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Sample records for genome tiling microarrays

  1. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor;

    2006-01-01

    Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species....... We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome. Udgivelsesdato: 2006-Jan...

  2. Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

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    Chen Tsute

    2010-02-01

    Full Text Available Abstract Background Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles. Results The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position. Conclusions The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.

  3. Identification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays.

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    Xiao Zheng

    Full Text Available Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST, ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs, among which 26 are putative genomic islands (GIs. Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.

  4. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.

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    Noam Leviatan

    Full Text Available Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

  5. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.

    Science.gov (United States)

    Leviatan, Noam; Alkan, Noam; Leshkowitz, Dena; Fluhr, Robert

    2013-01-01

    Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

  6. A brief introduction to tiling microarrays: principles, concepts, and applications.

    Science.gov (United States)

    Lemetre, Christophe; Zhang, Zhengdong D

    2013-01-01

    Technological achievements have always contributed to the advancement of biomedical research. It has never been more so than in recent times, when the development and application of innovative cutting-edge technologies have transformed biology into a data-rich quantitative science. This stunning revolution in biology primarily ensued from the emergence of microarrays over two decades ago. The completion of whole-genome sequencing projects and the advance in microarray manufacturing technologies enabled the development of tiling microarrays, which gave unprecedented genomic coverage. Since their first description, several types of application of tiling arrays have emerged, each aiming to tackle a different biological problem. Although numerous algorithms have already been developed to analyze microarray data, new method development is still needed not only for better performance but also for integration of available microarray data sets, which without doubt constitute one of the largest collections of biological data ever generated. In this chapter we first introduce the principles behind the emergence and the development of tiling microarrays, and then discuss with some examples how they are used to investigate different biological problems.

  7. Optimized design and assessment of whole genome tiling arrays.

    NARCIS (Netherlands)

    Graf, S.; Nielsen, F.G.G.; Kurtz, S.; Huynen, M.A.; Birney, E.; Stunnenberg, H.G.; Flicek, P.

    2007-01-01

    MOTIVATION: Recent advances in microarray technologies have made it feasible to interrogate whole genomes with tiling arrays and this technique is rapidly becoming one of the most important high-throughput functional genomics assays. For large mammalian genomes, analyzing oligonucleotide tiling arra

  8. Analysis of tiling microarray data by learning vector quantization and relevance learning

    NARCIS (Netherlands)

    Biehl, Michael; Breitling, Rainer; Li, Yang; Yin, H; Tino, P; Corchado, E; Byrne, W; Yao,

    2007-01-01

    We apply learning vector quantization to the analysis of tiling microarray data. As an example we consider the classification of C. elegans genomic probes as intronic or exonic. Training is based on the current annotation of the genome. Relevance learning techniques are used to weight and select fea

  9. Design optimization methods for genomic DNA tiling arrays.

    Science.gov (United States)

    Bertone, Paul; Trifonov, Valery; Rozowsky, Joel S; Schubert, Falk; Emanuelsson, Olof; Karro, John; Kao, Ming-Yang; Snyder, Michael; Gerstein, Mark

    2006-02-01

    A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences.

  10. Differential analysis for high density tiling microarray data

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    Kapranov Philipp

    2007-09-01

    Full Text Available Abstract Background High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. Results We have proposed a novel approach, based on a piece-wise function – to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. Conclusion The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value -13. The prototype R code has been made available as supplementary material [see Additional file 1]. Additional file 1 gsam_prototypercode.zip. File archive comprising of prototype R code for gSAM implementation including readme and examples. Click here for file

  11. Differential analysis for high density tiling microarray data.

    Science.gov (United States)

    Ghosh, Srinka; Hirsch, Heather A; Sekinger, Edward A; Kapranov, Philipp; Struhl, Kevin; Gingeras, Thomas R

    2007-09-24

    High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. We have proposed a novel approach, based on a piece-wise function - to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value < 0.003; it is most significant at the 5' end of genes, at a p-value < 10-13. The prototype R code has been made available as supplementary material [see Additional file 1].

  12. Efficient oligonucleotide probe selection for pan-genomic tiling arrays

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    Zhang Wei

    2009-09-01

    Full Text Available Abstract Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. Results This paper presents a new probe selection algorithm (PanArray that can tile multiple whole genomes using a minimal number of probes. Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. Conclusion PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on

  13. Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

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    Casey R Richardson

    Full Text Available BACKGROUND: MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery. PRINCIPAL FINDINGS: We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes. CONCLUSIONS: Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non

  14. Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray

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    Segura Víctor

    2012-09-01

    Full Text Available Abstract Background High-density oligonucleotide microarray is an appropriate technology for genomic analysis, and is particulary useful in the generation of transcriptional maps, ChIP-on-chip studies and re-sequencing of the genome.Transcriptome analysis of tiling microarray data facilitates the discovery of novel transcripts and the assessment of differential expression in diverse experimental conditions. Although new technologies such as next-generation sequencing have appeared, microarrays might still be useful for the study of small genomes or for the analysis of genomic regions with custom microarrays due to their lower price and good accuracy in expression quantification. Results Here, we propose a novel wavelet-based method, named ZCL (zero-crossing lines, for the combined denoising and segmentation of tiling signals. The denoising is performed with the classical SUREshrink method and the detection of transcriptionally active regions is based on the computation of the Continuous Wavelet Transform (CWT. In particular, the detection of the transitions is implemented as the thresholding of the zero-crossing lines. The algorithm described has been applied to the public Saccharomyces cerevisiae dataset and it has been compared with two well-known algorithms: pseudo-median sliding window (PMSW and the structural change model (SCM. As a proof-of-principle, we applied the ZCL algorithm to the analysis of the custom tiling microarray hybridization results of a S. aureus mutant deficient in the sigma B transcription factor. The challenge was to identify those transcripts whose expression decreases in the absence of sigma B. Conclusions The proposed method archives the best performance in terms of positive predictive value (PPV while its sensitivity is similar to the other algorithms used for the comparison. The computation time needed to process the transcriptional signals is low as compared with model-based methods and in the same range to those

  15. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Xia, Mian

    2005-01-01

    BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models...... definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice...

  16. Identification of a novel gene by whole human genome tiling array.

    Science.gov (United States)

    Ishida, Hirokazu; Yagi, Tomohito; Tanaka, Masami; Tokuda, Yuichi; Kamoi, Kazumi; Hongo, Fumiya; Kawauchi, Akihiro; Nakano, Masakazu; Miki, Tsuneharu; Tashiro, Kei

    2013-03-01

    When the whole human genome sequence was determined by the Human Genome Project, the number of identified genes was fewer than expected. However, recent studies suggest that undiscovered transcripts still exist in the human genome. Furthermore, a new technology, the DNA microarray, which can simultaneously characterize huge amounts of genome sequence data, has become a useful tool for analyzing genetic changes in various diseases. A version of this tool, the tiling DNA microarray, was designed to search all the transcripts of the entire human genome, and provides huge amounts of data, including both exon and intron sequences, by a simple process. Although some previous studies using tiling DNA microarray analysis have indicated that numerous novel transcripts can be found in the human genome, none of them has reported any novel full-length human genes. Here, to find novel genes, we analyzed all the transcripts expressed in normal human prostate cells using this microarray. Because the optimal analytical parameters for using tiling DNA microarray data for this purpose had not been established, we established parameters for extracting the most likely regions for novel transcripts. The three parameters we optimized were the threshold for positive signal intensity, the Max gap, and the Min run, which we set to detect all transcriptional regions that were above the average length of known exons and had a signal intensity in the top 5%. We succeeded in obtaining the full-length sequence of one novel gene, located on chromosome 12q24.13. We named the novel gene "POTAGE". Its 5841-bp mRNA consists of 26 exons. We detected part of exon 2 in the tiling data analysis. The full-length sequence was then obtained by RT-PCR and RACE. Although the function of POTAGE is unclear, its sequence showed high homology with genes in other species, suggesting it might have an important or essential function. This study demonstrates that the tiling DNA microarray can be useful for

  17. Analysis of DNA strand-specific differential expression with high density tiling microarrays

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    Antequera Francisco

    2010-03-01

    Full Text Available Abstract Background DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA contain probes for annotated open reading frames (ORF and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol to exploit the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts. Results We extensively filtered probes present in Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to generate custom Chip Description Files (CDF in order to compare their efficiency. We experimentally tested the potential of our approach by measuring the differential expression of 4904 genes in the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress. The results showed a Pearson correlation coefficient of 0.943 between both platforms, indicating that TMAs are as reliable as EMAs for quantitative expression analysis. A significant advantage of TMAs over EMAs is the possibility of detecting non-annotated transcripts generated only under specific physiological conditions. To take full advantage of this property, we have used a target-labelling protocol that preserves the original polarity of the transcripts and, therefore, allows the strand-specific differential expression of non-annotated transcripts to be determined. By using a segmentation algorithm prior to generating the corresponding custom CDFs, we identified and quantitatively measured the expression of 510 transcripts longer than 180 nucleotides and not overlapping previously annotated ORFs that were differentially expressed at least 2-fold under oxidative stress. Conclusions We show that the information derived from TMA

  18. Picky: oligo microarray design for large genomes

    National Research Council Canada - National Science Library

    Chou, Hui-Hsien; Hsia, An-Ping; Mooney, Denise L; Schnable, Patrick S

    2004-01-01

    Many large genomes are getting sequenced nowadays. Biologists are eager to start microarray analysis taking advantage of all known genes of a species, but existing microarray design tools were very inefficient for large genomes...

  19. Microarray Genomic Systems Development

    Science.gov (United States)

    2008-06-01

    D Canada Contract Report DRDC Suffield CR 2009-145 June 2008 V. Lam, M. Crichton , T. Dickinson Laing, and D.C. Mah Canada West Biosciences Inc...Genomic Systems Development V. Lam, M. Crichton , T. Dickinson Laing, and D.C. Mah Canada West Biosciences Inc. Canada West Biosciences Inc. 5429... Crichton , M.; Dickinson Laing, T.; Mah, D.C.; DRDC Suffield CR 2009- 145; Defence R&D Canada – Suffield; June 2008. Introduction: Conventional

  20. Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

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    Jee Justin

    2008-12-01

    Full Text Available Abstract Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C→A, C→G and T→A (yielding purine-purine mispairs are most disruptive, whereas A→X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa. This skew is small in highly-expressed regions (± 0.5% of total intensity range and large (± 2% or more elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM. Conclusion We investigate several parameters for oligonucleotide design, including the effects of each central nucleotide substitution on array signal intensity and of multiple MM per oligo. To avoid GC skew, individual substitutions should not alter probe GC content. RNA sample mixture complexity may increase the amount of nonspecific hybridization, magnify GC skew and boost the intensity of MM oligos at all levels.

  1. Flexible and efficient genome tiling design with penalized uniqueness score

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    Du Yang

    2012-12-01

    Full Text Available Abstract Background As a powerful tool in whole genome analysis, tiling array has been widely used in the answering of many genomic questions. Now it could also serve as a capture device for the library preparation in the popular high throughput sequencing experiments. Thus, a flexible and efficient tiling array design approach is still needed and could assist in various types and scales of transcriptomic experiment. Results In this paper, we address issues and challenges in designing probes suitable for tiling array applications and targeted sequencing. In particular, we define the penalized uniqueness score, which serves as a controlling criterion to eliminate potential cross-hybridization, and a flexible tiling array design pipeline. Unlike BLAST or simple suffix array based methods, computing and using our uniqueness measurement can be more efficient for large scale design and require less memory. The parameters provided could assist in various types of genomic tiling task. In addition, using both commercial array data and experiment data we show, unlike previously claimed, that palindromic sequence exhibiting relatively lower uniqueness. Conclusions Our proposed penalized uniqueness score could serve as a better indicator for cross hybridization with higher sensitivity and specificity, giving more control of expected array quality. The flexible tiling design algorithm incorporating the penalized uniqueness score was shown to give higher coverage and resolution. The package to calculate the penalized uniqueness score and the described probe selection algorithm are implemented as a Perl program, which is freely available at http://www1.fbn-dummerstorf.de/en/forschung/fbs/fb3/paper/2012-yang-1/OTAD.v1.1.tar.gz.

  2. Design of an Enterobacteriaceae Pan-genome Microarray Chip

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David

    2010-01-01

    -density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability...... to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination...

  3. SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

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    Davies Jonathan J

    2006-12-01

    Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

  4. Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays.

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    Soumaya Laalami

    Full Text Available RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis. Its characterization provided the first evidence that endonucleolytic cleavage plays a major role in the mRNA metabolism of this organism. RNase Y shares important functional features with the RNA decay initiating RNase E from Escherichia coli, notably a similar cleavage specificity and a preference for 5' monophosphorylated substrates. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. The downstream cleavage products are likely to be degraded by the 5' exonucleolytic activity of RNases J1/J2 as we show for a specific case. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% were in common in all three studies. This highlights that experimental conditions and data analysis play an important role in identifying RNase Y substrates by global transcriptional profiling. Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allow an exceptionally detailed view of the turnover of hundreds of new RNA substrates.

  5. Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

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    Swiatlo Edwin

    2010-06-01

    Full Text Available Abstract Background The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus, an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution. Results Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome. Conclusions In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence.

  6. The research progress of tiling array technology and applications

    Institute of Scientific and Technical Information of China (English)

    LANG XianYu; WANG Jun; CHI XueBin

    2008-01-01

    Tiling array technology was improved from microarray technology. Over the past five years, tiling array has become an important tool for gathering genome information. Its features of high density and high throughput allow people to probe into life from the whole-genome level. This paper is a survey of tiling array technology and its applications. In addition, some typical algorithms for identifying expressed probe signals are described and compared.

  7. Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

    Directory of Open Access Journals (Sweden)

    Huyen Yentram

    2008-08-01

    Full Text Available Abstract Background Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP calls from the microarray with known SNP among parasite isolates. Results We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes with high accuracy (≥ 94% and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV among the parasites was also cataloged and compared. Conclusion A large number of mSFP were discovered from the P. falciparum genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the P. falciparum parasite and provide useful resources for mapping important parasite traits.

  8. A hidden Markov model approach for determining expression from genomic tiling micro arrays

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    Krogh Anders

    2006-05-01

    Full Text Available Abstract Background Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. Results We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005 tiling array experiments on ten Human chromosomes 1. Results can be downloaded and viewed from our web site 2. Conclusion The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms of nucleotide sensitivity and transfrag specificity.

  9. DNA Microarrays in Comparative Genomics and Transcriptomics

    DEFF Research Database (Denmark)

    Willenbrock, Hanni

    2007-01-01

    of each method’s ability to analyze DNA copy number data. Moreover, our study shows that analysis methods developed for cancer research may also successfully be applied to DNA copy number profiles from bacterial genomes. However, here the purpose is to characterize variations in the gene content...... to verify predictions of highly expressed genes. Moreover, the codon bias of microbial genomes was found to constitute an environmental signature. For example, soil bacteria have very similar codon bias....

  10. Digital microarray analysis for digital artifact genomics

    Science.gov (United States)

    Jaenisch, Holger; Handley, James; Williams, Deborah

    2013-06-01

    We implement a Spatial Voting (SV) based analogy of microarray analysis for digital gene marker identification in malware code sections. We examine a famous set of malware formally analyzed by Mandiant and code named Advanced Persistent Threat (APT1). APT1 is a Chinese organization formed with specific intent to infiltrate and exploit US resources. Manidant provided a detailed behavior and sting analysis report for the 288 malware samples available. We performed an independent analysis using a new alternative to the traditional dynamic analysis and static analysis we call Spatial Analysis (SA). We perform unsupervised SA on the APT1 originating malware code sections and report our findings. We also show the results of SA performed on some members of the families associated by Manidant. We conclude that SV based SA is a practical fast alternative to dynamics analysis and static analysis.

  11. Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs

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    Ringnér Markus

    2008-07-01

    Full Text Available Abstract Background Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors. Methods 32 K tiling microarray-based comparative genomic hybridization (aCGH was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters. Results Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 × 10-5 unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29 displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses. Conclusion Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and

  12. A hidden Markov model approach for determining expression from genomic tiling micro arrays

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Gardner, P. P.; Arctander, Peter;

    2006-01-01

    HMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non......]. Results can be downloaded and viewed from our web site [2]. Conclusion The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms...

  13. Comparative analysis of genomic signal processing for microarray data clustering.

    Science.gov (United States)

    Istepanian, Robert S H; Sungoor, Ala; Nebel, Jean-Christophe

    2011-12-01

    Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides the best clustering accuracy compared to other digital signal processing and well known statistical methods.

  14. Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray

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    Lan Shu

    2008-07-01

    Full Text Available Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research because they enable massively-parallel assays and simultaneous monitoring of thousands of gene expression of biological samples. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding(LLE is proposed, and fuzzy K-nearest neighbors algorithm which denoises datasets will be introduced as a replacement to the classical LLE’s KNN algorithm. In addition, kernel method based support vector machine (SVM will be used to classify genomic microarray data sets in this paper. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results confirm the superiority and high success rates of the presented method.

  15. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

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    Albert Lee

    2008-12-01

    Full Text Available A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs, which are rapidly degraded and whose function(s within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

  16. Human genomics and microarrays: implications for the plastic surgeon.

    Science.gov (United States)

    Cole, Jana; Isik, Frank

    2002-09-01

    The Human Genome Project was launched in 1989 in an effort to sequence the entire span of human DNA. Although coding sequences are important in identifying mutations, the static order of DNA does not explain how a cell or organism may respond to normal and abnormal biological processes. By examining the mRNA content of a cell, researchers can determine which genes are being activated in response to a stimulus. Traditional methods in molecular biology generally work on a "one gene: one experiment" basis, which means that the throughput is very limited and the "whole picture" of gene function is hard to obtain. To study each of the 60,000 to 80,000 genes in the human genome under each biological circumstance is not practical. Recently, microarrays (also known as gene or DNA chips) have emerged; these allow for the simultaneous determination of expression for thousands of genes and analysis of genome-wide mRNA expression. The purpose of this article is twofold: first, to provide the clinical plastic surgeon with a working knowledge and understanding of the fields of genomics, microarrays, and bioinformatics and second, to present a case to illustrate how these technologies can be applied in the study of wound healing.

  17. Sequencing ebola and marburg viruses genomes using microarrays.

    Science.gov (United States)

    Hardick, Justin; Woelfel, Roman; Gardner, Warren; Ibrahim, Sofi

    2016-08-01

    Periodic outbreaks of Ebola and Marburg hemorrhagic fevers have occurred in Africa over the past four decades with case fatality rates reaching as high as 90%. The latest Ebola outbreak in West Africa in 2014 raised concerns that these infections can spread across continents and pose serious health risks. Early and accurate identification of the causative agents is necessary to contain outbreaks. In this report, we describe sequencing-by-hybridization (SBH) technique using high density microarrays to identify Ebola and Marburg viruses. The microarrays were designed to interrogate the sequences of entire viral genomes, and were evaluated with three species of Ebolavirus (Reston, Sudan, and Zaire), and three strains of Marburgvirus (Angola, Musoke, and Ravn). The results showed that the consensus sequences generated with four or more hybridizations had 92.1-98.9% accuracy over 95-99% of the genomes. Additionally, with SBH microarrays it was possible to distinguish between different strains of the Lake Victoria Marburgvirus. J. Med. Virol. 88:1303-1308, 2016. © 2016 Wiley Periodicals, Inc.

  18. Experimental annotation of the human genome using microarray technology.

    Science.gov (United States)

    Shoemaker, D D; Schadt, E E; Armour, C D; He, Y D; Garrett-Engele, P; McDonagh, P D; Loerch, P M; Leonardson, A; Lum, P Y; Cavet, G; Wu, L F; Altschuler, S J; Edwards, S; King, J; Tsang, J S; Schimmack, G; Schelter, J M; Koch, J; Ziman, M; Marton, M J; Li, B; Cundiff, P; Ward, T; Castle, J; Krolewski, M; Meyer, M R; Mao, M; Burchard, J; Kidd, M J; Dai, H; Phillips, J W; Linsley, P S; Stoughton, R; Scherer, S; Boguski, M S

    2001-02-15

    The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

  19. A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

    Directory of Open Access Journals (Sweden)

    Woodward Martin J

    2008-01-01

    Full Text Available Abstract Background Microarray based comparative genomic hybridisation (CGH experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity. Results The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data. Conclusion After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.

  20. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

    Directory of Open Access Journals (Sweden)

    Brahmbhatt Sonal

    2008-11-01

    Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

  1. Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

    Directory of Open Access Journals (Sweden)

    Ball Catherine A

    2004-10-01

    Full Text Available Abstract Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. Results We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files, as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. Conclusion Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context.

  2. Whole genome microarray analysis, from neonatal blood cards

    Directory of Open Access Journals (Sweden)

    Hogan Michael E

    2009-07-01

    Full Text Available Abstract Background Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. Results A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Conclusion Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.

  3. Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis

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    Chavez Adela

    2008-07-01

    Full Text Available Abstract Background Anaplasma phagocytophilum (Ap is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6 and pathogenesis (human; HL-60 and HMEC-1. Results Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6 and the human (HL-60 and HMEC-1 cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins paralogs (of 114 total, through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6. Conclusion Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.

  4. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

    Science.gov (United States)

    Jaing, Crystal J.; McLoughlin, Kevin S.; Thissen, James B.; Zemla, Adam; Vergez, Lisa M.; Bourguet, Feliza; Mabery, Shalini; Fofanov, Viacheslav Y.; Koshinsky, Heather; Jackson, Paul J.

    2016-01-01

    Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms. PMID:27668749

  5. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  6. A genome-wide 20 K citrus microarray for gene expression analysis.

    Science.gov (United States)

    Martinez-Godoy, M Angeles; Mauri, Nuria; Juarez, Jose; Marques, M Carmen; Santiago, Julia; Forment, Javier; Gadea, Jose

    2008-07-03

    Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database 1 was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in

  7. A genome-wide 20 K citrus microarray for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Gadea Jose

    2008-07-01

    Full Text Available Abstract Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database 1 was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. Conclusion This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global

  8. An efficient pseudomedian filter for tiling microrrays

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    Gerstein Mark B

    2007-06-01

    Full Text Available Abstract Background Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a O(n2logn calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution. Results We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of n numbers to O(nlogn from O(n2logn. For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple O(log n inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets. Conclusion Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that

  9. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.

    Directory of Open Access Journals (Sweden)

    Leighton Pritchard

    2009-08-01

    Full Text Available Microarray comparative genomic hybridisation (aCGH provides an estimate of the relative abundance of genomic DNA (gDNA taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043 and Dickeya dadantii 3937 (Dda3937; and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.

  10. Experimental genomics: The application of DNA microarrays in cellular and molecular biology studies

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellular and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quant itative fashion. DNA microarrays can be used to measure levels of gene expressio n for tens of thousands of gene simultaneously and take advantage of all availab le sequence information for experimental design and data interpretation in pursu it of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a catalogue of all the genes and informati on about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in genome and gene function analysis, gene expression studies, biological signal and defense system, cell cyclereg ulation, mechanism of transcriptional regulation, proteomics, and the functional ity of food component.

  11. A genome-wide 20 K citrus microarray for gene expression analysis

    OpenAIRE

    Gadea Jose; Forment Javier; Santiago Julia; Marques M Carmen; Juarez Jose; Mauri Nuria; Martinez-Godoy M Angeles

    2008-01-01

    Abstract Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-...

  12. A genome-wide 20 K citrus microarray for gene expression analysis

    OpenAIRE

    Martinez-Godoy, M Angeles; Mauri, Nuria; Juarez, Jose; Marques, M Carmen; Santiago, Julia; Forment, Javier; Gadea, Jose

    2008-01-01

    Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA...

  13. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis

    NARCIS (Netherlands)

    Skinner, M.; Robertson, L.B.; Tempest, H.G.; Langley, E.J.; Ioannou, D.; Fowler, K.E.; Crooijmans, R.P.M.A.

    2009-01-01

    Background: The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, w

  14. High-resolution genomic microarrays for X-linked mental retardation.

    NARCIS (Netherlands)

    Lugtenberg, D.; Veltman, J.A.; Bokhoven, J.H.L.M. van

    2007-01-01

    Developments in genomic microarray technology have revolutionized the study of human genomic copy number variation. This has significantly affected many areas in human genetics, including the field of X-linked mental retardation (XLMR). Chromosome X-specific bacterial artificial chromosomes

  15. High-resolution genomic microarrays for X-linked mental retardation.

    NARCIS (Netherlands)

    Lugtenberg, D.; Veltman, J.A.; Bokhoven, J.H.L.M. van

    2007-01-01

    Developments in genomic microarray technology have revolutionized the study of human genomic copy number variation. This has significantly affected many areas in human genetics, including the field of X-linked mental retardation (XLMR). Chromosome X-specific bacterial artificial chromosomes microarr

  16. Microarray-based genomic profiling as a diagnostic tool in acute lymphoblastic leukemia.

    Science.gov (United States)

    Simons, Annet; Stevens-Kroef, Marian; El Idrissi-Zaynoun, Najat; van Gessel, Sabine; Weghuis, Daniel Olde; van den Berg, Eva; Waanders, Esmé; Hoogerbrugge, Peter; Kuiper, Roland; van Kessel, Ad Geurts

    2011-12-01

    In acute lymphoblastic leukemia (ALL) specific genomic abnormalities provide important clinical information. In most routine clinical diagnostic laboratories conventional karyotyping, in conjunction with targeted screens using e.g., fluorescence in situ hybridization (FISH), is currently considered as the gold standard to detect such aberrations. Conventional karyotyping, however, is limited in its resolution and yield, thus hampering the genetic diagnosis of ALL. We explored whether microarray-based genomic profiling would be feasible as an alternative strategy in a routine clinical diagnostic setting. To this end, we compared conventional karyotypes with microarray-deduced copy number aberration (CNA) karyotypes in 60 ALL cases. Microarray-based genomic profiling resulted in a CNA detection rate of 90%, whereas for conventional karyotyping this was 61%. In addition, many small (< 5 Mb) genetic lesions were encountered, frequently harboring clinically relevant ALL-related genes such as CDKN2A/B, ETV6, PAX5, and IKZF1. From our data we conclude that microarray-based genomic profiling serves as a robust tool in the genetic diagnosis of ALL, outreaching conventional karyotyping in CNA detection both in terms of sensitivity and specificity. We also propose a practical workflow for a comprehensive and objective interpretation of CNAs obtained through microarray-based genomic profiling, thereby facilitating its application in a routine clinical diagnostic setting.

  17. Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization

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    Gibello Alicia

    2010-03-01

    Full Text Available Abstract Background Lactococcus garvieae is a bacterial pathogen that affects different animal species in addition to humans. Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study, the genomic content of L. garvieae CECT 4531 was analysed using bioinformatics tools and microarray-based comparative genomic hybridization (CGH experiments. Lactococcus lactis subsp. lactis IL1403 and Streptococcus pneumoniae TIGR4 were used as reference microorganisms. Results The combination and integration of in silico analyses and in vitro CGH experiments, performed in comparison with the reference microorganisms, allowed establishment of an inter-species hybridization framework with a detection threshold based on a sequence similarity of ≥ 70%. With this threshold value, 267 genes were identified as having an analogue in L. garvieae, most of which (n = 258 have been documented for the first time in this pathogen. Most of the genes are related to ribosomal, sugar metabolism or energy conversion systems. Some of the identified genes, such as als and mycA, could be involved in the pathogenesis of L. garvieae infections. Conclusions In this study, we identified 267 genes that were potentially present in L. garvieae CECT 4531. Some of the identified genes could be involved in the pathogenesis of L. garvieae infections. These results provide the first insight into the genome content of L. garvieae.

  18. Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC and its application for DNA methylation analysis

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    Ottaviani Diego

    2008-05-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP, methylated DNA immunoprecipitation (MeDIP, array comparative genomic hybridization (aCGH and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs. Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.

  19. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides.

    NARCIS (Netherlands)

    Carvalho, B; Ouwerkerk, E; Meijer, G.A.; Ylstra, B.

    2004-01-01

    BACKGROUND: Currently, comparative genomic hybridisation array (array CGH) is the method of choice for studying genome wide DNA copy number changes. To date, either amplified representations of bacterial artificial chromosomes (BACs)/phage artificial chromosomes (PACs) or cDNAs have been spotted as

  20. Two heuristic approaches to describe periodicities in genomic microarrays

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    Jörg Aßmus

    2009-09-01

    Full Text Available In the first part we discuss the filtering of panels of time series based on singular value decomposition. The discussion is based on an approach where this filtering is used to normalize microarray data. We point out effects on the periodicity and phases for time series panels. In the second part we investigate time dependent periodic panels with different phases. We align the time series in the panel and discuss the periodogram of the aligned time series with the purpose of describing the periodic structure of the panel. The method is quite powerful assuming known phases in the model, but it deteriorates rapidly for noisy data.  

  1. A 7872 cDNA microarray and its use in bovine functional genomics.

    Science.gov (United States)

    Everts, Robin E; Band, Mark R; Liu, Z Lewis; Kumar, Charu G; Liu, Lei; Loor, Juan J; Oliveira, Rosane; Lewin, Harris A

    2005-05-15

    The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, thereby facilitating data analysis and interpretation. A total of 3244 genes were annotated with GO terms. The array is rich in sequences encoding transcription factors, signal transducers and cell cycle regulators. Current research being conducted with this array is described, and an overview of planned improvements in our microarray platform for cattle functional genomics is presented.

  2. A genome-wide 20 K citrus microarray for gene expression analysis

    OpenAIRE

    Martínez-Godoy, M. Ángeles; Mauri, Nuria; Juárez, José; Marqués, M. Carmen; Santiago, Julia; Forment, Javier; Gadea Vacas, José

    2008-01-01

    Background: Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genomewide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results: We have designed and constructed a publicly available ...

  3. CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data

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    Rajashekara Gireesh

    2006-04-01

    Full Text Available Abstract Background Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. The density of oligonucleotide probes available on current microarray platforms is particularly well-suited for comparisons of organisms with smaller genomes like bacteria and yeast where an entire genome can be assayed on a single microarray with high resolution. Available methods for analyzing these experiments typically confine analyses to data from pre-defined annotated genome features, such as entire genes. Many of these methods are ill suited for datasets with the number of measurements typical of high-density microarrays. Results We present an algorithm for analyzing microarray hybridization data to aid identification of regions that vary between an unsequenced genome and a sequenced reference genome. The program, CGHScan, uses an iterative random walk approach integrating multi-layered significance testing to detect these regions from comparative genomic hybridization data. The algorithm tolerates a high level of noise in measurements of individual probe intensities and is relatively insensitive to the choice of method for normalizing probe intensity values and identifying probes that differ between samples. When applied to comparative genomic hybridization data from a published experiment, CGHScan identified eight of nine known deletions in a Brucella ovis strain as compared to Brucella melitensis. The same result was obtained using two different normalization methods and two different scores to classify data for individual probes as representing conserved or variable genomic regions. The undetected region is a small (58 base pair deletion that is below the resolution of CGHScan given the array design employed in the study

  4. Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

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    Ben Beheshti

    2003-01-01

    Full Text Available Conventional comparative genomic hybridization (CGH profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1 no amplifications evident, 2 a small MYCN amplicon as the only detectable imbalance, and 3 a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.

  5. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    Directory of Open Access Journals (Sweden)

    Carr Steven M

    2007-09-01

    Full Text Available Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by

  6. Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling

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    Beuf Kristof

    2012-09-01

    Full Text Available Abstract Background Existing statistical methods for tiling array transcriptome data either focus on transcript discovery in one biological or experimental condition or on the detection of differential expression between two conditions. Increasingly often, however, biologists are interested in time-course studies, studies with more than two conditions or even multiple-factor studies. As these studies are currently analyzed with the traditional microarray analysis techniques, they do not exploit the genome-wide nature of tiling array data to its full potential. Results We present an R Bioconductor package, waveTiling, which implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling the user is able to discover (1 group-wise expressed regions, (2 differentially expressed regions between any two groups in single-factor studies and in (3 multifactorial designs. Moreover, for time-course experiments it is also possible to detect (4 linear time effects and (5 a circadian rhythm of transcripts. By considering the expression values of the individual tiling probes as a function of genomic position, effect regions can be detected regardless of existing annotation. Three case studies with different experimental set-ups illustrate the use and the flexibility of the model-based transcriptome analysis. Conclusions The waveTiling package provides the user with a convenient tool for the analysis of tiling array trancriptome data for a multitude of experimental set-ups. Regardless of the study design, the probe-wise analysis allows for the detection of transcriptional effects in both exonic, intronic and intergenic regions, without prior consultation of existing annotation.

  7. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

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    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  8. Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays.

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    Mitchell Guttman

    2007-08-01

    Full Text Available Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication machinery that results in an accumulation of genomic aberrations in the form of duplications, deletions, translocations, and other genomic alterations. Microarray methods allow for finer mapping of these aberrations than has previously been possible; however, data processing and analysis methods have not taken full advantage of this higher resolution. Attention has primarily been given to analysis on the single sample level, where multiple adjacent probes are necessarily used as replicates for the local region containing their target sequences. However, regions of concordant aberration can be short enough to be detected by only one, or very few, array elements. We describe a method called Multiple Sample Analysis for assessing the significance of concordant genomic aberrations across multiple experiments that does not require a-priori definition of aberration calls for each sample. If there are multiple samples, representing a class, then by exploiting the replication across samples our method can detect concordant aberrations at much higher resolution than can be derived from current single sample approaches. Additionally, this method provides a meaningful approach to addressing population-based questions such as determining important regions for a cancer subtype of interest or determining regions of copy number variation in a population. Multiple Sample Analysis also provides single sample aberration calls in the locations of significant concordance, producing high resolution calls per sample, in concordant regions. The approach is demonstrated on a dataset representing a challenging but important resource: breast tumors that have been formalin-fixed, paraffin-embedded, archived, and subsequently UV-laser capture microdissected and hybridized to two

  9. Genomic Imbalances in Neonates With Birth Defects: High Detection Rates by Using Chromosomal Microarray Analysis

    Science.gov (United States)

    Lu, Xin-Yan; Phung, Mai T.; Shaw, Chad A.; Pham, Kim; Neil, Sarah E.; Patel, Ankita; Sahoo, Trilochan; Bacino, Carlos A.; Stankiewicz, Pawel; Lee Kang, Sung-Hae; Lalani, Seema; Chinault, A. Craig; Lupski, James R.; Cheung, Sau W.; Beaudet, Arthur L.

    2009-01-01

    OBJECTIVES Our aim was to determine the frequency of genomic imbalances in neonates with birth defects by using targeted array-based comparative genomic hybridization, also known as chromosomal microarray analysis. METHODS Between March 2006 and September 2007, 638 neonates with various birth defects were referred for chromosomal microarray analysis. Three consecutive chromosomal microarray analysis versions were used: bacterial artificial chromosome-based versions V5 and V6 and bacterial artificial chromosome emulated oligonucleotide-based version V6 Oligo. Each version had targeted but increasingly extensive genomic coverage and interrogated >150 disease loci with enhanced coverage in genomic rearrangement-prone pericentromeric and subtelomeric regions. RESULTS Overall, 109 (17.1%) patients were identified with clinically significant abnormalities with detection rates of 13.7%, 16.6%, and 19.9% on V5, V6, and V6 Oligo, respectively. The majority of these abnormalities would not be defined by using karyotype analysis. The clinically significant detection rates by use of chromosomal microarray analysis for various clinical indications were 66.7% for “possible chromosomal abnormality” ± “others” (other clinical indications), 33.3% for ambiguous genitalia ± others, 27.1% for dysmorphic features + multiple congenital anomalies ± others, 24.6% for dysmorphic features ± others, 21.8% for congenital heart disease ± others, 17.9% for multiple congenital anomalies ± others, and 9.5% for the patients referred for others that were different from the groups defined. In all, 16 (2.5%) patients had chromosomal aneuploidies, and 81 (12.7%) patients had segmental aneusomies including common microdeletion or microduplication syndromes and other genomic disorders. Chromosomal mosaicism was found in 12 (1.9%) neonates. CONCLUSIONS Chromosomal microarray analysis is a valuable clinical diagnostic tool that allows precise and rapid identification of genomic imbalances

  10. Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data

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    Kennedy Breandan

    2010-01-01

    Full Text Available Abstract Background The Affymetrix GeneChip is a widely used gene expression profiling platform. Since the chips were originally designed, the genome databases and gene definitions have been considerably updated. Thus, more accurate interpretation of microarray data requires parallel updating of the specificity of GeneChip probes. We propose a new probe remapping protocol, using the zebrafish GeneChips as an example, by removing nonspecific probes, and grouping the probes into transcript level probe sets using an integrated zebrafish genome annotation. This genome annotation is based on combining transcript information from multiple databases. This new remapping protocol, especially the new genome annotation, is shown here to be an important factor in improving the interpretation of gene expression microarray data. Results Transcript data from the RefSeq, GenBank and Ensembl databases were downloaded from the UCSC genome browser, and integrated to generate a combined zebrafish genome annotation. Affymetrix probes were filtered and remapped according to the new annotation. The influence of transcript collection and gene definition methods was tested using two microarray data sets. Compared to remapping using a single database, this new remapping protocol results in up to 20% more probes being retained in the remapping, leading to approximately 1,000 more genes being detected. The differentially expressed gene lists are consequently increased by up to 30%. We are also able to detect up to three times more alternative splicing events. A small number of the bioinformatics predictions were confirmed using real-time PCR validation. Conclusions By combining gene definitions from multiple databases, it is possible to greatly increase the numbers of genes and splice variants that can be detected in microarray gene expression experiments.

  11. Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

    Science.gov (United States)

    Yao, Jianchao; Chang, Chunqi; Salmi, Mari L; Hung, Yeung Sam; Loraine, Ann; Roux, Stanley J

    2008-06-18

    Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. This study shows that SCC is an alternative to the Pearson

  12. Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient

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    Loraine Ann

    2008-06-01

    Full Text Available Abstract Background Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. Results In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC, that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. Conclusion

  13. Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification

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    Norihisa Ishii

    2013-10-01

    Full Text Available The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA, labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.

  14. NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

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    Maija Wolf

    2005-01-01

    Full Text Available Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD inhibition and microarray analysis (NMD microarrays in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization in order to identify inactivation of tumor suppressor genes in cancer. Such a “mutatomics” screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.

  15. ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

    OpenAIRE

    Porter Christopher J; Palidwor Gareth; Palmer Claire; Muro Enrique M; McCann Jennifer A; Andrade-Navarro Miguel A; Rudnicki Michael A

    2007-01-01

    Abstract Background SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments. Results Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacety...

  16. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis

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    Fowler Katie E

    2009-08-01

    Full Text Available Abstract Background The availability of the complete chicken (Gallus gallus genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo and the first analysis of copy number variants (CNVs in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos, an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu. Results We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey. Conclusion Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots". Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies.

  17. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

    OpenAIRE

    Carter, Mark G.; Sharov, Alexei A; VanBuren, Vincent; Dudekula, Dawood B.; Carmack, Condie E; Nelson, Charlie; Ko, Minoru SH

    2005-01-01

    The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

  18. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

    Science.gov (United States)

    Carter, Mark G; Sharov, Alexei A; VanBuren, Vincent; Dudekula, Dawood B; Carmack, Condie E; Nelson, Charlie; Ko, Minoru SH

    2005-01-01

    The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance. PMID:15998450

  19. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2005-05-01

    Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

  20. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data

    Directory of Open Access Journals (Sweden)

    Chen Dongrong

    2003-07-01

    Full Text Available Abstract Background The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays. Results We designed PCR primers to amplify specific probes (180–500 bp for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (~13,000 spots/slide. Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts. Conclusions This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.

  1. Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports

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    Jing Liu

    2011-01-01

    Full Text Available Microarray-based comparative genomic hybridization (array CGH is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances. The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

  2. Parents' Experience with Pediatric Microarray: Transferrable Lessons in the Era of Genomic Counseling.

    Science.gov (United States)

    Hayeems, R Z; Babul-Hirji, R; Hoang, N; Weksberg, R; Shuman, C

    2016-04-01

    Advances in genome-based microarray and sequencing technologies hold tremendous promise for understanding, better-managing and/or preventing disease and disease-related risk. Chromosome microarray technology (array based comparative genomic hybridization [aCGH]) is widely utilized in pediatric care to inform diagnostic etiology and medical management. Less clear is how parents experience and perceive the value of this technology. This study explored parents' experiences with aCGH in the pediatric setting, focusing on how they make meaning of various types of test results. We conducted in-person or telephone-based semi-structured interviews with parents of 21 children who underwent aCGH testing in 2010. Transcripts were coded and analyzed thematically according to the principles of interpretive description. We learned that parents expect genomic tests to be of personal use; their experiences with aCGH results characterize this use as intrinsic in the test's ability to provide a much sought-after answer for their child's condition, and instrumental in its ability to guide care, access to services, and family planning. In addition, parents experience uncertainty regardless of whether aCGH results are of pathogenic, uncertain, or benign significance; this triggers frustration, fear, and hope. Findings reported herein better characterize the notion of personal utility and highlight the pervasive nature of uncertainty in the context of genomic testing. Empiric research that links pre-test counseling content and psychosocial outcomes is warranted to optimize patient care.

  3. Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis

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    Smith Maria W

    2006-05-01

    Full Text Available Abstract Background Many model systems of human viral disease involve human-mouse chimeric tissue. One such system is the recently developed SCID-beige/Alb-uPA mouse model of hepatitis C virus (HCV infection which involves a human-mouse chimeric liver. The use of functional genomics to study HCV infection in these chimeric tissues is complicated by the potential cross-hybridization of mouse mRNA on human oligonucleotide microarrays. To identify genes affected by mouse liver mRNA hybridization, mRNA from identical human liver samples labeled with either Cy3 or Cy5 was compared in the presence and absence of known amounts of mouse liver mRNA labeled in only one dye. Results The results indicate that hybridization of mouse mRNA to the corresponding human gene probe on Agilent Human 22 K oligonucleotide microarray does occur. The number of genes affected by such cross-hybridization was subsequently reduced to approximately 300 genes both by increasing the hybridization temperature and using liver samples which contain at least 80% human tissue. In addition, Real Time quantitative RT-PCR using human specific probes was shown to be a valid method to verify the expression level in human cells of known cross-hybridizing genes. Conclusion The identification of genes affected by cross-hybridization of mouse liver RNA on human oligonucleotide microarrays makes it feasible to use functional genomics approaches to study the chimeric SCID-beige/Alb-uPA mouse model of HCV infection. This approach used to study cross-species hybridization on oligonucleotide microarrays can be adapted to other chimeric systems of viral disease to facilitate selective analysis of human gene expression.

  4. Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization

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    Moerman Donald G

    2008-10-01

    Full Text Available Abstract Background Microarray comparative genomic hybridization (CGH is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. Results We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10°C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data

  5. Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions (Uranium and Chromium)

    Energy Technology Data Exchange (ETDEWEB)

    Fields, Matthew W.

    2005-06-01

    One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. Previous whole-genome microarrays constructed at ORNL have been PCR-amplimer based, and we wanted to re-evaluate the type of microarrays being built because oligonucleotide probes have several advantages. Microarrays have been generally constructed with two types of probes, PCR-generated probes that typically range in size between 200 and 2000 bp, and oligonucleotide probes with typical size of 20-70 nt. Producing PCR product-based DNA arrays can be a time-consuming procedure that includes PCR primer design, amplification, size verification, product purification, and product quantification. Also, some ORFs are difficult to amplify and thus the construction of comprehensive arrays can be a challenge. Recently, to alleviate some of the problems associated with PCR product-based microarrays, oligonucleotide microarrays that contain probes longer than 40 nt have been evaluated and used for whole genome expression studies. These microarrays should have higher specificity and are easy to construct, and can thus provide an important alternative approach to monitor gene expression. However, due to the smaller probe size, it is expected that the detection sensitivity of oligonucleotide arrays will be lower than PCR product-based probes.

  6. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system

    NARCIS (Netherlands)

    Hsiao, Nai-hua; Kirby, Ralph

    2008-01-01

    DNA/DNA microarray hybridization was used to compare the genome content of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens with that of Streptomyces coelicolor A3(2). The array data showed an about 93% agreement with the genome sequence data ava

  7. Construction and Evaluation of Desulfovibrio vulgaris Whole-Genome Oligonucleotide Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Z. He; Q. He; L. Wu; M.E. Clark; J.D. Wall; Jizhong Zhou; Matthew W. Fields

    2004-03-17

    Desulfovibrio vulgaris Hildenborough has been the focus of biochemical and physiological studies in the laboratory, and the metabolic versatility of this organism has been largely recognized, particularly the reduction of sulfate, fumarate, iron, uranium and chromium. In addition, a Desulfovibrio sp. has been shown to utilize uranium as the sole electron acceptor. D. vulgaris is a d-Proteobacterium with a genome size of 3.6 Mb and 3584 ORFs. The whole-genome microarrays of D. vulgaris have been constructed using 70mer oligonucleotides. All ORFs in the genome were represented with 3471 (97.1%) unique probes and 103 (2.9%) non-specific probes that may have cross-hybridization with other ORFs. In preparation for use of the experimental microarrays, artificial probes and targets were designed to assess specificity and sensitivity and identify optimal hybridization conditions for oligonucleotide microarrays. The results indicated that for 50mer and 70mer oligonucleotide arrays, hybridization at 45 C to 50 C, washing at 37 C and a wash time of 2.5 to 5 minutes obtained specific and strong hybridization signals. In order to evaluate the performance of the experimental microarrays, growth conditions were selected that were expected to give significant hybridization differences for different sets of genes. The initial evaluations were performed using D. vulgaris cells grown at logarithmic and stationary phases. Transcriptional analysis of D. vulgaris cells sampled during logarithmic phase growth indicated that 25% of annotated ORFs were up-regulated and 3% of annotated ORFs were downregulated compared to stationary phase cells. The up-regulated genes included ORFs predicted to be involved with acyl chain biosynthesis, amino acid ABC transporter, translational initiation factors, and ribosomal proteins. In the stationary phase growth cells, the two most up-regulated ORFs (70-fold) were annotated as a carboxynorspermidine decarboxylase and a 2C-methyl-D-erythritol-2

  8. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system

    OpenAIRE

    2007-01-01

    DNA/DNA microarray hybridization was used to compare the genome content of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens with that of Streptomyces coelicolor A3(2). The array data showed an about 93% agreement with the genome sequence data available for S. avermitilis and also showed a number of trends in the genome structure for Streptomyces and closely related Kitasatospora. A core central region was well conserved, which might be pre...

  9. Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures

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    Levine R Paul

    2005-04-01

    Full Text Available Abstract Background Genetic differences between yeast strains used in wine-making may account for some of the variation seen in their fermentation properties and may also produce differing sensory characteristics in the final wine product itself. To investigate this, we have determined genomic differences among several Saccharomyces cerevisiae wine strains by using a "microarray karyotyping" (also known as "array-CGH" or "aCGH" technique. Results We have studied four commonly used commercial wine yeast strains, assaying three independent isolates from each strain. All four wine strains showed common differences with respect to the laboratory S. cerevisiae strain S288C, some of which may be specific to commercial wine yeasts. We observed very little intra-strain variation; i.e., the genomic karyotypes of different commercial isolates of the same strain looked very similar, although an exception to this was seen among the Montrachet isolates. A moderate amount of inter-strain genomic variation between the four wine strains was observed, mostly in the form of depletions or amplifications of single genes; these differences allowed unique identification of each strain. Many of the inter-strain differences appear to be in transporter genes, especially hexose transporters (HXT genes, metal ion sensors/transporters (CUP1, ZRT1, ENA genes, members of the major facilitator superfamily, and in genes involved in drug response (PDR3, SNQ1, QDR1, RDS1, AYT1, YAR068W. We therefore used halo assays to investigate the response of these strains to three different fungicidal drugs (cycloheximide, clotrimazole, sulfomethuron methyl. Strains with fewer copies of the CUP1 loci showed hypersensitivity to sulfomethuron methyl. Conclusion Microarray karyotyping is a useful tool for analyzing the genome structures of wine yeasts. Despite only small to moderate variations in gene copy numbers between different wine yeast strains and within different isolates of a given

  10. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

    Energy Technology Data Exchange (ETDEWEB)

    Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M.; Hazen, T.C.; Zhou, J.

    2008-01-15

    The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

  11. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

    Directory of Open Access Journals (Sweden)

    Chan Alan

    2006-06-01

    Full Text Available Abstract Background Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A. Conclusion Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

  12. Development of a custom-designed, pan genomic DNA microarray to characterize strain-level diversity among Cronobacter spp.

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    Ben Davies Tall

    2015-04-01

    Full Text Available Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species: C. sakazakii, C. malonaticus, C. turicensis C. muytjensii, C. dublinensis, C. universalis, and C. condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically-related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically-related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite towards the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas.

  13. POLAR MODELLING AND SEGMENTATION OF GENOMIC MICROARRAY SPOTS USING MATHEMATICAL MORPHOLOGY

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    Jesús Angulo

    2011-05-01

    Full Text Available Robust image analysis of spots in microarrays (quality control + spot segmentation + quantification is a requirement for automated software which is of fundamental importance for a high-throughput analysis of genomics microarray-based data. This paper deals with the development of model-based image processing algorithms for qualifying/segmenting/quantifying adaptively each spot according to its morphology. A series of morphologicalmodels for spot intensities are introduced. The spot typologies representmost of the possible qualitative cases identified from a large database (different routines, techniques, etc.. Then, based on these spot models, a classification framework has been developed. The spot feature extraction and classification (without segmenting is based on converting the spot image to polar coordinates and, after computing the radial/angular projections, the calculation of granulometric curves and derived parameters from these projections. Spot contour segmentation can also be solved by working in polar coordinates, calculating the up/downminimal path, which is easily obtained with the generalized distance function. With this model-based technique, the segmentation can be regularised by controlling different elements of the algorithm. According to the spot typology (e.g., doughnut-like or egg-like spots, several minimal paths can be computed to obtain a multi-region segmentation. Moreover, this segmentation is more robust and sensible to weak spots, improving the previous approaches.

  14. An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays

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    Kapur Vivek

    2005-05-01

    Full Text Available Abstract Background DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values. Results We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions. Conclusion Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray

  15. Genome-wide microarray expression and genomic alterations by array-CGH analysis in neuroblastoma stem-like cells.

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    Raquel Ordóñez

    Full Text Available Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC, a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture. Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-β and contribute to CSC phenotype. We focused on the aberrant activation of TGF-β and Hh signalling pathways, confirming the inhibition of repressors of TGF-β pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells.

  16. Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design

    Directory of Open Access Journals (Sweden)

    Malloch Gaynor

    2007-11-01

    Full Text Available Abstract Background The green peach aphid, Myzus persicae (Sulzer, is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. Results Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs. Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection. The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. Conclusion New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible

  17. Distinguishing bacterial pathogens of potato using a genome-wide microarray approach.

    Science.gov (United States)

    Aittamaa, M; Somervuo, P; Pirhonen, M; Mattinen, L; Nissinen, R; Auvinen, P; Valkonen, J P T

    2008-09-01

    A set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. Gene-specific probes could be designed for all genes of Pectobacterium atrosepticum, c. 50% of the genes of Streptomyces scabies and c. 30% of the genes of Clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. For Streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing important virulence genes. In addition, probes were designed for the virulence-associated nip (necrosis-inducing protein) genes of P. atrosepticum, P. carotovorum and Dickeya dadantii and for the intergenic spacer (IGS) sequences of the 16S-23S rRNA gene region. Ralstonia solanacearum was not included in the study, because it is a quarantine organism and is not presently found in Finland, but a few probes were also designed for this species. The probes contained on average 40 target-specific nucleotides and were synthesized on the array in situ, organized as eight sub-arrays with an identical set of probes which could be used for hybridization with different samples. All bacteria were readily distinguished using a single channel system for signal detection. Nearly all of the c. 1000 probes designed for C. michiganensis ssp. sepedonicus, c. 50% and 40% of the c. 4000 probes designed for the genes of S. scabies and P. atrosepticum, respectively, and over 100 probes for S. turgidiscabies showed significant signals only with the respective species. P. atrosepticum, P. carotovorum and Dickeya strains were all detected with 110 common probes. By contrast, the strains of these species were found to differ in their signal profiles. Probes targeting the IGS region and nip genes could be used to place strains of Dickeya to two groups, which correlated with differences in virulence. Taken together, the approach of using a custom-designed, genome-wide microarray provided a robust means

  18. Comparative genomic analysis of Acidithiobacillus ferrooxidans strains using the A. ferrooxidans ATCC 23270 whole-genome oligonucleotide microarray.

    Science.gov (United States)

    Luo, Hailang; Shen, Li; Yin, Huaqun; Li, Qian; Chen, Qijiong; Luo, Yanjie; Liao, Liqin; Qiu, Guanzhou; Liu, Xueduan

    2009-05-01

    Acidithiobacillus ferrooxidans is an important microorganism used in biomining operations for metal recovery. Whole-genomic diversity analysis based on the oligonucleotide microarray was used to analyze the gene content of 12 strains of A. ferrooxidans purified from various mining areas in China. Among the 3100 open reading frames (ORFs) on the slides, 1235 ORFs were absent in at least 1 strain of bacteria and 1385 ORFs were conserved in all strains. The hybridization results showed that these strains were highly diverse from a genomic perspective. The hybridization results of 4 major functional gene categories, namely electron transport, carbon metabolism, extracellular polysaccharides, and detoxification, were analyzed. Based on the hybridization signals obtained, a phylogenetic tree was built to analyze the evolution of the 12 tested strains, which indicated that the geographic distribution was the main factor influencing the strain diversity of these strains. Based on the hybridization signals of genes associated with bioleaching, another phylogenetic tree showed an evolutionary relationship from which the co-relation between the clustering of specific genes and geochemistry could be observed. The results revealed that the main factor was geochemistry, among which the following 6 factors were the most important: pH, Mg, Cu, S, Fe, and Al.

  19. Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.

    Science.gov (United States)

    Oikawa, Masahiro; Yoshiura, Koh-ichiro; Kondo, Hisayoshi; Miura, Shiro; Nagayasu, Takeshi; Nakashima, Masahiro

    2011-12-07

    It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A

  20. Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Oikawa Masahiro

    2011-12-01

    Full Text Available Abstract Background It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN, which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH. Methods Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. Results The mean of the derivative log ratio spread (DLRSpread, which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05. The concordance of results between aCGH and fluorescence in situ hybridization (FISH for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively. The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15. Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40. Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005 independent factor which was associated with larger total length of CNA of breast cancers. Conclusions Thus, archival FFPE tissues from A-bomb survivors are useful for

  1. Surface ligation-based resonance light scattering analysis of methylated genomic DNA on a microarray platform.

    Science.gov (United States)

    Ma, Lan; Lei, Zhen; Liu, Xia; Liu, Dianjun; Wang, Zhenxin

    2016-05-10

    DNA methylation is a crucial epigenetic modification and is closely related to tumorigenesis. Herein, a surface ligation-based high throughput method combined with bisulfite treatment is developed for analysis of methylated genomic DNA. In this method, a DNA microarray is employed as a reaction platform, and resonance light scattering (RLS) of nanoparticles is used as the detection principle. The specificity stems from allele-specific ligation of Taq DNA ligase, which is further enhanced by improving the fidelity of Taq DNA ligase in a heterogeneous reaction. Two amplification techniques, rolling circle amplification (RCA) and silver enhancement, are employed after the ligation reaction and a gold nanoparticle (GNP) labeling procedure is used to amplify the signal. As little as 0.01% methylated DNA (i.e. 2 pmol L(-1)) can be distinguished from the cocktail of methylated and unmethylated DNA by the proposed method. More importantly, this method shows good accuracy and sensitivity in profiling the methylation level of genomic DNA of three selected colonic cancer cell lines. This strategy provides a high throughput alternative with reasonable sensitivity and resolution for cancer study and diagnosis.

  2. American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders.

    Science.gov (United States)

    Cooley, Linda D; Lebo, Matthew; Li, Marilyn M; Slovak, Marilyn L; Wolff, Daynna J

    2013-06-01

    Microarray methodologies, to include array comparative genomic hybridization and single-nucleotide polymorphism-based arrays, are innovative methods that provide genomic data. These data should be correlated with the results from the standard methods, chromosome and/or fluorescence in situ hybridization, to ascertain and characterize the genomic aberrations of neoplastic disorders, both liquid and solid tumors. Over the past several decades, standard methods have led to an accumulation of genetic information specific to many neoplasms. This specificity is now used for the diagnosis and classification of neoplasms. Cooperative studies have revealed numerous correlations between particular genetic aberrations and therapeutic outcomes. Molecular investigation of chromosomal abnormalities identified by standard methods has led to discovery of genes, and gene function and dysfunction. This knowledge has led to improved therapeutics and, in some disorders, targeted therapies. Data gained from the higher-resolution microarray methodologies will enhance our knowledge of the genomics of specific disorders, leading to more effective therapeutic strategies. To assist clinical laboratories in validation of the methods, their consistent use, and interpretation and reporting of results from these microarray methodologies, the American College of Medical Genetics and Genomics has developed the following professional standard and guidelines.

  3. Microarray data integration for genome-wide analysis of human tissue-selective gene expression

    OpenAIRE

    Wang, Liangjiang; Srivastava, Anand K; Schwartz, Charles E

    2010-01-01

    Background Microarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public microarray data requires integrating the expression profiles from heterogeneous sources. Results In this study, we have compiled a compendium of microarray expression profiles of various human tissue samples. The microarray raw data generated in different research laboratorie...

  4. Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

    Directory of Open Access Journals (Sweden)

    Christine M Costello

    2005-08-01

    Full Text Available BACKGROUND: The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD, Crohn disease (CD, and ulcerative colitis (UC are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression. METHODS AND FINDINGS: High-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11, CD patients (n = 10 and UC patients (n = 10. 33P-radiolabeled cDNA from purified poly(A+ RNA extracted from biopsies (unpooled was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome and CDH11 (cadherin 11, type 2. By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology. CONCLUSION: A comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches.

  5. In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans

    Directory of Open Access Journals (Sweden)

    Jiang Xu-Cheng

    2006-11-01

    Full Text Available Abstract Background Currently available vaccines against leptospirosis are of low efficacy, have an unacceptable side-effect profile, do not induce long-term protection, and provide no cross-protection against the different serovars of pathogenic leptospira. The current major focus in leptospirosis research is to discover conserved protective antigens that may elicit longer-term protection against a broad range of Leptospira. There is a need to screen vaccine candidate genes in the genome of Leptospira interrogans. Results Bioinformatics, comparative genomic hybridization (CGH analysis and transcriptional analysis were used to identify vaccine candidates in the genome of L. interrogans serovar Lai strain #56601. Of a total of 4727 open reading frames (ORFs, 616 genes were predicted to encode surface-exposed proteins by P-CLASSIFIER combined with signal peptide prediction, α-helix transmembrane topology prediction, integral β-barrel outer membrane protein and lipoprotein prediction, as well as by retaining the genes shared by the two sequenced L. interrogans genomes and by subtracting genes with human homologues. A DNA microarray of L. interrogans strain #56601 was constructed for CGH analysis and transcriptome analysis in vitro. Three hundred and seven differential genes were identified in ten pathogenic serovars by CGH; 1427 genes had high transcriptional levels (Cy3 signal ≥ 342 and Cy5 signal ≥ 363.5, respectively. There were 565 genes in the intersection between the set encoding surface-exposed proteins and the set of 307 differential genes. The number of genes in the intersection between this set of 565 and the set of 1427 highly transcriptionally active genes was 226. These 226 genes were thus identified as putative vaccine candidates. The proteins encoded by these genes are not only potentially surface-exposed in the bacterium, but also conserved in two sequenced L. interrogans. Moreover, these genes are conserved among ten epidemic

  6. Analysis Method of Citrus Genome Microarray%浅谈柑橘基因组芯片分析方法

    Institute of Scientific and Technical Information of China (English)

    杨雪莲; 贝学军; 朱友娟

    2012-01-01

    cDNA microarray and oligonucleotide microarray are currently used for analysing citrus gene expression profile.The data analysis of genome microarray include data preprocessing,screening differential expression genes,and further analysing the differential expression genes.Through data analysis and integration of biological information,this paper studies the plant physiological changes.%指出了cDNA芯片和寡核苷酸芯片是目前用于柑橘基因表达谱分析的方法,基因组芯片数据分析主要包括数据预处理,筛选差异基因,差异基因再进一步分析。通过数据分析及整合样点的生物学信息,研究了植物生理变化。

  7. Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

    Directory of Open Access Journals (Sweden)

    Gray Joanna

    2010-11-01

    Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

  8. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones.

    Science.gov (United States)

    Fiegler, Heike; Carr, Philippa; Douglas, Eleanor J; Burford, Deborah C; Hunt, Sarah; Scott, Carol E; Smith, James; Vetrie, David; Gorman, Patricia; Tomlinson, Ian P M; Carter, Nigel P

    2003-04-01

    We have designed DOP-PCR primers specifically for the amplification of large insert clones for use in the construction of DNA microarrays. A bioinformatic approach was used to construct primers that were efficient in the general amplification of human DNA but were poor at amplifying E. coli DNA, a common contaminant of DNA preparations from large insert clones. We chose the three most selective primers for use in printing DNA microarrays. DNA combined from the amplification of large insert clones by use of these three primers and spotted onto glass slides showed more than a sixfold increase in the human to E. coli hybridization ratio when compared to the standard DOP-PCR primer, 6MW. The microarrays reproducibly delineated previously characterized gains and deletions in a cancer cell line and identified a small gain not detected by use of conventional CGH. We also describe a method for the bulk testing of the hybridization characteristics of chromosome-specific clones spotted on microarrays by use of DNA amplified from flow-sorted chromosomes. Finally, we describe a set of clones selected from the publicly available Golden Path of the human genome at 1-Mb intervals and a view in the Ensembl genome browser from which data required for the use of these clones in array CGH and other experiments can be downloaded across the Internet.

  9. Preferences for results from genomic microarrays: comparing parents and health care providers.

    Science.gov (United States)

    Turbitt, E; Halliday, J L; Amor, D J; Metcalfe, S A

    2015-01-01

    Chromosomal microarray (CMA) testing is now performed frequently in paediatric care. Although CMAs improve diagnostic yields, they increase detection of variants of unknown and uncertain clinical significance (VUS). Understanding parents', paediatricians' and genetic health professionals' (GHPs) views regarding variant disclosure may reduce the potential for communication of unwanted information. A questionnaire was designed to compare disclosure preferences of these three groups in Australia. One hundred and forty-seven parents, 159 paediatricians and 69 GHPs hold similar views with at least 89% of respondents certainly or probably favouring disclosure of all categories of variants. However, some differences were observed between health care providers (HCPs: paediatricians and GHPs) and parents, who were less sure of their disclosure preferences. There was consensus among respondent groups that knowledge of a variant of certain clinical significance would provide more practical and emotional utility compared to VUS. Compared to HCPs, parents placed more emphasis on using knowledge of a VUS when considering future pregnancies (p exome/genome sequencing is integrated into clinical practice, the potential for differing views of parents and HCPs should be considered when developing guidelines for result disclosure.

  10. Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Hing Anne V

    2008-04-01

    Full Text Available Abstract Background Supernumerary marker chromosomes (SMCs are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients that were characterized by microarray comparative genomic hybridization (array CGH. Results In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. Conclusion The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.

  11. Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases

    DEFF Research Database (Denmark)

    Harris, R Alan; Nagy-Szakal, Dorottya; Pedersen, Natalia

    2012-01-01

    Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel disease (IBD). Monozygotic (MZ) twin discordance rates and epidemiologic data implicate that environmental changes and epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation...... of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. We investigated whether DNA methylation might be connected with IBD in peripheral blood leukocyte (PBL) DNA by utilizing genome-wide microarrays....

  12. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways.

    Science.gov (United States)

    Cogburn, L A; Wang, X; Carre, W; Rejto, L; Aggrey, S E; Duclos, M J; Simon, J; Porter, T E

    2004-01-01

    The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation-fasting and re-feeding-in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.

  13. Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

    Directory of Open Access Journals (Sweden)

    Cannon Steven

    2009-08-01

    Full Text Available Abstract Background Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient and iron deficient conditions. Results Transcriptional profiles of soybean (Glycine max, L. Merr near isogenic lines Clark (PI548553, iron efficient and IsoClark (PI547430, iron inefficient grown under Fe-sufficient and Fe-limited conditions were analyzed and compared using the Affymetrix® GeneChip® Soybean Genome Array. There were 835 candidate genes in the Clark (PI548553 genotype and 200 candidate genes in the IsoClark (PI547430 genotype putatively involved in soybean's iron stress response. Of these candidate genes, fifty-eight genes in the Clark genotype were identified with a genetic location within known iron efficiency QTL and 21 in the IsoClark genotype. The arrays also identified 170 single feature polymorphisms (SFPs specific to either Clark or IsoClark. A sliding window analysis of the microarray data and the 7X genome assembly coupled with an iterative model of the data showed the candidate genes are clustered in the genome. An analysis of 5' untranslated regions in the promoter of candidate genes identified 11 conserved motifs in 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier, confirming the cluster analysis results. Conclusion These analyses have identified the first genes with expression patterns that are affected by iron stress and are located within QTL specific to iron deficiency stress. The genetic location and promoter motif analysis results support the hypothesis that the differentially expressed genes are co-regulated. The combined results of all analyses lead us to postulate iron inefficiency in

  14. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Hallin, Peter Fischer; Wassenaar, Trudy

    2007-01-01

    Background: Microarrays have recently emerged as a novel procedure to evaluate the genetic content of bacterial species. So far, microarrays have mostly covered single or few strains from the same species. However, with cheaper high-throughput sequencing techniques emerging, multiple strains of t...

  15. Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma

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    García José

    2005-07-01

    Full Text Available Abstract Background Chromosomal Comparative Genomic Hybridization (CGH has been applied to all stages of cervical carcinoma progression, defining a specific pattern of chromosomal imbalances in this tumor. However, given its limited spatial resolution, chromosomal CGH has offered only general information regarding the possible genetic targets of DNA copy number changes. Methods In order to further define specific DNA copy number changes in cervical cancer, we analyzed 20 cervical samples (3 pre-malignant lesions, 10 invasive tumors, and 7 cell lines, using the GenoSensor microarray CGH system to define particular genetic targets that suffer copy number changes. Results The most common DNA gains detected by array CGH in the invasive samples were located at the RBP1-RBP2 (3q21-q22 genes, the sub-telomeric clone C84C11/T3 (5ptel, D5S23 (5p15.2 and the DAB2 gene (5p13 in 58.8% of the samples. The most common losses were found at the FHIT gene (3p14.2 in 47% of the samples, followed by deletions at D8S504 (8p23.3, CTDP1-SHGC- 145820 (18qtel, KIT (4q11-q12, D1S427-FAF1 (1p32.3, D9S325 (9qtel, EIF4E (eukaryotic translation initiation factor 4E, 4q24, RB1 (13q14, and DXS7132 (Xq12 present in 5/17 (29.4% of the samples. Conclusion Our results confirm the presence of a specific pattern of chromosomal imbalances in cervical carcinoma and define specific targets that are suffering DNA copy number changes in this neoplasm.

  16. Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma

    Science.gov (United States)

    Hidalgo, Alfredo; Baudis, Michael; Petersen, Iver; Arreola, Hugo; Piña, Patricia; Vázquez-Ortiz, Guelaguetza; Hernández, Dulce; González, José; Lazos, Minerva; López, Ricardo; Pérez, Carlos; García, José; Vázquez, Karla; Alatorre, Brenda; Salcedo, Mauricio

    2005-01-01

    Background Chromosomal Comparative Genomic Hybridization (CGH) has been applied to all stages of cervical carcinoma progression, defining a specific pattern of chromosomal imbalances in this tumor. However, given its limited spatial resolution, chromosomal CGH has offered only general information regarding the possible genetic targets of DNA copy number changes. Methods In order to further define specific DNA copy number changes in cervical cancer, we analyzed 20 cervical samples (3 pre-malignant lesions, 10 invasive tumors, and 7 cell lines), using the GenoSensor microarray CGH system to define particular genetic targets that suffer copy number changes. Results The most common DNA gains detected by array CGH in the invasive samples were located at the RBP1-RBP2 (3q21-q22) genes, the sub-telomeric clone C84C11/T3 (5ptel), D5S23 (5p15.2) and the DAB2 gene (5p13) in 58.8% of the samples. The most common losses were found at the FHIT gene (3p14.2) in 47% of the samples, followed by deletions at D8S504 (8p23.3), CTDP1-SHGC- 145820 (18qtel), KIT (4q11-q12), D1S427-FAF1 (1p32.3), D9S325 (9qtel), EIF4E (eukaryotic translation initiation factor 4E, 4q24), RB1 (13q14), and DXS7132 (Xq12) present in 5/17 (29.4%) of the samples. Conclusion Our results confirm the presence of a specific pattern of chromosomal imbalances in cervical carcinoma and define specific targets that are suffering DNA copy number changes in this neoplasm. PMID:16004614

  17. Genomic resources for the brown planthopper, Nilaparvata lugens: Transcriptome pyrosequencing and microarray design

    Institute of Scientific and Technical Information of China (English)

    Chris Bass; Martin Bay Hebsgaard; Joseph Hughes

    2012-01-01

    The brown planthopper,Nilaparvata lugens is a pest of cultivated rice throughout Asia and is controlled using insecticides and/or resistant rice varieties.This species has developed resistance to many classes of insecticide and biotypes have developed that are virulent against formerly resistant rice cultivars.Insects use a suite of detoxification enzymes,including cytochrome P450s,glutathione S-transferases and carboxyl/cholinesterases to defend themselves against plant secondary metabolites and pesticides.Pyrosequencing on the Roche 454-FLX platform was used to produce a substantial expressed sequence tag (EST) dataset to complement the existing Sanger sequenced ESTs in GenBank.A total of 78 959 reads were combined with the 37 392 publically available Sanger ESTs; these assembled into 8 911 contigs and 10 620 singletons.Analysis of the distribution of tentative unique genes (TUGs) with the gene ontology for biological processes and molecular functions suggests that the 454 and Sanger EST assembly is broadly representative of the N.lugens transcriptome.The brown planthopper transcriptome was found to contain 31 TUGs encoding P450s,nine encoding glutathione S-transferases and 26 encoding carboxyl/cholinesterases and many of these are putatively involved in the detoxification of xenobiotics.The Agilent eArray platform was used to construct an oligonucleotide microarray populated with probes for ~ 19 000 unigene sequences,including all those known to encode detoxification enzymes.The genomic resources developed in this study will be useful to the community studying this crop pest and will help elucidate the molecular mechanism underlying insecticide resistance and planthopper adaptation to resistant rice cultivars.

  18. A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain.

    Science.gov (United States)

    Band, Mark R; Olmstead, Colleen; Everts, Robin E; Liu, Zonglin L; Lewin, Harris A

    2002-05-01

    A cDNA microarray representing approximately 3800 cattle genes was created for functional genomic studies. The array elements were selected from > 7000 cDNA clones identified in a large-scale expressed sequence tag (EST) project that utilized spleen and normalized and subtracted placenta cDNA libraries. Sequence similarity searches of the 3820 ESTs represented on the array using BLASTN identified 3290 (86.1%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. Experiments were conducted with a prototype 768 gene microarray created from spleen cDNAs and with the 3800 gene array that included genes from spleen and placenta. The 768 gene array was used to profile RNA transcripts expressed by adult and fetal spleen. The 3800 gene array was used to profile transcripts expressed by adult brain and placenta. Microarray analysis of RNA extracted from fetal and adult spleen identified 29 genes that were differentially expressed two-fold or more. Transcriptional differences of two of these genes, IGJ and CTSS, were confirmed using TaqMan technology. The comparison of brain and placenta revealed 400 genes expressed at higher levels in brain and 72 genes expressed at higher levels in placenta. These results demonstrate the potential power of microarrays for understanding the molecular mechanisms of cattle development, disease resistance, nutrition, fertility and production traits.

  19. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system.

    Science.gov (United States)

    Hsiao, Nai-Hua; Kirby, Ralph

    2008-01-01

    DNA/DNA microarray hybridization was used to compare the genome content of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens with that of Streptomyces coelicolor A3(2). The array data showed an about 93% agreement with the genome sequence data available for S. avermitilis and also showed a number of trends in the genome structure for Streptomyces and closely related Kitasatospora. A core central region was well conserved, which might be predicted from previous research and this was linked to a low degree of gene conservation in the terminal regions of the linear chromosome across all four species. Between these regions there are two areas of intermediate gene conservation by microarray analysis where gene synteny is still detectable in S. avermitilis. Nonetheless, a range of conserved genes could be identified within the terminal regions. Variation in the genes involved in differentiation, transcription, DNA replication, etc. provides interesting insights into which genes in these categories are generally conserved and which are not. The results also provide target priorities for possible gene knockouts in a group of bacteria with a very large numbers of genes with unknown functions compared to most bacterial species.

  20. Prosecutor : parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

    NARCIS (Netherlands)

    Blom, E.J.; Breitling, R.; Hofstede, K.J.; Roerdink, J.B.T.M.; van Hijum, S.A F T; Kuipers, O.P.

    2008-01-01

    Background: Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar

  1. Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity

    OpenAIRE

    2001-01-01

    Campylobacter jejuni is the leading cause of bacterial food-borne diarrhoeal disease throughout the world, and yet is still a poorly understood pathogen. Whole genome microarray comparisons of 11 C. jejuni strains of diverse origin identified genes in up to 30 NCTC 11168 loci ranging from 0.7 to 18.7 kb that are either absent or highly divergent in these isolates. Many of these regions are associated with the biosynthesis of surface structures including flagella, lipo-oligosaccharide, and the...

  2. Differential Gene Expression Analysis of Placentas with Increased Vascular Resistance and Pre-Eclampsia Using Whole-Genome Microarrays

    Directory of Open Access Journals (Sweden)

    M. Centlow

    2011-01-01

    Full Text Available Pre-eclampsia is a pregnancy complication characterized by hypertension and proteinuria. There are several factors associated with an increased risk of developing pre-eclampsia, one of which is increased uterine artery resistance, referred to as “notching”. However, some women do not progress into pre-eclampsia whereas others may have a higher risk of doing so. The placenta, central in pre-eclampsia pathology, may express genes associated with either protection or progression into pre-eclampsia. In order to search for genes associated with protection or progression, whole-genome profiling was performed. Placental tissue from 15 controls, 10 pre-eclamptic, 5 pre-eclampsia with notching, and 5 with notching only were analyzed using microarray and antibody microarrays to study some of the same gene product and functionally related ones. The microarray showed 148 genes to be significantly altered between the four groups. In the preeclamptic group compared to notch only, there was increased expression of genes related to chemotaxis and the NF-kappa B pathway and decreased expression of genes related to antigen processing and presentation, such as human leukocyte antigen B. Our results indicate that progression of pre-eclampsia from notching may involve the development of inflammation. Increased expression of antigen-presenting genes, as seen in the notch-only placenta, may prevent this inflammatory response and, thereby, protect the patient from developing pre-eclampsia.

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

    Directory of Open Access Journals (Sweden)

    Ragupathy Viswanath

    2010-10-01

    Full Text Available Abstract Background For 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 a rapid and simple gold nanoparticle (NP-based genomic microarray assay for specific identification of avian influenza virus H5N1 and its discrimination from other major influenza A virus strains (H1N1, H3N2. Results Capture and intermediate oligonucleotides were designed based on the consensus sequences of the matrix (M gene of H1N1, H3N2 and H5N1 viruses, and sequences specific for the hemaglutinin (HA and neuraminidase (NA genes of the H5N1 virus. Viral RNA was detected within 2.5 hours using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining in the absence of RNA fragmentation, target amplification, and enzymatic reactions. The lower limit of detection (LOD of the assay was less than 100 fM for purified PCR fragments and 103 TCID50 units for H5N1 viral RNA. Conclusions The NP-based microarray assay was able to detect and distinguish H5N1 sequences from those of major influenza A viruses (H1N1, H3N2. The new method described here may be useful for simultaneous detection and subtyping of major influenza A viruses.

  4. Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides

    DEFF Research Database (Denmark)

    Bonde, Mads; Kosuri, Sriram; Genee, Hans Jasper

    2015-01-01

    operons in E. coli using this method, which we call Microarray-Oligonucleotide (MO)-MAGE. The resulting mutant library was characterized by high-throughput sequencing to show that all attempted insertions were estimated to have occurred at an average frequency of 0.02 % per loci with 0.4 average...

  5. Microarray-based Comparative Genomic Indexing of the Cronobacter genus (Enterobacter sakazakii)

    Science.gov (United States)

    Cronobacter is a recently defined genus synonymous with Enterobacter sakazakii. This new genus currently comprises 6 genomospecies. To extend our understanding of the genetic relationship between Cronobacter sakazakii BAA-894 and the other species of this genus, microarray-based comparative genomi...

  6. Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains

    Directory of Open Access Journals (Sweden)

    van Gent Marjolein

    2008-06-01

    Full Text Available Abstract Background Whooping cough caused by Bordetella pertussis in humans, is re-emerging in many countries despite vaccination. Several studies have shown that significant shifts have occurred in the B. pertussis population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. In the Netherlands, the resurgence of pertussis is associated with the rise of B. pertussis strains with an altered promoter region for pertussis toxin (ptxP3. Results We used Multi-Locus Sequence Typing (MLST, Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA and microarray-based comparative genomic hybridization (CGH to characterize the ptxP3 strains associated with the Dutch epidemic. For CGH analysis, we developed an oligonucleotide (70-mers microarray consisting of 3,581 oligonucleotides representing 94% of the gene repertoire of the B. pertussis strain Tohama I. Nine different MLST profiles and 38 different MLVA types were found in the period 1993 to 2004. Forty-three Dutch clinical isolates were analyzed with CGH, 98 genes were found to be absent in at least one of the B. pertussis strains tested, these genes were clustered in 8 distinct regions of difference. Conclusion The presented MLST, MLVA and CGH-analysis identified distinctive characteristics of ptxP3 B. pertussis strains -the most prominent of which was a genomic deletion removing about 23,000 bp. We propose a model for the emergence of ptxP3 strains.

  7. Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, J.; Wu, L.; Gentry, T.; Schadt, C.; He, Z.; Li, X.

    2006-04-05

    To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approximately 2000 unique and group-specific probes with <85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50 C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ({approx}1.3{sup o} 10{sup 7} cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r{sup 2} = 0.95-0.99). Application of this microarray to naphthalene-amended enrichments and soil microcosms demonstrated that composition of the microflora varied depending on incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in enrichments, the genes involved in naphthalene degradation from Gram-negative microorganisms such as Ralstonia, Comamonas, and Burkholderia were most abundant in the soil microcosms (as well as those for polyaromatic hydrocarbon and nitrotoluene degradation). Although naphthalene degradation is widely known and studied in Pseudomonas, Pseudomonas genes were not detected in either system. Real-time PCR analysis of 4 representative genes was consistent with microarray-based quantification (r{sup 2} = 0.95). Currently, we are also applying this microarray to the study of several

  8. DNA Microarray as Part of a Genomic-Assisted Breeding Approach

    DEFF Research Database (Denmark)

    Vincze, Éva; Bowra, Steve

    2010-01-01

    . tissue/pathway specific approaches using an example of focused microarray and how it follows predicted changes during grain development. We describe of an extension of the study to field grown material and conclude that such an approach is able to interpret differences in the gene expression profiles......In the struggle to achieve global food security, crop breeding retains an important role in crop production. A current trend is the diversification of the aims of crop production, to include an increased awareness of aspects and consequences of food quality. The added emphasis on food and feed...... and practical significances, fold changes, validation and possible additional regulatory mechanisms in gene expression. The subject of the fourth section is the applications of DNA microarrays to study of global gene expression during grain filling in monocot crops, especially barley. We compare large arrays vs...

  9. A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis.

    Science.gov (United States)

    Thomas, R; Duke, S E; Karlsson, E K; Evans, A; Ellis, P; Lindblad-Toh, K; Langford, C F; Breen, M

    2008-01-01

    Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species. We have used the dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.

  10. Science Letters: A robust statistical procedure to discover expression biomarkers using microarray genomic expression data

    Institute of Scientific and Technical Information of China (English)

    ZOU Yang-yun; YANG Jian; ZHU Jun

    2006-01-01

    Microarray has become increasingly popular biotechnology in biological and medical researches, and has been widely applied in classification of treatment subtypes using expression patterns of biomarkers. We developed a statistical procedure to identify expression biomarkers for treatment subtype classification by constructing an F-statistic based on Henderson method Ⅲ.Monte Carlo simulations were conducted to examine the robustness and efficiency of the proposed method. Simulation results showed that our method could provide satisfying power of identifying differentially expressed genes (DEGs) with false discovery rate (FDR) lower than the given type Ⅰ error rate. In addition, we analyzed a leukemia dataset collected from 38 leukemia patients with 27 samples diagnosed as acute lymphoblastic leukemia (ALL) and 11 samples as acute myeloid leukemia (AML). We compared our results with those from the methods of significance analysis of microarray (SAM) and microarray analysis of variance (MAANOVA). Among these three methods, only expression biomarkers identified by our method can precisely identify the three human acute leukemia subtypes.

  11. Determination of the relationship between group A streptococcal genome content, M type, and toxic shock syndrome by a mixed genome microarray.

    Science.gov (United States)

    Vlaminckx, Bart J M; Schuren, Frank H J; Montijn, Roy C; Caspers, Martien P M; Fluit, Ad C; Wannet, Wim J B; Schouls, Leo M; Verhoef, Jan; Jansen, Wouter T M

    2007-05-01

    Group A streptococci (GAS), or Streptococcus pyogenes, are associated with a remarkable variety of diseases, ranging from superficial infections to life-threatening diseases such as toxic-shock-like syndrome (TSS). GAS strains belonging to M types M1 and M3 are associated with TSS. This study aims to obtain insight into the gene profiles underlying different M types and disease manifestations. Genomic differences between 76 clinically well characterized GAS strains collected in The Netherlands were examined using a mixed-genome microarray. Inter-M-type genomic differences clearly outweighed intra-M-type genome variation. Phages were major contributors to observed genome diversification. We identified four novel genes, including two genes encoding fibronectin-binding-like proteins, which are highly specific to a subset of M types and thus may contribute to M-type-associated disease manifestations. All M12 strains were characterized by the unique absence of the citrate lyase complex and reduced growth under hypoxic, nutrient-deprived conditions. Furthermore, six virulence factors, including genes encoding a complement-inhibiting protein (sic), an exotoxin (speA), iron(III) binding factor, collagen binding factor (cpa), and fibrinogen binding factor (prt2-like), were unique to M1 and/or M3 strains. These virulence factors may contribute to the potential of these strains to cause TSS. Finally, in contrast to M-type-specific virulence profiles, we did not identify a common virulence profile among strains associated with TSS irrespective of their M type.

  12. FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays

    Science.gov (United States)

    Background: Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed the genomics tool ArrayTrackTM, which provides extensive functionalities to man...

  13. Genome-wide microarray analysis of human fibroblasts in response to γ radiation and the radiation-induced bystander effect.

    Science.gov (United States)

    Kalanxhi, Erta; Dahle, Jostein

    2012-01-01

    Radiation-induced bystander effects have been studied extensively due to their potential implications for cancer therapy and radiation protection; however, a complete understanding of the molecular mechanisms remains to be elucidated. In this study, we monitored transcriptional responses to γ radiation in irradiated and bystander fibroblasts simultaneously employing a genome-wide microarray approach to determine factors that may be modulated in the generation or propagation of the bystander effect. For the microarray data we employed analysis at both the single-gene and gene-set level to place the findings in a biological context. Unirradiated bystander fibroblasts that were recipients of growth medium harvested from irradiated cultures 2 h after exposure to 2 Gy displayed transient enrichment in gene sets belonging to ribosome, oxidative phosphorylation and neurodegenerative disease pathways associated with mitochondrial dysfunctions. The response to direct irradiation was characterized by induction of signaling and apoptosis genes and the gradual formation of a cellular immune response. A set of 14 genes, many of which were regulated by p53, were found to be induced early after irradiation (prior to medium transfer) and may be important in the generation or propagation of the bystander effect.

  14. A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus

    Directory of Open Access Journals (Sweden)

    Primmer Craig R

    2009-09-01

    Full Text Available Abstract Background The use of microarray technology for describing changes in mRNA expression to address ecological and evolutionary questions is becoming increasingly popular. Since three-spine stickleback are an important ecological and evolutionary model-species as well as an emerging model for eco-toxicology, the ability to have a functional and flexible microarray platform for transcriptome studies will greatly enhance the research potential in these areas. Results We designed 43,392 unique oligonucleotide probes representing 19,274 genes (93% of the estimated total gene number, and tested the hybridization performance of both DNA and RNA from different populations to determine the efficacy of probe design for transcriptome analysis using the Agilent array platform. The majority of probes were functional as evidenced by the DNA hybridization success, and 30,946 probes (14,615 genes had a signal that was significantly above background for RNA isolated from liver tissue. Genes identified as being expressed in liver tissue were grouped into functional categories for each of the three Gene Ontology groups: biological process, molecular function, and cellular component. As expected, the highest proportions of functional categories belonged to those associated with metabolic functions: metabolic process, binding, catabolism, and organelles. Conclusion The probe and microarray design presented here provides an important step facilitating transcriptomics research for this important research organism by providing a set of over 43,000 probes whose hybridization success and specificity to liver expression has been demonstrated. Probes can easily be added or removed from the current design to tailor the array to specific experiments and additional flexibility lies in the ability to perform either one-color or two-color hybridizations.

  15. Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi*

    Science.gov (United States)

    Atanasova, Lea; Druzhinina, Irina S.

    2010-01-01

    Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool. PMID:20205302

  16. Xenogenomics: Genomic Bioprospecting in Indigenous and Exotic Plants Through EST Discovery, cDNA Microarray-Based Expression Profiling and Functional Genomics

    Directory of Open Access Journals (Sweden)

    German C. Spangenberg

    2006-04-01

    Full Text Available To date, the overwhelming majority of genomics programs in plants have been directed at model or crop plant species, meaning that very little of the naturally occurring sequence diversity found in plants is available for characterization and exploitation. In contrast, ‘xenogenomics’ refers to the discovery and functional analysis of novel genes and alleles from indigenous and exotic species, permitting bioprospecting of biodiversity using high-throughput genomics experimental approaches. Such a program has been initiated to bioprospect for genetic determinants of abiotic stress tolerance in indigenous Australian flora and native Antarctic plants. Uniquely adapted Poaceae and Fabaceae species with enhanced tolerance to salt, drought, elevated soil aluminium concentration, and freezing stress have been identified, based primarily on their eco-physiology, and have been subjected to structural and functional genomics analyses. For each species, EST collections have been derived from plants subjected to appropriate abiotic stresses. Transcript profiling with spotted unigene cDNA micro-arrays has been used to identify genes that are transcriptionally modulated in response to abiotic stress. Candidate genes identified on the basis of sequence annotation or transcript profiling have been assayed in planta and other in vivo systems for their capacity to confer novel phenotypes. Comparative genomics analysis of novel genes and alleles identified in the xenogenomics target plant species has subsequently been undertaken with reference to key model and crop plants.

  17. Microarray-bioinformatics analysis of altered genomic expression profiles between human fetal and infant myocardium

    Institute of Scientific and Technical Information of China (English)

    KONG Bo; LIU Ying-long; L(U) Xiao-dong

    2008-01-01

    Background The physiological differences between fetal and postnatal heart have been well characterized at the cellular level. However, the genetic mechanisms governing and regulating these differences have only been partially elucidated. Elucidation of the differentially expressed genes profile before and after birth has never been systematically proposed and analyzed.Methods The human oligonuclectide microarray and bioinformatics analysis approaches were applied to isolate and classify the differentially expressed genes between fetal and infant cardiac tissue samples. Quantitative real-time PCR was used to confirm the results from the microarray.Results Two hundred and forty-two differentially expressed genes were discovered and classified into 13 categories, including genes related to energy metabolism, myocyte hyperplasia, development, muscle contraction, protein synthesis and degradation, extraceUular matrix components, transcription factors, apoptosis, signal pathway molecules, organelle organization and several other biological processes. Moreover, 95 genes were identified which had not previously been reported to be expressed in the heart.Conclusions The study systematically analyzed the alteration of the gene expression profile between the human fetal and infant myocardium. A number of genes were discovered which had not been reported to be expressed in the heart. The data provided insight into the physical development mechanisms of the heart before and after birth.KONG Bo and LU Xiao-dong contributed equally to this study.

  18. Repairing ceramic insulating tiles

    Science.gov (United States)

    Dunn, B. R.; Laymance, E. L.

    1980-01-01

    Fused-silica tiles containing large voids or gauges are repaired without adhesives by plug insertion method. Tiles are useful in conduits for high-temperature gases, in furnaces, and in other applications involving heat insulation.

  19. Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae

    Directory of Open Access Journals (Sweden)

    Aparicio Oscar M

    2006-10-01

    Full Text Available Abstract Background Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms remain poorly understood. A key to understanding the exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences that control origin function. In S. cerevisiae, Autonomously Replicating Sequences (ARSs contain a consensus sequence (ACS that binds the Origin Recognition Complex (ORC and is essential for origin function. However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites. Results To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen to map the ORC and Mcm2p binding sites at high resolution. These binding sites define a set of potential Autonomously Replicating Sequences (ARSs, which we term nimARSs. The nimARS set comprises 529 ORC and/or Mcm2p binding sites, which includes 95% of known ARSs, and experimental verification demonstrates that 94% are functional. The resolution of the analysis facilitated identification of potential ACSs (nimACSs within 370 nimARSs. Cross-validation shows that the nimACS predictions include 58% of known ACSs, and experimental verification indicates that 82% are essential for ARS activity. Conclusion These findings provide the most comprehensive, accurate, and detailed mapping of ORC binding sites to date, adding to the emerging picture of the chromatin organization of the budding yeast genome.

  20. Self-Directed Student Research through Analysis of Microarray Datasets: A Computer-Based Functional Genomics Practical Class for Masters-Level Students

    Science.gov (United States)

    Grenville-Briggs, Laura J.; Stansfield, Ian

    2011-01-01

    This report describes a linked series of Masters-level computer practical workshops. They comprise an advanced functional genomics investigation, based upon analysis of a microarray dataset probing yeast DNA damage responses. The workshops require the students to analyse highly complex transcriptomics datasets, and were designed to stimulate…

  1. The ATLAS tile calorimeter

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Louis Rose-Dulcina, a technician from the ATLAS collaboration, works on the ATLAS tile calorimeter. Special manufacturing techniques were developed to mass produce the thousands of elements in this detector. Tile detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

  2. Isoperimetric Pentagonal Tilings

    CERN Document Server

    Chung, Ping Ngai; Li, Yifei; Mara, Michael; Morgan, Frank; Plata, Isamar Rosa; Shah, Niralee; Vieira, Luis Sordo; Wikner, Elena

    2011-01-01

    We identify least-perimeter unit-area tilings of the plane by convex pentagons, namely tilings by Cairo and Prismatic pentagons, find infinitely many, and prove that they minimize perimeter among tilings by convex polygons with at most five sides.

  3. Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

    DEFF Research Database (Denmark)

    Jönsson, Mats; Isinger-Ekstrand, Anna; Johansson, Jan;

    2010-01-01

    /losses and gene expression profiles show strong similarity between cancers in the distal esophagus and the gastroesophageal junction with frequent upregulation of CDK6 and EGFR, whereas gastric cancer displays distinct genetic changes. These data suggest that molecular diagnostics and targeted therapies can......15, 13q34, and 12q13, whereas different profiles with gains at 5p15, 7p22, 2q35, and 13q34 characterized gastric cancers. CDK6 and EGFR were identified as putative target genes in cancers of the esophagus and the gastroesophageal junction, with upregulation in one quarter of the tumors. Gains......-resolution array-based comparative genomic hybridization and 27k oligo gene expression arrays, and putative target genes were validated in an extended series. Adenocarcinomas in the distal esophagus and the gastroesophageal junction showed strong similarities with the most common gains at 20q13, 8q24, 1q21-23, 5p...

  4. Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

    DEFF Research Database (Denmark)

    Isinger-Ekstrand, Anna; Johansson, Jan; Ohlsson, Mattias

    2010-01-01

    We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas by means of 32k high......15, 13q34, and 12q13, whereas different profiles with gains at 5p15, 7p22, 2q35, and 13q34 characterized gastric cancers. CDK6 and EGFR were identified as putative target genes in cancers of the esophagus and the gastroesophageal junction, with upregulation in one quarter of the tumors. Gains....../losses and gene expression profiles show strong similarity between cancers in the distal esophagus and the gastroesophageal junction with frequent upregulation of CDK6 and EGFR, whereas gastric cancer displays distinct genetic changes. These data suggest that molecular diagnostics and targeted therapies can...

  5. Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part B: ChIP-chip data analysis.

    Science.gov (United States)

    Göbel, Ulrike; Reimer, Julia; Turck, Franziska

    2010-01-01

    Genome-wide targets of chromatin-associated factors can be identified by a combination of chromatin-immunoprecipitation and oligonucleotide microarray hybridization. Genome-wide mircoarray data analysis represents a major challenge for the experimental biologist. This chapter introduces ChIPR, a package written in the R statistical programming language that facilitates the analysis of two-color microarrays from Roche-Nimblegen. The workflow of ChIPR is illustrated with sample data from Arabidopsis thaliana. However, ChIPR supports ChIP-chip data preprocessing, target identification, and cross-annotation of any species for which genome annotation data is available in GFF format. This chapter describes how to use ChIPR as a software tool without the requirement for programming skills in the R language.

  6. Predicting tile drainage discharge

    DEFF Research Database (Denmark)

    Iversen, Bo Vangsø; Kjærgaard, Charlotte; Petersen, Rasmus Jes;

    of the water load coming from the tile drainage system is therefore essential. This work aims at predicting tile drainage discharge using dynamic as well as a statistical predictive models. A large dataset of historical tile drain discharge data, daily discharge values as well as yearly average values were......More than 50 % of Danish agricultural areas are expected to be artificial tile drained. Transport of water and nutrients through the tile drain system to the aquatic environment is expected to be significant. For different mitigation strategies such as constructed wetlands an exact knowledge...... used in the analysis. For the dynamic modelling, a simple linear reservoir model was used where different outlets in the model represented tile drain as well as groundwater discharge outputs. This modelling was based on daily measured tile drain discharge values. The statistical predictive model...

  7. Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

    Directory of Open Access Journals (Sweden)

    MacInnes Janet I

    2009-02-01

    Full Text Available Abstract Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology.

  8. Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data.

    Science.gov (United States)

    Teng, Shaolei; Yang, Jack Y; Wang, Liangjiang

    2013-01-01

    Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene targets could provide useful information for biomarker development and drug target identification. In this study, we have developed a machine learning approach for predicting the human tissue-specific genes using microarray expression data. The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding. Random Forests (RFs) and Support Vector Machines (SVMs) were used to construct accurate classifiers. The RF classifiers were found to outperform SVM models for tissue-specific gene prediction. The results suggest that the candidate genes for brain or liver specific expression can provide valuable information for further experimental studies. Our approach was also applied for identifying tissue-selective gene targets for different types of tissues. A machine learning approach has been developed for accurately identifying the candidate genes for tissue specific/selective expression. The approach provides an efficient way to select some interesting genes for developing new biomedical markers and improve our knowledge of tissue-specific expression.

  9. Exploring host-pathogen interactions through genome wide protein microarray analysis.

    Science.gov (United States)

    Scietti, Luigi; Sampieri, Katia; Pinzuti, Irene; Bartolini, Erika; Benucci, Barbara; Liguori, Alessia; Haag, Andreas F; Lo Surdo, Paola; Pansegrau, Werner; Nardi-Dei, Vincenzo; Santini, Laura; Arora, Seguinde; Leber, Xavier; Rindi, Simonetta; Savino, Silvana; Costantino, Paolo; Maione, Domenico; Merola, Marcello; Speziale, Pietro; Bottomley, Matthew J; Bagnoli, Fabio; Masignani, Vega; Pizza, Mariagrazia; Scharenberg, Meike; Schlaeppi, Jean-Marc; Nissum, Mikkel; Liberatori, Sabrina

    2016-06-15

    During bacterial pathogenesis extensive contacts between the human and the bacterial extracellular proteomes take place. The identification of novel host-pathogen interactions by standard methods using a case-by-case approach is laborious and time consuming. To overcome this limitation, we took advantage of large libraries of human and bacterial recombinant proteins. We applied a large-scale protein microarray-based screening on two important human pathogens using two different approaches: (I) 75 human extracellular proteins were tested on 159 spotted Staphylococcus aureus recombinant proteins and (II) Neisseria meningitidis adhesin (NadA), an important vaccine component against serogroup B meningococcus, was screened against ≈2300 spotted human recombinant proteins. The approach presented here allowed the identification of the interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting; and of the interaction between meningococcal NadA and human LOX-1 (low-density oxidized lipoprotein receptor), an endothelial receptor. The novel interactions between bacterial and human extracellular proteins here presented might provide a better understanding of the molecular events underlying S. aureus and N. meningitidis pathogenesis.

  10. Microarray studies of genomic oxidative stress and cell cycle responses in obstructive sleep apnea.

    Science.gov (United States)

    Hoffmann, Michal S; Singh, Prachi; Wolk, Robert; Romero-Corral, Abel; Raghavakaimal, Sreekumar; Somers, Virend K

    2007-06-01

    Obstructive sleep apnea (OSA), the commonest form of sleep-disordered breathing, is characterized by recurrent episodes of intermittent hypoxia and sleep fragmentation. This study evaluated microarray measures of gene transcript levels in OSA subjects compared to age and BMI matched healthy controls. Measurements were obtained before and after: (a) a night of normal sleep in controls; and (b) a night of untreated apnea in OSA patients. All subjects underwent full polysomnography. mRNA from the whole blood samples was analyzed by HG-U133A and B Affymetrix GeneChip arrays using Spotfire 7.2 data analysis platform. After sleep in OSA patients, changes were noted in several genes involved in modulation of reactive oxygen species (ROS), including heme oxygenase 1, superoxide dismutase 1 and 2, and catalase. Changes were also observed in genes involved in cell growth, proliferation, and the cell cycle such as cell division cycle 25B, signaling lymphocyte activating molecule (SLAM), calgizzarin S100A11, B-cell translocation gene, Src-like adapter protein (SLAP), and eukaryotic translation initiation factor 4E binding protein 2. These overnight changes in OSA patients are suggestive of activation of several mechanisms to modulate, and adapt to, increased ROS developing in response to the frequent episodes of intermittent hypoxia.

  11. A three-dimensional waveguide structure as a support for genomic and proteomic microarrays

    Science.gov (United States)

    Dertinger, Stephan K.; Kluehr, Marco; Elsner, Christian A.; Sauermann, Alexander; Rueffer, Kristin; Nicklaus, Petra M.; Thein, Kerstin

    2004-12-01

    In this paper we present a three-dimensional waveguide structure with unique optical and fluidic properties and demonstrate its application as a substrate for DNA microarrays. The structure is fabricated by thermal oxidation of a macroporous silicon membrane with a periodic pattern of discrete pores running perpendicular through the substrate. Partial oxidation generates a SiO2 membrane, but leaves a rectangular grid of silicon walls dividing the membrane into compartments. We show that the SiO2 walls act as optical waveguides and characterize their optical properties; modes can be launched using Koehler illumination. The silicon walls optically isolate adjacent compartments and prevent light from spreading laterally in the membrane. In a DNA hybridization experiment, the detection of 100 attomol of a Cy-3 labeled DNA fragment (17 oligonucleotides) has been achieved with a signal to noise ratio of > 3:1. We believe that even lower detection limits can be achieved by further tuning the optical parameters of the three-dimensional waveguide structure.

  12. Exploring host-pathogen interactions through genome wide protein microarray analysis

    Science.gov (United States)

    Scietti, Luigi; Sampieri, Katia; Pinzuti, Irene; Bartolini, Erika; Benucci, Barbara; Liguori, Alessia; Haag, Andreas F.; Lo Surdo, Paola; Pansegrau, Werner; Nardi-Dei, Vincenzo; Santini, Laura; Arora, Seguinde; Leber, Xavier; Rindi, Simonetta; Savino, Silvana; Costantino, Paolo; Maione, Domenico; Merola, Marcello; Speziale, Pietro; Bottomley, Matthew J.; Bagnoli, Fabio; Masignani, Vega; Pizza, Mariagrazia; Scharenberg, Meike; Schlaeppi, Jean-Marc; Nissum, Mikkel; Liberatori, Sabrina

    2016-01-01

    During bacterial pathogenesis extensive contacts between the human and the bacterial extracellular proteomes take place. The identification of novel host-pathogen interactions by standard methods using a case-by-case approach is laborious and time consuming. To overcome this limitation, we took advantage of large libraries of human and bacterial recombinant proteins. We applied a large-scale protein microarray-based screening on two important human pathogens using two different approaches: (I) 75 human extracellular proteins were tested on 159 spotted Staphylococcus aureus recombinant proteins and (II) Neisseria meningitidis adhesin (NadA), an important vaccine component against serogroup B meningococcus, was screened against ≈2300 spotted human recombinant proteins. The approach presented here allowed the identification of the interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting; and of the interaction between meningococcal NadA and human LOX-1 (low-density oxidized lipoprotein receptor), an endothelial receptor. The novel interactions between bacterial and human extracellular proteins here presented might provide a better understanding of the molecular events underlying S. aureus and N. meningitidis pathogenesis. PMID:27302108

  13. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP

    2012-11-01

    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  14. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains

    OpenAIRE

    Salama, Nina; Guillemin, Karen; McDaniel, Timothy K.; Sherlock, Gavin; Tompkins, Lucy; Falkow, Stanley

    2000-01-01

    Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for these diverse clinical outcomes is not understood, more severe disease is associated with strains harboring a pathogenicity island. To characterize the genetic diversity of more and less virulent strains, we examined the genomic content of 15 H. pylori clinical isolate...

  15. Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

    Directory of Open Access Journals (Sweden)

    van Wieringen Wessel N

    2012-05-01

    Full Text Available Abstract Background An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrative analysis of genomic data. Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms. Results We describe, illustrate and discuss six matching procedures. They are implemented in the R-package sigaR (available from Bioconductor. The principles underlying the presented matching procedures are generic, and can be combined to form new matching approaches or be applied to the matching of other platforms. Illustration of the matching procedures on a variety of data sets reveals how the procedures differ in the use of the available data, and may even lead to different results for individual genes. Conclusions Matching of data from multiple genomics platforms is an important preprocessing step for many integrative bioinformatic analysis, for which we present six generic procedures, both old and new. They have been implemented in the R-package sigaR, available from Bioconductor.

  16. Rapid extraction of genomic DNA from saliva for HLA typing on microarray based on magnetic nanobeads

    Science.gov (United States)

    Xie, Xin; Zhang, Xu; Yu, Bingbin; Gao, Huafang; Zhang, Huan; Fei, Weiyang

    2004-09-01

    A series of simplified protocols are developed for extracting genomic DNA from saliva by using the magnetic nanobeads as absorbents. In these protocols, both the enrichment of the target cells and the adsorption of DNA can be achieved simultaneously by our functionally modified magnetic beads in one step, and the DNA-nanobeads complex can be used as PCR templates. HLA typing based on an oligonucleotide array was conducted by hybridization with the PCR products. The result shows that the protocols are robust and sensitive.

  17. Introduction to microarray technology.

    Science.gov (United States)

    Dufva, Martin

    2009-01-01

    DNA microarrays can be used for large number of application where high-throughput is needed. The ability to probe a sample for hundred to million different molecules at once has made DNA microarray one of the fastest growing techniques since its introduction about 15 years ago. Microarray technology can be used for large scale genotyping, gene expression profiling, comparative genomic hybridization and resequencing among other applications. Microarray technology is a complex mixture of numerous technology and research fields such as mechanics, microfabrication, chemistry, DNA behaviour, microfluidics, enzymology, optics and bioinformatics. This chapter will give an introduction to each five basic steps in microarray technology that includes fabrication, target preparation, hybridization, detection and data analysis. Basic concepts and nomenclature used in the field of microarray technology and their relationships will also be explained.

  18. In silico enhanced restriction enzyme based methylation analysis of the human glioblastoma genome using Agilent 244K CpG Island microarrays

    Directory of Open Access Journals (Sweden)

    Anh Tran

    2010-01-01

    Full Text Available Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive and MspI (methylation-insensitive restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC analysis to determine the optimal threshold (p ≤ 0.001. Based on this threshold, we identified ~2400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide more general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches.

  19. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

    Science.gov (United States)

    D’Ursi, Pasqualina; Milanesi, Luciano; Di Canito, Alessandra; Zampolli, Jessica; Collina, Elena; Decorosi, Francesca; Viti, Carlo; Fedi, Stefano; Presentato, Alessandro; Zannoni, Davide; Di Gennaro, Patrizia

    2015-01-01

    In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination

  20. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance.

    Science.gov (United States)

    Orro, Alessandro; Cappelletti, Martina; D'Ursi, Pasqualina; Milanesi, Luciano; Di Canito, Alessandra; Zampolli, Jessica; Collina, Elena; Decorosi, Francesca; Viti, Carlo; Fedi, Stefano; Presentato, Alessandro; Zannoni, Davide; Di Gennaro, Patrizia

    2015-01-01

    In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination

  1. Tilings in topological spaces

    Directory of Open Access Journals (Sweden)

    F. G. Arenas

    1999-01-01

    pairwise-disjoint interiors. Tilings of ℝ2 have received considerable attention (see [2] for a wealth of interesting examples and results as well as an extensive bibliography. On the other hand, the study of tilings of general topological spaces is just beginning (see [1, 3, 4, 6]. We give some generalizations for topological spaces of some results known for certain classes of tilings of topological vector spaces.

  2. Generalized quasiperiodic Rauzy tilings

    Science.gov (United States)

    Vidal, Julien; Mosseri, Rémy

    2001-05-01

    We present a geometrical description of new canonical d-dimensional codimension one quasiperiodic tilings based on generalized Fibonacci sequences. These tilings are made up of rhombi in 2d and rhombohedra in 3d as the usual Penrose and icosahedral tilings. Thanks to a natural indexing of the sites according to their local environment, we easily write down, for any approximant, the sites coordinates, the connectivity matrix and we compute the structure factor.

  3. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity.

    Science.gov (United States)

    Dorrell, N; Mangan, J A; Laing, K G; Hinds, J; Linton, D; Al-Ghusein, H; Barrell, B G; Parkhill, J; Stoker, N G; Karlyshev, A V; Butcher, P D; Wren, B W

    2001-10-01

    Campylobacter jejuni is the leading cause of bacterial food-borne diarrhoeal disease throughout the world, and yet is still a poorly understood pathogen. Whole genome microarray comparisons of 11 C. jejuni strains of diverse origin identified genes in up to 30 NCTC 11168 loci ranging from 0.7 to 18.7 kb that are either absent or highly divergent in these isolates. Many of these regions are associated with the biosynthesis of surface structures including flagella, lipo-oligosaccharide, and the newly identified capsule. Other strain-variable genes of known function include those responsible for iron acquisition, DNA restriction/modification, and sialylation. In fact, at least 21% of genes in the sequenced strain appear dispensable as they are absent or highly divergent in one or more of the isolates tested, thus defining 1300 C. jejuni core genes. Such core genes contribute mainly to metabolic, biosynthetic, cellular, and regulatory processes, but many virulence determinants are also conserved. Comparison of the capsule biosynthesis locus revealed conservation of all the genes in this region in strains with the same Penner serotype as strain NCTC 11168. By contrast, between 5 and 17 NCTC 11168 genes in this region are either absent or highly divergent in strains of a different serotype from the sequenced strain, providing further evidence that the capsule accounts for Penner serotype specificity. These studies reveal extensive genetic diversity among C. jejuni strains and pave the way toward identifying correlates of pathogenicity and developing improved epidemiological tools for this problematic pathogen.

  4. Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.

    Directory of Open Access Journals (Sweden)

    Christin Habig

    Full Text Available The Lohmann Selected Leghorn (LSL and Lohmann Brown (LB layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05 among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

  5. Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions

    Energy Technology Data Exchange (ETDEWEB)

    M.W. Fields; J.D. Wall; J. Keasling; J. Zhou

    2008-05-15

    We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a non-stretch probe (< 15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50mer probes or a 50-base stretch for 70mer probes had approximately 55% of the PM signal. Mismatches should be as close to the middle position of an oligonucleotide probe as possible to minimize cross-hybridization. Little cross-hybridization was observed for probes with a minimal binding free energy greater than -30 kcal/mol for 50mer probes or -40 kcal/mol for 70mer probes. Based on the

  6. Cyclotomic Aperiodic Substitution Tilings

    Directory of Open Access Journals (Sweden)

    Stefan Pautze

    2017-01-01

    Full Text Available The class of Cyclotomic Aperiodic Substitution Tilings (CASTs is introduced. Its vertices are supported on the 2 n -th cyclotomic field. It covers a wide range of known aperiodic substitution tilings of the plane with finite rotations. Substitution matrices and minimal inflation multipliers of CASTs are discussed as well as practical use cases to identify specimen with individual dihedral symmetry D n or D 2 n , i.e., the tiling contains an infinite number of patches of any size with dihedral symmetry D n or D 2 n only by iteration of substitution rules on a single tile.

  7. Preliminary report for analysis of genome wide mutations from four ciprofloxacin resistant B. anthracis Sterne isolates generated by Illumina, 454 sequencing and microarrays for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vergez, Lisa [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hinckley, Aubree [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ellingson, Sally [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hauser, Loren [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brettin, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fofanov, Viacheslav [Eureka Genomics, Hercules, CA (United States); Koshinsky, Heather [Eureka Genomics, Hercules, CA (United States); Fofanov, Yuriy [Univ. of Houston, TX (United States)

    2011-06-21

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzed the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.

  8. A predictive factor of the quality of microarray comparative genomic hybridization analysis for formalin-fixed paraffin-embedded archival tissue.

    Science.gov (United States)

    Nakao, Kenjiro; Oikawa, Masahiro; Arai, Junichi; Mussazhanova, Zhanna; Kondo, Hisayoshi; Shichijo, Kazuko; Nakashima, Masahiro; Hayashi, Tomayoshi; Yoshiura, Koh-Ichiro; Hatachi, Toshiko; Nagayasu, Takeshi

    2013-09-01

    Utilizing formalin-fixed paraffin-embedded (FFPE) archival tissue, the most common form of tissue preservation in routine practice, for cytogenetic analysis using microarray comparative genomic hybridization (aCGH) remains challenging. We searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types (31 breast cancers, 24 lung cancers, and 8 thyroid tumors), followed by aCGH analysis using high-density oligonucleotide microarrays. Tumor DNA from matched frozen samples and from FFPE samples after whole-genome amplification were also analyzed in 2 and 4 case, respectively. The derivative log ratio spread (DLRSpread) was used to assess the overall quality of each aCGH result. The DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5 (Parchival tissue samples can be utilized for aCGH analysis.

  9. Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

    Directory of Open Access Journals (Sweden)

    Zamboni Anita

    2012-03-01

    Full Text Available Abstract Background Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far. Results A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism. Conclusions The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

  10. Wang Tiles in Computer Graphics

    CERN Document Server

    Lagae, Ares

    2009-01-01

    Many complex signals in computer graphics, such as point distributions and textures, cannot be efficiently synthesized and stored. This book presents tile-based methods based on Wang tiles and corner tiles to solve both these problems. Instead of synthesizing a complex signal when needed, the signal is synthesized beforehand over a small set of Wang tiles or corner tiles. Arbitrary large amounts of that signal can then efficiently be generated when needed by generating a stochastic tiling, and storing only a small set of tiles reduces storage requirements. A tile-based method for generating a

  11. The tile assembly model is intrinsically universal

    CERN Document Server

    Doty, David; Patitz, Matthew J; Schweller, Robert T; Summers, Scott M; Woods, Damien

    2011-01-01

    We prove that the abstract Tile Assembly Model (aTAM) of nanoscale self-assembly is intrinsically universal. This means that there is a single tile assembly system U that, with proper initialization, simulates any tile assembly system T. The simulation is "intrinsic" in the sense that the self-assembly process carried out by U is exactly that carried out by T, with each tile of T represented by an m x m "supertile" of U. Our construction works for the full aTAM at any temperature, and it faithfully simulates the deterministic or nondeterministic behavior of each T. Our construction succeeds by solving an analog of the cell differentiation problem in developmental biology: Each supertile of U, starting with those in the seed assembly, carries the "genome" of the simulated system T. At each location of a potential supertile in the self-assembly of U, a decision is made whether and how to express this genome, i.e., whether to generate a supertile and, if so, which tile of T it will represent. This decision must ...

  12. Microarray based comparative genomic hybridization testing in deletion bearing patients with Angelman syndrome: genotype-phenotype correlations.

    Science.gov (United States)

    Sahoo, T; Peters, S U; Madduri, N S; Glaze, D G; German, J R; Bird, L M; Barbieri-Welge, R; Bichell, T J; Beaudet, A L; Bacino, C A

    2006-06-01

    Angelman syndrome (AS) is a neurodevelopmental disorder characterised by severe mental retardation, dysmorphic features, ataxia, seizures, and typical behavioural characteristics, including a happy sociable disposition. AS is caused by maternal deficiency of UBE3A (E6 associated protein ubiquitin protein ligase 3A gene), located in an imprinted region on chromosome 15q11-q13. Although there are four different molecular types of AS, deletions of the 15q11-q13 region account for approximately 70% of the AS patients. These deletions are usually detected by fluorescence in situ hybridisation studies. The deletions can also be subclassified based on their size into class I and class II, with the former being larger and encompassing the latter. We studied 22 patients with AS due to microdeletions using a microarray based comparative genomic hybridisation (array CGH) assay to define the deletions and analysed their phenotypic severity, especially expression of the autism phenotype, in order to establish clinical correlations. Overall, children with larger, class I deletions were significantly more likely to meet criteria for autism, had lower cognitive scores, and lower expressive language scores compared with children with smaller, class II deletions. Children with class I deletions also required more medications to control their seizures than did those in the class II group. There are four known genes (NIPA1, NIPA2, CYFIP1, & GCP5) that are affected by class I but not class II deletions, thus raising the possibility of a role for these genes in autism as well as the development of expressive language skills.

  13. Cancer immunotherapy using novel tumor-associated antigenic peptides identified by genome-wide cDNA microarray analyses.

    Science.gov (United States)

    Nishimura, Yasuharu; Tomita, Yusuke; Yuno, Akira; Yoshitake, Yoshihiro; Shinohara, Masanori

    2015-05-01

    Recent genome-wide cDNA microarray analysis of gene expression profiles in comprehensive tumor types coupled with isolation of cancer tissues by laser-microbeam microdissection have revealed ideal tumor-associated antigens (TAAs) that are frequently overexpressed in various cancers including head and neck squamous cell cancer (HNSCC) and lung cancer, but not in most normal tissues except for testis, placenta, and fetal organs. Preclinical studies using HLA-transgenic mice and human T cells in vitro showed that TAA-derived CTL-epitope short peptides (SPs) are highly immunogenic and induce HLA-A2 or -A24-restricted CTLs. Based on the accumulated evidence, we carried out a phase II clinical trial of the TAA-SP vaccine in advanced 37 HNSCC patients. This study showed a significant induction of TAA-specific CTLs in the majority of patients without serious adverse effects. Importantly, clinical responses including a complete response were observed in this study. Another phase II clinical trial of therapeutic TAA-SP vaccine, designed to evaluate the ability of prevention of recurrence, is ongoing in HNSCC patients who have received curative operations. Further studies in human preclinical studies and in vivo studies using HLA class I transgenic mice showed TAA-derived long peptides (TAA-LPs) have the capacity to induce not only promiscuous HLA class II-restricted CD4(+) T helper type 1 cells but also tumor-specific CTLs through a cross-presentation mechanism. Moreover, we observed an augmentation of TAA-LP-specific T helper type 1 cell responses and tumor antigen-spreading in HNSCC patients vaccinated with TAA-SPs. This accumulated evidence suggests that therapeutic TAA-SPs and LPs vaccines may provide a promising cancer immunotherapy.

  14. Carbon ion irradiation of the human prostate cancer cell line PC3: a whole genome microarray study.

    Science.gov (United States)

    Suetens, Annelies; Moreels, Marjan; Quintens, Roel; Chiriotti, Sabina; Tabury, Kevin; Michaux, Arlette; Grégoire, Vincent; Baatout, Sarah

    2014-04-01

    Hadrontherapy is a form of external radiation therapy, which uses beams of charged particles such as carbon ions. Compared to conventional radiotherapy with photons, the main advantage of carbon ion therapy is the precise dose localization along with an increased biological effectiveness. The first results obtained from prostate cancer patients treated with carbon ion therapy showed good local tumor control and survival rates. In view of this advanced treatment modality we investigated the effects of irradiation with different beam qualities on gene expression changes in the PC3 prostate adenocarcinoma cell line. For this purpose, PC3 cells were irradiated with various doses (0.0, 0.5 and 2.0 Gy) of carbon ions (LET=33.7 keV/µm) at the beam of the Grand Accélérateur National d'Ions Lourds (Caen, France). Comparative experiments with X-rays were performed at the Belgian Nuclear Research Centre. Genome-wide gene expression was analyzed using microarrays. Our results show a downregulation in many genes involved in cell cycle and cell organization processes after 2.0 Gy irradiation. This effect was more pronounced after carbon ion irradiation compared with X-rays. Furthermore, we found a significant downregulation of many genes related to cell motility. Several of these changes were confirmed using qPCR. In addition, recurrence-free survival analysis of prostate cancer patients based on one of these motility genes (FN1) revealed that patients with low expression levels had a prolonged recurrence-free survival time, indicating that this gene may be a potential prognostic biomarker for prostate cancer. Understanding how different radiation qualities affect the cellular behavior of prostate cancer cells is important to improve the clinical outcome of cancer radiation therapy.

  15. Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients

    DEFF Research Database (Denmark)

    Győrffy, Balázs; Lánczky, András; Szállási, Zoltán

    2012-01-01

    The validation of prognostic biomarkers in large independent patient cohorts is a major bottleneck in ovarian cancer research. We implemented an online tool to assess the prognostic value of the expression levels of all microarray-quantified genes in ovarian cancer patients. First, a database was...... biomarker validation platform that mines all available microarray data to assess the prognostic power of 22 277 genes in 1287 ovarian cancer patients. We specifically used this tool to evaluate the effect of 37 previously published biomarkers on ovarian cancer prognosis.......The validation of prognostic biomarkers in large independent patient cohorts is a major bottleneck in ovarian cancer research. We implemented an online tool to assess the prognostic value of the expression levels of all microarray-quantified genes in ovarian cancer patients. First, a database...... was set up using gene expression data and survival information of 1287 ovarian cancer patients downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (Affymetrix HG-U133A, HG-U133A 2.0, and HG-U133 Plus 2.0 microarrays). After quality control and normalization, only probes present on all...

  16. Two recombinant human interferon-beta 1a pharmaceutical preparations produce a similar transcriptional response determined using whole genome microarray analysis.

    Science.gov (United States)

    Prync, A E Sterin; Yankilevich, P; Barrero, P R; Bello, R; Marangunich, L; Vidal, A; Criscuolo, M; Benasayag, L; Famulari, A L; Domínguez, R O; Kauffman, M A; Diez, R A

    2008-02-01

    Recombinant human interferon-beta (IFN-b) is a well-established treatment for multiple sclerosis (MS). The regulatory process for marketing authorization of biosimilars is currently under debate in certain countries. In the EU, EMEA has clearly defined the process including overarching and product-specific guidelines, which includes clinical testing. Biosimilarity needs to be based on comparability criteria, including at least molecular characterization, biological activity relevant for the therapeutic effect and relative bioavailability ("bioequivalence"). In the case of such complex diseases as MS, where the effect of treatment is not so directly measurable, in vitro tools can provide additional data to support comparability. Genomic microarrays assays might be useful to compare multisource biopharmaceuticals. The aim of the present study was to compare the pharmacodynamic genomic effects (in terms of transcriptional regulation) of two recombinant human IFN-I(2)1a preparations on lymphocytes of multiple sclerosis patients using a whole genome microarray assay. We performed an ex vivo whole genome expression profiling of the effect of two preparations of IFN-I(2)1a on non-adherent mononuclears from five relapsing-remitting MS patients analyzing microarrays (CodeLink Human Whole Genome). Patients blood was drawn, PBMCs isolated and cultured in three different conditions: culture medium (control), 1,000 U/ml of IFN-I(2)1a (BLA- (STOFERON, Bio Sidus) and 1,000 U/ml of IFN-I(2)1a (REBIF, Serono) RNA was purified from non-adherent cells (mostly lymphocytes), amplified and hybridized. Raw data were generated by CodeLink proprietary software. Data normalization, quality control and analysis of differential gene expression between treatments were done using linear model for microarray data. Functional annotation analysis of IFN-I(2)1a MS treatment transcription was done using DAVID. Out of the approximately 45,000 human sequences examined, no evidence of differential

  17. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao

    2011-01-01

    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  18. Microarray Applications in Cancer Research

    Science.gov (United States)

    Kim, Il-Jin; Kang, Hio Chung

    2004-01-01

    DNA microarray technology permits simultaneous analysis of thousands of DNA sequences for genomic research and diagnostics applications. Microarray technology represents the most recent and exciting advance in the application of hybridization-based technology for biological sciences analysis. This review focuses on the classification (oligonucleotide vs. cDNA) and application (mutation-genotyping vs. gene expression) of microarrays. Oligonucleotide microarrays can be used both in mutation-genotyping and gene expression analysis, while cDNA microarrays can only be used in gene expression analysis. We review microarray mutation analysis, including examining the use of three oligonucleotide microarrays developed in our laboratory to determine mutations in RET, β-catenin and K-ras genes. We also discuss the use of the Affymetrix GeneChip in mutation analysis. We review microarray gene expression analysis, including the classifying of such studies into four categories: class comparison, class prediction, class discovery and identification of biomarkers. PMID:20368836

  19. Binary Non-tiles

    CERN Document Server

    Coppersmith, Don

    2009-01-01

    A subset V of GF(2)^n is a tile if GF(2)^n can be covered by disjoint translates of V. In other words, V is a tile if and only if there is a subset A of GF(2)^n such that V+A = GF(2)^n uniquely (i.e., v + a = v' + a' implies that v=v' and a=a' where v,v' in V and a,a' in A). In some problems in coding theory and hashing we are given a putative tile V, and wish to know whether or not it is a tile. In this paper we give two computational criteria for certifying that V is not a tile. The first involves impossibility of a bin-packing problem, and the second involves infeasibility of a linear program. We apply both criteria to a list of putative tiles given by Gordon, Miller, and Ostapenko in that none of them are, in fact, tiles.

  20. Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray generated from the shotgun libraries previously used in the sequencing of this bacterial genome

    Directory of Open Access Journals (Sweden)

    Zaini Paulo A

    2010-05-01

    Full Text Available Abstract Background From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC, clones that were representative of the largest possible number of coding sequences (CDSs were selected to create a DNA microarray platform on glass slides (XACarray. The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

  1. Distances on Lozenge Tilings

    CERN Document Server

    Bodini, Olivier; Fernique, Thomas

    2009-01-01

    In this paper, a structural property of the set of lozenge tilings of a 2n-gon is highlighted. We introduce a simple combinatorial value called Hamming-distance, which is a lower bound for the flipdistance (i.e. the number of necessary local transformations involving three lozenges) between two given tilings. It is here proven that, for n5, We show that there is some deficient pairs of tilings for which the flip connection needs more flips than the combinatorial lower bound indicates.

  2. Self-assembled random arrays: high-performance imaging and genomics applications on a high-density microarray platform

    Science.gov (United States)

    Barker, David L.; Theriault, Greg; Che, Diping; Dickinson, Todd; Shen, Richard; Kain, Robert C.

    2003-07-01

    Illumina is developing a BeadArrayTM technology that supports SNP genotyping, mRNA expression analysis and protein expression analysis on the same platform. We use fiber-optic bundles with a density of approximately 40,000 fibers/mm2. At hte end of each fiber, a derivatized silica bead forms an array element for reading out a genotyping or expression assay data point. Each bead contains oligonucleotide probes that hybridize with high specificity to complementary sequences in a complex nucleic acid mixture. We derivatize the beads in bulk, pool them to form a quality-controlled source of microarray elements, and allow them to assemble spontaneously into pits etched into the end of each optical fiber bundle. We load our fiber bundles, containing 49,777 fibers, with up to 1520 different bead types. The presence of many beads of each type greatly improves the accuracy of each assay. As the final step in our manufacturing process, we decode the identity of each bead by a series of rapid hybridizations with fluroescent oligos. Decoding accuracy and the number of beads of each type is recorded for each array. Decoding also serves as a quality control procedure for the performance of each element in the array. To facilitate high-throughput analysis of many samples, the fiber bundles are arranged in an array matrix (SentrixTM arrays). Using a 96-bundle array matrix, up to 1520 assays can be performed on each of 96 samples simultaneously for a total of 145,920 assays. Using a 384-bundle array matrix, up to 583,680 assays can be performed simultaneously. The BeadArray platform is the highest density microarray in commercial use, requiring development of a high-performance array scanner. To meet this need, we developed the SherlockTM system, a laser-scanning confocal imaging system that automatically scans all 96 bundles of an array matrix at variable resolution down to 0.8 micron. The system scans with both 532 and 635 nm lasers simultaneously, collecting two fluorescence

  3. Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance.

    Directory of Open Access Journals (Sweden)

    Alessandro Orro

    Full Text Available In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and

  4. Crosslinking in viral capsids via tiling theory.

    Science.gov (United States)

    Twarock, R; Hendrix, R W

    2006-06-07

    A vital part of a virus is its protein shell, called the viral capsid, that encapsulates and hence protects the viral genome. It has been shown in Twarock [2004. A tiling approach to vius capsids assembly explaining a structural puzzle in virology. J. Theor. Biol. 226, 477-482] that the surface structures of viruses with icosahedrally symmetric capsids can be modelled in terms of tilings that encode the locations of the protein subunits. This theory is extended here to multi-level tilings in order to model crosslinking structures. The new framework is demonstrated for the case of bacteriophage HK97, and it is shown, how the theory can be used in general to decide if crosslinking, and what type of crosslinking, is compatible from a mathematical point of view with the geometrical surface structure of a virus.

  5. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola;

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technol...

  6. Tiled Multicore Processors

    Science.gov (United States)

    Taylor, Michael B.; Lee, Walter; Miller, Jason E.; Wentzlaff, David; Bratt, Ian; Greenwald, Ben; Hoffmann, Henry; Johnson, Paul R.; Kim, Jason S.; Psota, James; Saraf, Arvind; Shnidman, Nathan; Strumpen, Volker; Frank, Matthew I.; Amarasinghe, Saman; Agarwal, Anant

    For the last few decades Moore’s Law has continually provided exponential growth in the number of transistors on a single chip. This chapter describes a class of architectures, called tiled multicore architectures, that are designed to exploit massive quantities of on-chip resources in an efficient, scalable manner. Tiled multicore architectures combine each processor core with a switch to create a modular element called a tile. Tiles are replicated on a chip as needed to create multicores with any number of tiles. The Raw processor, a pioneering example of a tiled multicore processor, is examined in detail to explain the philosophy, design, and strengths of such architectures. Raw addresses the challenge of building a general-purpose architecture that performs well on a larger class of stream and embedded computing applications than existing microprocessors, while still running existing ILP-based sequential programs with reasonable performance. Central to achieving this goal is Raw’s ability to exploit all forms of parallelism, including ILP, DLP, TLP, and Stream parallelism. Raw approaches this challenge by implementing plenty of on-chip resources - including logic, wires, and pins - in a tiled arrangement, and exposing them through a new ISA, so that the software can take advantage of these resources for parallel applications. Compared to a traditional superscalar processor, Raw performs within a factor of 2x for sequential applications with a very low degree of ILP, about 2x-9x better for higher levels of ILP, and 10x-100x better when highly parallel applications are coded in a stream language or optimized by hand.

  7. Different responsiveness to a high-fat/cholesterol diet in two inbred mice and underlying genetic factors: a whole genome microarray analysis

    Directory of Open Access Journals (Sweden)

    Jin Gang

    2009-10-01

    Full Text Available Abstract Background To investigate different responses to a high-fat/cholesterol diet and uncover their underlying genetic factors between C57BL/6J (B6 and DBA/2J (D2 inbred mice. Methods B6 and D2 mice were fed a high-fat/cholesterol diet for a series of time-points. Serum and bile lipid profiles, bile acid yields, hepatic apoptosis, gallstones and atherosclerosis formation were measured. Furthermore, a whole genome microarray was performed to screen hepatic genes expression profile. Quantitative real-time PCR, western blot and TUNEL assay were conducted to validate microarray data. Results After fed the high-fat/cholesterol diet, serum and bile total cholesterol, serum cholesterol esters, HDL cholesterol and Non-HDL cholesterol levels were altered in B6 but not significantly changed in D2; meanwhile, biliary bile acid was decreased in B6 but increased in D2. At the same time, hepatic apoptosis, gallstones and atherosclerotic lesions occurred in B6 but not in D2. The hepatic microarray analysis revealed distinctly different genes expression patterns between B6 and D2 mice. Their functional pathway groups included lipid metabolism, oxidative stress, immune/inflammation response and apoptosis. Quantitative real time PCR, TUNEL assay and western-blot results were consistent with microarray analysis. Conclusion Different genes expression patterns between B6 and D2 mice might provide a genetic basis for their distinctive responses to a high-fat/cholesterol diet, and give us an opportunity to identify novel pharmaceutical targets in related diseases in the future.

  8. Tiling Lattices with Sublattices, II

    CERN Document Server

    Feldman, David; Robins, Sinai

    2010-01-01

    Our earlier article proved that if $n > 1$ translates of sublattices of $Z^d$ tile $Z^d$, and all the sublattices are Cartesian products of arithmetic progressions, then two of the tiles must be translates of each other. We re-prove this Theorem, this time using generating functions. We also show that for $d > 1$, not every finite tiling of $Z^d$ by lattices can be obtained from the trivial tiling by the process of repeatedly subdividing a tile into sub-tiles that are translates of one another.

  9. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis: EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Directory of Open Access Journals (Sweden)

    Planas Josep V

    2008-10-01

    Full Text Available Abstract Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis, larval stages (pre-metamorphosis, metamorphosis, juvenile stages (post-metamorphosis, abnormal fish, and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs. Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34% had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.

  10. Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

    Science.gov (United States)

    Cerdà, Joan; Mercadé, Jaume; Lozano, Juan José; Manchado, Manuel; Tingaud-Sequeira, Angèle; Astola, Antonio; Infante, Carlos; Halm, Silke; Viñas, Jordi; Castellana, Barbara; Asensio, Esther; Cañavate, Pedro; Martínez-Rodríguez, Gonzalo; Piferrer, Francesc; Planas, Josep V; Prat, Francesc; Yúfera, Manuel; Durany, Olga; Subirada, Francesc; Rosell, Elisabet; Maes, Tamara

    2008-01-01

    Background The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. Results Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. Conclusion New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions. PMID:18973667

  11. Maize microarray annotation database

    Directory of Open Access Journals (Sweden)

    Berger Dave K

    2011-10-01

    Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to

  12. Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA – a Bayesian approach

    Directory of Open Access Journals (Sweden)

    Pin Carmen

    2007-11-01

    Full Text Available Abstract Background Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge. Results A computing tool (ArrayLeaRNA has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19, a published Bayesian approach also using predicted operon structure. The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements. ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at http://www.ifr.ac.uk/safety/ArrayLeaRNA/ Conclusion We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where

  13. Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.

    Directory of Open Access Journals (Sweden)

    Joseph Andrews

    Full Text Available BACKGROUND: We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis. METHODOLOGY/PRINCIPAL FINDINGS: We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model using Affymetrix gene expression (U133, promoter (1.0R, and SNP/CNV (SNP 6.0 microarray platforms to correlate data from gene expression, epigenetic (DNA methylation, and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo methylation with the loss (or gain of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis. CONCLUSIONS/SIGNIFICANCE: Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer

  14. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  15. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    -based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research.......In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...

  16. Genome Array on Differentially Expressed Genes of Skin Tissue in Cashmere Goat at Early Anagen of Cashmere Growth Cycle Using DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    DI Jiang; Marzeya Yasen; XU Xin-ming; Lazate Ainiwaer; ZHANG Yan-hua; TIAN Ke-chuan; YU Li-juan; WU Wei-wei; Hanikezi Tulafu; FU Xue-feng

    2014-01-01

    In order to study the molecular mechanism involved in cashmere regeneration, this study investigated the gene expression proifle of skin tissue at various stages of the cashmere growth cycle and screen differentially expressed genes at proangen in 10 cashmere goats at 2 years of age using agilent sheep oligo microarray. Signiifcance analysis of microarray (SAM) methods was used to identify the differentially expressed genes, Hierarchical clustering was performed to clarify these genes in association with different cashmere growth stages, and GO (Gene ontology) and the pathway analyses were con-ducted by a free web-based Molecular Annotation System3.0 (MAS 3.0). Approximately 10 200 probe sets were detected in skin tissue of 2-yr-old cashmere goat. After SAM analysis of the microarray data, totally 417 genes were shown to be differentially expressed at different cashmere growth stages, and 24 genes are signiifcantly up-regulated (21) or down-regulated (3) at proangen concurrently compared to angen and telogen. Hierarchical clustering analysis clearly distinguished the differentially expressed genes of each stage. GO analysis indicated that these altered genes at proangen were predominantly involved in collagen ifbril organization, integrin-mediated signaling pathway, cell-matrix adhesion, cell adhesion, transforming growth factor-β (TGF-β) receptor signaling pathway, regulation of cell growth. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that the signiifcant pathways involved mainly included focal adhesion and extracellular matrixc (ECM)-receptor interaction. Some important genes involved in these biological processes, such as COL1A1, COL1A2, COL3A1, SPARC, CYR61 and CTGF, were related to tissue remolding and repairing and detected by more than one probe with similar expression trends at different stages of cashmere growth cycle. The different expression of these genes may contribute to understanding the molecular mechanism of cashmere

  17. Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

    Directory of Open Access Journals (Sweden)

    Thijs Inge M

    2010-01-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of regulatory RNA elements have been predicted by computational methods, mostly in well-studied γ-proteobacteria but lately in several α-proteobacteria as well. Here, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a whole-genome high-resolution tiling array in the soil-dwelling α-proteobacterium Rhizobium etli. Results Expression of 89 candidate ncRNAs was detected, both on the chromosome and on the six megaplasmids encompassing the R. etli genome. Of these, 11 correspond to functionally well characterized ncRNAs, 12 were previously identified in other α-proteobacteria but are as yet uncharacterized and 66 were computationally predicted earlier but had not been experimentally identified and were therefore classified as novel ncRNAs. The latter comprise 17 putative sRNAs and 49 putative cis-regulatory ncRNAs. A selection of these candidate ncRNAs was validated by RT-qPCR, Northern blotting and 5' RACE, confirming the existence of 4 ncRNAs. Interestingly, individual transcript levels of numerous ncRNAs varied during free-living growth and during interaction with the eukaryotic host plant, pointing to possible ncRNA-dependent regulation of these specialized processes. Conclusions Our data support the practical value of previous ncRNA prediction algorithms and significantly expand the list of candidate ncRNAs encoded in the intergenic regions of R. etli and, by extension, of α-proteobacteria. Moreover, we show high-resolution tiling arrays to be suitable tools for studying intergenic ncRNA transcription profiles across the genome. The differential expression levels of some of these ncRNAs may indicate a role in adaptation to changing environmental conditions.

  18. Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.

    Science.gov (United States)

    Pardo, Belén G; Álvarez-Dios, José Antonio; Cao, Asunción; Ramilo, Andrea; Gómez-Tato, Antonio; Planas, Josep V; Villalba, Antonio; Martínez, Paulino

    2016-12-01

    The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in

  19. Genomic comparison of Yersinia pestis and Yersinia pseudotuberculosis by combination of suppression subtractive hybridization and DNA microarray

    DEFF Research Database (Denmark)

    Wang, Xiaoyi; Zhou, Dongsheng; Qin, Long

    2006-01-01

    a combination of suppression subtractive hybridization (SSH) and comparative genomic hybridization with DNAs from a diverse panel of Y. pestis and Y. pseudotuberculosis strains. SSH followed by BLAST analysis revealed 112 SSH fragments specific to strain ATCC29833, compared to the genomic sequence data of Y...

  20. Fixed Point and Aperiodic Tilings

    CERN Document Server

    Durand, Bruno; Shen, Alexander

    2008-01-01

    An aperiodic tile set was first constructed by R.Berger while proving the undecidability of the domino problem. It turned out that aperiodic tile sets appear in many topics ranging from logic (the Entscheidungsproblem) to physics (quasicrystals) We present a new construction of an aperiodic tile set that is based on Kleene's fixed-point construction instead of geometric arguments. This construction is similar to J. von Neumann self-reproducing automata; similar ideas were also used by P. Gacs in the context of error-correcting computations. The flexibility of this construction allows us to construct a ``robust'' aperiodic tile set that does not have periodic (or close to periodic) tilings even if we allow some (sparse enough) tiling errors. This property was not known for any of the existing aperiodic tile sets.

  1. Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements

    Indian Academy of Sciences (India)

    Jun Ge; Zheng Lou; Hong Cui; Lei Shang; Rasika M Harshey

    2011-09-01

    Of all known transposable elements, phage Mu exhibits the highest transposition efficiency and the lowest target specificity. In vitro, MuB protein is responsible for target choice. In this work, we provide a comprehensive assessment of the genome-wide distribution of MuB and its relationship to Mu target selection using high-resolution Escherichia coli tiling DNA arrays. We have also assessed how MuB binding and Mu transposition are influenced by chromosome-organizing elements such as AT-rich DNA signatures, or the binding of the nucleoid-associated protein Fis, or processes such as transcription. The results confirm and extend previous biochemical and lower resolution in vivo data. Despite the generally random nature of Mu transposition and MuB binding, there were hot and cold insertion sites and MuB binding sites in the genome, and differences between the hottest and coldest sites were large. The new data also suggest that MuB distribution and subsequent Mu integration is responsive to DNA sequences that contribute to the structural organization of the chromosome.

  2. Genome-wide expression profiling of the response to terbinafine in Candida albicans using a cDNA microarray analysis

    Institute of Scientific and Technical Information of China (English)

    ZENG Yue-bin; QIAN Yuan-shu; MA Lian; GU Hong-ni

    2007-01-01

    Background Candida albicans is the most frequently seen opportunistic human fungal pathogen. Terbinafine is an allylamine antifungal agent that has been proven to have high clinical efficacy in the therapy of fungal infections, the mechanism of action of terbinafine involves the specific inhibition of fungal squalene epoxidase, resulting in ergosterol deficiency and accumulation of intracellular squalene. We used cDNA microarray analysis technology to monitor global expression profile changes of Candida albicans genes in response to terbinafine treatment, and we anticipated a panoramic view of the responses of Candida albicans cells to the representatives of allylamine antifungal agents at the molecular level in an effort to identify drug class-specific and mechanism-independent changes in gene expression.Methods Candida albicans strain ATCC 90028 was exposed to either medium alone or terbinafine at a concentration equivalent to the 1/2 minimal inhibitory concentrations (MICs, 4 mg/L) for 90 minutes. RNA was isolated and gene expression profiles were compared to identify the changes in the gene expression profile using a cDNA microarray analysis. Differential expression of 10 select genes detected by cDNA microarray analysis was confirmed by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR).Results A total of 222 genes were found to be responsive to terbinafine, including 121 up-regulated genes and 101 down-regulated genes. These included genes encoding membrane transport proteins belonging to the members of the ATP-binding cassette (ABC) or major facilitator superfamily (MFS; CDR1, AGP2, GAP6, PHO84, HOL3, FCY23, VCX1),genes involved in stress response and detoxification (CDR1, AGP2, HOL3), and gene involved in the ergosterol biosynthesis pathway (ERG12). The results of semi-quantitative RT-PCR were consistent with that of the cDNA microarray analysis.Conclusions The up-regulation of the gene encoding the multidrug resistance efflux pump

  3. Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

    Directory of Open Access Journals (Sweden)

    van Hijum Sacha AFT

    2008-10-01

    Full Text Available Abstract Background Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes. Results We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for 11 prokaryotic organisms on a dedicated website. Conclusion The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.

  4. Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility

    Directory of Open Access Journals (Sweden)

    Qiongqiong eYan

    2013-09-01

    Full Text Available Outbreaks of human infection linked to the powdered infant formula (PIF food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC], pSP291-2, [52.1-kb (49.2% GC] and pSP291-3, [4.4 -kb (54.0% GC]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM, we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.

  5. Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility.

    Science.gov (United States)

    Yan, Qiongqiong; Power, Karen A; Cooney, Shane; Fox, Edward; Gopinath, Gopal R; Grim, Christopher J; Tall, Ben D; McCusker, Matthew P; Fanning, Séamus

    2013-01-01

    Outbreaks of human infection linked to the powdered infant formula (PIF) food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC) and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC)], pSP291-2, [52.1-kb (49.2% GC)], and pSP291-3, [4.4-kb (54.0% GC)]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM), we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.

  6. Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray

    Directory of Open Access Journals (Sweden)

    Rempei Yanagawa

    2001-01-01

    Full Text Available In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions.

  7. Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays.

    Science.gov (United States)

    Liu, Weiqiang; Zhang, Rui; Wei, Jun; Zhang, Huimin; Yu, Guojiu; Li, Zhihua; Chen, Min; Sun, Xiaofang

    2015-01-01

    Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD.

  8. Self Cleanable Tile Grout

    Directory of Open Access Journals (Sweden)

    Mehmet CANBAZ

    2016-03-01

    Full Text Available In this study, In this study, self-cleaning tile grout and white cement specimens are produced and the effect of self-cleaning mechanism of TiO2 is tested. Effects of TiO2 amount and TiO2 type are tested and compared. Anatase form and rutile TiO2 additive are used in the study. In addition, effects of silicate additives on the self-cleaning mechanism is determined. Studies are conducted with respect to Italian UNI code. This study presents a method for solving rust between the tiles of ceramic wet floor coverings with photocatalysis method and then removing the dirt with secondary effects such as water, wind etc.

  9. Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi

    National Research Council Canada - National Science Library

    Atanasova, Lea; Druzhinina, Irina S

    2010-01-01

    .... They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available...

  10. Producing superhydrophobic roof tiles

    Science.gov (United States)

    Carrascosa, Luis A. M.; Facio, Dario S.; Mosquera, Maria J.

    2016-03-01

    Superhydrophobic materials can find promising applications in the field of building. However, their application has been very limited because the synthesis routes involve tedious processes, preventing large-scale application. A second drawback is related to their short-term life under outdoor conditions. A simple and low-cost synthesis route for producing superhydrophobic surfaces on building materials is developed and their effectiveness and their durability on clay roof tiles are evaluated. Specifically, an organic-inorganic hybrid gel containing silica nanoparticles is produced. The nanoparticles create a densely packed coating on the roof tile surface in which air is trapped. This roughness produces a Cassie-Baxter regime, promoting superhydrophobicity. A surfactant, n-octylamine, was also added to the starting sol to catalyze the sol-gel process and to coarsen the pore structure of the gel network, preventing cracking. The application of ultrasound obviates the need to use volatile organic compounds in the synthesis, thereby making a ‘green’ product. It was also demonstrated that a co-condensation process effective between the organic and inorganic species is crucial to obtain durable and effective coatings. After an aging test, high hydrophobicity was maintained and water absorption was completely prevented for the roof tile samples under study. However, a transition from a Cassie-Baxter to a Wenzel state regime was observed as a consequence of the increase in the distance between the roughness pitches produced by the aging of the coating.

  11. Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness.

    Science.gov (United States)

    Hamed, Mohamed; Nitsche-Schmitz, Daniel Patric; Ruffing, Ulla; Steglich, Matthias; Dordel, Janina; Nguyen, Duy; Brink, Jan-Hendrik; Chhatwal, Gursharan Singh; Herrmann, Mathias; Nübel, Ulrich; Helms, Volkhard; von Müller, Lutz

    2015-12-01

    Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims to distinguish invasive (blood stream infection) and non-invasive (nasal colonization) MRSA isolates of the same CC5 into phylogenetic- and virulence-associated genotypic subgroups by WGS and MA. A cohort of twelve blood stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and t504) was selected. Isolates were propagated at the same period of time from unrelated patients treated at the University of Saarland Medical Center, Germany. Rooted phylotyping based on WGS with core-genome single nucleotide polymorphism (SNP) analysis revealed two local clusters of closely related CC5 subgroups (t504 and Clade1 t003) which were separated from other local t003 isolates and from unrelated CC5 MRSA reference isolates of German origin. Phylogenetic subtyping was not associated with invasiveness when comparing blood stream and nasal isolates. Clustering based on MA profiles was not concordant with WGS phylotyping, but MA profiles may identify subgroups of isolates with nasal and blood stream origin. Among the new putative virulence associated genes identified by WGS, the strongest association with blood stream infections was shown for ebhB mutants. Analysis of the core-genome together with the accessory genome enables subtyping of closely related MRSA isolates according to phylogeny and presumably also to the potential virulence capacity of isolates.

  12. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Wayne E Clarke

    Full Text Available Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38. The main goal of this project was to combine sequence capture with next generation sequencing (NGS to discover single nucleotide polymorphisms (SNPs in specific areas of the B. napus genome historically associated (via quantitative trait loci -QTL- analysis to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively. Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.

  13. Investigation of archived formalin-fixed paraffin-embedded pancreatic tissue with whole-genome gene expression microarray

    DEFF Research Database (Denmark)

    Michelsen, Nete Vinstrup; Brusgaard, Klaus; Tan, Qihua

    2011-01-01

    high amounts of ribonucleases compared to other tissues/organs. In choosing pancreatic tissue, we therefore indirectly address the applicability of other FFPE tissues to gene expression microarray (GEM). GEM was performed on archived, routinely fixed, FFPE pancreatic tissue from patients......The use of formalin-fixed, paraffin-embedded (FFPE) tissue overcomes the most prominent issues related to research on relatively rare diseases: limited sample size, availability of control tissue, and time frame. The use of FFPE pancreatic tissue in GEM may be especially challenging due to its very......, (b) amino acid metabolism, and (c) calcium ion homeostasis. These results should encourage future research and GEM studies on FFPE tissue from the invaluable biobanks available at the departments of pathology worldwide....

  14. Genomics of hepatitis B virus-related hepatocellular carcinoma and adjacent noncancerous tissues with cDNA microarray.

    Science.gov (United States)

    Huang, Yu-kun; Fan, Xue-gong; Qiu, Fu; Wang, Zhi-ming

    2011-07-05

    Hepatocellular carcinoma (HCC) is a common primary cancer frequently associated with hepatitis B virus (HBV) infection. However, whether these identified genes are particularly associated with HBV-related HCC remains unknown. The aim of this study was to investigate the differential gene expression between HBV-related HCC tissues and adjacent noncancerous tissues. cDNA microarray was used to detect the differential gene expression profile in the HBV-related HCC tissues and adjacent noncancerous tissues, and reverse transcription-polymerase chain reaction (RT-PCR) was performed to verify the differential expression of candidate genes obtained from cDNA microarray experiment. In this study, 1369 genes or expressed sequence tags (ESTs) including 121 genes or ESTs with at least two-fold expression alterations between cancerous and noncancerous tissues were identified. Special AT-rich sequence binding protein 1 (SATB-1) expression was positive in 73% (16/22) of cancerous tissues and negative (0/22) in all noncancerous tissues of HBV-related HCC patients. Transmembrane 4 superfamily member 1 (TM4SF-1) expression was positive in 86% (19/22) of cancerous tissues and negative (0/22) in all noncancerous tissues. Suppression of tumorigenicity 14 (ST-14) expression was positive in 73% (16/22) of noncancerous tissues in patients with HBV-related HCC and negative in all HCC tissues (0/22). This study provided the gene expression profile of HBV-related HCC and presented differential expression patterns of SATB-1, TM4SF-1 and ST-14 between cancerous and noncancerous tissues in patients with HBV-related HCC.

  15. Genomics of hepatitis B virus-related hepatocellular carcinoma and adjacent noncancerous tissues with cDNA microarray

    Institute of Scientific and Technical Information of China (English)

    HUANG Yu-kun; FAN Xue-gong; QIU Fu; WANG Zhi-ming

    2011-01-01

    Background Hepatocellular carcinoma (HCC) is a common primary cancer frequently associated with hepatitis B virus (HBV) infection. However, whether these identified genes are particularly associated with HBV-related HCC remains unknown. The aim of this study was to investigate the differential gene expression between HBV-related HCC tissues and adjacent noncancerous tissues.Methods cDNA microarray was used to detect the differential gene expression profile in the HBV-related HCC tissues and adjacent noncancerous tissues, and reverse transcription-polymerase chain reaction (RT-PCR) was performed to verify the differential expression of candidate genes obtained from cDNA microarray experiment.Results In this study, 1369 genes or expressed sequence tags (ESTs) including 121 genes or ESTs with at least two-fold expression alterations between cancerous and noncancerous tissues were identified. Special AT-rich sequence binding protein 1 (SATB-1) expression was positive in 73% (16/22) of cancerous tissues and negative (0/22) in all noncancerous tissues of HBV-related HCC patients. Transmembrane 4 superfamily member 1 (TM4SF-1) expression was positive in 86% (19/22) of cancerous tissues and negative (0/22) in all noncancerous tissues. Suppression of tumorigenicity 14 (ST-14) expression was positive in 73% (16/22) of noncancerous tissues in patients with HBV-related HCC and negative in all HCC tissues (0/22).Conclusion This study provided the gene expression profile of HBV-related HCC and presented differential expression patterns of SATB-1, TM4SF-1 and ST-14 between cancerous and noncancerous tissues in patients with HBV-related HCC.

  16. De novo monosomy 9p24.3-pter and trisomy 17q24.3-qter characterised by microarray comparative genomic hybridisation in a fetus with an increased nuchal translucency.

    Science.gov (United States)

    Brisset, Sophie; Kasakyan, Serdar; L'Herminé, Aurore Coulomb; Mairovitz, Valérie; Gautier, Evelyne; Aubry, Marie-Cécile; Benkhalifa, Moncef; Tachdjian, Gérard

    2006-03-01

    Increased nuchal translucency (NT) during the first trimester of pregnancy is a useful marker to detect chromosomal abnormalities. Here, we report a prenatal case with molecular cytogenetic characterisation of an abnormal derivative chromosome 9 identified through NT. Amniocentesis was performed because of an increased NT (4.4 mm) and showed an abnormal de novo 46,XX,add(9)(p24.3) karyotype. To characterise the origin of the small additional material on 9p, we performed a microarray comparative genomic hybridisation (microarray CGH) using a genomic DNA array providing an average of 1 Mb resolution. Microarray CGH showed a deletion of distal 9p and a trisomy of distal 17q. These results were confirmed by FISH analyses. Microarray CGH provided accurate information on the breakpoint regions and the size of both distal 9p deletion and distal 17q trisomy. The fetus was therefore a carrier of a de novo derivative chromosome 9 arising from a t(9;17)(p24.3;q24.3) translocation and generating a monosomy 9p24.3-pter and a trisomy 17q24.3-qter. This case illustrates that microarray CGH is a rapid, powerful and sensitive technology to identify small de novo unbalanced chromosomal abnormalities and can be applied in prenatal diagnosis. 2006 John Wiley & Sons, Ltd.

  17. A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Myburg Alexander A

    2010-06-01

    Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

  18. Unraveling the rat blood genome-wide transcriptome after oral administration of lavender oil by a two-color dye-swap DNA microarray approach

    Directory of Open Access Journals (Sweden)

    Motohide Hori

    2016-06-01

    Full Text Available Lavender oil (LO is a commonly used essential oil in aromatherapy as non-traditional medicine. With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. In this brief, we investigate the effect of LO ingestion in the blood of rat. Rats were administered LO at usual therapeutic dose (5 mg/kg in humans, and following collection of the venous blood from the heart and extraction of total RNA, the differentially expressed genes were screened using a 4 × 44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA in conjunction with a two-color dye-swap approach. A total of 834 differentially expressed genes in the blood were identified: 362 up-regulated and 472 down-regulated. These genes were functionally categorized using bioinformatics tools. The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO: GSE67499. The data will be a valuable resource in examining the effects of natural products, and which could also serve as a human model for further functional analysis and investigation.

  19. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities.

    Science.gov (United States)

    Kearney, Hutton M; South, Sarah T; Wolff, Daynna J; Lamb, Allen; Hamosh, Ada; Rao, Kathleen W

    2011-07-01

    Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray technology that targets the entire genome in the same manner as an assay that targets a specific gene or syndromic region, a new paradigm of validation and regulation is needed to regulate this important diagnostic technology. We suggest that these microarray platforms be evaluated and manufacturers regulated for the ability to accurately measure copy number gains or losses in DNA (analytical validation) and that the subsequent interpretation of the findings and assignment of clinical significance be determined by medical professionals with appropriate training and certification. To this end, the American College of Medical Genetics, as the professional organization of board-certified clinical laboratory geneticists, herein outlines recommendations for the design and performance expectations for clinical genomic copy number microarrays and associated software intended for use in the postnatal setting for detection of constitutional abnormalities.

  20. Identification of gene clusters associated with host adaptation and antibiotic resistance in Chinese Staphylococcus aureus isolates by microarray-based comparative genomics.

    Directory of Open Access Journals (Sweden)

    Henan Li

    Full Text Available A comparative genomic microarray comprising 2,457 genes from two whole genomes of S. aureus was employed for the comparative genome hybridization analysis of 50 strains of divergent clonal lineages, including methicillin-resistant S. aureus (MRSA, methicillin-susceptible S. aureus (MSSA, and swine strains in China. Large-scale validation was confirmed via polymerase chain reaction in 160 representative clinical strains. All of the 50 strains were clustered into seven different complexes by phylogenetic tree analysis. Thirteen gene clusters were specific to different S. aureus clones. Ten gene clusters, including seven known (vSa3, vSa4, vSaα, vSaβ, Tn5801, and phage ϕSa3 and three novel (C8, C9, and C10 gene clusters, were specific to human MRSA. Notably, two global regulators, sarH2 and sarH3, at cluster C9 were specific to human MRSA, and plasmid pUB110 at cluster C10 was specific to swine MRSA. Three clusters known to be part of SCCmec, vSa4 or Tn5801, and vSaα as well as one novel gene cluster C12 with homology with Tn554 of S. epidermidis were identified as MRSA-specific gene clusters. The replacement of ST239-spa t037 with ST239-spa t030 in Beijing may be a result of its acquisition of vSa4, phage ϕSa1, and ϕSa3. In summary, thirteen critical gene clusters were identified to be contributors to the evolution of host specificity and antibiotic resistance in Chinese S. aureus.

  1. Proximal genomic localization of STAT1 binding and regulated transcriptional activity

    Directory of Open Access Journals (Sweden)

    Smyth Gordon K

    2006-10-01

    Full Text Available Abstract Background Signal transducer and activator of transcription (STAT proteins are key regulators of gene expression in response to the interferon (IFN family of anti-viral and anti-microbial cytokines. We have examined the genomic relationship between STAT1 binding and regulated transcription using multiple tiling microarray and chromatin immunoprecipitation microarray (ChIP-chip experiments from public repositories. Results In response to IFN-γ, STAT1 bound proximally to regions of the genome that exhibit regulated transcriptional activity. This finding was consistent between different tiling microarray platforms, and between different measures of transcriptional activity, including differential binding of RNA polymerase II, and differential mRNA transcription. Re-analysis of tiling microarray data from a recent study of IFN-γ-induced STAT1 ChIP-chip and mRNA expression revealed that STAT1 binding is tightly associated with localized mRNA transcription in response to IFN-γ. Close relationships were also apparent between STAT1 binding, STAT2 binding, and mRNA transcription in response to IFN-α. Furthermore, we found that sites of STAT1 binding within the Encyclopedia of DNA Elements (ENCODE region are precisely correlated with sites of either enhanced or diminished binding by the RNA polymerase II complex. Conclusion Together, our results indicate that STAT1 binds proximally to regions of the genome that exhibit regulated transcriptional activity. This finding establishes a generalized basis for the positioning of STAT1 binding sites within the genome, and supports a role for STAT1 in the direct recruitment of the RNA polymerase II complex to the promoters of IFN-γ-responsive genes.

  2. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  3. A comparative genomic study in schizophrenic and in bipolar disorder patients, based on microarray expression profiling meta-analysis.

    Science.gov (United States)

    Logotheti, Marianthi; Papadodima, Olga; Venizelos, Nikolaos; Chatziioannou, Aristotelis; Kolisis, Fragiskos

    2013-01-01

    Schizophrenia affecting almost 1% and bipolar disorder affecting almost 3%-5% of the global population constitute two severe mental disorders. The catecholaminergic and the serotonergic pathways have been proved to play an important role in the development of schizophrenia, bipolar disorder, and other related psychiatric disorders. The aim of the study was to perform and interpret the results of a comparative genomic profiling study in schizophrenic patients as well as in healthy controls and in patients with bipolar disorder and try to relate and integrate our results with an aberrant amino acid transport through cell membranes. In particular we have focused on genes and mechanisms involved in amino acid transport through cell membranes from whole genome expression profiling data. We performed bioinformatic analysis on raw data derived from four different published studies. In two studies postmortem samples from prefrontal cortices, derived from patients with bipolar disorder, schizophrenia, and control subjects, have been used. In another study we used samples from postmortem orbitofrontal cortex of bipolar subjects while the final study was performed based on raw data from a gene expression profiling dataset in the postmortem superior temporal cortex of schizophrenics. The data were downloaded from NCBI's GEO datasets.

  4. A Comparative Genomic Study in Schizophrenic and in Bipolar Disorder Patients, Based on Microarray Expression Profiling Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Marianthi Logotheti

    2013-01-01

    Full Text Available Schizophrenia affecting almost 1% and bipolar disorder affecting almost 3%–5% of the global population constitute two severe mental disorders. The catecholaminergic and the serotonergic pathways have been proved to play an important role in the development of schizophrenia, bipolar disorder, and other related psychiatric disorders. The aim of the study was to perform and interpret the results of a comparative genomic profiling study in schizophrenic patients as well as in healthy controls and in patients with bipolar disorder and try to relate and integrate our results with an aberrant amino acid transport through cell membranes. In particular we have focused on genes and mechanisms involved in amino acid transport through cell membranes from whole genome expression profiling data. We performed bioinformatic analysis on raw data derived from four different published studies. In two studies postmortem samples from prefrontal cortices, derived from patients with bipolar disorder, schizophrenia, and control subjects, have been used. In another study we used samples from postmortem orbitofrontal cortex of bipolar subjects while the final study was performed based on raw data from a gene expression profiling dataset in the postmortem superior temporal cortex of schizophrenics. The data were downloaded from NCBI's GEO datasets.

  5. Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

    Science.gov (United States)

    Knijnenburg, Jeroen; van der Burg, Marja; Nilsson, Philomeen; Ploos van Amstel, Hans Kristian; Tanke, Hans; Szuhai, Károly

    2005-10-12

    A strategy is presented to select, pool and spot human BAC clones on an array in such a way that each spot contains five well performing BAC clones, covering one chromosome arm. A mini-array of 240 spots was prepared representing all human chromosome arms in a 5-fold as well as some controls, and used for comparative genomic hybridization (CGH) of 10 cell lines with aneusomies frequently found in clinical cytogenetics and oncology. Spot-to-spot variation within five replicates was below 6% and all expected abnormalities were detected 100% correctly. Sensitivity was such that replacing one BAC clone in a given spot of five by a BAC clone from another chromosome, thus resulting in a change in ratio of 20%, was reproducibly detected. Incubation time of the mini-array was varied and the fluorescently labelled target DNA was diluted. Typically, aneusomies could be detected using 30 ng of non-amplified random primed labelled DNA amounts in a 4 h hybridization reaction. Potential application of these mini-arrays for genomic profiling of disseminated tumour cells or of blastomeres for preimplantation genetic diagnosis, using specially designed DNA amplification methods, are discussed.

  6. Microarray and synchronization of neuronal differentiation with pathway changes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databank in nerve growth factor-treated PC12 cells.

    Science.gov (United States)

    Lin, Chih-Ming; Feng, Wayne

    2012-08-01

    The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database creates networks from interrelations between molecular biology and underlying chemical elements. This allows for analysis of biologic networks, genomic information, and higher-order functional information at a systems level. We performed microarray experiments and used the KEGG database, systems biology analysis, and annotation of pathway function to study nerve growth factor (NGF)-induced differentiation of PC12 cells. Cells were cultured to 70%-80% confluence, treated with NGF for 1 or 3 hours (h), and RNA was extracted. Stage 1 data analysis involved analysis of variance (ANOVA), and stage 2 involved cluster analysis and heat map generation. We identified 2020 NGF-induced PC12 genes (1038 at 1 h and 1554 at 3 h). Results showed changes in gene expression over time. We compared these genes with 6035 genes from the KEGG database. Cross-matching resulted in 830 genes. Among these, we identified 395 altered genes (155 at 1 h and 301 at 3 h; 2-fold increase from 1 h to 3 h). We identified 191 biologic pathways in the KEGG database; the top 15 showed correlations with neuronal differentiation (mitogen-activated protein kinase [MAPK] pathway: 35 genes at 1 h, 54 genes at 3 h; genes associated with axonal guidance: 12 at 1 h, 26 at 3 h; Wnt pathway: 16 at 1 h, 25 at 3 h; neurotrophin pathway: 4 at 1 h, 14 at 3 h). Thus, we identified changes in neuronal differentiation pathways with the KEGG database, which were synchronized with NGF-induced differentiation.

  7. Analysis of pigmented villonodular synovitis with genome-wide complementary DNA microarray and tissue array technology reveals insight into potential novel therapeutic approaches.

    Science.gov (United States)

    Finis, Katharina; Sültmann, Holger; Ruschhaupt, Markus; Buness, Andreas; Helmchen, Birgit; Kuner, Ruprecht; Gross, Marie-Luise; Fink, Bernd; Schirmacher, Peter; Poustka, Annemarie; Berger, Irina

    2006-03-01

    To characterize the gene expression profile and determine potential diagnostic markers and therapeutic targets in pigmented villonodular synovitis (PVNS). Gene expression patterns in 11 patients with PVNS, 18 patients with rheumatoid arthritis (RA), and 19 patients with osteoarthritis (OA) were investigated using genome-wide complementary DNA microarrays. Validation of differentially expressed genes was performed by real-time quantitative polymerase chain reaction and immunohistochemical analysis on tissue arrays (80 patients with PVNS, 51 patients with RA, and 20 patients with OA). The gene expression profile in PVNS was clearly distinct from those in RA and OA. One hundred forty-one up-regulated genes and 47 down-regulated genes were found in PVNS compared with RA, and 153 up-regulated genes and 89 down-regulated genes were found in PVNS compared with OA (fold change > or = 1.5; Q PVNS were involved in apoptosis regulation, matrix degradation, and inflammation (ALOX5AP, ATP6V1B2, CD53, CHI3L1, CTSL, CXCR4, HSPA8, HSPCA, LAPTM5, MMP9, MOAP1, and SPP1). The gene expression signature in PVNS is similar to that of activated macrophages and is consistent with the local destructive course of the disease. The gene and protein expression patterns suggest that the ongoing proliferation in PVNS is sustained by apoptosis resistance. This result suggests the possibility of a potential novel therapeutic intervention against PVNS.

  8. Case of 7p22.1 Microduplication Detected by Whole Genome Microarray (REVEAL in Workup of Child Diagnosed with Autism

    Directory of Open Access Journals (Sweden)

    Veronica Goitia

    2015-01-01

    Full Text Available Introduction. More than 60 cases of 7p22 duplications and deletions have been reported with over 16 of them occurring without concomitant chromosomal abnormalities. Patient and Methods. We report a 29-month-old male diagnosed with autism. Whole genome chromosome SNP microarray (REVEAL demonstrated a 1.3 Mb interstitial duplication of 7p22.1 ->p22.1 arr 7p22.1 (5,436,367–6,762,394, the second smallest interstitial 7p duplication reported to date. This interval included 14 OMIM annotated genes (FBXL18, ACTB, FSCN1, RNF216, OCM, EIF2AK1, AIMP2, PMS2, CYTH3, RAC1, DAGLB, KDELR2, GRID2IP, and ZNF12. Results. Our patient presented features similar to previously reported cases with 7p22 duplication, including brachycephaly, prominent ears, cryptorchidism, speech delay, poor eye contact, and outburst of aggressive behavior with autism-like features. Among the genes located in the duplicated segment, ACTB gene has been proposed as a candidate gene for the alteration of craniofacial development. Overexpression of RNF216L has been linked to autism. FSCN1 may play a role in neurodevelopmental disease. Conclusion. Characterization of a possible 7p22.1 Duplication Syndrome has yet to be made. Recognition of the clinical spectrum in patients with a smaller duplication of 7p should prove valuable for determining the minimal critical region, helping delineate a better prediction of outcome and genetic counseling

  9. An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome.

    Science.gov (United States)

    Jehee, Fernanda Sarquis; Rosenberg, Carla; Krepischi-Santos, Ana Cristina; Kok, Fernando; Knijnenburg, Jeroen; Froyen, Guy; Vianna-Morgante, Angela M; Opitz, John M; Passos-Bueno, Maria Rita

    2005-12-15

    FG syndrome is an X-linked multiple congenital anomalies (MCA) syndrome. It has been mapped to four distinct loci FGS1-4, through linkage analysis (Xq13, Xp22.3, and Xp11.4-p11.3) and based on the breakpoints of an X chromosome inversion (Xq11:Xq28), but so far no gene has been identified. We describe a boy with FG syndrome who has an inherited duplication at band Xq22.3 detected by comparative genomic hybridization microarray (Array-CGH). These duplication maps outside all four loci described so far for FG syndrome, representing therefore a new locus, which we propose to be called FGS5. MID2, a gene closely related to MID1, which is known to be mutated in Opitz G/BBB syndrome, maps within the duplicated segment of our patient. Since FG and Opitz G/BBB syndromes share many manifestations we considered MID2 a candidate gene for FG syndrome. We also discuss the involvement of other potential genes within the duplicated segment and its relationship with clinical symptoms of our patient, as well as the laboratory abnormalities found in his mother, a carrier of the duplication.

  10. Tiled QR factorization algorithms

    CERN Document Server

    Bouwmeester, Henricus; Langou, Julien; Robert, Yves

    2011-01-01

    This work revisits existing algorithms for the QR factorization of rectangular matrices composed of p-by-q tiles, where p >= q. Within this framework, we study the critical paths and performance of algorithms such as Sameh and Kuck, Modi and Clarke, Greedy, and those found within PLASMA. Although neither Modi and Clarke nor Greedy is optimal, both are shown to be asymptotically optimal for all matrices of size p = q^2 f(q), where f is any function such that \\lim_{+\\infty} f= 0. This novel and important complexity result applies to all matrices where p and q are proportional, p = \\lambda q, with \\lambda >= 1, thereby encompassing many important situations in practice (least squares). We provide an extensive set of experiments that show the superiority of the new algorithms for tall matrices.

  11. ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

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    Porter Christopher J

    2007-09-01

    Full Text Available Abstract Background SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs. These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments. Results Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes. Conclusion The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.

  12. Biolog phenotype microarrays.

    Science.gov (United States)

    Shea, April; Wolcott, Mark; Daefler, Simon; Rozak, David A

    2012-01-01

    Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism's physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog's reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis.

  13. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology

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    Ben D. Tall

    2017-03-01

    Full Text Available Cronobacter (previously known as Enterobacter sakazakii is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1 the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2 mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3 lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of

  14. Tiling a Rectangle with Polyominoes

    OpenAIRE

    2016-01-01

    International audience; A polycube in dimension $d$ is a finite union of unit $d$-cubes whose vertices are on knots of the lattice $\\mathbb{Z}^d$. We show that, for each family of polycubes $E$, there exists a finite set $F$ of bricks (parallelepiped rectangles) such that the bricks which can be tiled by $E$ are exactly the bricks which can be tiled by $F$. Consequently, if we know the set $F$, then we have an algorithm to decide in polynomial time if a brick is tilable or not by the tiles of...

  15. An ANOCEF Genomic and Transcriptomic Microarray Study of the Response to Irinotecan and Bevacizumab in Recurrent Glioblastomas

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    Julien Laffaire

    2014-01-01

    Full Text Available Background. We performed a retrospective study to assess whether the initial molecular characteristics of glioblastomas (GBMs were associated with the response to the bevacizumab/irinotecan chemotherapy regimen given at recurrence. Results. Comparison of the genomic and gene expression profiles of the responders (n=12 and nonresponders (n=13 demonstrated only slight differences and could not identify any robust biomarkers associated with the response. In contrast, a significant association was observed between GBMs molecular subtypes and response rates. GBMs assigned to molecular subtype IGS-18 and to classical subtype had a lower response rate than those assigned to other subtypes. In an independent series of 33 patients, neither EGFR amplification nor CDKN2A deletion (which are frequent in IGS-18 and classical GBMs was significantly associated with the response rate, suggesting that these two alterations are unlikely to explain the lower response rate of these GBMs molecular subtypes. Conclusion. Despite its limited sample size, the present study suggests that comparing the initial molecular profiles of responders and nonresponders might not be an effective strategy to identify biomarkers of the response to bevacizumab given at recurrence. Yet it suggests that the response rate might differ among GBMs molecular subtypes.

  16. Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system

    Directory of Open Access Journals (Sweden)

    Katz Jonathan D

    2004-10-01

    Full Text Available Abstract Background In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated, or in vitro activated T-cells. Results Gene clusters, formed based on similarity of expression-pattern across either all tissues or the immune tissues only, had highly significant associations both with immunological processes such as chemokine-mediated response, antigen processing, receptor-related signal transduction, and transcriptional regulation, and also with more general processes such as replication and cell cycle control. Within-cluster gene correlations implicated known associations of known genes, as well as immune process-related roles for poorly described genes. To characterize regulatory mechanisms and cis-elements of genes with similar patterns of expression, we used a new version of a comparative genomics-based cis-element analysis tool to identify clusters of cis-elements with compositional similarity among multiple genes. Several clusters contained genes that shared 5–6 cis-elements that included ETS and zinc-finger binding sites. cis-Elements AP2 EGRF ETSF MAZF SP1F ZF5F and AREB ETSF MZF1 PAX5 STAT were shared in a thymus-expressed set; AP4R E2FF EBOX ETSF MAZF SP1F ZF5F and CREB E2FF MAZF PCAT SP1F STAT cis-clusters occurred in activated T-cells; CEBP CREB NFKB SORY and GATA NKXH OCT1 RBIT occurred in stimulated lymph nodes. Conclusion This study demonstrates a series of analytic approaches that have allowed the implication of genes and regulatory elements that participate in the differentiation, maintenance, and function of the immune system. Polymorphism or mutation of these could adversely impact immune system functions.

  17. Cytotoxicity and genome-wide microarray analysis of intestinal smooth muscle cells in response to hexavalent chromium induction

    Institute of Scientific and Technical Information of China (English)

    Li-Fang JIN; Yuan-Yuan WANG; Zi-Dong ZHANG; Yi-Meng YUAN; Yi-Rui HU; Yang-Feng WEI; Jian NI

    2013-01-01

    Chronic ingestion of high concentrations of hexavalent chromium [Cr(Ⅵ)] in drinking water induces intestinal tumors in mice; however,information on its toxicity on intestinal smooth muscle cells is limited.The present study aimed to assess the in vitro and in vivo toxicological effects of Cr(Ⅵ) on intestinal smooth muscle cells.Human intestinal smooth muscle cells (HISM cells) were cultured with different concentrations of Cr(Ⅵ) to evaluate effects on cell proliferation ability,oxidative stress levels,and antioxidant system.Furthermore,tissue sections in Cr(Ⅵ) exposed rabbits were analyzed to evaluate toxicity on intestinal muscle cells in vivo.Gene chips were utilized to assess differential gene expression profiles at the genome-wide level in 1 μmol/L Cr(Ⅵ) treated cells.Intestinal tissue biopsy results showed that Cr(Ⅵ) increased the incidences of diffuse epithelial hyperplasia in intestinal jejunum but caused no obvious damage to the structure of the muscularis.Cell proliferation analysis revealed that high concentrations (≥64 μmol/L) but not low concentrations of Cr(Ⅵ) (≤16 μmol/L) significantly inhibited the growth of HISM cells.For oxidative stress levels,the expression of reactive oxygen species (ROS) and nitric oxide (NO) was elevated at high concentrations (≥64 μmol/L) but not at low concentrations of Cr(Ⅵ) (≤ 16 μmol/L).In addition,dose-dependent increases in the activity of oxidized glutathione (GSSH)/total-glutathione (T-GSH) were also observed.Gene chip screened 491 differentially expressed genes including genes associated with cell apoptosis,oxidations,and cytoskeletons.Some of these differentially expressed genes may be unique to smooth muscle cells in response to Cr(Ⅵ) induction.

  18. A genome-wide study of cytogenetic changes in colorectal cancer using SNP microarrays: opportunities for future personalized treatment.

    Directory of Open Access Journals (Sweden)

    Farzana Jasmine

    Full Text Available In colorectal cancer (CRC, chromosomal instability (CIN is typically studied using comparative-genomic hybridization (CGH arrays. We studied paired (tumor and surrounding healthy fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN and B-allele frequency (BAF--a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis. We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p. From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.

  19. Mathematical design of prokaryotic clone-based microarrays

    NARCIS (Netherlands)

    Pieterse, B.; Quirijns, E.J.; Schuren, F.H.J.; Werf, van der M.J.

    2005-01-01

    Background - Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a ran

  20. Mathematical design of prokaryotic clone-based microarrays

    NARCIS (Netherlands)

    Pieterse, B.; Quirijns, E.J.; Schuren, F.H.J.; Werf, M.J. van der

    2005-01-01

    Background: Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a rand

  1. Sub-megabase resolution tiling (SMRT array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines

    Directory of Open Access Journals (Sweden)

    Lam Wan L

    2008-01-01

    Full Text Available Abstract Background Hodgkin lymphoma (HL and Anaplastic Large Cell Lymphoma (ALCL, are forms of malignant lymphoma defined by unique morphologic, immunophenotypic, genotypic, and clinical characteristics, but both overexpress CD30. We used sub-megabase resolution tiling (SMRT array-based comparative genomic hybridization to screen HL-derived cell lines (KMH2 and L428 and ALCL cell lines (DEL and SR-786 in order to identify disease-associated gene copy number gains and losses. Results Significant copy number gains and losses were observed on several chromosomes in all four cell lines. Assessment of copy number alterations with 26,819 DNA segments identified an average of 20 genetic alterations. Of the recurrent minimally altered regions identified, 11 (55% were within previously published regions of chromosomal alterations in HL and ALCL cell lines while 9 (45% were novel alterations not previously reported. HL cell lines L428 and KMH2 shared gains in chromosome cytobands 2q23.1-q24.2, 7q32.2-q36.3, 9p21.3-p13.3, 12q13.13-q14.1, and losses in 13q12.13-q12.3, and 18q21.32-q23. ALCL cell lines SR-786 and DEL, showed gains in cytobands 5p15.32-p14.3, 20p12.3-q13.11, and 20q13.2-q13.32. Both pairs of HL and ALCL cell lines showed losses in 18q21.32-18q23. Conclusion This study is considered to be the first one describing HL and ALCL cell line genomes at sub-megabase resolution. This high-resolution analysis allowed us to propose novel candidate target genes that could potentially contribute to the pathogenesis of HL and ALCL. FISH was used to confirm the amplification of all three isoforms of the trypsin gene (PRSS1/PRSS2/PRSS3 in KMH2 and L428 (HL and DEL (ALCL cell lines. These are novel findings that have not been previously reported in the lymphoma literature, and opens up an entirely new area of research that has not been previously associated with lymphoma biology. The findings raise interesting possibilities about the role of signaling

  2. Medicina genómica: Aplicaciones del polimorfismo de un nucleótido y micromatrices de ADN Genomic Medicine: Polymorphisms and microarray applications

    Directory of Open Access Journals (Sweden)

    Monica P. Spalvieri

    2004-12-01

    Full Text Available Esta actualización tiene por objeto difundir un nuevo enfoque de las variaciones del ADN entre individuos y comentar las nuevas tecnologías para su detección. La secuenciación total del genoma humano es el comienzo para conocer la diversidad genética. La unidad de medida reconocida de esta variabilidad es el polimorfismo de un solo nucleótido (single nucleotide polymorphism o SNP. El estudio de los SNPs está restringido a la investigación pero las numerosas publicaciones sobre el tema hacen vislumbrar su entrada en la práctica clínica. Se presentan ejemplos del uso de SNPs como marcadores moleculares en la genotipificación étnica, la expresión génica de enfermedades y como potenciales blancos farmacológicos. Se comenta la técnica de las matrices (arrays que facilita el estudio de múltiples secuencias de genes mediante chips de diseño específico. Los métodos convencionales analizan hasta un máximo de 20 genes, mientras que una sola micromatriz provee información sobre decenas de miles de genes simultáneamente con una genotipificación rápida y exacta. Los avances de la biotecnología permitirán conocer, además de la secuencia de cada gen, la frecuencia y ubicación exacta de los SNPs y su influencia en los comportamientos celulares. Si bien la validez de los resultados y la eficiencia de las micromatrices son aún controvertidos, el conocimiento y caracterización del perfil genético de un paciente impulsará seguramente un cambio radical en la prevención, diagnóstico, pronóstico y tratamiento de las enfermedades humanas.This update shows new concepts related to the significance of DNA variations among individuals, as well as to their detection by using a new technology. The sequencing of the human genome is only the beginning of what will enable us to understand genetic diversity. The unit of DNA variability is the polymorphism of a single nucleotide (SNP. At present, studies on SNPs are restricted to basic research

  3. The EADGENE Microarray Data Analysis Workshop

    NARCIS (Netherlands)

    Koning, de D.J.; Jaffrezic, F.; Lund, M.S.; Watson, M.; Channing, C.; Hulsegge, B.; Pool, M.H.; Buitenhuis, B.; Hedegaard, J.; Hornshoj, H.; Sorensen, P.; Marot, G.; Delmas, C.; Lê Cao, K.A.; San Cristobal, M.; Baron, M.D.; Malinverni, R.; Stella, A.; Brunner, R.M.; Seyfert, H.M.; Jensen, K.; Mouzaki, D.; Waddington, D.; Jiménez-Marín, A.; Perez-Alegre, M.; Perez-Reinado, E.; Closset, R.; Detilleux, J.C.; Dovc, P.; Lavric, M.; Nie, H.; Janss, L.

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10

  4. Glass slides to DNA microarrays

    Directory of Open Access Journals (Sweden)

    Samuel D Conzone

    2004-03-01

    Full Text Available A tremendous interest in deoxyribonucleic acid (DNA characterization tools was spurred by the mapping and sequencing of the human genome. New tools were needed, beginning in the early 1990s, to cope with the unprecedented amount of genomic information that was being discovered. Such needs led to the development of DNA microarrays; tiny gene-based sensors traditionally prepared on coated glass microscope slides. The following review is intended to provide historical insight into the advent of the DNA microarray, followed by a description of the technology from both the application and fabrication points of view. Finally, the unmet challenges and needs associated with DNA microarrays will be described to define areas of potential future developments for the materials researcher.

  5. Genome-Wide lncRNA Microarray Profiling Identifies Novel Circulating lncRNAs for Detection of Gastric Cancer

    Science.gov (United States)

    Zhang, Kecheng; Shi, Hongzhi; Xi, Hongqing; Wu, Xiaosong; Cui, Jianxin; Gao, Yunhe; Liang, Wenquan; Hu, Chong; Liu, Yi; Li, Jiyang; Wang, Ning; Wei, Bo; Chen, Lin

    2017-01-01

    Long non-coding RNAs (lncRNAs) can serve as blood-based biomarkers for cancer detection. To identify novel lncRNA biomarkers for gastric cancer (GC), we conducted, for the first time, genome-wide lncRNA screening analysis in two sets of samples: five paired preoperative and postoperative day 14 plasma samples from GC patients, and tissue samples from tumor and adjacent normal tissues. Candidate tumor-related lncRNAs were then quantitated and evaluated in three independent phases comprising 321 participants. The expression levels of lncRNAs were also measured in GC cell lines and the corresponding culture medium. Biomarker panels, lncRNA-based Index I and carcinoembryonic antigen (CEA)-based Index II, were constructed using logistic regression, and their diagnostic performance compared. Fagan's nomogram was plotted to facilitate clinical application. As a result, we identified five novel plasma lncRNAs (TINCR, CCAT2, AOC4P, BANCR and LINC00857), which, when combined in the lncRNA-based Index I, outperformed the CEA-based Index II (P < 0.001) and could distinguish GC patients from healthy controls with an area under the receiver-operating curve (AUC) of 0.91 (95% confidence interval (CI): 0.88-0.95). The lncRNA-based index decreased significantly by postoperative day 14 (P = 0.016), indicating its ability to monitor tumor dynamics. High values of the lncRNA-based index were correlated with tumor size (P = 0.036), depth of invasion (P = 0.025), lymphatic metastasis (P = 0.012) and more advanced tumor stages (P = 0.003). The lncRNA-based index was also able to discriminate GC patients from precancerous individuals and patients with gastrointestinal stromal tumor with AUC values of 0.82 (95% CI: 0.71-0.92) and 0.80 (95% CI: 0.68-0.91), respectively. Taken together, our findings demonstrate that this panel of five plasma lncRNAs could serve as a set of novel diagnostic biomarkers for GC detection. PMID:28042329

  6. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a

  7. Combining microarrays and genetic analysis

    NARCIS (Netherlands)

    Alberts, Rudi; Fu, Jingyuan; Swertz, Morris A.; Lubbers, L. Alrik; Albers, Casper J.; Jansen, Ritsert C.

    2005-01-01

    Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a st

  8. The Current Status of DNA Microarrays

    Science.gov (United States)

    Shi, Leming; Perkins, Roger G.; Tong, Weida

    DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manufacturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthesized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microarrays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

  9. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features

    National Research Council Canada - National Science Library

    Shaw-Smith, C; Redon, R; Rickman, L; Rio, M; Willatt, L; Fiegler, H; Firth, H; Sanlaville, D; Winter, R; Colleaux, L; Bobrow, M; Carter, N P

    2004-01-01

    ...). The presence of subtle DNA copy number changes was investigated by array-CGH in 50 patients with learning disability and dysmorphism, employing a DNA microarray constructed from large insert clones...

  10. Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization: e95047

    National Research Council Canada - National Science Library

    Heike Horn; Julia Bausinger; Annette M Staiger; Maximilian Sohn; Christopher Schmelter; Kim Gruber; Claudia Kalla; M Michaela Ott; Andreas Rosenwald; German Ott

    2014-01-01

    ...), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded...

  11. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization

    National Research Council Canada - National Science Library

    Horn, Heike; Bausinger, Julia; Staiger, Annette M; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M Michaela; Rosenwald, Andreas; Ott, German

    2014-01-01

    ...), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded...

  12. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M

    2007-01-01

    BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human...... genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed. RESULTS: We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human...... of 3 of the hairpin structures and 3 out of 9 high covariance structures in SK-N-AS cells. CONCLUSION: Our results demonstrate that many human noncoding, structured and conserved RNA genes remain to be discovered and that tissue specific tiling array data can be used in combination with computational...

  13. Integrated Amplification Microarrays for Infectious Disease Diagnostics

    Directory of Open Access Journals (Sweden)

    Darrell P. Chandler

    2012-11-01

    Full Text Available This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.

  14. Brane Tilings and Specular Duality

    CERN Document Server

    Hanany, Amihay

    2012-01-01

    We study a new duality which pairs 4d N=1 supersymmetric quiver gauge theories. They are represented by brane tilings and are worldvolume theories of D3 branes at Calabi-Yau 3-fold singularities. The new duality identifies theories which have the same combined mesonic and baryonic moduli space, otherwise called the master space. We obtain the associated Hilbert series which encodes both the generators and defining relations of the moduli space. We illustrate our findings with a set of brane tilings that have reflexive toric diagrams.

  15. Methylation profiling using methylated DNA immunoprecipitation and tiling array hybridization.

    Science.gov (United States)

    Cheung, Hoi-Hung; Lee, Tin-Lap; Rennert, Owen M; Chan, Wai-Yee

    2012-01-01

    DNA methylation is an important epigenetic modification that regulates development and plays a role in the pathophysiology of many diseases. It is dynamically changed during germline development. Methylated DNA immunoprecipitation (MeDIP) is an efficient, cost-effective method for locus-specific and genome-wide analysis. Methylated DNA fragments are enriched by a 5-methylcytidine-recognizing antibody, therefore allowing the analysis of both CpG and non-CpG methylation. The enriched DNA fragments can be amplified and hybridized to tiling arrays covering CpG islands, promoters, or the entire genome. Comparison of different methylomes permits the discovery of differentially methylated regions that might be important in disease- or tissue-specific expression. Here, we describe an established MeDIP protocol and tiling array hybridization method for profiling methylation of testicular germ cells.

  16. Duality properties between spectra and tilings

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Spectra and tilings play an important role in analysis and geometry respectively.The relations between spectra and tilings have bafied the mathematicians for a long time.Many conjectures,such as the Fuglede conjecture,are placed on the establishment of relations between spectra and tilings,although there are no desired results.In the present paper we derive some characteristic properties of spectra and tilings which highlight certain duality properties between them.

  17. Composite treatment of ceramic tile armor

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, James G. R. [Oak Ridge, TN; Frame, Barbara J [Oak Ridge, TN

    2010-12-14

    An improved ceramic tile armor has a core of boron nitride and a polymer matrix composite (PMC) facing of carbon fibers fused directly to the impact face of the tile. A polyethylene fiber composite backing and spall cover are preferred. The carbon fiber layers are cured directly onto the tile, not adhered using a separate adhesive so that they are integral with the tile, not a separate layer.

  18. Composite treatment of ceramic tile armor

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, James G. R. [Oak Ridge, TN; Frame, Barbara J [Oak Ridge, TN

    2012-01-02

    An improved ceramic tile armor has a core of boron nitride and a polymer matrix composite (PMC) facing of carbon fibers fused directly to the impact face of the tile. A polyethylene fiber composite backing and spall cover are preferred. The carbon fiber layers are cured directly onto the tile, not adhered using a separate adhesive so that they are integral with the tile, not a separate layer.

  19. Production Process for Strong, Light Ceramic Tiles

    Science.gov (United States)

    Holmquist, G. R.; Cordia, E. R.; Tomer, R. S.

    1985-01-01

    Proportions of ingredients and sintering time/temperature schedule changed. Production process for lightweight, high-strength ceramic insulating tiles for Space Shuttle more than just scaled-up version of laboratory process for making small tiles. Boron in aluminum borosilicate fibers allows fusion at points where fibers contact each other during sintering, thereby greatly strengthening tiles structure.

  20. FIBONACCI TILINGS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    KAZLACHEVA Zlatina

    2016-05-01

    Full Text Available The Fibonacci sequence is a symbol of beauty and harmony and by this reason geometrical objects in its proportions are used in the design. There are some versions of Fibonacci series tiling, which are constructed with equilateral geometrical figures – squares or triangles, as the sides’ lengths are equal to the numbers of the Fibonacci series, or the lengths of the sides of the squares or equilateral triangles are each to other in proportions, which are equal to Fibonacci sequence. The paper presents design of ladies’ dresses with the both ways of constructing of Fibonacci tilings with squares, the variants in a spiral pattern and the variant with squares which are put side by side, and the version of Fibonacci tiling with triangles in form of double spiral named Fibonacci rose. Nine models of ladies’ dresses are shown. As a result of the use of Fibonacci tilings for designing of aesthetic, beautiful and harmonic clothing, it can be concluded that in fashion design Fibonacci squares and Fibonacci rose can be used in different ways of color combinations, proportions toward the clothing sizes, and as a frame of creations of design elements. The different position, proportions and color combinations of use of Fibonacci squares and Fibonacci rose in fashion design according to the body type and size can cover some bodily defects and enhance the beautiful forms.

  1. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes

    Directory of Open Access Journals (Sweden)

    Lin Ye

    2008-06-01

    Full Text Available Abstract Background Xanthomonas oryzae pv. oryzae (Xoo and X. oryzae pv. oryzicola (Xoc are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174. Results Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories. Conclusion We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21

  2. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts

    Science.gov (United States)

    Lohse, Matthew B.; Kongsomboonvech, Pisiwat; Madrigal, Maria; Hernday, Aaron D.; Nobile, Clarissa J.

    2016-01-01

    Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments. PMID:26483022

  3. Protein Microarrays Technology and Its Application in Genome-Wide Posttranslational Modification%蛋白质芯片技术及其在全基因组翻译后修饰分析中的应用

    Institute of Scientific and Technical Information of China (English)

    眭维国; 王惠; 曹翠辉; 薛雯; 陈洁晶

    2013-01-01

    Protein microarrays technology is an important part in the current biological research. It can be used to study the interactions of protein-DNA,protein-ligand,protein-protein. In recent years,its application in the biochemical analysis of genome-wide has obtained remarkable achievement. Here is to make a review focusing on protein microarrays technology and its application in the analysis of genome-wide post-translational modification.%蛋白质芯片技术可用于研究蛋白质-DNA、蛋白质-配基和蛋白质与蛋白质之间的相互作用,是当前生物科学研究中的重要内容.近年来,运用蛋白质芯片技术对全基因组进行生物化学分析的应用取得令人瞩目的 成就.现着重总结蛋白质芯片技术及其在全基因组翻译后修饰分析中的应用.

  4. Genomic and expression array profiling of chromosome 20q amplicon in human colon cancer cells

    Directory of Open Access Journals (Sweden)

    Carter Jennifer

    2005-01-01

    Full Text Available Background: Gain of the q arm of chromosome 20 in human colorectal cancer has been associated with poorer survival time and has been reported to increase in frequency from adenomas to metastasis. The increasing frequency of chromosome 20q amplification during colorectal cancer progression and the presence of this amplification in carcinomas of other tissue origin has lead us to hypothesize that 20q11-13 harbors one or more genes which, when over expressed promote tumor invasion and metastasis. Aims: Generate genomic and expression profiles of the 20q amplicon in human cancer cell lines in order to identify genes with increased copy number and expression. Materials and Methods: Utilizing genomic sequencing clones and amplification mapping data from our lab and other previous studies, BAC/ PAC tiling paths spanning the 20q amplicon and genomic microarrays were generated. Array-CGH on the custom array with human cancer cell line DNAs was performed to generate genomic profiles of the amplicon. Expression array analysis with RNA from these cell lines using commercial oligo microarrays generated expression profiles of the amplicon. The data were then combined in order to identify genes with increased copy number and expression. Results: Over expressed genes in regions of increased copy number were identified and a list of potential novel genetic tumor markers was assembled based on biological functions of these genes Conclusions: Performing high-resolution genomic microarray profiling in conjunction with expression analysis is an effective approach to identify potential tumor markers.

  5. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  6. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Egmont-Peterson, M.; Janssen, I.M.; Smeets, D.F.C.M.; Geurts van Kessel, A.H.M.; Veltman, J.A.

    2007-01-01

    Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a

  7. The Level-1 Tile-Muon Trigger in the Tile Calorimeter upgrade program

    Science.gov (United States)

    Ryzhov, A.

    2016-12-01

    The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). TileCal provides highly-segmented energy measurements for incident particles. Information from TileCal's outermost radial layer can assist in muon tagging in the Level-1 Muon Trigger by rejecting fake muon triggers due to slow charged particles (typically protons) without degrading the efficiency of the trigger. The main activity of the Tile-Muon Trigger in the ATLAS Phase-0 upgrade program was to install and to activate the TileCal signal processor module for providing trigger inputs to the Level-1 Muon Trigger. This report describes the Tile-Muon Trigger, focusing on the new detector electronics such as the Tile Muon Digitizer Board (TMDB) that receives, digitizes and then provides the signal from eight TileCal modules to three Level-1 muon endcap Sector-Logic Boards.

  8. Performance of the Tile PreProcessor Demonstrator for the ATLAS Tile Calorimeter Phase II Upgrade

    CERN Document Server

    Carrio Argos, Fernando; The ATLAS collaboration

    2015-01-01

    The Tile Calorimeter PreProcessor (TilePPr) demonstrator is a high performance double AMC board based on FPGA resources and QSFP modules. This board has been designed in the framework of the ATLAS Tile Calorimeter (TileCal) Demonstrator Project for the Phase II Upgrade as the first stage of the back-end electronics. The TilePPr demonstrator has been conceived for receiving and processing the data coming from the front-end electronics of the TileCal Demonstrator module, as well as for configuring it. Moreover, the TilePPr demonstrator handles the communication with the Detector Control System to monitor and control the front-end electronics. The TilePPr demonstrator represents 1/8 of the final TilePPr that will be designed and installed into the detector for the ATLAS Phase II Upgrade.

  9. Empirical evaluation of oligonucleotide probe selection for DNA microarrays.

    Directory of Open Access Journals (Sweden)

    Jennifer G Mulle

    Full Text Available DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs, and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.

  10. Empirical evaluation of oligonucleotide probe selection for DNA microarrays.

    Science.gov (United States)

    Mulle, Jennifer G; Patel, Viren C; Warren, Stephen T; Hegde, Madhuri R; Cutler, David J; Zwick, Michael E

    2010-03-29

    DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.

  11. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  12. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...... and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme...... and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices....

  13. Shuttle Upgrade Program: Tile TPS

    Science.gov (United States)

    Leiser, Daniel B.; Stewart, David A.; DiFiore, Robert; Irby, Ed; Arnold, James (Technical Monitor)

    2001-01-01

    One of the areas where the thermal protection system on the Space Shuttle Orbiter could be improved is the RSI (Reusable Surface Insulation) tile. The improvement would be in damage resistance that would reduce the resultant maintenance and inspection required. It has performed very well in every other aspect. Improving the system's damage resistance has been the subject of much research over the past several years. One of the results of that research was a new system developed for damage prone areas on the orbiter (i.e., base heat shield). That system, designated as TUFI, Toughened Uni-Piece Fibrous Insulation, was successfully demonstrated as an experiment on the Orbiter and is now baselined for the base heat shield. This paper describes the results of a current research program to further improve the TUFI tile system, thus making it applicable to more areas on the orbiter. The way to remove the current limitations of the TUFI system (i.e., weight or thermal conductivity differences between it and the baseline tile (LI-900)) is to improve the characteristics of LI-900 or AETB-8. Specifically this paper describes the results of two efforts. The first shows performance data of an improved LI-900 system involving the application of TUFI and the second describes data that shows a reduced difference in thermal conductivity between the advanced TUFI substrate (AETB-8) now used on the orbiter and LI-900.

  14. Optical properties of the new TileCal scintillating tiles. Comparison with 1999 production.

    CERN Document Server

    Zenine, A

    2000-01-01

    A few samples of the scintillating tiles made of BASF polystyrol for ATLAS Tile Calorimeter have been measured with a radioactive source. The results are represented in comparison with the first 1999 year batch produced of PSM-115 polystyrene.

  15. Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

    Directory of Open Access Journals (Sweden)

    Yuanhai You

    Full Text Available In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.

  16. Microarrays, Integrated Analytical Systems

    Science.gov (United States)

    Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

  17. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Egmont-Peterson, M.; Janssen, I.M.; Smeets, D.F.C.M.; Geurts van Kessel, A.H.M.; Veltman, J.A.

    2007-01-01

    Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a high

  18. Tetromino tilings and the Tutte polynomial

    Science.gov (United States)

    Lykke Jacobsen, Jesper

    2007-02-01

    We consider tiling rectangles of size 4m × 4n by T-shaped tetrominoes. Each tile is assigned a weight that depends on its orientation and position on the lattice. For a particular choice of the weights, the generating function of tilings is shown to be the evaluation of the multivariate Tutte polynomial ZG(Q, v) (known also to physicists as the partition function of the Q-state Potts model) on an (m - 1) × (n - 1) rectangle G, where the parameter Q and the edge weights v can take arbitrary values depending on the tile weights.

  19. Tetromino tilings and the Tutte polynomial

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, Jesper Lykke [Laboratoire de Physique Theorique et Modeles Statistiques, Universite Paris-Sud, Bat. 100, 91405 Orsay (France); Service de Physique Theorique, CEA Saclay, Orme des Merisiers, 91191 Gif-sur-Yvette (France)

    2007-02-16

    We consider tiling rectangles of size 4m x 4n by T-shaped tetrominoes. Each tile is assigned a weight that depends on its orientation and position on the lattice. For a particular choice of the weights, the generating function of tilings is shown to be the evaluation of the multivariate Tutte polynomial Z{sub G}(Q, v) (known also to physicists as the partition function of the Q-state Potts model) on an (m - 1) x (n - 1) rectangle G, where the parameter Q and the edge weights v can take arbitrary values depending on the tile weights.

  20. Beryllium coating on Inconel tiles

    Energy Technology Data Exchange (ETDEWEB)

    Bailescu, V.; Burcea, G.; Lungu, C.P.; Mustata, I.; Lungu, A.M. [Association EURATOM-MEC Romania, National Institute of Laser, Plasma and Radiation Physics, Bucharest (Romania); Rubel, M. [Alfven Laboratory, Royal Institute of Technology, Stockholm (Sweden); Coad, J.P. [Culham Science Centre, EURATOM-UKAEA Fusion Association, Abingdon, OX, Oxon (United Kingdom); Matthews, G.; Pedrick, L.; Handley, R. [UKAEA Fusion, Association Euratom-UKAEA, Culham Science and Engineering Centre, OX 3DB ABINGDON, Oxon (United Kingdom)

    2007-07-01

    Full text of publication follows: The Joint European Torus (JET) is a large experimental nuclear fusion device. Its aim is to confine and study the behaviour of plasma in conditions and dimensions approaching those required for a fusion reactor. The plasma is created in the toroidal shaped vacuum vessel of the machine in which it is confined by magnetic fields. In preparation for ITER a new ITER-like Wall (ILW) will be installed on Joint European Torus (JET), a wall not having any carbon facing the plasma [1]. In places Inconel tiles are to be installed, these tiles shall be coated with Beryllium. MEdC represented by the National Institute for Laser, Plasma and Radiation Physics, Magurele, Bucharest and in direct cooperation with Nuclear Fuel Plant Pitesti started to coat Inconel tiles with 8 {mu}m of Beryllium in accordance with the requirements of technical specification and fit for installation in the JET machine. This contribution provides an overview of the principles of manufacturing processes using thermal evaporation method in vacuum and the properties of the prepared coatings. The optimization of the manufacturing process (layer thickness, structure and purity) has been carried out on Inconel substrates (polished and sand blasted) The results of the optimization process and analysis (SEM, TEM, XRD, Auger, RBS, AFM) of the coatings will be presented. Reference [1] Takeshi Hirai, H. Maier, M. Rubel, Ph. Mertens, R. Neu, O. Neubauer, E. Gauthier, J. Likonen, C. Lungu, G. Maddaluno, G. F. Matthews, R. Mitteau, G. Piazza, V. Philipps, B. Riccardi, C. Ruset, I. Uytdenhouwen, R and D on full tungsten divertor and beryllium wall for JET TIER-like Wall Project, 24. Symposium on Fusion Technology - 11-15 September 2006 -Warsaw, Poland. (authors)

  1. Whole genome methylation profiling by immunoprecipitation of methylated DNA.

    Science.gov (United States)

    Sharp, Andrew J

    2012-01-01

    I provide a protocol for DNA methylation profiling based on immunoprecipitation of methylated DNA using commercially available monoclonal antibodies that specifically recognize 5-methylcytosine. Quantification of the level of enrichment of the resulting DNA enables DNA methylation to be assayed for any genomic locus, including entire chromosomes or genomes if appropriate microarray or high-throughput sequencing platforms are used. In previous studies (1, 2), I have used hybridization to oligonucleotide arrays from Roche Nimblegen Inc, which allow any genomic region of interest to be interrogated, dependent on the array design. For example, using modern tiling arrays comprising millions of oligonucleotide probes, several complete human chromosomes can be assayed at densities of one probe per 100 bp or greater, sufficient to yield high-quality data. However, other methods such as quantitative real-time PCR or high-throughput sequencing can be used, giving either measurement of methylation at a single locus or across the entire genome, respectively. While the data produced by single locus assays is relatively simple to analyze and interpret, global assays such as microarrays or high-throughput sequencing require more complex statistical approaches in order to effectively identify regions of differential methylation, and a brief outline of some approaches is given.

  2. Uniform tiling with electrical resistors

    Energy Technology Data Exchange (ETDEWEB)

    Cserti, Jozsef; Szechenyi, Gabor [Department of Physics of Complex Systems, Eoetvoes University, H-1117 Budapest, Pazmany Peter setany 1/A (Hungary); David, Gyula, E-mail: cserti@elte.hu [Department of Atomic Physics, Eoetvoes University, H-1117 Budapest, Pazmany Peter setany 1/A (Hungary)

    2011-05-27

    The electric resistance between two arbitrary nodes on any infinite lattice structure of resistors that is a periodic tiling of space is obtained. Our general approach is based on the lattice Green's function of the Laplacian matrix associated with the network. We present several non-trivial examples to show how efficient our method is. Deriving explicit resistance formulas it is shown that the Kagome, diced and decorated lattice can be mapped to the triangular and square lattice of resistors. Our work can be extended to the random walk problem or to electron dynamics in condensed matter physics.

  3. Uniform tiling with electrical resistors

    CERN Document Server

    Cserti, Jozsef; David, Gyula

    2011-01-01

    Electric resistances between two arbitrary nodes on any infinite lattice structure of resistor networks that is a periodic tiling of the space is obtained. Our general approach is based on the lattice Green's function of the Laplacian matrix associated with the network. We present several and non-trivial examples to show how efficient our method is. Deriving explicit resistance formulas it is shown that the Kagom\\'e, the diced and the decorated lattice can be mapped to the triangular and square lattice of resistors. Our work can be extended to random walk problem or electron dynamics in condensed matter physics.

  4. Quality Visualization of Microarray Datasets Using Circos

    Directory of Open Access Journals (Sweden)

    Martin Koch

    2012-08-01

    Full Text Available Quality control and normalization is considered the most important step in the analysis of microarray data. At present there are various methods available for quality assessments of microarray datasets. However there seems to be no standard visualization routine, which also depicts individual microarray quality. Here we present a convenient method for visualizing the results of standard quality control tests using Circos plots. In these plots various quality measurements are drawn in a circular fashion, thus allowing for visualization of the quality and all outliers of each distinct array within a microarray dataset. The proposed method is intended for use with the Affymetrix Human Genome platform (i.e., GPL 96, GPL570 and GPL571. Circos quality measurement plots are a convenient way for the initial quality estimate of Affymetrix datasets that are stored in publicly available databases.

  5. Latest news from the Tiles

    CERN Multimedia

    Costanzo, D

    The Tile hadronic calorimeter will be installed in the central region of ATLAS with an inner radius of 2.28 m, an outer radius of 4.25 m, a total length of about 12 m and a weight of about 2300 tons. The calorimeter is mechanically divided in one central barrel and two extended barrels, with a gap in between for the services of the internal part of ATLAS. The construction of the calorimeter is advanced, and installation in the ATLAS pit is foreseen to start in December 2003. After mechanical assembly the modules are instrumented with all the optical components. Scintillating tiles are inserted into the slots, and the read-out Wave Length Shifting fibers are coupled to scintillators and bundled to achieve the quasi-projective cell geometry of the calorimeter. The final modules are stored in bldg 185, shown in the first photo, and in bldg 175 at CERN. The barrel modules are mechanically assembled in Dubna and then transported to CERN to be optically instrumented, while the extended barrels are constructed in t...

  6. Mounting LHCb hadron calorimeter scintillating tiles

    CERN Multimedia

    Maximilien Brice

    2004-01-01

    Scintillating tiles are carefully mounted in the hadronic calorimeter for the LHCb detector. These calorimeters measure the energy of particles that interact via the strong force, called hadrons. The detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

  7. Tiling Problems on Baumslag-Solitar groups.

    Directory of Open Access Journals (Sweden)

    Nathalie Aubrun

    2013-09-01

    Full Text Available We exhibit a weakly aperiodic tile set for Baumslag-Solitar groups, and prove that the domino problem is undecidable on these groups. A consequence of our construction is the existence of an arecursive tile set on Baumslag-Solitar groups.

  8. Shaving Ceramic Tiles To Final Dimensions

    Science.gov (United States)

    Shaw, Ernest

    1992-01-01

    Combination of template and routing tool cuts ceramic tiles to final dimensions. Template guides router along precisely defined planes to accurately and uniformly shave chamfers on edge of tiles. Legs of template temporarily bonded to workpiece by double-backed adhesive tape. Adaptable to in-situ final machining of other nominally flat, narrow surfaces.

  9. Optimal Partial Tiling of Manhattan Polyominoes

    CERN Document Server

    Bodini, Olivier

    2009-01-01

    Finding an efficient optimal partial tiling algorithm is still an open problem. We have worked on a special case, the tiling of Manhattan polyominoes with dominoes, for which we give an algorithm linear in the number of columns. Some techniques are borrowed from traditional graph optimisation problems.

  10. Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae

    Directory of Open Access Journals (Sweden)

    Wang Xianhui

    2009-08-01

    Full Text Available Abstract Background Many species of stalk-eyed flies (Diopsidae possess highly-exaggerated, sexually dimorphic eye-stalks that play an important role in the mating system of these flies. Eye-stalks are increasingly being used as a model system for studying sexual selection, but little is known about the genetic mechanisms producing variation in these ornamental traits. Therefore, we constructed an EST database of genes expressed in the developing eye-antennal imaginal disc of the highly dimorphic species Teleopsis dalmanni. We used this set of genes to construct microarray slides and compare patterns of gene expression between lines of flies with divergent eyespan. Results We generated 33,229 high-quality ESTs from three non-normalized libraries made from the developing eye-stalk tissue at different developmental stages. EST assembly and annotation produced a total of 7,066 clusters comprising 3,424 unique genes with significant sequence similarity to a protein in either Drosophila melanogaster or Anopheles gambiae. Comparisons of the transcript profiles at different stages reveal a developmental shift in relative expression from genes involved in anatomical structure formation, transcription, and cell proliferation at the larval stage to genes involved in neurological processes and cuticle production during the pupal stages. Based on alignments of the EST fragments to homologous sequences in Drosophila and Anopheles, we identified 20 putative gene duplication events in T. dalmanni and numerous genes undergoing significantly faster rates of evolution in T. dalmanni relative to the other Dipteran species. Microarray experiments identified over 350 genes with significant differential expression between flies from lines selected for high and low relative eyespan but did not reveal any primary biological process or pathway that is driving the expression differences. Conclusion The catalogue of genes identified in the EST database provides a valuable

  11. The Level-1 Tile-Muon Trigger in the Tile Calorimeter Upgrade Program

    CERN Document Server

    Ryzhov, Andrey; The ATLAS collaboration

    2016-01-01

    The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). The TileCal provides highly-segmented energy measurements for incident particles. Information from TileCal's last radial layer can assist in muon tagging using Level-1 muon trigger. It can help in the rejection of fake muon triggers arising from background radiation (slow charged particles - protons) without degrading the efficiency of the trigger. The TileCal main activity for Phase-0 upgrade ATLAS program (2013-2014) was the activation of the TileCal third layer signal for assisting the muon trigger at 1.0<|η|<1.3 (Tile-Muon Trigger). This report describes the Tile-Muon Trigger at TileCal upgrade activities, focusing on the new on-detector electronics such as Tile Muon Digitizer Board (TMDB) to provide (receive and digitize) the signal from eight TileCal modules to three Level-1 muon endcap sector logic blocks.

  12. Performance of the TilePPr demonstrator for the ATLAS Tile Calorimeter Phase II Upgrade

    CERN Document Server

    Carrio Argos, Fernando; The ATLAS collaboration

    2015-01-01

    The Tile Calorimeter Pre-processor (TilePPr) demonstrator is a high performance double AMC board based on FPGA resources and QSFP modules. This board has been designed in the framework of the ATLAS Tile Calorimeter (TileCal) Demonstrator Project for the Phase II Upgrade as the first stage of the off-detector electronics. The TilePPr demonstrator has been conceived for receiving and processing the data coming from the on-detector electronics of the TileCal Demonstrator module, as well as for configuring it. Moreover, the TilePPr demonstrator handles the communication with the Detector Control System to monitor and control the on-detector electronics.

  13. The Importance of Normalization on Large and Heterogeneous Microarray Datasets

    Science.gov (United States)

    DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

  14. Consistency and Derangements in Brane Tilings

    CERN Document Server

    Hanany, Amihay; Ramgoolam, Sanjaye; Seong, Rak-Kyeong

    2015-01-01

    Brane tilings describe Lagrangians (vector multiplets, chiral multiplets, and the superpotential) of four dimensional $\\mathcal{N}=1$ supersymmetric gauge theories. These theories, written in terms of a bipartite graph on a torus, correspond to worldvolume theories on $N$ D$3$-branes probing a toric Calabi-Yau threefold singularity. A pair of permutations compactly encapsulates the data necessary to specify a brane tiling. We show that geometric consistency for brane tilings, which ensures that the corresponding quantum field theories are well behaved, imposes constraints on the pair of permutations, restricting certain products constructed from the pair to have no one-cycles. Permutations without one-cycles are known as derangements. We illustrate this formulation of consistency with known brane tilings. Counting formulas for consistent brane tilings with an arbitrary number of chiral bifundamental fields are written down in terms of delta functions over symmetric groups.

  15. Electrokinetic desalination of glazed ceramic tiles

    DEFF Research Database (Denmark)

    Ottosen, Lisbeth M.; Ferreira, Celia; Christensen, Iben Vernegren

    2010-01-01

    Electrokinetic desalination is a method where an applied electric DC field is the driving force for removal of salts from porous building materials. In the present paper, the method is tested in laboratory scale for desalination of single ceramic tiles. In a model system, where a tile...... was contaminated with NaCl during submersion and subsequently desalinated by the method, the desalination was completed in that the high and problematic initial Cl(-) concentration was reduced to an unproblematic concentration. Further conductivity measurements showed a very low conductivity in the tile after...... renovation due to damage of the glazing from the presence of salts. These tiles were severely contaminated with both chlorides and nitrates, and one of the tiles also contained sulphates though at a low concentration. The charge transfer was too low in the experiments to obtain full desalination...

  16. Performance of the ATLAS hadronic Tile calorimeter

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00304670; The ATLAS collaboration

    2016-01-01

    The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted to photomultiplier tubes (PMTs). Signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. Results on the calorimeter operation and performance are presented, including the calibration, stability, absolute energy scale, uniformity and time resolution. These results show that the TileCal performance is within the design requirements and has given essential contribution to reconstructed objects and physics results.

  17. Effect of DNA Hairpin Loops on the Twist of Planar DNA Origami Tiles

    Science.gov (United States)

    Li, Zhe; Wang, Lei; Yan, Hao; Liu, Yan

    2012-01-01

    The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D)DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved. PMID:22126326

  18. Micro-Scale Genomic DNA Copy Number Aberrations as Another Means of Mutagenesis in Breast Cancer

    Science.gov (United States)

    Chao, Hann-Hsiang; He, Xiaping; Parker, Joel S.; Zhao, Wei; Perou, Charles M.

    2012-01-01

    Introduction In breast cancer, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations, as shown by a previously described micro-deletion event in the PTEN gene in the Basal-like SUM149 breast cancer cell line. Methods We sought to identify if small regions of genomic DNA copy number changes exist by using a high density, gene-centric Comparative Genomic Hybridizations (CGH) array on cell lines and primary tumors. A custom tiling array for CGH (244,000 probes, 200 bp tiling resolution) was created to identify small regions of genomic change, which was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments were called micro-aberrations (micro-aberrations, most of which are undetectable using typical-density genome-wide aCGH arrays. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene. We confirmed the presence of the PTEN micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5′ regions of the affected genes, including the promoter region, and high frequency of micro-aberrations was associated with poor survival. Conclusion Using a high-probe-density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that can contribute to gene inactivation. These events may contribute to tumor formation through mechanisms not detected using conventional DNA copy number analyses. PMID:23284754

  19. Review: DNA microarray technology and drug development

    Directory of Open Access Journals (Sweden)

    Sana Khan

    2010-01-01

    Full Text Available On the contrary to slow and non specific traditional drug discovery methods, DNA microarray technology could accelerate the identification of potential drugs for treating diseases like cancer, AIDS and provide fruitful results in the drug discovery. The technique provides efficient automation and maximum flexibility to the researchers and can test thousand compounds at a time. Scientists find DNA microarray useful in disease diagnosis, monitoring desired and adverse outcomes of therapeutic interventions, as well as, in the selection, assessment and quality con-trol of the potential drugs. In the current scenario, where new pathogens are expected every year, DNA microarray promises as an efficient technology to detect new organisms in a short time. Classification of carcinomas at the molecular level and prediction of how various types of tumor respond to different therapeutic agents can be made possible with the use of microarray analysis. Also, microarray technique can prove instrumental in personalized medicines development by providing microarray data of a patient which could be used for identifying diseases, treatment specific to individual and trailing disease prognosis. Microarray analysis could be beneficial in the area of molecular medicines for analysis of genetic variations and functions of genes in normal individuals and diseased conditions. The technique can give satisfactory results in single nucleotide polymorphism (SNP analysis and pharmacogenomics studies. The challenges that arise with the technology are high degree of variability with data obtained, frequent up gradation of methods and machines and lack of trained manpower. Despite this, DNA micro-array promises to be the next generation sequencer which could explain how organisms evolve and adapt looking at the whole genome. In a nutshell, Microarray technology makes it possible for molecular biologists to analyze simultaneously thousands of DNA samples and monitor their

  20. Identification of mycotoxigenic fungi using an oligonucleotide microarray

    CSIR Research Space (South Africa)

    Barros, E

    2013-01-01

    Full Text Available , numerous detection tools have been developed for the detection and analysis of various mycotoxigenic fungi. These include PCR-based assays and microarrays targeting different areas of the fungal genome depending on its application. This chapter describes...

  1. HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data

    Directory of Open Access Journals (Sweden)

    Wouters Bas J

    2010-05-01

    Full Text Available Abstract Background Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased, the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with increased signal intensity (as a result of hybridization of labeled DNA in a region. Currently, no standard criteria are available to define these regions-of-interest as there is no single probe intensity cut-off level, different regions-of-interest can contain various numbers of probes, and can vary in genomic width. Furthermore, the chromosomal distance between neighboring probes can vary across the genome among different arrays. Results We have developed Hypergeometric Analysis of Tiling-arrays (HAT, and first evaluated its performance for tiling-array datasets from a Chromatin Immunoprecipitation study on chip (ChIP-on-chip for the identification of genome-wide DNA binding profiles of transcription factor Cebpa (used for method comparison. Using this assay, we can refine the detection of regions-of-interest by illustrating that regions detected by HAT are more highly enriched for expected motifs in comparison with an alternative detection method (MAT. Subsequently, data from a retroviral insertional mutagenesis screen were used to examine the performance of HAT among different applications of tiling-array datasets. In both studies, detected regions-of-interest have been validated with (qPCR. Conclusions We demonstrate that HAT has increased specificity for analysis of tiling-array data in comparison with the alternative method, and that it accurately detects regions-of-interest in two different applications of tiling-arrays. HAT has several advantages over previous methods: i as there is no single cut-off level for probe-intensity, HAT can detect regions-of-interest at various thresholds, ii it can

  2. The Level-1 Tile-Muon Trigger in the Tile Calorimeter Upgrade Program

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00414625; The ATLAS collaboration

    2016-01-01

    The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). The TileCal provides highly-segmented energy measurements for incident particles. Information from TileCal's outermost radial layer can assist in muon tagging in the Level-1 Muon Trigger by rejecting fake muon triggers arising from background radiation (slow charged particles - protons) without degrading the efficiency of the trigger. The TileCal main activity for the ATLAS Phase-0 upgrade program (2013-2014) was the activation of the TileCal outermost D-layer signal for assisting the Level-1 Muon Trigger at 1.0<|η|<1.3. This report describes the Tile-Muon Trigger within the TileCal upgrade activities, focusing on the new on-detector electronics such as the Tile Muon Digitizer Board (TMDB) providing (receive and digitize) the signal from eight TileCal modules to three Level-1 muon end-cap sector logic blocks.

  3. Seamless stitching of tile scan microscope images.

    Science.gov (United States)

    Legesse, F B; Chernavskaia, O; Heuke, S; Bocklitz, T; Meyer, T; Popp, J; Heintzmann, R

    2015-06-01

    For diagnostic purposes, optical imaging techniques need to obtain high-resolution images of extended biological specimens in reasonable time. The field of view of an objective lens, however, is often smaller than the sample size. To image the whole sample, laser scanning microscopes acquire tile scans that are stitched into larger mosaics. The appearance of such image mosaics is affected by visible edge artefacts that arise from various optical aberrations which manifest in grey level jumps across tile boundaries. In this contribution, a technique for stitching tiles into a seamless mosaic is presented. The stitching algorithm operates by equilibrating neighbouring edges and forcing the brightness at corners to a common value. The corrected image mosaics appear to be free from stitching artefacts and are, therefore, suited for further image analysis procedures. The contribution presents a novel method to seamlessly stitch tiles captured by a laser scanning microscope into a large mosaic. The motivation for the work is the failure of currently existing methods for stitching nonlinear, multimodal images captured by our microscopic setups. Our method eliminates the visible edge artefacts that appear between neighbouring tiles by taking into account the overall illumination differences among tiles in such mosaics. The algorithm first corrects the nonuniform brightness that exists within each of the tiles. It then compensates for grey level differences across tile boundaries by equilibrating neighbouring edges and forcing the brightness at the corners to a common value. After these artefacts have been removed further image analysis procedures can be applied on the microscopic images. Even though the solution presented here is tailored for the aforementioned specific case, it could be easily adapted to other contexts where image tiles are assembled into mosaics such as in astronomical or satellite photos.

  4. Fibrous-Ceramic/Aerogel Composite Insulating Tiles

    Science.gov (United States)

    White, Susan M.; Rasky, Daniel J.

    2004-01-01

    Fibrous-ceramic/aerogel composite tiles have been invented to afford combinations of thermal-insulation and mechanical properties superior to those attainable by making tiles of fibrous ceramics alone or aerogels alone. These lightweight tiles can be tailored to a variety of applications that range from insulating cryogenic tanks to protecting spacecraft against re-entry heating. The advantages and disadvantages of fibrous ceramics and aerogels can be summarized as follows: Tiles made of ceramic fibers are known for mechanical strength, toughness, and machinability. Fibrous ceramic tiles are highly effective as thermal insulators in a vacuum. However, undesirably, the porosity of these materials makes them permeable by gases, so that in the presence of air or other gases, convection and gas-phase conduction contribute to the effective thermal conductivity of the tiles. Other disadvantages of the porosity and permeability of fibrous ceramic tiles arise because gases (e.g., water vapor or cryogenic gases) can condense in pores. This condensation contributes to weight, and in the case of cryogenic systems, the heat of condensation undesirably adds to the heat flowing to the objects that one seeks to keep cold. Moreover, there is a risk of explosion associated with vaporization of previously condensed gas upon reheating. Aerogels offer low permeability, low density, and low thermal conductivity, but are mechanically fragile. The basic idea of the present invention is to exploit the best features of fibrous ceramic tiles and aerogels. In a composite tile according to the invention, the fibrous ceramic serves as a matrix that mechanically supports the aerogel, while the aerogel serves as a low-conductivity, low-permeability filling that closes what would otherwise be the open pores of the fibrous ceramic. Because the aerogel eliminates or at least suppresses permeation by gas, gas-phase conduction, and convection, the thermal conductivity of such a composite even at

  5. Microarray Analysis of Serum mRNA in Patients with Head and Neck Squamous Cell Carcinoma at Whole-Genome Scale

    Directory of Open Access Journals (Sweden)

    Markéta Čapková

    2014-01-01

    Full Text Available With the increasing demand for noninvasive approaches in monitoring head and neck cancer, circulating nucleic acids have been shown to be a promising tool. We focused on the global transcriptome of serum samples of head and neck squamous cell carcinoma (HNSCC patients in comparison with healthy individuals. We compared gene expression patterns of 36 samples. Twenty-four participants including 16 HNSCC patients (from 12 patients we obtained blood samples 1 year posttreatment and 8 control subjects were recruited. The Illumina HumanWG-6 v3 Expression BeadChip was used to profile and identify the differences in serum mRNA transcriptomes. We found 159 genes to be significantly changed (Storey’s P value <0.05 between normal and cancer serum specimens regardless of factors including p53 and B-cell lymphoma family members (Bcl-2, Bcl-XL. In contrast, there was no difference in gene expression between samples obtained before and after surgery in cancer patients. We suggest that microarray analysis of serum cRNA in patients with HNSCC should be suitable for refinement of early stage diagnosis of disease that can be important for development of new personalized strategies in diagnosis and treatment of tumours but is not suitable for monitoring further development of disease.

  6. A Whole-Genome Microarray Study of Arabidopis Thaliana Cell Cultures Exposed to Real and Simulated Partial-G Forces: A Comparison of Parabolic Flight and Clinostat Data

    Science.gov (United States)

    Fengler, S.; Spirer, I.; Neef, M.; Ecke, M.; Hauslage, J.; Hampp, R.

    2015-09-01

    Cell cultures of the plant model organism Arabidopsis thaliana were exposed to partial-g forces during parabolic flight and clinostat experiments (0.38 g, 0. 16 g and 0.5 g). To investigate gravity-dependent alterations in gene expression, samples were metabolically quenched and used for microarray analysis. An attempt to identify the potential threshold acceleration showed that the smaller the experienced g-force, the greater was the susceptibility of the cell cultures. Compared to short-term ~sg during a regular parabolic flight, the number of differentially expressed genes under partial-g was lower. In addition, the effect on the alteration of amounts of transcripts decreased during partial-g parabolic flight due to the sequence of the different parabolas (0.38 g, 0.16 g and ~sg). A time-dependent analysis under simulated 0.5 g indicates that adaptation occurs within minutes. Differentially expressed genes (at least 2-fold altered in expression) under real flight conditions were to some extent identical with those affected by clinorotation. The highest number of identical genes was detected within seconds of exposure to 0.38 g.

  7. Genome-wide profiling of long non-coding RNA expression patterns in the EGFR-TKI resistance of lung adenocarcinoma by microarray.

    Science.gov (United States)

    Wu, Ying; Yu, Dan-Dan; Hu, Yong; Yan, Dali; Chen, Xiu; Cao, Hai-Xia; Yu, Shao-Rong; Wang, Zhuo; Feng, Ji-Feng

    2016-06-01

    Mutations in the epidermal growth factor receptor (EGFR) make lung adenocarcinoma cells sensitive to EGFR tyrosine kinase inhibitors (TKIs). Long-term cancer therapy may cause the occurrence of acquired resistance to EGFR TKIs. Long non-coding RNAs (lncRNAs) play important roles in tumor formation, tumor metastasis and the development of EGFR-TKI resistance in lung cancer. To gain insight into the molecular mechanisms of EGFR-TKI resistance, we generated an EGFR-TKI-resistant HCC827-8-1 cell line and analyzed expression patterns by lncRNA microarray and compared it with its parental HCC827 cell line. A total of 1,476 lncRNA transcripts and 1,026 mRNA transcripts were dysregulated in the HCC827‑8-1 cells. The expression levels of 7 chosen lncRNAs were validated by real-time quantitative PCR. As indicated by functional analysis, several groups of lncRNAs may be involved in the bio-pathways associated with EGFR-TKI resistance through their cis- and/or trans‑regulation of protein-coding genes. Thus, lncRNAs may be used as novel candidate biomarkers and potential targets in EGFR-TKI therapy in the future.

  8. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Directory of Open Access Journals (Sweden)

    Heike Horn

    Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  9. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    Science.gov (United States)

    Horn, Heike; Bausinger, Julia; Staiger, Annette M; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M Michaela; Rosenwald, Andreas; Ott, German

    2014-01-01

    Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.

  10. Expression profile analysis of the oxygen response in the nitrogen-fixing Pseudomonas stutzeri A1501 by genome-wide DNA microarray

    Institute of Scientific and Technical Information of China (English)

    DOU YueTan; YAN YongLiang; PING ShuZhen; LU Wei; CHEN Ming; ZHANG Wei; WANG YiPing; JIN Qi; LIN Min

    2008-01-01

    Pseudomonas stutzeri A1501, an associative nitrogen-fixing bacterium, was isolated from the rice paddy rhizosphere. This bacterium fixes nitrogen under microaerobic conditions. In this study, ge-nome-wide DNA microarrays were used to analyze the global transcription profile of A1501 under aerobic and microaerobic conditions. The expression of 135 genes was significantly altered by more than 2-fold in response to oxygen stress. Among these genes, 68 were down-regulated under aerobic conditions; these genes included those responsible for nitrogen fixation and denitrification. Sixty-seven genes were up-regulated under aerobic conditions; these genes included sodC, encoding a copper-zinc superoxide dismutase, PST2179, encoding an NAD(P)-dependent oxidoreductase, PST3584, encoding a 2OG-Fe(Ⅱ) oxygenase, and PST3602, encoding an NAD(P)H-flavin oxidoreductase. Addi-tionally, seven genes involved in capsular polysaccharide and antigen oligosaccharide biosynthesis together with 17 genes encoding proteins of unknown function were up-regulated under aerobic con-ditions. The overall analysis suggests that the genes we identified are involved in the protection of the bacterium from oxygen, but the mechanisms of their action remain to be elucidated.

  11. Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

    Energy Technology Data Exchange (ETDEWEB)

    Railo, Antti [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Pajunen, Antti [Department of Biochemistry, University of Oulu (Finland); Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Vainio, Seppo, E-mail: Seppo.Vainio@oulu.fi [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland)

    2009-10-01

    Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays of gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.

  12. Introductory Tiling Theory for Computer Graphics

    CERN Document Server

    Kaplan, Craig

    2009-01-01

    Tiling theory is an elegant branch of mathematics that has applications in several areas of computer science. The most immediate application area is graphics, where tiling theory has been used in the contexts of texture generation, sampling theory, remeshing, and of course the generation of decorative patterns. The combination of a solid theoretical base (complete with tantalizing open problems), practical algorithmic techniques, and exciting applications make tiling theory a worthwhile area of study for practitioners and students in computer science. This synthesis lecture introduces the math

  13. Modular robotic tiles: experiments for children with autism

    DEFF Research Database (Denmark)

    Lund, Henrik Hautop; Dam Pedersen, Martin; Beck, Richard

    2009-01-01

    We developed a modular robotic tile and a system composed of a number of these modular robotic tiles. The system composed of the modular robotic tiles engages the user in physical activities, e.g., physiotherapy, sports, fitness, and entertainment. The modular robotic tiles motivate the user to p...

  14. Tile-Packing Tomography Is NP-hard

    DEFF Research Database (Denmark)

    Chrobak, Marek; Dürr, Christoph; Guíñez, Flavio;

    2010-01-01

    Discrete tomography deals with reconstructing finite spatial objects from their projections. The objects we study in this paper are called tilings or tile-packings, and they consist of a number of disjoint copies of a fixed tile, where a tile is defined as a connected set of grid points. A row pr...

  15. Towards standardization of microarray-based genotyping of Salmonella

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Grønlund, Hugo Ahlm; Riber, Leise

    2010-01-01

    Genotyping is becoming an increasingly important tool to improve risk assessments of Salmonella. DNA microarray technology is a promising diagnostic tool that can provide high resolution genomic profile of many genes simultaneously. However, standardization of DNA microarray analysis is needed...... of Salmonella at two different laboratories. The low-density array contained 281 of 57-60-mer oligonucleotide probes for detecting a wide range of specific genomic markers associated with antibiotic resistance, cell envelope structures, mobile genetic elements and pathogenicity. Several test parameters...... for a decentralized and simple-to-implement DNA microarray as part of a pan-European source-attribution model for risk assessment of Salmonella....

  16. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  17. Real-Time Texture Synthesis Using s-Tile Set

    Institute of Scientific and Technical Information of China (English)

    Feng Xue; You-Sheng Zhang; Ju-Lang Jiang; Min Hu; Xin-Dong Wu; Rong-Gui Wang

    2007-01-01

    This paper presents a novel method of generating a set of texture tiles from samples, which can be seamlessly tiled into arbitrary size textures in real-time. Compared to existing methods, our approach is simpler and more advantageous in eliminating visual seams that may exist in each tile of the existing methods, especially when the samples have elaborate features or distinct colors. Texture tiles generated by our approach can be regarded as single-colored tiles on each orthogonal direction border, which are easier for tiling and more suitable for sentence tiling. Experimental results demonstrate the feasibility and effectiveness of our approach.

  18. High-Strength, Low-Shrinkage Ceramic Tiles

    Science.gov (United States)

    Wheeler, W. H.; Creedon, J. F.

    1986-01-01

    Addition of refractory fibers and whiskers to insulating tiles composed primarily of fibrous silica, such as those used on the skin of Space Shuttle orbiter, greatly improves properties. New composition suitable for lightweight, thermally-stable mirror blanks and as furnace and kiln insulation. Improved tiles made with current tile-fabrication processes. For given density, tiles containing silicon carbide and boron additives stronger in flexure than tiles made from silica alone. In addition, tiles with additives nearly immune to heat distortion, whereas pure-silica tiles shrink and become severely distorted.

  19. Single-species microarrays and comparative transcriptomics.

    Directory of Open Access Journals (Sweden)

    Frédéric J J Chain

    Full Text Available BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.

  20. Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.

    Science.gov (United States)

    Kim, Byoung-Chan; Postier, Bradley L; Didonato, Raymond J; Chaudhuri, Swades K; Nevin, Kelly P; Lovley, Derek R

    2008-06-01

    Geobacter sulfurreducens effectively produces electricity in microbial fuel cells by oxidizing acetate with an electrode serving as the sole electron acceptor. Deletion of the gene encoding OmcF, a monoheme outer membrane c-type cytochrome, substantially decreased current production. Previous studies demonstrated that inhibition of Fe(III) reduction in the OmcF-deficient mutant could be attributed to poor transcription of the gene for OmcB, an outer membrane c-type cytochrome that is required for Fe(III) reduction. However, a mutant in which omcB was deleted produced electricity as well as wild type. Microarray analysis of the OmcF-deficient mutant versus the wild type revealed that many of the genes with the greatest decreases in transcript levels were genes whose expression was previously reported to be upregulated in cells grown with an electrode as the sole electron acceptor. These included genes with putative functions related to metal efflux and/or type I secretion and two hypothetical proteins. The outer membrane cytochromes, OmcS and OmcE, which previous studies have demonstrated are required for optimal current generation, were not detected on the outer surface of the OmcF-deficient mutant even though the omcS and omcE genes were still transcribed, suggesting that the putative secretion system could be involved in the export of outer membrane proteins necessary for electron transfer to the fuel cell anode. These results suggest that the requirement for OmcF for optimal current production is not because OmcF is directly involved in extracellular electron transfer but because OmcF is required for the appropriate transcription of other genes either directly or indirectly involved in electricity production.

  1. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    -linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting...... years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...

  2. Instrumented module of the ATLAS tile calorimeter

    CERN Multimedia

    Laurent Guiraud

    1998-01-01

    The ATLAS tile calorimeter consists of steel absorber plates interspersed with plastic scintillator tiles. Interactions of high-energy hadrons in the plates transform the incident energy into a 'hadronic shower'. When shower particles traverse the scintillating tiles, the latter emit an amount of light proportional to the incident energy. This light is transmitted along readout fibres to a photomultiplier, where a detectable electrical signal is produced. These pictures show one of 64 modules or 'wedges' of the barrel part of the tile calorimeter, which are arranged to form a cylinder around the beam axis. The wedge has been instrumented with scintillators and readout fibres. Photos 03, 06: Checking the routing of the readout fibres into the girder that houses the photomultipliers. Photo 04: A view of the fibre bundles inside the girder.

  3. ATLAS Tile calorimeter calibration and monitoring systems

    CERN Document Server

    Chomont, Arthur Rene; The ATLAS collaboration

    2016-01-01

    The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser and charge injection elements and it allows to monitor and equalize the calorimeter response at each stage of the signal production, from scin...

  4. The ATLAS Tile Calorimeter performance at LHC

    CERN Document Server

    Cuciuc, M; The ATLAS collaboration

    2012-01-01

    The Tile Calorimeter (TileCal), the central section of the hadronic calorimeter of the ATLAS experiment, is a key detector component to detect hadrons, jets and taus and to measure the missing transverse energy. Due to the very good muon signal to noise ratio it assists the spectrometer in the identification and reconstruction of muons. TileCal is built of steel and scintillating tiles coupled to optical fibers and read out by photomultipliers. The calorimeter is equipped with systems that allow to monitor and to calibrate each stage of the readout system exploiting different signal sources: laser light, charge injection and a radioactive source. The calorimeter performance and its stability has been evaluated with the rich sample of collision data in 2011 but also with calibration data, random triggered data, cosmic muons and splash events. Results on the absolute energy scale calibration precision, on the energy and timing uniformity, on the time resolution and on the synchronization precision are presented...

  5. 2011 Las Conchas Post Fire Tile Index

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This data set consists of an orthophotography tile index based on multi-spectral (red, green, blue, near-infrared) digital aerial imagery, collected and processed by...

  6. Electrochemical desalination of historic Portuguese tiles

    DEFF Research Database (Denmark)

    Ottosen, Lisbeth M.; Dias-Ferreira, Celia; Ribeiro, Alexandra B.

    2015-01-01

    Soluble salts cause severe decay of historic Portuguese tiles. Treatment options for removal of the salts to stop the decay are few. The present paper deals with development of a method for electrochemical desalination, where an electric DC field is applied to the tiles. Laboratory experiments were...... and glaze, where salt crystals were clearly identified by SEM-EDX before desalination. The concentrations of chloride and especially nitrate were very high in the tiles (around 280 mmol Cl−/kg and 450 mmol NO3−/kg respectively). Both anions were successfully removed to below 6 mmol/kg during...... was initially very low, but nevertheless, sulfate removal started at the point where chloride and nitrate concentrations were very low in the tiles. Investigating the interface between biscuit and glaze after the treatment showed no signs of crystallized salts, so also in this important point, the desalination...

  7. ATLAS Tile calorimeter calibration and monitoring systems

    CERN Document Server

    Chomont, Arthur Rene; The ATLAS collaboration

    2016-01-01

    The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser and charge injection elements and it allows to monitor and equalize the calorimeter response at each stage of the signal production, from scin...

  8. Applied physics: The virtues of tiling

    Science.gov (United States)

    Fratzl, Peter

    2014-12-01

    A cracked metal film on an elastic substrate has been shown to provide ultrahigh sensitivity in detecting mechanical vibrations. The result draws inspiration from principles of tiling that apply to many biological systems. See Letter p.222

  9. GIBS Web Map Tile Service (WMTS)

    Data.gov (United States)

    National Aeronautics and Space Administration — The WMTS implementation standard provides a standards-based solution for serviing digital maps using predefined image tiles. Through the constructs of the...

  10. Performance of the ATLAS Tile Calorimeter

    CERN Document Server

    Solodkov, Alexander; The ATLAS collaboration

    2015-01-01

    The Tile Calorimeter (TileCal), the central section of the hadronic calorimeter of the ATLAS experiment, is a key detector component to detect hadrons, jets and taus and to measure the missing transverse energy. Due to the very good muon signal to noise ratio it assists the spectrometer in the identification and reconstruction of muons. The calorimeter consists of thin steel plates and 460,000 scintillating tiles configured into 5182 cells, each viewed by two photomultipliers. The calorimeter response and its readout electronics is monitored to better than 1\\% using radioactive source, laser and charge injection systems. The performance of the calorimeter has been measured and monitored using calibration data, cosmic ray muons and the large sample of proton-proton collisions acquired in 2011 and 2012. The results demonstrate a very good understanding of the performance of the Tile Calorimeter that is well within the design expectations.

  11. Performance of the ATLAS Tile Calorimeter

    CERN Document Server

    Solodkov, Alexander; The ATLAS collaboration

    2015-01-01

    The ATLAS Tile hadronic calorimeter (TileCal) provides highly-segmented energy measurements of incoming particles. It is a key detector for the measurement of hadrons, jets, tau leptons and missing transverse energy. It is also useful for identification and reconstruction of muons due to good signal to noise ratio. The calorimeter consists of thin steel plates and 460,000 scintillating tiles configured into 5000 cells, each viewed by two photomultipliers. The calorimeter response and its readout electronics is monitored to better than 1% using radioactive source, laser and charge injection systems. The calibration and performance of the calorimeter have been established through test beam measurements, cosmic ray muons and the large sample of muons and single hadrons from proton-proton collisions acquired in 2011 and 2012. The results demonstrate that the Tile Calorimeter has performed well within the design requirements and it has given essential contribution to reconstructed objects and physics results.

  12. Electrochemical desalination of historic Portuguese tiles

    DEFF Research Database (Denmark)

    Ottosen, Lisbeth M.; Dias-Ferreira, Celia; Ribeiro, Alexandra B.

    2015-01-01

    Soluble salts cause severe decay of historic Portuguese tiles. Treatment options for removal of the salts to stop the decay are few. The present paper deals with development of a method for electrochemical desalination, where an electric DC field is applied to the tiles. Laboratory experiments were...... and glaze, where salt crystals were clearly identified by SEM-EDX before desalination. The concentrations of chloride and especially nitrate were very high in the tiles (around 280 mmol Cl−/kg and 450 mmol NO3−/kg respectively). Both anions were successfully removed to below 6 mmol/kg during...... was initially very low, but nevertheless, sulfate removal started at the point where chloride and nitrate concentrations were very low in the tiles. Investigating the interface between biscuit and glaze after the treatment showed no signs of crystallized salts, so also in this important point, the desalination...

  13. VB Platinum Tile & Carpet, Inc. Information Sheet

    Science.gov (United States)

    VB Platinum Tile & Carpet, Inc. (the Company) is located in Bristow, Virginia. The settlement involves renovation activities conducted at a property constructed prior to 1978, located in Washington, DC.

  14. On reconfigurable tiled multi-core programming

    NARCIS (Netherlands)

    Rovers, Kenneth C.; Burgwal, van de Marcel D.; Kuper, Jan; Kokkeler, Andre B.J.; Smit, Gerard J.M.

    2009-01-01

    For a generic flexible efficient array antenna receiver platform a hierarchical reconfigurable tiled architecture has been proposed. The architecture provides a flexible reconfigurable solution, but partitioning, mapping, modelling and programming such systems remains an issue. A semantic model has

  15. Notch sensitivity of space shuttle tile materials

    Science.gov (United States)

    Newman, J. C., Jr.

    1980-01-01

    Tests were conducted at room temperature to determine the notch sensitivity of the thermal protection tile for the space shuttle. Two types of RSI tile were studied: LI-900 and LI-2200. Three point bend specimens were cut from discarded tiles in the in-plane (ip) and through-the-thickness (ttt) directions. They were tested with or without a sharp notch. The LI-900 (ip and ttt) specimens were not very notch sensitive, but the LI-2200 (ip and ttt) specimens were. The LI-2200 material showed about a 35 percent reduction in strength due to the presence of the notch. This reduction in strength should be considered in the design of mechanically fastened tile concepts.

  16. Detector Control System of Tile Calorimeter

    CERN Document Server

    Arabidze, G; The ATLAS collaboration

    2009-01-01

    The subject of this presentation is to describe the Detector Control System (DCS) implementation for Tile Calorimeter sub-detector. It describes hardware layout and software components for main, infrastructure related and sub-detector calibration systems. It discusses implementation of the top level software Finite State Machine (FSM)and discusses state models of FSM objects. Presentation shows usage of Configuration and Conditions Data Bases, for Tile Calorimeter DCS.

  17. Cutting Symmetrical Recesses In Soft Ceramic Tiles

    Science.gov (United States)

    Nesotas, Tony C.; Tyler, Brent

    1989-01-01

    Simple tool cuts hemispherical recesses in soft ceramic tiles. Designed to expose wires of thermocouples embedded in tiles without damaging leads. Creates neat, precise holes around wires. End mill includes axial hole to accommodate thermocouple wires embedded in material to be cut. Wires pass into hole without being bent or broken. Dimensions in inches. Used in place of such tools as dental picks, tweezers, spatulas, and putty knives.

  18. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  19. Organizing DNA origami tiles into larger structures using preformed scaffold frames.

    Science.gov (United States)

    Zhao, Zhao; Liu, Yan; Yan, Hao

    2011-07-13

    Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as "superorigami" or "origami of origami" to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.

  20. TiArA: a virtual appliance for the analysis of Tiling Array data.

    Directory of Open Access Journals (Sweden)

    Jason A Greenbaum

    Full Text Available BACKGROUND: Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis. METHODOLOGY/PRINCIPAL FINDINGS: Tiling Array Analyzer (TiArA is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range. CONCLUSIONS/SIGNIFICANCE: TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.

  1. On the structure of quadrilateral brane tilings

    CERN Document Server

    de Medeiros, Paul

    2011-01-01

    Brane tilings provide the most general framework in string and M-theory for matching toric Calabi-Yau singularities probed by branes with superconformal fixed points of quiver gauge theories. The brane tiling data consists of a bipartite tiling of the torus which encodes both the classical superpotential and gauge-matter couplings for the quiver gauge theory. We consider the class of tilings which contain only tiles bounded by exactly four edges and present a method for generating any tiling within this class by iterating combinations of certain graph-theoretic moves. In the context of D3-branes in IIB string theory, we consider the effect of these generating moves within the corresponding class of supersymmetric quiver gauge theories in four dimensions. Of particular interest are their effect on the superpotential, the vacuum moduli space and the conditions necessary for the theory to reach a superconformal fixed point in the infrared. We discuss the general structure of physically admissible quadrilateral b...

  2. Performance of the ATLAS hadronic Tile calorimeter

    CERN Document Server

    Bartos, Pavol; The ATLAS collaboration

    2016-01-01

    Performance of the ATLAS hadronic Tile calorimeter The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter have been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations o...

  3. Glazed Tiles as Floor Finish in Nigeria

    Directory of Open Access Journals (Sweden)

    Toyin Emmanuel AKINDE

    2013-09-01

    Full Text Available Tile is no doubt rich in antiquity; its primordial  show, came as mosaic with primary prospect in sacred floor finish before its oblivion, courtesy of, later consciousness towards wall finish in banquets, kitchens, toilets, restaurants and even bars. Today, its renaissance as floor finish is apparent in private and public architectural structures with prevalence in residential, recreational, commercial, governmental and other spaces. In Nigeria, the use of glazed tiles as floor finish became apparent, supposedly in mid-twentieth century; and has since, witnessed ever increasing demands from all sundry; a development that is nascent and has necessitated its mass  production locally with pockets of firms in the country. The latter however, is a resultant response to taste cum glazed tiles affordability, whose divergent sophistication in design, colour, size and shape is believed preferred to terrazzo, carpet and floor flex tile. Accessible as glazed tile and production is, in recent times; its dearth of a holistic literature in Nigeria is obvious. In the light of the latter, this paper examine glazed tiles as floor finish in Nigeria, its advent, usage, production, challenge, benefit and prospect with the hope of opening further frontier in discipline specifics.

  4. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis

    DEFF Research Database (Denmark)

    Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A

    2017-01-01

    BACKGROUND: Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their d......BACKGROUND: Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account......, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. RESULTS: Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32......: Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors....

  5. Mass-deformed Brane Tilings

    CERN Document Server

    Bianchi, Massimo; Hanany, Amihay; Morales, Jose Francisco; Pacifici, Daniel Ricci; Seong, Rak-Kyeong

    2014-01-01

    We study renormalization group flows among N=1 SCFTs realized on the worldvolume of D3-branes probing toric Calabi-Yau singularities, thus admitting a brane tiling description. The flows are triggered by masses for adjoint or vector-like pairs of bifundamentals and are generalizations of the Klebanov-Witten construction of the N=1 theory for the conifold starting from the N=2 theory for the C^2/Z_2 orbifold. In order to preserve the toric condition pairs of masses with opposite signs have to be switched on. We offer a geometric interpretation of the flows as complex deformations of the Calabi-Yau singularity preserving the toric condition. For orbifolds, we support this interpretation by an explicit string amplitude computation of the gauge invariant mass terms generated by imaginary self-dual 3-form fluxes in the twisted sector. In agreement with the holographic a-theorem, the volume of the Sasaki-Einstein 5-base of the Calabi-Yau cone always increases along the flow.

  6. Microarray Analysis in Glioblastomas

    Science.gov (United States)

    Bhawe, Kaumudi M.; Aghi, Manish K.

    2016-01-01

    Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930–2942, 2012)To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013)To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59–70, 2013; Verhaak et al., Cancer Cell 17(1):98–110, 2010) While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here. PMID:26113463

  7. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

    Directory of Open Access Journals (Sweden)

    Zhou Jizhong

    2007-06-01

    Full Text Available Abstract Background Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. Results The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold

  8. A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

    Science.gov (United States)

    Ronald, Angelica; Butcher, Lee M; Docherty, Sophia; Davis, Oliver S P; Schalkwyk, Leonard C; Craig, Ian W; Plomin, Robert

    2010-01-01

    Two separate genome-wide association studies were conducted to identify single nucleotide polymorphisms (SNPs) associated with social and nonsocial autistic-like traits. We predicted that we would find SNPs associated with social and non-social autistic-like traits and that different SNPs would be associated with social and nonsocial. In Stage 1, each study screened for allele frequency differences in approximately 430,000 autosomal SNPs using pooled DNA on microarrays in high-scoring versus low-scoring boys from a general population sample (N = approximately 400/group). In Stage 2, 22 and 20 SNPs in the social and non-social studies, respectively, were tested for QTL association by individually genotyping an independent community sample of 1,400 boys. One SNP (rs11894053) was nominally associated (P < .05, uncorrected for multiple testing) with social autistic-like traits. When the sample was increased by adding females, 2 additional SNPs were nominally significant (P < .05). These 3 SNPs, however, showed no significant association in transmission disequilibrium analyses of diagnosed ASD families.

  9. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-05-17

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  10. An ANOCEF genomic and transcriptomic microarray study of the response to radiotherapy or to alkylating first-line chemotherapy in glioblastoma patients

    Directory of Open Access Journals (Sweden)

    Ducray François

    2010-09-01

    Full Text Available Abstract Background The molecular characteristics associated with the response to treatment in glioblastomas (GBMs remain largely unknown. We performed a retrospective study to assess the genomic characteristics associated with the response of GBMs to either first-line chemotherapy or radiation therapy. The gene expression (n = 56 and genomic profiles (n = 67 of responders and non-responders to first-line chemotherapy or radiation therapy alone were compared on Affymetrix Plus 2 gene expression arrays and BAC CGH arrays. Results According to Verhaak et al.'s classification system, mesenchymal GBMs were more likely to respond to radiotherapy than to first-line chemotherapy, whereas classical GBMs were more likely to respond to first-line chemotherapy than to radiotherapy. In patients treated with radiation therapy alone, the response was associated with differential expression of microenvironment-associated genes; the expression of hypoxia-related genes was associated with short-term progression-free survival ( 10 months. Consistently, infiltration of the tumor by both CD3 and CD68 cells was significantly more frequent in responders to radiotherapy than in non-responders. In patients treated with first-line chemotherapy, the expression of stem-cell genes was associated with resistance to chemotherapy, and there was a significant association between response to treatment and p16 locus deletions. Consistently, in an independent data set of patients treated with either radiotherapy alone or with both radiotherapy and adjuvant chemotherapy, we found that patients with the p16 deletion benefited from adjuvant chemotherapy regardless of their MGMT promoter methylation status, whereas in patients without the p16 deletion, this benefit was only observed in patients with a methylated MGMT promoter. Conclusion Differential expression of microenvironment genes and p16 locus deletion are associated with responses to radiation therapy and to first

  11. Global identification and characterization of transcriptionally active regions in the rice genome.

    Directory of Open Access Journals (Sweden)

    Lei Li

    Full Text Available Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs not encoded by annotated exons in the rice (Oryza. sativa subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83% japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.

  12. Genome-wide identification of gene expression in the epididymis of infertile rat induced by alpha-chlorohydrin using oligonucleotide microarray

    Institute of Scientific and Technical Information of China (English)

    XIE Shu-wu; ZHU Yan; MA Li; LI Zhi-ling; GUI You-lun; LU Ying-ying; ZHAO Zhi-fang; CAO Lin

    2008-01-01

    Objective To establish a rat model of sterility associated with epididymis and epididymal gene expression profiles relation to fertility by alpha-chlorohydrin. Methods Rats were treated with 10 mg·kg-1. d-1. alpha-chlorohydrin for 10 consecutive days. Sperm maturation and other fertility parameters were analyzed. The sperm motility and morphology were evaluated by computer-assisted sperm analysis (CASA);sperm survival rate was assessed by SYBR-14 and propidium iodide (PI) fluorescent staining; the weights of testes, epididymides, prostates and seminal vesicles were determined by electronic balance; histological examination of above tissues were evaluated by HE staining;and serumal dihydrotestosterone (DHT) and testosterone (T) of rats were detected by enzyme-labeled immunoassay. Each male rat was paired with 2 female rats in proestrus. Female rats were examined the next morning for the presence of sperm in vaginal smears and underwent a cesarean section on day 12 of gestation. Finally the reproductive indices were calculated as follows: copulation index (number of sperm positive females / number of pairings), pregnancy index (number of pregnancies / number of sperm positive females), and fertility index (number of pregnancies / number of pairings). After that we used Affymetrix Rat 230 2.0 oligo-microarray to identify epididymal special genes associated with fertility. Finally, we validated some of these genes by Real-Time quantitative polymerase chain reaction. Results The motility of spermatozoa from the cauda epididymidis of treated rats showed a significant decrease in percentage of motile, progressively motile sperm, and sperm survival rate. At the same time, the morphology of cauda epididymal spermatozoa was also adversely affected by the treatment. In addition, the serumal androgen levels of treated animals weren' t changed compared with the control group. Accordingly, matings with treated males resulted in no successful pregnancy. Then, we classified

  13. ATLAS Rewards Russian Supplier for Scintillating Tile Production

    CERN Multimedia

    2001-01-01

    At a ceremony held at CERN on 30 July, the ATLAS collaboration awarded Russian firm SIA Luch from Podolsk in the Moscow region an ATLAS Suppliers Award. This follows delivery by the company of the final batch of scintillating tiles for the collaboration's Tile Calorimeter some six months ahead of schedule.   Representatives of Russian firm Luch Podolsk received the ATLAS Suppliers Award in the collaboration's Tile Calorimeter instrumentation plant at CERN on 30 July. In front of one Tile Calorimeter module instrumented by scintillating tiles are (left to right) IHEP physicists Evgueni Startchenko and Andrei Karioukhine, Luch Podolsk representatives Igor Karetnikov and Yuri Zaitsev, Tile Calorimeter Project Leader Rupert Leitner, ATLAS spokesperson Peter Jenni, and CERN Tile Calorimeter group leader Ana Henriques-Correia. Scintillating tiles form the active part of the ATLAS hadronic Tile Calorimeter, which will measure the energy and direction of particles produced in LHC collisions. They are emb...

  14. A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8.

    Science.gov (United States)

    Fengler, Svenja; Spirer, Ina; Neef, Maren; Ecke, Margret; Nieselt, Kay; Hampp, Rüdiger

    2015-01-01

    The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

  15. A Whole-Genome Microarray Study of Arabidopsis thaliana Semisolid Callus Cultures Exposed to Microgravity and Nonmicrogravity Related Spaceflight Conditions for 5 Days on Board of Shenzhou 8

    Directory of Open Access Journals (Sweden)

    Svenja Fengler

    2015-01-01

    Full Text Available The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes, this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

  16. Genome-wide microarray-based analysis of miRNAs expression in patients with acute-on-chronic liver failure

    Institute of Scientific and Technical Information of China (English)

    Wen Chen; Ze-Hui Yan; Yu-Ming Wang; Bao-Yan Xu; Guo-Hong Deng

    2014-01-01

    BACKGROUND: Acute-on-chronic liver failure (ACLF) is a severe clinical syndrome that may cause a high mortality. However, the mechanism is still not clear. Characterization of the microRNA (miRNA) proifles in ACLF patients may provide new clues to the pathogenesis and management of this syndrome. METHODS: Genome-wide  microarray  was  performed  to compare the different miRNA expression proifles in peripheral blood mononuclear cells of a pair of monozygotic twins, an ACLF patient and an HBV asymptomatic carrier (AsC). The case-control miRNA proifles were compared and conifrmed by quantitative reverse transcription-polymerase chain reaction in 104 ACLF patients and 96 AsCs. A combined computational prediction algorithm was used to predict the potential target genes. RESULTS: Forty-ifve miRNAs were increased and eight miRNAs were decreased in the ACLF group. The expressions of hsa-let-7a and hsa-miR-16 were increased by 8.58- and 8.63-fold in ACLF patients compared with that in AsCs, respectively (P CONCLUSIONS: Our  results  showed  that  there  is  a  close relationship  between  speciifc  miRNAs  of  peripheral  blood mononuclear cells and ACLF. hsa-miR-16 and hsa-let-7a may contribute to the development of ACLF.

  17. Tiled WMS/KML Server V2

    Science.gov (United States)

    Plesea, Lucian

    2012-01-01

    This software is a higher-performance implementation of tiled WMS, with integral support for KML and time-varying data. This software is compliant with the Open Geospatial WMS standard, and supports KML natively as a WMS return type, including support for the time attribute. Regionated KML wrappers are generated that match the existing tiled WMS dataset. Ping and JPG formats are supported, and the software is implemented as an Apache 2.0 module that supports a threading execution model that is capable of supporting very high request rates. The module intercepts and responds to WMS requests that match certain patterns and returns the existing tiles. If a KML format that matches an existing pyramid and tile dataset is requested, regionated KML is generated and returned to the requesting application. In addition, KML requests that do not match the existing tile datasets generate a KML response that includes the corresponding JPG WMS request, effectively adding KML support to a backing WMS server.

  18. The Mu3e Tile Detector

    Energy Technology Data Exchange (ETDEWEB)

    Eckert, Hans Patrick

    2015-05-06

    The Mu3e experiment is designed to search for the lepton flavour violating decay μ→e{sup +}e{sup +}e{sup -} with a sensitivity of one in 10{sup 16} decays. An observation of such a decay would be a clear sign of physics beyond the Standard Model. Achieving the targeted sensitivity requires a high precision detector with excellent momentum, vertex and time resolution. The Mu3e Tile Detector is a highly granular sub-detector system based on scintillator tiles with Silicon Photomultiplier (SiPM) readout, and aims at measuring the timing of the muon decay products with a resolution of better than 100 ps. This thesis describes the development of the Tile Detector concept and demonstrates the feasibility of the elaborated design. In this context, a comprehensive simulation framework has been developed, in order to study and optimise the detector performance. The central component of this framework is a detailed simulation of the SiPM response. The simulation model has been validated in several measurements and shows good agreement with the data. Furthermore, a 16-channel prototype of a Tile Detector module has been constructed and operated in an electron beam. In the beam tests, a time resolution up to 56 ps has been achieved, which surpasses the design goal. The simulation and measurement results demonstrate the feasibility of the developed Tile Detector design and show that the required detector performance can be achieved.

  19. Performance of the ATLAS Tile calorimeter

    CERN Document Server

    Bertoli, Gabriele; The ATLAS collaboration

    2015-01-01

    The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau­particles and missing transverse energy. TileCal is a scintillator­steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal front­end electronics read out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. The read­out system is responsible for reconstructing the data in real­time. The digitized signals are reconstructed with the Optimal Filtering algorithm, which computes for each channel the signal amplitude, time and quality factor at the required high rate. Each stage of the signal production from scintillation light to the signal reconstruc...

  20. Performance of the ATLAS hadronic Tile calorimeter

    CERN Document Server

    Mlynarikova, Michaela; The ATLAS collaboration

    2017-01-01

    The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations of the LHC. Prompt isolated muons of high momentum from elec...

  1. Performance of the ATLAS hadronic Tile calorimeter

    CERN Document Server

    Mlynarikova, Michaela; The ATLAS collaboration

    2017-01-01

    The ATLAS Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations of the LHC. Prompt isolated muons of high momentum fro...

  2. Performance of the ATLAS Tile Calorimeter

    Science.gov (United States)

    Hrynevich, A.

    2017-06-01

    The Tile Calorimeter (TileCal) is the central scintillator-steel sampling hadronic calorimeter of the ATLAS experiment at the LHC . Jointly with other calorimeters it is designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV . Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been established with cosmic ray muons and the large sample of the proton-proton collisions. The response of high momentum isolated muons is used to study the energy response at the electromagnetic scale, isolated hadrons are used as a probe of the hadronic response and its modelling by the Monte Carlo simulations. The calorimeter time resolution is studied with multijet events. Results on the calorimeter operation and performance are presented, including the calibration, stability, absolute energy scale, uniformity and time resolution. These results show that the TileCal performance is within the design requirements and has given essential contribution to reconstructed objects and physics results.

  3. Ceramic tile glazes: design, trends and applications

    Energy Technology Data Exchange (ETDEWEB)

    Manfredini, T. [Modena Univ. (Italy). Faculty of Engineering

    2002-07-01

    The purpose of this lecture is to describe the state of the art of glazes for applications in ceramic tile industry. A glaze for application in ceramic tile industry must satisfy certain requirements, which may be divided into two large groups, one in relation to its preparation and industrial utilisation and the other specific of the product utilisation. In order to design glaze compositions certain aspects must be taken into account. Viscosity and surface tension of the melt matching the body requirements, linear thermal expansion, nucleation and crystal growth processes occurring during firing, durability and optical properties must be designed and adjusted in the industrial practice. Glass-ceramic systems are the more suitable compositions for innovative glazes for fast firing of wall and floor tiles. (orig.)

  4. Tile vaulting in the 21st century

    Directory of Open Access Journals (Sweden)

    D. López López

    2016-12-01

    Full Text Available New interactive equilibrium methods for the design and analysis of masonry structures have facilitated the construction of masonry structures with a formal language well beyond what is typically associated with compression-only architecture. These developments have also rekindled interest in tile vaulting, and led to a rediscovery of this traditional building technique. To ensure that tile vaults with new, complex shapes can still be built economically, the construction processes involved in the realisation of these structures have adapted. For example, cheaper and simpler falsework systems have been introduced. In addition, a wide variety of materials have been experimented with to be able to build more sustainable vaulted structures with local resources. This paper presents a review of the latest innovations in tile vaulting, based on the most representative works of the past few years with respect to shape, construction method and the use of materials.

  5. Improved Tiled Bitmap Forensic Analysis Algorithm

    Directory of Open Access Journals (Sweden)

    C. D. Badgujar, G. N. Dhanokar

    2012-12-01

    Full Text Available In Computer network world, the needs for securityand proper systems of control are obvious and findout the intruders who do the modification andmodified data. Nowadays Frauds that occurs incompanies are not only by outsiders but also byinsiders. Insider may perform illegal activity & tryto hide illegal activity. Companies would like to beassured that such illegal activity i.e. tampering hasnot occurred, or if it does, it should be quicklydiscovered. Mechanisms now exist that detecttampering of a database, through the use ofcryptographically-strong hash functions. This papercontains a survey which explores the various beliefsupon database forensics through differentmethodologies using forensic algorithms and toolsfor investigations. Forensic analysis algorithms areused to determine who, when, and what data hadbeen tampered. Tiled Bitmap Algorithm introducesthe notion of a candidate set (all possible locationsof detected tampering(s and provides a completecharacterization of the candidate set and itscardinality. Improved tiled bitmap algorithm willcover come the drawbacks of existing tiled bitmapalgorithm.

  6. Protein microarray applications: Autoantibody detection and posttranslational modification.

    Science.gov (United States)

    Atak, Apurva; Mukherjee, Shuvolina; Jain, Rekha; Gupta, Shabarni; Singh, Vedita Anand; Gahoi, Nikita; K P, Manubhai; Srivastava, Sanjeeva

    2016-10-01

    The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.

  7. Degenerate polygonal tilings in simple animal tissues

    Science.gov (United States)

    Ziherl, Primoz; Hocevar, Ana

    2009-03-01

    We study 2D polygonal tilings as models of the en-face structure of single-layer biological tissues. Using numerical simulations, we explore the phase diagram of equilibrium tilings of equal-area, equal-perimeter convex polygons whose energy is independent of their shape. We identify 3 distinct phases, which are all observed in simple epithelial tissues: The disordered phase of polygons with 4-9 sides, the hexatic phase, and the hexagonal phase with perfect 6-fold coordination. We quantify their structure using Edwards' statistical mechanics of cellular systems.

  8. Development of Prototype Reactive Armor Tile

    Science.gov (United States)

    2015-05-13

    Final Technical Status Report For DOTC 10-01-INIT-017 Development of Prototype Reactive Armor Tile Reporting Period: 13 May 2015 Ordnance...Final 3. DATES COVERED 4. TITLE AND SUBTITLE Final Report: Development of Prototype Reactive Armor Tile 5a. CONTRACT NUMBER OTA # W15QKN-09-9...1001 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER N/A 6. AUTHOR(S) Herbst /Diana-Lynn 5d. PROJECT NUMBER DOTC-11-01-INIT017 5e. TASK NUMBER N

  9. Preimplantation genetic screening for all 24 chromosomes by microarray comparative genomic hybridization significantly increases implantation rates and clinical pregnancy rates in patients undergoing in vitro fertilization with poor prognosis

    Directory of Open Access Journals (Sweden)

    Gaurav Majumdar

    2016-01-01

    Full Text Available CONTEXT: A majority of human embryos produced in vitro are aneuploid, especially in couples undergoing in vitro fertilization (IVF with poor prognosis. Preimplantation genetic screening (PGS for all 24 chromosomes has the potential to select the most euploid embryos for transfer in such cases. AIM: To study the efficacy of PGS for all 24 chromosomes by microarray comparative genomic hybridization (array CGH in Indian couples undergoing IVF cycles with poor prognosis. SETTINGS AND DESIGN: A retrospective, case–control study was undertaken in an institution-based tertiary care IVF center to compare the clinical outcomes of twenty patients, who underwent 21 PGS cycles with poor prognosis, with 128 non-PGS patients in the control group, with the same inclusion criterion as for the PGS group. MATERIALS AND METHODS: Single cells were obtained by laser-assisted embryo biopsy from day 3 embryos and subsequently analyzed by array CGH for all 24 chromosomes. Once the array CGH results were available on the morning of day 5, only chromosomally normal embryos that had progressed to blastocyst stage were transferred. RESULTS: The implantation rate and clinical pregnancy rate (PR per transfer were found to be significantly higher in the PGS group than in the control group (63.2% vs. 26.2%, P = 0.001 and 73.3% vs. 36.7%, P = 0.006, respectively, while the multiple PRs sharply declined from 31.9% to 9.1% in the PGS group. CONCLUSIONS: In this pilot study, we have shown that PGS by array CGH can improve the clinical outcome in patients undergoing IVF with poor prognosis.

  10. Electro-desalination of glazed tile panels - discussion of possibilities

    DEFF Research Database (Denmark)

    Dias-Ferreira, Célia; Ottosen, Lisbeth M.; Ribeiro, Alexandra B.

    2016-01-01

    Glaze is lost from tiles in tile panels due to presence of soluble salts and this means loss of important heritage. The present paper discusses the possibility to apply electro-desalination. An in-situ test has not been performed yet, but encouraging results have been obtained with different parts...... of the system. Single tiles, a variety of porous stones and the mortar on the back of a tile have all been electro-desalinated successfully in laboratory scale. Thus individually, all parts of the wall with tile panel can be electro-desalinated. The interface between mortar and tile can be problematic....... In the few experiments conducted on tiles with attached mortar, the mortar was desalinated to a higher degree than the biscuit and successful desalination of the biscuit through the mortar requires further research. In-situ pilot scale tests were performed on highly salt-contaminated walls without tiles...

  11. A new manufacturing plant for fired color tile

    Institute of Scientific and Technical Information of China (English)

    ZhaoZhoumin

    2005-01-01

    The article describes the new manufacturing plant for fired colour tile designed by Xian Research and Design Institute for Nei Mongolia Yinshan Ceramic Ltd. Company. The plant with an annual capacity of 10million fired color tiles.

  12. Review: DNA Microarray Technology and Drug Development

    Directory of Open Access Journals (Sweden)

    Sushma Drabu

    2010-01-01

    genome. In a nutshell, Microarray technology makes it possible for molecular biologists to analyze

simultaneously thousands of DNA samples and monitor their behavior patterns, which brings about a tremendous
improvement over the tedious "one gene per experiment” technology that prevailed previously.

  • chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

    Science.gov (United States)

    Dufour, Yann S.; Wesenberg, Gary E.; Tritt, Andrew J.; Glasner, Jeremy D.; Perna, Nicole T.; Mitchell, Julie C.; Donohue, Timothy J.

    2010-01-01

    chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols or the array manufacturer’s requirements. The algorithm optimizes probes to meet three objectives: (i) probes should be specific; (ii) probes should have similar thermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid significant gaps. The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays for bacteria and yeast. chipD is available at http://chipd.uwbacter.org/. PMID:20529880

  • Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

    Directory of Open Access Journals (Sweden)

    Hiroko Kubo

    Full Text Available The use of lavender oil (LO--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham, a total of 156 and 154 up (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes, 174 and 66 up- (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes, and 222 and 322 up- (≧ 1.5-fold- and down (≦ 0.75-fold-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA, differentially expressed genes were functionally categorized by their Gene Ontology (GO and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules, to be influenced by LO treatment in the small intestine, spleen and

  • Unraveling the Rat Intestine, Spleen and Liver Genome-Wide Transcriptome after the Oral Administration of Lavender Oil by a Two-Color Dye-Swap DNA Microarray Approach.

    Science.gov (United States)

    Kubo, Hiroko; Shibato, Junko; Saito, Tomomi; Ogawa, Tetsuo; Rakwal, Randeep; Shioda, Seiji

    2015-01-01

    The use of lavender oil (LO)--a commonly, used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate--in non-traditional medicine is increasing globally. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model in this current study, investigating the orally administered LO effects genome wide in the rat small intestine, spleen, and liver. The rats were administered LO at 5 mg/kg (usual therapeutic dose in humans) followed by the screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a dye-swap approach, a novelty of this study. Fourteen days after LO treatment and compared with a control group (sham), a total of 156 and 154 up (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, 174 and 66 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes, and 222 and 322 up- (≧ 1.5-fold)- and down (≦ 0.75-fold)-regulated genes showed differential expression at the mRNA level in the small intestine, spleen and liver, respectively. The reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-regulated genes confirmed the regulation of the Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes by LO as examples in these tissues. Using bioinformatics, including Ingenuity Pathway Analysis (IPA), differentially expressed genes were functionally categorized by their Gene Ontology (GO) and biological function and network analysis, revealing their diverse functions and potential roles in LO-mediated effects in rat. Further IPA analysis in particular unraveled the presence of novel genes, such as Papd4, Or8k5, Gprc5b, Taar5, Trpc6, Pld2 and Onecut3 (up-regulated top molecules) and Tnf, Slc45a4, Slc25a23 and Samt4 (down-regulated top molecules), to be influenced by LO treatment in the small intestine, spleen and liver

  • The Corona Limit of Penrose Tilings Is a Regular Decagon

    OpenAIRE

    Akiyama, Shigeki; Imai, Katsunobu

    2016-01-01

    Part 2: Regular Papers; International audience; We define and study the corona limit of a tiling, by investigating the signal propagations on cellular automata (CA) on tilings employing the simple growth CA. In particular, the corona limit of Penrose tilings is the regular decagon.

  • Penetration dynamics of AP8 in thin ceramic tiles

    NARCIS (Netherlands)

    Abadjieva, E.; Khoe, Y.S.

    2013-01-01

    The interaction of thin ceramic tiles with AP8 (WC core, 7,62 mm) at 1000 m/s velocity has been studied experimentally and numerically. “Thin” ceramic tiles refers here to ratio of the tile thickness (t) to the projectile diameter, (d), t/d@ 1, as they are both in the same order. The method applied

  • Installation of Ceramic Tile: Residential Thin-Set Methods.

    Science.gov (United States)

    Short, Sam

    This curriculum guide contains materials for use in teaching a course on residential thin-set methods of tile installation. Covered in the individual units are the following topics: the tile industry; basic math; tools; measurement; safety in tile setting; installation materials and guidelines for their use; floors; counter tops and backsplashes;…

  • Two Views of Islam: Ceramic Tile Design and Miniatures.

    Science.gov (United States)

    Macaulay, Sara Grove

    2001-01-01

    Describes an art project focusing on Islamic art that consists of two parts: (1) ceramic tile design; and (2) Islamic miniatures. Provides background information on Islamic art and step-by-step instructions for designing the Islamic tile and miniature. Includes learning objectives and resources on Islamic tile miniatures. (CMK)

  • Jagged Tiling for Intra-tile Parallelism and Fine-Grain Multithreading

    Energy Technology Data Exchange (ETDEWEB)

    Shrestha, Sunil; Manzano Franco, Joseph B.; Marquez, Andres; Feo, John T.; Gao, Guang R.

    2015-05-01

    In this paper, we have developed a novel methodology that takes into consideration multithreaded many-core designs to better utilize memory/processing resources and improve memory residence on tileable applications. It takes advantage of polyhedral analysis and transformation in the form of PLUTO, combined with a highly optimized finegrain tile runtime to exploit parallelism at all levels. The main contributions of this paper include the introduction of multi-hierarchical tiling techniques that increases intra tile parallelism; and a data-flow inspired runtime library that allows the expression of parallel tiles with an efficient synchronization registry. Our current implementation shows performance improvements on an Intel Xeon Phi board up to 32.25% against instances produced by state-of-the-art compiler frameworks for selected stencil applications.

    1. ATLAS: First rehearsal for the tile calorimeter

      CERN Multimedia

      2003-01-01

      The dry run assembly of the first barrel of the ATLAS tile hadron calorimeter has been successfully completed. It is now being dismantled again so that it can be lowered into the ATLAS cavern where it will be reassembled in October 2004.

    2. Upgrade of the ATLAS Tile Calorimeter Electronics

      CERN Document Server

      Carrio, F

      2015-01-01

      The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (P hase - II ) where the pea k luminosity will increase 5 times compared to the design luminosity (10 34 cm −2 s −1 ) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity levelling. This upgrade is expe cted to happen around 202 4 . The TileCal upgrade aims at replacing the majority of the on - and off - detector electronics to the extent that all calorimeter signals will be digitized and sent to the off - detector electronics in the counting room. To achieve th e required reliability, redundancy has been introduced at different levels. Three different options are presently being investiga...

    3. The ATLAS Tile Calorimeter gets into shape!

      CERN Multimedia

      2002-01-01

      The last of the 64 modules for one of the ATLAS Hadron tile calorimeter barrels has just arrived at CERN. This arrival puts an end to two and a half years work assembling and testing all the modules in the Institut de Física d'Altes Energies (IFAE), in Barcelona.

    4. Performance of the ATLAS Tile Calorimeter

      CERN Document Server

      Hrynevich, Aliaksei; The ATLAS collaboration

      2017-01-01

      The Tile Calorimeter (TileCal) is the central scintillator-steel sampling hadronic calorimeter of the ATLAS experiment at the LHC. Jointly with other calorimeters it is designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been established with cosmic ray muons and the large sample of the proton-proton collisions. The response of high momentum isolated muons is used to study the energy response at the electromagnetic scale, isolated hadr...

    5. Upgrade of the ATLAS Tile Calorimeter

      CERN Document Server

      Reed, Robert; The ATLAS collaboration

      2014-01-01

      The Tile Calorimeter (TileCal) is the main hadronic calorimeter covering the central region of the ATLAS experiment at LHC. TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC operation (Phase 2 around 2023) where the peak luminosity will increase 5x compared to the design luminosity (10^{34} cm^{-2}s^{-1}) but with maintained energy (i.e. 7+7 TeV). The TileCal upgrade aims to replace the majority of the on- and off-detector electronics so that all calorimeter signals can be digitized and directly sent to the off-detector electronics in the counting room. This will reduce pile-up problems and allow more complex trigger algorithms. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 Gbps optical links are used to read out all digitized data to t...

    6. Upgrade of the ATLAS Tile Calorimeter Electronics

      CERN Document Server

      Moreno, P; The ATLAS collaboration

      2014-01-01

      The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (phase 2) where the peak luminosity will increase 5x compared to the design luminosity (10^34 cm−2s−1) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity leveling. This upgrade is expected to happen around 2023. The TileCal upgrade aims at replacing the majority of the on- and off-detector electronics to the extent that all calorimeter signals will be digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 ...

    7. Upgrade of the ATLAS Tile Calorimeter

      CERN Document Server

      Moreno, P; The ATLAS collaboration

      2014-01-01

      The Tile Calorimeter (TileCal) is the central hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (Phase 2) where the peak luminosity will increase 5$\\times$ compared to the design luminosity ($10^{34} cm^{-2}s^{-1}$) but with maintained energy (i.e. 7+7 TeV). The TileCal upgrade aims at replacing the majority of the on- and off-detector electronics to the extent that all calorimeter signals will be digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 Gbps optical links are used to read out all digitized data to the counting room while 5 Gbps down-links are used for synchronization, c...

    8. Lozenge Tilings, Glauber Dynamics and Macroscopic Shape

      Science.gov (United States)

      Laslier, Benoît; Toninelli, Fabio Lucio

      2015-09-01

      We study the Glauber dynamics on the set of tilings of a finite domain of the plane with lozenges of side 1/ L. Under the invariant measure of the process (the uniform measure over all tilings), it is well known (Cohn et al. J Am Math Soc 14:297-346, 2001) that the random height function associated to the tiling converges in probability, in the scaling limit , to a non-trivial macroscopic shape minimizing a certain surface tension functional. According to the boundary conditions, the macroscopic shape can be either analytic or contain "frozen regions" (Arctic Circle phenomenon Cohn et al. N Y J Math 4:137-165, 1998; Jockusch et al. Random domino tilings and the arctic circle theorem, arXiv:math/9801068, 1998). It is widely conjectured, on the basis of theoretical considerations (Henley J Statist Phys 89:483-507, 1997; Spohn J Stat Phys 71:1081-1132, 1993), partial mathematical results (Caputo et al. Commun Math Phys 311:157-189, 2012; Wilson Ann Appl Probab 14:274-325, 2004) and numerical simulations for similar models (Destainville Phys Rev Lett 88:030601, 2002; cf. also the bibliography in Henley (J Statist Phys 89:483-507, 1997) and Wilson (Ann Appl Probab 14:274-325, 2004), that the Glauber dynamics approaches the equilibrium macroscopic shape in a time of order L 2+ o(1). In this work we prove this conjecture, under the assumption that the macroscopic equilibrium shape contains no "frozen region".

    9. The ATLAS Tile Calorimeter performance at LHC

      Science.gov (United States)

      Molander, Simon

      2014-05-01

      This paper gives an overview of the performance of the Tile Calorimeter of the ATLAS detector at the Large Hadron Collider. Detector performances with respect to electronic noise and cell response are presented. In addition, an overview of the partially overlapping calibration systems is given.

    10. PCI Opens Tile Adhesives Plant in Foshan

      Institute of Scientific and Technical Information of China (English)

      Jenny Du

      2007-01-01

      @@ On October 22nd, 2007 BASF celebrated the inauguration of Asia's first PCI tilead hesives plant in Foshan, Guangdong Province. The plant is designed to provide a platform for the transfer of cutting-edge tiling systems technologies and solutions from Germany to China to benefit local construction chemicals sector.

    11. Brane Tilings, M2-branes and Orbifolds

      CERN Document Server

      Davey, John

      2011-01-01

      Brane Tilings represent one of the largest classes of superconformal theories with known gravity duals in 3+1 and also 2+1 dimensions. They provide a useful link between a large class of quiver gauge theories and their moduli spaces, which are the toric Calabi-Yau (CY) singularities. This thesis includes a discussion of an algorithm that can be used to generate all brane tilings with any given number of superpotential terms. All tilings with at most 8 superpotential terms have been generated using an implementation of this method. Orbifolds are a subject of central importance in string theory. It is widely known that there may be two or more orbifolds of a space by a finite group. Abelian Calabi-Yau orbifolds of the form $\\BC^3 / \\Gamma$ can be counted according to the size of the group $|\\Gamma|$. Three methods of counting these orbifolds will be given. A brane tiling together with a set of Chern Simons levels is sufficient to define a quiver Chern-Simons theory which describes the worldvolume theory of the ...

    12. Radioactivity level in Chinese building ceramic tile.

      Science.gov (United States)

      Xinwei, L

      2004-01-01

      The activity concentrations of (226)Ra, (232)Th and (40)K have been determined by gamma ray spectrometry. The concentrations of (226)Ra, (232)Th and (40)K range from 158.3 to 1087.6, 91.7 to 1218.4, and 473.8 to 1031.3 Bq kg(-1) for glaze, and from 63.5 to 131.4, 55.4 to 106.5, and 386.7 to 866.8 Bq kg(-1) for ceramic tile, respectively. The measured activity concentrations for these radionuclides were compared with the reported data of other countries and with the typical world values. The radium equivalent activities (Ra(eq)), external hazard index (H(ex)) and internal hazard index (H(in)) associated with the radionuclides were calculated. The Ra(eq) values of all ceramic tiles are lower than the limit of 370 Bq kg(-1). The values of H(ex) and H(in) calculated according to the Chinese criterion for ceramic tiles are less than unity. The Ra(eq) value for the glaze of glazed tile collected from some areas are >370 Bq kg(-1).

    13. Split Tiling for GPUs: Automatic Parallelization Using Trapezoidal Tiles to Reconcile Parallelism and Locality, avoiding Divergence and Load Imbalance

      OpenAIRE

      Cohen, Albert; Grosser, Tobias; Kelly, Paul H. J.; Ramanujam, J.; Sadayappan, P.; Verdoolaege, Sven

      2013-01-01

      International audience; Tiling is a key technology to increase data reuse in computation kernels. For computations structured as one sequential outer "time" loop enclosing a set of parallel inner loops, the option of tiling only the parallel inner loops is generally not profitable because it does not enable enough data reuse. To combine parallelism and locality, several tiling algorithms propose to tile the time loop together with one or more of the parallel inner loops. However, all these al...

    14. Investigating amoebic pathogenesis using Entamoeba histolytica DNA microarrays

      Indian Academy of Sciences (India)

      Upinder Singh; Preetam Shah

      2002-11-01

      Entamoeba histolytica, a protozoan parasite, causes diarrhea and liver abscesses resulting in 50 million cases of infection worldwide annually. Elucidation of parasite virulence determinants has recently been investigated using genetic approaches. We have undertaken a genomics approach to identify novel virulence determinants in the parasite. A DNA microarray of E. histolytica is being developed based on sequenced genomic clones from the genome sequencing efforts of The Institute of Genomic Research (TIGR) and the Sanger Center. Hybridization of the slides with samples labelled differentially using fluorescent dyes allows the characterization of transcriptional profiles of genes under the biological conditions tested. Additionally, a genome-wide comparison of E. histolytica and E. dispar can be undertaken. The development of an E. histolytica microarray will be outlined and its uses in identifying novel virulence determinants and characterizing amoebic biology will be discussed.

    15. Solving Vertex Cover Problem Using DNA Tile Assembly Model

      Directory of Open Access Journals (Sweden)

      Zhihua Chen

      2013-01-01

      Full Text Available DNA tile assembly models are a class of mathematically distributed and parallel biocomputing models in DNA tiles. In previous works, tile assembly models have been proved be Turing-universal; that is, the system can do what Turing machine can do. In this paper, we use tile systems to solve computational hard problem. Mathematically, we construct three tile subsystems, which can be combined together to solve vertex cover problem. As a result, each of the proposed tile subsystems consists of Θ(1 types of tiles, and the assembly process is executed in a parallel way (like DNA’s biological function in cells; thus the systems can generate the solution of the problem in linear time with respect to the size of the graph.

    16. ATLAS rewards Russian supplier for scintillating tile production

      CERN Multimedia

      Patrice Loïez

      2001-01-01

      The ATLAS collaboration has awarded Russian firm SIA Luch from Podolsk in the Moscow region an ATLAS Supplier Award. This follows delivery by the company of the final batch of scintillating tiles for the collaboration's tile calorimeter some six months ahead of schedule. Representatives of the firm are seen here receiving the award at a ceremony held in the collaboration's tile calorimeter instrumentation plant at CERN on 30 July. In front of one tile calorimeter module instrumented by scintillating tiles are (left to right) IHEP physicists Evgueni Startchenko and Andrei Karioukhine, Luch Podolsk representatives Igor Karetnikov and Yuri Zaitsev, tile calorimeter project leader Rupert Leitner, ATLAS spokesperson Peter Jenni, and CERN tile calorimeter group leader Ana Henriques-Correia.

    17. Taylor–Socolar Hexagonal Tilings as Model Sets

      Directory of Open Access Journals (Sweden)

      Jeong-Yup Lee

      2012-12-01

      Full Text Available The Taylor–Socolar tilings are regular hexagonal tilings of the plane but are distinguished in being comprised of hexagons of two colors in an aperiodic way. We place the Taylor–Socolar tilings into an algebraic setting, which allows one to see them directly as model sets and to understand the corresponding tiling hull along with its generic and singular parts. Although the tilings were originally obtained by matching rules and by substitution, our approach sets the tilings into the framework of a cut and project scheme and studies how the tilings relate to the corresponding internal space. The centers of the entire set of tiles of one tiling form a lattice Q in the plane. If XQ denotes the set of all Taylor–Socolar tilings with centers on Q, then XQ forms a natural hull under the standard local topology of hulls and is a dynamical system for the action of Q.The Q-adic completion Q of Q is a natural factor of XQ and the natural mapping XQ → Q is bijective except at a dense set of points of measure 0 in /Q. We show that XQ consists of three LI classes under translation. Two of these LI classes are very small, namely countable Q-orbits in XQ. The other is a minimal dynamical system, which maps surjectively to /Q and which is variously 2 : 1, 6 : 1, and 12 : 1 at the singular points. We further develop the formula of what determines the parity of the tiles of a tiling in terms of the coordinates of its tile centers. Finally we show that the hull of the parity tilings can be identified with the hull XQ; more precisely the two hulls are mutually locally derivable.

    18. Porcelain tiles by the dry route

      Directory of Open Access Journals (Sweden)

      Boschi, A. O.

      2010-10-01

      Full Text Available In Brazil, the second largest tile producer of the world, at present, 70% of the tiles are produced by the dry route. One of the main reasons that lead to this development is the fact that the dry route uses approximately 30% less thermal energy them the traditional wet route. The increasing world concern with the environment and the recognition of the central role played by the water also has pointed towards privileging dry processes. In this context the objective of the present work is to study the feasibility of producing high quality porcelain tiles by the dry route. A brief comparison of the dry and wet route, in standard conditions industrially used today to produce tiles that are not porcelain tiles, shows that there are two major differences: the particle sizes obtained by the wet route are usually considerably finer and the capability of mixing the different minerals, the intimacy of the mixture, is also usually better in the wet route. The present work studied the relative importance of these differences and looked for raw materials and operational conditions that would result in better performance and glazed porcelain tiles of good quality.

      En Brasil, en este momento segundo productor mundial, el 70% de los pavimentos cerámicos se obtiene por vía seca. Una de las razones fundamentales se debe a que esta vía supone un consumo energético inferior, en un 30%, a la via húmeda tradicional. La creciente preocupación mundial sobre los problemas medioambientales y el reconocimiento del papel central que juega el agua en este proceso han favorecido el desarrollo de la vía seca. En este contexto, el objetivo del presente trabajo es estudiar la viabilidad de la producción de pavimentos porcelánicos de alta calidad por vía seca. Una breve comparación entre ambas vías, en las condiciones standard de producción vigentes para producciones que no son de porcelánico, indican que existen dos diferencias substanciales; el tamaño de

    19. Analyzing Microarray Data.

      Science.gov (United States)

      Hung, Jui-Hung; Weng, Zhiping

      2017-03-01

      Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.

    20. ATLAS Tile calorimeter calibration and monitoring systems

      CERN Document Server

      Cortes-Gonzalez, Arely; The ATLAS collaboration

      2017-01-01

      The ATLAS Tile Calorimeter is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes, located in the outer part of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two photomultiplier in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The calibration system comprises Cesium radioactive sources, laser, charge injection elements and an integrator based readout system. Combined information from all systems allows to monitor and equalise the calorimeter r...

    1. Tiling by rectangles and alternating current

      KAUST Repository

      Prasolov, M. V.

      2011-04-01

      This paper is on tilings of polygons by rectangles. A celebrated physical interpretation of such tilings by R.L. Brooks, C.A.B. Smith, A.H. Stone and W.T. Tutte uses direct-current circuits. The new approach of this paper is an application of alternating-current circuits. The following results are obtained: •a necessary condition for a rectangle to be tilable by rectangles of given shapes;•a criterion for a rectangle to be tilable by rectangles similar to it but not all homothetic to it;•a criterion for a "generic" polygon to be tilable by squares. These results generalize those of C. Freiling, R. Kenyon, M. Laczkovich, D. Rinne, and G. Szekeres. © 2010 Elsevier Inc.

    2. Tile-in-ONE.cern.ch

      CERN Document Server

      Sivolella Gomes, Andressa; The ATLAS collaboration; Ferreira, Fernando; Solans, Carlos; Solodkov, Alexander

      2015-01-01

      The ATLAS Tile Calorimeter assesses the quality of data in order to ensure its proper operation. A number of tasks are then performed by running several tools and systems, which were independently developed to meet distinct collaboration’s requirements and do not necessarily builds an effective connection among them. Thus, a program is usually implemented without a global perspective of the detector, requiring basic software features. In addition, functionalities may overlap in their objectives and frequently replicate resources retrieval mechanisms. Tile-in-ONE is a unique platform that assembles various web systems used by the calorimeter community through a single framework and a standard technology. It provides an infrastructure to support the code implementation, avoiding duplication of work while integrating with an overall view of the detector status. Database connectors smooth the process of information access since developers do not need to be aware of where records are placed and how to extract th...

    3. Laser calibration of the ATLAS Tile Calorimeter

      CERN Document Server

      Di Gregorio, Giulia; The ATLAS collaboration

      2017-01-01

      High performance stability of the ATLAS Tile calorimeter is achieved with a set of calibration procedures. One step of the calibrtion procedure is based on measurements of the response stability to laser excitation of the photomultipliers (PMTs) that are used to readout the calorimeter cells. A facility to study in lab the PMT stability response is operating in the PISA-INFN laboratories since 2015. Goals of the test in lab are to study the time evolution of the PMT response to reproduce and to understand the origin of the resonse drifts seen with the PMT mounted on the Tile calorimeter in its normal operation during LHC run I and run II. A new statistical approach was developed to measure the drift of the absolute gain. This approach was applied to both the ATLAS laser calibration data and to the data collected in the Pisa local laboratory. The preliminary results from these two studies are shown.

    4. Laser Calibration of the ATLAS Tile Calorimeter

      CERN Document Server

      Di Gregorio, Giulia; The ATLAS collaboration

      2017-01-01

      High performance stability of the ATLAS Tile Calorimeter is achieved with a set of calibration procedures. One step of the calibration procedure is based on measurements of the response stability to laser excitation of the PMTs that are used to readout the calorimeter cells. A facility to study in lab the PMT stability response is operating in the PISA-INFN laboratories since 2015. Goals of the tests in lab are to study the time evolution of the PMT response to reproduce and to understand the origin of the response drifts seen with the PMT mounted on the Tile calorimeter in its normal operating during LHC run I and run II. A new statistical approach was developed to measure drift of the absolute gain. This approach was applied to both the ATLAS laser calibration data and to data collected in the Pisa local laboratory. The preliminary results from these two studies are shown.

    5. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

      Energy Technology Data Exchange (ETDEWEB)

      Gardner, S; Jaing, C

      2012-03-27

      The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

    6. Mapping Signal Processing Kernels to Tiled Architectures

      Science.gov (United States)

      2007-11-02

      attractive alternatives to monolithic computer architecture designs because they allow a larger design to be built from smaller modules and limit the...Computer Architectures. ACM Transactions on Computer Systems, 2(4):289–308, November 1984. [12] Steven Swanson, Ken Michelson , Andrew Schwerin, and...Program MIT Lincoln LaboratoryHPEC 2004-3 JML 28 Sep 2004 Tiled Architectures • Monolithic single-chip architectures are becoming rare in the industry

    7. Open Tiled Manycore System-on-Chip

      OpenAIRE

      Wallentowitz, Stefan; Wagner, Philipp; Tempelmeier, Michael; Wild, Thomas; Herkersdorf, Andreas

      2013-01-01

      Manycore System-on-Chip include an increasing amount of processing elements and have become an important research topic for improvements of both hardware and software. While research can be conducted using system simulators, prototyping requires a variety of components and is very time consuming. With the Open Tiled Manycore System-on-Chip (OpTiMSoC) we aim at building such an environment for use in our and other research projects as prototyping platform. This paper describes the project goal...

    8. The EADGENE Microarray Data Analysis Workshop (Open Access publication

      Directory of Open Access Journals (Sweden)

      Jiménez-Marín Ángeles

      2007-11-01

      Full Text Available Abstract Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced. While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.

    9. Upgrading the ATLAS Tile Calorimeter electronics

      CERN Document Server

      Souza, J; The ATLAS collaboration

      2014-01-01

      The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. Its main upgrade will occur for the High Luminosity LHC phase (phase 2) where the peak luminosity will increase 5-fold compared to the design luminosity (10exp34 cm−2s−1) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity leveling. This upgrade will probably happen around 2023. The upgrade aims at replacing the majority of the on- and off-detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. The smallest independent on-detector electronics module has been reduced from 45 channels to 6, greatly reducing the consequences of a failure in the on-detector electronics. The size of t...

    10. Foam-on-Tile Damage Model

      Science.gov (United States)

      Koharchik, Michael; Murphy, Lindsay; Parker, Paul

      2012-01-01

      An impact model was developed to predict how three specific foam types would damage the Space Shuttle Orbiter insulating tiles. The inputs needed for the model are the foam type, the foam mass, the foam impact velocity, the foam impact incident angle, the type being impacted, and whether the tile is new or aged (has flown at least one mission). The model will determine if the foam impact will cause damage to the tile. If it can cause damage, the model will output the damage cavity dimensions (length, depth, entry angle, exit angle, and sidewall angles). It makes the calculations as soon as the inputs are entered (less than 1 second). The model allows for the rapid calculation of numerous scenarios in a short time. The model was developed from engineering principles coupled with significant impact testing (over 800 foam impact tests). This model is applicable to masses ranging from 0.0002 up to 0.4 pound (0.09 up to 181 g). A prior tool performed a similar function, but was limited to the assessment of a small range of masses and did not have the large test database for verification. In addition, the prior model did not provide outputs of the cavity damage length, entry angle, exit angle, or sidewall angles.

    11. Chemical Composition of Ceramic Tile Glazes

      Science.gov (United States)

      Anufrik, S. S.; Kurian, N. N.; Zhukova, I. I.; Znosko, K. F.; Belkov, M. V.

      2016-11-01

      We have carried out laser emission and x-ray fluorescence spectral analysis of glaze before and after its application to ceramic tile produced by Keramin JSC (Belarus). We have studied the internal microstructure of the ceramic samples. It was established that on the surface and within the bulk interior of all the samples, there are micropores of sizes ranging from a few micrometers to tens of micrometers and microcracks as long as several hundred micrometers. The presence of micropores on the surface of the ceramic tile leads to an increase in the water absorption level and a decrease in frost resistance. It was found that a decrease in the surface tension of ceramic tile coatings is promoted by substitution of sodium by potassium, silica by boric anhydride, magnesium and barium by calcium, CaO by sodium oxide, and SiO2 by chromium oxide. We carried out a comparative analysis of the chemical composition of glaze samples using S4 Pioneer and ElvaX x-ray fluorescence spectrometers and also an LIBS laser emission analyzer.

    12. Design, construction, characterization, and application of a hyperspectral microarray scanner.

      Science.gov (United States)

      Sinclair, Michael B; Timlin, Jerilyn A; Haaland, David M; Werner-Washburne, Margaret

      2004-04-01

      We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 microm and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to the underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.

    13. Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

      Directory of Open Access Journals (Sweden)

      Nobumasa Hitoshi

      2007-04-01

      Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

    14. Microarray-based Identification of Novel Biomarkers in Asthma

      Directory of Open Access Journals (Sweden)

      Kenji Izuhara

      2006-01-01

      Full Text Available Bronchial asthma is a complicated and diverse disorder affected by genetic and environmental factors. It is widely accepted that it is a Th2-type inflammation originating in lung and caused by inhalation of ubiquitous allergens. The complicated and diverse pathogenesis of this disease yet to be clarified. Functional genomics is the analysis of whole gene expression profiling under given condition, and microarray technology is now the most powerful tool for functional genomics. Several attempts to clarify the pathogenesis of bronchial asthma have been carried out using microarray technology, providing us some novel biomarkers for diagnosis, therapeutic targets or understanding pathogenic mechanisms of bronchial asthma. In this article, we review the outcomes of these analyses by the microarray approach as applied to this disease by focusing on the identification of novel biomarkers.

    15. Monomer-dimer tatami tilings of square regions

      CERN Document Server

      Erickson, Alejandro

      2011-01-01

      We prove that the number of monomer-dimer tilings of an $n\\times n$ square grid, with $mtiles meet at any point is $m2^m+(m+1)2^{m+1}$, when $m$ and $n$ have the same parity. In addition, we present a new proof of the result that there are $n2^{n-1}$ such tilings with $n$ monomers, which divides the tilings into $n$ classes of size $2^{n-1}$. The sum of these tilings over all monomer counts has the closed form $2^{n-1}(3n-4)+2$ and, curiously, this is equal to the sum of the squares of all parts in all compositions of $n$. We also describe two algorithms and a Gray code ordering for generating the $n2^{n-1}$ tilings with $n$ monomers, which are both based on our new proof.

    16. Operating experience of the tile carrier transfer facility during the JET remote tile exchange

      Energy Technology Data Exchange (ETDEWEB)

      Edwards, P.; Patel, B.; Davies, N.; Middleton, R.; Mills, S.; Palmer, J.; Pedrick, L.; Wilson, D.W. [JET Joint Undertaking, Abingdon, Oxon (United Kingdom); Hurd, F. [NET Team, Garching (Germany)

      1998-07-01

      During the Remote Tile Exchange shutdown at JET, the purpose built Tile Carrier Transfer Facility (TCTF) has been successfully used for the remote removal and storage of activated, tritiated and beryllium contaminated torus components. The short boom, end effector and tine arrangement was also used during the installation of the new Gas Box Divertor. Tritium levels required the use of techniques and practices which were successful in confining contamination and allowed the declassification of work areas. A holding area and posting facilities enabled ancillary equipment / tool logistics to be managed efficiently. This article presents and describes all the equipment used and reports the operational experience. (authors)

    17. Military Curriculum Materials for Vocational and Technical Education. Builders School, Ceramic Tile Setting 3-9.

      Science.gov (United States)

      Ohio State Univ., Columbus. National Center for Research in Vocational Education.

      This course, for individualized or group instruction on ceramic tile setting, was developed from military sources for use in vocational education. The course provides students with skills in mortar preparation, surface preparation, tile layout planning, tile setting, tile cutting, and the grouting of tile joints. Both theory and shop assignments…

    18. Quantification of global transcription patterns in prokaryotes using spotted microarrays

      OpenAIRE

      Sidders, B.; Withers, M; Kendall, SL; J. Bacon; Waddell, SJ; Hinds, J; Golby, P.; Movahedzadeh, F; Cox, RA; Frita, R.; Ten Bokum, AM; Wernisch, L; Stoker, NG

      2007-01-01

      \\ud \\ud We describe an analysis, applicable to any spotted microarray dataset produced using genomic DNA as a reference, that quantifies prokaryotic levels of mRNA on a genome-wide scale. Applying this to Mycobacterium tuberculosis, we validate the technique, show a correlation between level of expression and biological importance, define the complement of invariant genes and analyze absolute levels of expression by functional class to develop ways of understanding an organism's biology witho...

    19. Human brain evolution: insights from microarrays.

      Science.gov (United States)

      Preuss, Todd M; Cáceres, Mario; Oldham, Michael C; Geschwind, Daniel H

      2004-11-01

      Several recent microarray studies have compared gene-expression patterns n humans, chimpanzees and other non-human primates to identify evolutionary changes that contribute to the distinctive cognitive and behavioural characteristics of humans. These studies support the surprising conclusion that the evolution of the human brain involved an upregulation of gene expression relative to non-human primates, a finding that could be relevant to understanding human cerebral physiology and function. These results show how genetic and genomic methods can shed light on the basis of human neural and cognitive specializations, and have important implications for neuroscience, anthropology and medicine.

    20. Tiling a figure using a height in a tree

      Energy Technology Data Exchange (ETDEWEB)

      Remila, E. [Institut Universitaire de Technologie de Roanne, Paris (France)

      1996-12-31

      We first give a new presentation of an algorithm from Thurston of tiling with lozenges formed from two cells of the triangular lattice A. Secondly we extend the method to get a linear algorithm of tiling with leaning dominoes (parallelograms formed from four cells of {Lambda}) and triangles (formed from four cells of {Lambda}). Thirdly, we produce a quadratic algorithm of tiling with leaning dominoes.

    1. The exact solution of an octagonal rectangle triangle random tiling

      CERN Document Server

      De Gier, J; Gier, Jan de; Nienhuis, Bernard

      1996-01-01

      We present a detailed calculation of the recently published exact solution of a random tiling model possessing an eight-fold symmetric phase. The solution is obtained using Bethe Ansatz and provides closed expressions for the entropy and phason elastic constants. Qualitatively, this model has the same features as the square-triangle random tiling model. We use the method of P. Kalugin, who solved the Bethe Ansatz equations for the square-triangle tiling, which were found by M. Widom.

    2. Procreating Tiles of Double Commutative-Step Digraphs

      Institute of Scientific and Technical Information of China (English)

      Jian-qin Zhou

      2008-01-01

      Double commutative-step digraph generalizes the double-loop digraph. A double commutative-step digraph can be represented by an L-shaped tile, which periodically tessellates the plane. Given an initial tile L(l, h,x, y), Agniló et al. define a discrete iteration L(p) = L(l + 2p, h + 2p, x + p, y + p),p = 0, 1, 2,…, over L-shapes (equivalently over double commutative-step digraphs), and obtain an orbit generated by L(l, h, x, y),which is said to be a procreating k-tight tile if L(p)(p= 0, 1, 2,… ) are all k-tight tiles. They classify the set of L-shaped tiles by its behavior under the above-mentioned discrete dynamics and obtain some procreating tiles of double commutative-step digraphs. In this work, with an approach proposed by Li and Xu et al., we define some new discrete iteration over L-shapes and classify the set of tiles by the procreating condition. We also propose some approaches to find infinite families of realizable k-tight tiles starting from any realizable k-tight L-shaped tile L(l, h, x, y), 0≤|y - x|≤ 2k + 2. As an example, we present an infinite family of 3-tight optimal double-loop networks to illustrate our approaches.

    3. Talk about Han eaves tile art in our country

      Institute of Scientific and Technical Information of China (English)

      刘泽艺

      2015-01-01

      The Han Dynasty is the first in the history of the unified and powerful country. It is a huge momentum has also affected the development of art, especially the art of eaves tile. Pattern of Han eaves tile is the art of the Chinese nation in the classic, rich artistic value for tile study of traditional ceramic art is very necessary in China. Through the research on Eave Tile Art, can be in-jected into the power of ceramic art in China's new development.

    4. Geopolymers as potential repair material in tiles conservation

      Science.gov (United States)

      Geraldes, Catarina F. M.; Lima, Augusta M.; Delgado-Rodrigues, José; Mimoso, João Manuel; Pereira, Sílvia R. M.

      2016-03-01

      The restoration materials currently used to fill gaps in historical architectural tiles (e.g. lime or organic resin pastes) usually show serious drawbacks in terms of compatibility, effectiveness or durability. The existing solutions do not fully protect Portuguese faïence tiles ( azulejos) in outdoor conditions and frequently result in further deterioration. Geopolymers can be a potential solution for tile lacunae infill, given the chemical-mineralogical similitude to the ceramic body, and also the durability and versatile range of physical properties that can be obtained through the manipulation of their formulation and curing conditions. This work presents and discusses the viability of the use of geopolymeric pastes to fill lacunae in tiles or to act as "cold" cast ceramic tile surrogates reproducing missing tile fragments. The formulation of geopolymers, namely the type of activators, the alumino-silicate source, the quantity of water required for adequate workability and curing conditions, was studied. The need for post-curing desalination was also considered envisaging their application in the restoration of outdoor historical architectural tiles frequently exposed to adverse environmental conditions. The possible advantages and disadvantages of the use of geopolymers in the conservation of tiles are also discussed. The results obtained reveal that geopolymers pastes are a promising material for the restoration of tiles, when compared to other solutions currently in use.

    5. Compressive Sensing DNA Microarrays

      Directory of Open Access Journals (Sweden)

      Richard G. Baraniuk

      2009-01-01

      Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

    6. Preparation of high performance ceramic tiles using waste tile granules and ceramic polishing powder

      Institute of Scientific and Technical Information of China (English)

      WANG Gong-xun; SU Da-gen

      2008-01-01

      This paper presents an innovative approach to reusing waste tile granules (TG) and ceramic polishing powder (PP) to produce high performance ceramic tiles. We studied formulations each with a TG mass fraction of 25.0% and a different PP mass fraction between 1.0% and 7.0%. The formulations included a small amount of borax additive of a mass fracton between 0.2%and 1.2%. The effects of these industrial by-products on compressive strength, water absorption and microstructure of the new ceramic tiles were investigated. The results indicate that the compressive strength decreases and water absorption increases when TG with a mass fraction of 25.0% are added. Improvement of the compressive strength may be achieved when TG (up to 25.0%)and PP (up to 2.0%) are both used at the same time. In particular, the compressive strength improvement can be maximized and water absorption reduced when a borax additive of up to 0.5% is used as a flux. Scanning electron microscopy reveals that a certain amount of fine PP granules and a high content of fluxing oxides from borax avail the formation of glassy phase that fills up the pores in the new ceramic tiles, resulting in a dense product with high compressive strength and low water absorption.

    7. Performance of the ATLAS Tile Calorimeter

      Directory of Open Access Journals (Sweden)

      Shimizu Shima

      2013-05-01

      Full Text Available The Tile Calorimeter is the central section of the ATLAS hadronic calorimeter at the Large Hadron Collider. It is a key detector for the measurement of hadrons, jets, tau leptons and missing transverse energy. Because of its very good signal to noise ratio it is also useful for the identification and reconstruction of muons. The calibration and performance of the calorimeter have been established through test beam measurements, cosmic ray muons and the large sample of pp collisions. Results on the calorimeter performance are presented, including the absolute energy scale, time resolution, and associated stabilities.

    8. Tiling a Pyramidal Polycube with Dominoes

      Directory of Open Access Journals (Sweden)

      Olivier Bodini

      2007-05-01

      Full Text Available The notion of pyramidal polycubes, namely the piling-up of bricks of a non-increasing size, generalizes in ℝ n the concept of trapezoidal polyominoes. In the present paper, we prove that n-dimensional dominoes can tile a pyramidal polycube if and only if the latter is balanced, that is, if the number of white cubes is equal to the number of black ones for a chessboard-like coloration, generalizing the result of [BC92] when n=2

    9. Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species.

      Directory of Open Access Journals (Sweden)

      Eva Kucerova

      Full Text Available BACKGROUND: The genus Cronobacter (formerly called Enterobacter sakazakii is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified. METHODOLOGY/PRINCIPAL FINDINGS: We report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content and two plasmids; 31 kb (51% GC and 131 kb (56% GC. The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10-17% absence of genes. CONCLUSIONS/SIGNIFICANCE: CGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii

    10. The Production and Qualification of Scintillator Tiles for the ATLAS Hadronic Calorimeter

      CERN Document Server

      Abdallah, J; Alexa, C; Alves, R; Amaral, P; Ananiev, A; Anderson, K; Andresen, X; Antonaki, A; Batusov, V; Bednar, P; Bergeaas, E; Biscarat, C; Blanch, O; Blanchot, G; Bohm, C; Boldea, V; Bosi, F; Bosman, M; Bromberg, C; Budagov, Yu; Calvet, D; Cardeira, C; Carli, T; Carvalho, J; Cascella, M; Castillo, M V; Costello, J; Cavalli-Sforza, M; Cavasinni, V; Cerqueira, A S; Clément, C; Cobal, M; Cogswell, F; Constantinescu, S; Costanzo, D; Da Silva, P; David, M; Davidek, T; Dawson, J; De, K; Del Prete, T; Diakov, E; Di Girolamo, B; Dita, S; Dolejsi, J; Dolezal, Z; Dotti, A; Downing, R; Drake, G; Efthymiopoulos, I; Errede, D; Errede, S; Farbin, A; Fassouliotis, D; Feng, E; Fenyuk, A; Ferdi, C; Ferreira, B C; Ferrer, A; Flaminio, V; Flix, J; Francavilla, P; Fullana, E; Garde, V; Gellerstedt, K; Giakoumopoulou, V; Giangiobbe, V; Gildemeister, O; Gilewsky, V; Giokaris, N; Gollub, N; Gomes, A; González, V; Gouveia, J; Grenier, P; Gris, P; Guarino, V; Guicheney, C; Sen-Gupta, A; Hakobyan, H; Haney, M; Hellman, S; Henriques, A; Higón, E; Hill, N; Holmgren, S; Hruska, I; Hurwitz, M; Huston, J; Jen-La Plante, I; Jon-And, K; Junk, T; Karyukhin, A; Khubua, J; Klereborn, J; Konsnantinov, V; Kopikov, S; Korolkov, I; Krivkova, P; Kulchitskii, Yu A; Kurochkin, Yu; Kuzhir, P; Lapin, V; LeCompte, T; Lefèvre, R; Leitner, R; Li, J; Liablin, M; Lokajícek, M; Lomakin, Y; Lourtie, P; Lovas, L; Lupi, A; Maidantchik, C; Maio, A; Maliukov, S; Manousakis, A; Marques, C; Marroquim, F; Martin, F; Mazzoni, E; Merritt, F S; Myagkov, A; Miller, R; Minashvili, I; Miralles, L; Montarou, G; Némécek, S; Nessi, M; Nikitine, I; Nodulman, L; Norniella, O; Onofre, A; Oreglia, M; Palan, B; Pallin, D; Pantea, D; Pereira, A; Pilcher, J E; Pina, J; Pinhão, J; Pod, E; Podlyski, F; Portell, X; Poveda, J; Pribyl, a L; Price, L E; Proudfoot, J; Ramalho, M; Ramstedt, M; Raposeiro, L; Reis, J; Richards, R; Roda, C; Romanov, V; Rosnet, P; Roy, P; Ruiz, A; Rumiantsau, V; Rusakovich, N; Sada Costa, J; Salto, O; Salvachúa, B; Sanchis, E; Sanders, H; Santoni, C; Santos, J; Saraiva, J G; Sarri, F; Says, L P; Schlager, G; Schlereth, J L; Seixas, J M; Selldén, B; Shalanda, N; Shevtsov, P; Shochet, M; Silva, J; Simaitis, V; Simonyan, M; Sisakian, A; Sjölin, J; Solans, C; Solodkov, A; Solovyanov, O; Sosebee, M; Spanó, F; Speckmeyer, P; Stanek, R; Starchenko, E; Starovoitov, P; Suk, M; Sykora, I; Tang, F; Tas, P; Teuscher, R; Tischenko, M; Tokar, S; Topilin, N; Torres, J; Underwood, D; Usai, G; Valero, A; Valkár, S; Valls, J A; Vartapetian, A; Vazeille, F; Vellidis, C; Ventura, F; Vichou, I; Vivarelli, I; Volpi, M; White, A; Zaitsev, A; Zaytsev, Yu; Zenin, A; Zenis, T; Zenonos, Z; Zenz, S; Zilka, B

      2007-01-01

      The production of the scintillator tiles for the ATLAS Tile Calorimeter is presented. In addition to the manufacture and production, the properties of the tiles will be presented including light yield, uniformity and stability.

    11. A comparative analysis of DNA barcode microarray feature size

      Directory of Open Access Journals (Sweden)

      Smith Andrew M

      2009-10-01

      Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

    12. Challenges for MicroRNA Microarray Data Analysisf

      Directory of Open Access Journals (Sweden)

      Bin Wang

      2013-03-01

      Full Text Available Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1 the total number of target genes is large enough (>10,000; and (2 the expression level of the majority of genes is kept constant. However, microRNA (miRNA arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays.

    13. Optimized light-directed synthesis of aptamer microarrays.

      Science.gov (United States)

      Franssen-van Hal, Nicole L W; van der Putte, Pepijn; Hellmuth, Klaus; Matysiak, Stefan; Kretschy, Nicole; Somoza, Mark M

      2013-06-18

      Aptamer microarrays are a promising high-throughput method for ultrasensitive detection of multiple analytes, but although much is known about the optimal synthesis of oligonucleotide microarrays used in hybridization-based genomics applications, the bioaffinity interactions between aptamers and their targets is qualitatively different and requires significant changes to synthesis parameters. Focusing on streptavidin-binding DNA aptamers, we employed light-directed in situ synthesis of microarrays to analyze the effects of sequence fidelity, linker length, surface probe density, and substrate functionalization on detection sensitivity. Direct comparison with oligonucleotide hybridization experiments indicates that aptamer microarrays are significantly more sensitive to sequence fidelity and substrate functionalization and have different optimal linker length and surface probe density requirements. Whereas microarray hybridization probes generate maximum signal with multiple deletions, aptamer sequences with the same deletion rate result in a 3-fold binding signal reduction compared with the same sequences synthesized for maximized sequence fidelity. The highest hybridization signal was obtained with dT 5mer linkers, and the highest aptamer signal was obtained with dT 11mers, with shorter aptamer linkers significantly reducing the binding signal. The probe hybridization signal was found to be more sensitive to molecular crowding, whereas the aptamer probe signal does not appear to be constrained within the density of functional surface groups commonly used to synthesize microarrays.

    14. Development and validation of a bovine macrophage specific cDNA microarray

      Directory of Open Access Journals (Sweden)

      Waddington David

      2006-09-01

      Full Text Available Abstract Background The response of macrophages to danger signals is an important early stage in the immune response. Our understanding of this complex event has been furthered by microarray analysis, which allows the simultaneous investigation of the expression of large numbers of genes. However, the microarray resources available to study these events in livestock animals are limited. Results Here we report the development of a bovine macrophage specific (BoMP cDNA microarray. The BoMP microarray contains 5026 sequence elements (printed in duplicate and numerous controls. The majority of the clones incorporated on the microarray were derived from the BoMP cDNA library generated from bovine myeloid cells subjected to various stimuli, including over 900 sequences unique to the library. Additional clones representing immunologically important genes have been included on the BoMP microarray. The microarray was validated by investigating the response of bovine monocytes to stimulation with interferon-γ and lipopolysaccharide using amplified RNA. At 2 and 16 hours post stimulation 695 genes exhibited statistically significant differential expression, including; 26 sequences unique to the BoMP library, interleukin 6, prion protein and toll-like receptor 4. Conclusion A 5 K cDNA microarray has been successfully developed to investigate gene expression in bovine myeloid cells. The BoMP microarray is available from the ARK-Genomics Centre for Functional Genomics in Farm Animals, UK.

    15. Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use?

      Directory of Open Access Journals (Sweden)

      Evangelia Karampetsou

      2014-06-01

      Full Text Available The advantage of microarray (array over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP and designs (targeted, whole genome, whole genome, and targeted, custom and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations.

    16. DNA Microarray-Based Diagnostics.

      Science.gov (United States)

      Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

      2016-01-01

      The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

    17. The TileCal Barrel Test Assembly

      CERN Multimedia

      Leitner, R

      On 30th October, the mechanics test assembly of the central barrel of the ATLAS tile hadronic calorimeter was completed in building 185. It started on 23rd June and is the second wheel for the Tilecal completely assembled this year. The ATLAS engineers and technicians are quick: instead of the 27 weeks initially foreseen for assembling the central barrel of the tile hadronic calorimeter (Tilecal) in building 185, they inserted the last of the 64 modules on 30th October after only 19 weeks. In part, this was due to the experience gained in the dry run assembly of the first extended barrel, produced in Spain, in spring this year (see Bulletin 23/2003); however, the central barrel is twice as long - and twice as heavy. With a length of 6.4 metres, an outer diameter of 8.5 metres and an inner diameter of 4.5 metres, the object weight is 1300 tonnes. The whole barrel cylinder is supported by the stainless steel support structure weighing only 27 tons. The barrel also has to have the right shape: over the whole 8...

    18. Triangular dissections, aperiodic tilings and Jones algebras

      CERN Document Server

      Coquereaux, Robert

      1994-01-01

      The Brattelli diagram associated with a given bicolored Dynkin-Coxeter graph of type A_n determines planar fractal sets obtained by infinite dissections of a given triangle. All triangles appearing in the dissection process have angles that are multiples of \\pi/ (n+1). There are usually several possible infinite dissections compatible with a given n but a given one makes use of n/2 triangle types if n is even. Jones algebra with index [ 4 \\ \\cos^2{\\pi \\over n+1}]^{-1} (values of the discrete range) act naturally on vector spaces associated with those fractal sets. Triangles of a given type are always congruent at each step of the dissection process. In the particular case n=4, there are isometric and the whole structure lead, after proper inflation, to aperiodic Penrose tilings. The other "tilings" associated with other values of the index are discussed and shown to be encoded by equivalence classes of infinite sequences (with appropriate constraints) using only n/2 digits (if n is even) and generalizing the ...

    19. Future Armor Tiles MIL-STD-166O Tests.

      Science.gov (United States)

      1997-02-01

      The U.S. Army Defense Ammunition Center (DAC), Validation Engineering Division, was tasked by DAC to conduct MIL- STD -1660 tests on armor tile...containers on a wooden pallet. This report contains test results with the armor tile containers on a wooden pallet meeting MIL- STD -1660, Design Criteria for Ammunition Unit Loads, requirements.

    20. Drainage water management effects on tile discharge and water quality

      Science.gov (United States)

      Nitrogen (N) fluxes from tile drained watersheds have been implicated in water quality studies of the Mississippi River Basin, but the contribution of tile drains to N export in headwater watersheds is not well understood. The objective of this study was to ascertain seasonal and annual contribution...

    1. Computerized Machine for Cutting Space Shuttle Thermal Tiles

      Science.gov (United States)

      Ramirez, Luis E.; Reuter, Lisa A.

      2009-01-01

      A report presents the concept of a machine aboard the space shuttle that would cut oversized thermal-tile blanks to precise sizes and shapes needed to replace tiles that were damaged or lost during ascent to orbit. The machine would include a computer-controlled jigsaw enclosed in a clear acrylic shell that would prevent escape of cutting debris. A vacuum motor would collect the debris into a reservoir and would hold a tile blank securely in place. A database stored in the computer would contain the unique shape and dimensions of every tile. Once a broken or missing tile was identified, its identification number would be entered into the computer, wherein the cutting pattern associated with that number would be retrieved from the database. A tile blank would be locked into a crib in the machine, the shell would be closed (proximity sensors would prevent activation of the machine while the shell was open), and a "cut" command would be sent from the computer. A blade would be moved around the crib like a plotter, cutting the tile to the required size and shape. Once the tile was cut, an astronaut would take a space walk for installation.

    2. Performance of the ATLAS Tile LaserII Calibration System

      CERN Document Server

      AUTHOR|(INSPIRE)INSPIRE-00124895; The ATLAS collaboration

      2015-01-01

      The new laser calibration system of the ATLAS Tile hadron calorimeter is presented. The perfomances of the calibration and monitor tools internal to the laser system are given in terms of operation time stability. The use of the laser system in the normal Tile calibration procedures is also described.

    3. The house, the tile stove and the climate change

      DEFF Research Database (Denmark)

      Atzbach, Rainer

      2014-01-01

      The tile stove was invented in the North Alpine area between the 8th and 10th century. Apart from convection air heating and clay cupola ovens, this system provided the only possibility for a smoke-free heated living room. The innovation of the tile stove heating system itself did not reach...

    4. Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

      Science.gov (United States)

      Veneman, Wouter J; de Sonneville, Jan; van der Kolk, Kees-Jan; Ordas, Anita; Al-Ars, Zaid; Meijer, Annemarie H; Spaink, Herman P

      2015-03-01

      We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available.

    5. Organizing DNA Origami Tiles Into Larger Structures Using Pre-formed Scaffold Frames

      Science.gov (United States)

      Zhao, Zhao; Liu, Yan; Yan, Hao

      2012-01-01

      Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tiles units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as ‘super-origami’ or ‘origami of origami’ to scale up DNA origami technology. First, this method uses a collection of bridge strands to pre-fold a single stranded DNA scaffold into a loose framework. Subsequently, pre-formed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures. PMID:21682348

    6. Ceramic tiles: above and beyond traditional applications

      Directory of Open Access Journals (Sweden)

      Moreno, A.

      2006-04-01

      Full Text Available At present ceramic tiles are already being marketed with characteristics and performance features that make them products whose applications go far beyond traditional tile uses. These are not just future possibilities: their industrial and commercial reality already makes them immediately serviceable in multiple environments. And this is precisely the key concept in these new tile applications: their features make them useable for wholly different functions – functions till now reserved for other products – or, in certain cases, for entirely novel functions. In addition, the functionalities involved are destined to improve aspects directly related to the quality of life, conditions of habitability or, for instance, to using such a vital natural source of energy as solar radiation. It should, therefore, be stressed that these new generations of ceramic tiles are to be considered part of the range of architectural elements for both external and internal uses, since, as the following will show, they provide the surfaces they clad with a broad spectrum of properties and functions without detriment to the aesthetic qualities, always so characteristic, of ceramic tile. To illustrate the above, the present paper describes three new families of ceramic products. These groups of products are conceptually different and many-sided, which makes them serviceable as functional elements in different contexts.

      En estos momentos, ya hay en el mercado baldosas cerámicas dotadas de características y prestaciones que hacen de ellas productos con aplicaciones que van mucho más allá de los usos a que tradicionalmente han estado asociadas. No se trata tan sólo de posibilidades futuras, sino de productos con una realidad industrial y comercial, que permite su implantación inmediata en los diferentes ámbitos en los que pueden desarrollar su funcionalidad. Y este es precisamente el concepto clave de estas nuevas aplicaciones de las baldosas cer

    7. A fisheye viewer for microarray-based gene expression data

      OpenAIRE

      2006-01-01

      Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of ra...

    8. Tiling for Performance Tuning on Different Models of GPUs

      CERN Document Server

      Xu, Chang; Jenkins, Samantha

      2010-01-01

      The strategy of using CUDA-compatible GPUs as a parallel computation solution to improve the performance of programs has been more and more widely approved during the last two years since the CUDA platform was released. Its benefit extends from the graphic domain to many other computationally intensive domains. Tiling, as the most general and important technique, is widely used for optimization in CUDA programs. New models of GPUs with better compute capabilities have, however, been released, new versions of CUDA SDKs were also released. These updated compute capabilities must to be considered when optimizing using the tiling technique. In this paper, we implement image interpolation algorithms as a test case to discuss how different tiling strategies affect the program's performance. We especially focus on how the different models of GPUs affect the tiling's effectiveness by executing the same program on two different models of GPUs equipped testing platforms. The results demonstrate that an optimized tiling...

    9. Modular Interactive Tiles for Rehabilitation – Evidence and Effect

      DEFF Research Database (Denmark)

      Lund, Henrik Hautop

      2010-01-01

      years) in daily use in a hospital rehabilitation unit e.g. for cardiac patients. Also, the tiles were tested for performing physical rehabilitation of stroke patients both in hospital, rehabilitation centre and in their private home. In all test cases qualitative feedback indicate that the patients find......We developed modular interactive tiles to be used for playful physiotherapy, which is supposed to motivate patients to engage in and perform physical rehabilitation exercises. We report on evidence for elderly training. We tested the modular interactive tiles for an extensive period of time (4...... the playful use of modular interactive tiles engaging and motivating for them to perform the rehabilitation. Also, test data suggest that some playful exercises on the tiles demand an average heart rate of 75% and 86% of the maximum heart rate....

    10. High throughput genetic analysis of congenital myasthenic syndromes using resequencing microarrays.

      Directory of Open Access Journals (Sweden)

      Lisa Denning

      Full Text Available BACKGROUND: The use of resequencing microarrays for screening multiple, candidate disease loci is a promising alternative to conventional capillary sequencing. We describe the performance of a custom resequencing microarray for mutational analysis of Congenital Myasthenic Syndromes (CMSs, a group of disorders in which the normal process of neuromuscular transmission is impaired. METHODOLOGY/PRINCIPAL FINDINGS: Our microarray was designed to assay the exons and flanking intronic regions of 8 genes linked to CMSs. A total of 31 microarrays were hybridized with genomic DNA from either individuals with known CMS mutations or from healthy controls. We estimated an overall microarray call rate of 93.61%, and we found the percentage agreement between the microarray and capillary sequencing techniques to be 99.95%. In addition, our microarray exhibited 100% specificity and 99.99% reproducibility. Finally, the microarray detected 22 out of the 23 known missense mutations, but it failed to detect all 7 known insertion and deletion (indels mutations, indicating an overall sensitivity of 73.33% and a sensitivity with respect to missense mutations of 95.65%. CONCLUSIONS/SIGNIFICANCE: Overall, our microarray prototype exhibited strong performance and proved highly efficient for screening genes associated with CMSs. Until indels can be efficiently assayed with this technology, however, we recommend using resequencing microarrays for screening CMS mutations after common indels have been first assayed by capillary sequencing.

    11. Perspectives of DNA microarray and next-generation DNA sequencing technologies

      Institute of Scientific and Technical Information of China (English)

      2009-01-01

      DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

    12. Perspectives of DNA microarray and next-generation DNA sequencing technologies

      Institute of Scientific and Technical Information of China (English)

      TENG XiaoKun; XIAO HuaSheng

      2009-01-01

      DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequenc-ing method was first introduced by the 454 Company in 2003, immediately followed by the establish-ment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

    13. A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data.

      Science.gov (United States)

      Gelfond, Jonathan A L; Gupta, Mayetri; Ibrahim, Joseph G

      2009-12-01

      We propose a unified framework for the analysis of chromatin (Ch) immunoprecipitation (IP) microarray (ChIP-chip) data for detecting transcription factor binding sites (TFBSs) or motifs. ChIP-chip assays are used to focus the genome-wide search for TFBSs by isolating a sample of DNA fragments with TFBSs and applying this sample to a microarray with probes corresponding to tiled segments across the genome. Present analytical methods use a two-step approach: (i) analyze array data to estimate IP-enrichment peaks then (ii) analyze the corresponding sequences independently of intensity information. The proposed model integrates peak finding and motif discovery through a unified Bayesian hidden Markov model (HMM) framework that accommodates the inherent uncertainty in both measurements. A Markov chain Monte Carlo algorithm is formulated for parameter estimation, adapting recursive techniques used for HMMs. In simulations and applications to a yeast RAP1 dataset, the proposed method has favorable TFBS discovery performance compared to currently available two-stage procedures in terms of both sensitivity and specificity.

    14. Genomic and Transcriptomic Analyses of Foodborne Bacterial Pathogens

      Science.gov (United States)

      Zhang, Wei; Dudley, Edward G.; Wade, Joseph T.

      DNA microarrays (often interchangeably called DNA chips or DNA arrays) are among the most popular analytical tools for high-throughput comparative genomic and transcriptomic analyses of foodborne bacterial pathogens. A typical DNA microarray contains hundreds to millions of small DNA probes that are chemically attached (or "printed") onto the surface of a microscopic glass slide. Depending on the specific "printing" and probe synthesis technologies for different microarray platforms, such DNA probes can be PCR amplicons or in situ synthesized short oligonucleotides. DNA microarray technologies have revolutionized the way that we investigate the biology of foodborne bacterial pathogens. The major advantage of these technologies is that DNA microarrays allow comparison of subtle genomic or transcriptomic variations between two bacterial samples, such as genomic variations between two different bacterial strains or transcriptomic alterations of same bacterial strain under two different treatments. Some applications of comparative genomic hybridization microarrays and global gene expression microarrays have been covered in previous chapters of this book.

    15. Carbohydrate Microarrays in Plant Science

      DEFF Research Database (Denmark)

      Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

      2012-01-01

      industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high......-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

    16. Transfection microarray and the applications.

      Science.gov (United States)

      Miyake, Masato; Yoshikawa, Tomohiro; Fujita, Satoshi; Miyake, Jun

      2009-05-01

      Microarray transfection has been extensively studied for high-throughput functional analysis of mammalian cells. However, control of efficiency and reproducibility are the critical issues for practical use. By using solid-phase transfection accelerators and nano-scaffold, we provide a highly efficient and reproducible microarray-transfection device, "transfection microarray". The device would be applied to the limited number of available primary cells and stem cells not only for large-scale functional analysis but also reporter-based time-lapse cellular event analysis.

    17. Elliptically distributed lozenge tilings of a hexagon

      CERN Document Server

      Betea, Dan

      2011-01-01

      We present a detailed study of a 4 parameter family of elliptic weights on tilings of a hexagon introduced by Borodin, Gorin and Rains, and generalize some of their results. In the process, we connect the combinatorics of the model with the theory of elliptic special functions. We first analyze some properties of the measure and introduce canonical coordinates that are useful for combinatorially interpreting results. We then show how the computed $n$-point function (called the elliptic Selberg density) and transitional probabilities connect to the theory of $BC_n$-symmetric multivariate elliptic special functions and difference operators discovered by Rains. In particular, the difference operators intrinsically capture the combinatorial model under study, while the elliptic Selberg density is a generalization (deformation) of probability distributions pervasive in the theory of random matrices and interacting particle systems. Based on quasi-commutation relations between elliptic difference operators, we cons...

    18. Tiling a unit square with 8 squares

      CERN Document Server

      Praton, Iwan

      2011-01-01

      Put n nonoverlapping squares inside the unit square. Let f(n) and g(n) denote the maximum values of the sum of the edge lengths of the n small squares, where in the case of f(n) the maximum is taken over all arbitrary packings of the unit square, and in the case of g(n) it is taken over all tilings of the unit square (i.e., the total area of the n small squares is 1). Benton and Tyler asked for which values of n we have f(n)=g(n). We show that f(8)>g(8). More precisely, we show that g(8)=13/5; it is known that f(8) is at least 8/3.

    19. Upgrade of the ATLAS Tile Calorimeter Electronics

      CERN Document Server

      Carrio, F; The ATLAS collaboration

      2014-01-01

      This presentation summarizes the status of the on-detector and off-detector electronics developments for the Phase II Upgrade of the ATLAS Tile Calorimeter at the LHC scheduled around 2024. A demonstrator prototype for a slice of the calorimeter including most of the new electronics is planned to be installed in ATLAS in middle 2014 during the Long Shutdown. For the on-detector readout, three different front-end boards (FEB) alternatives are being studied: a new version of the 3-in-1 card, the QIE chip and a dedicated ASIC called FATALIC. The MainBoard will provide communication and control to the FEBs and the DaughterBoard will transmit the digitized data to the off-detector electronics in the counting room, where the sROD will perform processing tasks on them.

    20. Upgrading the ATLAS Tile Calorimeter Electronics

      Directory of Open Access Journals (Sweden)

      Carrió Fernando

      2013-11-01

      Full Text Available This work summarizes the status of the on-detector and off-detector electronics developments for the Phase 2 Upgrade of the ATLAS Tile Calorimeter at the LHC scheduled around 2022. A demonstrator prototype for a slice of the calorimeter including most of the new electronics is planned to be installed in ATLAS in the middle of 2014 during the first Long Shutdown. For the on-detector readout, three different front-end boards (FEB alternatives are being studied: a new version of the 3-in-1 card, the QIE chip and a dedicated ASIC called FATALIC. The Main Board will provide communication and control to the FEBs and the Daughter Board will transmit the digitized data to the off-detector electronics in the counting room, where the super Read-Out Driver (sROD will perform processing tasks on them and will be the interface to the trigger levels 0, 1 and 2.

    1. Work on a ATLAS tile calorimeter Barrel

      CERN Multimedia

      Laurent Guiraud

      2000-01-01

      The Tile Calorimeter is designed as one barrel and two extended barrel hadron parts. The calorimeter consists of a cylindrical structure with inner and outer radius of 2280 and 4230 mm respectively. The barrel part is 5640 mm in length along the beam axis, while each of the extended barrel cylinders is 2910 mm long. Each detector cylinder is built of 64 independent wedges along the azimuthal direction. Between the barrel and the extended barrels there is a gap of about 600 mm, which is needed for the Inner Detector and the Liquid Argon cables, electronics and services. The barrel covers the region -1.0

    2. Are tiled display walls needed for astronomy?

      CERN Document Server

      Meade, Bernard F; Manos, Steven; Sinnott, Richard O

      2014-01-01

      Clustering commodity displays into a Tiled Display Wall (TDW) provides a cost-effective way to create an extremely high resolution display, capable of approaching the image sizes now gen- erated by modern astronomical instruments. Astronomers face the challenge of inspecting single large images, many similar images simultaneously, and heterogeneous but related content. Many research institutions have constructed TDWs on the basis that they will improve the scientific outcomes of astronomical imagery. We test this concept by presenting sample images to astronomers and non- astronomers using a standard desktop display (SDD) and a TDW. These samples include standard English words, wide field galaxy surveys and nebulae mosaics from the Hubble telescope. These experiments show that TDWs provide a better environment for searching for small targets in large images than SDDs. It also shows that astronomers tend to be better at searching images for targets than non-astronomers, both groups are generally better when em...

    3. Tile-Compressed FITS Kernel for IRAF

      Science.gov (United States)

      Seaman, R.

      2011-07-01

      The Flexible Image Transport System (FITS) is a ubiquitously supported standard of the astronomical community. Similarly, the Image Reduction and Analysis Facility (IRAF), developed by the National Optical Astronomy Observatory, is a widely used astronomical data reduction package. IRAF supplies compatibility with FITS format data through numerous tools and interfaces. The most integrated of these is IRAF's FITS image kernel that provides access to FITS from any IRAF task that uses the basic IMIO interface. The original FITS kernel is a complex interface of purpose-built procedures that presents growing maintenance issues and lacks recent FITS innovations. A new FITS kernel is being developed at NOAO that is layered on the CFITSIO library from the NASA Goddard Space Flight Center. The simplified interface will minimize maintenance headaches as well as add important new features such as support for the FITS tile-compressed (fpack) format.

    4. Surface manipulation of biomolecules for cell microarray applications.

      Science.gov (United States)

      Hook, Andrew L; Thissen, Helmut; Voelcker, Nicolas H

      2006-10-01

      Many biological events, such as cellular communication, antigen recognition, tissue repair and DNA linear transfer, are intimately associated with biomolecule interactions at the solid-liquid interface. To facilitate the study and use of these biological events for biodevice and biomaterial applications, a sound understanding of how biomolecules behave at interfaces and a concomitant ability to manipulate biomolecules spatially and temporally at surfaces is required. This is particularly true for cell microarray applications, where a range of biological processes must be duly controlled to maximize the efficiency and throughput of these devices. Of particular interest are transfected-cell microarrays (TCMs), which significantly widen the scope of microarray genomic analysis by enabling the high-throughput analysis of gene function within living cells. This article reviews this current research focus, discussing fundamental and applied research into the spatial and temporal surface manipulation of DNA, proteins and other biomolecules and the implications of this work for TCMs.

    5. Fixed-point tile sets and their applications

      CERN Document Server

      Durand, Bruno; Shen, Alexander

      2009-01-01

      An aperiodic tile set was first constructed by R. Berger while proving the undecidability of the domino problem. It turned out that aperiodic tile sets appear in many topics ranging from logic (the Entscheidungsproblem) to physics (quasicrystals). We present a new construction of an aperiodic tile set that is based on Kleene's fixed-point construction instead of geometric arguments. This construction is similar to J. von Neumann self-reproducing automata; similar ideas were also used by P. Gacs in the context of error-correcting computations. This construction it rather flexible, so it can be used in many ways: we show how it can be used to implement substitution rules, to construct strongly aperiodic tile sets (any tiling is far from any periodic tiling), to give a new proof for the undecidability of the domino problem and related results, characterize effectively closed 1D subshift it terms of 2D shifts of finite type (improvement of a result by M. Hochman), to construct a tile set which has only complex ti...

    6. Influence of Polymer Restraint on Ballistic Performanceof Alumina Ceramic Tiles

      Directory of Open Access Journals (Sweden)

      P.R.S. Reddy

      2008-03-01

      Full Text Available An experimental study has been carried out to evaluate the influence of confinement ofalumina ceramic tiles through polymer restraint, on its ballistic performance. Tiles of 99.5 per centpurity alumina were subjected to ballistic impact against 7.62 mm armour piercing projectiles atvelocities of about 820 m/s. The tiles of size 75 mm x 75 mm x 7 mm were confined on both facesby effectively bonding varying numbers of layers of polymer fabrics. These were then bondedto a 10 mm thick fibre glass laminate as a backing using epoxy resin. High performance polyethyleneand aramid polymer fabrics were used in the current set of experiments for restraining the tiles.Comparative effects of confinement on energy absorption of tiles with varied number of layersof fabrics were evaluated. It was observed that by providing effective confinement to the tile,energy absorption could be doubled with increase in areal density by about 13 per cent.Photographs of the damage and the effects of restraint on improvement in energy absorptionof ceramic tiles are presented and discussed.

    7. Spectral response data for development of cool coloured tile coverings

      Science.gov (United States)

      Libbra, Antonio; Tarozzi, Luca; Muscio, Alberto; Corticelli, Mauro A.

      2011-03-01

      Most ancient or traditional buildings in Italy show steep-slope roofs covered by red clay tiles. As the rooms immediately below the roof are often inhabited in historical or densely urbanized centres, the combination of low solar reflectance of tile coverings and low thermal inertia of either wooden roof structures or sub-tile insulation panels makes summer overheating a major problem. The problem can be mitigated by using tiles coated with cool colours, that is colours with the same spectral response of clay tiles in the visible, but highly reflecting in the near infrared range, which includes more than half of solar radiation. Cool colours can yield the same visible aspect of common building surfaces, but higher solar reflectance. Studies aimed at developing cool colour tile coverings for traditional Italian buildings have been started. A few coating solutions with the typical red terracotta colour have been produced and tested in the laboratory, using easily available materials. The spectral response and the solar reflectance have been measured and compared with that of standard tiles.

    8. Peptide based diagnostics: are random-sequence peptides more useful than tiling proteome sequences?

      Science.gov (United States)

      Navalkar, Krupa Arun; Johnston, Stephan Albert; Stafford, Phillip

      2015-02-01

      Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.

    9. Development of a new resequencing pathogen microarray based assay for detection of broad-spectrum respiratory tract viruses in patients with community-acquired pneumonia.

      Directory of Open Access Journals (Sweden)

      Hongwei Shen

      Full Text Available A Resequencing Pathogen Microarray (RPM is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism's nucleotide sequence. In this study, a new RPM (RPM-IVDC1 that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5 and adult patients (above age 18, respiratory syncytial virus (RSV and rhinovirus (RV were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens.

    10. Microarray Scanner for Fluorescence Detection

      Institute of Scientific and Technical Information of China (English)

      Wang Liqiang; Lu zukang; Li Yingsheng; Zheng Xufeng

      2003-01-01

      A novel pseudo confocal microarray scanner is introduced, in which one dimension scanning is performed by a galvanometer optical scanner and a telecentric objective, another dimension scanning is performed by a stepping motor.

    11. Passive cooling of porous tile used on external wall

      Institute of Scientific and Technical Information of China (English)

      罗庆; 刘庆开; 夏煦

      2009-01-01

      The porous tiles under the dry and wet conditions were studied. The simplified mathematical model was put forward to simulate the procedure of moisture evaporating for the densely porous tile. The results show that the capability of passive cooling of the porous tile is more than 5 ℃ with moisture content of 30% in Yangtze river region. Through the comparison between the measuring and simulating data,it can be proved that the simplified math model can be fully used to the engineering application,which provides a reference to explore the thermal performance of other porous material.

    12. Modular Interactive Tiles for Rehabilitation – Evidence and Effect

      DEFF Research Database (Denmark)

      Lund, Henrik Hautop

      2010-01-01

      We developed modular interactive tiles to be used for playful physiotherapy, which is supposed to motivate patients to engage in and perform physical rehabilitation exercises. We report on evidence for elderly training. We tested the modular interactive tiles for an extensive period of time (4...... years) in daily use in a hospital rehabilitation unit e.g. for cardiac patients. Also, the tiles were tested for performing physical rehabilitation of stroke patients both in hospital, rehabilitation centre and in their private home. In all test cases qualitative feedback indicate that the patients find...

    13. Monte Carlo estimation of the number of tatami tilings

      CERN Document Server

      Kimura, Kenji

      2016-01-01

      Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local interaction on the dual lattice. We use a variant of the Hamiltonian replica exchange Monte Carlo method and the multi-parameter reweighting technique to study the model. The properties of the quantity are studied beyond exact enumeration and combinatorial method. The logarithm of the number of the tilings is linear in the boundary length of the region for all the regions studied.

    14. Advanced spot quality analysis in two-colour microarray experiments

      Directory of Open Access Journals (Sweden)

      Vetter Guillaume

      2008-09-01

      Full Text Available Abstract Background Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings We evaluated the performance of two image analysis packages MAIA and GenePix (GP using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5% than GP with default spot filtering conditions. Conclusion Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.

    15. Microarray analysis in the archaeon Halobacterium salinarum strain R1.

      Directory of Open Access Journals (Sweden)

      Jens Twellmeyer

      Full Text Available BACKGROUND: Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea. METHODOLOGY/PRINCIPAL FINDINGS: We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis. CONCLUSION/SIGNIFICANCE: This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.

    16. A fisheye viewer for microarray-based gene expression data

      Directory of Open Access Journals (Sweden)

      Munson Ethan V

      2006-10-01

      Full Text Available Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface – an electronic table (E-table that uses fisheye distortion technology. Results The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. Conclusion This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

    17. Mathematical design of prokaryotic clone-based microarrays

      Directory of Open Access Journals (Sweden)

      Quirijns Elisabeth J

      2005-09-01

      Full Text Available Abstract Background Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome. Results This paper describes the development of two complementary equations for determining the genome coverage at the gene level. The first equation predicts the fraction of genes that is represented on the array in a detectable way and cover at least a set part (the minimal insert coverage of the genomic fragment by which these genes are represented. The higher this minimal insert coverage, the larger the chance that changes in expression of a specific gene can be detected and attributed to that gene. The second equation predicts the fraction of genes that is represented in spots on the array that only represent genes from a single transcription unit, which information can be interpreted in a quantitative way. Conclusion Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays.

    18. Viral discovery and sequence recovery using DNA microarrays.

      Directory of Open Access Journals (Sweden)

      David Wang

      2003-11-01

      Full Text Available Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

    19. Broad spectrum microarray for fingerprint-based bacterial species identification

      Directory of Open Access Journals (Sweden)

      Frey Jürg E

      2010-02-01

      Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

    20. The Utility of Chromosomal Microarray Analysis in Developmental and Behavioral Pediatrics

      Science.gov (United States)

      Beaudet, Arthur L.

      2013-01-01

      Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism…

    1. A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria

      NARCIS (Netherlands)

      Boesten, R.J.; Schuren, F.H.; Vos, de W.M.

      2009-01-01

      A genomic DNA-based microarray was constructed containing over 6000 randomly cloned genomic fragments of approximately 1-2 kb from six mammalian intestinal Bifidobacterium spp. including B. adolescentis, B. animalis, B. bifidum, B. catenulatum, B. longum and B. pseudolongum. This Bifidobacterium Mix

    2. Optimization of RNA Isolation from the Archaebacterium Methanosarcina Barkeri and Validation for Oligonucleotide Microarray Analysis

      Energy Technology Data Exchange (ETDEWEB)

      Culley, David E.; Kovacik, William P.; Brockman, Fred J.; Zhang, Weiwen

      2006-10-01

      ABSTRACT-The recent completion of a draft genome sequence for Methanosarcina barkeri has allowed the application of various high throughput post-genomics technologies, such as nucleic acid microarrays and mass spectrometry of proteins to detect global changes in transcription and translation that occur in response to experimental treatments...

    3. A gene expression map for the euchromatic genome of Drosophila melanogaster.

      Science.gov (United States)

      Stolc, Viktor; Gauhar, Zareen; Mason, Christopher; Halasz, Gabor; van Batenburg, Marinus F; Rifkin, Scott A; Hua, Sujun; Herreman, Tine; Tongprasit, Waraporn; Barbano, Paolo Emilio; Bussemaker, Harmen J; White, Kevin P

      2004-10-22

      We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult males and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.

    4. The Art of Space Filling in Penrose Tilings and Fractals

      CERN Document Server

      Le, San

      2011-01-01

      Incorporating designs into the tiles that form tessellations presents an interesting challenge for artists. Creating a viable MC Escher like image that works esthetically as well as functionally requires resolving incongruencies at a tile's edge while constrained by its shape. Escher was the most well known practitioner in this style of mathematical visualization, but there are significant mathematical shapes to which he never applied his artistry. These shapes can incorporate designs that form images as appealing as those produced by Escher, and our paper explores this for traditional tessellations, Penrose Tilings, fractals, and fractal/tessellation combinations. To illustrate the versatility of tiling art, images were created with multiple figures and negative space leading to patterns distinct from the work of others.

    5. Natural radioactivity in imported ceramic tiles used in Serbia

      Directory of Open Access Journals (Sweden)

      Marija M. Janković

      2013-09-01

      Full Text Available Ceramic tiles are one of the commonly used decorative building materials. Body of ceramic tiles is a mixture of different raw materials including clays, quartz materials and feldspat, and may be glazed or left unglazed. Due to the presence of zircon in the glaze, ceramic tiles can show natural radioactivity concentration significantly higher than the average values for building materials. This study presents a summary of results obtained by a survey which was consisted of measurements of activity concentrations of natural radionuclides in imported ceramic tile samples used in Serbia using a gamma spectrometer with HPGe detector. Based on the obtained concentrations, gamma index, radium equivalent activity, the indoor absorbed dose rate and the corresponding annual effective dose were evaluated to assess the potential radiological hazard associated with these building materials.

    6. REFINABLE DISTRIBUTIONS SUPPORTED ON SELF-AFFINE TILES

      Institute of Scientific and Technical Information of China (English)

      DaiXinrong

      2002-01-01

      In this paper,some conditions which assure the compactly supported refinable distributions supported on a self-affine tile to be Lebesgue-Stieltjes measures or absolutely continuous measures with respect to Lebesgue-Stieltjes measures are given.

    7. Correlation and principal component analysis in ceramic tiles characterization

      Directory of Open Access Journals (Sweden)

      Podunavac-Kuzmanović Sanja O.

      2015-01-01

      Full Text Available The present study deals with the analysis of the characteristics of ceramic wall and floor tiles on the basis of their quality parameters: breaking force, flexural strenght, absorption and shrinking. Principal component analysis was applied in order to detect potential similarities and dissimilarities among the analyzed tile samples, as well as the firing regimes. Correlation analysis was applied in order to find correlations among the studied quality parameters of the tiles. The obtained results indicate particular differences between the samples on the basis of the firing regimes. However, the correlation analysis points out that there is no statistically significant correlation among the quality parameters of the studied samples of the wall and floor ceramic tiles.[Projekat Ministarstva nauke Republike Srbije, br. 172012 i br. III 45008

    8. Utilization of red mud in the manufacture of ceramic tiles

      Energy Technology Data Exchange (ETDEWEB)

      Youssef, N.F.; Shater, M.O. [Housing and Building Research Center, Cairo (Egypt); Abadir, M.F.; Ibrahim, O.A. [Cairo Univ., Giza (Egypt). Faculty of Engineering

      2002-07-01

      Red mud, which is a pollutant residue from the extraction of alumina from bauxite ore, was utilized as an additive to a well blended mixture of three Egyptian clays, feldspar, quartz and grog. This was added in gradual proportions to study its effect on the vitrification properties of fired samples. Samples were moulded under a pressure of 20.7 MPa and fired at temperatures ranging from 950 C to 1100 C for soaking periods up to three hours. Compressive strength was determined as function of percent red mud added and firing temperature. A semi-exponential relation was established between strength and apparent porosity. 50 x 50 mm tiles containing 70% red mud addition and fired at 1100 C for one hour were tested. They were found to match the standards required for glazed wall tiles bodies. Tiles fired at 1100 C for 3 hours were compatible with the standards for glazed floor tiles. (orig.)

    9. Aerodynamic heat transfer to RSI tile surfaces and gap intersections. [Reusable Surface Insulation

      Science.gov (United States)

      Dunavant, J. C.; Throckmorton, D. A.

      1974-01-01

      Review of the results of aerothermal heating tests of a simulated reusable surface insulation (RSI) tile array, performed on the sidewall of a Mach-10 hypersonic tunnel. In particular, the heating characteristics of the tile array, such as they result from heating inside the tile-expansion-space providing gaps between individual tiles, are investigated. The results include the finding that heating on the upstream face of a tile is strongly affected by the interacting longitudinal gap flow.

    10. Characterization of Mechanical Properties of Porcelain Tile Using Ultrasonics

      OpenAIRE

      KURAMA, Semra; Eren, Elif

      2012-01-01

      Ultrasound affords a very useful and versatile non-destructive method, using a large application area, for evaluating the microstructure and mechanical properties of materials. In this study, porcelain tiles were sintered at different temperatures to change their porosity. Following this, the time of flight of both longitudinal and shear waves was measured through the tile. The time of flight of ultrasonic waves was measured using a contact ultrasonic transducer operating on a pulse-echo mode...

    11. ATLAS Tile Calorimeter performance with Run 1 data

      Energy Technology Data Exchange (ETDEWEB)

      Cerdá Alberich, L., E-mail: lcerdaal@cern.ch

      2016-07-11

      The performance of the central hadronic calorimeter, TileCal, in the ATLAS Experiment at the Large Hadron Collider is studied using cosmic-ray muons and the large sample of proton-proton collisions acquired during the Run 1 of LHC (2010–2012). Results are presented for the precision of the absolute energy scale and timing, noise characterization, and time-stability of the detector. The results show that the Tile Calorimeter performance is within the design requirements of the detector.

    12. Ternary and senary representations using DNA double-crossover tiles

      CERN Document Server

      Kim, Byeonghoon; Son, Junyoung; Kim, Junghoon; Hwang, Si Un; Dugasani, Sreekantha Reddy; Kim, Min Hyeok; Kim, Byung-Dong; Chang, Iksoo; Liu, Wing Kam; Kim, Moon Ki; Park, Sung Ha

      2016-01-01

      The information capacity of double-crossover (DX) tiles was successfully increased beyond a binary representation to higher base representations. By controlling the length and the position of DNA hairpins on the DX tile, ternary and senary (base-3 and base-6) digit representations were realized and verified by atomic force microscopy (AFM). Also, normal mode analysis (NMA) was carried out to study the mechanical characteristics of each structure.

    13. Numerical optimization of tungsten monoblock tile in EAST divertor

      Energy Technology Data Exchange (ETDEWEB)

      Chen, Xiahua [Harbin Engineering University, Harbin 150001 (China); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Ding, Fang, E-mail: fding@ipp.ac.cn [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Mao, Hongmin; Luo, Guangnan; Hu, Zhenhua; Xu, Feng; Niu, Guojian [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China)

      2016-10-15

      Highlights: • A method based on Kriging model and Uniform Design is developed and applied to the geometry optimization of EAST W tile. • An optimized chamfering geometry is obtained and significantly reduces the maximum temperature on W monoblock. • The incident angle of plasma flux has a strong impact on the optimized chamfering geometry. - Abstract: The ITER-like tungsten divertor with toroidally symmetric 1 mm × 1 mm chamfers on monoblock tiles has been installed in EAST in 2014. Hot spots were experimentally observed mostly along the toridial facing gaps between two columns of W/Cu monoblock units, which are often aggravated by installation misalignment. These hot spots can significantly degrade the power handling capability of W divertor and need to be alleviated. A numerical optimization model for tile chamfering design is built based on the finite element method (FEM), in which the numerical experiments are designed by the uniform table. The calculation results in ANSYS for these experiments are then processed employing the code Design and Analysis of Computer Experiments (DACE) in which the Kriging method is adopted to reconstruct a response surface. The optimum geometry can be derived from the minimum point on the surface. The results show that, under 200 MW/m{sup 2} parallel heat flux with an inclination angle of 3° with respect to tile surface, the maximum temperature on W tile with a 0.5 mm misalignment can be decreased to 2084 °C by adopting an optimized single-sided chamfer, 1.8 times lower than 1 mm × 1 mm symmetrically chamfered tile. The optimum chamfering geometry has a strong dependence on the inclination angle of plasma flux to tile surface. As a result, the monoblock tiles in a flat cassette module need to be chamfered differently to adapt to the varied inclination angles.

    14. A portable interferometric micro-array reader on image sensor

      OpenAIRE

      Villar Zafra, Aitor

      2014-01-01

      [ANGLÈS] Microarrays constitute a valuable analytical tool for multiplex and high-throughput analysis and are widely used in genomics and proteomics with many potential applications. During the last decades, protein chips have found increasing acceptance for diagnostic applications due to several advantages over conventional bioanalysis such as miniaturization, parallelization, real-time and sensitivity. Even though the majority of DNA-sensor systems relies on labeling of DNA, the recent prog...

    15. Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

      National Research Council Canada - National Science Library

      Miller, David T; Adam, Margaret P; Aradhya, Swaroop; Biesecker, Leslie G; Brothman, Arthur R; Carter, Nigel P; Church, Deanna M; Crolla, John A; Eichler, Evan E; Epstein, Charles J; Faucett, W. Andrew; Feuk, Lars; Friedman, Jan M; Hamosh, Ada; Jackson, Laird; Kaminsky, Erin B; Kok, Klaas; Krantz, Ian D; Kuhn, Robert M; Lee, Charles; Ostell, James M; Rosenberg, Carla; Scherer, Stephen W; Spinner, Nancy B; Stavropoulos, Dimitri J; Tepperberg, James H; Thorland, Erik C; Vermeesch, Joris R; Waggoner, Darrel J; Watson, Michael S; Martin, Christa Lese; Ledbetter, David H

      2010-01-01

      ... and (2) testing for common single-gene disorders, such as fragile X syndrome. 4 Microarray-based genomic copy-number analysis is now a commonly ordered clinical genetic test for this patient populat...

    16. Data Quality system of the ATLAS hadronic Tile calorimeter

      CERN Document Server

      Nemecek, S; The ATLAS collaboration

      2012-01-01

      The Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment. It is subdivided into a large central barrel and two smaller lateral extended barrels. Each barrel consists of 64 wedges, made of iron plates and scintillating tiles. Two edges of each scintillating tile are air-coupled to wave-length shifting fibres which collect the scintillating light and transmit it to photo-multipliers. The total number of channels is about 10000. An essential part of the TileCal detector is the Data Quality (DQ) system. The DQ system is designed to check the status of the electronic channels. It is designed to provide information at two levels - online and offline. The online TileCal DQ system monitors continuously the data while they are recorded and provides a fast feedback. The offline DQ system allows a detailed study, if needed it provides corrections to be applied to the recorded data and it allows to validate the data for physics analysis. In addition to the check of physics...

    17. Preparation and characterization of photo chromic effect for ceramic tiles

      Energy Technology Data Exchange (ETDEWEB)

      Atay, B.; Goktas, A.; Dogan, A.

      2011-07-01

      Ceramic tile industry is developing due to the technological researches in scientific area and new tiles which are not only a traditional ceramic also have many multiple functionalities have been marketed nowadays. These tiles like photo catalytic, photovoltaic, antibacterial and etc. improve the quality of life and provide lots of benefits such as self cleaning, energy production, climate control. The goal of this study was to enhance the photo chromic function on ceramic tiles which is the attitude of changing color in a reversible way by electromagnetic radiation and widely used in many areas because of its aesthetic and also functional properties. High response time of photo chromic features of ceramic tiles have been achieved by employing of polymeric gel with additives of photoactive dye onto the ceramic surface. Photo chromic layer with a thickness of approximately 45- 50 {mu}m was performed by using spray coating technique which provided homogeneous deposition on surface. Photo chromic ceramic tiles with high photo chromic activity such as reversibly color change between {delta}E= 0.29 and 26.31 were obtained successfully. The photo chromic performance properties and coloring-bleaching mechanisms were analyzed by spectrophotometer. The microstructures of coatings were investigated both by stereo microscopy and scanning electron microscopy (SEM). (Author) 13 refs.

    18. Coxeter Pairs, Ammann Patterns and Penrose-like Tilings

      CERN Document Server

      Boyle, Latham

      2016-01-01

      We identify a precise geometric relationship between: (i) certain natural pairs of irreducible reflection groups ("Coxeter pairs"); (ii) self-similar quasicrystalline patterns formed by superposing sets of 1D quasi-periodically-spaced lines, planes or hyper-planes ("Ammann patterns"); and (iii) the tilings dual to these patterns ("Penrose-like tilings"). We use this relationship to obtain all irreducible Ammann patterns and their dual Penrose-like tilings, along with their key properties in a simple, systematic and unified way, expanding the number of known examples from four to infinity. For each symmetry, we identify the minimal Ammann patterns (those composed of the fewest 1d quasiperiodic sets) and construct the associated Penrose-like tilings: six in 2D, five in 3D and one in 4D. These include the original Penrose tiling, the three other previously known Penrose-like tilings, and eight that are new. We also complete the enumeration of the quasicrystallographic space groups corresponding to the irreducibl...

    19. The ATLAS Tile Calorimeter DCS for Run 2

      CERN Document Server

      Pedro Martins, Filipe Manuel; The ATLAS collaboration

      2016-01-01

      TileCal is one of the ATLAS sub-detectors operating at the Large Hadron Collider (LHC), which is taking data since 2010. The Detector Control System (DCS) was developed to ensure the coherent and safe operation of the whole ATLAS detector. Seventy thousand (70000) parameters are used for control and monitoring purposes of TileCal, requiring an automated system. The TileCal DCS is mainly responsible for the control and monitoring of the high and low voltage systems but it also supervises the detector infrastructure (cooling and racks), calibration systems, data acquisition and safety. During the first period of data taking (Run 1, 2010-12) the TileCal DCS allowed a smooth detector operation and should continue to do so for the second period (Run 2) that started in 2015. The TileCal DCS was updated in order to cope with the hardware and software requirements for Run 2 operation. These updates followed the general ATLAS guidelines on the software and hardware upgrade but also the new requirements from the TileCa...

    20. Microarray analysis of p-anisaldehyde-induced transcriptome of Saccharomyces cerevisiae.

      Science.gov (United States)

      Yu, Lu; Guo, Na; Yang, Yi; Wu, Xiuping; Meng, Rizeng; Fan, Junwen; Ge, Fa; Wang, Xuelin; Liu, Jingbo; Deng, Xuming

      2010-03-01

      p-Anisaldehyde (4-methoxybenzaldehyde), an extract from Pimpinella anisum L. seeds, is a potential novel preservative. To reveal the possible action mechanism of p-anisaldehyde against microorganisms, yeast-based commercial oligonucleotide microarrays were used to analyze the genome-wide transcriptional changes in response to p-anisaldehyde. Quantitative real-time RT-PCR was performed for selected genes to verify the microarray results. We interpreted our microarray data with the clustering tool, T-profiler. Analysis of microarray data revealed that p-anisaldehyde induced the expression of genes related to sulphur assimilation, aromatic aldehydes metabolism, and secondary metabolism, which demonstrated that the addition of p-anisaldehyde may influence the normal metabolism of aromatic aldehydes. This genome-wide transcriptomics approach revealed first insights into the response of Saccharomyces cerevisiae (S. cerevisiae) to p-anisaldehyde challenge.