a-madman annotation-based microarray: Topics by WorldWideScience.org

Evaluating concentration estimation errors in ELISA microarray experiments

Tissue microarray technology (TMA) is a relatively new approach for efficiently and economically assessing protein and gene expression across large ensembles of tissue specimens. Tissue microarray technology...Full Text Available

High Throughput Screening on Angiogenesis Inhibitor and Promoter of Medicinal Plants using a Protein Microarray Chip

BackgroundEnzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to estimate a protein's concentration in a sample. Deploying ELISA in a microarray format permits simultaneous...Full Text Available

KoreaScience (Korea)

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2007-04-01

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

BackgroundMicroarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection...Full Text Available

Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture....Full Text Available

2008-08-01

Feature Selection and Classification of MAQC-II Breast Cancer and Multiple Myeloma Microarray Gene Expression Data

BackgroundFor more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe...Full Text Available

Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task...Full Text Available

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens....Full Text Available

2006-03-30

A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently...Full Text Available

2005-09-01

A Nonparametric Mean-Variance Smoothing Method to Assess Arabidopsis Cold Stress Transcriptional Regulator CBF2 Overexpression Microarray Data

BackgroundWith the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across...Full Text Available

Spectral Analysis of Breast Cancer on Tissue Microarrays ...

Microarray is a powerful tool for genome-wide gene expression analysis. In microarray expression data, often mean and variance have certain relationships. We present a non-parametric mean-variance smoothing...Full Text Available

Microarray-based gene expression profiles of silkworm brains

... Although cytologic evaluation of urine specimens is a standard Cesar Angeletti, MD ... 3. Rodriguez-Alonso A, Pita-Fernandez S, Gonzalez-Carrero J, ...

2005-04-01

Global Transcriptional Responses of Fission Yeast to Environmental Stress

BackgroundMolecular genetic studies of Bombyx mori have led to profound advances in our understanding of the regulation of development. Bombyx mori brain,...Full Text Available

Development of a microarray for identification of pathogenic Clostridium species

We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression...Full Text Available

2003-01-01

Comparative Analysis of the Anti-inflammatory Activity of Huang-lian Extracts in Lipopolysaccharide-stimulated RAW264.7 Murine Macrophage-like Cells Using Oligonucleotide Microarrays

In recent years, Clostridium species have rapidly reemerged as human and animal pathogens. The detection and identification of pathogenic Clostridium species...Full Text Available

2010-02-01

KoreaScience (Korea)

Full Text Available

2010-08-01

A Hybrid Multi Objective Particle Swarm Optimization Method to Discover Biclusters in Microarray Data

CERN Document Server

In recent years, with the development of microarray technique, discovery of useful knowledge from microarray data has become very important. Biclustering is a very useful data mining technique for discovering genes which have similar behavior. In microarray data, several objectives have to be optimized simultaneously and often these objectives are in conflict with each other. A Multi Objective model is capable of solving such problems. Our method proposes a Hybrid algorithm which is based on the Multi Objective Particle Swarm Optimization for discovering biclusters in gene expression data. In our method, we will consider a low level of overlapping amongst the biclusters and try to cover all elements of the gene expression matrix. Experimental results in the bench mark database show a significant improvement in both overlap among biclusters and coverage of elements in the gene expression matrix.

2009-01-01

Groundtruth approach to accurate quantitation of fluorescence microarrays

Using a Pan-Viral Microarray Assay (Virochip) to Screen Clinical Samples for Viral Pathogens

To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

2000-12-01

Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.)

The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus...Full Text Available

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Studying bacterial transcriptomes using RNA-seq

BackgroundSelection programs for growth and stress traits in cultured fish are fundamental to the improvement of aquaculture production. The gilthead sea bream (Sparus aurata)...Full Text Available

Sequential interim analyses of survival data in DNA microarray experiments

Genome-wide studies of bacterial gene expression are shifting from microarray technology to second generation sequencing platforms. RNA-seq has a number of advantages over hybridization-based techniques,...Full Text Available

2010-10-01

Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

BackgroundDiscovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently,...Full Text Available

SWISS MADE: Standardized WithIn Class Sum of Squares to Evaluate Methodologies and Dataset Elements

BackgroundThe study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray...Full Text Available

Recent Applications of DNA Microarray Technology to Toxicology and Ecotoxicology

Contemporary high dimensional biological assays, such as mRNA expression microarrays, regularly involve multiple data processing steps, such as experimental processing, computational processing, sample...Full Text Available

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs

Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be...Full Text Available

2006-01-01

Protein expression based multimarker analysis of breast cancer samples

Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of ‘DNA processing elements’...Full Text Available

2004-01-01

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

BackgroundTissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification...Full Text Available

Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray

BackgroundDifferent microarray studies have compiled gene lists for predicting outcomes of a range of treatments and diseases. These have produced gene lists that have little overlap,...Full Text Available

Molecular and clinico-pathological markers in rectal cancer: a tissue micro-array study

PurposeRetinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations...Full Text Available

Light-Powered Molecular Engineering : a new technology for medical safety applications

AimsThe aims of the study were to study the effect of pre-operative treatment on the expression of tumour-related proteins and to correlate the expression of these...Full Text Available

2009-02-01

DEFF Research Database (Denmark)

We present a new photonic technology and demonstrate that it allows for precise immobilisation of biomolecules to sensor surfaces. The technology secures spatially controlled molecular immobilisation since immobilisation of each molecule to a support surface can be limited to the focal point of the ultraviolet (UV) beam, as small as a few micrometers. We can immobilise molecules according to any pattern, from classical microarrays to diffraction patterns creating unique watermarking safety patterns. Given that suitable protein markers exists for all relevant diseases it is entirely feasible to test for a range of disease indicators (antigens and other markers) in a single test. Few micrometer spotsize allows for a virtually unlimited number of protein spots in a multipotent microarray. This new technology produces radically new photonics based microarray sensing technology and watermarking and has clear potential for ...

2007-01-01

Inferring gene regulatory networks from asynchronous microarray data with AIRnet

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

BackgroundModern approaches to treating genetic disorders, cancers and even epidemics rely on a detailed understanding of the underlying gene signaling network. Previous work has...Full Text Available

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest

BackgroundSpecies with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic...Full Text Available

Full genome gene expression analysis of the heat stress response in Drosophila melanogaster

BackgroundMicroarray data are often used for patient classification and gene selection. An appropriate tool for end users and biomedical researchers should combine user friendliness...Full Text Available

Epitope tagging of endogenous proteins for genome wide Chromatin immunoprecipitation analysis

The availability of full genome sequences has allowed the construction of microarrays, with which screening of the full genome for changes in gene expression is possible. This method can provide a wealth...Full Text Available

2005-10-01

Effect of dietary monosodium glutamate on trans fat-induced nonalcoholic fatty liver disease

The development of chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) technology has enabled genome-wide identification of cis-DNA regulatory elements to which transcription...Full Text Available

2009-01-01

Development of a novel data mining tool to find cis-elements in rice gene promoter regions

The effects of dietary monosodium glutamate (MSG) on trans-fatty acid (TFA)-induced nonalcoholic fatty liver disease (NAFLD) are addressed in an animal model. We used Affymetrix microarray...Full Text Available

2009-08-01

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

BackgroundInformation on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment...Full Text Available

Design of 240,000 orthogonal 25mer DNA barcode probes

BackgroundMicroorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential...Full Text Available

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Clustering gene expression data with a penalized graph-based metric

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow...Full Text Available

2009-02-17

An Integrated Genomics Approach to Define Niche Establishment by Rhodococcus fascians1[C][W][OA

BackgroundThe search for cluster structure in microarray datasets is a base problem for the so-called "-omic sciences". A difficult problem in clustering is how to handle data with...Full Text Available

A supervised approach for predicting patient survival with gene expression data

Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined...Full Text Available

2009-03-01

A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray

Rapid development in genomics in recent years has allowed the simultaneous measurement of the expression levels of thousands of genes using DNA microarrays. This has offered tremendous potential...Full Text Available

2010-01-01

A polyacetylene compound from herbal medicine regulates genes associated with thrombosis in endothelial cells

Abs are central to malaria immunity, which is only acquired after years of exposure to Plasmodium falciparum (Pf). Despite the enormous worldwide burden of malaria,...Full Text Available

2010-04-13

A caGRID-ENABLED, LEARNING BASED IMAGE SEGMENTATION METHOD FOR HISTOPATHOLOGY SPECIMENS

From Toki-shakuyaku-san, an herbal formulation for “cleansing stagnated blood,” a key gene regulatory compound was purified and identified through a screening based on DNA microarray...Full Text Available

2007-12-15

A Predictive Risk Probability Approach for Microarray Data with Survival as an Endpoint

Accurate segmentation of tissue microarrays is a challenging topic because of some of the similarities exhibited by normal tissue and tumor regions. Processing speed is another consideration...Full Text Available

2009-07-01

Algorithms for Internal Validation Clustering Measures in the Post Genomic Era

Gene expression profiling has played an important role in cancer risk classification and has shown promising results. Since gene expression profiling often involves determination of a set of...Full Text Available

2008-01-01

CERN Document Server

Inferring cluster structure in microarray datasets is a fundamental task for the -omic sciences. A fundamental question in Statistics, Data Analysis and Classification, is the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. In this dissertation, a study of internal validation measures is given, paying particular attention to the stability based ones. Indeed, this class of measures is particularly prominent and promising in order to have a reliable estimate the number of clusters in a dataset. For those measures, a new general algorithmic paradigm is proposed here that highlights the richness of measures in this class and accounts for the ones already available in the literature. Moreover, some of the most representative validation ...

2011-01-01

The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)

Sustainable phosphorous fertilisation of potatoes (Potato CHIPS)

We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our...Full Text Available

2008-09-01

Environmental Research Database

DescriptionThis project has two independent aims: (1) to investigate the use of struvite as an alternative to chemical P fertilisers and (2) to develop an oligonucleotide microarray to monitor the P status of the potato crop. The UK horticultural and agricultural industries rely on large inputs of phosphate (P) fertilisers to maintain crop yields and quality. However, the use of non-renewable, chemical P fertilisers is unsustainable, and the alternatives to chemical P-fertilisers must be identified as an [continued...

2008-01-31

Detecting and Genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

Bioinformatics in the information age

Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFU ml-1 ...

2000-12-01

Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.).

There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our ...

2000-02-01

Gene expression analysis after low dose ionising radiation exposure of the developing organism

High salinity is one of the main factors limiting cotton growth and productivity. The genes that regulate salt stress in TM-1 upland cotton were monitored using microarray and real-time PCR (RT-PCR) with samples taken from roots. Microarray analysis showed that 1503 probe sets were up-regulated and 1490 probe sets were down-regulated in plants exposed for 3h to 100mM NaCl, and RT-PCR analysis validated 42 relevant/related genes. The distribution of enriched gene ontology terms showed such important processes as the response to water stress and pathways of hormone metabolism and signal transduction were induced by the NaCl treatment. Some key regulatory gene families involved in abiotic and biotic sources of stress such as WRKY, ERF, and JAZ were differentially expressed. Our transcriptome analysis might provide some useful insights into salt-mediated signal transduction pathways in cotton and offer a number of candidate genes as potential ...

2011-04-30

International Nuclear Information System (INIS)

Measuring gene expression using microarrays is relevant to many areas of biology and medicine, such as follow up of developmental stages and diseases onset, and treatment study. Since there can be tens of thousands of distinct probes on an array, each micro array experiment can accomplish the equivalent number of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations. For example, microarrays can be used to identify stress response genes by comparing gene expression in challenged versus normal cells. In the Molecular and Cellular Biology lab (MCB), the micro array experiments are performed within the Genomic Platform, fully equipped to analyse either the behaviour of bacteria during long space flight, the effect of low dose ionising radiation on the developing organism in mice, or the human individual radiation sensitivity. For the low dose effect, two main stages of development are of interest; ...

2007-09-01

Translational bioinformatics and healthcare informatics: computational and ethical challenges.

Reporting bias when using real data sets to analyze classification performance

Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from ...

2009-09-16

British Library Electronic Table of Contents (United Kingdom)

Motivation: It is commonplace for authors to propose a new classification rule, either the operator construction part or feature selection, and demonstrate its performance on real data sets, which often come from high-dimensional studies, such as from gene-expression microarrays, with small samples. Owing to the variability in feature selection and error estimation, individual reported performances are highly imprecise. Hence, if only the best test results are reported, then these will be biased relative to the overall performance of the proposed procedure. Results: This article characterizes reporting bias with several statistics and computes these statistics in a large simulation study using both modeled and real data. The results appear as curves giving the different reporting biases as...

2010-01-01

Overexpression of MAD2 predicts clinical outcome in primary lung cancer patients

British Library Electronic Table of Contents (United Kingdom)

High-level expression of mitotic arrest defective protein 2 (MAD2), a central component of the spindle assembly checkpoint, has been observed in a variety of human malignancies. Aim of the present study was to observe the expression of MAD2 in human non-small-cell lung cancer (NSCLC) and explore its clinicopathologic significance and evaluate MAD2 expression as a prognostic marker. MAD2 transcript was found to be overexpressed in the great majority of lung cancers by semi-quantitative RT-PCR. A total of 358 NSCLCs were analyzed immunohistochemically on tissue microarrays. High-level MAD2 expression was observed in 26.3% (94 of 358 cases), and correlated with male sex (P=0.0002), tumor progression (pT status) (P=0.0009), visceral or parietal pleural invasion (P=0.0151), non-adenocarcinoma, ...

2011-01-01

Effect of postharvest water deficit stress on gene expression in heads of broccoli (Brassica oleracea var. italica)

British Library Electronic Table of Contents (United Kingdom)

Harvested plant organs such as heads of broccoli (Brassica oleracea L. var. italica) experience a range of stresses that can lead to premature reduction in quality and eventual senescence. Understanding plant responses to stress may open up novel opportunities to extend postharvest life. One of the first stresses experienced by harvested organs is likely to be water deficit stress since severance of the vascular system halts the normal flux of water into the tissue. For broccoli branchlets with their cut ends held in water, transcriptome analysis based on hybridization of broccoli floret mRNA to a heterologous Arabidopsis microarray revealed that the transcript abundance of 431 genes reliably changed within 48h of harvest. Of these, transcripts of 146 genes increased and 34 genes decreased...

2011-01-01

Cell culture and gene transcription effects of copper sulfate on Chinese hamster ovary cells

British Library Electronic Table of Contents (United Kingdom)

Abstract This study reports the effects of varying concentrations of copper sulfate on the metabolic and gene transcriptional profile of a recombinant Chinese hamster ovary (CHO) cell line producing an immunoglobulin G (IgG)-fusion protein (B0). Addition of 50 M copper sulfate significantly decreased lactate accumulation in the cultures while increasing viable cell density and protein titer. These changes could be seen from day 6 and became increasingly evident with culture duration. Reducing the copper sulfate concentration to 5 M retained all the above beneficial effects, but with the added benefit of reduced levels of the aggregated form of the B0 protein. To profile the cellular changes due to copper sulfate addition at the transcriptional level, Affymetrix CHO microarrays were used to...

2011-01-01

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BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium

British Library Electronic Table of Contents (United Kingdom)

The cAMP response element-binding protein (CREB) is a highly conserved transcription factor that integrates signaling through the cAMP-dependent protein kinase A (PKA) in many eukaryotes. PKA plays a critical role in Dictyostelium development but no CREB homologue has been identified in this system. Here we show that Dictyostelium utilizes a CREB-like protein, BzpF, to integrate PKA signaling during late development. bzpF^- mutants produce compromised spores, which are extremely unstable and germination defective. Previously, we have found that BzpF binds the canonical CRE motif in vitro. In this paper, we determined the DNA binding specificity of BzpF using protein binding microarray (PBM) and showed that the motif with the highest specificity is a CRE-like sequence. BzpF is necessary to ...

2011-01-01

Blood gene expression markers to detect and distinguish target organ toxicity

British Library Electronic Table of Contents (United Kingdom)

The purpose of this study was to investigate whether the expression of specific genes in peripheral blood can be used as surrogate marker(s) to detect and distinguish target organ toxicity induced by chemicals in rats. Rats were intraperitoneally administered a single, acute dose of a well-established hepatotoxic (acetaminophen) or a neurotoxic (methyl parathion) chemical. Administration of acetaminophen (AP) in the rats resulted in hepatotoxicity as evidenced from elevated blood transaminase activities. Similarly, administration of methyl parathion (MP) resulted in neurotoxicity in the rats as evidenced from the inhibition of acetyl cholinesterase activity in their blood. Administration of either chemical also resulted in mild hematotoxicity in the rats. Microarray analysis of the global ...

2010-01-01

A signature of six genes highlights defects on cell growth and specific metabolic pathways in murine and human hepatocellular carcinoma

British Library Electronic Table of Contents (United Kingdom)

Hepatocellular carcinoma (HCC) represents a major health problem as it afflicts an increasing number of patients worldwide. Albeit most of the risk factors for HCC are known, this is a deadly syndrome with a life expectancy at the time of diagnosis of less than 1?year. Definition of the molecular principles governing the neoplastic transformation of the liver is an urgent need to facilitate the clinical management of patients, based on innovative methods to detect the disease in its early stages and on more efficient therapies. In the present study, we have combined the analysis of a murine model and human samples of HCC to identify genes differentially expressed early in the process of hepatocarcinogenesis, using a microarray-based approach. Expression of 190 genes was impaired in murine ...

2011-01-01

Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis

Using light to bioactivate surfaces: A new way of creating oriented, active immunobiosensors

Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called signal to both standard deviations ratio (SSDR) was developed, and evaluated along with other two methods, signal to standard deviation ratio (SSR), and signal to background ratio (SBR). At a low stringency, the thresholds of SSR, SBR, and SSDR were 2.5, 1.60 and 0.80 with oligonucleotide and PCR amplicon as target templates, and 2.0, 1.60 and 0.70 with genomic DNA as target templates. Slightly higher thresholds were obtained at the high stringency condition. The thresholds of SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types), and the presence of background DNA, and a decrease in the composition of targets, while SBR remained unchanged under all situations. ...

2008-03-06

International Nuclear Information System (INIS)

Ultraviolet light can be used to immobilize biomolecules onto thiol reactive surfaces in order to, e.g., make biosensors. The mechanism involves light-induced formation of free, reactive thiol groups in disulphide containing molecules. This technology allows for the creation of arrays of biomolecules with a high degree of reproducibility, circumventing the need for often expensive nano/micro-dispensing technologies. The ultimate size of the immobilized spots is defined by the focal area of the UV beam. Light-induced immobilization has the added benefit that the immobilized molecules will be spatially oriented and covalently bound to the surface. In this paper, we demonstrate the utility of a sensor array created with the new sensor technology when integrated into a microfluidic system. Protein arrays made using light-induced immobilization showed successful antigen/antibody binding in a flow cell allowing the visualisation of real time binding and enzyme activity. This new technology ...

2007-12-15

Roles for Rat Hepatocyte Malignant Transforming Factor (HMTF) in Late Stage of Hepatocarcinogenesis.

Primary adenocarcinoma of the urinary bladder: value of cell cycle biomarkers.

In a previous study, to identify genes of importance for hepatocellular carcinogenesis, and especially for processes involved in malignant transformation, the authors investigated differences in gene expression between adenomas and carcinomas by DNA microarray. In the present study, the authors investigated AW434047, one of the sequences that was upregulated in carcinomas. The investigation led to the identification of a novel gene, which the authors named hepatocyte malignant transforming factor (HMTF), of unknown function whose expression was increased in hepatocellular carcinomas. Northern blot and in situ hybridization also demonstrated high levels of HMTF in rat hepatocellular carcinoma (HCC) cell lines, lymphocytes in the spleen, colon mucosal epithelia, spermatocytes, and granule cells of the hippocampus. Reduction of HMTF by RNA interference (RNAi) in N1 cells, an HCC cell line, caused suppression of cell proliferation, invasion, and migration. Suppression ...

2011-09-20

Data Merging for Integrated Microarray and Proteomic Analysis

Primary adenocarcinomas of the urinary bladder are uncommon, and the molecular pathways are currently not well defined. In this study, we assessed the association between biologic markers and clinicopathologic characteristics in a cohort of 21 patients with primary urinary bladder adenocarcinoma. Immunohistochemical staining for cell cycle-specific markers, including p53, p21, p27, Ki-67, and cyclin E, were performed on sections of a tissue microarray construct. The tumors were high grade in 12 (57%) and pT2 or higher in 18 (86%); lymph nodes were involved in 6 cases (29%); and there was pathologic evidence of schistosomiasis in 14 (67%). The best prognostic combination of markers was combined alterations in p27 and Ki-67 and was associated with stage (P = .012), grade (P = .005), DNA ploidy (P = .005), and lymph node involvement (P = .04). Stage, lymph node involvement, combined alterations of p27 and Ki-67, and combined alterations of all 5 biomarkers were ...

2011-06-01

Cluster Analysis of Gene Expression Data

The functioning of even a simple system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will lead to the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is to extract the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modeling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this review, we highlight ...

2006-05-10

CERN Document Server

The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical experiment uses a few tens of such chips, each dedicated to a single sample - such as tissue extracted from a particular tumor. The results of such an experiment contain several hundred thousand numbers, that come in the form of a table, of several thousand rows (one for each gene) and 50 - 100 columns (one for each sample). We developed a clustering methodology to mine such data. In this review I provide a very basic introduction to the subject, aimed at a physics audience with no prior knowledge of either gene expression or clustering methods. I explain what genes are, what is gene expression and how it is measured by DNA chips. Next I explain what is meant by "clustering" and how we analyze the massive amounts of data from such ...

2002-01-01

Global Molecular Characterization of the Chromate Stress Response in Shewanella oneidensis MR-1: Identification of a Putative DNA-Binding Response Regulator and Azoreductase Involved in Cr(VI) Detoxification

Transcriptional Profiling Analysis of the Global Regulator NorG, a GntR-Like Protein of Staphylococcus aureus.

Shewanella oneidensis MR-1 is a model environmental organism that possesses diverse respiratory capacities, including the ability to reduce soluble Cr(VI) to sparingly soluble, less toxic Cr(III). Effective bioremediation of Cr-contaminated sites requires knowledge of the molecular mechanisms and regulation of heavy metal resistance and biotransformation by dissimilatory metal-reducing bacteria. Towards this goal, our ERSP-funded work is focused on the identification and functional analysis of genes/proteins comprising the response pathways for chromate detoxification and/or reduction. Previous transcriptomic profiling and whole-cell proteomic analyses implicated the involvement of a functionally undefined DNA-binding response regulator (SO2426) and a putative azoreductase (SO3585) in the chromate stress response of MR-1. Here we describe a detailed functional analysis of SO2426 and SO3585 in order to begin to understand the role of these proteins in the cellular response to chromate. ...

2006-04-05

Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent.

The GntR-like protein NorG has been shown to affect Staphylococcus aureus genes involved in the resistance to quinolones and ?-lactams, such as those encoding the NorB and AbcA transporters. To identify the target genes regulated by NorG, we carried out transcriptional profiling assays using S. aureus RN6390 and its isogenic norG::cat mutant. Our data showed that NorG positively affected the transcription of global regulators mgrA, arlS, and sarZ. The three putative drug efflux pump genes most positively affected by NorG were the NorB efflux pump (5.1-fold), the MmpL-like protein SACOL2566 (5.2-fold), and the BcrA-like drug transporter SACOL2525 (5.7-fold). The S. aureus predicted MmpL protein showed 53% homology with the MmpL lipid transporter of Mycobacterium tuberculosis, and the putative SACOL2525 protein showed 87% homology with the bacitracin drug transporter BcrA of Staphylococcus hominis. Two pump genes most negatively affected by NorG were NorC (4-fold) and AbcA (6-fold). ...

2011-09-01

Insulin-like growth factor binding protein-7 (IGFBP7) functions as a potential tumor suppressor in hepatocellular carcinoma (HCC).

The epidermal compartment is complex and organized into several strata composed of keratinocytes (KCs), including basal, spinous, granular, and cornified layers. The continuous process of self-renewal and barrier formation is dependent on a homeostatic balance achieved amongst KCs involving proliferation, differentiation, and cell death. To determine genes responsible for initiating and maintaining a cornified epidermis, organotypic cultures comprised entirely of stratified KCs creating epidermal equivalents (EE) were raised from a submerged state to an air/liquid (A/L) interface. Compared to the array profile of submerged cultures containing KCs predominantly in a proliferative (relatively undifferentiated) state, EEs raised to an A/L interface displayed a remarkably consistent and distinct profile of mRNAs. Cultures lifted to an A/L interface triggered the induction of gene groups that regulate proliferation, differentiation, and cell death. Next, differentially expressed microRNAs ...

2010-05-25

Glial inflammation and neurodegeneration induced by candoxin, a novel neurotoxin from Bungarus candidus venom: global gene expression analysis using microarray.

PURPOSE: Hepatocellular carcinoma (HCC) is a highly virulent malignancy with no effective treatment thus requiring innovative and effective targeted therapies. The oncogene Astrocyte elevated gene-1 (AEG-1) plays a seminal role in hepatocarcinogenesis and profoundly downregulates insulin-like growth factor binding protein-7 (IGFBP7). The present study focuses on analyzing potential tumor suppressor functions of IGFBP7 in HCC and the relevance of IGFBP7 downregulation in mediating AEG-1 function.EXPERIMENTAL DESIGN: IGFBP7 expression was detected by immunohistochemistry in HCC tissue microarray and real-time PCR and ELISA in human HCC cell lines. Dual Fluorescence in situ hybridization was performed to detect loss of heterozygosity at IGFBP7 locus. Stable IGFBP7-overexpressing clones were established in the background of AEG-1-overexpressing human HCC cells and were analyzed for in vitro proliferation and senescence and in vivo tumorigenesis and ...

2011-09-16

Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress.

Candoxin (PDB #1JGK), a three-finger neurotoxin from Bungarus candidus venom, inhibits post-synaptic neuromuscular and neuronal alpha7nACh-receptors, and induces delayed cell-death throughout the glial population. When applied to cultured human glial cell lines, candoxin (CDX) induced cell death in a concentration (EC(50) approximately 1muM) and time dependent manner. Results of TUNEL-histochemistry further confirm CDX-induced brain (hippocampus, frontal cortex, and temporal regions) damage when administered intracerebroventricularly (i.c.v) in adult mice. In this study, we explored differential gene expression profiles following exposure of human glial (Hs 683) cell lines to CDX at various time intervals using Affymetrix-GeneChips. By means of MAS and GeneSpring analyses, 105 genes whose expression was significantly (P<0.01) altered by at least 3-fold were selected. Results of the genome analysis reveal that the potential role of CDX at molecular level involves the regulation of ...

2005-11-23

Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile, and amino acid composition

Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core ...

2010-01-08

DEFF Research Database (Denmark)

Antisense- or RNAi-mediated suppression of the biosynthesis of nutritionally inferior storage proteins is a promising strategy for improving the amino acid profile of seeds. However, the potential pleiotropic effects of this on interconnected pathways and the agronomic quality traits need to be addressed. In the current study, a transcriptomic analysis of an antisense C-hordein line of barley was performed, using a grain-specific cDNA array. The C-hordein antisense line is characterized by marked changes in storage protein and amino acid profiles, while the seed weight is within the normal range and no external morphological irregularities were observed. The results of the transcriptome analysis showed excellent correlation with data on changes in the relative proportions of storage proteins and amino acid composition. The antisense line had a lower C-hordein level and down-regulated transcript encoding C-hordein. The production of the S-rich B/gamma- and D-hordeins was increased and ...

2007-01-01

Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile and amino acid composition

DEFF Research Database (Denmark)

2007-01-01

Anticancer activity and cDNA microarray studies of a (RS)-1,2,3,5-tetrahydro-4,1-benzoxazepine-3-yl]-6-chloro-9H-purine, and an acyclic (RS)-O,N-acetalic 6-chloro-7H-purine

British Library Electronic Table of Contents (United Kingdom)

Completing a SAR study, a series of (RS)-6-substituted-7- or 9-(1,2,3,5-tetrahydro-4,1-benzoxazepine-3-yl)-7H or 9H-purines was previously prepared. The most potent antiproliferative agent against the MCF-7 adenocarcinoma cell line that belongs to the benzoxazepine O,N-acetalic family is (RS)-9-[1-(9H-fluorenyl-9-methoxycarbonyl)-1,2,3,5-tetrahydro-4,1-benzo xazepine-3-yl]-6-chloro-9H-purine (16, IC50 = 0.67 +- 0.18 mM), whilst (RS)-7-{2-(N-hydroxymethylphenyl)-2-nitrobenzenesulfonamido]-1-methoxye thyl}-6-chloro-7H-purine (37) shows the lowest IC50 value between the family of acyclic O,N-acetals (IC50 = 3.25 +- 0.23 mM). Moreover, 16 showed the better in vitro Therapeutic Index in breast cell lines (3.19), whilst 37 was found to be 3.69-fold more active against HT-29 human colon cancer ce...

2011-01-01

Activation of rapid signaling pathways and the subsequent transcriptional regulation for the proliferation of breast cancer MCF-7 cells by the treatment with an extract of Glycyrrhiza glabra root.

A novel glioblastoma cancer gene therapy using AAV-mediated long-term expression of human TERT C-terminal polypeptide.

Glycyrrhiza glabra root is one of the common traditional Chinese medicines and used as flavoring and sweetening agents for tobaccos, chewing gums, candies, toothpaste and beverages. While glycyrrhizin is one of the main components in the extract of G. glabra root and has been characterized, the other components have not been well characterized. The mechanism of growth activation of breast cancer MCF-7 cells, including the activation of Erk1/2 and Akt, and the transcriptional regulation of estrogen-responsive genes, was examined by means of sulforhodamine B, luciferase reporter gene, real-time RT-PCR and Western blotting assays after the induction of the cells with the extract of G. glabra root. The extract has similar activity to that induced by 17beta-estradiol (E(2)), although glycyrrhizin did not show such an activity. Moreover, the estrogen receptor alpha-dependent neurite outgrowth induced by the extract was similar to that by E(2), whereas glycyrrhizin had no effect. Furthermore, ...

2007-06-24

A Wheat Homolog of MOTHER OF FT AND TFL1 Acts in the Regulation of Germination.

Glioblastoma multiforme is the most aggressive form of human brain tumor, which has no effective cure. Previously, we have demonstrated that overexpression of the C-terminal fragment of the human telomerase reverse transcriptase (hTERTC27) inhibits the growth and tumorigenicity of human cervical cancer HeLa cells. In this study, the therapeutic effect and molecular mechanisms of hTERTC27-mediated cancer gene therapy were further explored in vivo in established human glioblastoma xenografts in nude mice. We showed that intratumoral injection of adeno-associated virus carrying hTERTC27 (rAAV-hTERTC27) is highly effective in reducing the growth of the subcutaneously transplanted glioblastoma tumors. Histological analyses showed that rAAV-hTERTC27 treatment leads to profound necrosis, apoptosis, infiltration of polymorphonuclear neutrophils and reduced microvessel density in the tumor samples. To study the molecular mechanism of rAAV-hTERTC27-mediated antitumor effects, we analyzed the ...

2007-03-23

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Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39.

Seed dormancy is an adaptive mechanism and an important agronomic trait. Temperature during seed development strongly affects seed dormancy in wheat (Triticum aestivum) with lower temperatures producing higher levels of seed dormancy. To identify genes important for seed dormancy, we used a wheat microarray to analyze gene expression in embryos from mature seeds grown at lower and higher temperatures. We found that a wheat homolog of MOTHER OF FT AND TFL1 (MFT) was upregulated after physiological maturity in dormant seeds grown at the lower temperature. In situ hybridization analysis indicated that MFT was exclusively expressed in the scutellum and coleorhiza. Mapping analysis showed that MFT on chromosome 3A (MFT-3A) colocalized with the seed dormancy quantitative trait locus (QTL) QPhs.ocs-3A.1. MFT-3A expression levels in a dormant cultivar used for the detection of the QTL were higher after physiological maturity; this increased expression correlated with a ...

2011-09-01