWWP2B enhances cellular sensitivity to ionizing radiation (IR) and impairs IR-induced foci formation of RAD51. PWWP2B interacts with MRE11 and participates in homologous recombination via promoting DNA end-resection. Taken together, our data show that PWWP2B facilitates the recruitment of DNA repair machinery to sites of DNA damage and promotes HR-mediated DNA double-strand break repair. Impaired PWWP2B function might thus cause genome instability and promote gastric cancer development.
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Affiliation(s)
- Min Kyung Ju
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Joo Rak Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Yeonsong Choi
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Seon Young Park
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hee Jung Sul
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Hee Jin Chung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Soyeong An
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Semin Lee
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Eunyoung Jung
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Bohyun Kim
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bo Youn Choi
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bum Jun Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyeong Su Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyun Lim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Ho Suk Kang
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Jae Seung Soh
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Kyungjae Myung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Kab Choong Kim
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Ji Woong Cho
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Jinwon Seo
- Department of PathologyHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Ja Yil Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Yonghwan Kim
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hongtae Kim
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Dae Young Zang
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
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11
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Son SM, Yun SH, Kwon JW. Motor Imagery Combined With Physical Training Improves Response Inhibition in the Stop Signal Task. Front Psychol 2022; 13:905579. [PMID: 35795413 PMCID: PMC9251501 DOI: 10.3389/fpsyg.2022.905579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMotor imagery training has a similar effect to that of physical training on motor performance. The objective of this study was to investigate the short-term effectiveness of motor imagery training on response inhibition using the stop signal task (SST).MethodsParticipants were divided into a physical training group (PT, n = 17), a motor imagery training group (MIT, n = 17), and a motor imagery combined with physical training group (MIPT, n = 17). All participants performed 10 SST training sessions over 5 days. Both stop signal reaction time (SSRT) and non-signal reaction time (NSRT) were measured before and after SST training.ResultsThere were significant interaction (time × group) and time effects, although the group effect was not statistically significant. Bonferroni post hoc analysis showed that MIPT group revealed a significantly greater change in SSRT than PT and MIT groups, while there was no significant difference between PT and MIT groups. SSRT significantly decreased after training in all groups. In NSRT, there was a significant effect of time, but there was no significant interaction effect (time × group) or group effect.ConclusionResponse inhibition could be enhanced via training, and it was most effective when motor imagery and physical training were combined. We demonstrate that motor imagery training significantly improves response inhibition and should be accompanied by physical training when performing SST.
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Affiliation(s)
- Sung Min Son
- Department of Physical Therapy, College of Health Science, Cheongju University, Cheongju, South Korea
| | - Seong Ho Yun
- Department of Public Health Sciences, Graduate School, Dankook University, Cheonan, South Korea
| | - Jung Won Kwon
- Department of Physical Therapy, College of Health and Welfare Sciences, Cheonan, South Korea
- *Correspondence: Jung Won Kwon,
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12
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Nam S, Downer B, Bae S, Hong I. Social, behavioural, and functional characteristics of community-dwelling South Korean adults with moderate and severe cognitive impairment. Int J Methods Psychiatr Res 2022; 31:e1908. [PMID: 35278012 PMCID: PMC9159685 DOI: 10.1002/mpr.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES This study used the 2016 Korean Longitudinal Study on Aging to investigate the social, behavioural, and functional characteristics of community-dwelling South Korean adults with cognitive impairment. METHODS Participants were classified as normal, moderate impairment, and severe impairment according to an algorithm that combined the Korean Mini-Mental State Examination score and the number of difficulties in performing instrumental activities of daily living. Selected characteristics included grip strength, depression, participation in exercise and social activities, and living in a rural, urban, or suburban community. RESULTS Most (72.7%) participants were classified as having normal cognition, 20.1% were classified as moderate impairment, and 7.2% were classified as severe impairment. Regardless of sex, the differences in grip strength across the cognitive status classifications were statistically significant, except for the difference between moderate and severe cognitive impairment in males (p = 0.8477). Greater number of depressive symptoms and living in rural areas were associated with significantly higher odds for severe cognitive impairment. Participants with moderate (OR = 0.51) and severe (OR = 0.33) cognitive impairment were less likely to participate in social activities than those with normal cognition. CONCLUSIONS The study findings revealed that social, behavioural, and functional characteristics are closely related to the cognitive status of community-dwelling adults in South Korea.
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Affiliation(s)
- Sanghun Nam
- Department of Occupational TherapyGraduate SchoolYonsei UniversityWonju‐siGangwon‐doRepublic of Korea
| | - Brian Downer
- Division of Rehabilitation SciencesUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Suyeong Bae
- Department of Occupational TherapyGraduate SchoolYonsei UniversityWonju‐siGangwon‐doRepublic of Korea
| | - Ickpyo Hong
- Department of Occupational TherapyCollege of Software and Digital Healthcare ConvergenceYonsei UniversityWonju‐siGangwon‐doRepublic of Korea
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13
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Choi J, Henze DK, Cao H, Nowlan CR, González Abad G, Kwon H, Lee H, Oak YJ, Park RJ, Bates KH, Maasakkers JD, Wisthaler A, Weinheimer AJ. An Inversion Framework for Optimizing Non-Methane VOC Emissions Using Remote Sensing and Airborne Observations in Northeast Asia During the KORUS-AQ Field Campaign. J Geophys Res Atmos 2022; 127:e2021JD035844. [PMID: 35865789 PMCID: PMC9285978 DOI: 10.1029/2021jd035844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/09/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
We aim to reduce uncertainties in CH2O and other volatile organic carbon (VOC) emissions through assimilation of remote sensing data. We first update a three-dimensional (3D) chemical transport model, GEOS-Chem with the KORUSv5 anthropogenic emission inventory and inclusion of chemistry for aromatics and C2H4, leading to modest improvements in simulation of CH2O (normalized mean bias (NMB): -0.57 to -0.51) and O3 (NMB: -0.25 to -0.19) compared against DC-8 aircraft measurements during KORUS-AQ; the mixing ratio of most VOC species are still underestimated. We next constrain VOC emissions using CH2O observations from two satellites (OMI and OMPS) and the DC-8 aircraft during KORUS-AQ. To utilize data from multiple platforms in a consistent manner, we develop a two-step Hybrid Iterative Finite Difference Mass Balance and four-dimensional variational inversion system (Hybrid IFDMB-4DVar). The total VOC emissions throughout the domain increase by 47%. The a posteriori simulation reduces the low biases of simulated CH2O (NMB: -0.51 to -0.15), O3 (NMB: -0.19 to -0.06), and VOCs. Alterations to the VOC speciation from the 4D-Var inversion include increases of biogenic isoprene emissions in Korea and anthropogenic emissions in Eastern China. We find that the IFDMB method alone is adequate for reducing the low biases of VOCs in general; however, 4D-Var provides additional refinement of high-resolution emissions and their speciation. Defining reasonable emission errors and choosing optimal regularization parameters are crucial parts of the inversion system. Our new hybrid inversion framework can be applied for future air quality campaigns, maximizing the value of integrating measurements from current and upcoming geostationary satellite instruments.
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Affiliation(s)
- Jinkyul Choi
- Environmental Engineering ProgramUniversity of ColoradoBoulderCOUSA
| | - Daven K. Henze
- Department of Mechanical EngineeringUniversity of ColoradoBoulderCOUSA
| | - Hansen Cao
- Department of Mechanical EngineeringUniversity of ColoradoBoulderCOUSA
| | | | | | | | - Hyung‐Min Lee
- Department of Environmental Science and EngineeringEwha Womans UniversitySeoulSouth Korea
| | - Yujin J. Oak
- School of Earth and Environmental SciencesSeoul National UniversitySeoulSouth Korea
| | - Rokjin J. Park
- School of Earth and Environmental SciencesSeoul National UniversitySeoulSouth Korea
| | - Kelvin H. Bates
- School of Engineering and Applied SciencesHarvard UniversityCambridgeMAUSA
| | | | - Armin Wisthaler
- Institute for Ion Physics and Applied PhysicsUniversity of InnsbruckInnsbruckAustria
- Department of ChemistryUniversity of OsloOsloNorway
| | - Andrew J. Weinheimer
- Atmospheric Chemistry Observations and Modeling LaboratoryNational Center for Atmospheric ResearchBoulderCOUSA
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14
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Abstract
In plants senescence is the final stage of plant growth and development that ultimately leads to death. Plants experience age-related as well as stress-induced developmental ageing. Senescence involves significant changes at the transcriptional, post-translational and metabolomic levels. Furthermore, phytohormones also play a critical role in the programmed senescence of plants. Nitric oxide (NO) is a gaseous signalling molecule that regulates a plethora of physiological processes in plants. Its role in the control of ageing and senescence has just started to be elucidated. Here, we review the role of NO in the regulation of programmed cell death, seed ageing, fruit ripening and senescence. We also discuss the role of NO in the modulation of phytohormones during senescence and the significance of NO-ROS cross-talk during programmed cell death and senescence.
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Affiliation(s)
- Adil Hussain
- Department of Entomology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Farooq Shah
- Department of Agronomy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Farman Ali
- Department of Entomology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Byung-Wook Yun
- Department of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, South Korea
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15
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Ahn G, Jung IJ, Cha JY, Jeong SY, Shin GI, Ji MG, Kim MG, Lee SY, Kim WY. Phytochrome B Positively Regulates Red Light-Mediated ER Stress Response in Arabidopsis. Front Plant Sci 2022; 13:846294. [PMID: 35283886 PMCID: PMC8905361 DOI: 10.3389/fpls.2022.846294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Light plays a crucial role in plant growth and development, and light signaling is integrated with various stress responses to adapt to different environmental changes. During this process, excessive protein synthesis overwhelms the protein-folding ability of the endoplasmic reticulum (ER), causing ER stress. Although crosstalk between light signaling and ER stress response has been reported in plants, the molecular mechanisms underlying this crosstalk are poorly understood. Here, we demonstrate that the photoreceptor phytochrome B (phyB) induces the expression of ER luminal protein chaperones as well as that of unfolded protein response (UPR) genes. The phyB-5 mutant was less sensitive to tunicamycin (TM)-induced ER stress than were the wild-type plants, whereas phyB-overexpressing plants displayed a more sensitive phenotype under white light conditions. ER stress response genes (BiP2 and BiP3), UPR-related bZIP transcription factors (bZIP17, bZIP28, and bZIP60), and programmed cell death (PCD)-associated genes (OXI1, NRP1, and MC8) were upregulated in phyB-overexpressing plants, but not in phyB-5, under ER stress conditions. The ER stress-sensitive phenotype of phyB-5 under red light conditions was eliminated with a reduction in photo-equilibrium by far-red light and darkness. The N-terminal domain of phyB is essential for signal transduction of the ER stress response in the nucleus, which is similar to light signaling. Taken together, our results suggest that phyB integrates light signaling with the UPR to relieve ER stress and maintain proper plant growth.
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Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - In Jung Jung
- National Institute of Wildlife Disease Control and Prevention (NIWDC), Ministry of Environment, Gwangju, South Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
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16
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Jongen HJ, Steeneveld GJ, Beringer J, Christen A, Chrysoulakis N, Fortuniak K, Hong J, Hong JW, Jacobs CMJ, Järvi L, Meier F, Pawlak W, Roth M, Theeuwes NE, Velasco E, Vogt R, Teuling AJ. Urban Water Storage Capacity Inferred From Observed Evapotranspiration Recession. Geophys Res Lett 2022; 49:e2021GL096069. [PMID: 35859568 PMCID: PMC9285425 DOI: 10.1029/2021gl096069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
Water storage plays an important role in mitigating heat and flooding in urban areas. Assessment of the water storage capacity of cities remains challenging due to the inherent heterogeneity of the urban surface. Traditionally, effective storage has been estimated from runoff. Here, we present a novel approach to estimate effective water storage capacity from recession rates of observed evaporation during precipitation-free periods. We test this approach for cities at neighborhood scale with eddy-covariance based latent heat flux observations from 14 contrasting sites with different local climate zones, vegetation cover and characteristics, and climates. Based on analysis of 583 drydowns, we find storage capacities to vary between 1.3 and 28.4 mm, corresponding to e-folding timescales of 1.8-20.1 days. This makes the urban storage capacity at least five times smaller than all the observed values for natural ecosystems, reflecting an evaporation regime characterized by extreme water limitation.
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Affiliation(s)
- H. J. Jongen
- Hydrology and Quantitative Water ManagementWageningen UniversityWageningenThe Netherlands
- Meteorology and Air QualityWageningen UniversityWageningenThe Netherlands
| | - G. J. Steeneveld
- Meteorology and Air QualityWageningen UniversityWageningenThe Netherlands
| | - J. Beringer
- School of Agriculture and EnvironmentUniversity of Western AustraliaCrawleyWAAustralia
| | - A. Christen
- Chair of Environmental MeteorologyFaculty of Environment and Natural ResourcesUniversity of FreiburgFreiburgGermany
| | - N. Chrysoulakis
- Foundation for Research and Technology HellasInstitute of Applied and Computational MathematicsThe Remote Sensing LabHeraklionGreece
| | - K. Fortuniak
- Department of Meteorology and ClimatologyFaculty of Geographical SciencesUniversity of ŁódźŁódźPoland
| | - J. Hong
- Department of Atmospheric SciencesYonsei UniversitySeoulSouth Korea
| | - J. W. Hong
- Korea Environment InstituteSejongSouth Korea
| | - C. M. J. Jacobs
- Wageningen Environmental ResearchWageningen University and ResearchWageningenThe Netherlands
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - L. Järvi
- Institute for Atmospheric and Earth System Research / PhysicsUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability ScienceUniversity of HelsinkiHesinkiFinland
| | - F. Meier
- Chair of ClimatologyTechnische Universität BerlinBerlinGermany
| | - W. Pawlak
- Department of Meteorology and ClimatologyFaculty of Geographical SciencesUniversity of ŁódźŁódźPoland
| | - M. Roth
- Department of GeographyNational University of SingaporeSingaporeSingapore
| | - N. E. Theeuwes
- Department of MeteorologyUniversity of ReadingReadingUK
- Royal Netherlands Meteorological Institute (KNMI)De BiltThe Netherlands
| | - E. Velasco
- Independent Research ScientistSingaporeSingapore
| | - R. Vogt
- Department of Environmental SciencesUniversity of BaselAtmospheric SciencesBaselSwitzerland
| | - A. J. Teuling
- Hydrology and Quantitative Water ManagementWageningen UniversityWageningenThe Netherlands
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17
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Che S, Nan D, Kamphuis P, Zhang S, Kim JH. Examining Crisis Communication Using Semantic Network and Sentiment Analysis: A Case Study on NetEase Games. Front Psychol 2022; 13:823415. [PMID: 35185736 PMCID: PMC8854284 DOI: 10.3389/fpsyg.2022.823415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/11/2022] [Indexed: 11/22/2022] Open
Abstract
The mobile game “Immortal Conquest,” created by NetEase Games, caused a dramatic user dissatisfaction event after an introduction of a sudden and uninvited “pay-to-win” update. As a result, many players filed grievances against NetEase in a court. The official game website issued three apologies, with mix results, to mitigate the crisis. The goal of the present study is to understand user feedback content from the perspective of Situational Crisis Communication Theory through semantic network analysis and sentiment analysis to explore how an enterprise’s crisis communication strategy affects users’ attitudes. First, our results demonstrate that the diminishing crisis communication strategies (excuse and justification) do not change players’ negative attitudes. It was not a failure because it successfully alleviated the players’ legal complaints and refocused their attention on the game itself. Second, the rebuild (apology & compensation) strategy was effective because it significantly increased the percentage of positive emotions and regenerated expectations for the game. The litigation crisis was identified within gamer communications with respect to Chinese gaming companies for the first time. Nevertheless, this does not indicate an increase in overall legal awareness among the larger Chinese population. It may only reflect greater legal awareness among Chinese online gamers. Fourth, gamers emphasized that they and enterprises should be equally involved when communicating with each other. Finally, in-game paid items should be reasonably priced, otherwise, they will drive users to competitors.
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Affiliation(s)
- ShaoPeng Che
- Department of Human-Artificial Intelligence Interaction, Sungkyunkwan University, Seoul, South Korea
- Department of Interaction Science, Sungkyunkwan University, Seoul, South Korea
| | - Dongyan Nan
- Department of Human-Artificial Intelligence Interaction, Sungkyunkwan University, Seoul, South Korea
- Department of Interaction Science, Sungkyunkwan University, Seoul, South Korea
| | - Pim Kamphuis
- Department of Interaction Science, Sungkyunkwan University, Seoul, South Korea
| | - Shunan Zhang
- Department of Interaction Science, Sungkyunkwan University, Seoul, South Korea
| | - Jang Hyun Kim
- Department of Human-Artificial Intelligence Interaction, Sungkyunkwan University, Seoul, South Korea
- Department of Interaction Science, Sungkyunkwan University, Seoul, South Korea
- *Correspondence: Jang Hyun Kim,
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18
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Lee K, Lee J, Lee P, Jeon BC, Song MY, Kwak S, Lee J, Kim J, Kim D, Kim JH, Tesh VL, Lee M, Park S. Inhibition of O-GlcNAcylation protects from Shiga toxin-mediated cell injury and lethality in host. EMBO Mol Med 2022; 14:e14678. [PMID: 34842355 PMCID: PMC8749473 DOI: 10.15252/emmm.202114678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
Shiga toxins (Stxs) produced by enterohemorrhagic Escherichia coli (EHEC) are the major virulence factors responsible for hemorrhagic colitis, which can lead to life-threatening systemic complications including acute renal failure (hemolytic uremic syndrome) and neuropathy. Here, we report that O-GlcNAcylation, a type of post-translational modification, was acutely increased upon induction of endoplasmic reticulum (ER) stress in host cells by Stxs. Suppression of the abnormal Stx-mediated increase in O-GlcNAcylation effectively inhibited apoptotic and inflammatory responses in Stx-susceptible cells. The protective effect of O-GlcNAc inhibition for Stx-mediated pathogenic responses was also verified using three-dimensional (3D)-cultured spheroids or organoids mimicking the human kidney. Treatment with an O-GlcNAcylation inhibitor remarkably improved the major disease symptoms and survival rate for mice intraperitoneally injected with a lethal dose of Stx. In conclusion, this study elucidates O-GlcNAcylation-dependent pathogenic mechanisms of Stxs and demonstrates that inhibition of aberrant O-GlcNAcylation is a potential approach to treat Stx-mediated diseases.
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Affiliation(s)
- Kyung‐Soo Lee
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
| | - Jieun Lee
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
| | - Pureum Lee
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
| | - Bong Chan Jeon
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
- Immunotherapy Convergence Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
| | - Min Yeong Song
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
| | - Sojung Kwak
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
| | - Jungwoon Lee
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
| | - Jun‐Seob Kim
- Department of Nano‐BioengineeringIncheon National UniversityIncheonKorea
| | - Doo‐Jin Kim
- Infectious Disease Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
| | - Ji Hyung Kim
- Infectious Disease Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
| | - Vernon L Tesh
- Department of Microbial Pathogenesis and ImmunologyCollege of MedicineTexas A&M UniversityBryanTXUSA
| | - Moo‐Seung Lee
- Environmental Diseases Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
- Department of Biomolecular ScienceKRIBB School of BioscienceKorea University of Science and Technology (UST)DaejeonKorea
| | - Sung‐Kyun Park
- Infectious Disease Research CenterKorea Research Institute of Bioscience & Biotechnology (KRIBB)DaejeonKorea
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Hwang IS, Oh EJ, Song E, Park IW, Lee Y, Sohn KH, Choi D, Oh CS. An Apoplastic Effector Pat-1 Cm of the Gram-Positive Bacterium Clavibacter michiganensis Acts as Both a Pathogenicity Factor and an Immunity Elicitor in Plants. Front Plant Sci 2022; 13:888290. [PMID: 35432427 PMCID: PMC9006514 DOI: 10.3389/fpls.2022.888290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 05/09/2023]
Abstract
Clavibacter michiganensis, a Gram-positive plant-pathogenic bacterium, utilizes apoplastic effectors for disease development in host plants. Here, we determine the roles of Pat-1Cm (a putative serine protease) in pathogenicity and plant immunity. Pat-1Cm was found to be a genuine secreted protein, and the secreted mature form did not carry the first 33 amino acids predicted to be a signal peptide (SP). The pat-1Cm mutant impaired to cause wilting, but still caused canker symptom in tomato. Moreover, this mutant failed to trigger the hypersensitive response (HR) in a nonhost Nicotiana tabacum. Among orthologs and paralogs of pat-1Cm , only chp-7Cs from Clavibacter sepedonicus, a potato pathogen, successfully complemented pat-1Cm function in pathogenicity in tomato, whereas all failed to complement pat-1Cm function in HR induction in N. tabacum. Based on the structural prediction, Pat-1Cm carried a catalytic triad for putative serine protease, and alanine substitution of any amino acids in the triad abolished both pathogenicity and HR-inducing activities of Pat-1Cm in C. michiganensis. Ectopic expression of pat-1Cm with an SP from tobacco secreted protein triggered HR in N. tabacum, but not in tomato, whereas a catalytic triad mutant failed to induce HR. Inoculation of the pat-1Cm mutant mixed with the mutant of another apoplastic effector CelA (cellulase) caused severe wilting in tomato, indicating that these two apoplastic effectors can functionally cooperate in pathogenicity. Overall, these results indicate that Pat-1Cm is a distinct secreted protein carrying a functional catalytic triad for serine protease and this enzymatic activity might be critical for both pathogenicity and HR-eliciting activities of Pat-1Cm in plants.
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Affiliation(s)
- In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eunbee Song
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Woong Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Doil Choi
- Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- *Correspondence: Chang-Sik Oh,
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Fuentes A, Yoon S, Lee MH, Park DS. Improving Accuracy of Tomato Plant Disease Diagnosis Based on Deep Learning With Explicit Control of Hidden Classes. Front Plant Sci 2021; 12:682230. [PMID: 34975931 PMCID: PMC8716922 DOI: 10.3389/fpls.2021.682230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Recognizing plant diseases is a major challenge in agriculture, and recent works based on deep learning have shown high efficiency in addressing problems directly related to this area. Nonetheless, weak performance has been observed when a model trained on a particular dataset is evaluated in new greenhouse environments. Therefore, in this work, we take a step towards these issues and present a strategy to improve model accuracy by applying techniques that can help refine the model's generalization capability to deal with complex changes in new greenhouse environments. We propose a paradigm called "control to target classes." The core of our approach is to train and validate a deep learning-based detector using target and control classes on images collected in various greenhouses. Then, we apply the generated features for testing the inference of the system on data from new greenhouse conditions where the goal is to detect target classes exclusively. Therefore, by having explicit control over inter- and intra-class variations, our model can distinguish data variations that make the system more robust when applied to new scenarios. Experiments demonstrate the effectiveness and efficiency of the proposed approach on our extended tomato plant diseases dataset with 14 classes, from which 5 are target classes and the rest are control classes. Our detector achieves a recognition rate of target classes of 93.37% mean average precision on the inference dataset. Finally, we believe that our study offers valuable guidelines for researchers working in plant disease recognition with complex input data.
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Affiliation(s)
- Alvaro Fuentes
- Department of Electronics Engineering, Jeonbuk National University, Jeonju, South Korea
- Core Research Institute of Intelligent Robots, Jeonbuk National University, Jeonju, South Korea
| | - Sook Yoon
- Department of Computer Engineering, Mokpo National University, Muan, South Korea
| | - Mun Haeng Lee
- Fruit Vegetable Research Institute, Chungnam A.R.E.S, Buyeo, South Korea
| | - Dong Sun Park
- Department of Electronics Engineering, Jeonbuk National University, Jeonju, South Korea
- Core Research Institute of Intelligent Robots, Jeonbuk National University, Jeonju, South Korea
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21
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Yu JE, Kim S, Hwang J, Hong JT, Hwang J, Soung N, Cha‐Molstad H, Kwon YT, Kim BY, Lee KH. Phosphorylation of β-catenin Ser60 by polo-like kinase 1 drives the completion of cytokinesis. EMBO Rep 2021; 22:e51503. [PMID: 34585824 PMCID: PMC8647012 DOI: 10.15252/embr.202051503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
β-Catenin is a multifunctional protein and participates in numerous processes required for embryonic development, cell proliferation, and homeostasis through various molecular interactions and signaling pathways. To date, however, there is no direct evidence that β-catenin contributes to cytokinesis. Here, we identify a novel p-S60 epitope on β-catenin generated by Plk1 kinase activity, which can be found at the actomyosin contractile ring of early telophase cells and at the midbody of late telophase cells. Depletion of β-catenin leads to cytokinesis-defective phenotypes, which eventually result in apoptotic cell death. In addition, phosphorylation of β-catenin Ser60 by Plk1 is essential for the recruitment of Ect2 to the midbody, activation of RhoA, and interaction between β-catenin, Plk1, and Ect2. Time-lapse image analysis confirmed the importance of β-catenin phospho-Ser60 in furrow ingression and the completion of cytokinesis. Taken together, we propose that phosphorylation of β-catenin Ser60 by Plk1 in cooperation with Ect2 is essential for the completion of cytokinesis. These findings may provide fundamental knowledge for the research of cytokinesis failure-derived human diseases.
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Affiliation(s)
- Ji Eun Yu
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
- Department of Drug Discovery and DevelopmentCollege of PharmacyChungbuk National UniversityCheongjuKorea
| | - Sun‐Ok Kim
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Jeong‐Ah Hwang
- Department of PhysiologyResearch Institute of Medical SciencesCollege of MedicineChungnam National UniversityDaejeonKorea
| | - Jin Tae Hong
- Department of Drug Discovery and DevelopmentCollege of PharmacyChungbuk National UniversityCheongjuKorea
| | - Joonsung Hwang
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Nak‐Kyun Soung
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Hyunjoo Cha‐Molstad
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical SciencesCollege of MedicineSeoul National UniversitySeoulKorea
| | - Bo Yeon Kim
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
- Department of Biomolecular ScienceUniversity of Science and TechnologyDaejeonKorea
| | - Kyung Ho Lee
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
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22
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Sampson J, Richards MW, Choi J, Fry AM, Bayliss R. Phase-separated foci of EML4-ALK facilitate signalling and depend upon an active kinase conformation. EMBO Rep 2021; 22:e53693. [PMID: 34661367 PMCID: PMC8647013 DOI: 10.15252/embr.202153693] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 12/11/2022] Open
Abstract
Variants of the oncogenic EML4-ALK fusion protein contain a similar region of ALK encompassing the kinase domain, but different portions of EML4. Here, we show that EML4-ALK V1 and V3 proteins form cytoplasmic foci that contain components of the MAPK, PLCγ and PI3K signalling pathways. The ALK inhibitors ceritinib and lorlatinib dissolve these foci and EML4-ALK V3 but not V1 protein re-localises to microtubules, an effect recapitulated in a catalytically inactive EML4-ALK mutant. Mutations that promote a constitutively active ALK stabilise the cytoplasmic foci even in the presence of these inhibitors. In contrast, the inhibitor alectinib increases foci formation of both wild-type and catalytically inactive EML4-ALK V3 proteins, but not a Lys-Glu salt bridge mutant. We propose that EML4-ALK foci formation occurs as a result of transient association of stable EML4-ALK trimers mediated through an active conformation of the ALK kinase domain. Our results demonstrate the formation of EML4-ALK cytoplasmic foci that orchestrate oncogenic signalling and reveal that their assembly depends upon the conformational state of the catalytic domain and can be differentially modulated by structurally divergent ALK inhibitors.
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Affiliation(s)
- Josephina Sampson
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
| | - Mark W Richards
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
| | - Jene Choi
- Department of PathologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoulKorea
| | - Andrew M Fry
- Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | - Richard Bayliss
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
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23
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Kim J, Rahman MH, Lee WH, Suk K. Chemogenetic stimulation of the G i pathway in astrocytes suppresses neuroinflammation. Pharmacol Res Perspect 2021; 9:e00822. [PMID: 34676988 PMCID: PMC8532135 DOI: 10.1002/prp2.822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/30/2021] [Indexed: 11/06/2022] Open
Abstract
Engineered G protein-coupled receptors (GPCRs) are commonly used in chemogenetics as designer receptors exclusively activated by designer drugs (DREADDs). Although several GPCRs have been studied in astrocytes using a chemogenetic approach, the functional role of the astrocytic Gi pathway is not clear, as the literature is conflicting depending on the brain regions or behaviors investigated. In this study, we evaluated the role of the astrocytic Gi pathway in neuroinflammation using a Gi -coupled DREADD (hM4Di). Gi -DREADD was expressed in hippocampal astrocytes of a lipopolysaccharide (LPS)-induced neuroinflammation mouse model using adeno-associated viruses. We found that astrocyte Gi -DREADD stimulation using clozapine N-oxide (CNO) inhibits neuroinflammation, as characterized by decreased levels of proinflammatory cytokines, glial activation, and cognitive impairment in mice. Subsequent experiments using primary astrocyte cultures revealed that Gi -DREADD stimulation significantly downregulated LPS-induced expression of Nos2 mRNA and nitric oxide production. Similarly, in vitro calcium imaging showed that activation of the astrocytic Gi pathway attenuated intracellular calcium transients triggered by LPS treatment, suggesting a positive correlation between enhanced calcium transients and the inflammatory phenotype of astrocytes observed in the inflamed brain. Taken together, our results indicate that the astrocytic Gi pathway plays an inhibitory role in neuroinflammation, providing an opportunity to identify potential cellular and molecular targets to control neuroinflammation.
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Affiliation(s)
- Jae‐Hong Kim
- Department of PharmacologySchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
- BK21 Plus KNU Biomedical Convergence ProgramDepartment of Biomedical SciencesSchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
| | - Md Habibur Rahman
- Department of PharmacologySchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
- BK21 Plus KNU Biomedical Convergence ProgramDepartment of Biomedical SciencesSchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Brain Science & Engineering InstituteKyungpook National UniversityDaeguRepublic of Korea
| | - Won Ha Lee
- School of Life SciencesBrain Korea 21 Plus KNU Creative BioResearch GroupKyungpook National UniversityDaeguRepublic of Korea
| | - Kyoungho Suk
- Department of PharmacologySchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
- BK21 Plus KNU Biomedical Convergence ProgramDepartment of Biomedical SciencesSchool of MedicineKyungpook National UniversityDaeguRepublic of Korea
- Brain Science & Engineering InstituteKyungpook National UniversityDaeguRepublic of Korea
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24
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Ohn J, Been KW, Kim JY, Kim EJ, Park T, Yoon H, Ji JS, Okada‐Iwabu M, Iwabu M, Yamauchi T, Kim YK, Seok C, Kwon O, Kim KH, Lee HH, Chung JH. Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth. EMBO Mol Med 2021; 13:e13790. [PMID: 34486824 PMCID: PMC8495455 DOI: 10.15252/emmm.202013790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/30/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022] Open
Abstract
Alopecia induced by aging or side effects of medications affects millions of people worldwide and impairs the quality of life; however, there is a limit to the current medications. Here, we identify a small transdermally deliverable 5-mer peptide (GLYYF; P5) that activates adiponectin receptor 1 (AdipoR1) and promotes hair growth. P5 sufficiently reproduces the biological effect of adiponectin protein via AMPK signaling pathway, increasing the expression of hair growth factors in the dermal papilla cells of human hair follicle. P5 accelerates hair growth ex vivo and induces anagen hair cycle in mice in vivo. Furthermore, we elucidate a key spot for the binding between AdipoR1 and adiponectin protein using docking simulation and mutagenesis studies. This study suggests that P5 could be used as a topical peptide drug for alleviating pathological conditions, which can be improved by adiponectin protein, such as alopecia.
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Affiliation(s)
- Jungyoon Ohn
- Department of Translational MedicineSeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Kyung Wook Been
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Jin Yong Kim
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Eun Ju Kim
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Taeyong Park
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Hye‐Jin Yoon
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Jeong Seok Ji
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Miki Okada‐Iwabu
- Department of Diabetes and Metabolic DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Masato Iwabu
- Department of Diabetes and Metabolic DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Yeon Kyung Kim
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Chaok Seok
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Ohsang Kwon
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Kyu Han Kim
- Department of Translational MedicineSeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
| | - Hyung Ho Lee
- Department of ChemistryCollege of Natural SciencesSeoul National UniversitySeoulKorea
| | - Jin Ho Chung
- Department of DermatologySeoul National University College of MedicineSeoulKorea
- Department of DermatologySeoul National University HospitalSeoulKorea
- Institute of Human‐Environment Interface BiologySeoul National UniversitySeoulKorea
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25
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Park J, Choi Y, Jung E, Lee S, Sohn J, Chung W. Microglial MERTK eliminates phosphatidylserine-displaying inhibitory post-synapses. EMBO J 2021; 40:e107121. [PMID: 34013588 PMCID: PMC8327958 DOI: 10.15252/embj.2020107121] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 01/11/2023] Open
Abstract
Glia contribute to synapse elimination through phagocytosis in the central nervous system. Despite the important roles of this process in development and neurological disorders, the identity and regulation of the "eat-me" signal that initiates glia-mediated phagocytosis of synapses has remained incompletely understood. Here, we generated conditional knockout mice with neuronal-specific deletion of the flippase chaperone Cdc50a, to induce stable exposure of phosphatidylserine, a well-known "eat-me" signal for apoptotic cells, on the neuronal outer membrane. Surprisingly, acute Cdc50a deletion in mature neurons causes preferential phosphatidylserine exposure in neuronal somas and specific loss of inhibitory post-synapses without effects on other synapses, resulting in abnormal excitability and seizures. Ablation of microglia or the deletion of microglial phagocytic receptor Mertk prevents the loss of inhibitory post-synapses and the seizure phenotype, indicating that microglial phagocytosis is responsible for inhibitory post-synapse elimination. Moreover, we found that phosphatidylserine is used for microglia-mediated pruning of inhibitory post-synapses in normal brains, suggesting that phosphatidylserine serves as a general "eat-me" signal for inhibitory post-synapse elimination.
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Affiliation(s)
- Jungjoo Park
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Yeeun Choi
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Eunji Jung
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Seung‐Hee Lee
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Jong‐Woo Sohn
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Won‐Suk Chung
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
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26
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Choi Y, Lee J, Lee H, Song JE, Kim D, Song H. Offset of apparent hyperpolarized 13 C lactate flux by the use of adjuvant metformin in ionizing radiation therapy in vivo. NMR Biomed 2021; 34:e4561. [PMID: 34080736 PMCID: PMC8365667 DOI: 10.1002/nbm.4561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 05/13/2023]
Abstract
An increase in hyperpolarized (HP) [1-13 C]lactate production has been suggested as a biomarker for cancer occurrence as well as for response monitoring of cancer treatment. Recently, the use of metformin has been suggested as an anticancer or adjuvant treatment. By regulating the cytosolic NAD+ /NADH redox state, metformin stimulates lactate production and increases the HP [1-13 C]lactate conversion rate in the kidney, liver, and heart. In general, increased HP [1-13 C]lactate is regarded as a sign of cancer occurrence or tumor growth. Thus, the relationship between the tumor suppression effect of metformin and the change in metabolism monitored by HP [1-13 C]pyruvate MRS in cancer treatment needs to be investigated. The present study was performed using a brain metastasis animal model with MDA-MB-231(BR)-Luc breast cancer cells. HP [1-13 C]pyruvate MRS, T2 -weighted MRI, and bioluminescence imaging were performed in groups treated with metformin or adjuvant metformin and radiation therapy. Metformin treatment alone did not display a tumor suppression effect, and the HP [1-13 C]lactate conversion rate increased. In radiation therapy, the HP [1-13 C]lactate conversion rate decreased with tumor suppression, with a p-value of 0.028. In the adjuvant metformin and radiation treatment, the tumor suppression effect increased, with a p-value of 0.001. However, the apparent HP [1-13 C]lactate conversion rate (Kpl ) was observed to be offset by two opposite effects: a decrease on radiation therapy and an increase caused by metformin treatment. Although HP [1-13 C]pyruvate MRS could not evaluate the tumor suppression effect of adjuvant metformin and radiation therapy due to the offset phenomenon, metabolic changes following only metformin pre-treatment could be monitored. Therefore, our results indicate that the interpretation of HP [1-13 C]pyruvate MRS for response monitoring of cancer treatment should be carried out with caution when metformin is used as an adjuvant cancer therapy.
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Affiliation(s)
- Young‐Suk Choi
- Department of Radiology and Research Institute of Radiological ScienceYonsei University College of MedicineSeoulSouth Korea
| | - Joonsung Lee
- Biomedical Science InstituteYonsei University College of MedicineSeoulSouth Korea
- GE HealthcareSeoulSouth Korea
| | - Han‐Sol Lee
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Jae Eun Song
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Dong‐Hyun Kim
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Ho‐Taek Song
- Department of Radiology and Research Institute of Radiological ScienceYonsei University College of MedicineSeoulSouth Korea
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27
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Shin YK, Bhandari SR, Lee JG. Monitoring of Salinity, Temperature, and Drought Stress in Grafted Watermelon Seedlings Using Chlorophyll Fluorescence. Front Plant Sci 2021; 12:786309. [PMID: 35003172 PMCID: PMC8727525 DOI: 10.3389/fpls.2021.786309] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 05/17/2023]
Abstract
Chlorophyll fluorescence (CF) is used to measure the physiological status of plants affected by biotic and abiotic stresses. Therefore, we aimed to identify the changes in CF parameters in grafted watermelon seedlings exposed to salt, drought, and high and low temperatures. Grafted watermelon seedlings at the true three-leaf stage were subjected to salinity levels (0, 50, 100, 150, and 200 mM) and temperature [low (8°C), moderate (24°C), and high (40°C)] stresses for 12 days under controlled environmental conditions independently. Eight CF parameters were measured at 2-day intervals using the FluorCam machine quenching protocol of the FluorCam machine. The seedlings were also exposed to drought stress for 3 days independent of salinity and temperature stress; CF parameters were measured at 1-day intervals. In addition, growth parameters, proline, and chlorophyll content were evaluated in all three experiments. The CF parameters were differentially influenced depending on the type and extent of the stress conditions. The results showed a notable effect of salinity levels on CF parameters, predominantly in maximum quantum yield (Fv/Fm), non-photochemical quenching (NPQ), the ratio of the fluorescence decrease (Rfd), and quantum yield of non-regulated energy dissipation in PSII [Y(NO)]. High temperature had significant effects on Rfd and NPQ, whereas low temperature showed significant results in most CF parameters: Fv/Fm, Y(NO), NPQ, Rfd, the efficiency of excitation capture of open photosystem II (PSII) center (Fv'/Fm'), and effective quantum yield of photochemical energy conversion in PSII [Y(PSII)]. Only NPQ and Rfd were significantly influenced by severe drought stress. Approximately, all the growth parameters were significantly influenced by the stress level. Proline content increased with an increase in stress levels in all three experiments, whereas the chlorophyll (a and b) content either decreased or increased depending upon the stressor. The results provided here may be useful for understanding the effect of abiotic stresses on CF parameters and the selection of index CF parameters to detect abiotic stresses in grafted watermelon seedlings.
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Affiliation(s)
- Yu Kyeong Shin
- Department of Horticulture, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Shiva Ram Bhandari
- Department of Horticulture, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, South Korea
- Core Research Institute of Intelligent Robots, Jeonbuk National University, Jeonju, South Korea
- Shiva Ram Bhandari,
| | - Jun Gu Lee
- Department of Horticulture, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, South Korea
- Core Research Institute of Intelligent Robots, Jeonbuk National University, Jeonju, South Korea
- Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju, South Korea
- *Correspondence: Jun Gu Lee,
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28
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Lee J, Hwang J, Lee K. Prediction and comparison of postural discomfort based on MLP and quadratic regression. J Occup Health 2021; 63:e12292. [PMID: 34766414 PMCID: PMC8586791 DOI: 10.1002/1348-9585.12292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE The objective of this study was to predict postural discomfort based on the deep learning-based regression (multilayer perceptron [MLP] model). METHODS A total of 95 participants performed 45 different static postures as a combination of 3 neck angles, 5 trunk angles, and 3 knee angles and rated the whole-body discomfort. Two different combinations of variables including model 1 (all variables: gender, height, weight, exercise, body segment angles) and model 2 (gender, body segment angles) were tested. The MLP regression and a conventional regression (quadratic regression) were both conducted, and the performance was compared. RESULTS In the overall regression analysis, the quadratic regression showed better performance than the MLP regression. For the postural discomfort group-specific analysis, MLP regression showed greater performance than the quadratic regression especially in the high postural discomfort group. The MLP regression also showed better performance in predicting postural discomfort among individuals who had a variability of subjective rating among different postures compared to the quadratic regression. The deep learning for postural discomfort prediction would be useful for the efficient job risk assessment for various industries that involve prolonged static postures. CONCLUSIONS The deep learning for postural discomfort prediction would be useful for the efficient job risk assessment for various industries that involve prolonged static postures. This information would be meaningful as basic research data to study in predicting psychophysical data in ergonomics.
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Affiliation(s)
- Jinwon Lee
- School of Mechanical EngineeringKorea UniversitySeoulRepublic of Korea
| | - Jaejin Hwang
- Department of Industrial and Systems EngineeringNorthern Illinois UniversityDeKalbIllinoisUSA
| | - Kyung‐Sun Lee
- Division of Energy Resources Engineering and Industrial EngineeringKangwon National UniversityChuncheonRepublic of Korea
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29
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Choi G, Jang KK, Lim JG, Lee ZW, Im H, Choi SH. The transcriptional regulator IscR integrates host-derived nitrosative stress and iron starvation in activation of the vvhBA operon in Vibrio vulnificus. J Biol Chem 2020; 295:5350-5361. [PMID: 32169898 PMCID: PMC7170529 DOI: 10.1074/jbc.ra120.012724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/09/2020] [Indexed: 12/30/2022] Open
Abstract
For successful infection of their hosts, pathogenic bacteria recognize host-derived signals that induce the expression of virulence factors in a spatiotemporal manner. The fulminating food-borne pathogen Vibrio vulnificus produces a cytolysin/hemolysin protein encoded by the vvhBA operon, which is a virulence factor preferentially expressed upon exposure to murine blood and macrophages. The Fe-S cluster containing transcriptional regulator IscR activates the vvhBA operon in response to nitrosative stress and iron starvation, during which the cellular IscR protein level increases. Here, electrophoretic mobility shift and DNase I protection assays revealed that IscR directly binds downstream of the vvhBA promoter P vvhBA , which is unusual for a positive regulator. We found that in addition to IscR, the transcriptional regulator HlyU activates vvhBA transcription by directly binding upstream of P vvhBA , whereas the histone-like nucleoid-structuring protein (H-NS) represses vvhBA by extensively binding to both downstream and upstream regions of its promoter. Of note, the binding sites of IscR and HlyU overlapped with those of H-NS. We further substantiated that IscR and HlyU outcompete H-NS for binding to the P vvhBA regulatory region, resulting in the release of H-NS repression and vvhBA induction. We conclude that concurrent antirepression by IscR and HlyU at regions both downstream and upstream of P vvhBA provides V. vulnificus with the means of integrating host-derived signal(s) such as nitrosative stress and iron starvation for precise regulation of vvhBA transcription, thereby enabling successful host infection.
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Affiliation(s)
- Garam Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea
| | - Kyung Ku Jang
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea
| | - Jong Gyu Lim
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea
| | - Zee-Won Lee
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea
| | - Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, South Korea.
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De Leoz MLA, Duewer DL, Fung A, Liu L, Yau HK, Potter O, Staples GO, Furuki K, Frenkel R, Hu Y, Sosic Z, Zhang P, Altmann F, Grunwald-Grube C, Shao C, Zaia J, Evers W, Pengelley S, Suckau D, Wiechmann A, Resemann A, Jabs W, Beck A, Froehlich JW, Huang C, Li Y, Liu Y, Sun S, Wang Y, Seo Y, An HJ, Reichardt NC, Ruiz JE, Archer-Hartmann S, Azadi P, Bell L, Lakos Z, An Y, Cipollo JF, Pucic-Bakovic M, Štambuk J, Lauc G, Li X, Wang PG, Bock A, Hennig R, Rapp E, Creskey M, Cyr TD, Nakano M, Sugiyama T, Leung PKA, Link-Lenczowski P, Jaworek J, Yang S, Zhang H, Kelly T, Klapoetke S, Cao R, Kim JY, Lee HK, Lee JY, Yoo JS, Kim SR, Suh SK, de Haan N, Falck D, Lageveen-Kammeijer GSM, Wuhrer M, Emery RJ, Kozak RP, Liew LP, Royle L, Urbanowicz PA, Packer NH, Song X, Everest-Dass A, Lattová E, Cajic S, Alagesan K, Kolarich D, Kasali T, Lindo V, Chen Y, Goswami K, Gau B, Amunugama R, Jones R, Stroop CJM, Kato K, Yagi H, Kondo S, Yuen CT, Harazono A, Shi X, Magnelli PE, Kasper BT, Mahal L, Harvey DJ, O'Flaherty R, Rudd PM, Saldova R, Hecht ES, Muddiman DC, Kang J, Bhoskar P, Menard D, Saati A, Merle C, Mast S, Tep S, Truong J, Nishikaze T, Sekiya S, Shafer A, Funaoka S, Toyoda M, de Vreugd P, Caron C, Pradhan P, Tan NC, Mechref Y, Patil S, Rohrer JS, Chakrabarti R, Dadke D, Lahori M, Zou C, Cairo C, Reiz B, Whittal RM, Lebrilla CB, Wu L, Guttman A, Szigeti M, Kremkow BG, Lee KH, Sihlbom C, Adamczyk B, Jin C, Karlsson NG, Örnros J, Larson G, Nilsson J, Meyer B, Wiegandt A, Komatsu E, Perreault H, Bodnar ED, Said N, Francois YN, Leize-Wagner E, Maier S, Zeck A, Heck AJR, Yang Y, Haselberg R, Yu YQ, Alley W, Leone JW, Yuan H, Stein SE. NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods. Mol Cell Proteomics 2020; 19:11-30. [PMID: 31591262 PMCID: PMC6944243 DOI: 10.1074/mcp.ra119.001677] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/26/2019] [Indexed: 01/24/2023] Open
Abstract
Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.
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Affiliation(s)
- Maria Lorna A De Leoz
- Mass Spectrometry Data Center, Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive Gaithersburg, Maryland 20899.
| | - David L Duewer
- Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive Gaithersburg, Maryland 20899
| | - Adam Fung
- Analytical Development, Agensys, Inc., 1800 Steward Street Santa Monica, California 90404
| | - Lily Liu
- Analytical Development, Agensys, Inc., 1800 Steward Street Santa Monica, California 90404
| | - Hoi Kei Yau
- Analytical Development, Agensys, Inc., 1800 Steward Street Santa Monica, California 90404
| | - Oscar Potter
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd Santa Clara, California 95051
| | - Gregory O Staples
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd Santa Clara, California 95051
| | - Kenichiro Furuki
- Astellas Pharma, 5-2-3 Tokodai, Tsukiba, Ibaraki, 300-2698, Japan
| | - Ruth Frenkel
- Analytical Development, Biogen, 14 Cambridge Center Cambridge, Massachusetts 02142
| | - Yunli Hu
- Analytical Development, Biogen, 14 Cambridge Center Cambridge, Massachusetts 02142
| | - Zoran Sosic
- Analytical Development, Biogen, 14 Cambridge Center Cambridge, Massachusetts 02142
| | - Peiqing Zhang
- Bioprocessing Technology Institute, 20 Biopolis Way, Level 3 Singapore 138668
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Science, Vienna (BOKU), Muthgasse 18 1190 Wien, Austria
| | - Clemens Grunwald-Grube
- Department of Chemistry, University of Natural Resources and Life Science, Vienna (BOKU), Muthgasse 18 1190 Wien, Austria
| | - Chun Shao
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street Boston, Massachusetts 02118
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street Boston, Massachusetts 02118
| | - Waltraud Evers
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | | | - Detlev Suckau
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Anja Wiechmann
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Anja Resemann
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Wolfgang Jabs
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany; Department of Life Sciences & Technology, Beuth Hochschule für Technik Berlin, Seestraβe 64, 13347 Berlin, Germany
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre, 5 Avenue Napoléon III, BP 60497, 74164 St Julien-en-Genevois, France
| | - John W Froehlich
- Department of Urology, Boston Children's Hospital, 300 Longwood Avenue Boston Massachusetts 02115
| | - Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Da Tun Road, Chaoyang District, Beijing 100101 China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Da Tun Road, Chaoyang District, Beijing 100101 China
| | - Yaming Liu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Da Tun Road, Chaoyang District, Beijing 100101 China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 15 Da Tun Road, Chaoyang District, Beijing 100101 China
| | - Yaojun Wang
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 15 Da Tun Road, Chaoyang District, Beijing 100101 China
| | - Youngsuk Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Gung-dong 220, Yuseong-Gu, Daejeon 305-764, Korea (South)
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Gung-dong 220, Yuseong-Gu, Daejeon 305-764, Korea (South)
| | | | | | - Stephanie Archer-Hartmann
- Analytical Services, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road Athens, Georgia 30602
| | - Parastoo Azadi
- Analytical Services, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road Athens, Georgia 30602
| | - Len Bell
- BioCMC Solutions (Large Molecules), Covance Laboratories Limited, Otley Road, Harrogate, North Yorks HG3 1PY, United Kingdom
| | - Zsuzsanna Lakos
- Biochemistry Method Development & Validation, Eurofins Lancaster Laboratories, Inc., 2425 New Holland Pike Lancaster, Pennsylvania 17601
| | - Yanming An
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993
| | - John F Cipollo
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993
| | - Maja Pucic-Bakovic
- Glycoscience Research Laboratory, Genos, Borongajska cesta 83h, 10 000 Zagreb, Croatia
| | - Jerko Štambuk
- Glycoscience Research Laboratory, Genos, Borongajska cesta 83h, 10 000 Zagreb, Croatia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos, Borongajska cesta 83h, 10 000 Zagreb, Croatia; Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Xu Li
- Department of Chemistry, Georgia State University, 100 Piedmont Avenue, Atlanta, Georgia 30303
| | - Peng George Wang
- Department of Chemistry, Georgia State University, 100 Piedmont Avenue, Atlanta, Georgia 30303
| | - Andreas Bock
- glyXera GmbH, Brenneckestrasse 20 * ZENIT / 39120 Magdeburg, Germany
| | - René Hennig
- glyXera GmbH, Brenneckestrasse 20 * ZENIT / 39120 Magdeburg, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestrasse 20 * ZENIT / 39120 Magdeburg, Germany; AstraZeneca, Granta Park, Cambridgeshire, CB21 6GH United Kingdom
| | - Marybeth Creskey
- Health Products and Foods Branch, Health Canada, AL 2201E, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9 Canada
| | - Terry D Cyr
- Health Products and Foods Branch, Health Canada, AL 2201E, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9 Canada
| | - Miyako Nakano
- Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan
| | - Taiki Sugiyama
- Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan
| | | | - Paweł Link-Lenczowski
- Department of Medical Physiology, Jagiellonian University Medical College, ul. Michalowskiego 12, 31-126 Krakow, Poland
| | - Jolanta Jaworek
- Department of Medical Physiology, Jagiellonian University Medical College, ul. Michalowskiego 12, 31-126 Krakow, Poland
| | - Shuang Yang
- Department of Pathology, Johns Hopkins University, 400 N. Broadway Street Baltimore, Maryland 21287
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, 400 N. Broadway Street Baltimore, Maryland 21287
| | - Tim Kelly
- Mass Spec Core Facility, KBI Biopharma, 1101 Hamlin Road Durham, North Carolina 27704
| | - Song Klapoetke
- Mass Spec Core Facility, KBI Biopharma, 1101 Hamlin Road Durham, North Carolina 27704
| | - Rui Cao
- Mass Spec Core Facility, KBI Biopharma, 1101 Hamlin Road Durham, North Carolina 27704
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongwon-gu, Cheongju Chungbuk, 363-883 Korea (South)
| | - Hyun Kyoung Lee
- Division of Mass Spectrometry, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongwon-gu, Cheongju Chungbuk, 363-883 Korea (South)
| | - Ju Yeon Lee
- Division of Mass Spectrometry, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongwon-gu, Cheongju Chungbuk, 363-883 Korea (South)
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongwon-gu, Cheongju Chungbuk, 363-883 Korea (South)
| | - Sa-Rang Kim
- Advanced Therapy Products Research Division, Korea National Institute of Food and Drug Safety, 187 Osongsaengmyeong 2-ro Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 363-700, Korea (South)
| | - Soo-Kyung Suh
- Advanced Therapy Products Research Division, Korea National Institute of Food and Drug Safety, 187 Osongsaengmyeong 2-ro Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 363-700, Korea (South)
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robert J Emery
- Ludger Limited, Culham Science Centre, Abingdon, Oxfordshire, OX14 3EB, United Kingdom
| | - Radoslaw P Kozak
- Ludger Limited, Culham Science Centre, Abingdon, Oxfordshire, OX14 3EB, United Kingdom
| | - Li Phing Liew
- Ludger Limited, Culham Science Centre, Abingdon, Oxfordshire, OX14 3EB, United Kingdom
| | - Louise Royle
- Ludger Limited, Culham Science Centre, Abingdon, Oxfordshire, OX14 3EB, United Kingdom
| | - Paulina A Urbanowicz
- Ludger Limited, Culham Science Centre, Abingdon, Oxfordshire, OX14 3EB, United Kingdom
| | - Nicolle H Packer
- Biomolecular Discovery and Design Research Centre and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, North Ryde, Australia
| | - Xiaomin Song
- Biomolecular Discovery and Design Research Centre and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, North Ryde, Australia
| | - Arun Everest-Dass
- Biomolecular Discovery and Design Research Centre and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, North Ryde, Australia
| | - Erika Lattová
- Proteomics, Central European Institute for Technology, Masaryk University, Kamenice 5, A26, 625 00 BRNO, Czech Republic
| | - Samanta Cajic
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Kathirvel Alagesan
- Department of Biomolecular Sciences, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Daniel Kolarich
- Department of Biomolecular Sciences, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Toyin Kasali
- AstraZeneca, Granta Park, Cambridgeshire, CB21 6GH United Kingdom
| | - Viv Lindo
- AstraZeneca, Granta Park, Cambridgeshire, CB21 6GH United Kingdom
| | - Yuetian Chen
- Merck, 2015 Galloping Hill Rd, Kenilworth, New Jersey 07033
| | - Kudrat Goswami
- Merck, 2015 Galloping Hill Rd, Kenilworth, New Jersey 07033
| | - Brian Gau
- Analytical R&D, MilliporeSigma, 2909 Laclede Ave. St. Louis, Missouri 63103
| | - Ravi Amunugama
- MS Bioworks, LLC, 3950 Varsity Drive Ann Arbor, Michigan 48108
| | - Richard Jones
- MS Bioworks, LLC, 3950 Varsity Drive Ann Arbor, Michigan 48108
| | | | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787 Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603 Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603 Japan
| | - Sachiko Kondo
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603 Japan; Medical & Biological Laboratories Co., Ltd, 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858 Japan
| | - C T Yuen
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG United Kingdom
| | - Akira Harazono
- Division of Biological Chemistry & Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501 Japan
| | - Xiaofeng Shi
- New England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938
| | - Paula E Magnelli
- New England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938
| | - Brian T Kasper
- New York University, 100 Washington Square East New York City, New York 10003
| | - Lara Mahal
- New York University, 100 Washington Square East New York City, New York 10003
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - Roisin O'Flaherty
- GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Pauline M Rudd
- GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Radka Saldova
- GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Elizabeth S Hecht
- Department of Chemistry, North Carolina State University, 2620 Yarborough Drive Raleigh, North Carolina 27695
| | - David C Muddiman
- Department of Chemistry, North Carolina State University, 2620 Yarborough Drive Raleigh, North Carolina 27695
| | - Jichao Kang
- Pantheon, 201 College Road East Princeton, New Jersey 08540
| | | | | | - Andrew Saati
- Pfizer Inc., 1 Burtt Road Andover, Massachusetts 01810
| | - Christine Merle
- Proteodynamics, ZI La Varenne 20-22 rue Henri et Gilberte Goudier 63200 RIOM, France
| | - Steven Mast
- ProZyme, Inc., 3832 Bay Center Place Hayward, California 94545
| | - Sam Tep
- ProZyme, Inc., 3832 Bay Center Place Hayward, California 94545
| | - Jennie Truong
- ProZyme, Inc., 3832 Bay Center Place Hayward, California 94545
| | - Takashi Nishikaze
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho Nakagyo-ku, Kyoto, 604 8511 Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho Nakagyo-ku, Kyoto, 604 8511 Japan
| | - Aaron Shafer
- Children's GMP LLC, St. Jude Children's Research Hospital, 262 Danny Thomas Place Memphis, Tennessee 38105
| | - Sohei Funaoka
- Sumitomo Bakelite Co., Ltd., 1-5 Muromati 1-Chome, Nishiku, Kobe, 651-2241 Japan
| | - Masaaki Toyoda
- Sumitomo Bakelite Co., Ltd., 1-5 Muromati 1-Chome, Nishiku, Kobe, 651-2241 Japan
| | - Peter de Vreugd
- Synthon Biopharmaceuticals, Microweg 22 P.O. Box 7071, 6503 GN Nijmegen, The Netherlands
| | - Cassie Caron
- Takeda Pharmaceuticals International Co., 40 Landsdowne Street Cambridge, Massachusetts 02139
| | - Pralima Pradhan
- Takeda Pharmaceuticals International Co., 40 Landsdowne Street Cambridge, Massachusetts 02139
| | - Niclas Chiang Tan
- Takeda Pharmaceuticals International Co., 40 Landsdowne Street Cambridge, Massachusetts 02139
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, Texas 79409
| | - Sachin Patil
- Thermo Fisher Scientific, 1214 Oakmead Parkway Sunnyvale, California 94085
| | - Jeffrey S Rohrer
- Thermo Fisher Scientific, 1214 Oakmead Parkway Sunnyvale, California 94085
| | - Ranjan Chakrabarti
- United States Pharmacopeia India Pvt. Ltd. IKP Knowledge Park, Genome Valley, Shamirpet, Turkapally Village, Medchal District, Hyderabad 500 101 Telangana, India
| | - Disha Dadke
- United States Pharmacopeia India Pvt. Ltd. IKP Knowledge Park, Genome Valley, Shamirpet, Turkapally Village, Medchal District, Hyderabad 500 101 Telangana, India
| | - Mohammedazam Lahori
- United States Pharmacopeia India Pvt. Ltd. IKP Knowledge Park, Genome Valley, Shamirpet, Turkapally Village, Medchal District, Hyderabad 500 101 Telangana, India
| | - Chunxia Zou
- Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2 Canada; Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
| | - Christopher Cairo
- Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2 Canada; Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
| | - Randy M Whittal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, One Shields Ave, Davis, California 95616
| | - Lauren Wu
- Department of Chemistry, University of California, One Shields Ave, Davis, California 95616
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory for Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Egyetem ter 1, Hungary
| | - Marton Szigeti
- Horváth Csaba Memorial Laboratory for Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Egyetem ter 1, Hungary; Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Egyetem ut 10, Hungary
| | - Benjamin G Kremkow
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way Newark, Delaware 19711
| | - Kelvin H Lee
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way Newark, Delaware 19711
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Medicinaregatan 1G SE 41390 Gothenburg, Sweden
| | - Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Institute of Biomedicine, Sahlgrenska Academy, Medicinaregatan 9A, Box 440, 405 30, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Institute of Biomedicine, Sahlgrenska Academy, Medicinaregatan 9A, Box 440, 405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Institute of Biomedicine, Sahlgrenska Academy, Medicinaregatan 9A, Box 440, 405 30, Gothenburg, Sweden
| | - Jessica Örnros
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Institute of Biomedicine, Sahlgrenska Academy, Medicinaregatan 9A, Box 440, 405 30, Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Bruna Straket 16, 41345 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Bruna Straket 16, 41345 Gothenburg, Sweden
| | - Bernd Meyer
- Department of Chemistry, University of Hamburg, Martin Luther King Pl. 6 20146 Hamburg, Germany
| | - Alena Wiegandt
- Department of Chemistry, University of Hamburg, Martin Luther King Pl. 6 20146 Hamburg, Germany
| | - Emy Komatsu
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Helene Perreault
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Edward D Bodnar
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, Canada R3T 2N2; Agilent Technologies, Inc., 5301 Stevens Creek Blvd Santa Clara, California 95051
| | - Nassur Said
- Laboratory of Mass Spectrometry of Interactions and Systems, University of Strasbourg, UMR Unistra-CNRS 7140, France
| | - Yannis-Nicolas Francois
- Laboratory of Mass Spectrometry of Interactions and Systems, University of Strasbourg, UMR Unistra-CNRS 7140, France
| | - Emmanuelle Leize-Wagner
- Laboratory of Mass Spectrometry of Interactions and Systems, University of Strasbourg, UMR Unistra-CNRS 7140, France
| | - Sandra Maier
- Natural and Medical Sciences Institute, University of Tübingen, Markwiesenstraβe 55, 72770 Reutlingen, Germany
| | - Anne Zeck
- Natural and Medical Sciences Institute, University of Tübingen, Markwiesenstraβe 55, 72770 Reutlingen, Germany
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Yang Yang
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rob Haselberg
- Division of Bioanalytical Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ying Qing Yu
- Department of Chemistry, Waters Corporation, 34 Maple Street Milford, Massachusetts 01757
| | - William Alley
- Department of Chemistry, Waters Corporation, 34 Maple Street Milford, Massachusetts 01757
| | | | - Hua Yuan
- Zoetis, 333 Portage St. Kalamazoo, Michigan 49007
| | - Stephen E Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive Gaithersburg, Maryland 20899
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Jung Y, Ryu HG, Kim SW, Lee KH, Gu S, Yi H, Ku HO, Jang SK, Kim KT. The RNA-binding protein hnRNP Q represses translation of the clock gene Bmal1 in murine cells. J Biol Chem 2019; 294:7682-7691. [PMID: 30948510 PMCID: PMC6514626 DOI: 10.1074/jbc.ra118.006947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/28/2019] [Indexed: 11/06/2022] Open
Abstract
Most living creatures have a circadian rhythm that is generated by a precisely regulated transcriptional-translational feedback loop of clock genes. Brain and muscle ARNT-like 1 (BMAL1) is one of the core clock genes and transcription factors that represents a positive arm of this autoregulatory circadian clock system. Despite the indispensable role of BMAL1 in the circadian rhythm, the molecular mechanisms underlying translational control of BMAL1 are largely unknown. Here, using murine NIH-3T3 cells, gene constructs, and a variety of biochemical approaches, including RNAi- and luciferase reporter gene-based assays, along with immunoblotting, in vitro transcription, quantitative real-time PCR, and real-time bioluminescence experiments, we show that translation of Bmal1 is negatively regulated by an RNA-binding protein, heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Interestingly, we found that hnRNP Q rhythmically binds to a specific region of the Bmal1 mRNA 5' UTR and controls its time-dependent expression. Moreover, we demonstrate that knockdown of hnRNP Q modulates BMAL1 protein oscillation amplitude without affecting mRNA rhythmic patterns. Furthermore, hnRNP Q depletion increases the mRNA oscillation amplitudes of BMAL1-regulated target genes. Together, our results suggest that hnRNP Q plays a pivotal role in both Bmal1 translation and BMAL1-regulated gene expression.
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Affiliation(s)
- Youngseob Jung
- From the Division of Integrative Biosciences and Biotechnology and
| | - Hye Guk Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sung Wook Kim
- From the Division of Integrative Biosciences and Biotechnology and
| | - Kyung-Ha Lee
- the Division of Cosmetic Science and Technology, Daegu Haany University, Gyeongsan, Gyeongbuk 38610, Republic of Korea, and
| | - Sohyun Gu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hee Yi
- the Vet Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongbuk 39660, Republic of Korea
| | - Hyun-Ok Ku
- the Vet Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongbuk 39660, Republic of Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyong-Tai Kim
- From the Division of Integrative Biosciences and Biotechnology and
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
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Jang SY, Hwang J, Kim BS, Lee EY, Oh BH, Kim MH. Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogen Vibrio vulnificus. J Biol Chem 2018; 293:18110-18122. [PMID: 30282804 PMCID: PMC6254334 DOI: 10.1074/jbc.ra118.004857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are secreted by Gram-negative bacteria and function as primary virulence-promoting macromolecules that deliver multiple cytopathic and cytotoxic effector domains into the host cytoplasm. Among these effectors, Ras/Rap1-specific endopeptidase (RRSP) catalyzes the sequence-specific cleavage of the Switch I region of the cellular substrates Ras and Rap1 that are crucial for host innate immune defenses during infection. To dissect the molecular basis underpinning RRSP-mediated substrate inactivation, we determined the crystal structure of an RRSP from the sepsis-causing bacterial pathogen Vibrio vulnificus (VvRRSP). Structural and biochemical analyses revealed that VvRRSP is a metal-independent TIKI family endopeptidase composed of an N-terminal membrane-localization and substrate-recruitment domain (N lobe) connected via an inter-lobe linker to the C-terminal active site-coordinating core β-sheet-containing domain (C lobe). Structure-based mutagenesis identified the 2His/2Glu catalytic residues in the core catalytic domain that are shared with other TIKI family enzymes and that are essential for Ras processing. In vitro KRas cleavage assays disclosed that deleting the N lobe in VvRRSP causes complete loss of enzymatic activity. Endogenous Ras cleavage assays combined with confocal microscopy analysis of HEK293T cells indicated that the N lobe functions both in membrane localization via the first α-helix and in substrate assimilation by altering the functional conformation of the C lobe to facilitate recruitment of cellular substrates. Collectively, these results indicate that RRSP is a critical virulence factor that robustly inactivates Ras and Rap1 and augments the pathogenicity of invading bacteria via the combined effects of its N and C lobes.
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Affiliation(s)
- Song Yee Jang
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,; the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and
| | - Jungwon Hwang
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and.
| | - Byoung Sik Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and; the Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea
| | - Eun-Young Lee
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and
| | - Byung-Ha Oh
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,.
| | - Myung Hee Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and.
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Kang SK, Seo S, Shin SA, Byun MS, Lee DY, Kim YK, Lee DS, Lee JS. Adaptive template generation for amyloid PET using a deep learning approach. Hum Brain Mapp 2018; 39:3769-3778. [PMID: 29752765 PMCID: PMC6866631 DOI: 10.1002/hbm.24210] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/26/2022] Open
Abstract
Accurate spatial normalization (SN) of amyloid positron emission tomography (PET) images for Alzheimer's disease assessment without coregistered anatomical magnetic resonance imaging (MRI) of the same individual is technically challenging. In this study, we applied deep neural networks to generate individually adaptive PET templates for robust and accurate SN of amyloid PET without using matched 3D MR images. Using 681 pairs of simultaneously acquired 11 C-PIB PET and T1-weighted 3D MRI scans of AD, MCI, and cognitively normal subjects, we trained and tested two deep neural networks [convolutional auto-encoder (CAE) and generative adversarial network (GAN)] that produce adaptive best PET templates. More specifically, the networks were trained using 685,100 pieces of augmented data generated by rotating 527 randomly selected datasets and validated using 154 datasets. The input to the supervised neural networks was the 3D PET volume in native space and the label was the spatially normalized 3D PET image using the transformation parameters obtained from MRI-based SN. The proposed deep learning approach significantly enhanced the quantitative accuracy of MRI-less amyloid PET assessment by reducing the SN error observed when an average amyloid PET template is used. Given an input image, the trained deep neural networks rapidly provide individually adaptive 3D PET templates without any discontinuity between the slices (in 0.02 s). As the proposed method does not require 3D MRI for the SN of PET images, it has great potential for use in routine analysis of amyloid PET images in clinical practice and research.
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Affiliation(s)
- Seung Kwan Kang
- Department of Biomedical SciencesSeoul National UniversitySeoulKorea
- Department of Nuclear MedicineSeoul National UniversitySeoulKorea
| | - Seongho Seo
- Department of Neuroscience, College of MedicineGachon UniversityIncheonKorea
| | - Seong A. Shin
- Department of Biomedical SciencesSeoul National UniversitySeoulKorea
- Department of Nuclear MedicineSeoul National University Boramae Medical CenterSeoulKorea
| | - Min Soo Byun
- Department of NeuropsychiatrySeoul National UniversitySeoulKorea
| | - Dong Young Lee
- Department of NeuropsychiatrySeoul National UniversitySeoulKorea
| | - Yu Kyeong Kim
- Department of Nuclear MedicineSeoul National University Boramae Medical CenterSeoulKorea
| | - Dong Soo Lee
- Department of Nuclear MedicineSeoul National UniversitySeoulKorea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and TechnologySeoul National UniversitySuwonKorea
- Institute of Radiation MedicineMedical Research Center, Seoul National UniversitySeoulKorea
| | - Jae Sung Lee
- Department of Biomedical SciencesSeoul National UniversitySeoulKorea
- Department of Nuclear MedicineSeoul National UniversitySeoulKorea
- Institute of Radiation MedicineMedical Research Center, Seoul National UniversitySeoulKorea
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Jin H, Roy U, Lee G, Schärer OD, Cho Y. Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease. J Biol Chem 2018; 293:6482-6496. [PMID: 29514982 PMCID: PMC5925792 DOI: 10.1074/jbc.ra118.002171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/05/2018] [Indexed: 01/04/2023] Open
Abstract
DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway. Recent structural studies have proposed two different mechanistic features for ICL unhooking by human FAN1: a specific basic pocket that recognizes the terminal phosphate of a 1-nucleotide (nt) 5' flap or FAN1 dimerization. Herein, we show that despite lacking these features, Pseudomonas aeruginosa FAN1 (PaFAN1) cleaves substrates at ∼3-nt intervals and resolves ICLs. Crystal structures of PaFAN1 bound to various DNA substrates revealed that its conserved basic Arg/Lys patch comprising Arg-228 and Lys-260 recognizes phosphate groups near the 5' terminus of a DNA substrate with a 1-nt flap or a nick. Substitution of Lys-260 did not affect PaFAN1's initial endonuclease activity but significantly decreased its subsequent exonuclease activity and ICL unhooking. The Arg/Lys patch also interacted with phosphates at a 3-nt gap, and this interaction could drive movement of the scissile phosphates into the PaFAN1-active site. In human FAN1, the ICL-resolving activity was not affected by individual disruption of the Arg/Lys patch or basic pocket. However, simultaneous substitution of both FAN1 regions significantly reduced its ICL-resolving activity, suggesting that these two basic regions play a complementary role in ICL repair. On the basis of these findings, we propose a conserved role for two basic regions in FAN1 to guide ICL unhooking and to maintain genomic stability.
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Affiliation(s)
- Hyeonseok Jin
- From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Upasana Roy
- the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794
| | - Gwangrog Lee
- the Department of Biology, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Orlando D Schärer
- the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea, and
- the Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Yunje Cho
- From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea,
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