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Liu R, Han M, Liu X, Yu K, Bai X, Dong Y. Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle. Front Genet 2022; 13:849399. [PMID: 35651943 PMCID: PMC9149217 DOI: 10.3389/fgene.2022.849399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
There is an increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. In this study, the transcriptome numbers of longissimus muscle of different beef cattle (Shandong black catle and Luxi catlle) were used to construct muscle related lncRNAs-miRNA-mRNA interaction network through bioinformatics analysis. This is helpful to clarify the molecular mechanism of bovine muscle development, and can be used to promote animal husbandry and improve animal husbandry production. According to the screening criteria of |FC|≧2 and q < 0.05, a total of 1,415 transcripts (of which 480 were LncRNAs) were differentially expressed (q < 0.05) in the different breeds. Further, we found that the most differentially expressed LncRNAs were found on chromosome 9, in which the differentially expressed LncRNAs targeted 1,164 protein coding genes (MYORG, Wnt4, PAK1, ADCY7,etc) (upstream and downstream<50 Kb). In addition, Pearson’s correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may combined miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds.
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Affiliation(s)
- Ruili Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Mingxuan Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xianxun Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Kun Yu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xuejin Bai
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Yajuan Dong
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
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Ramirez I, Gholkar AA, Velasquez EF, Guo X, Tofig B, Damoiseaux R, Torres JZ. The myosin regulatory light chain Myl5 localizes to mitotic spindle poles and is required for proper cell division. Cytoskeleton (Hoboken) 2021; 78:23-35. [PMID: 33641240 DOI: 10.1002/cm.21654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022]
Abstract
Myosins are ATP-dependent actin-based molecular motors critical for diverse cellular processes like intracellular trafficking, cell motility, and cell invasion. During cell division, myosin MYO10 is important for proper mitotic spindle assembly, the anchoring of the spindle to the cortex, and positioning of the spindle to the cell mid-plane. However, myosins are regulated by myosin regulatory light chains (RLCs), and whether RLCs are important for cell division has remained unexplored. Here, we have determined that the previously uncharacterized myosin RLC Myl5 associates with the mitotic spindle and is required for cell division. We show that Myl5 localizes to the leading edge and filopodia during interphase and to mitotic spindle poles and spindle microtubules during early mitosis. Importantly, depletion of Myl5 led to defects in mitotic spindle assembly, chromosome congression, and chromosome segregation and to a slower transition through mitosis. Furthermore, Myl5 bound to MYO10 in vitro and co-localized with MYO10 at the spindle poles. These results suggest that Myl5 is important for cell division and that it may be performing its function through MYO10.
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Affiliation(s)
- Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Erick F Velasquez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Xiao Guo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Bobby Tofig
- California NanoSystems Institute, Los Angeles, California, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, Los Angeles, California, USA.,Department of Molecular and Medical Pharmacology, Los Angeles, California, USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA.,Molecular Biology Institute, University of California, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
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Ling Y, Zheng Q, Sui M, Zhu L, Xu L, Zhang Y, Liu Y, Fang F, Chu M, Ma Y, Zhang X. Comprehensive Analysis of LncRNA Reveals the Temporal-Specific Module of Goat Skeletal Muscle Development. Int J Mol Sci 2019; 20:ijms20163950. [PMID: 31416143 PMCID: PMC6719106 DOI: 10.3390/ijms20163950] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022] Open
Abstract
A series of complex processes regulate muscle development, and lncRNAs play essential roles in the regulation of skeletal myogenesis. Using RNA sequencing, we profiled the lncRNA expression during goat (Capra hircus) skeletal muscle development, which included seven stages across fetal 45 (F45), 65 (F65), 90 (F90), 120 (F120), 135 (F135) days, born for 24 h (B1) and 90 (B90) days. A total of 15,079 lncRNAs were identified in the seven stages, and they were less conservative with other species (human, cow, and mouse). Among them, 547 were differentially expressed, and they divided the seven stages into three functional transition periods. Following weighted gene co-expression network analysis (WGCNA), five lncRNA modules specific for developmental stages were defined as three types: 'Early modules', 'late modules', and 'individual-stage-specific modules'. The enrichment content showed that 'early modules' were related to muscle structure formation, 'late modules' participated in the 'p53 signaling pathway' and other pathways, the F90-highly related module was involved in the 'MAPK signaling pathway', and other pathways. Furthermore, we identified hub-lncRNA in three types of modules, and LNC_011371, LNC_ 007561, and LNC_001728 may play important roles in goat skeletal muscle. These data will facilitate further exploration of skeletal muscle lncRNA functions at different developmental stages in goats.
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Affiliation(s)
- Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Lu Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Lina Xu
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230036, China
| | - Yunhai Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Ya Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuehui Ma
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
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Turathum B, Roytrakul S, Changsangfa C, Sroyraya M, Tanasawet S, Kitiyanant Y, Saikhun K. Missing and overexpressing proteins in domestic cat oocytes following vitrification and in vitro maturation as revealed by proteomic analysis. Biol Res 2018; 51:27. [PMID: 30124164 PMCID: PMC6100730 DOI: 10.1186/s40659-018-0176-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/12/2018] [Indexed: 12/18/2022] Open
Abstract
Background The domestic cat serves as an animal model for assisted reproductive studies of endangered felid species. To date, there are no data on the protein alterations following cryopreservation of oocytes in felid family. Methods Immature (germinal vesicle) domestic cat oocytes were vitrified in the vitrification solution containing 35% ethylene glycol, 20% DMSO and 0.5 mM sucrose. The vitrified-warmed oocytes were matured (metaphase II) in vitro and subjected to proteomic analysis using 1DE SDS-PAGE prefractionation combined with LC–MS/MS. Results A total of 1712 proteins were identified in in vitro matured oocytes. Of the 1712 proteins, 1454 proteins were found in both groups, whereas, 258 proteins were differentially expressed between control and vitrified-warmed groups. In vitrified-warmed oocytes, the missing proteins were membrane and nuclear proteins; whereas, apoptosis and DNA repair proteins were overrepresented. Conclusions The identified missing and overexpressed proteins in vitrified-warmed oocytes represent potential markers of cryoinjuries and the developmental pathways of oocytes. The findings of differential expressed proteins may contribute to effective ways of proteome analysis of oocyte/embryo quality in order to assess safety of cryopreservation in felid species.
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Affiliation(s)
- Bongkoch Turathum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, 12121, Thailand
| | - Chinarat Changsangfa
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Morakot Sroyraya
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Supita Tanasawet
- Department of Anatomy, Faculty of Science, Prince of Songkla University, Hat Yai, 90110, Thailand
| | - Yindee Kitiyanant
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kulnasan Saikhun
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Bennett RD, Pittelkow MR, Strehler EE. Immunolocalization of the tumor-sensitive calmodulin-like protein CALML3 in normal human skin and hyperproliferative skin disorders. PLoS One 2013; 8:e62347. [PMID: 23638045 PMCID: PMC3630146 DOI: 10.1371/journal.pone.0062347] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/20/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Calmodulin-like protein CALML3 is an epithelial-specific protein regulated during keratinocyte differentiation in vitro. CALML3 expression is downregulated in breast cancers and transformed cell lines making it an attractive marker for tumor formation. The objective of this study was to survey CALML3 localization in normal epidermis and in hyperproliferative skin diseases including actinic keratosis, squamous and basal cell carcinoma as well as verruca and psoriasis and to compare CALML3 immunoreactivity with the proliferation marker Ki-67. METHODS Paraffin-embedded tissue sections from normal human skin and hyperproliferative skin disorders were examined by immunohistochemistry and analyzed for localization and expression of CALML3 and Ki-67. RESULTS CALML3 was strongly expressed in differentiating layers of normal skin, staining the periphery in suprabasal cells and exhibiting nuclear localization in the stratum granulosum. CALML3 nuclear localization was inversely correlated to Ki-67 staining in each disease, indicating that CALML3 nuclear presence is related to terminal cell differentiation and postmitotic state. CONCLUSIONS Increased CALML3 expression in suprabasal layers is characteristic for differentiating keratinocytes in normal epidermis, and nuclear expression of CALML3 inversely correlates with expression of the proliferation marker Ki-67. This suggests that CALML3 is a useful marker for normal and benign hyperplastic epidermal development, whereas the loss of nuclear CALML3 indicates progression to a proliferative and potentially malignant phenotype.
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Affiliation(s)
- Richard D. Bennett
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- Department of Cell Biology and Genetics Program, Graduate School, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Mark R. Pittelkow
- Department of Dermatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Emanuel E. Strehler
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * E-mail:
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Yu H, Wang N, Ju X, Yang Y, Sun D, Lai M, Cui L, Sheikh MA, Zhang J, Wang X, Zhu X. PtdIns (3,4,5) P3 recruitment of Myo10 is essential for axon development. PLoS One 2012; 7:e36988. [PMID: 22590642 PMCID: PMC3349655 DOI: 10.1371/journal.pone.0036988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 04/11/2012] [Indexed: 02/03/2023] Open
Abstract
Myosin X (Myo10) with pleckstrin homology (PH) domains is a motor protein acting in filopodium initiation and extension. However, its potential role has not been fully understood, especially in neuronal development. In the present study the preferential accumulation of Myo10 in axon tips has been revealed in primary culture of hippocampal neurons with the aid of immunofluorescence from anti-Myo10 antibody in combination with anti-Tuj1 antibody as specific marker. Knocking down Myo10 gene transcription impaired outgrowth of axon with loss of Tau-1-positive phenotype. Interestingly, inhibition of actin polymerization by cytochalasin D rescued the defect of axon outgrowth. Furthermore, ectopic expression of Myo10 with enhanced green fluorescence protein (EGFP) labeled Myo10 mutants induced multiple axon-like neurites in a motor-independent way. Mechanism studies demonstrated that the recruitment of Myo10 through its PH domain to phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5) P3) was essential for axon formation. In addition, in vivo studies confirmed that Myo10 was required for neuronal morphological transition during radial neuronal migration in the developmental neocortex.
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Affiliation(s)
- Huali Yu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Nannan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Xingda Ju
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Yan Yang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Dong Sun
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Mingming Lai
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Lei Cui
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Muhammad Abid Sheikh
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Jianhua Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Xingzhi Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Xiaojuan Zhu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
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Abstract
Myosin-X (Myo10) is an unconventional myosin with MyTH4-FERM domains that is best known for its striking localization to the tips of filopodia and its ability to induce filopodia. Although the head domain of Myo10 enables it to function as an actin-based motor, its tail contains binding sites for several molecules with central roles in cell biology, including phosphatidylinositol (3,4,5)-trisphosphate, microtubules and integrins. Myo10 also undergoes fascinating long-range movements within filopodia, which appear to represent a newly recognized system of transport. Myo10 is also unusual in that it is a myosin with important roles in the spindle, a microtubule-based structure. Exciting new studies have begun to reveal the structure and single-molecule properties of this intriguing myosin, as well as its mechanisms of regulation and induction of filopodia. At the cellular and organismal level, growing evidence demonstrates that Myo10 has crucial functions in numerous processes ranging from invadopodia formation to cell migration.
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Affiliation(s)
- Michael L Kerber
- Department of Cell and Molecular Physiology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7545, USA
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Caride AJ, Bennett RD, Strehler EE. Kinetic analysis reveals differences in the binding mechanism of calmodulin and calmodulin-like protein to the IQ motifs of myosin-10. Biochemistry 2010; 49:8105-16. [PMID: 20731332 DOI: 10.1021/bi100644q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Myo10 is an unconventional myosin with important functions in filopodial motility, cell migration, and cell adhesion. The neck region of Myo10 contains three IQ motifs that bind calmodulin (CaM) or the tissue-restricted calmodulin-like protein (CLP) as light chains. However, little is known about the mechanism of light chain binding to the IQ motifs in Myo10. Binding of CaM and CLP to each IQ motif was assessed by nondenaturing gel electrophoresis and by stopped-flow experiments using fluorescence-labeled CaM and CLP. Although the binding kinetics are different in each case, there are similarities in the mechanism of binding of CaM and CLP to IQ1 and IQ2: for both IQ motifs Ca(2+) increased the binding affinity, mainly by increasing the rate of the forward steps. The general kinetic mechanism comprises a two-step process, which in some cases may involve the binding of a second IQ motif with lower affinity. For IQ3, however, the kinetics of CaM binding is very different from that of CLP. In both cases, binding in the absence of Ca(2+) is poor, and addition of Ca(2+) decreases the K(d) to below 10 nM. However, while the CaM binding kinetics are complex and best fitted by a multistep model, binding of CLP is fitted by a relatively simple two-step model. The results show that, in keeping with growing structural evidence, complexes between CaM or CaM-like myosin light chains and IQ motifs are highly diverse and depend on the specific sequence of the particular IQ motif as well as the light chain.
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Affiliation(s)
- Ariel J Caride
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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