Search results for " microarray"

Expression profiling of glial genes during Drosophila embryogenesis

2006

AbstractIn the central nervous system of Drosophila, the induction of the glial cell fate is dependent on the transcription factor glial cells missing (gcm). Though a considerable number of other genes have been shown to be expressed in all or in subsets of glial cells, the course of glial cell differentiation and subtype specification is only poorly understood. This prompted us to design a whole genome microarray approach comparing gcm gain-of-function and, for the first time, gcm loss-of-function genetics to wildtype in time course experiments along embryogenesis. The microarray data were analyzed with special emphasis on the temporal profile of differential regulation. A comparison of bo…

FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing

2019

RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon. We present Fedro, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidi…

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechan…

2021

[EN] Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,0…

Current Technologies for Pseudomonas spp. And Ralstonia solanacearum Detection and Molecular Typing

2008

Standard protocols for detection of phytopathogenic Pseudomonas spp. and Ralstonia solanacearum in plant material, soil, water or other sources, often still rely on the isolation of bacterial colonies on appropriate media, and/or on the use of serological techniques. However, over the last several years, molecular techniques, mainly based on PCR methods after extraction of nucleic acids from samples, have improved enough to allow a more rapid, reliable detection of these bacteria. When maximum accuracy is required the use of multiple techniques in an integrated approach is advised. Other promising technologies like flow cytometry, electronic nose or microarrays are emerging due to the need …

Systematic Comparative Protein Expression Profiling of Clear Cell Renal Cell Carcinoma

2009

Proteome-based technologies represent powerful tools for the analysis of protein expression profiles, including the identification of potential cancer candidate biomarkers. Thus, here we provide a comprehensive protein expression map for clear cell renal cell carcinoma established by systematic comparative two-dimensional gel electrophoresis-based protein expression profiling of 16 paired tissue systems comprising clear cell renal cell carcinoma lesions and corresponding tumor-adjacent renal epithelium using overlapping narrow pH gradients. This approach led to the mapping of 348 distinct spots corresponding to 248 different protein identities. By implementing restriction criteria concernin…

Genomic response programs of Candida albicans following protoplasting and regeneration

2005

Transcription profiling of Candida albicans cells responding to the elimination of the wall (protoplasts) and posterior regeneration was explored. DNA microarrays were used to measure changes in the expression of 6039 genes, and the upregulated genes during regeneration at 28 degrees C were assigned to fourteen categories. A total of 407 genes were upregulated during the process, of which 144 reached a maximum after 1 h. MKC1, a gene encoding a member of the regulatory pathway involved in cell wall integrity was overexpressed. Time-dependent expression divided the genes into 40 clusters. Clusters 1-19 were highly expressed initially (time 0) and downregulated following incubation, whereas t…

Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity

2009

Ad-Hoc Segmentation Pipeline for Microarray Image Analysis

2006

Microarray is a new class of biotechnologies able to help biologist researches to extrapolate new knowledge from biological experiments. Image Analysis is devoted to extrapolate, process and visualize image information. For this reason it has found application also in Microarray, where it is a crucial step of this technology (e.g. segmentation). In this paper we describe MISP (Microarray Image Segmentation Pipeline), a new segmentation pipeline for Microarray Image Analysis. The pipeline uses a recent segmentation algorithm based on statistical analysis coupled with K-Means algorithm. The Spot masks produced by MISP are used to determinate spots information and quality measures. A software …

Neurobeachin (NBEA) is downregulated in blood cells from a patient with autism spectrum disorders (ASD)

2007

Identification of pathways involved in aneuploidy onset and its tolerance using a DNA microarray approach

2013

Genomic instability is a hallmark of the majority of human tumors explaining the heterogeneity shown by tumor cells. This phenomenon is often associated with chromosomal instability (CIN) and aneuploidy, a condition in which tumor cells lose or gain chromosomes. Previously, we showed that posttranscriptional silencing by RNAi of pRb1, DNMT12 and MAD2 is associated with aneuploidy in cultured human cells reinforcing the idea that there are several roads leading to aneuploidy. In the attempt to understand if a common molecular signature exists underlying aneuploidy and its tolerance in tumor cells, we induced aneuploidy in human fibroblasts (IMR90) by depleting Rb, MAD2 and DNMT1 genes and an…