Possible gene dosage effect of glutathione-S-transferases on atopic asthma: Using real-time PCR for quantification of GSTM1 and GSTT1 gene copy numbers

2004 ◽  
Vol 24 (3) ◽  
pp. 208-214 ◽  
Author(s):  
Charlotte Brasch-Andersen ◽  
Lene Christiansen ◽  
Qihua Tan ◽  
Annette Haagerup ◽  
J�rgen Vestbo ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Gene Dosage ◽  
Atopic Asthma ◽  
Gene Copy ◽  
Gene Dosage Effect ◽  
Gstt1 Gene ◽  
Copy Numbers ◽  
Glutathione S Transferases ◽  
Gene Copy Numbers

scholarly journals Photo-Induced Electron Transfer Real-Time PCR for Detection ofPlasmodium falciparum plasmepsin 2Gene Copy Number

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Samaly Santos Souza ◽  
Mariangela L'Episcopia ◽  
Carlo Severini ◽  
Venkatachalam Udhayakumar ◽  
Naomi W. Lucchi
Keyword(s):  
Electron Transfer ◽  
Real Time ◽  
Real Time Pcr ◽  
Copy Number ◽  
Gene Copy ◽  
Content Type ◽  
Copy Numbers ◽  
Ofplasmodium Falciparum ◽  
Photo Induced Electron Transfer ◽  
Gene Copy Numbers

ABSTRACTPiperaquine is an important partner drug used in artemisinin-based combination therapies (ACTs). An increase in theplasmepsin 2and3gene copy numbers has been associated with decreased susceptibility ofPlasmodium falciparumto piperaquine in Cambodia. Here, we developed a photo-induced electron transfer real-time PCR (PET-PCR) assay to quantify the copy number of theP. falciparumplasmepsin 2gene (PfPM2) that can be used in countries whereP. falciparumis endemic to enhance molecular surveillance.

scholarly journals Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG, nirK, and nosZ Genes in Soils

2006 ◽  
Vol 72 (8) ◽  
pp. 5181-5189 ◽  
Author(s):  
S. Henry ◽  
D. Bru ◽  
B. Stres ◽  
S. Hallet ◽  
L. Philippot
Keyword(s):  
Nitrous Oxide ◽  
16S Rrna ◽  
Real Time ◽  
Real Time Pcr ◽  
Gene Copy ◽  
Nitrous Oxide Reductase ◽  
Gene Encoding ◽  
Copy Numbers ◽  
Dry Soil ◽  
Gene Copy Numbers

ABSTRACT Nitrous oxide (N2O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N2O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different soils. Detection limits were between 101 and 102 target molecules per reaction for all assays. Sequence analysis of 128 cloned quantitative PCR products confirmed the specificity of the designed primers. The abundance of nosZ genes ranged from 105 to 107 target copies g−1 of dry soil, whereas genes for 16S rRNA were found at 108 to 109 target copies g−1 of dry soil. The abundance of narG and nirK genes was within the upper and lower limits of the 16S rRNA and nosZ gene copy numbers. The two sets of nosZ primers gave similar gene copy numbers for all tested soils. The maximum abundance of nosZ and nirK relative to 16S rRNA was 5 to 6%, confirming the low proportion of denitrifiers to total bacteria in soils.

scholarly journals Quantitative Real-Time PCR for Determination of Microcystin Synthetase E Copy Numbers for Microcystis and Anabaena in Lakes

2003 ◽  
Vol 69 (12) ◽  
pp. 7289-7297 ◽  
Author(s):  
Jaana Vaitomaa ◽  
Anne Rantala ◽  
Katrianna Halinen ◽  
Leo Rouhiainen ◽  
Petra Tallberg ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Quantitative Methods ◽  
Gene Copy ◽  
Quantitative Real Time Pcr ◽  
Microcystin Synthetase ◽  
Copy Numbers ◽  
Restoration Strategies ◽  
Cell Densities ◽  
Gene Copy Numbers

ABSTRACT Cyanobacterial mass occurrences in freshwater lakes are generally formed by Anabaena, Microcystis, and Planktothrix, which may produce cyclic heptapeptide hepatotoxins, microcystins. Thus far, identification of the most potent microcystin producer in a lake has not been possible due to a lack of quantitative methods. The aim of this study was to identify the microcystin-producing genera and to determine the copy numbers of microcystin synthetase gene E (mcyE) in Lake Tuusulanjärvi and Lake Hiidenvesi in Finland by quantitative real-time PCR. The microcystin concentrations and cyanobacterial cell densities of these lakes were also determined. The microcystin concentrations correlated positively with the sum of Microcystis and Anabaena mcyE copy numbers from both Lake Tuusulanjärvi and Lake Hiidenvesi, indicating that mcyE gene copy numbers can be used as surrogates for hepatotoxic Microcystis and Anabaena. The main microcystin producer in Lake Tuusulanjärvi was Microcystis spp., since average Microcystis mcyE copy numbers were >30 times more abundant than those of Anabaena. Lake Hiidenvesi seemed to contain both nontoxic and toxic Anabaena as well as toxic Microcystis strains. Identifying the most potent microcystin producer in a lake could be valuable for designing lake restoration strategies, among other uses.

Real-time PCR-based determination of gene copy numbers inPichia pastoris

2010 ◽  
Vol 5 (4) ◽  
pp. 413-420 ◽  
Author(s):  
Sandra Abad ◽  
Kerstin Kitz ◽  
Astrid Hörmann ◽  
Ulrike Schreiner ◽  
Franz S. Hartner ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Gene Copy Numbers

scholarly journals The profile of ErbB/Her family genes copy number assessed by real-time PCR in parathyroid adenoma and hyperplasia associated with sporadic primary hyperparathyroidism.

2009 ◽  
Vol 56 (1) ◽  
Author(s):  
Natalia Bednarz ◽  
Krzysztof Błaut ◽  
Krzysztof Sworczak ◽  
Tomasz Oseka ◽  
Krzysztof P Bielawski
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Molecular Mechanisms ◽  
Gene Dosage ◽  
Parathyroid Tissue ◽  
Gene Copy ◽  
Clinical Parameters ◽  
Her Family ◽  
Egfr Expression ◽  
Her Genes

Hyperparathyroidism (pHPT) is a relatively frequent endocrinopathy, however, the molecular mechanisms of its etiology remain poorly understood. This disorder is mainly associated with benign tumours (adenoma) and hyperplasia of the parathyroid, hence, the focus is directed also to genes that are likely to be involved in carcinogenesis. Among such genes are ErbB/Her family genes already used in diagnosis of other tumours (e.g., breast carcinoma) and reported also to play a role in development of endocrine lesions. So far, ErbB-1/Her-1/EGFR expression has been detected in pHPT-associated adenomas and hyperplasia as opposed to no expression in normal parathyroid tissue. Moreover, losses or gains of the fragments of chromosomes where ErbB/Her genes are located have been reported. In this study, the gene dosage of ErbB/Her family genes were determined for the first time in parathyroid adenomas, hyperplasia and morphologically unchanged tissue in order to establish their putative role in the development of the disease. Genomic DNA was isolated from 33 patients with sporadic hyperparathyroidism and the gene copy numbers were assessed using real-time PCR. The ErbB/Her genes' profile was unaltered in most of the examined samples. Two low-level amplifications of ErbB-1/Her-1/EGFR gene, two deletions of ErbB-2/Her-2, and six deletions of ErbB-4/Her-4 were found. The ErbB-3/Her-3 gene remained unaffected. No correlation with clinical parameters was found for any gene. Both the low number of alterations and a lack of their associations with clinical parameters exclude the prognostic value of the ErbB/Her genes family in parathyroid tumourigenesis. Nevertheless, the ErbB-4/Her-4 deletions seem to be interesting for further investigations, especially in the context of PTH secretion.

scholarly journals Comparison of Different Approaches To QuantifyStaphylococcus aureus Cells by Real-Time Quantitative PCR and Application of This Technique for Examination of Cheese

2001 ◽  
Vol 67 (7) ◽  
pp. 3122-3126 ◽  
Author(s):  
Ingeborg Hein ◽  
Angelika Lehner ◽  
Petra Rieck ◽  
Kurt Klein ◽  
Ernst Brandl ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Taqman Probe ◽  
Gene Copy ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers ◽  
Gene Copies ◽  
Different Types ◽  
Pure Cultures ◽  
Gene Copy Numbers

ABSTRACT Two different real-time quantitative PCR (RTQ-PCR) approaches were applied for PCR-based quantification of Staphylococcus aureus cells by targeting the thermonuclease (nuc) gene. Purified DNA extracts from pure cultures ofS. aureus were quantified in a LightCycler system using SYBR Green I. Quantification proved to be less sensitive (60nuc gene copies/μl) than using a fluorigenic TaqMan probe (6 nuc gene copies/μl). Comparison of the LightCycler system and the well-established ABI Prism 7700 SDS with TaqMan probes revealed no statistically significant differences with respect to sensitivity and reproducibility. Application of the RTQ-PCR assay to quantify S. aureus cells in artificially contaminated cheeses of different types achieved sensitivities from 1.5 � 102 to 6.4 � 102 copies of the nuc gene/2 g, depending on the cheese matrix. The coefficients of correlation between log CFU and nuc gene copy numbers ranged from 0.979 to 0.998, thus enabling calculation of the number of CFU of S. aureus in cheese by performing RTQ-PCR.

scholarly journals The ribosomal RNA gene cluster in aneuploid chickens: evidence for increased gene dosage and regulation of gene expression.

1985 ◽  
Vol 101 (5) ◽  
pp. 1749-1756 ◽  
Author(s):  
D E Muscarella ◽  
V M Vogt ◽  
S E Bloom
Keyword(s):  
Ribosomal Rna ◽  
Gene Dosage ◽  
Regulation Of Gene Expression ◽  
Nucleolar Organizer ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Gene Copy ◽  
Multiple Generations ◽  
Copy Numbers ◽  
Gene Copy Numbers

In the chicken, the nucleolus organizer regions, or sites of the genes encoding 18S, 5.8S, and 28S ribosomal RNA (rRNA), map to one pair of microchromosomes that can be identified by silver nitrate cytochemistry. This nucleolar organizer chromosome also contains the major histocompatibility complex. Chickens aneuploid for this chromosome have been identified and reproduced for over seven generations. Crossing two trisomic parents results in the production of viable disomic, trisomic, and tetrasomic progeny, showing two, three, and four nucleoli and nucleolar organizers per cell, respectively. A molecular analysis of rRNA genes was undertaken to establish the gene copy numbers in the aneuploid genotypes, and to determine if elevated numbers of rRNA genes are stably maintained and inherited over multiple generations. Gene copy numbers were determined using hybridization analysis of erythrocyte DNA obtained from individuals comprising a family which segregated disomic, trisomic, and tetrasomic genotypes. The values obtained were 290, 420, and 570 rDNA repeats per cell for disomic, trisomic, and tetrasomic animals, respectively. These results provide molecular confirmation of the two aneuploid states and show that elevated gene copy numbers have been maintained over multiple generations. Fibroblasts derived from disomic and tetrasomic embryos were found to grow at similar rates in culture, and mature rRNA levels in chicken embryo fibroblasts from disomic, trisomic and tetrasomic embryos were also found to have similar levels of mature rRNA. Therefore, despite the increase in rDNA content, the level of rRNA is regulated to diploid amounts in aneuploid fibroblasts.

scholarly journals Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae

2021 ◽  
Vol 118 (49) ◽  
pp. e2111841118
Author(s):  
Kenneth Wu ◽  
Namrita Dhillon ◽  
Kelvin Du ◽  
Rohinton T. Kamakaka
Keyword(s):  
Gene Silencing ◽  
Gene Dosage ◽  
Gene Copy ◽  
Promoter Strength ◽  
Protein Levels ◽  
Copy Numbers ◽  
Upstream Activating Sequence ◽  
Functional Consequences ◽  
Gene Copy Numbers ◽  
Silent State

Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.

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