Papers by Keyword: Micro-Array

Abstract: DNA microarray analysis has become the most widely used functional genomics approach in the bioinformatics field. Biologists are vastly plagued by the enormous amount of unprecedented qualities of genome-wide data produced by the DNA Microarray experiment.Clustering is the process of grouping data objects into set of disjoint classes called clusters so that objects within a class are highly similar with one another and dissimilar with the objects in other classes. It is presently the far most used method for gene expression analysis which provides a divide-and–conquer strategy to extract meaningful information from expression profile.In transcriptomics,clustering is used to build groups of genes with related expression patterns (also known as coexpressed genes). Often such groups contain functionally related proteins, such as enzymes for a specific pathway, or genes that are co-regulated. This paper presents a review on the recently development of microarray clustering techniques followed by the different categories of gene expression data clustering.

Abstract: Biclustering is one of the important techniques for gene expression data analysis. A bicluster is a set of genes coherently expressed for a set of biological conditions. Various biclustering algorithms have been proposed to find biclusters of different types. However, most of them are not efficient. We propose a novel algorithm MRCluster to mine constant row biclusters from real-valued dataset. MRCluster uses Apriori property and several novel pruning techniques to mine biclusters efficiently. We compare our algorithm with a recent approach RAP, and experimental results show that MRCluster is much more efficient than RAP in mining biclusters with constant rows from real-valued gene expression data.

Abstract: Pure titanium and titanium alloys are materials widely used in orthopaedics and dental surgery because of their mechanical properties, chemical stability and biocompatibility. Although excellent clinical results have been shown, traditional porous metals have several inherent limitations (low volumetric porosity, relatively high modulus of elasticity and low frictional characteristics, availability as a coating only). With the aim of moving beyond these limits, improving the potentiality of osteointegration and consequently the stability of prosthetic implants, a new highly porous titanium biomaterial (Trabecular Titanium™, TT) has been developed. In this in vitro study, we are testing the effects of TT on osteoblast-like cells (MG63) cultured on disks of this biomaterial by using DNA microarrays containing 20,000 genes. We identified several genes covering a broad range of functional activities whose expression was significantly up- or down-regulated. Findings from this study can give a detailed description of the genetic effects TT has on human osteoblast-like cells in vitro. We demonstrated that TT stimulates osteoblast proliferation and differentiation, and reduces osteoblast apoptosis. Moreover, TT limits osteoclastogenesis, inflammation and reduces the immunologic events against the material, modulating genes related to the immune system. Therefore, all these effects contribute to improve osseointegration and consequently survival of the prosthetic implants. These reported data encourage the clinical application of Trabecular Titanium™ to prosthetic devices.

Abstract: Heap bioleaching is presently the most successful technology for copper extraction from low-grade sulfide ores. Metabolic behaviors and adaptation mechanisms of microbial communities to this system remain unknown. A combination of molecular approaches has been used to determine the key microorganisms in the Escondida Sulphide Heap. This work reports the global gene expression in industrial bioleaching samples by using a specific DNA microarray of Leptospirillum ferrooxidans to better understand the metabolic functions displayed by Leptospirillum spp. iron oxidizers as mineral leaching proceeds. Quantitative real-time PCR analysis showed low cell numbers of Leptospirillum species during the first part of the irrigation period, however, it became the most abundant and active in the second part of the cycle. Transcriptome analysis by DNA microarray could provide specifics transcription patterns in the different stages of the industrial process. We studied the gene expression from bioleaching heap samples with variable Leptospirillum cell numbers, operation times and with different chemical and physical conditions. The results showed induction of genes involved in energetic metabolism, electron transport, ribosomal proteins, DNA repair and response to heavy metals when Leptospirillum species were most abundant and active. We suggest that up- and down-regulation of specifics genes could be used as indicators of physiological responses to operational conditions in the bioleaching systems.

Abstract: Bioleaching is the extraction of metals, such as copper or gold, from ore by microorganisms. Bacterial attachment increases leaching activities due to the formation of a "reaction space" between the metal sulfide surface and the cell. This process depends on abiotic characteristics such as purity and degree of crystallization of the metal sulfide, as well as biotic ones such as the capacity of the bacteria for detecting favourable attachment sites and synthesizing a suitable cell envelope (EPS), for adhesion. Planktonic and sessile cells should differ significantly in their metabolic activities and therefore in their gene expression patterns. To help to understand At. ferrooxidans biofilm formation, microarray transcript profiling was carried out to compare planktonic and sessile cells. The high contents of EPS and ferric iron of the biofilms are interfering with RNA extraction, causing inhibition of DNAse, reverse transcriptase and/or polymerase activities required to get labelled target cDNA. In order to have sufficient high quality RNA suitable for transcriptomic analysis, we have optimized the biofilm formation of At. ferrooxidans on pyrite (FeS2) and the RNA extraction from the sessile cell population. DNA microarrays have been hybridized with labelled cDNAs from sessile and planktonic cells and preliminary data suggest that some genes are differently expressed between these two subpopulations. The understanding of these differences may help us to shift populations of leaching bacteria from the planktonic state towards the sessile state in order to influence bioleaching.

Abstract: Results from a high density microarray having 32,392 50-mer oligonucleotides, termed BMS2.1, were analyzed and used for the design of a new slide, called BMS 3.0, with 560 specific oligonucleotides manufactured in standard slides to be used in any open platform. Hybridizations of several samples, either known microorganisms or environmental samples, were performed. Automatic microarray analysis software was built in order to handle these data in a quick an efficient way. While oligonucleotides designed for microorganisms with known genome sequence showed a very good behavior, according to predicted design, variations were detected when different strains were hybridized, probably due to inadequate specificity of probes. Appropriate parameterization of the analysis software will improve prediction of presence for most of the microorganisms.

Abstract: In this paper emphasis is placed on the wet micromachining of silicon micro-arrays constituted by very small holes. Microfabrication of various Silicon plates is performed in a KOH etchant maintained at constant temperature. Limitations due to the process are given. A self elaborated simulator is used to predict etching shapes of several micro holes. A comparison between experiments and simulation is presented.

Abstract: Micropatterned PEGylated substrates with two-dimensional arrays of plasma-etched circular domains (diameter:100 micro-m) were prepared by coating of mercapto-functionalized poly(ethylene glycol) (PEG) on Au surface, followed by plasma-etching through a metal mask pattern with circular holes. The PEGylated region on the patterned substrate works to repel proteins, consequently, inhibits cell adhesion. Then the micro-patterning of bovine articular chondrocytes or rat primary hepatocytes hetero-spheroids underlaid with human umbilical endothelial cells (HUVEC) was achieved on the plasma-etched circular domains, exposing the base gold surface. Obtained results suggested that the efficiency of inhibiting non-specific protein adsorption significantly affects on construction of micro-patterned cell adhesion and hetero-spheroids. The formation of hetero-spheroid thus suggested is significantly modulated by suface properties, particularly non-fouling character of PEG region. These arrayed spheroids is promising materials for tissue and cell-based biosensors (TBB/CBB) as well as tissue engineering technologies.

Abstract: We have obtained Er-doped ZnO thin film in a micropattern of reverse trapezoids processed on Si substrate by sputtering and ultrafine polishing techniques. Near-infrared light emission was detected successfully from the thin film filling a single micropit with 10 μm square. Transmission electron microscopy (TEM) observation showed epitaxial growth of ZnO crystals along the curvature of the micropit.