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Genorm hypoxia

Anja Nilsen, Marte Jonsson, Eva-Katrine Aarnes, Gunnar Balle Kristensen, Heidi Lyng
MicroRNA (miRNA) expressions in tumor biopsies have shown potential as biomarkers in cervical cancer, but suitable reference RNAs for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays in patient cohorts with different clinicopathological characteristics are not available. We aimed to identify the optimal reference miRNAs and apply these to investigate the potential of miR-9-5p as human papilloma virus (HPV) 16 biomarker and miR-210-3p as hypoxia biomarker in cervical cancer...
January 17, 2019: Translational Oncology
Dhananjay Kumar, Prasanta Kumar Das, Bidyut Kumar Sarmah
Study on expression of genes for the traits associated with hypoxia tolerance during the germination demands robust choice of reference genes for transcript data normalization and gene validation through real-time quantitative polymerase chain reaction (RT-qPCR). However, reliability and stability of reference genes across different rice germplasms under hypoxic condition have not been accessed yet. Stability performance of reference genes such as eukaryotic elongation factor 1 α (eEF1α), ubiquitin 10 (UBQ10), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA (18SrRNA), 25S ribosomal RNA (25SrRNA), β-tublin (β-TUB), actin11 (ACT11), ubiquitin C (UBC), eukaryotic elongation factor 4 α (eIF4α), and ubiquitin5 (UBQ5) was accessed through statistical algorithms like geNorm, NormFinder, Comparative ΔCt method, BestKeeper, and RefFinder in three rice germplasms (KHO, RKB, and IR-64) with varied level of tolerance to hypoxic condition during germination...
November 2018: Journal of Applied Genetics
Yuning Hu, Hongtuo Fu, Hui Qiao, Shengming Sun, Wenyi Zhang, Shubo Jin, Sufei Jiang, Yongsheng Gong, Yiwei Xiong, Yan Wu
Quantitative real-time PCR (qPCR) is widely used in molecular biology, although the accuracy of the quantitative results is determined by the stability of the reference genes used. Recent studies have investigated suitable reference genes for some crustaceans under various conditions, but studies in Macrobrachium nipponense are currently lacking. In this study, we selected the following seven genes from among 35 commonly used housekeeping genes as candidate qPCR reference genes for temporal and spatial expression: EIF ( eukaryotic translation initiation factor 5A ), 18S ( 18S ribosomal RNA ), EF-1α ( elongation factor-1α ), GAPDH ( glyceraldehyde-3-phosphate dehydrogenase ), TUB ( α-tubulin ), β-act ( β-actin ), and RPL18 ( Ribosomal protein L18 )...
August 1, 2018: International Journal of Molecular Sciences
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
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
Guilherme Silva Julian, Renato Watanabe de Oliveira, Sergio Tufik, Jair Ribeiro Chagas
Obstructive sleep apnea (OSA) has been associated with oxidative stress and various cardiovascular consequences, such as increased cardiovascular disease risk. Quantitative real-time PCR is frequently employed to assess changes in gene expression in experimental models. In this study, we analyzed the effects of chronic intermittent hypoxia (an experimental model of OSA) on housekeeping gene expression in the left cardiac ventricle of rats. Analyses via four different approaches-use of the geNorm, BestKeeper, and NormFinder algorithms; and 2-ΔCt (threshold cycle) data analysis-produced similar results: all genes were found to be suitable for use, glyceraldehyde-3-phosphate dehydrogenase and 18S being classified as the most and the least stable, respectively...
May 2016: Jornal Brasileiro de Pneumologia: Publicaça̋o Oficial da Sociedade Brasileira de Pneumologia e Tisilogia
Jia'nan Xie, Xin Liu, Ying Li, Yang Liu, Guanfang Su
Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become the most common technique to investigate mRNA expression levels of target genes. In order to obtain accurate results, stable reference genes need to be selected for normalization in an experimental study. Human retinal endothelial cells (HREC) cultured in a hypoxic and hyperglycemic environment is a potential cell model to study diabetic retinopathy (DR), but the proper reference genes for RNA analysis have not yet been determined...
July 1, 2016: Gene
Xin Liu, Jia'nan Xie, Zaoxia Liu, Qiaoyun Gong, Rui Tian, Guanfang Su
Retinal pigment epithelium (RPE) cell-based gene expression studies performed under hypoxia and/or hyperglycemia show huge potential for modeling cell responses in diabetic retinopathy, retinopathy of prematurity and other retinal diseases. However, normalization of gene expression on RPE cells under those conditions has commonly been done using either GAPDH or β-actin as reference genes without any validation of their expression stability. Therefore, we aimed to establish a suitable set of reference genes for studies on RPE cells cultured under both normal culturing glucose and atmospheric oxygen tension (normoxia, 21%), under a low oxygen tension (hypoxia, 1%), under a high glucose growth medium (25 mmol/l) and under the combination of the two changed conditions above for distinct time points taking together from 24h to 7 days...
April 10, 2016: Gene
Lesia Kurlak, Hiten Mistry, Tereza Cindrova-Davies, Martha Tissot van Patot, Graham Burton, Fiona Broughton Pipkin
INTRODUCTION: We have previously shown the activation of placental RAS in high altitude normotensive (NT) pregnancies [1], presumably related to hypoxia during placental development. PE incidence is increased at high altitude; hypoxia-reoxygenation injury contributes to the elevated oxidative stress seen in this condition. Binding of Angiotensin II to its type I receptor (AT1R) increases generation of reactive oxygen species and we have shown an increase in AT1R in PE [2]. Therefore we investigated whether the RAS is further augmented in PE at high altitudes...
April 2013: Pregnancy Hypertension
Guilherme Silva Julian, Renato Watanabe de Oliveira, Juliana Cini Perry, Sergio Tufik, Jair Ribeiro Chagas
Obstructive sleep apnea (OSA) is a syndrome characterized by intermittent nocturnal hypoxia, sleep fragmentation, hypercapnia and respiratory effort, and it has been associated with several complications, such as diabetes, hypertension and obesity. Quantitative real-time PCR has been performed in previous OSA-related studies; however, these studies were not validated using proper reference genes. We have examined the effects of chronic intermittent hypoxia (CIH), which is an experimental model mainly of cardiovascular consequences of OSA, on reference genes, including beta-actin, beta-2-microglobulin, glyceraldehyde-3-phosphate dehydrogenase, hypoxanthine guanine phosphoribosyl transferase and eukaryotic 18S rRNA, in different areas of the brain...
2014: PloS One
Konstantinos Kagias, Agnieszka Podolska, Roger Pocock
BACKGROUND: Quantitative real-time PCR (qPCR) has become the "gold standard" for measuring expression levels of individual miRNAs. However, little is known about the validity of reference miRNAs, the improper use of which can result in misleading interpretation of data. RESULTS: Here we undertook a systematic approach to identify highly stable miRNAs in different stress conditions such as low oxygen (hypoxia), UV-stress and high temperature (heat-stress) in the nematode Caenorhabditis elegans...
March 21, 2014: BMC Genomics
De-Jian Zhao, Kun Guo, Le Kang
Real-time quantitative polymerase chain reaction (qPCR) is a routine and robust approach for measuring gene expression. The stability of reference genes in qPCR is crucial for the accurate quantification of gene expression. To provide reliable reference genes for studying the transcriptional responses of locust muscles to hypobaric hypoxia, we first examined the gene expression stability of the frequently used housekeeping genes 18S, GAPDH, and β-actin. However, the expression of these three housekeeping genes was influenced by hypobaric hypoxia...
2012: FEBS Open Bio
A B Brito, J S Lima, D C Brito, L N Santana, N N Costa, M S Miranda, O M Ohashi, R R Santos, S F S Domingues
There is no tradition in studies reporting the effect of exposure to cryoprotectants or simply hypoxia and hypothermia on gene expression in the ovarian tissue and there has been only one study on reference or target genes quantification, and comparisons of normoxic with hypoxic, hypothermic and toxic conditions. Our aim in the present study was to investigate the stability of three reference genes in the ovarian tissue of capuchin monkeys (Cebus apella). To this end, fresh and cryoprotectant-exposed ovarian biopsies were used...
May 2013: Zygote: the Biology of Gametes and Early Embryos
Suat Cheng Tan, Carolyn A Carr, Kar Kheng Yeoh, Christopher J Schofield, Kay E Davies, Kieran Clarke
Infarction irreversibly damages the heart, with formation of an akinetic scar that may lead to heart failure. Endogenous cardiac stem cells (CSCs) are a promising candidate cell source for restoring lost tissue and thereby preventing heart failure. CSCs may be isolated in vitro, via the formation of cardiospheres, to give cardiosphere-derived cells (CDCs). Although qRT-PCR analyses of CDCs have been performed, no justification for the selection of the housekeeping gene has been published. Here, we evaluated the most suitable housekeeping gene for RNA expression analysis in CDCs cultured under normoxia, hypoxia or with prolyl-4-hydroxylase inhibitors (PHDIs), from both neonatal and adult rats, to determine the effects of ageing and different culture conditions on the stability of the housekeeping gene for CDCs...
April 2012: Molecular Biology Reports
Cristina Della Beffa, Frank Klawonn, Joseph P Menetski, H Ralph Schumacher, Frank Pessler
BACKGROUND: The murine air pouch membrane represents an easily accessible tissue for studies on gene regulation in acute inflammation. Considering that acute inflammation may affect expression of molecular reference genes, we evaluated the expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prolylpeptidyl isomerase A (PPIA) in the air pouch membrane during a complete time course of urate crystal inflammation and correlated the results with expression of interleukin (IL)-1β and hypoxia inducible factor (HIF)-1α...
2011: BMC Research Notes
Insook Kim, Dongjin Yang, Xinyu Tang, John L Carroll
BACKGROUND: The carotid bodies are the main arterial oxygen chemoreceptors in mammals. Afferent neural output from the carotid bodies to brainstem respiratory and cardiovascular nuclei provides tonic input and mediates important protective responses to acute and chronic hypoxia. It is widely accepted that the selection of reference genes for mRNA normalization in quantitative real-time PCR must be validated for a given tissue and set of conditions. This is particularly important for studies in carotid body during early postnatal maturation as the arterial oxygen tension undergoes major changes from fetal to postnatal life, which may affect reference gene expression...
2011: BMC Research Notes
F Brugè, E Venditti, L Tiano, G P Littarru, E Damiani
Data normalization of gene expression on human dermal fibroblasts (HDF) exposed to UVA has commonly been done using either GAPDH or β-actin as reference genes without any validation of their expression stability. Since this aspect, important for accurate normalization, has been overlooked, we aimed to establish a suitable set of reference genes for studies on UVA-treated HDF cultured under both standard atmospheric oxygen tension (normoxia, 21%) and under a physiological, low oxygen tension for these cells (hypoxia, 5%)...
December 10, 2011: Journal of Biotechnology
Lu Yao, Xinlin Chen, Yingfang Tian, Haixia Lu, Pengbo Zhang, Qindong Shi, Junfeng Zhang, Yong Liu
Gene expression analysis under various conditions using real-time reverse transcription polymerase chain reaction (RT-PCR) needs reliable control genes. Housekeeping genes are commonly used as the control. However, no validated housekeeping gene is available for study of hypoxic neural stem cell culture. To choose appropriate internal control genes, the expression of eight commonly used housekeeping genes was examined in rat neural stem cell model to find one or more stably expressed genes under hypoxic/ischemic conditions...
January 2012: Molecular Biology Reports
Kalle T Rytkönen, Gillian M C Renshaw, Kevin J Ashton, Grant Williams-Pritchard, Erica H Leder, Mikko Nikinmaa
BACKGROUND: Elasmobranch fishes are an ancient group of vertebrates which have high potential as model species for research into evolutionary physiology and genomics. However, no comparative studies have established suitable reference genes for quantitative PCR (qPCR) in elasmobranchs for any physiological conditions. Oxygen availability has been a major force shaping the physiological evolution of vertebrates, especially fishes. Here we examined the suitability of 9 reference candidates from various functional categories after a single hypoxic insult or after hypoxia preconditioning in epaulette shark (Hemiscyllium ocellatum)...
April 23, 2010: BMC Molecular Biology
Casper Bindzus Foldager, Samir Munir, Michael Ulrik-Vinther, Kjeld Søballe, Cody Bünger, Martin Lind
BACKGROUND: Hypoxic culturing of chondrocytes is gaining increasing interest in cartilage research. Culturing of chondrocytes under low oxygen tension has shown several advantages, among them increased synthesis of extracellular matrix and increased redifferentiation of dedifferentiated chondrocytes. Quantitative gene expression analyses such as quantitative real-time PCR (qRT-PCR) are powerful tools in the investigation of underlying mechanisms of cell behavior and are used routinely for differentiation and phenotype assays...
2009: BMC Molecular Biology
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