Search results for "Reference genes"
showing 8 items of 8 documents
Validation of a set of reference genes to study response to herbicide stress in grasses
2012
Abstract Background Non-target-site based resistance to herbicides is a major threat to the chemical control of agronomically noxious weeds. This adaptive trait is endowed by differences in the expression of a number of genes in plants that are resistant or sensitive to herbicides. Quantification of the expression of such genes requires normalising qPCR data using reference genes with stable expression in the system studied as internal standards. The aim of this study was to validate reference genes in Alopecurus myosuroides, a grass (Poaceae) weed of economic and agronomic importance with no genomic resources. Results The stability of 11 candidate reference genes was assessed in plants res…
Bypassing hazard of housekeeping genes: their evaluation in rat granule neurons treated with cerebrospinal fluid of multiple sclerosis subjects
2015
Gene expression studies employing real-time PCR has become an intrinsic part of biomedical research. Appropriate normalization of target gene transcript(s) based on stably expressed housekeeping genes is crucial in individual experimental conditions to obtain accurate results. In multiple sclerosis (MS), several gene expression studies have been undertaken, however, the suitability of housekeeping genes to express stably in this disease is not yet explored. Recent research suggests that their expression level may vary under different experimental conditions. Hence it is indispensible to evaluate their expression stability to accurately normalize target gene transcripts. The present study ai…
Influence of Age on Cerebral Housekeeping Gene Expression for Normalization of Quantitative Polymerase Chain Reaction after Acute Brain Injury in Mice
2015
To prevent methodological errors of quantitative PCR (qPCR) normalization with reference genes is obligatory. Although known to influence gene expression, impact of age on housekeeping gene expression has not been determined after acute brain lesions such as traumatic brain injury (TBI). Therefore, expression of eight common control genes was investigated at 15 min, 24 h, and 72 h after experimental TBI in 2- and 21-month-old C57Bl6 mice. Expression of β2-microglobulin (B2M), β-actin (ActB), and porphobilinogen deaminase (PBGD) increased after TBI in both ages. β2M demonstrated age-dependent differences and highest inter- and intragroup variations. Expression of cyclophilin A, glyceraldehyd…
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
2019
Abstract Motivation Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. Results To address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, re…
Optimised lyophilisation-based method for different biomolecule single-extractions from the same rat brain sample: Suitability for RNA and protein ex…
2019
Abstract Background Optimisation of tissue processing procedures in preclinical studies reduces the number of animals used and allows integrated multilevel study in the same sample. Multiple extraction of different biomolecules from the same sample has several limitations. New method Using brain samples from rats subjected to ischemic stroke, we combined lyophilisation of flash-frozen tissue, mechanical pulverisation and cryopreservation in a method to optimise tissue handling and preservation for independent RNA or protein single-extract methods, and subsequent RT-qPCR or Western blot analyses. Results Lyophilisation resulted in 70% tissue weight loss. RNA (OD260/280∼1.8) and protein yield…
Selection of suitable housekeeping genes for expression analysis in glioblastoma using quantitative RT-PCR
2009
Abstract Background Considering the broad variation in the expression of housekeeping genes among tissues and experimental situations, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. For glioblastoma, the most common type of tumor in the central nervous system, there was no previous report regarding this issue. Results Here we show that amongst seven frequently used housekeeping genes TBP and HPRT1 are adequate references for glioblastoma gene expression analysis. Evaluation of the expression levels of 12 target genes utilizing different endogenous controls revealed that the normalization method applied might introduce errors in the estimation of…
β-Aminobutyric Acid (BABA)-Induced Resistance in Arabidopsis thaliana: Link with Iron Homeostasis
2014
International audience; Bêta-Aminobutyric acid (BABA) is a nonprotein amino acid inducing resistance in many different plant species against a wide range of abiotic and biotic stresses. Nevertheless, how BABA primes plant natural defense reactions remains poorly understood. Based on its structure, we hypothesized and confirmed that BABA is able to chelate iron (Fe) in vitro. In vivo, we showed that it led to a transient Fe deficiency response in Arabidopsis thaliana plants exemplified by a reduction of ferritin accumulation and disturbances in the expression of genes related to Fe homeostasis. This response was not correlated to changes in Fe concentrations, suggesting that BABA affects the…
Prognostic and Predictive Significance of Pharmacogenetic Analysis in Patients with Carcinomas of Unknown Primary (CAUP)
2012
ABSTRACT Purpose To investigate the prognostic/predictive significance of the expression of BRCA1, ERCC1, RRM1, TOPO-I, TOPO-IIa, TOPO-IIb, TXR1 TYMS and HIF1a mRNA in patients with Carcinomas of Unknown Primary (CaUP). Material and methods Ninety-three patients with CaUP and available tumoral samples diagnosed in three institutions were included in the study. The mRNA levels of the target genes were determined by quantitative real-time PCR from microdissected cells derived from patients' tumoral specimens. β-actin and PGK1 were used as reference genes. Results Successful amplification of at least one gene was achieved in all samples. BRCA1, ERCC1, HIF1a and TXR1 were amplified in all sampl…