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Beaudier P, Devès G, Plawinski L, Dupuy D, Barberet P, Seznec H. Proton Microbeam Targeted Irradiation of the Gonad Primordium Region Induces Developmental Alterations Associated with Heat Shock Responses and Cuticle Defense in Caenorhabditis elegans. BIOLOGY 2023; 12:1372. [PMID: 37997971 PMCID: PMC10669138 DOI: 10.3390/biology12111372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
We describe a methodology to manipulate Caenorhabditis elegans (C. elegans) and irradiate the stem progenitor gonad region using three MeV protons at a specific developmental stage (L1). The consequences of the targeted irradiation were first investigated by considering the organogenesis of the vulva and gonad, two well-defined and characterized developmental systems in C. elegans. In addition, we adapted high-throughput analysis protocols, using cell-sorting assays (COPAS) and whole transcriptome analysis, to the limited number of worms (>300) imposed by the selective irradiation approach. Here, the presented status report validated protocols to (i) deliver a controlled dose in specific regions of the worms; (ii) immobilize synchronized worm populations (>300); (iii) specifically target dedicated cells; (iv) study the radiation-induced developmental alterations and gene induction involved in cellular stress (heat shock protein) and cuticle injury responses that were found.
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Affiliation(s)
- Pierre Beaudier
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France; (P.B.); (G.D.); (L.P.); (P.B.)
| | - Guillaume Devès
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France; (P.B.); (G.D.); (L.P.); (P.B.)
| | - Laurent Plawinski
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France; (P.B.); (G.D.); (L.P.); (P.B.)
| | - Denis Dupuy
- University Bordeaux, INSERM, U1212, 33607 Pessac, France
| | - Philippe Barberet
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France; (P.B.); (G.D.); (L.P.); (P.B.)
| | - Hervé Seznec
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France; (P.B.); (G.D.); (L.P.); (P.B.)
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2
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Kumar AV, Mills J, Parker WM, Leitão JA, Rodriguez DI, Daigle SE, Ng C, Patel R, Aguilera JL, Johnson JR, Wong SQ, Lapierre LR. Lipid droplets modulate proteostasis, SQST-1/SQSTM1 dynamics, and lifespan in C. elegans. iScience 2023; 26:107960. [PMID: 37810233 PMCID: PMC10551902 DOI: 10.1016/j.isci.2023.107960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 06/01/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
In several long-lived Caenorhabditis elegans strains, such as insulin/IGF-1 receptor daf-2 mutants, enhanced proteostatic mechanisms are accompanied by elevated intestinal lipid stores, but their role in longevity is unclear. Here, while determining the regulatory network of the selective autophagy receptor SQST-1/SQSTM1, we uncovered an important role for lipid droplets in proteostasis and longevity. Using genome-wide RNAi screening, we identified several SQST-1 modulators, including lipid droplets-associated and aggregation-prone proteins. Expansion of intestinal lipid droplets by silencing the conserved cytosolic triacylglycerol lipase gene atgl-1/ATGL enhanced autophagy, and extended lifespan. Notably, a substantial amount of ubiquitinated proteins were found on lipid droplets. Reducing lipid droplet levels exacerbated the proteostatic collapse when autophagy or proteasome function was compromised, and significantly reduced the lifespan of long-lived daf-2 animals. Altogether, our study uncovered a key role for lipid droplets in C. elegans as a proteostatic mediator that modulates ubiquitinated protein accumulation, facilitates autophagy, and promotes longevity.
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Affiliation(s)
- Anita V Kumar
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Joslyn Mills
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Biology Department, Wheaton College, 26 E. Main Street, Norton, MA 02766, USA
| | - Wesley M Parker
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Joshua A Leitão
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Diego I Rodriguez
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Sandrine E Daigle
- New Brunswick Center for Precision Medicine, 27 rue Providence, Moncton, NB E1C 8X3, Canada
- Département de chimie et biochimie, Université de Moncton, 18 Antonine Maillet, Moncton, NB E1A 3E9, Canada
| | - Celeste Ng
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Rishi Patel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Joseph L Aguilera
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Joseph R Johnson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Shi Quan Wong
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Louis R Lapierre
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- New Brunswick Center for Precision Medicine, 27 rue Providence, Moncton, NB E1C 8X3, Canada
- Département de chimie et biochimie, Université de Moncton, 18 Antonine Maillet, Moncton, NB E1A 3E9, Canada
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3
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Liska D, Wolfe Z, Norris A. VISTA: visualizing the spatial transcriptome of the C.elegans nervous system. BIOINFORMATICS ADVANCES 2023; 3:vbad127. [PMID: 37810458 PMCID: PMC10560093 DOI: 10.1093/bioadv/vbad127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023]
Abstract
Summary Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm Caenorhabditis elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future. Availability and implementation VISTA is freely available at the following URL: https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University, Dallas, TX 75205, United States
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
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4
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Liska D, Wolfe Z, Norris A. VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538711. [PMID: 37163055 PMCID: PMC10168398 DOI: 10.1101/2023.04.28.538711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm C. elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently-generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation, and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University. Dallas, TX USA
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
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5
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Xiao Y, Yee C, Zhao CZ, Martinez MAQ, Zhang W, Shen K, Matus DQ, Hammell C. An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans. Genetics 2023; 223:iyad013. [PMID: 36722258 PMCID: PMC10319979 DOI: 10.1093/genetics/iyad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 02/02/2023] Open
Abstract
The auxin-inducible degradation system has been widely adopted in the Caenorhabditis elegans research community for its ability to empirically control the spatiotemporal expression of target proteins. This system can efficiently degrade auxin-inducible degron (AID)-tagged proteins via the expression of a ligand-activatable AtTIR1 protein derived from A. thaliana that adapts target proteins to the endogenous C. elegans proteasome. While broad expression of AtTIR1 using strong, ubiquitous promoters can lead to rapid degradation of AID-tagged proteins, cell type-specific expression of AtTIR1 using spatially restricted promoters often results in less efficient target protein degradation. To circumvent this limitation, we have developed an FLP/FRT3-based system that functions to reanimate a dormant, high-powered promoter that can drive sufficient AtTIR1 expression in a cell type-specific manner. We benchmark the utility of this system by generating a number of tissue-specific FLP-ON::TIR1 drivers to reveal genetically separable cell type-specific phenotypes for several target proteins. We also demonstrate that the FLP-ON::TIR1 system is compatible with enhanced degron epitopes. Finally, we provide an expandable toolkit utilizing the basic FLP-ON::TIR1 system that can be adapted to drive optimized AtTIR1 expression in any tissue or cell type of interest.
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Affiliation(s)
- Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chris Z Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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A preliminary analysis of prognostic genes in advanced laryngeal squamous cell carcinoma patients with postoperative radiotherapy. Pathol Res Pract 2023; 241:154229. [PMID: 36509010 DOI: 10.1016/j.prp.2022.154229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Advanced laryngeal squamous cell carcinoma (LSCC) has a high mortality rate, and the prognosis is poor. However, the underlying molecular biological mechanisms bringing about the development and progression of advanced LSCC are not entirely clarified. This study aimed to find out the potential biomarkers to predict the prognosis in advanced LSCC patients who had undergone postoperative radiotherapy alone. The next-generation sequencing of RNA was performed to detect the mRNAs expression profiling in 10 advanced LSCC samples, comprised of 5 samples from LSCC patients with favorable outcome and 5 samples from paired patients with poor outcome. Then bioinformatics analysis including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to find out functional core genes that were significantly different between the two groups. 1630 differentially expressed genes (DEGs) were confirmed to have significant differences between the two groups. 53 GO terms and 19 pathways which were closely related to the DEGs were identified. Finally, 52 intersection DEGs which were both related to the top three GO terms and pathways were identified. The expression of several core genes was confirmed with RT-qPCR in tissues from another 75 patients. RT-qPCR confirmed that the genes of c-JUN, LYN, PIK3R2, and TNFAIP3 were significantly differentially expressed between the two groups, which was in accordance with the RNA sequencing data. The DEGs identified above may be potential prognostic markers for advanced LSCC patients with postoperative radiotherapy, and may provide essential guidance for following-up.
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7
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Li N, Amatjan M, He P, Wu M, Yan H, Shao X. Whole transcriptome expression profiles in kidney samples from rats with hyperuricaemic nephropathy. PLoS One 2022; 17:e0276591. [PMID: 36534664 PMCID: PMC9762607 DOI: 10.1371/journal.pone.0276591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Hyperuricaemic nephropathy (HN) is a common clinical complication of hyperuricaemia (HUA) and poses a huge threat to human health. Hence, we aimed to prospectively investigate the dysregulated genes, pathways and networks involved in HN by performing whole transcriptome sequencing using RNA sequencing. Six kidney samples from HN group (n = 3) and a control group (n = 3) were obtained to conduct RNA sequencing. To disclose the relevant signalling pathways, we conducted the analysis of differentially expressed genes (DEGs), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A competitive endogenous RNA (ceRNA) network was established to reveal the interactions between lncRNAs, circRNAs, mRNAs and miRNAs and investigate the potential mechanisms of HN. Ultimately, 2250 mRNAs, 306 lncRNAs, 5 circRNAs, and 70 miRNAs were determined to be significantly differentially expressed in the HN group relative to the control group. We further authenticated 8 differentially expressed (DE)-ncRNAs by quantitative real-time polymerase chain reaction, and these findings were in accordance with the sequencing results. The analysis results evidently showed that these DE-ncRNAs were significantly enriched in pathways related to inflammatory reaction. In conclusion, HUA may generate abnormal gene expression changes and regulate signalling pathways in kidney samples. Potentially related genes and pathways involved in HN were identified.
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Affiliation(s)
- Na Li
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Mukaram Amatjan
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Pengke He
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Meiwei Wu
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Hengxiu Yan
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Xiaoni Shao
- College of Pharmacy, Southwest Minzu University, Chengdu, China
- * E-mail:
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8
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Johnson CA, Behbehani R, Buss F. Unconventional Myosins from Caenorhabditis elegans as a Probe to Study Human Orthologues. Biomolecules 2022; 12:biom12121889. [PMID: 36551317 PMCID: PMC9775386 DOI: 10.3390/biom12121889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Unconventional myosins are a superfamily of actin-based motor proteins that perform a number of roles in fundamental cellular processes, including (but not limited to) intracellular trafficking, cell motility, endocytosis, exocytosis and cytokinesis. 40 myosins genes have been identified in humans, which belong to different 12 classes based on their domain structure and organisation. These genes are widely expressed in different tissues, and mutations leading to loss of function are associated with a wide variety of pathologies while over-expression often results in cancer. Caenorhabditis elegans (C. elegans) is a small, free-living, non-parasitic nematode. ~38% of the genome of C. elegans has predicted orthologues in the human genome, making it a valuable tool to study the function of human counterparts and human diseases. To date, 8 unconventional myosin genes have been identified in the nematode, from 6 different classes with high homology to human paralogues. The hum-1 and hum-5 (heavy chain of an unconventional myosin) genes encode myosin of class I, hum-2 of class V, hum-3 and hum-8 of class VI, hum-6 of class VII and hum-7 of class IX. The hum-4 gene encodes a high molecular mass myosin (307 kDa) that is one of the most highly divergent myosins and is a member of class XII. Mutations in many of the human orthologues are lethal, indicating their essential properties. However, a functional characterisation for many of these genes in C. elegans has not yet been performed. This article reviews the current knowledge of unconventional myosin genes in C. elegans and explores the potential use of the nematode to study the function and regulation of myosin motors to provide valuable insights into their role in diseases.
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9
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Jing J, Yang P, Wang Y, Qu Q, An J, Fu B, Hu X, Zhou Y, Hu T, Cao Y. Identification of Competing Endogenous RNAs (ceRNAs) Network Associated with Drought Tolerance in Medicago truncatula with Rhizobium Symbiosis. Int J Mol Sci 2022; 23:14237. [PMID: 36430715 PMCID: PMC9696283 DOI: 10.3390/ijms232214237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
Drought, bringing the risks of agricultural production losses, is becoming a globally environmental stress. Previous results suggested that legumes with nodules exhibited superior drought tolerance compared with the non-nodule group. To investigate the molecular mechanism of rhizobium symbiosis impacting drought tolerance, transcriptome and sRNAome sequencing were performed to identify the potential mRNA-miRNA-ncRNA dynamic network. Our results revealed that seedlings with active nodules exhibited enhanced drought tolerance by reserving energy, synthesizing N-glycans, and medicating systemic acquired resistance due to the early effects of symbiotic nitrogen fixation (SNF) triggered in contrast to the drought susceptible with inactive nodules. The improved drought tolerance might be involved in the decreased expression levels of miRNA such as mtr_miR169l-5p, mtr_miR398b, and mtr_miR398c and its target genes in seedlings with active nodules. Based on the negative expression pattern between miRNA and its target genes, we constructed an mRNA-miR169l-ncRNA ceRNA network. During severe drought stress, the lncRNA alternative splicings TCONS_00049507 and TCONS_00049510 competitively interacted with mtr_miR169l-5p, which upregulated the expression of NUCLEAR FACTOR-Y (NF-Y) transcription factor subfamily NF-YA genes MtNF-YA2 and MtNF-YA3 to regulate their downstream drought-response genes. Our results emphasized the importance of SNF plants affecting drought tolerance. In conclusion, our work provides insight into ceRNA involvement in rhizobium symbiosis contributing to drought tolerance and provides molecular evidence for future study.
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Affiliation(s)
- Jiaxian Jing
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yue Wang
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Qihao Qu
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Jie An
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory of Agrobiotechnology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100083, China
| | - Bingzhe Fu
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xiaoning Hu
- Shaanxi Academy of Forestry, Xi’an 710082, China
| | - Yi Zhou
- School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
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10
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Wu C, Liu Y, Wan K, Lan Y, Jia M, Lin L, Gao S, Chen K, Yang J, Pan HL, Li M, Mao H. Long Non-Coding RNA and mRNA Profiles in the Spinal Cord of Rats with Resiniferatoxin-Induced Neuropathic Pain. J Pain Res 2022; 15:2149-2160. [PMID: 35935680 PMCID: PMC9348574 DOI: 10.2147/jpr.s368599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Caihua Wu
- Department of Acupuncture, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Yongmin Liu
- Department of Neurobiology, School of Basic medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Kexing Wan
- Department of Neurobiology, School of Basic medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Yuye Lan
- Department of Neurobiology, School of Basic medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Min Jia
- Clinical Laboratories, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Lixue Lin
- Department of Rehabilitation, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Shan Gao
- Department of Acupuncture, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Ke Chen
- Department of Acupuncture, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Jinmei Yang
- Department of Acupuncture, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Hui-Lin Pan
- Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Man Li
- Department of Neurobiology, School of Basic medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, People’s Republic of China
| | - Hongrong Mao
- Department of Acupuncture, Wuhan First Hospital, Wuhan, Hubei Province, 430030, People’s Republic of China
- Correspondence: Hongrong Mao, Department of Acupuncture, Wuhan First Hospital, 215 Zhongshan Avenue, Wuhan, Hubei Province, 430030, People’s Republic of China, Tel +86-13277912052, Email
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11
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Filgueiras CC, Kim Y, Wickings KG, El Borai F, Duncan LW, Willett DS. The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification. Biosens Bioelectron 2022; 221:114417. [PMID: 35690558 DOI: 10.1016/j.bios.2022.114417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.
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Affiliation(s)
- Camila C Filgueiras
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, 28804, NC, USA.
| | - Yongwoon Kim
- Union Biometrica, 84 October Hill Rd, Holliston, 01746, MA, USA
| | - Kyle G Wickings
- Department of Entolomogy, Cornell University, Cornell AgriTech, 15 Castle Creek Drive, Geneva, 14456, NY, USA
| | - Faheim El Borai
- Department of Entolomogy and Nematology, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, 33598, FL, USA
| | - Larry W Duncan
- Department of Entolomogy and Nematology, University of Florida, Citrus Research and Education Center, 700 Experiment Station Rd, Lake Alfred, 33850, FL, USA
| | - Denis S Willett
- North Carolina Institute for Climate Studies, North Carolina State University, 151 Patton Avenue, Asheville, 28801, NC, USA.
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12
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Cao X, Shi T, Zhang C, Jin W, Song L, Zhang Y, Liu J, Yang F, Rotimi CN, Xu A, Yang J. ACE2 pathway regulates thermogenesis and energy metabolism. eLife 2022; 11:72266. [PMID: 35014608 PMCID: PMC8776250 DOI: 10.7554/elife.72266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/09/2022] [Indexed: 12/02/2022] Open
Abstract
Identification of key regulators of energy homeostasis holds important therapeutic promise for metabolic disorders, such as obesity and diabetes. ACE2 cleaves angiotensin II (Ang II) to generate Ang-(1-7) which acts mainly through the Mas1 receptor. Here, we identify ACE2 pathway as a critical regulator in the maintenance of thermogenesis and energy expenditure. We found that ACE2 is highly expressed in brown adipose tissue (BAT) and that cold stimulation increases ACE2 and Ang-(1-7) levels in BAT and serum. Ace2 knockout mice (Ace2-/y) and Mas1 knockout mice (Mas1-/-) displayed impaired thermogenesis. Mice transplanted with brown adipose tissue from Mas1-/- display metabolic abnormalities consistent with those seen in the Ace2 and Mas1 knockout mice. In contrast, impaired thermogenesis of Leprdb/db obese diabetic mice and high-fat diet-induced obese mice were ameliorated by overexpression of Ace2 or continuous infusion of Ang-(1-7). Activation of ACE2 pathway was associated with improvement of metabolic parameters, including blood glucose, lipids, and energy expenditure in multiple animal models. Consistently, ACE2 pathway remarkably enhanced the browning of white adipose tissue. Mechanistically, we showed that ACE2 pathway activated Akt/FoxO1 and PKA pathway, leading to induction of UCP1 and activation of mitochondrial function. Our data propose that adaptive thermogenesis requires regulation of ACE2 pathway and highlight novel potential therapeutic targets for the treatment of metabolic disorders.
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Affiliation(s)
- Xi Cao
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Tingting Shi
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chuanhai Zhang
- Department of Physiology, University of Texas Meical Center at Dallas, Dallas, United States
| | - Wanzhu Jin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lini Song
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yichen Zhang
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jingyi Liu
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Fangyuan Yang
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Charles N Rotimi
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Aimin Xu
- Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Jinkui Yang
- Beijing Diabetes Institute, Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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13
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Smanski M. Spotlight on Genetic Design in a Spotted Wing Crop Killer. CRISPR J 2021; 4:628-630. [PMID: 34661432 DOI: 10.1089/crispr.2021.29136.msm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michael Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
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14
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Hippocampus chronic deep brain stimulation induces reversible transcript changes in a macaque model of mesial temporal lobe epilepsy. Chin Med J (Engl) 2021; 134:1845-1854. [PMID: 34267068 PMCID: PMC8367040 DOI: 10.1097/cm9.0000000000001644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Deep brain stimulation (DBS) has seizure-suppressing effects but the molecular mechanisms underlying its therapeutic action remain unclear. This study aimed to systematically elucidate the mechanisms underlying DBS-induced seizure suppression at a molecular level. METHODS We established a macaque model of mesial temporal lobe epilepsy (mTLE), and continuous high-frequency hippocampus DBS (hip-DBS) was applied for 3 months. The effects of hip-DBS on hippocampus gene expression were examined using high-throughput microarray analysis followed by bioinformatics analysis. Moreover, the microarray results were validated using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analyses. RESULTS The results showed that chronic hip-DBS modulated the hippocampal gene expression. We identified 4119 differentially expressed genes and assigned these genes to 16 model profiles. Series test of cluster analysis showed that profiles 5, 3, and 2 were the predominant expression profiles. Moreover, profile 5 was mainly involved in focal adhesion and extracellular matrix-receptor interaction pathway. Nine dysregulated genes (Arhgap5, Col1a2, Itgb1, Pik3r1, Lama4, Fn1, Col3a1, Itga9, and Shc4) and three genes (Col1a2, Itgb1, and Flna) in these two pathways were further validated by qRT-PCR and Western blot analyses, respectively, which showed a concordance. CONCLUSION Our findings suggest that hip-DBS could markedly reverse mTLE-induced abnormal gene expression. Findings from this study establish the basis for further investigation of the underlying regulatory mechanisms of DBS for mTLE.
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15
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Rödelsperger C, Ebbing A, Sharma DR, Okumura M, Sommer RJ, Korswagen HC. Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution. Mol Biol Evol 2021; 38:229-243. [PMID: 32785688 PMCID: PMC8480184 DOI: 10.1093/molbev/msaa207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence of gene function and expression during development can give rise to phenotypic differences at the level of cells, tissues, organs, and ultimately whole organisms. To gain insights into the evolution of gene expression and novel genes at spatial resolution, we compared the spatially resolved transcriptomes of two distantly related nematodes, Caenorhabditis elegans and Pristionchus pacificus, that diverged 60–90 Ma. The spatial transcriptomes of adult worms show little evidence for strong conservation at the level of single genes. Instead, regional expression is largely driven by recent duplication and emergence of novel genes. Estimation of gene ages across anatomical structures revealed an enrichment of novel genes in sperm-related regions. This provides first evidence in nematodes for the “out of testis” hypothesis that has been previously postulated based on studies in Drosophila and mammals. “Out of testis” genes represent a mix of products of pervasive transcription as well as fast evolving members of ancient gene families. Strikingly, numerous novel genes have known functions during meiosis in Caenorhabditis elegans indicating that even universal processes such as meiosis may be targets of rapid evolution. Our study highlights the importance of novel genes in generating phenotypic diversity and explicitly characterizes gene origination in sperm-related regions. Furthermore, it proposes new functions for previously uncharacterized genes and establishes the spatial transcriptome of Pristionchus pacificus as a catalog for future studies on the evolution of gene expression and function.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annabel Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Devansh Raj Sharma
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands.,Developmental Biology, Department of Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht, The Netherlands
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16
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Aberrant lncRNA Profiles Are Associated With Chronic Benzene Poisoning and Acute Myelocytic Leukemia. J Occup Environ Med 2021; 62:e308-e317. [PMID: 32730034 DOI: 10.1097/jom.0000000000001875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVE This study investigates the mechanisms of benzene hematotoxicity. METHODS We used microarray to detect expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in peripheral lymphocytes from chronic benzene poisoning, acute myelocytic leukemia, and healthy controls. The lncRNAs and mRNAs were validated using real-time quantitative PCR (RT-qPCR). Cytokinesis-block micronucleus assay was used to analyze chromosomal aberration. RESULTS We found 173 upregulated and 258 downregulated lncRNAs, and 695 upregulated and 804 downregulated mRNAs. The lncRNA CUST_40243 and mRNA PDGFC and CDKN1A associated with chronic benzene poisoning. Relevant inflammatory response, hematopoietic cell lineage, and cell cycle may be important pathways for the sifted lncRNAs and mRNAs. Furthermore, micronuclei frequency was significantly higher in off-post chronic benzene poisoning patients. CONCLUSIONS Chromosomal aberration induced by benzene exposure is irreversible. The lncRNA CUST_40243 and mRNA PDGFC and CDKN1A are related to chronic benzene poisoning.
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17
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Li X, Chen R, Lei X, Wang P, Zhu X, Zhang R, Yang L. Quercetin regulates ERα mediated differentiation of BMSCs through circular RNA. Gene 2020; 769:145172. [PMID: 33065239 DOI: 10.1016/j.gene.2020.145172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/04/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022]
Abstract
Circular RNA (circRNA) participates in regulation of gene transcription, while estrogen receptor alpha (ERα) and quercetin (QUE) positively regulate bone formation, but little is known about the correlation among circRNA, ERα and QUE. In this experiment, we created an ERα-deficient rBMSC model treated with QUE and evaluated the effects of ERα or QUE on rBMSCs, then analyzed differentially-expressed circRNAs by RNA-Seq and bioinformatics. The results showed that ERα deficiency constrained osteogenic differentiation and stimulated adipocytic differentiation of rBMSCs, while QUE abrogated those effects. We identified 136 differentially-expressed circRNAs in the Lv-shERα group and 120 differentially-expressed circRNAs in the Lv-shERα + QUE group. Thirty-two circRNAs retroregulated by ERα and QUE were involved in Rap1 and Wnt signaling, and four of them together sponged miR-326-5p, the target genes of which are osteogenic and adipogenic differentiation factors. Further study showed that over-expressed miR-326-5p could stimulate osteogenic differentiation, while attenuating adipogenic differentiation of rBMSCs. Therefore, we concluded that ERα and QUE might regulate the differentiation of rBMSCs through the circRNA-miR-326-5p-mRNA axis.
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Affiliation(s)
- Xiaoyun Li
- College of Traditional Chinese Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China
| | - Rumeng Chen
- College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China
| | - Xiaotong Lei
- College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China
| | - Panpan Wang
- Department of the First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong 510630, PR China
| | - Xiaofeng Zhu
- College of Traditional Chinese Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China; Department of the First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West, Guangzhou, Guangdong 510630, PR China
| | - Ronghua Zhang
- College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China.
| | - Li Yang
- College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, PR China.
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18
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Chen C, Weng J, Fang D, Chen J, Chen M. Transcriptomic study of lipopolysaccharide-induced sepsis damage in a mouse heart model. Exp Ther Med 2020; 20:3782-3790. [PMID: 32855727 PMCID: PMC7444370 DOI: 10.3892/etm.2020.9086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Sepsis is an emergency systemic illness caused by pathogen infection and the combined result of the underactivity and overactivity of a patient's own immune system. However, the molecular mechanism of this illness remains largely unknown. Lipopolysaccharide (LPS) was injected to establish a sepsis model, and heart tissue was used to analyze transcriptome changes in mice. LPS injection was used to develop a sepsis model, which resulted in cardiac tissue rearrangement and inflammatory response activation. An RNA-sequencing-based transcriptome assay using mouse heart tissue with or without LPS injection showed that 3,326 and 1,769 genes were upregulated and downregulated, respectively (>2-fold changes; P<0.05). Furthermore, these differentially expressed genes were classified into 20 pathways, including ‘Wnt signaling pathway’, ‘VEGF signaling pathway’ and ‘TGF-β signaling pathway’, and these altered genes were enriched in 41 Gene Ontology terms. The application of Wnt3a inhibited the activation of the LPS-induced inflammatory response and activated Wnt signaling, as well as protecting against LPS-mediated cardiac tissue damage in mice. In contrast, inhibition of Wnt signaling by injection of its inhibitor IWR induced plasminogen activator inhibitor-1 expression and resulted in cardiac structure derangement, which was similar to the symptoms caused by injection of LPS, suggesting that LPS-induced damage to heart tissue may be via inhibition of Wnt signaling. The present analyses showed that Wnt signaling serves a pivotal role in sepsis development and may improve our understanding of the molecular basis underlying sepsis.
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Affiliation(s)
- Cunrong Chen
- Department of Critical Care Medicine, Union Hospital Affiliated to Fujian Medical University, Fuzhou, Fujian 350000, P.R. China
| | - Junting Weng
- Department of Critical Care Medicine, Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Dexiang Fang
- Department of Critical Care Medicine, Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Jianfei Chen
- Department of Critical Care Medicine, Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Min Chen
- Department of Critical Care Medicine, Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
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19
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Kim B, Lee J, Kim Y, Lee SJV. Regulatory systems that mediate the effects of temperature on the lifespan of Caenorhabditis elegans. J Neurogenet 2020; 34:518-526. [PMID: 32633588 DOI: 10.1080/01677063.2020.1781849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Temperature affects animal physiology, including aging and lifespan. How temperature and biological systems interact to influence aging and lifespan has been investigated using model organisms, including the nematode Caenorhabditis elegans. In this review, we discuss mechanisms by which diverse cellular factors modulate the effects of ambient temperatures on aging and lifespan in C. elegans. C. elegans thermosensory neurons alleviate lifespan-shortening effects of high temperatures via sterol endocrine signaling and probably through systemic regulation of cytosolic proteostasis. At low temperatures, C. elegans displays a long lifespan by upregulating the cold-sensing TRPA channel, lipid homeostasis, germline-mediated prostaglandin signaling, and autophagy. In addition, co-chaperone p23 amplifies lifespan changes affected by high and low temperatures. Our review summarizes how external temperatures modulate C. elegans lifespan and provides information regarding responses of biological processes to temperature changes, which may affect health and aging at an organism level.
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Affiliation(s)
- Byounghun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongsun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Younghun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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20
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Zhang J, Hartman JH, Chen C, Yang S, Li Q, Tian Z, Huang PH, Wang L, Meyer JN, Huang TJ. Fluorescence-based sorting of Caenorhabditis elegans via acoustofluidics. LAB ON A CHIP 2020; 20:1729-1739. [PMID: 32292982 PMCID: PMC7239761 DOI: 10.1039/d0lc00051e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Effectively isolating and categorizing large quantities of Caenorhabditis elegans (C. elegans) based on different phenotypes is important for most worm research, especially genetics. Here we present an integrated acoustofluidic chip capable of identifying worms of interest based on expression of a fluorescent protein in a continuous flow and then separate them accordingly in a high-throughput manner. Utilizing planar fiber optics as the detection unit, our acoustofluidic device requires no temporary immobilization of worms for interrogation/detection, thereby improving the throughput. Implementing surface acoustic waves (SAW) as the sorting unit, our device provides a contact-free method to move worms of interest to the desired outlet, thus ensuring the biocompatibility for our chip. Our device can sort worms of different developmental stages (L3 and L4 stage worms) at high throughput and accuracy. For example, L3 worms can be processed at a throughput of around 70 worms per min with a sample purity over 99%, which remains over 90% when the throughput is increased to around 115 worms per min. In our acoustofluidic chip, the time period to complete the detection and sorting of one worm is only 50 ms, which outperforms nearly all existing microfluidics-based worm sorting devices and may be further reduced to achieve higher throughput.
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Affiliation(s)
- Jinxin Zhang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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21
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Bulcha JT, Giese GE, Ali MZ, Lee YU, Walker MD, Holdorf AD, Yilmaz LS, Brewster RC, Walhout AJM. A Persistence Detector for Metabolic Network Rewiring in an Animal. Cell Rep 2020; 26:460-468.e4. [PMID: 30625328 PMCID: PMC6368391 DOI: 10.1016/j.celrep.2018.12.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 12/14/2018] [Indexed: 11/25/2022] Open
Abstract
Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental inputs. Caenorhabditis elegans has two breakdown pathways for the short-chain fatty acid propionate: a canonical, vitamin B12-dependent pathway and a propionate shunt that is used when vitamin B12 levels are low. The shunt pathway is kept off when there is sufficient flux through the canonical pathway, likely to avoid generating shunt-specific toxic intermediates. Here, we discovered a transcriptional regulatory circuit that activates shunt gene expression upon propionate buildup. Nuclear hormone receptor 10 (NHR-10) and NHR-68 function together as a "persistence detector" in a type 1, coherent feed-forward loop with an AND-logic gate to delay shunt activation upon propionate accumulation and to avoid spurious shunt activation in response to a non-sustained pulse of propionate. Together, our findings identify a persistence detector in an animal, which transcriptionally rewires propionate metabolism to maintain homeostasis.
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Affiliation(s)
- Jote T Bulcha
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabrielle E Giese
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Md Zulfikar Ali
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yong-Uk Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Melissa D Walker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy D Holdorf
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - L Safak Yilmaz
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Robert C Brewster
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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22
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Zhou Y, Zhao D, Shuang L, Xiao D, Xuan Y, Duan Y, Chen L, Wang Y, Liu X, Fan H, Zhu X. Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection. Int J Mol Sci 2020; 21:ijms21030848. [PMID: 32013011 PMCID: PMC7037758 DOI: 10.3390/ijms21030848] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.
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Affiliation(s)
- Yuan Zhou
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Di Zhao
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Li Shuang
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, Shaanxi 716000, China;
| | - Dongxue Xiao
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuanhu Xuan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuxi Duan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Lijie Chen
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuanyuan Wang
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Xiaoyu Liu
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Haiyan Fan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Xiaofeng Zhu
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
- Correspondence: ; Tel.: +86-135-1603-9056
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23
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Wang C, Cao H, Gu S, Shi C, Chen X, Han X. Expression analysis of microRNAs and mRNAs in myofibroblast differentiation of lung resident mesenchymal stem cells. Differentiation 2019; 112:10-16. [PMID: 31838455 DOI: 10.1016/j.diff.2019.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2019] [Accepted: 11/17/2019] [Indexed: 12/11/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a serious lung disease that involved the myofibroblast differentiation of lung resident mesenchymal stem cells (LR-MSCs). However, the specific molecular mechanisms of myofibroblast differentiation of LR-MSCs still remain a mystery. In this study, a comprehensive analysis of miRNAs and mRNAs changes in LR-MSCs treated with TGF-β1 was performed. Through computational approaches, the pivotal roles of differentially expressed miRNAs that were associated with tight junction, pathways in cancer, focal adhesion, and cytokine-cytokine receptor interaction were shown. Kruppel-like factor 4 (Klf4) and inhibitor of growth family, member 5 (Ing5) may be the targets for the therapy of pulmonary fibrosis by inhibiting myofibroblast differentiation of LR-MSCs and EMT. Collectively, a molecular paradigm for understanding myofibroblast differentiation of LR-MSCs in IPF was provided by the integrated miRNA/mRNA analyses.
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Affiliation(s)
- Cong Wang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of New Drug Discovery, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Honghui Cao
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Shen Gu
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Chaowen Shi
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xiang Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China.
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Large-scale analyses identify a cluster of novel long noncoding RNAs as potential competitive endogenous RNAs in progression of hepatocellular carcinoma. Aging (Albany NY) 2019; 11:10422-10453. [PMID: 31761783 PMCID: PMC6914412 DOI: 10.18632/aging.102468] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
The abnormal expression of noncoding RNAs has attracted increasing interest in the field of hepatocellular carcinoma progression. However, the underlying molecular mechanisms mediated by noncoding RNAs in these processes are unclear. Here, we obtained the expression profiles of long noncoding RNAs, microRNAs, and mRNAs from the Gene Expression Omnibus database and identified hepatocarcinogenesis-specific differentially expressed transcripts. Next, we identified significant Gene Ontology and pathway terms that the differentially expressed transcripts involved in. Using functional analysis and target prediction, we constructed a hepatocellular carcinoma-associated deregulated competitive endogenous RNA network to reveal the potential mechanisms underlying tumor progression. By analyzing The Cancer Genome Atlas dataset, six key long noncoding RNAs showed significant association with overall survival as well as strong correlation with some microRNAs and mRNAs in the competitive endogenous RNA network. We further validated the above results and determined their diagnostic and prognostic value in clinical samples. Importantly, by large-scale analyses, we identified a cluster of long noncoding RNAs, GBAP1, MCM3AP-AS1, SLC16A1-AS1, C3P1, DIO3OS, and HNF4A-AS1 as candidate biomarkers for the diagnosis and prognosis of hepatocellular carcinoma, which will improve our understanding of competitive endogenous RNA-mediated regulatory mechanisms underlying hepatocellular carcinoma development and will provide novel therapeutic targets in the future.
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25
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Zhang X, Zhang L, Wang Q, Sun X, Dong Y, Xing Y, Ma X. Exploration of the potential mechanism of Danggui Shaoyao powder in the treatment of endometriosis based on bioinformatics. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2019. [DOI: 10.1016/j.jtcms.2019.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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26
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Chaudhuri P, Imam HT, Essig Y, Krasauskas J, Webb SM, Blindauer CA, Stürzenbaum SR. Molecular genetic and biochemical characterization of a putative family of zinc metalloproteins in Caenorhabditis elegans. Metallomics 2019; 10:1814-1823. [PMID: 30444224 PMCID: PMC6336089 DOI: 10.1039/c8mt00169c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The first characterization of W08E12.2, W08E12.3, W08E12.4 and W08E12.5, four putative metalloproteins in C. elegans. (A) phase contrast microscopy, (B) fluorescence microscopy of PW08E12.3;W08E12.4::GFP.
Four highly similar genes (W08E12.2, W08E12.3, W08E12.4 and W08E12.5) which are consecutively aligned on chromosome IV of the C. elegans genome are predicted to code for small (120–141aa) yet cysteine rich (18–19 cysteines) proteins. Cloning and sequencing of the genomic regions of the isoforms confirmed the presence and order of all genes. The generation of transgenic worms strains with an integrated single copy or extrachromosomal multi-copy PW08E12.3;W08E12.4::GFP uncovered that W08E12.3 and W08E12.4 are constitutively expressed in the pharynx and significantly induced in worms exposed to 100 μM Zn. Knockdown by RNAi did not have a marked consequence on reproductive performance nor was a Zn-dependent effect on nematode growth observed. However, RNAi of these genes led to an accumulation of Zn in the intestinal cells. W08E12.3 was recombinantly expressed in E. coli and the purified protein was shown to be able to bind up to 6.5 Zn molecules at neutral pH. Zn-binding was acid-labile and the apo protein was observed at pH < 4.3. This characterization suggests W08E12.2, W08E12.3, W08E12.4 and W08E12.5 belong to a family of putative Metalloproteins which, akin to metallothioneins, may play an important role in Zn-sensing, homeostasis and/or detoxification.
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Affiliation(s)
- Poulami Chaudhuri
- King's College London, School of Population Health & Environmental Sciences, Faculty of Life Sciences & Medicine, 150 Stamford Street, London, SE1 9NH, UK.
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27
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Jones LM, Eves-van den Akker S, van-Oosten Hawle P, Atkinson HJ, Urwin PE. Duplication of hsp-110 Is Implicated in Differential Success of Globodera Species under Climate Change. Mol Biol Evol 2019; 35:2401-2413. [PMID: 29955862 PMCID: PMC6188557 DOI: 10.1093/molbev/msy132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Managing the emergence and spread of crop pests and pathogens is essential for global food security. Understanding how organisms have adapted to their native climate is key to predicting the impact of climate change. The potato cyst nematodes Globodera pallida and G. rostochiensis are economically important plant pathogens that cause yield losses of up to 50% in potato. The two species have different thermal optima that may relate to differences in the altitude of their regions of origin in the Andes. Here, we demonstrate that juveniles of G. pallida are less able to recover from heat stress than those of G. rostochiensis. Genome-wide analysis revealed that while both Globodera species respond to heat stress by induction of various protective heat-inducible genes, G. pallida experiences heat stress at lower temperatures. We use C. elegans as a model to demonstrate the dependence of the heat stress response on expression of Heat Shock Factor-1 (HSF-1). Moreover, we show that hsp-110 is induced by heat stress in G. rostochiensis, but not in the less thermotolerant G. pallida. Sequence analysis revealed that this gene and its promoter was duplicated in G. rostochiensis and acquired thermoregulatory properties. We show that hsp-110 is required for recovery from acute thermal stress in both C. elegans and in G. rostochiensis. Our findings point towards an underlying molecular mechanism that allows the differential expansion of one species relative to another closely related species under current climate change scenarios. Similar mechanisms may be true of other invertebrate species with pest status.
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Affiliation(s)
- Laura M Jones
- Center for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Patricija van-Oosten Hawle
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Howard J Atkinson
- Center for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Peter E Urwin
- Center for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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28
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Huang Y, Xu Y, Lu Y, Zhu S, Guo Y, Sun C, Xu L, Chen X, Zhao Y, Yu B, Yang Y, Wang Z. lncRNA Gm10451 regulates PTIP to facilitate iPSCs-derived β-like cell differentiation by targeting miR-338-3p as a ceRNA. Biomaterials 2019; 216:119266. [PMID: 31220795 DOI: 10.1016/j.biomaterials.2019.119266] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 02/08/2023]
Abstract
iPSCs-derived insulin-producing cell transplantation is a promising strategy for diabetes therapy. Although there have been many protocols of mature, glucose-responsive β cells induced in vitro over the past few years, many underlying problems remain to be resolved. As a crucial regulator, long noncoding RNAs (lncRNAs) participate in numerous biological processes, including the maintenance of pluripotency, and stem cell differentiation. In this study, we identified a novel lncRNA Gm10451 as a functional regulator for β-like cell differentiation. Localized to the cytoplasm, Gm10451 regulates histone H3K4 methyltransferase complex PTIP to facilitate Insulin+/Nkx6.1+ β-like cell differentiation by targeting miR-338-3p as a competing endogenous RNA (ceRNA). miR-338-3p has also been shown to suppress Nkx6.1+ early-stage β-like cell differentiation by targeting PTIP. Following transplantation into streptozotocin (STZ)-mice, Gm10451 loss in β-like cells prevented the expression of mature β-cell makers, such as Insulin, Nkx6.1, and Mafa. Accordingly, hyperglycemia in the mice was not resolved. Taken together, this study provides an efficient epigenetic target for generating more mature and functional iPSCs-derived β-like cells. We anticipate that pancreatic organoids, which are generated from human stem cells, biological materials, and epigenetic modifications, can be used in the future as a novel diabetes treatment option.
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Affiliation(s)
- Yan Huang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yang Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yuhua Lu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China.
| | - Shajun Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yibing Guo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Cheng Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Lianchen Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Xiaolan Chen
- Department of Nephrology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yahong Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China; Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yumin Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
| | - Zhiwei Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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Zhang Q, Feng M, Zhang H, Xu J, Zhang L, Wang X, Cheng Z, Qian L. Long noncoding RNA uc.4 inhibits cell differentiation in heart development by altering DNA methylation. J Cell Biochem 2019; 120:8061-8068. [PMID: 30426569 DOI: 10.1002/jcb.28084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
In previous studies, we have demonstrated that long noncoding RNA uc.4 may influence the cell differentiation through the TGF-β signaling pathway, suppressed the heart development of zebrafish and resulting cardiac malformation. DNA methylation plays a significant role in the heart development and disordered of DNA methylation may cause disruption of control of gene promoter. In this study, methylated DNA immunoprecipitation was performed to identify the different expression levels of methylation regions. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were also performed to identify the possible biological process and pathway that uc.4 may join, associated with Rap1 signaling pathway, gonadotropin-releasing hormone signaling pathway, and Calcium signaling pathway. We found that the distribution of differentially methylated regions peaks was mainly located in intergenic and intron regions. Altogether, our result showed that differentially methylated genes are significantly expressed in uc.4-overexpression cells, providing valuable data for further exploration of the role of uc.4 in heart development.
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Affiliation(s)
- Qijun Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengwen Feng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia Xu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xuejun Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zijie Cheng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lingmei Qian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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30
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Sun T, Zhao Q, Zhang C, Cao L, Song M, Maimela NR, Liu S, Wang J, Gao Q, Qin G, Wang L, Zhang Y. Screening common signaling pathways associated with drug resistance in non-small cell lung cancer via gene expression profile analysis. Cancer Med 2019; 8:3059-3071. [PMID: 31025554 PMCID: PMC6558586 DOI: 10.1002/cam4.2190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer‐related deaths worldwide. Although several therapeutic strategies have been employed to curb lung cancer, the survival rate is still poor owing to the development of drug resistance. The mechanisms underlying drug resistance development are incompletely understood. Here, we aimed to identify the common signaling pathways involved in drug resistance in non‐small cell lung cancer (NSCLC). Three published transcriptome microarray data were downloaded from the Gene Expression Omnibus (GEO) database comprising different drug‐resistant cell lines and their parental cell lines. Differentially expressed genes (DEGs) were identified and used to perform Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. An overlapping analysis was performed for KEGG pathways enriched from all the three datasets to identify the common signaling pathways. As a result, we found that metabolic pathways, ubiquitin‐mediated proteolysis, and mitogen‐activated protein kinase (MAPK) signaling were the most aberrantly expressed signaling pathways. The knockdown of nicotinamide phosphoribosyltransferase (NAMPT), the gene involved in metabolic pathways and known to be upregulated in drug‐resistant tumor cells, was shown to increase the apoptosis of cisplatin‐resistant A549 cells following cisplatin treatment. Thus, our results provide an in‐depth analysis of the signaling pathways that are commonly altered in drug‐resistant NSCLC cell lines and highlight the potential strategy that facilitates the development of interventions to interfere with upregulated signaling pathways as well as to boost downregulated signaling pathways in drug‐resistant tumors for the elimination of multiple resistance of NSCLC.
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Affiliation(s)
- Ting Sun
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Respiratory medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qitai Zhao
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaoqi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Cao
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengjia Song
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Shasha Liu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinjin Wang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qun Gao
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Qin
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liping Wang
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China.,Engineering Key Laboratory for Cell Therapy of Henan Province, Zhengzhou, China
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31
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Xiang J, Zhang Y, Tuo L, Liu R, Gou D, Liang L, Chen C, Xia J, Tang N, Wang K. Transcriptomic changes associated with PCK1 overexpression in hepatocellular carcinoma cells detected by RNA-seq. Genes Dis 2019; 7:150-159. [PMID: 32181286 PMCID: PMC7063442 DOI: 10.1016/j.gendis.2019.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
Phosphoenolpyruvate carboxykinase 1 (PCK1), a step limiting enzyme of gluconeogenesis, is downregulated in hepatocellular carcinoma (HCC). Overexpression of PCK1 has been shown to suppress hepatoma cell growth, but the underlying mechanism remains unclear. We used recombinant adenovirus overexpressing PCK1 or GFP in Huh7 cells, and the differentially expressed genes (DEGs) were identified by RNA-Seq. 180 were upregulated by PCK1 overexpression, whereas 316 were downregulated. Pathway analysis illustrated that PCK1 was closely correlated with Wnt signaling pathway and TGF-beta signaling pathway. Hence, Wnt signaling pathway and its downstream component, FZD2, FZD6, FZD7 and β-catenin were confirmed by qRT-PCR and Western blot. In vivo we also observed that PCK1 had restrained tumor growth as a result of decreasing expression of β-catenin. Whole-transcriptomic profile analysis discovered that overexpression of PCK1 downregulates several oncogenic signaling pathways in HCC, providing potential therapeutic targets for improving HCC therapy.
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Affiliation(s)
- Jin Xiang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Lin Tuo
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Rui Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Dongmei Gou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Li Liang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Chang Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Jie Xia
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
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32
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Worms on a Chip. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Li L, Peng M, Xue W, Fan Z, Wang T, Lian J, Zhai Y, Lian W, Qin D, Zhao J. Integrated analysis of dysregulated long non-coding RNAs/microRNAs/mRNAs in metastasis of lung adenocarcinoma. J Transl Med 2018; 16:372. [PMID: 30587197 PMCID: PMC6307237 DOI: 10.1186/s12967-018-1732-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/06/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), largely remains a primary cause of cancer-related death worldwide. The molecular mechanisms in LUAD metastasis have not been completely uncovered. METHODS In this study, we identified differentially expressed genes (DEGs), miRNAs (DEMs) and lncRNAs (DELs) underlying metastasis of LUAD from The Cancer Genome Atlas database. Intersection mRNAs were used to perform gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and co-expression network analysis. In addition, survival analyses of intersection mRNAs were conducted. Finally, intersection mRNAs, miRNAs and lncRNAs were subjected to construct miRNA-mRNA-lncRNA network. RESULTS A total of 1015 DEGs, 54 DEMs and 22 DELs were identified in LUAD metastasis and non-metastasis samples. GO and KEGG pathway analysis had proven that the functions of intersection mRNAs were closely related with many important processes in cancer pathogenesis. Among the co-expression interactions network, 22 genes in the co-expression network were over the degree 20. These genes imply that they have connections with many other gene nodes. In addition, 14 target genes (ARHGAP11A, ASPM, HELLS, PRC1, TMPO, ARHGAP30, CD52, IL16, IRF8, P2RY13, PRKCB, PTPRC, SASH3 and TRAF3IP3) were found to be associated with survival in patients with LUAD significantly (log-rank P < 0.05). Two lncRNAs (LOC96610 and ADAM6) acting as ceRNAs were identified based on the miRNA-mRNA-lncRNA network. CONCLUSIONS Taken together, the results may provide a novel perspective to develop a multiple gene diagnostic tool for LUAD prognosis, which might also provide potential biomarkers or therapeutic targets for LUAD.
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Affiliation(s)
- Lifeng Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China
| | - Mengle Peng
- Department of Clinical Laboratory, The Third People's Hospital of Henan Province, Zhengzhou, 450052, Henan, China
| | - Wenhua Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhirui Fan
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Tian Wang
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jingyao Lian
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yunkai Zhai
- National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China
| | - Wenping Lian
- Department of Clinical Laboratory, The Third People's Hospital of Henan Province, Zhengzhou, 450052, Henan, China
| | - Dongchun Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, 450052, Henan, China.
| | - Jie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China.
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34
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Ebbing A, Vértesy Á, Betist MC, Spanjaard B, Junker JP, Berezikov E, van Oudenaarden A, Korswagen HC. Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns. Dev Cell 2018; 47:801-813.e6. [DOI: 10.1016/j.devcel.2018.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/31/2018] [Accepted: 10/12/2018] [Indexed: 12/15/2022]
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35
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McDiarmid TA, Au V, Loewen AD, Liang J, Mizumoto K, Moerman DG, Rankin CH. CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance. Dis Model Mech 2018; 11:dmm.036517. [PMID: 30361258 PMCID: PMC6307914 DOI: 10.1242/dmm.036517] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole-exome and whole-genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization, based on CRISPR-Cas9 genome engineering in the genetic model organism Caenorhabditis elegans, that will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of the C. elegans ortholog (daf-18) with the critical human disease-associated gene phosphatase and tensin homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion of daf-18, including complex chemosensory and mechanosensory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E), and showed that our automated in vivo phenotypic assays could accurately and efficiently classify this missense variant as loss of function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines the identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used as in vivo functional assays to decipher variants of uncertain significance.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Vinci Au
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Aaron D Loewen
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada .,Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
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Asweto CO, Hu H, Liang S, Wang L, Liu M, Yang H, Duan J, Sun Z. Gene profiles to characterize the combined toxicity induced by low level co-exposure of silica nanoparticles and benzo[a]pyrene using whole genome microarrays in zebrafish embryos. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 163:47-55. [PMID: 30036756 DOI: 10.1016/j.ecoenv.2018.07.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/12/2018] [Accepted: 07/15/2018] [Indexed: 06/08/2023]
Abstract
Several studies have suggested that air pollutants combine exposure have greater adverse effects. However, limited studies were available on the combined toxicity of silica nanoparticles (SiNPs) and benzo[a]pyrene (B[a]P). The study was to evaluate the toxic effect and mechanisms of low-dose exposure of SiNPs, B[a]P and co-exposure in zebrafish embryos. In this study, zebrafish embryos received intravenous microinjection of SiNPs and B[a]P, and then was used to select differentially expressed genes by microarray analysis. Multiple bioinformatics analyses and STC analysis were done to identify key genes, pathways and biological processes and the expression trend of genes in each group. 1) 3065 differentially expressed genes were identified in zebrafish embryos. 2) These differentially expressed genes were involved in multiple biological processes and cellular processes such as immunity, response to stimuli, cell proliferation, adhesion, signaling transduction, and embryonic development. 3) Dynamic Gene Network analysis was used to identify a subgroup of 26 core genes that involved in multiple biological processes and cellular processes. 4) Pathway analysis and Signal-net analysis indicated that the MAPK signaling pathway, calcium signaling pathway, p53 signaling pathway, PI3k/Akt signaling pathway, and several pathways associated with immune response were the most prominent significant pathways induced by co-exposure of SiNPs and B[a]P in zebrafish embryos. Our study demonstrated that the molecular actions of co-treated with SiNPs and B[a]P on the immune system, inflammatory process and cardiovascular development had more severe toxicity than single exposure.
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Affiliation(s)
- Collins Otieno Asweto
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Hejing Hu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Shuang Liang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Lijing Wang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China
| | - Mengdi Liu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China
| | - Han Yang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
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Yu AJ, McDiarmid TA, Ardiel EL, Rankin CH. High-Throughput Analysis of Behavior Under the Control of Optogenetics in Caenorhabditis elegans. ACTA ACUST UNITED AC 2018; 86:e57. [DOI: 10.1002/cpns.57] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alex J. Yu
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia; Vancouver British Columbia Canada
| | - Troy A. McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia; Vancouver British Columbia Canada
| | - Evan L. Ardiel
- Department of Molecular Biology, Massachusetts General Hospital; Boston Massachusetts
| | - Catharine H. Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia; Vancouver British Columbia Canada
- Department of Psychology, University of British Columbia; Vancouver, British Columbia Canada
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38
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Jiang H, Hong T, Wang T, Wang X, Cao L, Xu X, Zheng M. Gene expression profiling of human bone marrow mesenchymal stem cells during osteogenic differentiation. J Cell Physiol 2018; 234:7070-7077. [PMID: 30378112 DOI: 10.1002/jcp.27461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/29/2018] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Osteogenesis is a multiple-step process through which osteoblasts are derived from bone marrow mesenchymal stem cells (MSCs) with multilineage differentiation potential. This study aimed to analyze gene expression profiling during osteogenic differentiation of MSCs. MATERIALS AND METHODS Human MSCs were isolated and induced for differentiation in osteogenic medium. Full-genome gene expression microarrays and gene ontology analysis were performed. RESULTS A total of 1,680 differentially expressed genes in differentiated MSCs were identified including 430 upregulated and 1,250 downregulated. Moreover, pathway-act-network analysis showed that cell cycle, p53 signaling pathway and focal adhesion, had high degree (>5). The ribonucleotide reductase M1, thymidine kinase 1 and histone cluster 1 H3e also showed high degree (>10). Polymerase chain reaction analysis confirmed the differential expression of insulin-like growth factor binding protein 3, SMAD family member 3, transforming growth factor beta 2, and fibroblast growth factor 14 in differentiated MSCs. CONCLUSIONS Gene expression profiling provides a foundation to reveal the mechanisms that regulate osteogenic differentiation of MSCs.
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Affiliation(s)
- He Jiang
- Key Laboratory for System Bio-medicine of Jiangxi Province, Jiujiang University, Jiujiang, Jiangxi, China
| | - Tao Hong
- Department of Ultrasound, The First Hospital of Jiujiang City, Jiangxi, China
| | - Tao Wang
- Key Laboratory for System Bio-medicine of Jiangxi Province, Jiujiang University, Jiujiang, Jiangxi, China
| | - Xinping Wang
- Key Laboratory for System Bio-medicine of Jiangxi Province, Jiujiang University, Jiujiang, Jiangxi, China
| | - Lingling Cao
- Department of Ultrasound, The First Hospital of Jiujiang City, Jiangxi, China
| | - Xiaoyuan Xu
- Key Laboratory for System Bio-medicine of Jiangxi Province, Jiujiang University, Jiujiang, Jiangxi, China
| | - Meirong Zheng
- Key Laboratory for System Bio-medicine of Jiangxi Province, Jiujiang University, Jiujiang, Jiangxi, China
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Chen F, Wang RJ, Li GZ, Zhang Y, Yu S, Liu YF, Chen XY, Hou SK. miRNA array analysis of plasma miRNA alterations in rats exposed to a high altitude hypoxic environment. Mol Med Rep 2018; 18:5502-5510. [PMID: 30365091 PMCID: PMC6236226 DOI: 10.3892/mmr.2018.9570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 03/20/2017] [Indexed: 11/06/2022] Open
Abstract
In the present study, the microRNA (miRNA) expression profiles of rats exposed to high altitude hypoxia and normal conditions were obtained from miRNA array analysis. Bioinformatics analyses, including the use of the Gene Oncology and Kyoto Encyclopedia of Genes and Genomes databases, were used to identify the genes and pathways, which were specifically associated with high altitude hypoxic environment‑associated miRNAs. A total of 26 miRNAs were differentially expressed in the two groups, comprising six upregulated and 20 downregulated miRNAs. In the present study, a novel pattern of upregulated miRNAs and their associated pathways were constructed, including proteoglycans in cancer, spliceosome, gluamatergic synapse, glycolysis/gluconeogenesis, Foxo, cGMP‑PKG and p53 signaling pathways, which may provide novel targets for diagnosing and understanding the mechanism of high altitude hypoxia‑induced disease.
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Affiliation(s)
- Feng Chen
- Graduate School, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Ren-Jie Wang
- Department of Neurosurgery, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Guang-Zong Li
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Yi Zhang
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Shuo Yu
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Ying-Fu Liu
- Department of Cell Biology, Logistics University of Chinese People's Armed Police Forces, Tianjin 300309, P.R. China
| | - Xiao-Yi Chen
- Department of Cell Biology, Logistics University of Chinese People's Armed Police Forces, Tianjin 300309, P.R. China
| | - Shi-Ke Hou
- Graduate School, Tianjin Medical University, Tianjin 300070, P.R. China
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Wu J, Zhang R, Shen F, Yang R, Zhou D, Cao H, Chen G, Pan Q, Fan J. Altered DNA Methylation Sites in Peripheral Blood Leukocytes from Patients with Simple Steatosis and Nonalcoholic Steatohepatitis (NASH). Med Sci Monit 2018; 24:6946-6967. [PMID: 30270343 PMCID: PMC6180948 DOI: 10.12659/msm.909747] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background The aim of this study was to identify DNA methylation sites in peripheral blood leukocytes from patients with histologically confirmed nonalcoholic fatty liver disease (NAFLD) that included simple hepatic steatosis and nonalcoholic steatohepatitis (NASH). Material/Methods DNA was isolated from peripheral blood leukocytes from patients with histologically diagnosed NAFLD (n=35), including simple hepatic steatosis (n=18) and NASH (n=17). Healthy controls included individuals without liver disease (n=30). DNA was hybridized, and DNA methylation was interrogated in an epigenome-wide association study (EWAS). DNA methylation levels (β-values) were correlated with serum lipid profiles, liver enzymes, and liver histology. Results Circulating blood leukocytes from 35 patients with NAFLD (simple steatosis and NASH) contained 65 CpG sites, which represented 60 genes that were differentially methylated when compared with healthy controls. In the simple hepatic steatosis group (n=18), 42 methylated CpG sites were found to be associated with increased levels of serum alanine aminotransferase (ALT), and 32 methylated CpG sites were associated with increased serum lipid profiles. In the NASH group (n=17), when compared with the simple hepatic steatosis group, methylated CpG sites showed significant correlations with the presence of lobular inflammation compared with hepatic steatosis and fibrosis. Six differentially methylated CpG sites were identified in the ACSL4, CRLS1, CTP1A, SIGIRR, SSBP1 and ZNF622 genes, which were associated with histologically confirmed simple hepatic steatosis and NASH. Conclusions The study identified some key methylated CpG sites from peripheral blood leukocytes, which might be used as serum biomarkers to stratify NAFLD patients into simple hepatic steatosis and NASH.
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Affiliation(s)
- Jiayu Wu
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Ruinan Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Feng Shen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Ruixu Yang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Da Zhou
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Haixia Cao
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Guangyu Chen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Qin Pan
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Jiangao Fan
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland).,Shanghai Key Laboratory of Children's Digestion and Nutrition, Shanghai, China (mainland).,Shanghai Institute of Pediatrics, Shanghai, China (mainland)
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Ovarian transcriptomic analysis reveals the alternative splicing events associated with fecundity in different sheep breeds. Anim Reprod Sci 2018; 198:177-183. [PMID: 30318312 DOI: 10.1016/j.anireprosci.2018.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Alternative splicing (AS) is one of the most common mechanisms that accounts for the greater macromolecular and cellular complexity of higher eukaryotic organisms. This study focused on the splicing events in the ovaries of different sheep breeds, namely the Han and Dorset breeds. Of the groups studied, cassette splicing events accounted for the maximum number of the AS events with significant differences, whereas the splicing events that were mutually exclusive with introns accounted for the smallest proportion of splicing events. Greater than 1000 AS events with significant differences were identified between the Han BB and Dorset sheep. The number of AS events with significant differences between Han ++ and Dorset sheep, however, was fewer than that of the comparison of Han BB and Dorset sheep. Seven randomly selected genes with AS events were detected in this study and were validated by reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, there are many genes which were common to the two genotype groups (Han BB and Dorset sheep, as well as the Han ++ and Dorset sheep). In addition, genes detected in the present study were involved in different pathways, including the pathways related with fertility or fecundity. The present study could provide the detailed understanding on the mechanisms of alternative splicing events associated with fecundity in different sheep breeds.
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Yuan DP, Zhang C, Wang ZY, Zhu XF, Xuan YH. RAVL1 Activates Brassinosteroids and Ethylene Signaling to Modulate Response to Sheath Blight Disease in Rice. PHYTOPATHOLOGY 2018; 108:1104-1113. [PMID: 29767552 DOI: 10.1094/phyto-03-18-0085-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Rhizoctonia solani causes sheath blight disease in rice; however, the defense mechanism of rice plants against R. solani remains elusive. To analyze the roles of brassinosteroid (BR) and ethylene signaling on rice defense to R. solani, wild-type (WT) rice and several mutants and overexpressing (OX) lines were inoculated with R. solani. Mutants d61-1 and d2 were less susceptible to sheath blight disease, bri1-D was more susceptible, and ravl1 and d61-1/EIL1 Ri5 were similarly susceptible compared with WT. The double mutant ravl1/d61-1 was phenotypically similar to the ravl1 mutant. Transcriptome analysis, chromatin immunoprecipitation assay, electrophoretic mobility shift assay, and transient assays indicted that RAVL1 might directly activate Ethylene insensitive 3-like 1 (EIL1), a master regulator of ethylene signaling. Mutants ers1 and d61-1/RAVL1 OX were resistant to sheath blight disease, whereas EIL1 RNAi mutants and RAVL1 OX were more susceptible than WT. BRI1 and D2 expression in EIL1 Ri5/RAVL1 OX and EIL1 expression in d61-1/RAVL1 OX indicated that RAVL1 activates BRI1/D2 and EIL1, respectively, independent of BR and ethylene signaling. Our analyses provide information on how BR and ethylene signaling regulate sheath blight disease and on the regulatory function of RAVL1 in rice sheath blight disease.
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Affiliation(s)
- De Peng Yuan
- All authors: College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866 China
| | - Chong Zhang
- All authors: College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866 China
| | - Zi Yuan Wang
- All authors: College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866 China
| | - Xiao Feng Zhu
- All authors: College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866 China
| | - Yuan Hu Xuan
- All authors: College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866 China
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Wang C, Ren Q, Chen XT, Song ZQ, Ning ZC, Gan JH, Ma XL, Liang DR, Guan DG, Liu ZL, Lu AP. System Pharmacology-Based Strategy to Decode the Synergistic Mechanism of Zhi-zhu Wan for Functional Dyspepsia. Front Pharmacol 2018; 9:841. [PMID: 30127739 PMCID: PMC6087764 DOI: 10.3389/fphar.2018.00841] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
Functional dyspepsia (FD) is a widely prevalent gastrointestinal disorder throughout the world, whereas the efficacy of current treatment in the Western countries is limited. As the symptom is equivalent to the traditional Chinese medicine (TCM) term "stuffiness and fullness," FD can be treated with Zhi-zhu Wan (ZZW) which is a kind of Chinese patent medicine. However, the "multi-component" and "multi-target" feature of Chinese patent medicine makes it challenge to elucidate the potential therapeutic mechanisms of ZZW on FD. Presently, a novel system pharmacology model including pharmacokinetic parameters, pharmacological data, and component contribution score (CS) is constructed to decipher the potential therapeutic mechanism of ZZW on FD. Finally, 61 components with favorable pharmacokinetic profiles and biological activities were obtained through ADME (absorption, distribution, metabolism, and excretion) screening in silico. The related targets of these components are identified by component targeting process followed by GO analysis and pathway enrichment analysis. And systematic analysis found that through acting on the target related to inflammation, gastrointestinal peristalsis, and mental disorder, ZZW plays a synergistic and complementary effect on FD at the pathway level. Furthermore, the component CS showed that 29 components contributed 90.18% of the total CS values of ZZW for the FD treatment, which suggested that the effective therapeutic effects of ZZW for FD are derived from all active components, not a few components. This study proposes the system pharmacology method and discovers the potent combination therapeutic mechanisms of ZZW for FD. This strategy will provide a reference method for other TCM mechanism research.
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Affiliation(s)
- Chun Wang
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Qing Ren
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Xue-Tong Chen
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
- Center of Bioinformatics, College of Life Science, Northwest A & F University, Yangling, China
| | - Zhi-Qian Song
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhang-Chi Ning
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Jia-He Gan
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xin-Ling Ma
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dong-Rui Liang
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dao-Gang Guan
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Zhen-Li Liu
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ai-Ping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong
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Altered DNA Methylation of Long Noncoding RNA uc.167 Inhibits Cell Differentiation in Heart Development. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4658024. [PMID: 30003100 PMCID: PMC5998154 DOI: 10.1155/2018/4658024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022]
Abstract
In previous studies, we have demonstrated the function of uc.167 in the heart development. DNA methylation plays a crucial role in regulating the expression of developmental genes during embryonic development. In this study, the methylomic landscape was investigated in order to identify the DNA methylation alterations. Methylated DNA immunoprecipitation (MeDIP) was performed to examine the differences in methylation status of overexpressed uc.167 in P19 cells. GO and KEGG pathway analyses of differentially methylated genes were also conducted. We found that the distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in intergenic regions and intron. The biological process associated with uc.167 was focal adhesion and Rap1 signaling pathway. MEF2C was significantly decreased in uc.167 overexpressed group, suggesting that uc.167 may influence the P19 differentiation through MEF2C reduction. Taken together, our findings revealed that the effect of uc.167 on P19 differentiation may be attributed to the altered methylation of specific genes.
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Yang J, Qu Y, Huang Y, Lei F. Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck. BMC Genomics 2018; 19:391. [PMID: 29793441 PMCID: PMC5968480 DOI: 10.1186/s12864-018-4778-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 05/10/2018] [Indexed: 11/14/2022] Open
Abstract
Background Feathers with complex and fine structure are hallmark avian integument appendages, which have contributed significantly to the survival and breeding for birds. Here, we aimed to explore the differentiation, morphogenesis and development of diverse feathers in the domestic duck. Results Transcriptome profiles of skin owing feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the development of plumulaceous and flight feather structures. The venn analysis of differentially expressed genes (DEGs) between abdomen and wing skin tissues at three developmental stages showed that 38 genes owing identical differentially expression pattern. Together, our data suggest that feather morphological and structural diversity can be possibly related to the homeobox proteins. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcriptomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns. Conclusions Overall, this study detected many functional genes and showed differences in the molecular mechanisms of diverse feather developments. The findings in WNT, FGF and BMP, which were consistent with biological experiments, showed more possible complex modulations. A correlative role of HOX genes was also suggested but future biological verification experiments are required. This work provided valuable information for subsequent research on the morphogenesis of feathers. Electronic supplementary material The online version of this article (10.1186/s12864-018-4778-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Yang
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China.,School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Yanhua Qu
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuan Huang
- Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Lin X, Meng G, Liu X, Yu T, Bai C, Fei X, Deng S, Zhao J, Ren S, Zhang J, Wu Z, Wang S, Zhang J, Zhang L. The Differentially Expressed Genes of Human Sporadic Cerebral Cavernous Malformations. World Neurosurg 2018; 113:e247-e270. [DOI: 10.1016/j.wneu.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
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47
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Hernando-Rodríguez B, Erinjeri AP, Rodríguez-Palero MJ, Millar V, González-Hernández S, Olmedo M, Schulze B, Baumeister R, Muñoz MJ, Askjaer P, Artal-Sanz M. Combined flow cytometry and high-throughput image analysis for the study of essential genes in Caenorhabditis elegans. BMC Biol 2018; 16:36. [PMID: 29598825 PMCID: PMC5875015 DOI: 10.1186/s12915-018-0496-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/06/2018] [Indexed: 12/28/2022] Open
Abstract
Background Advances in automated image-based microscopy platforms coupled with high-throughput liquid workflows have facilitated the design of large-scale screens utilising multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high-throughput approaches, and a systematic way to analyse genetic interactions of essential genes in multicellular organisms has been lacking. Results In C. elegans, non-conditional lethal mutations can be maintained in heterozygosity using chromosome balancers, commonly expressing green fluorescent protein (GFP) in the pharynx. However, gene expression or function is typically monitored by the use of fluorescent reporters marked with the same fluorophore, presenting a challenge to sort worm populations of interest, particularly at early larval stages. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at the second larval stage. Because sorting is not completely error-free, we develop an automated high-throughput image analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image analysis in a functional genomic RNA interference (RNAi) screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both known and new PHB genetic interactors affecting the UPRmt and growth. Conclusions The method presented here allows the study of balanced lethal mutations in a high-throughput manner. It can be easily adapted depending on the user’s requirements and should serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks. Electronic supplementary material The online version of this article (10.1186/s12915-018-0496-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Blanca Hernando-Rodríguez
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Annmary Paul Erinjeri
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Val Millar
- GE Healthcare Life Sciences, Maynard Centre, Forest Farm, Whitchurch, Cardiff, UK.,Present address: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sara González-Hernández
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.,Present address: Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - María Olmedo
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.,Present address: Department of Genetics, University of Seville, Seville, Spain
| | - Bettina Schulze
- Centre for Biological Signalling Studies (BIOSS), Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, and ZBMZ Center for Biochemistry and Molecular Cell Biology (Faculty of Medicine), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Ralf Baumeister
- Centre for Biological Signalling Studies (BIOSS), Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, and ZBMZ Center for Biochemistry and Molecular Cell Biology (Faculty of Medicine), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Manuel J Muñoz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain. .,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain.
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48
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Yu S, Mao C, Yu J, Qi X, Wang J, Lu H. A study of the key genes and inflammatory signaling pathways involved in HLA-B27-associated acute anterior uveitis families. Int J Mol Med 2018; 42:259-269. [PMID: 29620146 PMCID: PMC5979938 DOI: 10.3892/ijmm.2018.3596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/21/2018] [Indexed: 12/13/2022] Open
Abstract
The present study was conducted to investigate the key genes and the inflammatory signaling pathways involved in HLA-B27-associated acute anterior uveitis (AAU) families. Four families with HLA-B27-positive AAU patients and their HLA-B27-positive blood relatives were included in the study. Peripheral blood monocytes were isolated from the subjects and stimulated by lipopolysaccharides (LPS). Gene expression microarrays were used to identify the differentially expressed genes (DEGs), and the DEGs were analyzed by a range of bioinformatics-based techniques, including Gene Ontology (GO), Pathway analysis, Signal-Net analysis and Gene Relation Network (Gene-Rel-Net). Finally, ELISA was used to quantify cytokines in the supernatant. The gene expression microarrays identified 801 DEGs, including 349 upregulated and 452 downregulated genes. The GO analysis revealed several important functions, including metabolic, immune and inflammatory responses. The pathway analysis highlighted the enhanced activity of Staphylococcus aureus infection, chemokine and metabolic signaling pathways, as well as cytokine-to-cytokine receptor interactions. A total of 18 DEGs that were found to play critical roles by Signal-Net and Gene-Rel-Net and verified by quantitative polymerase chain reaction analysis were identified as key genes. In conclusion, monocytes from the AUU patients were more sensitive and exhibited a more prominent inflammatory response to stimulation by LPS compared with monocytes from healthy HLA-B27-positive blood relatives. These characterized DEGs may provide new evidence for the pathogenesis of AAU and help identify new therapeutic targets.
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Affiliation(s)
- Shuo Yu
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100083, P.R. China
| | - Cui Mao
- Department of Ophthalmology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jinyi Yu
- Department of Ophthalmology, Yantai Yuhuangding Hospital, Affiliated Hospital of Medical College, Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Xin Qi
- Department of Ophthalmology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jing Wang
- Department of Ophthalmology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Hong Lu
- Department of Ophthalmology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
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49
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Zhang RN, Pan Q, Zheng RD, Mi YQ, Shen F, Zhou D, Chen GY, Zhu CY, Fan JG. Genome-wide analysis of DNA methylation in human peripheral leukocytes identifies potential biomarkers of nonalcoholic fatty liver disease. Int J Mol Med 2018; 42:443-452. [PMID: 29568887 DOI: 10.3892/ijmm.2018.3583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/12/2018] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to uncover the role of leukocytic DNA methylation in the evaluation of nonalcoholic fatty liver disease (NAFLD). Patients with biopsy-proven NAFLD (n=35) and normal controls (n=30) were recruited from Chinese Han population. Their DNA methylation in peripheral leukocytes was subjected to genome-wide profiling. The association between differential methylation of CpG sites and NAFLD was further investigated on the basis of histopathological classification, bioinformatics, and pyrosequencing. A panel of 863 differentially methylated CpG sites dominated by global hypomethylation, characterized the NAFLD patients. Hypomethylated CpG sites of Acyl-CoA synthetase long-chain family member 4 (ACSL4) (cg15536552) and carnitine palmitoyltransferase 1C (CPT1C) (cg21604803) associated with the increased risk of NAFLD [cg15536552, odds ratio (OR): 11.44, 95% confidence interval (CI): 1.04‑125.37, P=0.046; cg21604803, OR: 6.57, 95% CI: 1.02-42.15, P=0.047] at cut-off β-values of <3.36 (ACSL4 cg15536552) and <3.54 (CPT1C cg21604803), respectively, after the adjustment of age, sex, body mass index (BMI) and homeostasis model assessment of insulin resistant (HOMA-IR). Their methylation levels also served as biomarkers of NAFLD (ACSL4 cg15536552, AUC: 0.80, 95% CI: 0.62-0.98, P=0.009; CPT1C cg21604803, AUC: 0.78, 95% CI: 0.65-0.91, P=0.001). Pathologically, lowered methylation level (β-values <3.26) of ACSL4 (cg15536552) conferred susceptibility to nonalcoholic steatohepatitis (NASH). Taken together, genome-wide hypomethylation of peripheral leukocytes may differentiate NAFLD patients from normal controls. The leukocytic hypomethylated ACSL4 (cg15536552) was suggested to be a biomarker for the pathological characteristics of NAFLD.
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Affiliation(s)
- Rui-Nan Zhang
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Qin Pan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Rui-Dan Zheng
- Diagnosis and Treatment Center for Liver Diseases, Zhengxing Hospital, Zhangzhou, Fujian 363000, P.R. China
| | - Yu-Qiang Mi
- Department of Infective Diseases, Tianjin Infectious Disease Hospital, Tianjin 300192, P.R. China
| | - Feng Shen
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Da Zhou
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Guang-Yu Chen
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Chan-Yan Zhu
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Jian-Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
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50
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Zhu Z, Li Y, Liu W, He J, Zhang L, Li H, Li P, Lv L. Comprehensive circRNA expression profile and construction of circRNA-associated ceRNA network in fur skin. Exp Dermatol 2018; 27:251-257. [DOI: 10.1111/exd.13502] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Zhiwei Zhu
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Yuan Li
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Wenyan Liu
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Junping He
- College of Animal Science and Technology; Shanxi Agricultural University; Taigu China
| | - Lihuan Zhang
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Huifeng Li
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Pengfei Li
- College of Life Sciences; Shanxi Agricultural University; Taigu China
| | - Lihua Lv
- College of Animal Science and Technology; Shanxi Agricultural University; Taigu China
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