The Experts below are selected from a list of 204 Experts worldwide ranked by ideXlab platform
Xuguo Zhou - One of the best experts on this subject based on the ideXlab platform.
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Selection of Reference Genes for RT-qPCR Analysis Under Intrinsic Conditions in the Hawthorn Spider Mite, Amphitetranychus viennensis (Acarina: Tetranychidae)
Frontiers in physiology, 2019Co-Authors: Yang Jing, Xuguo Zhou, Gao Yue, Liu Zhongfang, Yuying Zhang, Zhang Pengjiu, Fan Jianbin, Fan RenjunAbstract:Hawthorn spider mite, Amphitetranychus viennensis Zacher, is one of the most devastating sap-sucking pest of deciduous fruit trees. Most recently, we sequenced the genome of A. viennensis. To take advantage of the newly established genomic resources, however, we need to develop a standardized protocol for Real-Time Quantitative Reverse Transcription PCR (RT-qPCR), one of the most effective and broadly adopted methods to quantify gene expression. Following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guidelines, inteRNAl references are required to counter the innate technical errors and biases in RT-qPCR analysis. Based on previous knowledge, we hypothesized that inteRNAl references for RT-qPCR analysis reside in housekeeping genes. To examine this hypothesis, we assessed the stability of nine housekeeping genes from A. viennensis transcriptome. These candidates, including 18S ribosomal RNA(18S), 28S ribosomal RNA (28S), Elongation factor 1-alpha (EF1A), Actin3, V-ATP vacuolar-type H+-ATPase (V-ATPase), α-tubulin (α-tubulin), Ribosomal protein L13 (RPL13), 40S ribosomal protein S9 (RPS9), and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), have been used extensively as the reference genes for RT-qPCR analysis. The expression of these candidates under intrinsic conditions, across developmental stage, sex, and diapause, was evaluated by a panel of computational programs, including geNorm, Normfinder, BestKeeper, and ΔCt method. Finally, a specific set of reference genes is recommended for each intrinsic conditions, respectively, based on RefFinder, a comprehensive analytical platform integrating all four above-mentioned algorisms. Overall, V-ATPase, Actin3, and GAPDH are consistently stably expressed across all the intrinsic conditions in A. viennensis. In addition, we compared reference genes recommended for different developmental stages among the nine sap-sucking arthropods, including four spider mites, A. viennensis, Tetranychus urticae, Tetranychus cinnabarinus, and Panonychus citri, and five hemipterans, Myzus persicae, Aphis gossypii, Toxoptera citricida, Lipaphis erysimi, and Sogatella furcifera. Not surprisingly, rRNAs and ribosomal proteins, the most abundant RNA species, is the top choice for the reference gene(s), and follows by EF1A, Actin, GAPDH, and tubulin, which all exceed 10% chance of been selected. Information present here lays the foundation for the genomic and functional genomic research in sap-sucking arthropods in general and A. viennensis in particular.
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A Comprehensive Selection of Reference Genes for RT-qPCR Analysis in a Predatory Lady Beetle, Hippodamia convergens (Coleoptera: Coccinellidae)
PloS one, 2015Co-Authors: Huipeng Pan, Xiaowei Yang, Blair D. Siegfried, Xuguo ZhouAbstract:Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable, rapid, and reproducible technique for measuring and evaluating changes in gene expression. To facilitate gene expression studies and obtain more accurate RT-qPCR data, normalization relative to stable reference genes is required. In this study, expression profiles of seven candidate reference genes, including β-actin (Actin), elongation factor 1 α (EF1A), glyceralde hyde-3-phosphate dehydro-genase (GAPDH), cyclophilins A (CypA), vacuolar-type H+-ATPase (ATPase), 28S ribosomal RNA (28S), and 18S ribosomal RNA (18S) from Hippodamia convergens were investigated. H. convergens is an abundant predatory species in the New World, and has been widely used as a biological control agent against sap-sucking insect pests, primarily aphids. A total of four analytical methods, geNorm, Normfinder, BestKeeper, and the ΔCt method, were employed to evaluate the performance of these seven genes as endogenous controls under diverse experimental conditions. Additionally, RefFinder, a comprehensive evaluation platform integrating the four above mentioned algorithms, ranked the overall stability of these candidate genes. A suite of reference genes were specifically recommended for each experimental condition. Among them, 28S, EF1A, and CypA were the best reference genes across different development stages; GAPDH, 28S, and CypA were most stable in different tissues. GAPDH and CypA were most stable in female and male adults and photoperiod conditions, 28S and EF1A were most stable under a range of temperatures, Actin and CypA were most stable under dietary RNAi condition. This work establishes a standardized RT-qPCR analysis in H. convergens. Additionally, this study lays a foundation for functional genomics research in H. convergens and sheds light on the ecological risk assessment of RNAi-based biopesticides on this non-target biological control agent.
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stably expressed housekeeping genes across developmental stages in the two spotted spider mite tetranychus urticae
PLOS ONE, 2015Co-Authors: Chunxiao Yang, Huipeng Pan, Yong Liu, Xuguo ZhouAbstract:Quantitative real-time PCR (qRT-PCR) is a reliable and reproducible technique for measuring mRNA expression. To facilitate gene expression studies and obtain more accurate qRT-PCR analysis, normalization relative to stable housekeeping genes is mandatory. In this study, ten housekeeping genes, including beta-actin (Actin) , elongation factor 1 α (EF1A) , glyceralde hyde-3-phosphate dehydrogenase (GAPDH) , ribosomal protein L13 (RPL13) , ribosomal protein 49 (RP49) , α-tubulin (Tubulin) , vacuolar-type H+-ATPase (v-ATPase) , succinate dehydrogenase subunit A (SDHA) , 28S ribosomal RNA (28S) , and 18S ribosomal RNA (18S) from the two-spotted spider mite, Tetranychus urticae, were selected as the candidate reference genes. Four algorithms, geNorm, Normfinder, BestKeeper, and the ΔCt method, were used to evaluate the performance of these candidates as endogenous controls across different developmental stages. In addition, RefFinder, which integrates the above-mentioned software tools, provided the overall ranking of the stability/suitability of these candidate reference genes. Among them, PRL13 and v-ATPase were the two most stable housekeeping genes across different developmental stages. This work is the first step toward establishing a standardized qRT-PCR analysis in T. urticae following the MIQE guideline. With the recent release of the T. urticae genome, results from this study provide a critical piece for the subsequent genomics and functional genomics research in this emerging model system.
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Selection of reference genes for expression analysis using quantitative real-time PCR in the pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera, Aphidiae).
PLOS ONE, 2014Co-Authors: Chunxiao Yang, Xuguo ZhouAbstract:To facilitate gene expression study and obtain accurate qRT-PCR analysis, normalization relative to stable expressed housekeeping genes is required. In this study, expression profiles of 11 candidate reference genes, including actin (Actin), elongation factor 1 α (EF1A), TATA-box-binding protein (TATA), ribosomal protein L12 (RPL12), β-tubulin (Tubulin), NADH dehydrogenase (NADH), vacuolar-type H+-ATPase (v-ATPase), succinate dehydrogenase B (SDHB), 28S ribosomal RNA (28S), 16S ribosomal RNA (16S), and 18S ribosomal RNA (18S) from the pea aphid Acyrthosiphon pisum, under different developmental stages and temperature conditions, were investigated. A total of four analytical tools, geNorm, Normfinder, BestKeeper, and the ΔCt method, were used to evaluate the suitability of these genes as endogenous controls. According to RefFinder, a web-based software tool which integrates all four above-mentioned algorithms to compare and rank the reference genes, SDHB, 16S, and NADH were the three most stable house-keeping genes under different developmental stages and temperatures. This work is intended to establish a standardized qRT-PCR protocol in pea aphid and serves as a starting point for the genomics and functional genomics research in this emerging insect model.
Yin-yin Yang - One of the best experts on this subject based on the ideXlab platform.
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Selection of Suitable Housekeeping Genes for Real-Time Quantitative PCR in CD4+ Lymphocytes from Asthmatics with or without Depression
PloS one, 2012Co-Authors: Ting Wang, Zong-an Liang, Andrew J. Sandford, Xing-yu Xiong, Yin-yin YangAbstract:Objective No optimal housekeeping genes (HKGs) have been identified for CD4+ T cells from non-depressive asthmatic and depressive asthmatic adults for normalizing quantitative real-time PCR (qPCR) assays. The aim of present study was to select appropriate HKGs for gene expression analysis in purified CD4+ T cells from these asthmatics. Methods Three groups of subjects (Non-depressive asthmatic, NDA, n = 10, Depressive asthmatic, DA, n = 11, and Healthy control, HC, n = 10 respectively) were studied. qPCR for 9 potential HKGs, namely RNA, 28S ribosomal 1 (RN28S1), ribosomal protein, large, P0 (RPLP0), actin, beta (ACTB), cyclophilin A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), beta-2-microglobulin (B2M), glucuronidase, beta (GUSB) and ribosomal protein L13a (RPL13A), was performed. Then the data were analyzed with three different applications namely BestKeeper, geNorm, and NormFinder. Results The analysis of gene expression data identified B2M and RPLP0 as the most stable reference genes and showed that the level of PPIA was significantly different among subjects of three groups when the two best HKGs identified were applied. Post-hoc analysis by Student-Newman-Keuls correction shows that depressive asthmatics and non-depressive asthmatics exhibited lower expression level of PPIA than healthy controls (p
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Selection of suitable housekeeping genes for real-time quantitative PCR in CD4+ lymphocytes from asthmatics with or without depression
European Respiratory Journal, 2012Co-Authors: Ting Wang, Zong-an Liang, Andrew J. Sandford, Xing-yu Xiong, Yin-yin YangAbstract:Objective: No optimal housekeeping genes (HKGs) have been identified for CD4+ T cells from non-depressive asthmatic and depressive asthmatic adults for normalizing quantitative real-time PCR (qPCR) assays. The aim of present study was to select appropriate HKGs for gene expression analysis in purified CD4+ T cells from these asthmatics. Methods: Three groups of subjects (Non-depressive asthmatic, NDA, n = 10, Depressive asthmatic, DA, n = 11, and Healthy control, HC, n = 10 respectively) were studied. qPCR for 9 potential HKGs, namely RNA, 28S ribosomal 1 (RN28S1), ribosomal protein, large, P0 (RPLP0), actin, beta (ACTB), cyclophilin A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), beta-2-microglobulin (B2M), glucuronidase, beta (GUSB) and ribosomal protein L13a (RPL13A), was performed. Then the data were analyzed with three different applications namely BestKeeper, geNorm, and NormFinder. Results: The analysis of gene expression data identified B2M and RPLP0 as the most stable reference genes and showed that the level of PPIA was significantly different among subjects of three groups when the two best HKGs identified were applied. Post hoc analysis by Student-Newman-Keuls correction shows that depressive asthmatics and non-depressive asthmatics exhibited lower expression level of PPIA than healthy controls. Conclusions: B2M and RPLP0 were identified as the most optimal HKGs in gene expression studies involving human blood CD4+ T cells derived from normal, depressive asthmatics and non-depressive asthmatics.
Ting Wang - One of the best experts on this subject based on the ideXlab platform.
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Selection of Suitable Housekeeping Genes for Real-Time Quantitative PCR in CD4+ Lymphocytes from Asthmatics with or without Depression
PloS one, 2012Co-Authors: Ting Wang, Zong-an Liang, Andrew J. Sandford, Xing-yu Xiong, Yin-yin YangAbstract:Objective No optimal housekeeping genes (HKGs) have been identified for CD4+ T cells from non-depressive asthmatic and depressive asthmatic adults for normalizing quantitative real-time PCR (qPCR) assays. The aim of present study was to select appropriate HKGs for gene expression analysis in purified CD4+ T cells from these asthmatics. Methods Three groups of subjects (Non-depressive asthmatic, NDA, n = 10, Depressive asthmatic, DA, n = 11, and Healthy control, HC, n = 10 respectively) were studied. qPCR for 9 potential HKGs, namely RNA, 28S ribosomal 1 (RN28S1), ribosomal protein, large, P0 (RPLP0), actin, beta (ACTB), cyclophilin A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), beta-2-microglobulin (B2M), glucuronidase, beta (GUSB) and ribosomal protein L13a (RPL13A), was performed. Then the data were analyzed with three different applications namely BestKeeper, geNorm, and NormFinder. Results The analysis of gene expression data identified B2M and RPLP0 as the most stable reference genes and showed that the level of PPIA was significantly different among subjects of three groups when the two best HKGs identified were applied. Post-hoc analysis by Student-Newman-Keuls correction shows that depressive asthmatics and non-depressive asthmatics exhibited lower expression level of PPIA than healthy controls (p
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Selection of suitable housekeeping genes for real-time quantitative PCR in CD4+ lymphocytes from asthmatics with or without depression
European Respiratory Journal, 2012Co-Authors: Ting Wang, Zong-an Liang, Andrew J. Sandford, Xing-yu Xiong, Yin-yin YangAbstract:Objective: No optimal housekeeping genes (HKGs) have been identified for CD4+ T cells from non-depressive asthmatic and depressive asthmatic adults for normalizing quantitative real-time PCR (qPCR) assays. The aim of present study was to select appropriate HKGs for gene expression analysis in purified CD4+ T cells from these asthmatics. Methods: Three groups of subjects (Non-depressive asthmatic, NDA, n = 10, Depressive asthmatic, DA, n = 11, and Healthy control, HC, n = 10 respectively) were studied. qPCR for 9 potential HKGs, namely RNA, 28S ribosomal 1 (RN28S1), ribosomal protein, large, P0 (RPLP0), actin, beta (ACTB), cyclophilin A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK1), beta-2-microglobulin (B2M), glucuronidase, beta (GUSB) and ribosomal protein L13a (RPL13A), was performed. Then the data were analyzed with three different applications namely BestKeeper, geNorm, and NormFinder. Results: The analysis of gene expression data identified B2M and RPLP0 as the most stable reference genes and showed that the level of PPIA was significantly different among subjects of three groups when the two best HKGs identified were applied. Post hoc analysis by Student-Newman-Keuls correction shows that depressive asthmatics and non-depressive asthmatics exhibited lower expression level of PPIA than healthy controls. Conclusions: B2M and RPLP0 were identified as the most optimal HKGs in gene expression studies involving human blood CD4+ T cells derived from normal, depressive asthmatics and non-depressive asthmatics.
Fan Renjun - One of the best experts on this subject based on the ideXlab platform.
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Selection of Reference Genes for RT-qPCR Analysis Under Intrinsic Conditions in the Hawthorn Spider Mite, Amphitetranychus viennensis (Acarina: Tetranychidae)
Frontiers in physiology, 2019Co-Authors: Yang Jing, Xuguo Zhou, Gao Yue, Liu Zhongfang, Yuying Zhang, Zhang Pengjiu, Fan Jianbin, Fan RenjunAbstract:Hawthorn spider mite, Amphitetranychus viennensis Zacher, is one of the most devastating sap-sucking pest of deciduous fruit trees. Most recently, we sequenced the genome of A. viennensis. To take advantage of the newly established genomic resources, however, we need to develop a standardized protocol for Real-Time Quantitative Reverse Transcription PCR (RT-qPCR), one of the most effective and broadly adopted methods to quantify gene expression. Following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guidelines, inteRNAl references are required to counter the innate technical errors and biases in RT-qPCR analysis. Based on previous knowledge, we hypothesized that inteRNAl references for RT-qPCR analysis reside in housekeeping genes. To examine this hypothesis, we assessed the stability of nine housekeeping genes from A. viennensis transcriptome. These candidates, including 18S ribosomal RNA(18S), 28S ribosomal RNA (28S), Elongation factor 1-alpha (EF1A), Actin3, V-ATP vacuolar-type H+-ATPase (V-ATPase), α-tubulin (α-tubulin), Ribosomal protein L13 (RPL13), 40S ribosomal protein S9 (RPS9), and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), have been used extensively as the reference genes for RT-qPCR analysis. The expression of these candidates under intrinsic conditions, across developmental stage, sex, and diapause, was evaluated by a panel of computational programs, including geNorm, Normfinder, BestKeeper, and ΔCt method. Finally, a specific set of reference genes is recommended for each intrinsic conditions, respectively, based on RefFinder, a comprehensive analytical platform integrating all four above-mentioned algorisms. Overall, V-ATPase, Actin3, and GAPDH are consistently stably expressed across all the intrinsic conditions in A. viennensis. In addition, we compared reference genes recommended for different developmental stages among the nine sap-sucking arthropods, including four spider mites, A. viennensis, Tetranychus urticae, Tetranychus cinnabarinus, and Panonychus citri, and five hemipterans, Myzus persicae, Aphis gossypii, Toxoptera citricida, Lipaphis erysimi, and Sogatella furcifera. Not surprisingly, rRNAs and ribosomal proteins, the most abundant RNA species, is the top choice for the reference gene(s), and follows by EF1A, Actin, GAPDH, and tubulin, which all exceed 10% chance of been selected. Information present here lays the foundation for the genomic and functional genomic research in sap-sucking arthropods in general and A. viennensis in particular.
Felix A. H. Sperling - One of the best experts on this subject based on the ideXlab platform.
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Molecular phylogeny of the diverse parasitoid wasp genus Ophion Fabricius (Hymenoptera: Ichneumonidae: Ophioninae)
Systematic Entomology, 2015Co-Authors: Marla D. Schwarzfeld, Gavin R. Broad, Felix A. H. SperlingAbstract:Ophion Fabricius is a diverse genus of noctuRNAl ichneumonid wasps (Insecta: Hymenoptera) that is particularly species-rich in temperate areas, yet has received little taxonomic attention in the Holarctic region, where most species occur. While there have been some attempts to divide Ophion into monophyletic species groups, the vast majority of species have been lumped into a single, paraphyletic group, the O. luteus species group, which is defined only by the lack of characters specific to the other groups. The challenging morphology of this large catch-all group has limited attempts to subdivide it, and no phylogenetic hypothesis has been proposed for the genus as a whole. In this study, we use DNA sequence data [28S ribosomal RNA (28S), cytochrome oxidase 1 (COI) and inteRNAl transcribed spacer 2 (ITS2)] to present the first molecular phylogeny of Ophion. We also describe the secondary structure of ITS2 for the first time in Ichneumonidae, and explore its implications for phylogeny estimation. We define 13 species groups, nine of which were previously considered part of the O. luteus species group s.l. The included species groups are the O. minutus, O. areolaris, O. scutellaris, O. flavidus, O. parvulus, O. slossonae, O. nigrovarius, O. pteridis, O. luteus s.s., and O. obscuratus species groups, along with three groups lacking described species (Species group 1, New Zealand group, Madagascar group). This study provides a framework for future studies of this diverse and morphologically challenging genus.
