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https://www.readbyqxmd.com/read/28328930/validation-of-qpcr-reference-genes-in-lymphocytes-from-patients-with-amyotrophic-lateral-sclerosis
#1
Ewa Usarek, Anna Barańczyk-Kuźma, Beata Kaźmierczak, Beata Gajewska, Magdalena Kuźma-Kozakiewicz
Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines-LCLs) were used for qPCR analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28326094/selection-and-validation-of-reference-genes-for-accurate-rt-qpcr-data-normalization-in-coffea-spp-under-a-climate-changes-context-of-interacting-elevated-co2-and-temperature
#2
Madlles Q Martins, Ana S Fortunato, Weverton P Rodrigues, Fábio L Partelli, Eliemar Campostrini, Fernando C Lidon, Fábio M DaMatta, José C Ramalho, Ana I Ribeiro-Barros
World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO2] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted...
2017: Frontiers in Plant Science
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
#3
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/28300076/evaluation-of-reference-genes-at-different-developmental-stages-for-quantitative-real-time-pcr-in-aedes-aegypti
#4
Najat Dzaki, Karima N Ramli, Azali Azlan, Intan H Ishak, Ghows Azzam
The mosquito Aedes aegypti (Ae. aegypti) is the most notorious vector of illness-causing viruses such as Dengue, Chikugunya, and Zika. Although numerous genetic expression studies utilizing quantitative real-time PCR (qPCR) have been conducted with regards to Ae. aegypti, a panel of genes to be used suitably as references for the purpose of expression-level normalization within this epidemiologically important insect is presently lacking. Here, the usability of seven widely-utilized reference genes i.e. actin (ACT), eukaryotic elongation factor 1 alpha (eEF1α), alpha tubulin (α-tubulin), ribosomal proteins L8, L32 and S17 (RPL8, RPL32 and RPS17), and glyceraldeyde 3-phosphate dehydrogenase (GAPDH) were investigated...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299307/identification-of-appropriate-housekeeping-genes-for-gene-expression-analysis-in-long-term-hypoxia-treated-kidney-cells
#5
Shiva Moein, Shaghayegh Haghjooy Javanmard, Maryam Abedi, Mohammad Hosein Izadpanahi, Yousof Gheisari
BACKGROUND: Selection of stably expressing housekeeping genes (HKGs) is a crucial step in gene expression analysis. However, there are no universal HKGs for all experiments, and they should be determined by each biologic condition. The aim of this study was to detect appropriate HKGs for kidney cells cultured in long-term hypoxia. MATERIALS AND METHODS: Based on a screening step using a microarray data available from gene expression omnibus database, a set of candidate HKGs were chosen to be assessed in human kidney cells cultured in hypoxic or normoxic conditions for about 2 weeks in a time course manner...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28294410/reference-gene-selection-for-reverse-transcription-quantitative-polymerase-chain-reaction-in-chicken-hypothalamus-under-different-feeding-status
#6
Á Simon, A Jávor, P Bai, J Oláh, L Czeglédi
This study was designed to investigate the stability of 10 candidate reference genes, namely ACTB, B2M, GAPDH, HMBS, LBR, POLR2B, RN18S, RPS17, TBP, and YWHAZ for the normalization of gene expression data obtained by quantitative real-time polymerase chain reaction (qPCR) in studies related to feed intake of chicken. Samples were isolated from hypothalamus under three different nutritional status (ad libitum, fasted for 24 hr, fasted for 24 hr then refed for 2 hr). Five different algorithms were applied for the analysis of reference gene stability: BestKeeper, geNorm, NormFinder, the comparative ΔCt method, and a novel approach using multivariate linear mixed-effects modelling for stable reference gene selection...
March 15, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28262749/identification-of-stable-housekeeping-genes-in-response-to-ionizing-radiation-in-cancer-research
#7
Gopal Iyer, Albert R Wang, Sean R Brennan, Shay Bourgeois, Eric Armstrong, Pari Shah, Paul M Harari
Housekeeping genes (HKGs) are essential for basic maintenance of a variety of cellular processes. They ideally maintain uniform expression independent of experimental conditions. However, the effects of ionizing radiation (IR) on HKG expression is unclear. Statistical algorithms, geNorm and Normfinder were used for estimating the stability of HKGs as raw quantification cycle (Cq) values were not a reliable factor for normalization. Head and neck, non-small lung and pancreas cells were exposed to 2, 4 and 6 Gy IR doses and expression of fourteen HKGs was measured at 5 min to 48 h post-irradiation within a given tissue...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28261247/selection-of-candidate-reference-genes-for-gene-expression-analysis-in-kentucky-bluegrass-poa-pratensis-l-under-abiotic-stress
#8
Kuiju Niu, Yi Shi, Huiling Ma
Kentucky bluegrass (Poa pratensis L.) belong to Gramineae and is widely used in lawns, golf courses, landscapes, and sport fields as a prominent cool-season grass. Gene expression patterns during different stages of plant development can provide clues toward the understanding of its biological functions. The selection and validation of reference genes are the first steps in any real-time quantitative PCR gene expression study. Therefore, suitable reference genes are necessary for obtaining reliable results in real-time quantitative PCR analyses of Kentucky bluegrass...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28198810/reference-genes-for-quantitative-real-time-pcr-analysis-in-symbiont-entomomyces-delphacidicola-of-nilaparvata-lugens-st%C3%A3-l
#9
Pin-Jun Wan, Yao-Hua Tang, San-Yue Yuan, Jia-Chun He, Wei-Xia Wang, Feng-Xiang Lai, Qiang Fu
Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) is a major rice pest that harbors an endosymbiont ascomycete fungus, Entomomyces delphacidicola str. NLU (also known as yeast-like symbiont, YLS). Driving by demand of novel population management tactics (e.g. RNAi), the importance of YLS has been studied and revealed, which greatly boosts the interest of molecular level studies related to YLS. The current study focuses on reference genes for RT-qPCR studies related to YLS. Eight previously unreported YLS genes were cloned, and their expressions were evaluated for N...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28184026/identification-of-tmem208-and-pqlc2-as-reference-genes-for-normalizing-mrna-expression-in-colorectal-cancer-treated-with-aspirin
#10
Yuanyuan Zhu, Chao Yang, Mingjiao Weng, Yan Zhang, Chunhui Yang, Yinji Jin, Weiwei Yang, Yan He, Yiqi Wu, Yuhua Zhang, Guangyu Wang, Riju James RajkumarEzakiel Redpath, Lei Zhang, Xiaoming Jin, Ying Liu, Yuchun Sun, Ning Ning, Yu Qiao, Fengmin Zhang, Zhiwei Li, Tianzhen Wang, Yanqiao Zhang, Xiaobo Li
Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts...
February 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28182746/selection-and-evaluation-of-new-reference-genes-for-rt-qpcr-analysis-in-epinephelus-akaara-based-on-transcriptome-data
#11
Huan Wang, Xiang Zhang, Qiaohong Liu, Xiaochun Liu, Shaoxiong Ding
Groupers are an economically important fish species in world fishery markets. Because many studies using RT-qPCR have addressed gene expression in groupers, appropriate reference genes are required to obtain reliable and accurate results. In this study, the most suitable reference genes were identified from eleven candidate genes of one of the most valuable species, Epinephelus akaara, in a range of different experimental conditions. Using the software packages geNorm, NormFinder, BestKeeper and refFinder, three traditionally used reference genes, β-actin (β-ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-2-microglobulin (B2M), were identified as not suitable for E...
2017: PloS One
https://www.readbyqxmd.com/read/28182697/identification-of-reference-genes-for-qpcr-analysis-during-hasc-long-culture-maintenance
#12
Silvia Palombella, Cristina Pirrone, Mario Cherubino, Luigi Valdatta, Giovanni Bernardini, Rosalba Gornati
Up to now quantitative PCR based assay is the most common method for characterizing or confirming gene expression patterns and comparing mRNA levels in different sample populations. Since this technique is relative easy and low cost compared to other methods of characterization, e.g. flow cytometry, we used it to typify human adipose-derived stem cells (hASCs). hASCs possess several characteristics that make them attractive for scientific research and clinical applications. Accurate normalization of gene expression relies on good selection of reference genes and the best way to choose them appropriately is to follow the common rule of the "Best 3", at least three reference genes, three different validation software and three sample replicates...
2017: PloS One
https://www.readbyqxmd.com/read/28160493/analysis-of-transcriptional-responses-of-normalizing-genes-on-crassostrea-brasiliana-under-different-experimental-conditions
#13
Gabrielle do Amaral E Silva Müller, Daína de Lima, Flávia Lucena Zacchi, Rômi Sharon Piazza, Karim Hahn Lüchmann, Jacó Joaquim Mattos, Daniel Schlenk, Afonso Celso Dias Bainy
Bivalves show remarkable plasticity to environmental changes and have been proposed as sentinel organisms in biomonitoring. Studies related to transcriptional analysis using quantitative real-time polymerase chain reaction (qRT-PCR) in these organisms have notably increased, imposing a need to identify and validate adequate reference genes for an accurate and reliable analysis. In the present study, 9 reference genes were selected from transcriptome data of Crassostrea brasiliana to identify their suitability as qRT-PCR normalizer genes...
February 4, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28133578/selection-and-evaluation-of-reference-genes-for-analysis-of-mouse-mus-musculus-sex-dimorphic-brain-development
#14
Tanya T Cheung, Mitchell K Weston, Megan J Wilson
The development of the brain is sex-dimorphic, and as a result so are many neurological disorders. One approach for studying sex-dimorphic brain development is to measure gene expression in biological samples using RT-qPCR. However, the accuracy and consistency of this technique relies on the reference gene(s) selected. We analyzed the expression of ten reference genes in male and female samples over three stages of brain development, using popular algorithms NormFinder, GeNorm and Bestkeeper. The top ranked reference genes at each time point were further used to quantify gene expression of three sex-dimorphic genes (Wnt10b, Xist and CYP7B1)...
2017: PeerJ
https://www.readbyqxmd.com/read/28120870/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-gene-expression-analysis-in-salix-matsudana-under-different-abiotic-stresses
#15
Yunxing Zhang, Xiaojiao Han, Shuangshuang Chen, Liu Zheng, Xuelian He, Mingying Liu, Guirong Qiao, Yang Wang, Renying Zhuo
Salix matsudana is a deciduous, rapidly growing willow species commonly cultivated in China, which can tolerate drought, salt, and heavy metal stress conditions. Selection of suitable reference genes for quantitative real-time PCR is important for normalizing the expression of the key genes associated with various stresses. To validate suitable reference genes, we selected 11 candidate reference genes (five traditional housekeeping genes and six novel genes) and analyzed their expression stability in various samples, including different tissues and under different abiotic stress treatments...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28117343/selection-of-reference-genes-is-critical-for-mirna-expression-analysis-in-human-cardiac-tissue-a-focus-on-atrial-fibrillation
#16
Michela Masè, Margherita Grasso, Laura Avogaro, Elvira D'Amato, Francesco Tessarolo, Angelo Graffigna, Michela Alessandra Denti, Flavia Ravelli
MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28115499/selection-and-evaluation-of-reference-genes-for-expression-analysis-using-qrt-pcr-in-chilo-suppressalis-lepidoptera-pyralidae
#17
Jing Xu, Ming-Xing Lu, Ya-Dong Cui, Yu-Zhou Du
Quantitative real-time polymerase chain reaction (qRT-PCR) is a valuable tool for estimating gene expression; however, the validity is largely dependent on the selection of stable reference genes. The suitability of various reference genes for qRT-PCR analysis was evaluated in, Chilo suppressalis (Walker). The ΔCt method, geNorm, NormFinder, and BestKeeper were used to evaluate the suitability of nine candidate reference genes for normalizing gene expression in larval tissues and organs and during high and low temperature stress...
January 22, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28090788/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-in-trabecular-meshwork-cells-under-oxidative-stress
#18
Jing Zhao, HongYan Zhou, Lixia Sun, Ben Yang, Lin Zhang, Hongfeng Shi, Yajuan Zheng
Oxidative stress-induced dysfunction in trabecular meshwork (TM) cells is considered a major alteration that can lead to glaucoma. Hydrogen peroxide (H2O2) is the most widely used agent for inducing oxidation in TM cells in vitro. Quantitative real-time PCR (qPCR) is an important method for studying alterations in gene expression, and suitable (i.e. invariant) reference genes must be defined to normalize expression levels. In this study, eight common reference genes, i.e. PRS18, ACTB, B2M, GAPDH, PPIA, HPRT1, YWHAZ, and TBP, were evaluated for use in studies of H2O2-induced dysfunction in TM cells...
January 2017: Free Radical Research
https://www.readbyqxmd.com/read/28067273/validation-of-reference-genes-for-cryopreservation-studies-with-the-gorgonian-coral-endosymbiont-symbiodinium
#19
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/28056110/selection-of-reference-genes-for-qrt-pcr-analysis-of-gene-expression-in-stipa-grandis-during-environmental-stresses
#20
Dongli Wan, Yongqing Wan, Qi Yang, Bo Zou, Weibo Ren, Yong Ding, Zhen Wang, Ruigang Wang, Kai Wang, Xiangyang Hou
Stipa grandis P. Smirn. is a dominant plant species in the typical steppe of the Xilingole Plateau of Inner Mongolia. Selection of suitable reference genes for the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is important for gene expression analysis and research into the molecular mechanisms underlying the stress responses of S. grandis. In the present study, 15 candidate reference genes (EF1 beta, ACT, GAPDH, SamDC, CUL4, CAP, SNF2, SKIP1, SKIP5, SKIP11, UBC2, UBC15, UBC17, UCH, and HERC2) were evaluated for their stability as potential reference genes for qRT-PCR under different stresses...
2017: PloS One
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