Search results for "oligonucleotide"

A simple DNA extraction method suitable for PCR detection of genetically modified maize.

2010

BACKGROUND: The polymerase chain reaction (PCR) is a powerful tool that is being increasingly used for detection of transgenic DNA. PCR requires only a minute quantity of template, but sensitive and accurate testing requires DNA of sufficient purity and free from inhibitors such as plant polysaccharides. Several standard protocols are available for this purpose, but they usually involve several steps, imply destruction of the maize kernel, or are time-consuming. Our aim was to develop a fast and simple extraction method to isolate a raw DNA-containing solution from maize tissues suitable for use as a template in a PCR-based detection assay with specific oligonucleotides directed to the iden…

Genetics of hepatocellular carcinoma.

2007

The completely assembled human genome has made it possible for modern medicine to step into an era rich in genetic information and high-throughput genomic analysis. These novel and readily available genetic resources and analytical tools may be the key to unravel the molecular basis of hepatocellular carcinoma (HCC). Moreover, since an efficient treatment for this disease is lacking, further understanding of the genetic background of HCC will be crucial in order to develop new therapies aimed at selected targets. We report on the current status and recent developments in HCC genetics. Special emphasis is given to the genetics and regulation of major signalling pathways involved in HCC such …

Genomic response programs of Saccharomyces cerevisiae following protoplasting and regeneration.

2007

Abstract Global transcription profiling during regeneration of Saccharomyces cerevisiae protoplasts was explored. DNA microarrays measured the expression of 6388 genes and wall removal resulted initially in over-expression of 861 genes that decayed later on, a behaviour expected from a transient stress response. Kinetics of expression divided the genes into 25 clusters. Transcription of the genes from clusters 14–25 was initially up-regulated, suggesting that the grouped genes permitted cell adaptation to the removal of the wall. Clustering of genes involved in “wall structure and biosynthesis” showed that most of them had initially low levels of expression that increased along the process.…

2004

Background Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet.

A new method for the mapping of 5' ends of RNAs.

2008

In this article, we describe a new procedure to map 5' ends of RNAs. The procedure consists in the use of specific RNase H digestion of a hybrid formed by the RNA and a complementary DNA oligonucleotide. Northern blot hybridization of the resulting RNA fragment allows an accurate measurement of its length. Although we generally use this procedure as a control of previously performed primer extension analyses, the absence of nonspecific bands, which often occur in primer extensions on RNA templates with extended secondary structures, suggests that our method may be preferable when these difficult templates are analyzed.

4p16.1-p15.31 duplication and 4p terminal deletion in a 3-years old Chinese girl: Array-CGH, genotype-phenotype and neurological characterization

2014

Abstract Background Microscopically chromosome rearrangements of the short arm of chromosome 4 include the two known clinical entities: partial trisomy 4p and deletions of the Wolf-Hirschhorn critical regions 1 and 2 (WHSCR-1 and WHSCR-2, respectively), which cause cranio-facial anomalies, congenital malformations and developmental delay/intellectual disability. Methods/results We report on clinical findings detected in a Chinese patient with a de novo 4p16.1-p15.32 duplication in association with a subtle 4p terminal deletion of 6 Mb in size. This unusual chromosome imbalance resulted in WHS classical phenotype, while clinical manifestations of 4p trisomy were practically absent. Conclusio…

Synthesis of undulin by rat liver fat-storing cells: Comparison with fibronectin and tenascin

1992

Abstract Fat-storing cells (FSCs) are known to synthesize various components of the hepatic extracellular matrix and thereby play an important role during liver fibrogenesis. The aim of our study was to investigate the synthesis of undulin, a recently described connective tissue protein belonging to the fibronectin—tenascin superfamily of glycoproteins, by fat-storing cells in primary culture. SDS-PAGE analysis of immunoprecipitates from cell layer lysates or media pulse-labeled with radioactive methionine revealed undulin-specific bands A (270 kDa), B1 (190 kDa), and B2 (180 kDa) after reduction. A single undulin-specific transcript was detected at about 7 kb. Undulin synthesized by cell-f…

Generation of reporter plasmids containing defined base modifications in the DNA strand of choice

2012

Physiological effects of DNA bases other than A, G, C, and T as well as ways of removal of such bases from genomes are studied intensely. Methods for targeted insertion of modified bases into DNA, therefore, are highly demanded in the fields of DNA repair and epigenetics. This article describes efficient procedures for incorporation of modified DNA bases into a plasmid-borne enhanced green fluorescent protein (EGFP) gene. The procedure exploits excision of a stretch of 18 nt from either the transcribed or nontranscribed DNA strand with the help of the sequence-specific nicking endonucleases Nb.Bpu10I and Nt.Bpu10I. The excised single-stranded oligonucleotide is then swapped for a synthetic …

Are we sure we know how to measure 8-oxo-7,8-dihydroguanine in DNA from human cells?

2004

The most commonly measured marker of oxidative DNA damage is 8-oxo-7,8-dihydroguanine (8-oxoGua) or its deoxyribonucleoside (8-oxodGuo). Published estimates of the concentration of 8-oxoGua/8-oxodGuo in DNA of normal human cells vary over a range of three orders of magnitude. Analysis by chromatographic methods (GC-MS, HPLC with electrochemical detection (ECD) or HPLC-MS/MS) is beset by the problem of adventitious oxidation of guanine during sample preparation. An alternative approach, based on the use of the DNA repair enzyme formamidopyrimidine DNA N-glycosylase (FPG) to make breaks in the DNA at sites of the oxidised base, gives much lower values. ESCODD, the European Standards Committee…

H89 enhances the sensitivity of cancer cells to glyceryl trinitrate through a purinergic receptor-dependent pathway

2014

// Marion Cortier 1, 2, 3 , Rahamata Boina-Ali 1, 2, 3 , Cindy Racoeur 1, 2, 3 , Catherine Paul 1, 2, 3 , Eric Solary 2, 4, 5 , Jean-Francois Jeannin 1, 2, 3 , Ali Bettaieb 1, 2, 3 1 EPHE, Tumor Immunology and Immunotherapy Laboratory, Dijon, F-21000, France 2 Inserm U866, Dijon, F-21000, France 3 EA7269, University of Burgundy, Dijon, F-21000, France 4 Inserm UMR1009, Gustave Roussy Institute, Villejuif F-94805, France 5 University Paris-Sud, Faculty of Medicine, Le Kremlin-Bicetre, F-94800, France Correspondence to: Ali Bettaieb, e-mail: ali.bettaieb@u-bourgogne.fr Keywords: H89, GTN, cancer, purinergic receptors, cGMP Received: October 08, 2014      Accepted: January 09, 2015      Publis…