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https://www.readbyqxmd.com/read/28919905/candidate-reference-genes-selection-and-application-for-rt-qpcr-analysis-in-kenaf-with-cytoplasmic-male-sterility-background
#1
Bujin Zhou, Peng Chen, Aziz Khan, Yanhong Zhao, Lihong Chen, Dongmei Liu, Xiaofang Liao, Xiangjun Kong, Ruiyang Zhou
Cytoplasmic male sterility (CMS) is a maternally inherited trait that results in the production of dysfunctional pollen. Based on reliable reference gene-normalized real-time quantitative PCR (RT-qPCR) data, examining gene expression profile can provide valuable information on the molecular mechanism of kenaf CMS. However, studies have not been conducted regarding selection of reference genes for normalizing RT-qPCR data in the CMS and maintainer lines of kenaf crop. Therefore, we studied 10 candidate reference genes (ACT3, ELF1A, G6PD, PEPKR1, TUB, TUA, CYP, GAPDH, H3, and 18S) to assess their expression stability at three stages of pollen development in CMS line 722A and maintainer line 722B of kenaf...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28810828/suitable-reference-gene-for-quantitative-real-time-pcr-analysis-of-gene-expression-in-gonadal-tissues-of-minnow-puntius-sophore-under-high-temperature-stress
#2
Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak, Bimal Prasanna Mohanty
BACKGROUND: High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poorly understood. Gonadal gene expression influence the gonadal development, physiology and the quality of egg/sperm produced in teleosts and the mechanistic understanding of spatio-temporal changes in the gonadal gene expression could be instrumental in controlling the fate of egg/sperm and the quality of seed produced...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28763741/expression-stability-and-selection-of-optimal-reference-genes-for-gene-expression-normalization-in-early-life-stage-rainbow-trout-exposed-to-cadmium-and-copper
#3
Kamran Shekh, Song Tang, Som Niyogi, Markus Hecker
Gene expression analysis represents a powerful approach to characterize the specific mechanisms by which contaminants interact with organisms. One of the key considerations when conducting gene expression analyses using quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is the selection of appropriate reference genes, which is often overlooked. Specifically, to reach meaningful conclusions when using relative quantification approaches, expression levels of reference genes must be highly stable and cannot vary as a function of experimental conditions...
September 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28746411/selection-and-validation-of-reference-genes-for-quantitative-real-time-pcr-analysis-under-different-experimental-conditions-in-the-leafminer-liriomyza-trifolii-diptera-agromyzidae
#4
Ya-Wen Chang, Jing-Yun Chen, Ming-Xing Lu, Yuan Gao, Zi-Hua Tian, Wei-Rong Gong, Wei Zhu, Yu-Zhou Du
Liriomyza trifolii is a highly-invasive leafmining insect that causes significant damage to vegetables and horticultural crops worldwide. Relatively few studies have quantified gene expression in L. trifolii using real-time quantitative PCR (RT-qPCR), which is a reliable and sensitive technique for measuring gene expression. RT-qPCR requires the selection of reference genes to normalize gene expression data and control for internal differences between samples. In this study, nine housekeeping genes from L. trifolii were selected for their suitability in normalizing gene expression using geNorm, Normfinder, BestKeeper, the ΔCt method and RefFinder...
2017: PloS One
https://www.readbyqxmd.com/read/28699725/evaluation-of-candidate-reference-genes-for-quantitative-expression-studies-in-asian-seabass-lates-calcarifer-during-ontogenesis-and-in-tissues-of-healthy-and-infected-fishes
#5
Anutosh Paria, Jie Dong, P P Suresh Babu, M Makesh, Aparna Chaudhari, A R Thirunavukkarasu, C S Purushothaman, K V Rajendran
Quantitative real-time PCR (qRT-PCR), used to determine the gene expression profile, is an important tool in functional genomic research, including fishes. To obtain more robust and meaningful result, the best possible normalization of the data is of utmost significance. In the present study, we have evaluated the potential of five commonly used housekeeping genes i.e., elongation factor 1-α (EF1A), β-Actin (ACTB), 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-2-Microglobulin (B2M) in normal physiological conditions, developmental stages and in response to bacterial infection in Asian seabass, Lates calcarifer (Bloch), an important food fish cultured in the Asia-Pacific region...
September 2016: Indian Journal of Experimental Biology
https://www.readbyqxmd.com/read/28671969/reference-gene-selection-for-the-shell-gland-of-laying-hens-in-response-to-time-points-of-eggshell-formation-and-nicarbazin
#6
Sami Samiullah, Juliet Roberts, Shu-Biao Wu
Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (18S rRNA), ribosomal protein L4 (RPL4) and HMBS, RPL4, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28598997/selection-of-reference-genes-for-quantitative-real-time-rt-pcr-assays-in-different-morphological-forms-of-dimorphic-zygomycetous-fungus-benjaminiella-poitrasii
#7
Ejaj K Pathan, Vandana Ghormade, Mukund V Deshpande
Benjaminiella poitrasii, a dimorphic non-pathogenic zygomycetous fungus, exhibits a morphological yeast (Y) to hypha (H) reversible transition in the vegetative phase, sporangiospores (S) in the asexual phase and zygospores (Z) in the sexual phase. To study the gene expression across these diverse morphological forms, suitable reference genes are required. In the present study, 13 genes viz. ACT, 18S rRNA, eEF1α, eEF-Tu,eIF-1A, Tub-α, Tub-b, Ubc, GAPDH, Try, WS-21, NADGDH and NADPGDH were evaluated for their potential as a reference, particularly for studying gene expression during the Y-H reversible transition and also for other asexual and sexual life stages of B...
2017: PloS One
https://www.readbyqxmd.com/read/28559905/validation-of-suitable-reference-genes-for-rt-qpcr-data-in-achyranthes-bidentata-blume-under-different-experimental-conditions
#8
Jinting Li, Xueping Han, Can Wang, Wanzhen Qi, Weiyu Zhang, Li Tang, Xiting Zhao
Real-time quantitative polymerase chain reaction (RT-qPCR) is a sensitive technique for gene expression studies. However, choosing the appropriate reference gene is essential to obtain reliable results for RT-qPCR assays. In the present work, the expression of eight candidate reference genes, EF1-α (elongation factor 1-α), GAPDH (glyceraldehyde 3-phosphate dehydrogenase), UBC (ubiquitin-conjugating enzyme), UBQ (polyubiquitin), ACT (actin), β-TUB (β-tubulin), APT1 (adenine phosphoribosyltransferase 1), and 18S rRNA (18S ribosomal RNA), was evaluated in Achyranthes bidentata samples using two algorithms, geNorm and NormFinder...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28523004/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-in-sapium-sebiferum
#9
Xue Chen, Yingji Mao, Shengwei Huang, Jun Ni, Weili Lu, Jinyan Hou, Yuting Wang, Weiwei Zhao, Minghao Li, Qiaojian Wang, Lifang Wu
Chinese tallow (Sapium sebiferum L.) is a promising landscape and bioenergy plant. Measuring gene expression by quantitative real-time polymerase chain reaction (qRT-PCR) can provide valuable information on gene function. Stably expressed reference genes for normalization are a prerequisite for ensuring the accuracy of the target gene expression level among different samples. However, the reference genes in Chinese tallow have not been systematically validated. In this study, 12 candidate reference genes (18S, GAPDH, UBQ, RPS15, SAND, TIP41, 60S, ACT7, PDF2, APT, TBP, and TUB) were investigated with qRT-PCR in 18 samples, including those from different tissues, from plants treated with sucrose and cold stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515733/stable-internal-reference-genes-for-normalizing-real-time-quantitative-pcr-in-baphicacanthus-cusia-under-hormonal-stimuli-and-uv-irradiation-and-in-different-plant-organs
#10
Yuxiang Huang, Hexin Tan, Jian Yu, Yue Chen, Zhiying Guo, Guoquan Wang, Qinglei Zhang, Junfeng Chen, Lei Zhang, Yong Diao
Baphicacanthus cusia (Nees) Bremek, the plant source for many kinds of drugs in traditional Chinese medicine, is widely distributed in South China, especially in Fujian. Recent studies about B. cusia mainly focus on its chemical composition and pharmacological effects, but further analysis of the plant's gene functions and expression is required to better understand the synthesis of its effective compounds. Real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful method for gene expression analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28453515/reliable-reference-genes-for-normalization-of-gene-expression-data-in-tea-plants-camellia-sinensis-exposed-to-metal-stresses
#11
Ming-Le Wang, Qing-Hui Li, Hua-Hong Xin, Xuan Chen, Xu-Jun Zhu, Xing-Hui Li
Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems...
2017: PloS One
https://www.readbyqxmd.com/read/28407308/methods-of-rna-preparation-affect-mrna-abundance-quantification-of-reference-genes-in-pig-maturing-oocytes
#12
Y-K Wang, X Li, Z-Q Song, C-X Yang
To ensure accurate normalization and quantification of target RNA transcripts using reverse transcription quantitative polymerase chain reaction (RT-qPCR), most studies focus on the identification of stably expressed gene(s) as internal reference. However, RNA preparation methods could also be an important factor, especially for test samples of limited quantity (e.g. oocytes). In this study, we aimed to select appropriate reference gene(s), and evaluate the effect of RNA preparation methods on gene expression quantification in porcine oocytes and cumulus cells during in vitro maturation...
April 13, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28362875/identification-and-validation-of-reference-genes-for-quantitative-real-time-pcr-studies-in-long-yellow-daylily-hemerocallis-citrina-borani
#13
Feifan Hou, Sen Li, Jinyao Wang, Xiuping Kang, Yiqun Weng, Guoming Xing
Gene expression analysis using reverse transcription quantitative real-time PCR (RT-qPCR) requires the use of reference gene(s) in the target species. The long yellow daylily, Hemerocallis citrina Baroni. is rich in beneficial secondary metabolites and is considered as a functional vegetable. It is widely cultivated and consumed in East Asian countries. However, reference genes for use in RT-qPCR in H. citrina are not available. In the present study, six potential reference genes, actin (ACT), AP-4 complex subunit (AP4), tubulin (TUB), ubiquitin (UBQ), 18S and 60S ribosomal RNA, were selected and their expression stability in different developmental stages, organs and accessions was evaluated using four statistical software packages (geNorm, NormFinder, BestKeeper, and RefFinder)...
2017: PloS One
https://www.readbyqxmd.com/read/28323834/selection-and-validation-of-reference-genes-for-qrt-pcr-analysis-during-biological-invasions-the-thermal-adaptability-of-bemisia-tabaci-med
#14
Tian-Mei Dai, Zhi-Chuang Lü, Wan-Xue Liu, Fang-Hao Wan
The Bemisia tabaci Mediterranean (MED) cryptic species has been rapidly invading to most parts of the world owing to its strong ecological adaptability, which is considered as a model insect for stress tolerance studies under rapidly changing environments. Selection of a suitable reference gene for quantitative stress-responsive gene expression analysis based on qRT-PCR is critical for elaborating the molecular mechanisms of thermotolerance. To obtain accurate and reliable normalization data in MED, eight candidate reference genes (β-act, GAPDH, β-tub, EF1-α, GST, 18S, RPL13A and α-tub) were examined under various thermal stresses for varied time periods by using geNorm, NormFinder and BestKeeper algorithms, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28067273/validation-of-reference-genes-for-cryopreservation-studies-with-the-gorgonian-coral-endosymbiont-symbiodinium
#15
Gabriella Chong, Fu-Wen Kuo, Sujune Tsai, Chiahsin Lin
Quantification by real-time RT-PCR requires a stable internal reference known as a housekeeping gene (HKG) for normalising the mRNA levels of target genes. The present study identified and validated stably expressed HKGs in post-thaw Symbiodinium clade G. Six potential HKGs, namely, pcna, gapdh, 18S rRNA, hsp90, rbcl, and ps1, were analysed using three different algorithms, namely, GeNorm, NormFinder, and BestKeeper. The GeNorm algorithm ranked the candidate genes as follows in the order of decreasing stability: pcna and gapdh > ps1 > 18S rRNA > hsp90 > rbcl...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27974876/evaluation-of-housekeeping-genes-for-quantitative-gene-expression-analysis-in-the-equine-kidney
#16
Sara Azarpeykan, Keren E Dittmer
Housekeeping genes (HKGs) are used as internal controls for normalising and calculating the relative expression of target genes in RT-qPCR experiments. There is no unique universal HKG and HKGs vary among organisms and tissues, so this study aimed to determine the most stably expressed HKGs in the equine kidney. The evaluated HKGs included 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), ribosomal protein L32 (RPL32), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), succinate dehydrogenase complex (SDHA), zeta polypeptide (YWHAZ), and hypoxanthine phosphoribosyltransferase 1 (HPRT1)...
2016: Journal of Equine Science
https://www.readbyqxmd.com/read/27957397/validation-of-internal-reference-genes-for-relative-quantitation-studies-of-gene-expression-in-human-laryngeal-cancer
#17
Xiaofeng Wang, Jinting He, Wei Wang, Ming Ren, Sujie Gao, Guanjie Zhao, Jincheng Wang, Qiwei Yang
BACKGROUND: The aim of this study was to determine the expression stabilities of 12 common internal reference genes for the relative quantitation analysis of target gene expression performed by reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) in human laryngeal cancer. METHODS: Hep-2 cells and 14 laryngeal cancer tissue samples were investigated. The expression characteristics of 12 internal reference gene candidates (18S rRNA, GAPDH, ACTB, HPRT1, RPL29, HMBS, PPIA, ALAS1, TBP, PUM1, GUSB, and B2M) were assessed by RT-qPCR...
2016: PeerJ
https://www.readbyqxmd.com/read/27889881/identification-of-reference-genes-and-mirnas-for-qrt-pcr-in-human-esophageal-squamous-cell-carcinoma
#18
Li Chen, Yulin Jin, Lin Wang, Fenghao Sun, Xiaodong Yang, Mengkun Shi, Cheng Zhan, Yu Shi, Qun Wang
It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs...
January 2017: Medical Oncology
https://www.readbyqxmd.com/read/27835695/reference-genes-for-addressing-gene-expression-of-bladder-cancer-cell-models-under-hypoxia-a-step-towards-transcriptomic-studies
#19
Luís Lima, Cristiana Gaiteiro, Andreia Peixoto, Janine Soares, Manuel Neves, Lúcio Lara Santos, José Alexandre Ferreira
Highly aggressive, rapidly growing tumors contain significant areas of hypoxia or anoxia as a consequence of inadequate and/or irregular blood supply. During oxygen deprivation, tumor cells withstand a panoply of adaptive responses, including a shift towards anaerobic metabolism and the reprogramming of the transcriptome. One of the major mediators of the transcriptional hypoxic response is the hypoxia-inducible factor 1 (HIF-1), whose stabilization under hypoxia acts as an oncogenic stimulus contributing to chemotherapy resistance, invasion and metastasis...
2016: PloS One
https://www.readbyqxmd.com/read/27824922/identification-of-reference-genes-for-quantitative-real-time-pcr-in-date-palm-phoenix-dactylifera-l-subjected-to-drought-and-salinity
#20
Himanshu V Patankar, Dekoum V M Assaha, Rashid Al-Yahyai, Ramanjulu Sunkar, Mahmoud W Yaish
Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt- and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression...
2016: PloS One
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