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Dithiobis(succinimidyl propionate) modified gold microarray electrode based electrochemical immunosensor for ultrasensitive detection of cortisol.

Gold microelectrode arrays functionalized with dithiobis(succinimidyl propionate) self-assembled monolayer (SAM) have been used to fabricate an ultrasensitive, disposable, electrochemical cortisol immunosensor. Cortisol specific monoclonal antibody (C-Mab) was covalently immobilized on the surface of gold microelectrode array and the sensors were exposed to solutions with different cortisol concentration. After C-Mab binding, unreacted active groups of DTSP were blocked using ethanol amine (EA) and label-free electrochemical impedance (EIS) technique was used to determine cortisol concentratio

A gradient microarray electronic nose based on percolating SnO(2) nanowire sensing elements.

Fabrication, characterization, and tests of the practical gradient microarray electronic nose with SnO(2) nanowire gas-sensing elements are reported. This novel device has demonstrated an excellent performance as a gas sensor and e-nose system capable of promptly detecting and reliably discriminating between several reducing gases in air at a ppb level of concentration. It has been found that, in addition to the temperature gradient across the nanowire layer, the density and morphological inhomogeneities of nanowire mats define the discriminating power of the electronic nose.

Finding consistent disease subnetworks across microarray datasets.

BACKGROUND: While contemporary methods of microarray analysis are excellent tools for studying individual microarray datasets, they have a tendency to produce different results from different datasets of the same disease. We aim to solve this reproducibility problem by introducing a technique (SNet). SNet provides both quantitative and descriptive analysis of microarray datasets by identifying specific connected portions of pathways that are significant. We term such portions within pathways as "subnetworks". RESULTS: We tested SNet on independent datasets of several diseases, including child…

Genes involved in the balance between neuronal survival and death during inflammation.

Glucocorticoids are potent regulators of the innate immune response, and alteration in this inhibitory feedback has detrimental consequences for the neural tissue. This study profiled and investigated functionally candidate genes mediating this switch between cell survival and death during an acute inflammatory reaction subsequent to the absence of glucocorticoid signaling. Oligonucleotide microarray analysis revealed that following lipopolysaccharide (LPS) intracerebral administration at striatum level, more modulated genes presented transcription impairment than exacerbation upon glucocortic…

Evaluation of natural and synthetic stimulants of plant immunity by microarray technology.

Induction of local defence, as well as systemic resistance, of plants is associated with transcriptional reprogramming. Here we report on defence gene induction by natural and synthetic stimulants of plant immunity. Gene expression changes in Arabidopsis thaliana were monitored in response to several plant immunity stimulants (plant activators) using Northern blotting and an application-based array representing c. 750 genes involved in several aspects of plant defence and/or plant stress. The commercial plant activators Bio-S, Neudo-Vital and PRORADIX have been shown to induce systemic resista

DNA microarrays provide new options for allergen testing.

Microarray studies are increasingly used for toxicological research and even for the development of new toxicological test methods. Since gene-expression changes in cultured cells can be conveniently measured with microarrays, this method might be of use for in vitro toxicity testing, for example, in the field of contact sensitization. Allergic contact dermatitis, the clinical manifestation of contact sensitization, may occur when sensitizing chemicals enter the skin and get in contact with epidermal and dermal antigen-presenting cells. The resulting maturation process in these cells can be me

Overexpression of glucose transporter-1 (GLUT-1) predicts poor prognosis in epithelial ovarian cancer.

Illumina microarray was used to identify differentially expressed genes in three epithelial ovarian cancer (EOC) cells. To validate the microarray data, mRNA and protein level of glucose transporter-1 (GLUT-1) was examined. GLUT-1 had an EOC/normal cells ratio of 5.51 based on microarray. Real-time PCR and immunohistochemistry demonstrated that GLUT-1 expression was significantly increased in EOC (p = .029 and p < .001, respectively). On survival analysis, GLUT-1 overexpression (HR = 4.80, p = .027) and lymph node metastases (HR = 8.35, p = .016) conferred a significantly worse overall surviva

New protocol for oligonucleotide microarray fabrication using SU-8-coated glass microslides.

Microarray technology has become an important tool for detection and analysis of nucleic acid targets. Immobilization of modified and unmodified oligonucleotides on epoxy-functionalized glass surfaces is often used in microarray fabrication. Here, we demonstrate a protocol that employs coating of SU-8 (glycidyl ether of bisphenol A) onto glass microslides to obtain high density of epoxy functions for efficient immobilization of aminoalkyl-, thiophosphoryl-, and phosphorylated oligonucleotides with uniform spot morphology. The resulting microarrays exhibited high immobilization (∼65%) and hybri

Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.

A pan-viral DNA microarray, the Virochip (University of California, San Francisco), was used to detect human parainfluenzavirus 4 (HPIV-4) infection in an immunocompetent adult presenting with a life-threatening acute respiratory illness. The virus was identified in an endotracheal aspirate specimen, and the microarray results were confirmed by specific polymerase chain reaction and serological analysis for HPIV-4. Conventional clinical laboratory testing using an extensive panel of microbiological tests failed to yield a diagnosis. This case suggests that the potential severity of disease cau

Analysis of genes linked to depressive-like behaviors in interleukin-18-deficient mice: Gene expression profiles in the brain.

Interleukin (IL)-18 is an interferon γ-inducing inflammatory cytokine associated with function of the immune system and other physiological … the depressive-like behaviors and other impairments displayed by Il18 -/- mice. Using whole genome microarray analysis, gene expression patterns in the brains of Il18 +/+ and Il18 -/- mice at 6 and 12 weeks of age were examined and compared. Subsequently, genes were categorized using Ingenuity® Pathway Analysis (IPA). At 12 weeks of age, 2,805 genes were identified …

DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment.

Visceral leishmaniasis (VL) is one of the major infectious diseases affecting the poorest regions of the world. Current therapy is not very much satisfactory. The alarming rise of drug resistance and the unavailability of an effective vaccine against VL urges research towards identifying new targets or biomarkers for its effective treatment. New technology developments offer some fresh hope in its diagnosis, treatment, and control. DNA microarray approach is now broadly used in parasitology research to facilitate the thoughtful of mechanisms of disease and identification of drug targets and bi

Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology.

BACKGROUND: Gene set analysis based on Gene Ontology (GO) can be a promising method for the analysis of differential expression patterns. However, current studies that focus on individual GO terms have limited analytical power, because the complex structure of GO introduces strong dependencies among the terms, and some genes that are annotated to a GO term cannot be found by statistically significant enrichment. RESULTS: We proposed a method for enriching clustered GO terms based on semantic similarity, namely cluster enrichment analysis based on GO (CeaGO), to extend the individual term anal

Design of Hydrogel Silk-Based Microarrays and Molecular Beacons for Reagentless Point-of-Care Diagnostics.

We have developed a novel microarray system based on three technologies: 1) molecular beacons designed to interact with DNA targets at room temperature (25-27°C), 2) tridimensional silk-based microarrays containing the molecular beacons immersed in the silk hydrogel, and 3) shallow angle illumination, which uses separated optical pathways for excitation and emission. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing, and stringency control, and measure only end-point results, our microarray technology provides enhance

Integration of gene expression profiling and mutation analysis via RNA sequencing: transitioning the 95-gene classifier to a next-generation platform in early-stage HR+/HER2- breast cancer.

BACKGROUND: Curebest™ 95GC breast is a multigene assay independently developed in Japan, that utilizes DNA microarray technology to analyze … ases and a validation set of 117 cases. Whole RNAseq was performed using residual RNA samples after microarray analysis. The 95GC scores calculated from RNAseq were compared with those from microarray, and comprehensive mutation profiling was conducted. RESULTS: The correlation coefficients between the 95GC score (microarray) and the 95GC score (RNAseq) were high in …

Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies.

BACKGROUND: Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ Transplant (B-HOT) probe set panel, derived from validated microarrays, can identify the relevant allograft diagnoses directly from archival human renal transplant formalin-fixed paraffin-embedded biopsies. To test this hypothesis, principal components (PCs) of gene expressions were used to identify allograft diagnoses, to classify diagnoses, and to de

Towards the integration, annotation and association of historical microarray experiments with RNA-seq.

BackgroundTranscriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via cluster assignment, and a 70 gene risk score. Both enabled an improved molecular understanding of MM, and have provided prognostic information for the purposes of clinical management. Many researchers are now transitioning to Next Generation Sequencing (NGS) approaches and RNA-seq in particular, due to its discovery-based nature, improved sensitivity, and dynamic range. Additiona

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… Compared to microarray analysis the computational requirements for RNA-seq are much more complex. The term "cost" refers to financial cost, and reflects computational hardware including infrastructure, as well as the time and expertise for data analysis. …

Selection of control genes for quantitative RT-PCR based on microarray data.

Use of internal reference gene(s) is necessary for adequate quantification of target gene expression by RT-PCR. Herein, we elaborated a strategy of control gene selection based on microarray data and illustrated it by analyzing endomyocardial biopsies with acute cardiac rejection and infection. Using order statistics and binomial distribution we evaluated the probability of finding low-varying genes by chance. For analysis, the microarray data were divided into two sample subsets. Among the first 10% of genes with the lowest standard deviations, we found 14 genes common to both subsets. After

Early Trichinella spiralis and Trichinella nativa infections induce similar gene expression profiles in rat jejunal mucosa.

Trichinella spiralis causes a significantly higher parasite burden in rat muscle than Trichinella nativa. To assess whether the difference in infectivity is due to the early intestinal response, we analyzed gene expression changes in the rat jejunum during Trichinella infection with a whole-genome microarray. The rats were euthanized on day five of infection, and their jejunal mucosa was sampled for microarray analysis. In addition, intestinal histology and hematology were examined. Against our expectations, the gene expression changes were similar in both T.nativa- and T. spiralis-infected gr…

Development of a miniaturized protein microarray as a new serological IgG screening test for zoonotic agents and production diseases in pigs.

In order to monitor the occurrence of zoonotic agents in pig herds as well as to improve herd health management, the development of new cost … he different pathogens were conducted with the purpose of creating a panel of reference samples for microarray analysis. To evaluate the accuracy of the antigens on the microarray, receiver operating characteristic (ROC) curve analysis using the ELISA test results as reference was performed for the different antigens. High area under curve values were achieved for th …

Potential role of circulating microRNAs as a biomarker for unexplained recurrent spontaneous abortion.

OBJECTIVE: To compare circulating microRNA (miRNA) profiles between unexplained recurrent spontaneous abortion (URSA) and normal early pregnancies (NEP) and to evaluate the potential role of circulating miRNA as a biomarker for URSA. DESIGN: Laboratory study using human plasma samples. SETTING: Special hospital and research institutes. PATIENT(S): From September 2012 to April 2013, samples of plasma were obtained from 27 URSA patients and 28 NEP patients at 6-10 weeks of gestation at the Department of Reproductive Immunology in Family Planning Special Hospital of Guangdong Province. INTERV