Search results for "microarray"

Application of Nanogen microarray technology for forensic SNP analysis

2006

Abstract The NanoChip® Molecular Biology Workstation using electronic microarrays is an approach for rapid and high throughput analysis of SNPs. This instrument is fully automated and uses a microchip for electronic addressing of capture probes to specific array sites followed by electronic hybridisation of the single stranded PCR products, and passive hybridisation of fluorescently labelled reporter probes. Discrimination is achieved by applying thermal stringency to denature the mismatched reporters. 48 SNP assays have been designed using the ‘capture down’ assay which applies a thermal ‘touch down’ strategy to obtain the best reporter probe discrimination.

Stress responses in citrus peel: Comparative analysis of host responses to Huanglongbing disease and puffing disorder

2015

Abstract A comparison between transcriptomic responses to puffing disorder and Huanglongbing disease was conducted to decipher differences and similarities in gene and pathway regulation induced by abiotic (puffing) and biotic stresses (Huanglongbing) in citrus peel tissues. We functionally analyzed two previously published datasets: the first obtained for the study of puffing disorder using an Affymetrix citrus microarray and the second consisting of a deep sequencing analysis of symptomatic responses to Huanglongbing disease. Transcriptomic data were mined using bioinformatic tools to highlight genes and pathways playing a key role in modulating responses to different types of stress in c…

2013

Abstract Background The cumulus cells (CCs) enveloping antral and ovulated oocytes have been regarded as putative source of non-invasive markers of the oocyte developmental competence. A number of studies have indeed observed a correlation between CCs gene expression, embryo quality, and final pregnancy outcome. Here, we isolated CCs from antral mouse oocytes of known developmental incompetence (NSN-CCs) or competence (SN-CCs) and compared their transcriptomes with the aim of identifying distinct marker transcripts. Results Global gene expression analysis highlighted that both types of CCs share similar transcriptomes, with the exception of 422 genes, 97.6% of which were down-regulated in N…

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.…

Molecular biology approaches utilized in preimplantation genetics: real-time PCR, microarrays, next-generation sequencing, karyomapping, and others

2020

Abstract Over the past few decades the development of new molecular technologies has revolutionized diagnosis in the reproductive medicine field, with the evaluation of the two main factors involved in a successful pregnancy: the embryo and the endometrium. The detection of genetically abnormal embryos, as well as the identification of an optimum endometrium using transcriptomics have become a priority in assisted reproductive treatments to increase pregnancy rates. This chapter provides an overview of the molecular techniques currently employed in assisted reproduction for embryo evaluation such as preimplantation genetic testing karyotyping, fluorescence in situ hybridization, polymerase …

Selective phenotyping, entropy reduction, and the mastermind game.

2011

Abstract Background With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. Results Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of p…

EFFECTIVENESS OF G-CSF+PLERIXAFOR MOBILIZATION IN β- THALASSEMIA PATIENTS AND WHOLE GENE EXPRESSION ANALYSIS OF THE HARVESTED CD34+ CELLS

2014

Identification of ELF3 as an early transcriptional regulator of human urothelium

2014

AbstractDespite major advances in high-throughput and computational modelling techniques, understanding of the mechanisms regulating tissue specification and differentiation in higher eukaryotes, particularly man, remains limited. Microarray technology has been explored exhaustively in recent years and several standard approaches have been established to analyse the resultant datasets on a genome-wide scale. Gene expression time series offer a valuable opportunity to define temporal hierarchies and gain insight into the regulatory relationships of biological processes. However, unless datasets are exactly synchronous, time points cannot be compared directly.Here we present a data-driven ana…

“Default” versus “pre-atopic” IgG responses to foodborne and airborne pathogenesis-related group 10 protein molecules in birch-sensitized and nonatop…

2014

Background The route and dose of exposure are believed to be relevant factors in the sensitization process. Pathogenesis-related group 10 protein (PR-10) molecules are a family of allergenic proteins shared by many pollens (eg, birch and alder) and foods (eg, apple, peach, and soy). Children are exposed to both pollen-derived (inhaled) and food-derived (ingested) PR-10 molecules. Objective We sought to investigate the role of route and dose of exposure in the evolution of IgG and IgE responses to recombinant PR-10 molecules. Methods The German Multicentre Allergy Study examined a birth cohort born in 1990. Blood samples were collected at the ages of 1, 2, 3, 5, 6, 7, 10, and 13 years. Parti…