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Sample records for two-color microarray experiments

  1. Statistical analysis of efficient unbalanced factorial designs for two-color microarray experiments.

    Science.gov (United States)

    Tempelman, Robert J

    2008-01-01

    Experimental designs that efficiently embed a fixed effects treatment structure within a random effects design structure typically require a mixed-model approach to data analyses. Although mixed model software tailored for the analysis of two-color microarray data is increasingly available, much of this software is generally not capable of correctly analyzing the elaborate incomplete block designs that are being increasingly proposed and used for factorial treatment structures. That is, optimized designs are generally unbalanced as it pertains to various treatment comparisons, with different specifications of experimental variability often required for different treatment factors. This paper uses a publicly available microarray dataset, as based upon an efficient experimental design, to demonstrate a proper mixed model analysis of a typical unbalanced factorial design characterized by incomplete blocks and hierarchical levels of variability.

  2. EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments

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    Craven Mark

    2009-09-01

    Full Text Available Abstract Background The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of data generated, has implications when it comes to effective storage, analysis and sharing of these data. A number of software tools have been developed to store, analyze, and share microarray data. However, a majority of these tools do not offer all of these features nor do they specifically target the commonly used two color Agilent DNA microarray platform. Thus, the motivating factor for the development of EDGE3 was to incorporate the storage, analysis and sharing of microarray data in a manner that would provide a means for research groups to collaborate on Agilent-based microarray experiments without a large investment in software-related expenditures or extensive training of end-users. Results EDGE3 has been developed with two major functions in mind. The first function is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy the first function, EDGE3 has been developed as a means to establish a well defined experimental workflow and information system for microarray generation. To satisfy the second function, the software application utilized as the user interface of EDGE3 is a web browser. Within the web browser, a user is able to access the entire functionality, including, but not limited to, the ability to perform a number of bioinformatics based analyses, collaborate between research groups through a user-based security model, and access to the raw data files and quality control files generated by the software used to extract the signals from an array image. Conclusion Here, we present EDGE3, an open-source, web

  3. An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments

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    Barillot Emmanuel

    2005-12-01

    Full Text Available Abstract Background Although DNA microarray technologies are very powerful for the simultaneous quantitative characterization of thousands of genes, the quality of the obtained experimental data is often far from ideal. The measured microarrays images represent a regular collection of spots, and the intensity of light at each spot is proportional to the DNA copy number or to the expression level of the gene whose DNA clone is spotted. Spot quality control is an essential part of microarray image analysis, which must be carried out at the level of individual spot identification. The problem is difficult to formalize due to the diversity of instrumental and biological factors that can influence the result. Results For each spot we estimate the ratio of measured fluorescence intensities revealing differential gene expression or change in DNA copy numbers between the test and control samples. We also define a set of quality characteristics and a model for combining these characteristics into an overall spot quality value. We have developed a training procedure to evaluate the contribution of each individual characteristic in the overall quality. This procedure uses information available from replicated spots, located in the same array or over a set of replicated arrays. It is assumed that unspoiled replicated spots must have very close ratios, whereas poor spots yield greater diversity in the obtained ratio estimates. Conclusion The developed procedure provides an automatic tool to quantify spot quality and to identify different types of spot deficiency occurring in DNA microarray technology. Quality values assigned to each spot can be used either to eliminate spots or to weight contribution of each ratio estimate in follow-up analysis procedures.

  4. Assessing probe-specific dye and slide biases in two-color microarray data

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    Goldberg Zelanna

    2008-07-01

    Full Text Available Abstract Background A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue. Results We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function, though numerical results are also obtained. Conclusion We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor.

  5. Goulphar: rapid access and expertise for standard two-color microarray normalization methods

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    Servant Nicolas

    2006-10-01

    Full Text Available Abstract Background Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packages but it is often difficult to identify the most appropriate method. Furthermore, the use of R commands for functions and graphics can introduce mistakes that are difficult to trace. We present here a script written in R that provides a flexible means of access to and monitoring of data normalization for two-color microarrays. This script combines the power of BioConductor and R analysis functions and reduces the amount of R programming required. Results Goulphar was developed in and runs using the R language and environment. It combines and extends functions found in BioConductor packages (limma and marray to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters for excluding incorrect signals during the pre-processing step. It displays informative output plots, enabling the user to monitor the normalization process, and helps adapt the normalization method appropriately to the data. All these analyses and graphical outputs are presented in a single PDF report. Conclusion Goulphar provides simple, rapid access to the power of the R/BioConductor statistical analysis packages, with precise control and visualization of the results obtained. Complete documentation, examples and online forms for setting script parameters are available from http://transcriptome.ens.fr/goulphar/.

  6. Normalization for triple-target microarray experiments

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    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  7. Two-color CO{sub 2}/HeNe laser interferometer for C-2 experiment

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    Gornostaeva, O.; Deng, B. H.; Garate, E.; Gota, H.; Kinley, J.; Schroeder, J.; Tuszewski, M. [Tri Alpha Energy, Inc., P.O. Box 7010, Rancho Santa Margarita, California 92688 (United States)

    2010-10-15

    A six-channel two-color interferometer has been developed for plasma electron density measurements in the C-2 field reversed configuration experiment. A CO{sub 2} laser is utilized as the main probe beams, while copropagating visible HeNe laser beams are mainly sensitive to vibration. Density measurements in C-2 plasmas have shown that this is a reliable turn-key system. The maximum residual phase noise after vibration compensation is less than {+-}5 deg., corresponding to a line integral density of 3x10{sup 18} m{sup -2}. The time resolution for routine operation is 2 {mu}s.

  8. Two-color CO2/HeNe laser interferometer for C-2 experiment.

    Science.gov (United States)

    Gornostaeva, O; Deng, B H; Garate, E; Gota, H; Kinley, J; Schroeder, J; Tuszewski, M

    2010-10-01

    A six-channel two-color interferometer has been developed for plasma electron density measurements in the C-2 field reversed configuration experiment. A CO(2) laser is utilized as the main probe beams, while copropagating visible HeNe laser beams are mainly sensitive to vibration. Density measurements in C-2 plasmas have shown that this is a reliable turn-key system. The maximum residual phase noise after vibration compensation is less than ±5°, corresponding to a line integral density of 3×10(18) m(-2). The time resolution for routine operation is 2 μs.

  9. Opportunities for two-color experiments at the SASE3 undulator line of the European XFEL

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    Geloni, Gianluca; Mazza, Tommaso; Meyer, Michael; Serkez, Svitozar [European XFEL GmbH, Hamburg (Germany); Kocharyan, Vitali; Saldin, Evgeni [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2017-06-15

    X-ray Free Electron Lasers (XFELs) have been proven to generate short and powerful radiation pulses allowing for a wide class of novel experiments. If an XFEL facility supports the generation of two X-ray pulses with different wavelengths and controllable delay, the range of possible experiments is broadened even further to include X-ray-pump/X-ray-probe applications. In this work we discuss the possibility of applying a simple and cost-effective method for producing two-color pulses at the SASE3 soft X-ray beamline of the European XFEL. The technique is based on the installation of a magnetic chicane in the baseline undulator and can be accomplished in several steps. We discuss the scientific interest of this upgrade for the Small Quantum Systems (SQS) instrument, in connection with the high-repetition rate of the European XFEL, and we provide start-to-end simulations up to the radiation focus on the sample, proving the feasibility of our concept.

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

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    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.

  11. Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

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    Verjovski-Almeida Sergio

    2006-02-01

    Full Text Available Abstract Background Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies. For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. Results We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool. To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as

  12. Spotting effect in microarray experiments

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    Mary-Huard Tristan

    2004-05-01

    Full Text Available Abstract Background Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio and intensity across the array. Results Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. Conclusions The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.

  13. Two-color femtosecond experiments by use of two independently tunable Ti:sapphire lasers with a sample-and-hold switch.

    Science.gov (United States)

    Sohn, J Y; Ahn, Y H; Yee, K J; Kim, D S

    1999-09-20

    We performed femtosecond two-color experiments (four-wave mixing and pump probe) using two independently tunable, partially synchronized femtosecond lasers. Despite the fact that the jitter is of the order of 5-10 ps, the time resolution is limited only by the pulse width when a homemade sample-and-hold switch is used.

  14. Weighted analysis of general microarray experiments

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    Kristiansson Erik

    2007-10-01

    Full Text Available Abstract Background In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be invalid and typically lead to too optimistic p-values. A method called WAME has been proposed where a variance is estimated for each sample and a covariance is estimated for each pair of samples. The current version of WAME is, however, limited to experiments with paired design, e.g. two-channel microarrays. Results The WAME procedure is extended to general microarray experiments, making it capable of handling both one- and two-channel datasets. Two public one-channel datasets are analysed and WAME detects both unequal variances and correlations. WAME is compared to other common methods: fold-change ranking, ordinary linear model with t-tests, LIMMA and weighted LIMMA. The p-value distributions are shown to differ greatly between the examined methods. In a resampling-based simulation study, the p-values generated by WAME are found to be substantially more correct than the alternatives when a relatively small proportion of the genes is regulated. WAME is also shown to have higher power than the other methods. WAME is available as an R-package. Conclusion The WAME procedure is generalized and the limitation to paired-design microarray datasets is removed. The examined other methods produce invalid p-values in many cases, while WAME is shown to produce essentially valid p-values when a relatively small proportion of genes is regulated. WAME is also shown to have higher power than the examined alternative methods.

  15. Triple-target microarray experiments: a novel experimental strategy

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    Cooke Howard J

    2004-02-01

    Full Text Available Abstract Background High-throughput, parallel gene expression analysis by means of microarray technology has become a widely used technique in recent years. There are currently two main dye-labelling strategies for microarray studies based on custom-spotted cDNA or oligonucleotides arrays: (I Dye-labelling of a single target sample with a particular dye, followed by subsequent hybridisation to a single microarray slide, (II Dye-labelling of two different target samples with two different dyes, followed by subsequent co-hybridisation to a single microarray slide. The two dyes most frequently used for either method are Cy3 and Cy5. We propose and evaluate a novel experiment set-up utilising three differently labelled targets co-hybridised to one microarray slide. In addition to Cy3 and Cy5, this incorporates Alexa 594 as a third dye-label. We evaluate this approach in line with current data processing and analysis techniques for microarrays, and run separate analyses on Alexa 594 used in single-target, dual-target and the intended triple-target experiment set-ups (a total of 18 microarray slides. We follow this by pointing out practical applications and suitable analysis methods, and conclude that triple-target microarray experiments can add value to microarray research by reducing material costs for arrays and related processes, and by increasing the number of options for pragmatic experiment design. Results The addition of Alexa 594 as a dye-label for an additional – third – target sample works within the framework of more commonplace Cy5/Cy3 labelled target sample combinations. Standard normalisation methods are still applicable, and the resulting data can be expected to allow identification of expression differences in a biological experiment, given sufficient levels of biological replication (as is necessary for most microarray experiments. Conclusion The use of three dye-labelled target samples can be a valuable addition to the standard

  16. Statistical implications of pooling RNA samples for microarray experiments

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    Landfield Philip W

    2003-06-01

    Full Text Available Abstract Background Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarray chip to help defray the cost of microarray experiments as well as to correct for the technical difficulty in getting sufficient RNA from a single subject. However, the statistical, technical and financial implications of pooling have not been explicitly investigated. Results Modeling the resulting gene expression from sample pooling as a mixture of individual responses, we derived expressions for the experimental error and provided both upper and lower bounds for its value in terms of the variability among individuals and the number of RNA samples pooled. Using "virtual" pooling of data from real experiments and computer simulations, we investigated the statistical properties of RNA sample pooling. Our study reveals that pooling biological samples appropriately is statistically valid and efficient for microarray experiments. Furthermore, optimal pooling design(s can be found to meet statistical requirements while minimizing total cost. Conclusions Appropriate RNA pooling can provide equivalent power and improve efficiency and cost-effectiveness for microarray experiments with a modest increase in total number of subjects. Pooling schemes in terms of replicates of subjects and arrays can be compared before experiments are conducted.

  17. Advanced spot quality analysis in two-colour microarray experiments

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    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.

  18. A methodology for global validation of microarray experiments

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    Sladek Robert

    2006-07-01

    Full Text Available Abstract Background DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with data publicly available for mining by other investigators. Under most circumstances, validation of differential expression of genes is performed on a gene to gene basis. Thus, it is not possible to generalize validation results to the remaining majority of non-validated genes or to evaluate the overall quality of these studies. Results We present an approach for the global validation of DNA microarray experiments that will allow researchers to evaluate the general quality of their experiment and to extrapolate validation results of a subset of genes to the remaining non-validated genes. We illustrate why the popular strategy of selecting only the most differentially expressed genes for validation generally fails as a global validation strategy and propose random-stratified sampling as a better gene selection method. We also illustrate shortcomings of often-used validation indices such as overlap of significant effects and the correlation coefficient and recommend the concordance correlation coefficient (CCC as an alternative. Conclusion We provide recommendations that will enhance validity checks of microarray experiments while minimizing the need to run a large number of labour-intensive individual validation assays.

  19. Fast Gene Ontology based clustering for microarray experiments

    OpenAIRE

    Ovaska Kristian; Laakso Marko; Hautaniemi Sampsa

    2008-01-01

    Abstract Background Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. Results We present fa...

  20. Gene set analyses for interpreting microarray experiments on prokaryotic organisms

    OpenAIRE

    Heffron Fred; Van Bruggen Dirk; DeJongh Matthew; Best Aaron A; Tintle Nathan L; Porwollik Steffen; Taylor Ronald C

    2008-01-01

    Abstract Background Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use biologically defined sets of genes in interpretation, instead of examining results gene-by-gene. Despite a serious limitation, a method based on Fisher's exact test remains one of the few plausible options for gene set analysis when an experiment has few replicates, ...

  1. Two-color infrared detector

    Science.gov (United States)

    Klem, John F; Kim, Jin K

    2014-05-13

    A two-color detector includes a first absorber layer. The first absorber layer exhibits a first valence band energy characterized by a first valence band energy function. A barrier layer adjoins the first absorber layer at a first interface. The barrier layer exhibits a second valence band energy characterized by a second valence band energy function. The barrier layer also adjoins a second absorber layer at a second interface. The second absorber layer exhibits a third valence band energy characterized by a third valence band energy function. The first and second valence band energy functions are substantially functionally or physically continuous at the first interface and the second and third valence band energy functions are substantially functionally or physically continuous at the second interface.

  2. 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.

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    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

  3. 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

  4. Sequential interim analyses of survival data in DNA microarray experiments

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    Jung Klaus

    2011-04-01

    Full Text Available Abstract Background Discovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently, microarray studies are performed to identify genes of which the expression levels in pretherapeutic tissue samples are correlated to survival times of patients. Typically, such a study can take several years until the full planned sample size is available. Therefore, interim analyses are desirable, offering the possibility of stopping the study earlier, or of performing additional laboratory experiments to validate the role of the detected genes. While many methods correcting the multiple testing bias introduced by interim analyses have been proposed for studies of one single feature, there are still open questions about interim analyses of multiple features, particularly of high-dimensional microarray data, where the number of features clearly exceeds the number of samples. Therefore, we examine false discovery rates and power rates in microarray experiments performed during interim analyses of survival studies. In addition, the early stopping based on interim results of such studies is evaluated. As stop criterion we employ the achieved average power rate, i.e. the proportion of detected true positives, for which a new estimator is derived and compared to existing estimators. Results In a simulation study, pre-specified levels of the false discovery rate are maintained in each interim analysis, where reduced levels as used in classical group sequential designs of one single feature are not necessary. Average power rates increase with each interim analysis, and many studies can be stopped prior to their planned end when a certain pre-specified power rate is achieved. The new estimator for the power rate slightly deviates from the true power rate but is comparable to other estimators. Conclusions Interim analyses of microarray experiments can provide

  5. Visualization of Growth Curve Data from Phenotype MicroarrayExperiments

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    Jacobsen, Janet S.; Joyner, Dominique C.; Borglin, Sharon E.; Hazen, Terry C.; Arkin, Adam P.; Bethel, E. Wes

    2007-04-19

    Phenotype microarrays provide a technology to simultaneouslysurvey the response of an organism to nearly 2,000 substrates, includingcarbon, nitrogen and potassium sources; varying pH; varying saltconcentrations; and antibiotics. In order to more quickly and easily viewand compare the large number of growth curves produced by phenotypemicroarray experiments, we have developed software to produce and displaycolor images, each of which corresponds to a set of 96 growth curves.Using color images to represent growth curves data has proven to be avaluable way to assess experiment quality, compare replicates, facilitatecomparison of the responses of different organisms, and identifysignificant phenotypes. The color images are linked to traditional plotsof growth versus time, as well as to information about the experiment,organism, and substrate. In order to share and view information and dataproject-wide, all information, plots, and data are accessible using onlya Web browser.

  6. Visualization of Growth Curve Data from Phenotype MicroarrayExperiments

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, Janet S.; Joyner, Dominique C.; Borglin, Sharon E.; Hazen, Terry C.; Arkin, Adam P.; Bethel, E. Wes

    2007-04-19

    Phenotype microarrays provide a technology to simultaneouslysurvey the response of an organism to nearly 2,000 substrates, includingcarbon, nitrogen and potassium sources; varying pH; varying saltconcentrations; and antibiotics. In order to more quickly and easily viewand compare the large number of growth curves produced by phenotypemicroarray experiments, we have developed software to produce and displaycolor images, each of which corresponds to a set of 96 growth curves.Using color images to represent growth curves data has proven to be avaluable way to assess experiment quality, compare replicates, facilitatecomparison of the responses of different organisms, and identifysignificant phenotypes. The color images are linked to traditional plotsof growth versus time, as well as to information about the experiment,organism, and substrate. In order to share and view information and dataproject-wide, all information, plots, and data are accessible using onlya Web browser.

  7. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  8. Development and application of a microarray meter tool to optimize microarray experiments

    Directory of Open Access Journals (Sweden)

    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  9. Gene set analyses for interpreting microarray experiments on prokaryotic organisms.

    Energy Technology Data Exchange (ETDEWEB)

    Tintle, Nathan; Best, Aaron; Dejongh, Matthew; VanBruggen, Dirk; Heffron, Fred; Porwollik, Steffen; Taylor, Ronald C.

    2008-11-05

    Background: Recent advances in microarray technology have brought with them the need for enhanced methods of biologically interpreting gene expression data. Recently, methods like Gene Set Enrichment Analysis (GSEA) and variants of Fisher’s exact test have been proposed which utilize a priori biological information. Typically, these methods are demonstrated with a priori biological information from the Gene Ontology. Results: Alternative gene set definitions are presented based on gene sets inferred from the SEED: open-source software environment for comparative genome annotation and analysis of microbial organisms. Many of these gene sets are then shown to provide consistent expression across a series of experiments involving Salmonella Typhimurium. Implementation of the gene sets in an analysis of microarray data is then presented for the Salmonella Typhimurium data. Conclusions: SEED inferred gene sets can be naturally defined based on subsystems in the SEED. The consistent expression values of these SEED inferred gene sets suggest their utility for statistical analyses of gene expression data based on a priori biological information

  10. Scheme for femtosecond-resolution pump-probe experiments at XFELs with two-color ten GW-level X-ray pulses

    CERN Document Server

    Geloni, Gianluca; Saldin, Evgeni

    2010-01-01

    This paper describes a scheme for pump-probe experiments that can be performed at LCLS and at the European XFEL and determines what additional hardware development will be required to bring these experiments to fruition. It is proposed to derive both pump and probe pulses from the same electron bunch, but from different parts of the tunable-gap baseline undulator. This eliminates the need for synchronization and cancels jitter problems. The method has the further advantage to make a wide frequency range accessible at high peak-power and high repetition-rate. An important feature of the proposed scheme is that the hardware requirement is minimal. Our technique is based in essence on the "fresh" bunch technique. For its implementation it is sufficient to substitute a single undulator module with short magnetic delay line, i.e. a weak magnetic chicane, which delays the electron bunch with respect to the SASE pulse of half of the bunch length in the linear stage of amplification. This installation does not pertur...

  11. Two-color QCD at high density

    Energy Technology Data Exchange (ETDEWEB)

    Boz, Tamer; Skullerud, Jon-Ivar [Department of Mathematical Physics, Maynooth University, Maynooth, Co. Kildare (Ireland); Centre for the Subatomic Structure of Matter, Adelaide University, Adelaide, SA 5005 (Australia); Giudice, Pietro [Universität Münster, Institut für Theoretische Physik, Münster (Germany); Hands, Simon [Department of Physics, College of Science, Swansea University, Swansea (United Kingdom); Williams, Anthony G. [Centre for the Subatomic Structure of Matter, Adelaide University, Adelaide, SA 5005 (Australia)

    2016-01-22

    QCD at high chemical potential has interesting properties such as deconfinement of quarks. Two-color QCD, which enables numerical simulations on the lattice, constitutes a laboratory to study QCD at high chemical potential. Among the interesting properties of two-color QCD at high density is the diquark condensation, for which we present recent results obtained on a finer lattice compared to previous studies. The quark propagator in two-color QCD at non-zero chemical potential is referred to as the Gor’kov propagator. We express the Gor’kov propagator in terms of form factors and present recent lattice simulation results.

  12. Unscaled Bayes factors for multiple hypothesis testing in microarray experiments.

    Science.gov (United States)

    Bertolino, Francesco; Cabras, Stefano; Castellanos, Maria Eugenia; Racugno, Walter

    2015-12-01

    Multiple hypothesis testing collects a series of techniques usually based on p-values as a summary of the available evidence from many statistical tests. In hypothesis testing, under a Bayesian perspective, the evidence for a specified hypothesis against an alternative, conditionally on data, is given by the Bayes factor. In this study, we approach multiple hypothesis testing based on both Bayes factors and p-values, regarding multiple hypothesis testing as a multiple model selection problem. To obtain the Bayes factors we assume default priors that are typically improper. In this case, the Bayes factor is usually undetermined due to the ratio of prior pseudo-constants. We show that ignoring prior pseudo-constants leads to unscaled Bayes factor which do not invalidate the inferential procedure in multiple hypothesis testing, because they are used within a comparative scheme. In fact, using partial information from the p-values, we are able to approximate the sampling null distribution of the unscaled Bayes factor and use it within Efron's multiple testing procedure. The simulation study suggests that under normal sampling model and even with small sample sizes, our approach provides false positive and false negative proportions that are less than other common multiple hypothesis testing approaches based only on p-values. The proposed procedure is illustrated in two simulation studies, and the advantages of its use are showed in the analysis of two microarray experiments.

  13. Stochastic Oscillations in Genetic Regulatory Networks: Application to Microarray Experiments

    Directory of Open Access Journals (Sweden)

    Rosenfeld Simon

    2006-01-01

    Full Text Available We analyze the stochastic dynamics of genetic regulatory networks using a system of nonlinear differential equations. The system of -functions is applied to capture the role of RNA polymerase in the transcription-translation mechanism. Using probabilistic properties of chemical rate equations, we derive a system of stochastic differential equations which are analytically tractable despite the high dimension of the regulatory network. Using stationary solutions of these equations, we explain the apparently paradoxical results of some recent time-course microarray experiments where mRNA transcription levels are found to only weakly correlate with the corresponding transcription rates. Combining analytical and simulation approaches, we determine the set of relationships between the size of the regulatory network, its structural complexity, chemical variability, and spectrum of oscillations. In particular, we show that temporal variability of chemical constituents may decrease while complexity of the network is increasing. This finding provides an insight into the nature of "functional determinism" of such an inherently stochastic system as genetic regulatory network.

  14. ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

    Science.gov (United States)

    Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

    2016-01-01

    Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools.

  15. A Web-based multi-database system supporting distributed collaborative management and sharing of microarray experiment information.

    Science.gov (United States)

    Burgarella, Sarah; Cattaneo, Dario; Masseroli, Marco

    2006-01-01

    We developed MicroGen, a multi-database Web based system for managing all the information characterizing spotted microarray experiments. It supports information gathering and storing according to the Minimum Information About Microarray Experiments (MIAME) standard. It also allows easy sharing of information and data among all multidisciplinary actors involved in spotted microarray experiments.

  16. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA

    NARCIS (Netherlands)

    Nueda, M.J.; Conesa, A.; Westerhuis, J.A.; Hoefsloot, H.C.J.; Smilde, A.K.; Talón, M.; Ferrer, A.

    2007-01-01

    Motivation: Designed microarray experiments are used to investigate the effects that controlled experimental factors have on gene expression and learn about the transcriptional responses associated with external variables. In these datasets, signals of interest coexist with varying sources of unwant

  17. MicroGen: a MIAME compliant web system for microarray experiment information and workflow management

    Directory of Open Access Journals (Sweden)

    Pinciroli Francesco

    2005-12-01

    Full Text Available Abstract Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

  18. poolMC: Smart pooling of mRNA samples in microarray experiments

    Directory of Open Access Journals (Sweden)

    Schiefelbein John

    2010-06-01

    Full Text Available Abstract Background Typically, pooling of mRNA samples in microarray experiments implies mixing mRNA from several biological-replicate samples before hybridization onto a microarray chip. Here we describe an alternative smart pooling strategy in which different samples, not necessarily biological replicates, are pooled in an information theoretic efficient way. Further, each sample is tested on multiple chips, but always in pools made up of different samples. The end goal is to exploit the compressibility of microarray data to reduce the number of chips used and increase the robustness to noise in measurements. Results A theoretical framework to perform smart pooling of mRNA samples in microarray experiments was established and the software implementation of the pooling and decoding algorithms was developed in MATLAB. A proof-of-concept smart pooled experiment was performed using validated biological samples on commercially available gene chips. Differential-expression analysis of the smart pooled data was performed and compared against the unpooled control experiment. Conclusions The theoretical developments and experimental demonstration in this paper provide a useful starting point to investigate smart pooling of mRNA samples in microarray experiments. Although the smart pooled experiment did not compare favorably with the control, the experiment highlighted important conditions for the successful implementation of smart pooling - linearity of measurements, sparsity in data, and large experiment size.

  19. Statistical tests for differential expression in cDNA microarray experiments

    OpenAIRE

    Cui, Xiangqin; Churchill, Gary A.

    2003-01-01

    Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (ANOVA) can be used, and the mixed ANOVA model is a general and powerful approach for microarray experiments with multiple factors and/or several sources of variation.

  20. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration

    Science.gov (United States)

    Romualdi, Chiara; Trevisan, Silvia; Celegato, Barbara; Costa, Germano; Lanfranchi, Gerolamo

    2003-01-01

    The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests. PMID:14627839

  1. Two-color walking Peregrine solitary waves.

    Science.gov (United States)

    Baronio, Fabio; Chen, Shihua; Mihalache, Dumitru

    2017-09-15

    We study the extreme localization of light, evolving upon a non-zero background, in two-color parametric wave interaction in nonlinear quadratic media. We report the existence of quadratic Peregrine solitary waves, in the presence of significant group-velocity mismatch between the waves (or Poynting vector beam walk-off), in the regime of cascading second-harmonic generation. This finding opens a novel path for the experimental demonstration of extreme rogue waves in ultrafast quadratic nonlinear optics.

  2. Identifying genes relevant to specific biological conditions in time course microarray experiments.

    Science.gov (United States)

    Singh, Nitesh Kumar; Repsilber, Dirk; Liebscher, Volkmar; Taher, Leila; Fuellen, Georg

    2013-01-01

    Microarrays have been useful in understanding various biological processes by allowing the simultaneous study of the expression of thousands of genes. However, the analysis of microarray data is a challenging task. One of the key problems in microarray analysis is the classification of unknown expression profiles. Specifically, the often large number of non-informative genes on the microarray adversely affects the performance and efficiency of classification algorithms. Furthermore, the skewed ratio of sample to variable poses a risk of overfitting. Thus, in this context, feature selection methods become crucial to select relevant genes and, hence, improve classification accuracy. In this study, we investigated feature selection methods based on gene expression profiles and protein interactions. We found that in our setup, the addition of protein interaction information did not contribute to any significant improvement of the classification results. Furthermore, we developed a novel feature selection method that relies exclusively on observed gene expression changes in microarray experiments, which we call "relative Signal-to-Noise ratio" (rSNR). More precisely, the rSNR ranks genes based on their specificity to an experimental condition, by comparing intrinsic variation, i.e. variation in gene expression within an experimental condition, with extrinsic variation, i.e. variation in gene expression across experimental conditions. Genes with low variation within an experimental condition of interest and high variation across experimental conditions are ranked higher, and help in improving classification accuracy. We compared different feature selection methods on two time-series microarray datasets and one static microarray dataset. We found that the rSNR performed generally better than the other methods.

  3. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.

    NARCIS (Netherlands)

    M.J. Nueda; A. Conessa; J.A. Westerhuis; H.C.J. Hoefsloot; A.K. Smilde; M. Talon; A. Ferrer

    2007-01-01

    In this work, we develop the application of the Analysis of variance-simultaneous component analysis (ANOVA-SCA) Smilde et al. Bioinformatics, (2005) to the analysis of multiple series time course microarray data as an example of multifactorial gene expression profiling experiments. We denoted this

  4. Factorial and time course designs for cDNA microarray experiments.

    Science.gov (United States)

    Glonek, G F V; Solomon, P J

    2004-01-01

    Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.

  5. Two Color QCD beyond the BEC regime

    CERN Document Server

    Hands, S; Skullerud, J I; Hands, Simon; Kim, Seyong; Skullerud, Jon-Ivar

    2005-01-01

    We present results of simulations of Two Color QCD using two flavors of Wilson quark in the fundamental representation, at non-zero quark chemical potential mu, on an 8^3x16 lattice. Results for the quark number density, quark and gluon energy densities, and superfluid condensate are qualitatively distinct from the behaviour expected on the assumption that the dominant degrees of freedom are tightly bound scalar diquarks which Bose condense; rather the scaling with mu is more suggestive of a Fermi surface disrupted by a Cooper pair condensate. We also present evidence both for screening of the static potential, and color deconfinement, arising solely as a result of a non-zero quark density.

  6. Position dependent mismatch discrimination on DNA microarraysexperiments and model

    Directory of Open Access Journals (Sweden)

    Michel Wolfgang

    2008-12-01

    Full Text Available Abstract Background The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. Results We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. Conclusion Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.

  7. Interpreting the gene expression microarray results: a user-based experience.

    Science.gov (United States)

    Melissari, Erika; Di Russo, Manuela; Mariotti, Veronica; Righi, Marco; Iofrida, Caterina; Pellegrini, Silvia

    2013-06-01

    In recent years many tools have been developed to cope with the interpretation of gene expression results from microarray experiments. The effectiveness of these tools largely depends on their ease of use by biomedical researchers. Tools based on effective computational methods, indeed, cannot be fully exploited by users if they are not supported by an intuitive interface, a large set of utilities and effective outputs. In this paper, 10 tools for the interpretation of gene expression microarray results have been tested on 11 microarray datasets and evaluated according to eight assessment criteria: 1. interface design and usability, 2. easiness of input submission, 3. effectiveness of output representation and 4. of the downloaded outputs, 5. possibility to submit multiple gene IDs, 6. sources of information, 7. provision of different statistical tests and 8. of multiple test correction methods. Strengths and weaknesses of each tool are highlighted to: a. provide useful tips to users dealing with the biological interpretation of microarray results; b. draw the attention of software developers on the usability of their tools.

  8. Sample size calculation for microarray experiments with blocked one-way design

    Directory of Open Access Journals (Sweden)

    Jung Sin-Ho

    2009-05-01

    Full Text Available Abstract Background One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments. Results In this paper, we consider discovery of the genes that are differentially expressed among K (> 2 treatments when each set of K arrays consists of a block. In this case, the array data among K treatments tend to be correlated because of block effect. We propose to use the blocked one-way ANOVA F-statistic to test if each gene is differentially expressed among K treatments. The marginal p-values are calculated using a permutation method accounting for the block effect, adjusting for the multiplicity of the testing procedure by controlling the false discovery rate (FDR. We propose a sample size calculation method for microarray experiments with a blocked one-way design. With FDR level and effect sizes of genes specified, our formula provides a sample size for a given number of true discoveries. Conclusion The calculated sample size is shown via simulations to provide an accurate number of true discoveries while controlling the FDR at the desired level.

  9. Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

    Directory of Open Access Journals (Sweden)

    Hedegaard Jakob

    2009-07-01

    Full Text Available Abstract Background The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.

  10. Development of a two-color FQI

    Energy Technology Data Exchange (ETDEWEB)

    Butcher, T.; Wei, G. [Brookhaven National Lab., Upton, NY (United States)

    1996-07-01

    The Flame Quality Indicator (FQI) concept was developed at Brookhaven National Laboratory as a simple device which could be used to monitor oil burner flames and indicate when a problem was starting to occur. Fault situations which could be identified by the FQI include: fouled nozzle, increased or decreased excess air, blocked air inlet or flue, and use of low quality oil. The basic concept of the FQI is quite simple. A conventional cadmium sulfide photocell is used to measure the amount of light emitted from an oil burner flame when the appliance is fully warmed-up. The measured amount of light is compared to a set point, established during burner tune-up. If the two intensities differ by more than a set range, a {open_quotes}service required{close_quotes} signal is produced. The amount of light which is emitted from an oil burner flame depends upon the amount of {open_quotes}soot{close_quotes} or carbon in the flame, the size and shape of the flame, and the flame temperature. The quality of flame is practically judged by the amount of soot which it is producing and for this reason it is necessary to eliminate effects of other parameters. Temperature is expected to be the most important of these. The FQI eliminates effects due to the chamber environment by establishing a set point for each specific appliance. The transient temperature effects are accounted for by examining the flame brightness only at a single time during the firing cycle. BNL is currently involved with the development of a two-color approach to the monitoring of flame quality. The basic concept involved is the measurement of both flame temperature and total amount of light emitted to allow a more direct estimate to be made of the amount of soot being produced and so the flame quality. The objective is to develop a more sensitive measurement which may be more universally applicable. This paper provides a summary of our approach and results to date in this project.

  11. D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis

    Directory of Open Access Journals (Sweden)

    Marcelo F. Carazzolle

    2009-01-01

    Full Text Available The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix. Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner. In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

  12. 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.

  13. Extending the Interpretation of Gene Profiling Microarray Experiments to Pathway Analysis Through the Use of Gene Ontology Terms

    Science.gov (United States)

    Chatziioannou, Aristotelis; Moulos, Panagiotis

    Microarray technology allows the survey of gene expression at a global level by measuring mRNA abundance. However, the grand complexity characterizing a microarray experiment entails the development of computationally powerful tools apt for probing the biological problem studied. Here we propose a suite for flexible, adaptable to a wide range of possible needs of the biological end-user, data-driven interpretation of microarray experiments. The suite is implemented in MATLAB and is making use of two modules, able to perform all steps of typical microarray data analysis starting from data standardization and normalization up to statistical selection and pathway analysis utilizing Gene Ontology Term annotations for the species genomes interrogated, whereas due to its modular structure it is scalable thus enabling the incorporation or its seamless assembly with other existing tools.

  14. HAMSTER: visualizing microarray experiments as a set of minimum spanning trees

    Directory of Open Access Journals (Sweden)

    Harada Hajime

    2009-11-01

    Full Text Available Abstract Background Visualization tools allow researchers to obtain a global view of the interrelationships between the probes or experiments of a gene expression (e.g. microarray data set. Some existing methods include hierarchical clustering and k-means. In recent years, others have proposed applying minimum spanning trees (MST for microarray clustering. Although MST-based clustering is formally equivalent to the dendrograms produced by hierarchical clustering under certain conditions; visually they can be quite different. Methods HAMSTER (Helpful Abstraction using Minimum Spanning Trees for Expression Relations is an open source system for generating a set of MSTs from the experiments of a microarray data set. While previous works have generated a single MST from a data set for data clustering, we recursively merge experiments and repeat this process to obtain a set of MSTs for data visualization. Depending on the parameters chosen, each tree is analogous to a snapshot of one step of the hierarchical clustering process. We scored and ranked these trees using one of three proposed schemes. HAMSTER is implemented in C++ and makes use of Graphviz for laying out each MST. Results We report on the running time of HAMSTER and demonstrate using data sets from the NCBI Gene Expression Omnibus (GEO that the images created by HAMSTER offer insights that differ from the dendrograms of hierarchical clustering. In addition to the C++ program which is available as open source, we also provided a web-based version (HAMSTER+ which allows users to apply our system through a web browser without any computer programming knowledge. Conclusion Researchers may find it helpful to include HAMSTER in their microarray analysis workflow as it can offer insights that differ from hierarchical clustering. We believe that HAMSTER would be useful for certain types of gradient data sets (e.g time-series data and data that indicate relationships between cells/tissues. Both

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

    Directory of Open Access Journals (Sweden)

    Chinnaiyan Arul M

    2007-09-01

    Full Text Available Abstract Background With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies. Results In this article, we describe a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models. A key feature of the model is the use of latent variables that represent quantities that can be combined across diverse platforms. We consider two methods for estimation of an index termed the probability of expression (POE. The first, reported in previous work by the authors, involves Markov Chain Monte Carlo (MCMC techniques. The second method is a faster algorithm based on the expectation-maximization (EM algorithm. The methods are illustrated with application to a meta-analysis of datasets for metastatic cancer. Conclusion The statistical methods described in the paper are available as an R package, metaArray 1.8.1, which is at Bioconductor, whose URL is http://www.bioconductor.org/.

  16. A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments.

    Science.gov (United States)

    Broët, Philippe; Lewin, Alex; Richardson, Sylvia; Dalmasso, Cyril; Magdelenat, Henri

    2004-11-01

    Multiclass response (MCR) experiments are those in which there are more than two classes to be compared. In these experiments, though the null hypothesis is simple, there are typically many patterns of gene expression changes across the different classes that led to complex alternatives. In this paper, we propose a new strategy for selecting genes in MCR that is based on a flexible mixture model for the marginal distribution of a modified F-statistic. Using this model, false positive and negative discovery rates can be estimated and combined to produce a rule for selecting a subset of genes. Moreover, the method proposed allows calculation of these rates for any predefined subset of genes. We illustrate the performance our approach using simulated datasets and a real breast cancer microarray dataset. In this latter study, we investigate predefined subset of genes and point out interesting differences between three distinct biological pathways. http://www.bgx.org.uk/software.html

  17. Two-color lattice QCD with staggered quarks

    Energy Technology Data Exchange (ETDEWEB)

    Scheffler, David

    2015-07-20

    The study of quantum chromodynamics (QCD) at finite temperature and density provides important contributions to the understanding of strong-interaction matter as it is present e.g. in nuclear matter and in neutron stars or as produced in heavy-ion collision experiments. Lattice QCD is a non-perturbative approach, where equations of motion for quarks and gluons are discretized on a finite space-time lattice. The method successfully describes the behavior of QCD in the vacuum and at finite temperature, however it cannot be applied to finite baryon density due to the fermion sign problem. Various QCD-like theories, that offer to draw conclusions about QCD, allow simulations also at finite densities. In this work we investigate two-color QCD as a popular example of a QCD-like theory free from the sign problem with methods from lattice gauge theory. For the generation of gauge configurations with two dynamical quark flavors in the staggered formalism with the ''rooting trick'' we apply the Rational Hybrid Monte Carlo (RHMC) algorithm. We carry out essential preparatory work for future simulations at finite density. As a start, we concentrate on the calculation of the effective potential for the Polyakov loop, which is an order parameter for the confinement-deconfinement transition, in dependence of the temperature and quark mass. It serves as an important input for effective models of QCD. We obtain the effective potential via the histogram method from local distributions of the Polyakov loop. To study the influence of dynamical quarks on gluonic observables, the simulations are performed with large quark masses and are compared to calculations in the pure gauge theory. In the second part of the thesis we examine aspects of the chiral phase transition along the temperature axis. The symmetry group of chiral symmetry in two-color QCD is enlarged to SU(2N{sub f}). Discretized two-color QCD in the staggered formalism exhibits a chiral symmetry breaking

  18. Combining Digital Watermarks with Two-Color Bitmap Image

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A technology for combining digital watermarks with two-color bitmap image based on the threshold watermarking method is presented. Our technology doesn't add any thing to the digital media, but combines the watermarks in two-color bitmap image by looking for some characteristic values in the bitmap and uses the relationship between the watermarks and the characteristic values to prove the copyright protection. The choice of the characteristic values depends on the choice of a cryptographic key known by the owner of the bitmap. The benefit of using a cryptographic key is to combine the watermarks with the bitmap in a high secure way.

  19. Rational choices for the wavelengths of a two color interferometer

    Energy Technology Data Exchange (ETDEWEB)

    Jobes, F.C.

    1995-07-01

    If in a two color interferometer for plasma density measurements, the two wavelengths are chosen to have a ratio that is a rational number, and if the signals from each of the wavelengths are multiplied in frequency by the appropriate integer of the rational number and then heterodyned together, the resultant signal will have all effects of component motion nulled out. A phase measurement of this signal will have only plasma density information in it. With CO{sub 2} lasers, it is possible to find suitable wavelength pairs which are close enough to rational numbers to produce an improvement of about 100 in density resolution, compared to standard two color interferometers.

  20. A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments.

    Science.gov (United States)

    Newton, Richard; Hinds, Jason; Wernisch, Lorenz

    2006-01-01

    Whole genome DNA microarray genomotyping experiments compare the gene content of different species or strains of bacteria. A statistical approach to analysing the results of these experiments was developed, based on a Hidden Markov model (HMM), which takes adjacency of genes along the genome into account when calling genes present or absent. The model was implemented in the statistical language R and applied to three datasets. The method is numerically stable with good convergence properties. Error rates are reduced compared with approaches that ignore spatial information. Moreover, the HMM circumvents a problem encountered in a conventional analysis: determining the cut-off value to use to classify a gene as absent. An Apache Struts web interface for the R script was created for the benefit of users unfamiliar with R. The application may be found at http://hmmgd.cryst.bbk.ac.uk/hmmgd. The source code illustrating how to run R scripts from an Apache Struts-based web application is available from the corresponding author on request. The application is also available for local installation if required.

  1. Determination of the differentially expressed genes in microarray experiments using local FDR

    Directory of Open Access Journals (Sweden)

    Daudin J-J

    2004-09-01

    Full Text Available Abstract Background Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the False Discovery Rate (FDR, has been proposed to measure the statistical significance of this set. Various procedures exist for controlling the FDR. However the threshold (generally 5% is arbitrary and a specific measure associated with each gene would be worthwhile. Results Using process intensity estimation methods, we define and give estimates of the local FDR, which may be considered as the probability for a gene to be a false positive. After a global assessment rule controlling the false positive error, the local FDR is a valuable guideline for deciding wether a gene is differentially expressed. The interest of the method is illustrated on three well known data sets. A R routine for computing local FDR estimates from p-values is available at http://www.inapg.fr/ens_rech/mathinfo/recherche/mathematique/outil.html. Conclusions The local FDR associated with each gene measures the probability that it is a false positive. It gives the opportunity to compute the FDR of any given group of clones (of the same gene or genes pertaining to the same regulation network or the same chromosomic region.

  2. Femtosecond Non-degenerate Four Wave Mixing Spectroscopy: The Two Color Photon Echo Peak Shift

    CERN Document Server

    Prall, B S

    2005-01-01

    The couplings between multiple electronic states and electronic and nuclear coordinates are examined for condensed phase systems by femtosecond degenerate and non-degenerate four wave mixing. The two-color photon echo peak shift experiment is developed which allows measurement of the correlation between transition frequencies in two different spectral regions. Two-color photon echo peak shift (2C3PEPS) experiments are used to study coupling between electronic states in the lutetium bisphthalocyanine anion, LuPc2−. Electronically induced mixing between exciton and charge resonance states leads to correlations in transition energies for the two observed transitions. This correlation generates non-zero 2C3PEPS which, when compared with 1C3PEPS, allows experimental determination of the degree of mixing, which was in good agreement with theoretical predictions. By exploiting a coherently excited nuclear wavepacket, the nuclear dependence on the electronic mixing between exciton and charge resonance state...

  3. Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.

    Science.gov (United States)

    Zilina, Olga; Teek, Rita; Tammur, Pille; Kuuse, Kati; Yakoreva, Maria; Vaidla, Eve; Mölter-Väär, Triin; Reimand, Tiia; Kurg, Ants; Ounap, Katrin

    2014-03-01

    Chromosomal microarray analysis (CMA) is now established as the first-tier cytogenetic diagnostic test for fast and accurate detection of chromosomal abnormalities in patients with developmental delay/intellectual disability (DD/ID), multiple congenital anomalies (MCA), and autism spectrum disorders (ASD). We present our experience with using CMA for postnatal and prenatal diagnosis in Estonian patients during 2009-2012. Since 2011, CMA is on the official service list of the Estonian Health Insurance Fund and is performed as the first-tier cytogenetic test for patients with DD/ID, MCA or ASD. A total of 1191 patients were analyzed, including postnatal (1072 [90%] patients and 59 [5%] family members) and prenatal referrals (60 [5%] fetuses). Abnormal results were reported in 298 (25%) patients, with a total of 351 findings (1-3 per individual): 147 (42%) deletions, 106 (30%) duplications, 89 (25%) long contiguous stretches of homozygosity (LCSH) events (>5 Mb), and nine (3%) aneuploidies. Of all findings, 143 (41%) were defined as pathogenic or likely pathogenic; for another 143 findings (41%), most of which were LCSH, the clinical significance remained unknown, while 61 (18%) reported findings can now be reclassified as benign or likely benign. Clinically relevant findings were detected in 126 (11%) patients. However, the proportion of variants of unknown clinical significance was quite high (41% of all findings). It seems that our ability to detect chromosomal abnormalities has far outpaced our ability to understand their role in disease. Thus, the interpretation of CMA findings remains a rather difficult task requiring a close collaboration between clinicians and cytogeneticists.

  4. Streaking temporal double slit interference by an orthogonal two-color laser field

    CERN Document Server

    Richter, Martin; Schöffler, Markus; Jahnke, Till; Schmidt, Lothar P H; Li, Min; Liu, Yunquan; Dörner, Reinhard

    2015-01-01

    We investigate electron momentum distributions from single ionization of Ar by two orthogonally polarized laser pulses of different color. The two-color scheme is used to experimentally control the interference between electron wave packets released at different times within one laser cycle. This intracycle interference pattern is typically hard to resolve in an experiment. With the two-color control scheme these features become the dominant contribution to the electron momentum distribution. Furthermore the second color can be used for streaking of the otherwise interfering wave packets establishing a which-way marker. Our investigation shows that the visibility of the interference fringes depends on the degree of the which-way information determined by the controllable phase between the two pulses.

  5. A Computer-Based Microarray Experiment Design-System for Gene-Regulation Pathway Discovery

    OpenAIRE

    2003-01-01

    This paper reports the methods and evaluation of a computer-based system that recommends microarray experimental design for biologists — causal discovery in Gene Expression data using Expected Value of Experimentation (GEEVE). The GEEVE system uses causal Bayesian networks and generates a decision tree for recommendations.

  6. Noninferiority tests based on concordance correlation coefficient for assessment of the agreement for gene expression data from microarray experiments.

    Science.gov (United States)

    Liao, Chen-Tuo; Lin, Chia-Ying; Liu, Jen-Pei

    2007-01-01

    Microarray is one of the breakthrough technologies in the twenty-first century. Despite of its great potential, transition and realization of microarray technology into the clinically useful commercial products have not been as rapid as the technology could promise. One of the primary reasons is lack of agreement and poor reproducibility of the intensity measurements on gene expression obtained from microarray experiments. Current practices often use the testing the hypothesis of zero Pearson correlation coefficient to assess the agreement of gene expression levels between the technical replicates from microarray experiments. However, Pearson correlation coefficient is to evaluate linear association between two variables and fail to take into account changes in accuracy and precision. Hence, it is not appropriate for evaluation of agreement of gene expression levels between technical replicates. Therefore, we propose to use the concordance correlation coefficient to assess agreement of gene expression levels between technical replicates. We also apply the Generalized Pivotal Quantities to obtain the exact confidence interval for concordance coefficient. In addition, based on the concept of noninferiority test, a one-sided (1 - alpha) lower confidence limit for concordance correlation coefficient is employed to test the hypothesis that the agreement of expression levels of the same genes between two technical replicates exceeds some minimal requirement of agreement. We conducted a simulation study, under various combinations of mean differences, variability, and sample size, to empirically compare the performance of different methods for assessment of agreement in terms of coverage probability, expected length, size, and power. Numerical data from published papers illustrate the application of the proposed methods.

  7. Femtosecond laser-induced periodic surface structures on silicon upon polarization controlled two-color double-pulse irradiation.

    Science.gov (United States)

    Höhm, Sandra; Herzlieb, Marcel; Rosenfeld, Arkadi; Krüger, Jörg; Bonse, Jörn

    2015-01-12

    Two-color double-fs-pulse experiments were performed on silicon wafers to study the temporally distributed energy deposition in the formation of laser-induced periodic surface structures (LIPSS). A Mach-Zehnder interferometer generated parallel or cross-polarized double-pulse sequences at 400 and 800 nm wavelength, with inter-pulse delays up to a few picoseconds between the sub-ablation 50-fs-pulses. Multiple two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample. The resulting LIPSS characteristics (periods, areas) were analyzed by scanning electron microscopy. A wavelength-dependent plasmonic mechanism is proposed to explain the delay-dependence of the LIPSS. These two-color experiments extend previous single-color studies and prove the importance of the ultrafast energy deposition for LIPSS formation.

  8. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.

    Science.gov (United States)

    Peyser, Brian D; Irizarry, Rafael A; Tiffany, Carol W; Chen, Ou; Yuan, Daniel S; Boeke, Jef D; Spencer, Forrest A

    2005-09-15

    Saccharomyces cerevisiae knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. TAG arrays report abundance of unique oligonucleotide 'TAG' sequences incorporated into each deletion mutation of the yeast knockout collection, allowing measurement of relative strain representation across experimental conditions for all knockout mutants simultaneously. One application of TAG arrays is to perform genome-wide synthetic lethality screens, known as synthetic lethality analyzed by microarray (SLAM). We designed a fully defined spike-in pool to resemble typical SLAM experiments and performed TAG microarray hybridizations. We describe a method for analyzing two-color array data to efficiently measure the differential knockout strain representation across two experimental conditions, and use the spike-in pool to show that the sensitivity and specificity of this method exceed typical current approaches.

  9. "It wasn't a disaster or anything": Parents' experiences of their child's uncertain chromosomal microarray result.

    Science.gov (United States)

    Wilkins, Ella J; Archibald, Alison D; Sahhar, Margaret A; White, Susan M

    2016-11-01

    Chromosomal microarray is an increasingly utilized diagnostic test, particularly in the pediatric setting. However, the clinical significance of copy number variants detected by this technology is not always understood, creating uncertainties in interpreting and communicating results. The aim of this study was to explore parents' experiences of an uncertain microarray result for their child. This research utilized a qualitative approach with a phenomenological methodology. Semi-structured interviews were conducted with nine parents of eight children who received an uncertain microarray result for their child, either a 16p11.2 microdeletion or 15q13.3 microdeletion. Interviews were transcribed verbatim and thematic analysis was used to identify themes within the data. Participants were unprepared for the abnormal test result. They had a complex perception of the extent of their child's condition and a mixed understanding of the clinical relevance of the result, but were accepting of the limitations of medical knowledge, and appeared to have adapted to the result. The test result was empowering for parents in terms of access to medical and educational services; however, they articulated significant unmet support needs. Participants expressed hope for the future, in particular that more information would become available over time. This research has demonstrated that parents of children who have an uncertain microarray result appeared to adapt to uncertainty and limited availability of information and valued honesty and empathic ongoing support from health professionals. Genetic health professionals are well positioned to provide such support and aid patients' and families' adaptation to their situation as well as promote empowerment. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. LIMaS: the JAVA-based application and database for microarray experiment tracking.

    Science.gov (United States)

    Webb, Sarah C; Attwood, Anthony; Brooks, Tony; Freeman, Tom; Gardner, Phil; Pritchard, Clare; Williams, Debbie; Underhill, Peter; Strivens, Mark A; Greenfield, Andy; Pilicheva, Ekaterina

    2004-09-01

    Microarrays allow monitoring of gene expression for tens of thousands of genes in parallel and are being used routinely to generate huge amounts of valuable data. Handling and analysis of such data are becoming major bottlenecks in the utilization of the technology. To enable the researcher to interpret the results postanalysis, we have developed a laboratory information management system for microarrays (LIMaS) with an n-tier Java front-end and relational database to record and manage large-scale expression data preanalysis. This system enables the laboratory to replace the paper trail with an efficient and fully customizable interface giving it the ability to adapt to any working practice, e.g., handling many resources used to form many products (chaining of resources). The ability to define sets of activities, resources, and workflows makes LIMaS MIAME-supportive.

  11. 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...

  12. The tissue micro-array data exchange specification: a web based experience browsing imported data

    Directory of Open Access Journals (Sweden)

    Ayers Leona W

    2005-08-01

    Full Text Available Abstract Background The AIDS and Cancer Specimen Resource (ACSR is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI Division of Cancer Treatment and Diagnosis (DCTD. The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API extensible mark-up language (XML TMA data exchange specification (TMA DES proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT scripts that convert XML data into Hyper-Text Mark-up Language (HTML web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core

  13. Tests for differential gene expression using weights in oligonucleotide microarray experiments

    Directory of Open Access Journals (Sweden)

    Beyene Joseph

    2006-02-01

    Full Text Available Abstract Background Microarray data analysts commonly filter out genes based on a number of ad hoc criteria prior to any high-level statistical analysis. Such ad hoc approaches could lead to conflicting conclusions with no clear guidance as to which method is most likely to be reproducible. Furthermore, the number of tests performed with concomitant inflation in type I error also plagues the statistical analysis of microarray data, since the number of tested quantities in a study significantly affects the family-wise error rate. It would, therefore, be very useful to develop and adopt strategies that allow quantification of the quality of each probeset, to filter out or give little credence to low-quality or unexpressed probesets, and to incorporate these strategies into gene selection within a multiple testing framework. Results We have proposed a unified scheme for filtering and gene selection. For Affymetrix gene expression microarrays, we developed new methods for measuring the reliability of a particular probeset in a single array, and we used these to develop measures for a set of arrays. These measures are then used as weights in standard t-statistic calculations, and are incorporated into the multiple testing procedures. We demonstrated the advantages of our methods using simulated data, publicly available spiked-in data as well as data comparing normal muscle to muscle from patients with Duchenne muscular dystrophy (DMD, in which a set of truly differentially expressed genes is known. Conclusion Our quality measures provide convenient ways to search for individual genes of high quality. The quality weighting strategies we proposed for testing differential gene expression have demonstrable improvement on the traditional filtering methods, the standard t-statistic and a regularized t-statistic in Affymetrix data analysis.

  14. Exploratory Visual Analysis of Statistical Results from Microarray Experiments Comparing High and Low Grade Glioma

    Directory of Open Access Journals (Sweden)

    Jason H. Moore

    2007-01-01

    Full Text Available The biological interpretation of gene expression microarray results is a daunting challenge. For complex diseases such as cancer, wherein the body of published research is extensive, the incorporation of expert knowledge provides a useful analytical framework. We have previously developed the Exploratory Visual Analysis (EVA software for exploring data analysis results in the context of annotation information about each gene, as well as biologically relevant groups of genes. We present EVA as a fl exible combination of statistics and biological annotation that provides a straightforward visual interface for the interpretation of microarray analyses of gene expression in the most commonly occurring class of brain tumors, glioma. We demonstrate the utility of EVA for the biological interpretation of statistical results by analyzing publicly available gene expression profi les of two important glial tumors. The results of a statistical comparison between 21 malignant, high-grade glioblastoma multiforme (GBM tumors and 19 indolent, low-grade pilocytic astrocytomas were analyzed using EVA. By using EVA to examine the results of a relatively simple statistical analysis, we were able to identify tumor class-specifi c gene expression patterns having both statistical and biological signifi cance. Our interactive analysis highlighted the potential importance of genes involved in cell cycle progression, proliferation, signaling, adhesion, migration, motility, and structure, as well as candidate gene loci on a region of Chromosome 7 that has been implicated in glioma. Because EVA does not require statistical or computational expertise and has the fl exibility to accommodate any type of statistical analysis, we anticipate EVA will prove a useful addition to the repertoire of computational methods used for microarray data analysis. EVA is available at no charge to academic users and can be found at http://www.epistasis.org.

  15. Two-color beam generation based on wakefield excitation

    Science.gov (United States)

    Bettoni, S.; Prat, E.; Reiche, S.

    2016-05-01

    Several beam manipulation methods have been studied and experimentally tested to generate two-color photon beams in free electron laser facilities to accommodate the user requests. We propose to use the interaction of the beam with an oscillating longitudinal wakefield source to obtain a suitable electron beam structure. The bunch generates two subpulses with different energies and delayed in time passing through a magnetic chicane after its longitudinal phase space has been modulated by the wakefield source. According to this approach the power of the emitted radiation is not degraded compared to the monochromatic beam, and the setup in the machine is quite simple because the bunch is manipulated only in the high energy section, where it is more rigid. We present the design applied to SwissFEL. We identified the parameters and the corresponding range of tunability of the time and energy separation among the two subbunches.

  16. Semiconductor cluster beams: One and two color ionization studies of Six and Gex

    OpenAIRE

    Heath, J R; Liu, Yuan; O'Brien, S. C.; Zhang, Qing-ling; Curl, R. F.; Tittel, F.K.; Smalley, R.E.

    1985-01-01

    Supersonic beams of clusters of Si and Ge atoms have been produced by laser vaporization followed by supersonic expansion in a helium carrier. The cluster beams were characterized by F2(7.9 eV) and ArF(6.4 eV) excimer laser ionization accompanied by time-of-flight mass analysis. In addition, the feasibility of a resonant two-photon ionization (R2PI) spectroscopic study was explored by two-color experiments involving initial excitation with the second (2.36 eV) and third (3.54 eV) harmonics of...

  17. OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

    Directory of Open Access Journals (Sweden)

    Arkin Adam P

    2006-01-01

    Full Text Available Abstract Background Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Conclusion Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

  18. OpWise: Operons aid the identification of differentially expressedgenes in bacterial microarray experiments

    Energy Technology Data Exchange (ETDEWEB)

    Price, Morgan N.; Arkin, Adam P.; Alm, Eric J.

    2005-11-23

    Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results-OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

  19. Technical variability is greater than biological variability in a microarray experiment but both are outweighed by changes induced by stimulation.

    Directory of Open Access Journals (Sweden)

    Penelope A Bryant

    Full Text Available INTRODUCTION: A central issue in the design of microarray-based analysis of global gene expression is that variability resulting from experimental processes may obscure changes resulting from the effect being investigated. This study quantified the variability in gene expression at each level of a typical in vitro stimulation experiment using human peripheral blood mononuclear cells (PBMC. The primary objective was to determine the magnitude of biological and technical variability relative to the effect being investigated, namely gene expression changes resulting from stimulation with lipopolysaccharide (LPS. METHODS AND RESULTS: Human PBMC were stimulated in vitro with LPS, with replication at 5 levels: 5 subjects each on 2 separate days with technical replication of LPS stimulation, amplification and hybridisation. RNA from samples stimulated with LPS and unstimulated samples were hybridised against common reference RNA on oligonucleotide microarrays. There was a closer correlation in gene expression between replicate hybridisations (0.86-0.93 than between different subjects (0.66-0.78. Deconstruction of the variability at each level of the experimental process showed that technical variability (standard deviation (SD 0.16 was greater than biological variability (SD 0.06, although both were low (SD<0.1 for all individual components. There was variability in gene expression both at baseline and after stimulation with LPS and proportion of cell subsets in PBMC was likely partly responsible for this. However, gene expression changes after stimulation with LPS were much greater than the variability from any source, either individually or combined. CONCLUSIONS: Variability in gene expression was very low and likely to improve further as technical advances are made. The finding that stimulation with LPS has a markedly greater effect on gene expression than the degree of variability provides confidence that microarray-based studies can be used to

  20. Using the ratio of means as the effect size measure in combining results of microarray experiments

    Directory of Open Access Journals (Sweden)

    Greenwood Celia MT

    2009-11-01

    Full Text Available Abstract Background Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference when sample sizes in each group are small. Results We propose a re-parameterization of the traditional mean difference based effect measure by using the log ratio of means as an effect size measure for each gene in each study. The estimated effect sizes for all studies were then combined under two modeling frameworks: the quality-unweighted random effects models and the quality-weighted random effects models. We defined the quality measure as a function of the detection p-value, which indicates whether a transcript is reliably detected or not on the Affymetrix gene chip. The new effect size measure is evaluated and compared under the quality-weighted and quality-unweighted data integration frameworks using simulated data sets, and also in several data sets of prostate cancer patients and controls. We focus on identifying differentially expressed biomarkers for prediction of cancer outcomes. Conclusion Our results show that the proposed effect size measure (log ratio of means has better power to identify differentially expressed genes, and that the detected genes have better performance in predicting cancer outcomes than the commonly used effect size measure, the standardized mean difference (SMD, under both quality-weighted and quality

  1. Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

    Directory of Open Access Journals (Sweden)

    Tözeren Aydin

    2007-03-01

    Full Text Available Abstract Background Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. Methods This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B, percentage occupied by stroma-like regions (P, and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. Results Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. Conclusion These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists as hundreds of tumors that are used to develop an array have typically been evaluated

  2. Statistical methodology for the analysis of dye-switch microarray experiments

    Directory of Open Access Journals (Sweden)

    Mansouri-Attia Nadera

    2008-02-01

    Full Text Available Abstract Background In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurements that must be taken into account in the statistical analysis. Results We present two original statistical procedures for the statistical analysis of individually balanced designs. These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data. Conclusion The UP procedure we propose as an alternative to usual mixed model procedures is more efficient and significantly faster to compute. This result provides some useful guidelines for the analysis of complex designs.

  3. A computer-based microarray experiment design-system for gene-regulation pathway discovery.

    Science.gov (United States)

    Yoo, Changwon; Cooper, Gregory F

    2003-01-01

    This paper reports the methods and evaluation of a computer-based system that recommends microarray experimental design for biologists - causal discovery in Gene Expression data using Expected Value of Experimentation (GEEVE). The GEEVE system uses causal Bayesian networks and generates a decision tree for recommendations. To evaluate the GEEVE system, we first built an expression simulation model based on a gene regulation model assessed by an expert biologist. Using the simulation model, we conducted a controlled study that involved 10 biologists, some of whom used GEEVE and some of whom did not. The results show that biologists who used GEEVE reached correct causal assessments about gene regulation more often than did those biologists who did not use GEEVE.

  4. Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments

    Directory of Open Access Journals (Sweden)

    Kitchen Robert R

    2011-12-01

    Full Text Available Abstract Background Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR and individual or pooled breast-tumour RNA. Results A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependant upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. Conclusions The magnitude of systematic

  5. Noise in two-color electronic distance meter measurements revisited

    Science.gov (United States)

    Langbein, J.

    2004-01-01

    Frequent, high-precision geodetic data have temporally correlated errors. Temporal correlations directly affect both the estimate of rate and its standard error; the rate of deformation is a key product from geodetic measurements made in tectonically active areas. Various models of temporally correlated errors are developed and these provide relations between the power spectral density and the data covariance matrix. These relations are applied to two-color electronic distance meter (EDM) measurements made frequently in California over the past 15-20 years. Previous analysis indicated that these data have significant random walk error. Analysis using the noise models developed here indicates that the random walk model is valid for about 30% of the data. A second 30% of the data can be better modeled with power law noise with a spectral index between 1 and 2, while another 30% of the data can be modeled with a combination of band-pass-filtered plus random walk noise. The remaining 10% of the data can be best modeled as a combination of band-pass-filtered plus power law noise. This band-pass-filtered noise is a product of an annual cycle that leaks into adjacent frequency bands. For time spans of more than 1 year these more complex noise models indicate that the precision in rate estimates is better than that inferred by just the simpler, random walk model of noise.

  6. Two-color, double-slit in vivo flow cytometer.

    Science.gov (United States)

    Novak, J; Puoris'haag, M

    2007-10-15

    The in vivo flow cytometer enables the real-time detection and quantification of fluorescent cells circulating within a live animal without the need for incisions or extraction of blood. It has been used in demonstrating flow velocity disparities in biological flows, and in the investigation of the circulation kinetics of various types of cells. However, a shortcoming of this in vivo flow cytometer is that it provides only one excitation slit at one wavelength, resulting in several performance limitations. Therefore, a second in vivo flow cytometer that provides two different laser wavelengths, 473 and 633 nm, and one or two excitation slits has been designed and built. Thus far, the two-color system has been used to acquire circulation kinetics data of two different cell populations each labeled with a different marker, one cell population labeled with two different markers, and one cell population expressing the green-fluorescent protein gene. In addition, accurate arterial red blood cell velocities within a mouse have been determined using the cytometer.

  7. Towards the phase diagram of dense two-color matter

    CERN Document Server

    Cotter, Seamus; Hands, Simon; Skullerud, Jon-Ivar

    2012-01-01

    We study two-color QCD with two flavors of Wilson fermion as a function of quark chemical potential mu and temperature T. We find evidence of a superfluid phase at intermediate mu and low T where the quark number density and diquark condensate are both very well described by a Fermi sphere of nearly-free quarks disrupted by a BCS condensate. Our results suggest that the quark contribution to the energy density is negative (and balanced by a positive gauge contribution), although this result is highly sensitive to details of the energy renormalisation. We also find evidence that the chiral condensate in this region vanishes in the massless limit. This region gives way to a region of deconfined quark matter at higher T and mu, with the deconfinement temperature, determined from the renormalised Polyakov loop, decreasing only very slowly with increasing chemical potential. The quark number susceptibility chi_q does not exhibit any qualitative change at the deconfinement transition. We argue that this is because ...

  8. Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

    Science.gov (United States)

    Harrison, Andrew; Binder, Hans; Buhot, Arnaud; Burden, Conrad J.; Carlon, Enrico; Gibas, Cynthia; Gamble, Lara J.; Halperin, Avraham; Hooyberghs, Jef; Kreil, David P.; Levicky, Rastislav; Noble, Peter A.; Ott, Albrecht; Pettitt, B. Montgomery; Tautz, Diethard; Pozhitkov, Alexander E.

    2013-01-01

    Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized. PMID:23307556

  9. A control study to evaluate a computer-based microarray experiment design recommendation system for gene-regulation pathways discovery.

    Science.gov (United States)

    Yoo, Changwon; Cooper, Gregory F; Schmidt, Martin

    2006-04-01

    The main topic of this paper is evaluating a system that uses the expected value of experimentation for discovering causal pathways in gene expression data. By experimentation we mean both interventions (e.g., a gene knock-out experiment) and observations (e.g., passively observing the expression level of a "wild-type" gene). We introduce a system called GEEVE (causal discovery in Gene Expression data using Expected Value of Experimentation), which implements expected value of experimentation in discovering causal pathways using gene expression data. GEEVE provides the following assistance, which is intended to help biologists in their quest to discover gene-regulation pathways: Recommending which experiments to perform (with a focus on "knock-out" experiments) using an expected value of experimentation (EVE) method. Recommending the number of measurements (observational and experimental) to include in the experimental design, again using an EVE method. Providing a Bayesian analysis that combines prior knowledge with the results of recent microarray experimental results to derive posterior probabilities of gene regulation relationships. In recommending which experiments to perform (and how many times to repeat them) the EVE approach considers the biologist's preferences for which genes to focus the discovery process. Also, since exact EVE calculations are exponential in time, GEEVE incorporates approximation methods. GEEVE is able to combine data from knock-out experiments with data from wild-type experiments to suggest additional experiments to perform and then to analyze the results of those microarray experimental results. It models the possibility that unmeasured (latent) variables may be responsible for some of the statistical associations among the expression levels of the genes under study. To evaluate the GEEVE system, we used a gene expression simulator to generate data from specified models of gene regulation. Using the simulator, we evaluated the GEEVE

  10. 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...

  11. Making and using inexpensive manually constructed tissue micro-array: Experience of a tertiary care hospital in India

    Directory of Open Access Journals (Sweden)

    Singh Deepak

    2009-07-01

    Full Text Available Background: Tissue micro-array enables the analysis of a large number of tissues simultaneously. Widespread use of this technology is hampered by the high cost of commercial array instruments. We describe our experience of constructing tissue micro-array in a simple method using easily available and inexpensive instruments. Materials and Methods: We used an 11-19 gauge (G bone marrow trephine biopsy needle/ small sized slotted screwdriver to punch holes in the wax blocks. Cores were taken from donor tissue blocks using a bone marrow trephine biopsy needle and arrayed into host paraffin wax blocks. A detailed database was constructed for each array constructed. Results: The array blocks were used over a period of one year as internal control for immunohistochemistry (IHC, quality control and research. It took about 10 minutes to construct a nine-dot array and about one hour for a 56-dot array. During IHC, the average loss of control dots was less than one per cent. We did not see any loss of antigenicity in the control sections even after four weeks storage. Discussion: Tissue array construction by the technique described here is inexpensive and reliable alternative to automated instruments. Because it is easy to modify the arrays by varying the core size, it is easy to adapt this to individual labs and requirements. We recommend using blocks with cores in 3 x 3 to 5 x 4 grids as controls in IHC and for standardizing antibodies and array blocks with a larger number of cores for research.

  12. Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments

    Directory of Open Access Journals (Sweden)

    Pistoia Vito

    2008-10-01

    Full Text Available Abstract Background Most microarray experiments are carried out with the purpose of identifying genes whose expression varies in relation with specific conditions or in response to environmental stimuli. In such studies, genes showing similar mean expression values between two or more groups are considered as not differentially expressed, even if hidden subclasses with different expression values may exist. In this paper we propose a new method for identifying differentially expressed genes, based on the area between the ROC curve and the rising diagonal (ABCR. ABCR represents a more general approach than the standard area under the ROC curve (AUC, because it can identify both proper (i.e., concave and not proper ROC curves (NPRC. In particular, NPRC may correspond to those genes that tend to escape standard selection methods. Results We assessed the performance of our method using data from a publicly available database of 4026 genes, including 14 normal B cell samples (NBC and 20 heterogeneous lymphomas (namely: 9 follicular lymphomas and 11 chronic lymphocytic leukemias. Moreover, NBC also included two sub-classes, i.e., 6 heavily stimulated and 8 slightly or not stimulated samples. We identified 1607 differentially expressed genes with an estimated False Discovery Rate of 15%. Among them, 16 corresponded to NPRC and all escaped standard selection procedures based on AUC and t statistics. Moreover, a simple inspection to the shape of such plots allowed to identify the two subclasses in either one class in 13 cases (81%. Conclusion NPRC represent a new useful tool for the analysis of microarray data.

  13. Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies.

    Science.gov (United States)

    Drobyshev, Alexei L; Machka, Christine; Horsch, Marion; Seltmann, Matthias; Liebscher, Volkmar; Hrabé de Angelis, Martin; Beckers, Johannes

    2003-01-15

    The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the specificity of hybridisation. SAFE (specificity assessment from fractionation experiments) is a novel method to discriminate between non- specific cross-hybridisation and specific signals. We applied in situ fractionation of hybridised target on DNA-chips by means of repeated washes with increasing stringencies. Different fractions of hybridised target are washed off at defined stringencies and the collected fluorescence intensity data at each step comprise the fractionation curve. Based on characteristic features of the fractionation curve, unreliable data can be filtered and eliminated from subsequent analyses. The approach described here provides a novel experimental tool to identify probes that produce specific hybridisation signals in DNA-chip expression profiling approaches. The iterative use of the SAFE procedure will result in increasingly reliable sets of probes for microarray experiments and significantly improve the overall efficiency and reliability of RNA expression profiling data from DNA-chip experiments.

  14. A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment

    NARCIS (Netherlands)

    Aguirre von Wobeser, E.; Huisman, J.; Ibelings, B.; Matthijs, H.C.P.; Matthijs, H.C.P.

    2005-01-01

    A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment Eneas Aguirre-von-Wobeser 1, Jef Huisman1, Bas Ibelings2 and Hans C.P. Matthijs1 1 Universiteit van Amsterdam, Amsterdam, The Netherla

  15. Calibration of a two-color soft x-ray diagnostic for electron temperature measurement

    Energy Technology Data Exchange (ETDEWEB)

    Reusch, L. M., E-mail: lmmcguire@wisc.edu; Den Hartog, D. J.; Goetz, J.; McGarry, M. B. [University of Wisconsin - Madison, Madison, Wisconsin 53703 (United States); Franz, P. [Consorzio RFX, Padova (Italy); Stephens, H. D. [University of Wisconsin - Madison, Madison, Wisconsin 53703 (United States); Pierce College Fort Steilacoom, Lakewood, Washington 98498 (United States)

    2016-11-15

    The two-color soft x-ray (SXR) tomography diagnostic on the Madison Symmetric Torus is capable of making electron temperature measurements via the double-filter technique; however, there has been a 15% systematic discrepancy between the SXR double-filter (SXR{sub DF}) temperature and Thomson scattering (TS) temperature. Here we discuss calibration of the Be filters used in the SXR{sub DF} measurement using empirical measurements of the transmission function versus energy at the BESSY II electron storage ring, electron microprobe analysis of filter contaminants, and measurement of the effective density. The calibration does not account for the TS and SXR{sub DF} discrepancy, and evidence from experiments indicates that this discrepancy is due to physics missing from the SXR{sub DF} analysis rather than instrumentation effects.

  16. Mechanisms of two-color laser-induced field-free molecular orientation.

    Science.gov (United States)

    Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

    2012-09-14

    Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

  17. Two-color resonance photoionization spectrum of nickelocene in a supersonic jet

    Science.gov (United States)

    Ketkov, S. Yu.; Selzle, H. L.; Schlag, E. W.; Titova, S. N.; Kalakutskaya, L. V.

    2004-10-01

    Two-color photoionization of nickelocene molecules cooled in a supersonic jet is performed using a tunable nanosecond pulsed laser. The first stage of the multiphoton excitation is the transition from the highest occupied molecular orbital of nickelocene to the lowest Rydberg level. Conditions are found under which molecular ions (η 5-C5H5)2Ni+ are the only product of the multiphoton ionization in the one-color experiment. Irradiation of an excited molecule by an intense pulse of another laser increases significantly the yield of molecular ions. The dependence of the yield of (η5-C5H5)2Ni+ ions on the frequency of the second laser makes it possible to determine the adiabatic ionization potential of nickelocene as 6.138±0.012eV.

  18. Calibration of a two-color soft x-ray diagnostic for electron temperature measurement

    Science.gov (United States)

    Reusch, L. M.; Den Hartog, D. J.; Franz, P.; Goetz, J.; McGarry, M. B.; Stephens, H. D.

    2016-11-01

    The two-color soft x-ray (SXR) tomography diagnostic on the Madison Symmetric Torus is capable of making electron temperature measurements via the double-filter technique; however, there has been a 15% systematic discrepancy between the SXR double-filter (SXRDF) temperature and Thomson scattering (TS) temperature. Here we discuss calibration of the Be filters used in the SXRDF measurement using empirical measurements of the transmission function versus energy at the BESSY II electron storage ring, electron microprobe analysis of filter contaminants, and measurement of the effective density. The calibration does not account for the TS and SXRDF discrepancy, and evidence from experiments indicates that this discrepancy is due to physics missing from the SXRDF analysis rather than instrumentation effects.

  19. On Two Color and CCD Methods for the Determination of Astronomic Position.

    Science.gov (United States)

    1986-03-14

    INTRODUCTION .................................... 2 A. Astroposition Objectives As Related to Two-Color Refractometry .................. 2 B. Results...value for the astronomic longitude and latitude.-_ A. Astroposition Objectives As Related to Two-Color Refractometry The long term objectives consist...The interior of the box was divided into 4 bays containing the telescope, the refractometry optics, the power supplies and the refralctometry

  20. Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data

    Directory of Open Access Journals (Sweden)

    Burtt Glyn J

    2007-01-01

    Full Text Available Abstract Background There are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments. Resulting analyses therefore often choose between the unacceptable inclusion of poor quality data or the unpalatable exclusion of some (possibly a lot of good quality data along with the bad. Two such approaches would be a single channel analysis using some of the data from all of the arrays, and an analysis of all of the data, but only from unaffected arrays. In this paper we examine a 'combined' approach to the analysis of such affected experiments that uses all of the unaffected data. Results A simulation experiment shows that while a single channel analysis performs relatively well when the majority of arrays are affected, and excluding affected arrays performs relatively well when few arrays are affected (as would be expected in both cases, the combined approach out-performs both. There are benefits to actively estimating the key-parameter of the approach, but whether these compensate for the increased computational cost and complexity over just setting that parameter to take a fixed value is not clear. Inclusion of ozone-affected data results in poor performance, with a clear spatial effect in the damage being apparent. Conclusion There is no need to exclude unaffected data in order to remove those which are damaged. The combined approach discussed here is shown to out-perform more usual approaches, although it seems that if the damage is limited to very few arrays, or extends to very nearly all, then the benefits will be limited. In other circumstances though, large improvements in performance can be achieved by adopting such an approach.

  1. Identification of Differentially Expressed IGFBP5-Related Genes in Breast Cancer Tumor Tissues Using cDNA Microarray Experiments

    OpenAIRE

    2015-01-01

    IGFBP5 is an important regulatory protein in breast cancer progression. We tried to identify differentially expressed genes (DEGs) between breast tumor tissues with IGFBP5 overexpression and their adjacent normal tissues. In this study, thirty-eight breast cancer and adjacent normal breast tissue samples were used to determine IGFBP5 expression by qPCR. cDNA microarrays were applied to the highest IGFBP5 overexpressed tumor samples compared to their adjacent normal breast tissue. Microarray a...

  2. Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening

    Directory of Open Access Journals (Sweden)

    Vitulli Federico

    2008-04-01

    Full Text Available Abstract Background Since its discovery more than 100 years ago, potato (Solanum tuberosum tuber cold-induced sweetening (CIS has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in the process. However, many uncertainties still exist, as the relative contribution of each gene to the process is often unclear, possibly as the consequence of the heterogeneity of experimental systems. Some enzymes associated with CIS, such as β-amylases and invertases, have still to be identified at a sequence level. In addition, little is known about the early events that trigger CIS and on the involvement/association with CIS of genes different from carbohydrate-associated genes. Many of these uncertainties could be resolved by profiling experiments, but no GeneChip is available for the potato, and the production of the potato cDNA spotted array (TIGR has recently been discontinued. In order to obtain an overall picture of early transcriptional events associated with CIS, we investigated whether the commercially-available tomato Affymetrix GeneChip could be used to identify which potato cold-responsive gene family members should be further studied in detail by Real-Time (RT-PCR (qPCR. Results A tomato-potato Global Match File was generated for the interpretation of various aspects of the heterologous dataset, including the retrieval of best matching potato counterparts and annotation, and the establishment of a core set of highly homologous genes. Several cold-responsive genes were identified, and their expression pattern was studied in detail by qPCR over 26 days. We detected biphasic behaviour of mRNA accumulation for carbohydrate-associated genes and our combined GeneChip-qPCR data identified, at a sequence level, enzymatic activities such as β-amylases and invertases previously reported as being involved in CIS. The GeneChip data also unveiled important processes accompanying CIS, such as the induction of redox

  3. Two-color above threshold ionization of atoms and ions in XUV Bessel beams and combined with intense laser light

    CERN Document Server

    Seipt, D; Surzhykov, A; Fritzsche, S

    2016-01-01

    The two-color above-threshold ionization (ATI) of atoms and ions is investigated for a vortex Bessel beam in the presence of a strong near-infrared (NIR) light field. While the photoionization is caused by the photons from the weak but extreme ultra-violet (XUV) vortex Bessel beam, the energy and angular distribution of the photoelectrons and their sideband structure are affected by the plane-wave NIR field. We here explore the energy spectra and angular emission of the photoelectrons in such two-color fields as a function of the size and location of the target (atoms) with regard to the beam axis. In addition, analogue to the circular dichroism in typical two-color ATI experiments with circularly polarized light, we define and discuss seven different dichroism signals for such vortex Bessel beams that arise from the various combinations of the orbital and spin angular momenta of the two light fields. For localized targets, it is found that these dichroism signals strongly depend on the size and position of t...

  4. Development of two color laser diagnostics for the ITER poloidal polarimeter.

    Science.gov (United States)

    Kawahata, K; Akiyama, T; Tanaka, K; Nakayama, K; Okajima, S

    2010-10-01

    Two color laser diagnostics using terahertz laser sources are under development for a high performance operation of the Large Helical Device and for future fusion devices such as ITER. So far, we have achieved high power laser oscillation lines simultaneously oscillating at 57.2 and 47.7 μm by using a twin optically pumped CH(3)OD laser, and confirmed the original function, compensation of mechanical vibration, of the two color laser interferometer. In this article, application of the two color laser diagnostics to the ITER poloidal polarimeter and recent hardware developments will be described.

  5. In situ spatial mapping of Gouy phase slip with terahertz generation in two-color field.

    Science.gov (United States)

    Meng, Chao; Lü, Zhihui; Huang, Yindong; Wang, Xiaowei; Chen, Wenbo; Zhang, Dongwen; Zhao, Zengxiu; Yuan, Jianmin

    2016-05-30

    We establish a one-to-one mapping between the local phase slip and the spatial position near the focus by scanning a thin jet along the propagation direction of laser beams. The measurement shows that the optimal phase of terahertz can be utilized to characterize in situ the spatially dependent relative phase of the two-color field. We also investigate the role of the Gouy phase shift on terahertz generation from two-color laser-induced plasma. The result is of critical importance for phase-dependent applications of two-color laser-field, including high-order harmonic and terahertz generation.

  6. Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Chan Frances

    2006-03-01

    Full Text Available Abstract Background DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of different technologies and non-standard methods of data analysis and interpretation. In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective and conflicting conclusions. To address this issue we have conducted a large scale TaqMan® Gene Expression Assay based real-time PCR experiment and used this data set as the reference to evaluate the performance of two representative commercial microarray platforms. Results In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR using two representative commercial long-oligonucleotide microarray platforms: (1 Applied Biosystems Human Genome Survey Microarrays (based on single-color detection; (2 Agilent Whole Human Genome Oligo Microarrays (based on two-color detection. 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan® Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer's standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference. Using the TaqMan® Gene Expression Assay based real-time PCR data set as the reference set, the performance of the two microarray platforms was evaluated focusing on the following criteria: (1 Sensitivity and accuracy in detection of expression; (2 Fold change correlation with real-time PCR data in pair

  7. Maternal detection of neonatal jaundice during birth hospitalization using a novel two-color icterometer

    National Research Council Canada - National Science Library

    Bolajoko O Olusanya; Tina M Slusher; Donald O Imosemi; Abieyuwa A Emokpae

    2017-01-01

    .... This study therefore, set out to evaluate the performance of a -two-color icterometer (BilistripTM) as a possible screening tool for detecting significant jaundice by mothers or care-givers in the first week of life...

  8. The intraclass correlation coefficient applied for evaluation of data correction, labeling methods and rectal biopsy sampling in DNA microarray experiments

    NARCIS (Netherlands)

    Pellis, E.P.M.; Franssen-Hal, van N.L.W.; Burema, J.; Keijer, J.

    2003-01-01

    We show that the intraclass correlation coefficient (ICC) can be used as a relatively simple statistical measure to assess methodological and biological variation in DNA microarray analysis. The ICC is a measure that determines the reproducibility of a variable, which can easily be calculated from a

  9. Trajectory selection in high harmonic generation by controlling the phase between orthogonal two-color fields.

    Science.gov (United States)

    Brugnera, Leonardo; Hoffmann, David J; Siegel, Thomas; Frank, Felix; Zaïr, Amelle; Tisch, John W G; Marangos, Jonathan P

    2011-10-07

    We demonstrate control of short and long quantum trajectories in high harmonic emission through the use of an orthogonally polarized two-color field. By controlling the relative phase ϕ between the two fields we show via classical and quantum calculations that we can steer the two-dimensional trajectories to return, or not, to the core and so control the relative strength of the short or long quantum trajectory contribution. In experiments, we demonstrate that this leads to robust control over the trajectory contributions using a drive field from a femtosecond laser composed of the fundamental ω at 800 nm (intensity ∼1.2×10(14)  W cm(-2)) and its weaker orthogonally polarized second harmonic 2ω (intensity ∼0.3×10(14)  W cm(-2)) with the relative phase between the ω and 2ω fields varied simply by tilting a fused silica plate. This is the first demonstration of short and long quantum trajectory control at the single-atom level.

  10. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  11. Two-Color Magneto-Optical Trap with Small Magnetic Field for Ytterbium

    CERN Document Server

    Kawasaki, Akio; Yu, QinQin; Vuletić, Vladan

    2015-01-01

    We report a two-color magneto-optical trap (MOT) for ytterbium atoms operating at a low magnetic field gradient down to 2 G/cm where a conventional MOT using the singlet transition (6s^2 1S0 -> 6s6p 1P1) is unable to trap atoms. By simultaneously applying laser light on both the broad-linewidth singlet transition and the narrow-linewidth triplet transition (6s^2 1S0 -> 6s6p 3P1), we load and trap 4.0 x 10^5 atoms directly from an atomic beam at 700 K. In the two-color MOT, the slowing and trapping functions are separately performed by the singlet transition light and the triplet transition light, respectively. The two-color MOT is highly robust against laser power imbalance even at very low magnetic field gradients.

  12. Inkjet printing the three organic functional layers of two-colored organic light emitting diodes

    Energy Technology Data Exchange (ETDEWEB)

    Coenen, Michiel J.J., E-mail: Michiel.Coenen@tmc.nl [Holst Centre, PO BOX 8550, 5605 KN Eindhoven (Netherlands); Slaats, Thijs M.W.L.; Eggenhuisen, Tamara M. [Holst Centre, PO BOX 8550, 5605 KN Eindhoven (Netherlands); Groen, Pim [Holst Centre, PO BOX 8550, 5605 KN Eindhoven (Netherlands); Novel Aerospace Materials Group, Faculty of Aerospace Engineering, Delft University of Technology, Kluyverweg 1, 2629HS Delft (Netherlands)

    2015-05-29

    Inkjet printing allows for the roll-2-roll fabrication of organic electronic devices at an industrial scale. In this paper we demonstrate the fabrication of two-colored organic light emitting diodes (OLEDs) in which three adjacent organic device layers were inkjet printed from halogen free inks. The resulting devices demonstrate the possibilities offered by this technique for the fabrication of OLEDs for signage and personalized electronics. - Highlights: • Two-colored organic light emitting diodes with 3 inkjet printed device layers were fabricated. • All materials were printed from halogen free inks. • Inkjet printing of emissive materials is suitable for signage applications.

  13. Electron Correlation in Nonsequential Double Ionization of Helium by Two-Color Pulses

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yue-Ming; LIAO Qing; HUANG Cheng; TONG Ai-Hong; LU Pei-Xiang

    2010-01-01

    @@ We investigate the momentum and energy correlations between the two electrons from nonsequential double ionization(NSDI)of helium by strong two-color pulses with the classical three-dimensional ensemble model.The correlated momentum distribution in the direction parallel to the laser field exhibits an arc-like structure and the sum-energy spectrum shows a sharp peak for the NSDI of helium in the two-color fields.Back analysis reveals that the narrow time interval during which recollisions occur,the low returning energy and the short time delay between recollision and double ionization lead to the novel momentum and energy correlations.

  14. A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments

    Directory of Open Access Journals (Sweden)

    Vassal Aurélien

    2008-01-01

    Full Text Available Abstract Background The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix® technology provides both a quantitative fluorescence signal and a decision (detection call: absent or present based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM patients. Results After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i determine a sex predictor with the normal donor group classifying gender with no error in all patient groups except for male MM samples with a Y chromosome deletion, (ii predict the immunoglobulin light and heavy chains expressed by the malignant myeloma clones of the validation group and (iii predict sex, light and heavy chain nature for every new patient. Finally, this method was shown powerful when compared to the popular classification method Prediction Analysis of Microarray (PAM. Conclusion This normalization-free method is routinely used for quality control and correction of collection errors in patient reports to clinicians. It can be easily extended to multiple class prediction suitable with

  15. MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data.

    Science.gov (United States)

    Brock, Guy N; Mukhopadhyay, Partha; Pihur, Vasyl; Webb, Cynthia; Greene, Robert M; Pisano, M Michele

    2013-01-08

    MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is an effective means of acquiring genome-level information of miRNA activation and inhibition, as well as the potential regulatory role that these genes play within a biological system. As with mRNA expression profiling arrays, miRNA microarrays come in a variety of platforms from numerous manufacturers, and there are a multitude of techniques available for reducing and analyzing these data. In this paper, we present an analysis of a typical two-color miRNA microarray experiment using publicly available packages from R and Bioconductor, the open-source software project for the analysis of genomic data. Covered topics include visualization, normalization, quality checking, differential expression, cluster analysis, miRNA target identification, and gene set enrichment analysis. Many of these tools carry-over from the analysis of mRNA microarrays, but with some notable differences that require special attention. The paper is presented as a "compendium" which, along with the accompanying R package MmPalateMiRNA, contains all of the experimental data and source code to reproduce the analyses contained in the paper. The compendium presented in this paper will provide investigators with an access point for applying the methods available in R and Bioconductor for analysis of their own miRNA array data.

  16. Identification of Differentially Expressed IGFBP5-Related Genes in Breast Cancer Tumor Tissues Using cDNA Microarray Experiments.

    Science.gov (United States)

    Akkiprik, Mustafa; Peker, İrem; Özmen, Tolga; Amuran, Gökçe Güllü; Güllüoğlu, Bahadır M; Kaya, Handan; Özer, Ayşe

    2015-11-10

    IGFBP5 is an important regulatory protein in breast cancer progression. We tried to identify differentially expressed genes (DEGs) between breast tumor tissues with IGFBP5 overexpression and their adjacent normal tissues. In this study, thirty-eight breast cancer and adjacent normal breast tissue samples were used to determine IGFBP5 expression by qPCR. cDNA microarrays were applied to the highest IGFBP5 overexpressed tumor samples compared to their adjacent normal breast tissue. Microarray analysis revealed that a total of 186 genes were differentially expressed in breast cancer compared with normal breast tissues. Of the 186 genes, 169 genes were downregulated and 17 genes were upregulated in the tumor samples. KEGG pathway analyses showed that protein digestion and absorption, focal adhesion, salivary secretion, drug metabolism-cytochrome P450, and phenylalanine metabolism pathways are involved. Among these DEGs, the prominent top two genes (MMP11 and COL1A1) which potentially correlated with IGFBP5 were selected for validation using real time RT-qPCR. Only COL1A1 expression showed a consistent upregulation with IGFBP5 expression and COL1A1 and MMP11 were significantly positively correlated. We concluded that the discovery of coordinately expressed genes related with IGFBP5 might contribute to understanding of the molecular mechanism of the function of IGFBP5 in breast cancer. Further functional studies on DEGs and association with IGFBP5 may identify novel biomarkers for clinical applications in breast cancer.

  17. Laser-induced periodic surface structures on titanium upon single- and two-color femtosecond double-pulse irradiation.

    Science.gov (United States)

    Höhm, Sandra; Rosenfeld, Arkadi; Krüger, Jörg; Bonse, Jörn

    2015-10-05

    Single- and two-color double-fs-pulse experiments were performed on titanium to study the dynamics of the formation of laser-induced periodic surface structures (LIPSS). A Mach-Zehnder inter-ferometer generated polarization controlled (parallel or cross-polarized) double-pulse sequences in two configurations - either at 800 nm only, or at 400 and 800 nm wavelengths. The inter-pulse delays of the individual 50-fs pulses ranged up to some tens of picoseconds. Multiple of these single- or two-color double-fs-pulse sequences were collinearly focused by a spherical mirror to the sample surface. In both experimental configurations, the peak fluence of each individual pulse was kept below its respective ablation threshold and only the joint action of both pulses lead to the formation of LIPSS. Their resulting characteristics were analyzed by scanning electron microscopy and the periods were quantified by Fourier analyses. The LIPSS periods along with the orientation allow a clear identification of the pulse which dominates the energy coupling to the material. A plasmonic model successfully explains the delay-dependence of the LIPSS on titanium and confirms the importance of the ultrafast energy deposition stage for LIPSS formation.

  18. Long-range predissociation in two-color photoassociation of ultracold Na atoms

    NARCIS (Netherlands)

    Molenaar, P.A.; Straten, P. van der; Heideman, H.G.M.

    1997-01-01

    We report two-color photo-associative ionization of sodium in a Magneto-Optical Trap. The experimental results yield information on both singly and doubly excited states. We find that the highest bound vibrational levels (v > 20) of the singly-excited 0^- g state predissociate into the 3²P3/2

  19. A Method of Microarray Data Storage Using Array Data Type

    OpenAIRE

    Tsoi, Lam C.; Zheng, W Jim

    2007-01-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store ...

  20. 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.

  1. Differential expression of 114 oxidative stressrelated genes in peripheral blood mononuclear cells of acute cerebral infarction patients A gene microarray experiment

    Institute of Scientific and Technical Information of China (English)

    Jing Yang; Fei Zhong; Mingshan Ren; Jiangming Zhao

    2010-01-01

    Previous studies have focused on the analysis of single or several function-related genes in oxidative stress;however,little information is available regarding altered expression of oxidative stress-related genes in the process of ischemia-reperfusion injury from microarray experiments.The aim of the present study was to investigate the changes in cell oxidative stress-and toxicity-related gene expression utilizing microarray screening in patients with acute cerebral infarction during cerebral ischemia-reperfusion injury.Of the included 114 genes,expression was significantly upregulated in eight genes,including three heat shock protein-related genes,one oxidative and metabolic stress-related gene,one cell growth arrest/senescence related gene,two apoptosis signal-related genes,and one DNA damage and repair related gene.Expression was significantly downregulated in four genes,including one cell proliferation/cancer related gene,two oxidative and metabolic stress-related genes and one DNA damage and repair related gene.The results demonstrated that cerebral ischemia-reperfusion injury in patients with acute cerebral infarction was affected by many genes including oxidative stress-,heat shock-,DNA damage and repair-,and apoptosis signal-related genes.Therefore,it could be suggested that cerebral ischemia-reperfusion injury may be subjected to complex genetic regulation mechanisms.

  2. Formation of laser-induced periodic surface structures on fused silica upon two-color double-pulse irradiation

    Science.gov (United States)

    Höhm, S.; Herzlieb, M.; Rosenfeld, A.; Krüger, J.; Bonse, J.

    2013-12-01

    The formation of laser-induced periodic surface structures (LIPSS) upon irradiation of fused silica with multiple irradiation sequences consisting of laser pulse pairs (50 fs single-pulse duration) of two different wavelengths (400 and 800 nm) is studied experimentally. Parallel polarized double-pulse sequences with a variable delay Δt between -10 and +10 ps and between the individual fs-laser pulses were used to investigate the LIPSS periods versus Δt. These two-color experiments reveal the importance of the ultrafast energy deposition to the silica surface by the first laser pulse for LIPSS formation. The second laser pulse subsequently reinforces the previously seeded spatial LIPSS frequencies.

  3. Formation of laser-induced periodic surface structures on fused silica upon two-color double-pulse irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Höhm, S.; Herzlieb, M.; Rosenfeld, A. [Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Straße 2A, D-12489 Berlin (Germany); Krüger, J.; Bonse, J. [BAM Bundesanstalt für Materialforschung und –prüfung, Unter den Eichen 87, D-12205 Berlin (Germany)

    2013-12-16

    The formation of laser-induced periodic surface structures (LIPSS) upon irradiation of fused silica with multiple irradiation sequences consisting of laser pulse pairs (50 fs single-pulse duration) of two different wavelengths (400 and 800 nm) is studied experimentally. Parallel polarized double-pulse sequences with a variable delay Δt between −10 and +10 ps and between the individual fs-laser pulses were used to investigate the LIPSS periods versus Δt. These two-color experiments reveal the importance of the ultrafast energy deposition to the silica surface by the first laser pulse for LIPSS formation. The second laser pulse subsequently reinforces the previously seeded spatial LIPSS frequencies.

  4. Simultaneous measurement of temperature and velocity of air flow over 1000°C using two color phosphor thermometry

    Science.gov (United States)

    Fukuta, Masatoshi; Someya, Satoshi; Munakata, Tetsuo; LCS Team

    2016-11-01

    Thermal barrier coatings were applied to the gas turbines and the internal combustion engines for the high thermal efficiency. The evaluation and the improvement of coatings require to measure transient gaseous flow near the wall with coatings. An aim of this study is to combine a two color phosphor thermometry with the PIV to measure simultaneously temperature and velocity of the gas over 1000°C. The temperature and velocity distribution of an impinging jet of high temperature air was simultaneously visualized in experiments. The temperature was estimated from an intensity ratio of luminescent in different ranges of wavelength, 500 600 nm and 400 480 nm. Uncertainty of measured temperature was less than 10°C. Temperatures measured by the developed method and by thermocouples were agreed well. The measured velocity by the PIV with phosphor particles were also agreed well with the velocity measured by a Laser Doppler Velocimeter.

  5. APPLICATION OF TWO-COLOR INTERPHASE FISH USING SEX PROBE IN ALLOGENEIC STEM CELL TRANSPLANTATION

    Institute of Scientific and Technical Information of China (English)

    曾慧兰; 李建勇; 朱康儿; 薛永权; 李杨秋; 刘晓力; 过宇

    2002-01-01

    Objective: To evaluate the significance of two-color interphase fluorescence in situ hybridization (FISH) using X and Y centromere probe in the engraftment estimation and minimal residual disease (MRD) monitoring after allogeneic stem cell transplantation (alloSCT). Methods: Samples from 12 cases patients in different periods after alloSCT were detected by interphase FISH. Results: All of the 12 patients were proved to obtain engraftment 22(35 days after alloSCT. While traditional karyotype showed as 100%XX or 100%XY invariably, FISH showed different percentages of donor original sex chromosome. Conclusion: Two-color interphase FISH is a more sensitive and simple test for engraftment evaluation and MRD monitoring post SCT, though, it can not entirely replace traditional karyotype analysis and gene detection by RT-PCR.

  6. Effects of a static electric field on two-color photoassociation of heteronuclear atom-pairs

    CERN Document Server

    Chakraborty, Debashree

    2013-01-01

    We study non-perturbative effects of a static electric field on two-color photoassociation of heteronuclear atom-pairs. A static electric field induces anisotropy in scattering between two heteronuclear atoms and hybridizes field-free rotational states of heteronuclear dimers or polar molecules. In a previous paper [D. Chakraborty $\\it {et.}$ $\\it {al.}$, J. Phys. B 44, 095201 (2011)], the effects of a static electric field on one-color photoassociation between heteronuclear atoms has been described through field-modified ground-state scattering states, neglecting electric field effects on heteronuclear diatomic bound states. To study the effects of a static electric field on heteronuclear bound states, and the resulting influence on Raman-type two-color photoassociation between heteronuclear atoms in the presence of a static electric field, we develop a non-perturbative numerical method to calculate static electric field-dressed heteronuclear bound states. We show that the static electric field induced scatt...

  7. Two-color mid-infrared thermometer with a hollow glass optical fiber.

    Science.gov (United States)

    Small, W; Celliers, P M; Da Silva, L B; Matthews, D L; Soltz, B A

    1998-10-01

    We have developed a low-temperature optical-fiber-based two-color infrared thermometer. A single 700-mum-bore hollow glass optical fiber collects and transmits radiation that is then modulated and split into two paths by a reflective optical chopper. Two different thermoelectrically cooled mid-infrared HgCdZnTe photoconductors monitor the chopped signals that are recovered with lock-in amplification. With the two previously obtained blackbody calibration equations, a computer algorithm calculates the true temperature and emissivity of a target in real time, taking into account reflection of the ambient radiation field from the target surface. The small numerical aperture of the hollow glass fiber and the fast response of the detectors, together with the two-color principle, permit high spatial and temporal resolution while allowing the user to dynamically alter the fiber-to-target distance.

  8. Low-temperature characteristics of two-color InAs/InP quantum dots laser

    Institute of Scientific and Technical Information of China (English)

    Shiguo Li; Qian Gong; Xinzhong Wang; Li Yue; Oingbo Liu; Hailong Wang

    2012-01-01

    We report on the lasing characteristics of a two-color InAs/InP quantum dots (QDs) laser at a low temperature.Two lasing peaks with a tunable gap are simultaneously observed.At a low temperature of 80 K,a tunable range greater than a 20-nm wavelength is demonstrated by varying the injection current from 30 to 500 mA.Under a special condition,we even observe three lasing peaks,which are in contrast to those observed at room temperature.The temperature coefficient of the lasing wavelength was obtained for the two colors in the 80-280 K temperature range,which is lower than that of the reference quantum well (QW) laser working in the same wavelength region.

  9. Dirac Spectrum of the Wilson Dirac Operator for QCD with Two Colors

    CERN Document Server

    Kieburg, Mario; Zafeiropoulos, Savvas

    2015-01-01

    We study the lattice artefacts of the Wilson Dirac operator for QCD with two colors and fermions in the fundamental representation from the viewpoint of chiral perturbation theory. These effects are studied with the help of the following spectral observables: the level density of the Hermitian Wilson Dirac operator, the distribution of chirality over the real eigenvalues, and the chiral condensate for the quenched as well as for the unquenched theory. We provide analytical expressions for all these quantities. Moreover we derive constraints for the level density of the real eigenvalues of the non-Hermitian Wilson Dirac operator and the number of additional real modes. The latter is a good measure for the strength of lattice artefacts. All computations are confirmed by Monte Carlo simulations of the corresponding random matrix theory which agrees with chiral perturbation theory of two color QCD with Wilson fermions.

  10. Autler-Townes splitting in two-color photoassociation of 6Li

    CERN Document Server

    Schloeder, U; Silber, C; Zimmermann, C; Schloeder, Ulrike; Deuschle, Thomas; Silber, Christian; Zimmermann, Claus

    2003-01-01

    We report on high-resolution two-color photoassociation spectroscopy in the triplet system of magneto-optically trapped 6Li. The absolute transition frequencies have been measured. Strong optical coupling of the bound molecular states has been observed as Autler-Townes splitting in the photoassociation signal. The spontaneous bound-bound transition rate is determined and the molecule formation rate is estimated. The observed lineshapes are in good agreement with the theoretical model.

  11. Lowest eigenvalues of the Dirac operator for two color QCD at finite density

    CERN Document Server

    Bittner, E; Markum, H; Pullirsch, R; Bittner, Elmar; Lombardo, Maria-Paola; Markum, Harald; Pullirsch, Rainer

    2001-01-01

    We investigate the eigenvalue spectrum of the staggered Dirac matrix in full QCD with two colors and finite chemical potential. Along the strong-coupling axis up to the temperature phase transition, the low-lying Dirac spectrum is well described by random matrix theory (RMT) and exhibits universal behavior. The situation is discussed in the chirally symmetric phase and no universality is seen for the microscopic spectral density.

  12. Polyakov-Quark-Meson-Diquark Model for two-color QCD

    CERN Document Server

    Strodthoff, Nils

    2013-01-01

    We present an update on the phase diagram of two-color QCD from a chiral effective model approach based on a quark-meson-diquark model using the Functional Renormalization Group (FRG). We discuss the impact of perturbative UV contributions, the inclusion of gauge field dynamics via a phenomenological Polyakov loop potential, and the impact of matter backcoupling on the gauge sector. The corresponding phase diagram including these effects is found to be in qualitative agreement with recent lattice investigations.

  13. The study of two-color excitation upconversion of Pr(0.5)Yb(3):ZBLAN

    Institute of Scientific and Technical Information of China (English)

    CHEN; Xiaobo; SONG; Zengfu

    2006-01-01

    The excited state absorption upconversion of Pr(0.5)Yb(3):ZBLAN glass material, under two-color excitation of the 960 nm semiconductor laser and the Xe lamp light simultaneously, is reported in this article. It was found that the upconversion emission spectra of 480.1, 519.0, 601.9 and 631.8 nm coincide with the common emission spectra. Meanwhile, the upconversion-excitation spectrum has three obvious peaks under two-color excitation, and they respectively correspond to the 856.0 nm upconversion excitation transition [1G4(Pr3+)→1I6(Pr3+) and 1G4(Pr3+)→3P1(Pr3+)], the 789.0 nm upconversion excitation transition 1G4(Pr3+)→3P2(Pr3+), and the 803.7 nm upconversion excitation transition 3H6(Pr3+)→1D2(Pr3+). The upconversion excitation transition 1G4(Pr3+)→1I6(Pr3+) is strong because its oscillator strength f = 23.040(10-6 is large, which results in a large peak appearing in the upconversion excitation spectrum. That is just the new interesting two-color excitation upconversion luminescence phenomenon of Pr(0.5)Yb(3):ZBLAN induced by one laser and one continuous normal light simultaneously.

  14. SIMAGE : simulation of DNA-microarray gene expression data

    NARCIS (Netherlands)

    Albers, Casper J.; Jansen, Ritsert C.; Kok, Jan; Kuipers, Oscar P.; Hijum, Sacha A.F.T. van

    2006-01-01

    Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best analysis of a given DNA microarray experiment, (iii) educating students, lab-workers and other

  15. Dynamics of the formation of laser-induced periodic surface structures (LIPSS) upon femtosecond two-color double-pulse irradiation of metals, semiconductors, and dielectrics

    Science.gov (United States)

    Höhm, S.; Herzlieb, M.; Rosenfeld, A.; Krüger, J.; Bonse, J.

    2016-06-01

    In order to address the dynamics and physical mechanisms of LIPSS formation for three different classes of materials (metals, semiconductors, and dielectrics), two-color double-fs-pulse experiments were performed on Titanium, Silicon and Fused Silica. For that purpose a Mach-Zehnder interferometer generated polarization controlled (parallel or cross-polarized) double-pulse sequences at 400 nm and 800 nm wavelength, with inter-pulse delays up to a few picoseconds. Multiple of these two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample surfaces. The fluence of each individual pulse (400 nm and 800 nm) was always kept below its respective ablation threshold and only the joint action of both pulses lead to the formation of LIPSS. Their resulting characteristics (periods, areas) were analyzed by scanning electron microscopy. The periods along with the LIPSS orientation allow a clear identification of the pulse which dominates the energy coupling to the material. For strong absorbing materials (Silicon, Titanium), a wavelength-dependent plasmonic mechanism can explain the delay-dependence of the LIPSS. In contrast, for dielectrics (Fused Silica) the first pulse always dominates the energy deposition and LIPSS orientation, supporting a non-plasmonic formation scenario. For all materials, these two-color experiments confirm the importance of the ultrafast energy deposition stage for LIPSS formation.

  16. Laser-induced periodic surface structures on fused silica upon cross-polarized two-color double-fs-pulse irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Höhm, S., E-mail: hoehm@mbi-berlin.de.de [Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Straße 2A, D-12489 Berlin (Germany); Herzlieb, M.; Rosenfeld, A. [Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Straße 2A, D-12489 Berlin (Germany); Krüger, J. [BAM Bundesanstalt für Materialforschung und–prüfung, Unter den Eichen 87, D-12205 Berlin (Germany); Bonse, J., E-mail: joern.bonse@bam.de [BAM Bundesanstalt für Materialforschung und–prüfung, Unter den Eichen 87, D-12205 Berlin (Germany)

    2015-05-01

    Graphical abstract: - Highlights: • LIPSS formation on fused silica is studied upon cross-polarized two-color (400 and 800 nm) double-fs-pulse irradiation. • LIPSS orientation follows the polarization of the first pulse. • LIPSS periods are determined by the wavelength of the first pulse. • LIPSS area is increased for temporally overlapping pulses due to nonlinear absorption. - Abstract: The dynamics of the formation of laser-induced periodic surface structures (LIPSS) on fused silica upon irradiation with linearly polarized fs-laser pulses (50 fs pulse duration) is studied by cross-polarized two-color double-fs-pulse experiments. In order to analyze the relevance of temporally distributed energy deposition in the early stage of LIPSS formation, a Mach-Zehnder interferometer was used for generating multiple double-pulse sequences at two different wavelengths (400 and 800 nm). The inter-pulse delay between the individual cross-polarized pulses of each sequence was systematically varied in the sub-ps range and the resulting LIPSS morphologies were characterized by scanning electron microscopy. It is found that the polarization of the first laser pulse arriving to the surface determines the orientation and the periodicity of the LIPSS. These two-color experiments further confirm the importance of the ultrafast energy deposition to the silica surface for LIPSS formation, particularly by the first laser pulse of each sequence. The second laser pulse subsequently reinforces the previously seeded spatial LIPSS characteristics (period, orientation)

  17. Nonvolatile two-color holographic recording in near-stoichiometric lithium niobate crystals gated by incoherent ultraviolet light

    Institute of Scientific and Technical Information of China (English)

    Shaolin Chen; Xiangming Liu; Bo Fu; Guoquan Zhang

    2009-01-01

    Nonvolatile two-color holographic recording gated by incoherent ultraviolet (UV) light centered at 365 nm is investigated in near-stoichiometric lithium niobate crystals. The influence of thermal treatment on the two-color recording is studied. The results show that thermal reduction tends to improve the two-color recording performance, whereas thermal oxidation degrades the two-color recording. With an incoherent 0.2-W/cm2 UV gating light and a 0.25-W/cm2 semiconductor recording laser at 780 nm, a two-color recording sensitivity of 4 x 10-3 cm/J and a recording dynamic range characterized by M/# of 0.12 are achieved in a 2.2-mm thermally reduced near-stoichiometric lithium niobate crystal. We attribute the improvement to the prolonged lifetime of small polarons and the increased absorption at the gating wavelength due to thermal reduction.

  18. Dynamics of the formation of laser-induced periodic surface structures (LIPSS) upon femtosecond two-color double-pulse irradiation of metals, semiconductors, and dielectrics

    Energy Technology Data Exchange (ETDEWEB)

    Höhm, S.; Herzlieb, M.; Rosenfeld, A. [Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Straße 2A, D-12489 Berlin (Germany); Krüger, J. [BAM Bundesanstalt für Materialforschung und –prüfung, Unter den Eichen 87, D-12205 Berlin (Germany); Bonse, J., E-mail: joern.bonse@bam.de [BAM Bundesanstalt für Materialforschung und –prüfung, Unter den Eichen 87, D-12205 Berlin (Germany)

    2016-06-30

    Graphical abstract: - Highlights: • LIPSS formation on Fused Silica, Silicon, and Titanium is studied upon parallel and cross-polarized two-color (400 and 800 nm) double-fs-pulse irradiation. • LIPSS orientation on Fused Silica follows the polarization of the first pulse. • LIPSS formation on Silicon and Titanium can be explained by a plasmonic model. - Abstract: In order to address the dynamics and physical mechanisms of LIPSS formation for three different classes of materials (metals, semiconductors, and dielectrics), two-color double-fs-pulse experiments were performed on Titanium, Silicon and Fused Silica. For that purpose a Mach–Zehnder interferometer generated polarization controlled (parallel or cross-polarized) double-pulse sequences at 400 nm and 800 nm wavelength, with inter-pulse delays up to a few picoseconds. Multiple of these two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample surfaces. The fluence of each individual pulse (400 nm and 800 nm) was always kept below its respective ablation threshold and only the joint action of both pulses lead to the formation of LIPSS. Their resulting characteristics (periods, areas) were analyzed by scanning electron microscopy. The periods along with the LIPSS orientation allow a clear identification of the pulse which dominates the energy coupling to the material. For strong absorbing materials (Silicon, Titanium), a wavelength-dependent plasmonic mechanism can explain the delay-dependence of the LIPSS. In contrast, for dielectrics (Fused Silica) the first pulse always dominates the energy deposition and LIPSS orientation, supporting a non-plasmonic formation scenario. For all materials, these two-color experiments confirm the importance of the ultrafast energy deposition stage for LIPSS formation.

  19. 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.

  20. Phenotypic MicroRNA Microarrays

    OpenAIRE

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the bio...

  1. Control of the polarization of attosecond pulses using a two-color field

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz, Camilo; Hoffmann, David J; Torres, Ricardo; Chipperfield, Luke E; Marangos, Jonathan P [Blackett Laboratory, Imperial College London, London SW7 2BW (United Kingdom)], E-mail: camilo@usal.es

    2009-11-15

    Control over the polarization of an attosecond pulse train (APT) is demonstrated theoretically using orthogonally polarized two-color fields. The carrier envelope phase of the two pulses is used as a control parameter to generate both an APT with linear polarization in two nearly perpendicular planes or a train of elliptically polarized pulses of alternating helicity. By using few-cycle driving laser fields an isolated attosecond pulse with elliptical polarization is shown to be generated after selecting the cut-off region of the harmonic spectrum. The control mechanism is explained in terms of classical trajectories.

  2. Tomographic imaging of asymmetric molecular orbitals with a two-color multicycle laser field

    CERN Document Server

    Qin, Meiyan; Zhang, Qingbin; Lu, Peixiang

    2013-01-01

    We theoretically demonstrate a scheme for tomographic reconstruction of asymmetric molecular orbitals based on high-order harmonic generation with a two-color multicycle laser field. It is shown that by adjusting the relative phase of the two fields, the returning electrons can be forced to recollide from one direction for all the orientations of molecules. Thus the reconstruction of the asymmetric orbitals can be carried out with multicycle laser field. This releases the stringent requirement of a single-cycle pulse with a stabilized and controllable carrier-envelop phase for the tomographic imaging of asymmetric molecular orbitals.

  3. Two-Color Fabry-Perot Laser Diode with THz Primary Mode Spacing

    CERN Document Server

    O'Brien, S; Buckley, K; Fehse, R; Amann, A; O'Reilly, E P; Barry, L P; Anandarajah, P; Patchell, J; O'Gorman, J

    2006-01-01

    A class of multiwavelength Fabry-Perot lasers is introduced where the spectrum is tailored through a non-periodic patterning of the cavity effective index. The cavity geometry is obtained using an inverse scattering approach and can be designed such that the spacing of discrete Fabry-Perot lasing modes is limited only by the bandwidth of the inverted gain medium. A specific two-color semiconductor laser with a mode spacing in the THz regime is designed, and measurements are presented demonstrating the simultaneous oscillation of the two wavelengths. The extension of the Fabry-Perot laser concept described presents significant new possibilities in laser cavity design.

  4. Two-color QCD with non-zero chiral chemical potential

    Energy Technology Data Exchange (ETDEWEB)

    Braguta, V.V. [Institute for High Energy Physics NRC “Kurchatov Institute' ,142281 Protvino (Russian Federation); Far Eastern Federal University, School of Biomedicine,690950 Vladivostok (Russian Federation); Goy, V.A. [Far Eastern Federal University, School of Natural Sciences,690950 Vladivostok (Russian Federation); Ilgenfritz, E.M. [Joint Institute for Nuclear Research,BLTP, 141980 Dubna (Russian Federation); Kotov, A.Yu. [Institute of Theoretical and Experimental Physics,117259 Moscow (Russian Federation); Molochkov, A.V. [Far Eastern Federal University, School of Biomedicine,690950 Vladivostok (Russian Federation); Müller-Preussker, M.; Petersson, B. [Humboldt-Universität zu Berlin, Institut für Physik,12489 Berlin (Germany)

    2015-06-16

    The phase diagram of two-color QCD with non-zero chiral chemical potential is studied by means of lattice simulation. We focus on the influence of a chiral chemical potential on the confinement/deconfinement phase transition and the breaking/restoration of chiral symmetry. The simulation is carried out with dynamical staggered fermions without rooting. The dependences of the Polyakov loop, the chiral condensate and the corresponding susceptibilities on the chiral chemical potential and the temperature are presented. The critical temperature is observed to increase with increasing chiral chemical potential.

  5. Flank transparency: transparent filters seen in dynamic two-color displays.

    Science.gov (United States)

    Wollschläger, D; Rodriguez, A M; Hoffman, D D

    2001-01-01

    Flank transparency is the perception of a colored transparent filter evoked by apparent-motion displays containing as few as two colors. Displays of flank transparency contain a random array of line segments placed on a uniform background. Small flanks are added to the line segments if the segments fall in the interior of a moving virtual shape, such as a virtual disk. This leads to the perception of a colored transparent disk with well-defined boundaries moving over the array of lines. Current qualitative and quantitative models of luminance and color conditions for perceptual transparency do not account for flank transparency as they require displays containing at least three different colors.

  6. Spatial properties of a terahertz beam generated from a two-color air plasma

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Wang, Tianwu; Buron, Jonas Christian Due

    2013-01-01

    We present a spatial characterization of terahertz (THz) beams generated from a two-color air plasma under different conditions by measuring full 3D beam profiles using a commercial THz camera. We compare two THz beam profiles emitted from plasmas generated by 35 fs and 100 fs laser pulses......, and show that the spatial properties of the two THz beams do not change significantly. For the THz beam profile generated by the 35 fs pulse, the spatial effect of eliminating the lower frequencies is investigated by implementing two crossed polarizers working as a high-pass filter. We show...

  7. Controlling Nonsequential Double Ionization in Two-Color Circularly Polarized Femtosecond Laser Fields

    Science.gov (United States)

    Mancuso, Christopher A.; Dorney, Kevin M.; Hickstein, Daniel D.; Chaloupka, Jan L.; Ellis, Jennifer L.; Dollar, Franklin J.; Knut, Ronny; Grychtol, Patrik; Zusin, Dmitriy; Gentry, Christian; Gopalakrishnan, Maithreyi; Kapteyn, Henry C.; Murnane, Margaret M.

    2016-09-01

    Atoms undergoing strong-field ionization in two-color circularly polarized femtosecond laser fields exhibit unique two-dimensional photoelectron trajectories and can emit bright circularly polarized extreme ultraviolet and soft-x-ray beams. In this Letter, we present the first experimental observation of nonsequential double ionization in these tailored laser fields. Moreover, we can enhance or suppress nonsequential double ionization by changing the intensity ratio and helicity of the two driving laser fields to maximize or minimize high-energy electron-ion rescattering. Our experimental results are explained through classical simulations, which also provide insight into how to optimize the generation of circularly polarized high harmonic beams.

  8. Stokes image reconstruction for two-color microgrid polarization imaging systems.

    Science.gov (United States)

    Lemaster, Daniel A

    2011-07-18

    The Air Force Research Laboratory has developed a new microgrid polarization imaging system capable of simultaneously reconstructing linear Stokes parameter images in two colors on a single focal plane array. In this paper, an effective method for extracting Stokes images is presented for this type of camera system. It is also shown that correlations between the color bands can be exploited to significantly increase overall spatial resolution. Test data is used to show the advantages of this approach over bilinear interpolation. The bounds (in terms of available reconstruction bandwidth) on image resolution are also provided.

  9. Statistical approaches for the analysis of DNA methylation microarray data.

    Science.gov (United States)

    Siegmund, Kimberly D

    2011-06-01

    Following the rapid development and adoption in DNA methylation microarray assays, we are now experiencing a growth in the number of statistical tools to analyze the resulting large-scale data sets. As is the case for other microarray applications, biases caused by technical issues are of concern. Some of these issues are old (e.g., two-color dye bias and probe- and array-specific effects), while others are new (e.g., fragment length bias and bisulfite conversion efficiency). Here, I highlight characteristics of DNA methylation that suggest standard statistical tools developed for other data types may not be directly suitable. I then describe the microarray technologies most commonly in use, along with the methods used for preprocessing and obtaining a summary measure. I finish with a section describing downstream analyses of the data, focusing on methods that model percentage DNA methylation as the outcome, and methods for integrating DNA methylation with gene expression or genotype data.

  10. 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.

  11. Generation of strong terahertz field from two-color laser filamentation and optical rectification

    Science.gov (United States)

    Kuk, Donghoon; Yoo, Yungjun; Oh, Taek Il; You, Yong Sing; Kim, Ki-Yong

    2015-04-01

    We have demonstrated strong-field (>8 MV/cm), high-peak-power (12 MW) THz generation with a bandwidth of >20 THz via two-color laser filamentation. Moderate average power (1.4 mW) is also achieved by using a cryogenically-cooled Ti:sapphire amplifier capable of producing 30 fs, 15 mJ pulses at a 1 kHz repetition rate. For maximal THz generation and transmission, we have used a combination of a thin dichroic waveplate and a large Brewster-angled silicon filter. Here we have used a thin BBO crystal for frequency doubling (800 nm to 400 nm) and observed strong terahertz emission from the crystal itself. We also find that this type of terahertz emission can be optimized to yield more output power compared to two-color photoionization. In both cases, we have used a microbolometer camera for real-time THz beam profiling. This cost-effective THz camera along with our intense THz sources can be a useful tool for nonlinear THz studies including broadband THz spectroscopy and imaging. Work supported by DOE, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award No. 014216-001.

  12. Two-color HgCdTe infrared staring focal plane arrays

    Science.gov (United States)

    Smith, Edward P.; Pham, Le T.; Venzor, Gregory M.; Norton, Elyse; Newton, Michael; Goetz, Paul; Randall, Valerie; Pierce, Gregory; Patten, Elizabeth A.; Coussa, Raymond A.; Kosai, Ken; Radford, William A.; Edwards, John; Johnson, Scott M.; Baur, Stefan T.; Roth, John A.; Nosho, Brett; Jensen, John E.; Longshore, Randolph E.

    2003-12-01

    Raytheon Vision Systems (RVS) in collaboration with HRL Laboratories is contributing to the maturation and manufacturing readiness of third-generation two-color HgCdTe infrared staring focal plane arrays (FPAs). This paper will highlight data from the routine growth and fabrication of 256x256 30μm unit-cell staring FPAs that provide dual-color detection in the mid-wavelength infrared (MWIR) and long-wavelength infrared (LWIR) spectral regions. FPAs configured for MWIR/MWIR, MWIR/LWIR and LWIR/LWIR detection are used for target identification, signature recognition and clutter rejection in a wide variety of space and ground-based applications. Optimized triple-layer-heterojunction (TLHJ) device designs and molecular beam epitaxy (MBE) growth using in-situ controls has contributed to individual bands in all two-color FPA configurations exhibiting high operability (>99%) and both performance and FPA functionality comparable to state-of-the-art single-color technology. The measured spectral cross talk from out-of-band radiation for either band is also typically less than 10%. An FPA architecture based on a single mesa, single indium bump, and sequential mode operation leverages current single-color processes in production while also providing compatibility with existing second-generation technologies.

  13. Evolution of the THz Beam Profile from a Two-Color Air Plasma Through a Beam Waist

    DEFF Research Database (Denmark)

    Strikwerda, Andrew; Pedersen, Pernille Klarskov; Jepsen, Peter Uhd

    2013-01-01

    We experimentally measure the profile of a THz beam generated by a two-color air plasma as it passes through a beam waist, and show that it can be approximated as a Bessel-Gauss beam.......We experimentally measure the profile of a THz beam generated by a two-color air plasma as it passes through a beam waist, and show that it can be approximated as a Bessel-Gauss beam....

  14. Two dye combinations suitable for two-color/two-dye laser-induced fluorescence thermography for ethanol

    Science.gov (United States)

    Fenner, Andreas; Stephan, Peter

    2017-06-01

    This paper presents two dye combinations suitable for two-color/two-dye laser-induced fluorescence thermography for ethanol. Besides the temperature dependency of the fluorescence, the influences of laser fluence, dye concentration, pressure, dissolved air, and photobleaching are also discussed. The experimental data are compared with models and data available in literature. Based on this, parameter ranges for two-color/two-dye laser-induced fluorescence thermography applications can be determined.

  15. In control: systematic assessment of microarray performance.

    Science.gov (United States)

    van Bakel, Harm; Holstege, Frank C P

    2004-10-01

    Expression profiling using DNA microarrays is a powerful technique that is widely used in the life sciences. How reliable are microarray-derived measurements? The assessment of performance is challenging because of the complicated nature of microarray experiments and the many different technology platforms. There is a mounting call for standards to be introduced, and this review addresses some of the issues that are involved. Two important characteristics of performance are accuracy and precision. The assessment of these factors can be either for the purpose of technology optimization or for the evaluation of individual microarray hybridizations. Microarray performance has been evaluated by at least four approaches in the past. Here, we argue that external RNA controls offer the most versatile system for determining performance and describe how such standards could be implemented. Other uses of external controls are discussed, along with the importance of probe sequence availability and the quantification of labelled material.

  16. 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...

  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. A Method of Microarray Data Storage Using Array Data Type

    Science.gov (United States)

    Tsoi, Lam C.; Zheng, W. Jim

    2009-01-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store microarray data by using array data type in an object-relational database management system – PostgreSQL. The implemented database can store all the microarray data from the same chip in an array data structure. The variable length array data type in PostgreSQL can store microarray data from same chip. The implementation of our schema can help to increase the data retrieval and space efficiency. PMID:17392028

  19. Multiscale Monte Carlo equilibration: Two-color QCD with two fermion flavors

    CERN Document Server

    Detmold, William

    2016-01-01

    We demonstrate the applicability of a recently proposed multi-scale thermalization algorithm to two-color quantum chromodynamics (QCD) with two mass-degenerate fermion flavors. The algorithm involves refining an ensemble of gauge configurations that had been generated using a renormalization group (RG) matched coarse action, thereby producing a fine ensemble that is close to the thermalized distribution of a target fine action; the refined ensemble is subsequently rethermalized using conventional algorithms. Although the generalization of this algorithm from pure Yang-Mills theory to QCD with dynamical fermions is straight-forward, we find that in the latter case, the method is susceptible to numerical instabilities during the initial stages of rethermalization when using the hybrid Monte Carlo algorithm. We find that these instabilities arise from large fermion forces in the evolution, which are attributed to an accumulation of spurious near-zero modes of the Dirac operator. We propose a simple strategy for ...

  20. Two-color Photodetectors%双波段光电探测器

    Institute of Scientific and Technical Information of China (English)

    刘铁权; 但伟

    2000-01-01

    Photodetectors are the critical parts for implementation of optoelectoronic detection and various optoelectronic technology. The paper introduces two-color photodetectors made of silicon integrated with InGaAs. These photodetectors can detect and respond incident light with the range of 400~1 100 nm and 1 100~1 650 nm simultaneously.%光电探测器是实现光电检测及各种光电技术的核心部件。文章介绍采用Si和In-GaAs两种材料集成制作的双波段光电探测器,它能同时探测并区分400~1100nm和1100~1 650 nm波段的入射光。

  1. Remote creation of strong and coherent emissions in air with two-color ultrafast laser pulses

    CERN Document Server

    Yao, Jinping; Jing, Chenrui; Zeng, Bin; Chu, Wei; Ni, Jielei; Zhang, Haisu; Xie, Hongqiang; Zhang, Chaojin; Li, Helong; Xu, Huailiang; Chin, See Leang; Cheng, Ya; Xu, Zhizhan

    2012-01-01

    We experimentally demonstrate generation of strong narrow-bandwidth emissions with excellent coherent properties at ~391 nm and ~428 nm from molecular ions of nitrogen inside a femtosecond filament in air by an orthogonally polarized two-color driver field (i. e., 800 nm laser pulse and its second harmonic). The durations of the coherent emissions at 391 nm and 428 nm are measured to be ~2.4 ps and ~7.8 ps respectively, both of which are much longer than the duration of the pump and its second harmonic pulses. Furthermore, the measured temporal decay characteristics of the excited molecular systems suggest an "instantaneous" population inversion mechanism that may be achieved in molecular nitrogen ions at an ultrafast time scale comparable to the 800 nm pump pulse.

  2. Fabrication of optical multilayer for two-color phase plate in super-resolution microscope.

    Science.gov (United States)

    Iketaki, Yoshinori; Kitagawa, Katsuichi; Hidaka, Kohjiro; Kato, Naoki; Hirabayashi, Akira; Bokor, Nandor

    2014-07-01

    In super-resolution microscopy based on fluorescence depletion, the two-color phase plate (TPP) is an indispensable optical element, which can independently control the phase shifts for two beams of different color, i.e., the pump and erase beams. By controlling a phase shift of the erase beam through the TPP, the erase beam can be modulated into a doughnut shape, while the pump beam maintains the initial Gaussian shape. To obtain a reliable optical multiplayer (ML) for the TPP, we designed a ML with only two optical layers by performing numerical optimization. The measured phase shifts generated by the fabricated ML using interferometry correspond to the design values. The beam profiles in the focal plane are also consistent with theoretical results. Although the fabricated ML consists of only two optical layers, the ML can provide a suitable phase modulation function for the TPP in a practical super-resolution microscope.

  3. Magnetic catalysis (and inverse catalysis) at finite temperature in two-color lattice QCD

    CERN Document Server

    Ilgenfritz, E -M; Petersson, B; Schreiber, A

    2013-01-01

    Two-color lattice QCD with N_f=4 staggered fermion degrees of freedom (no rooting trick is applied) with equal electric charge q is studied in a homogeneous magnetic background field B and at non-zero temperature T. In order to circumvent renormalization as a function of the bare coupling we apply a fixed-scale approach. We study the influence of the magnetic field on the critical temperature. At rather small pseudo-scalar meson mass (m_pi \\approx 175 MeV \\approx T_c(B=0)) we confirm magnetic catalysis for sufficiently strong magnetic field strength, while at T=195 MeV and weak magnetic field (qB {\\lesssim} 0.8 GeV^2) we find a rise of the Polyakov loop with qB and thus, indications for an inverse magnetic catalysis.

  4. Synthesis of Two-Color Laser Pulses for the Harmonic Cutoff Extension

    Science.gov (United States)

    Wang, Guo-Li; Zhou, Li-Hua; Zhao, Song-Feng; Zhou, Xiao-Xin

    2016-05-01

    Increasing simultaneously both the cutoff energy and efficiency is a big challenge to all applications of high-order harmonic generation (HHG). For this purpose, the shaping of the waveform of driving pulse is an alternative approach. Here, we show that the harmonic cutoff can be extended by about two times without reducing harmonic yield after considering macroscopic propagation effects, by adopting a practical way to synthesize two-color fields with fixed energy. Our results, combined with the experimental techniques, show the great potential of HHG as a tabletop light source. Supported by the National Natural Science Foundation of China under Grant Nos. 11264036, 11164025, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  5. Biosynthetic labeling and two-color imaging of phospholipids in cells.

    Science.gov (United States)

    Jao, Cindy Y; Roth, Mary; Welti, Ruth; Salic, Adrian

    2015-02-09

    Phospholipids with a choline head group are abundant components of all biological membranes, performing critical functions in cellular structure, metabolism, and signaling. In spite of their importance, our ability to visualize choline phospholipids in vivo remains very limited. We present a simple and robust chemical strategy to image choline phospholipids, based on the metabolic incorporation of azidocholine analogues, that accurately reflects the normal biosynthetic incorporation of choline into cellular phospholipids. Azidocholine-labeled phospholipids can be imaged in cells with high sensitivity and resolution, following derivatization with fluorophores, by bio-orthogonal chemical reactions compatible with live-cell imaging. We used this method to visualize the subcellular localization of choline phospholipids. We also demonstrate that double metabolic labeling with azidocholine and propargylcholine allows sensitive two-color imaging of choline phospholipids. Our method represents a powerful approach to directly image phospholipids, and to study their dynamics in cells and tissues.

  6. Enhanced hole boring with two-color relativistic laser pulses in the fast ignition scheme

    Science.gov (United States)

    Yu, Changhai; Deng, Aihua; Tian, Ye; Li, Wentao; Wang, Wentao; Zhang, Zhijun; Qi, Rong; Wang, Cheng; Liu, Jiansheng

    2016-08-01

    A scheme of using two-color laser pulses for hole boring into overdense plasma as well as energy transfer into electron and ion beams has been studied using particle-in-cell simulations. Following an ultra-short ultra-intense hole-boring laser pulse with a short central wavelength in extreme ultra-violet range, the main infrared driving laser pulse can be guided in the hollow channel preformed by the former laser and propagate much deeper into an overdense plasma, as compared to the case using the infrared laser only. In addition to efficiently transferring the main driving laser energy into energetic electrons and ions generation deep inside the overdense plasma, the ion beam divergence can be greatly reduced. The results might be beneficial for the fast ignition concept of inertial confinement fusion.

  7. THz wave emission from argon in two-color laser field

    Institute of Scientific and Technical Information of China (English)

    杜玲玲; 赵松峰; 周效信; 赵增秀

    2015-01-01

    Terahertz (THz) wave emission from argon atom in a two-color laser pulses is studied numerically by solving the one-dimensional (1D) time-dependent Schr ¨odinger equation. The THz spectra we obtained include both discontinuous and continuum ones. By using the special basis functions that we previously proposed, our analysis points out that the discontinuous and continuum parts are contributed by bound–bound and continuum–continuum transition of atomic energy levels. Although the atomic wave function is strongly dressed during the interaction with laser fields, our identification for the discontinuous part of the THz wave shows that the transition between highly excited bound states can still be well described by the field-free basis function in the tunneling ionization regime.

  8. BEC-BCS crossover in a cold and magnetized two color NJL model

    CERN Document Server

    Duarte, Dyana C; Farias, R L S; Manso, Pedro H A; Ramos, Rudnei O; Scoccola, N N

    2016-01-01

    The BEC-BCS crossover for a NJL model with diquark interactions is studied in the presence of an external magnetic field. Particular attention is paid to different regularization schemes used in the literature. A thorough comparison of results is performed for the case of a cold and magnetized two-color NJL model. According to our results, the critical chemical potential for the BEC transition exhibits a clear inverse magnetic catalysis effect for magnetic fields in the range $ 1 \\lesssim eB/m_\\pi^2 \\lesssim 20 $. As for the BEC-BCS crossover, the corresponding critical chemical potential is very weakly sensitive to magnetic fields up to $eB \\sim 9\\ m_\\pi^2$, showing a much smaller inverse magnetic catalysis as compared to the BEC transition, and displays a strong magnetic catalysis from this point on.

  9. Two-color in vivo imaging of photoreceptor apoptosis and development in Drosophila.

    Science.gov (United States)

    Gambis, Alexis; Dourlen, Pierre; Steller, Hermann; Mollereau, Bertrand

    2011-03-01

    We report a new two-color fluorescent imaging system to visualize the mosaic adult photoreceptor neurons (PRs) in real-time. Using this method, we examined a collection of 434 mutants and identified genes required for PR survival, planar cell polarity (PCP), patterning and differentiation. We could track the progression of PR degeneration in living flies. By introducing the expression of p35, a caspase inhibitor, we found mutations that specifically activate caspase-dependent death. Moreover, we showed that grh is required in R3 for correct PCP establishment. The "Tomato/GFP-FLP/FRT" method allows high-throughput, rapid and precise identification of survival and developmental pathways in living adult PRs at single-cell resolution.

  10. Frequency doubler and two-color mode of operation at free electron laser FLASH2

    Science.gov (United States)

    Kuhlmann, M.; Schneidmiller, E. A.; Yurkov, M. V.

    2017-06-01

    We report on the results of the first operation of a frequency doubler at FLASH2. The scheme uses the feature of the variable gap of the undulator. Undulator is divided in two parts. The second part of the undulator is tuned to the double frequency of the first part. Modulated electron beam enters the second part of the undulator and generates radiation at the 2nd harmonic. Depending on a balance between the gain of undulator sections, frequency doubler allows operation in a two-color mode and operation at shorter wavelengths with respect to standard SASE scheme. The shortest wavelength of 3.1 nm (photon energy 400 eV) has been achieved at FLASH2 with frequency doubler scheme, which is significantly below the design value for the standard SASE option.

  11. P1-9: Relationship between Color Shifts in Land's Two-Color Method and Higher- and Lower-Level Visual Information

    Directory of Open Access Journals (Sweden)

    Saki Iwaida

    2012-10-01

    Full Text Available Land's two-color method gives rise to apparent full-color perception, even though only two colors (e.g., red and gray are used. Previous studies indicate that chromatic adaptation, color memory, and inductive effects contribute to the shifts of color perception from real to illusory colors (e.g., Kuriki, 2006 Vision Research 46 3055–3066. This paper investigates the relationship between the color shifts induced by Land images and the skewness of the luminance histogram. In Experiment 1, several Land images are created based on a yellow ball, and the magnitude of the color shifts of the images are measured. The results of Experiment 1 show a significant correlation between the magnitude of the color shifts and skewness, suggesting that skewness is critical for the color shifts. In Experiment 2, we test the hypothesis that color shifts depends on just skewness; the color shifts should be invariant even if the Land images are scrambled. However, the results of Experiment 2 demonstrate that scrambled Land images exhibit less intense color shifts, suggesting that color shifts are determined by the object's overall shape or surface gloss, not just skewness. Taken together, we conclude that both low-level visual processes, such as those associated with luminance histogram skew, and high-level cognitive functions, such as object interpretation or understanding of surface gloss, are involved in the color shift of Land images.

  12. 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.

  13. 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.

  14. Two-color two-photon excited fluorescence of indole: Determination of wavelength-dependent molecular parameters

    Energy Technology Data Exchange (ETDEWEB)

    Herbrich, Sebastian; Al-Hadhuri, Tawfik; Gericke, Karl-Heinz, E-mail: k.Gericke@tu-bs.de [Institut für Physikalische und Theoretische Chemie, TU Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig (Germany); Shternin, Peter S., E-mail: pshternin@gmail.com; Vasyutinskii, Oleg S., E-mail: osv@pms.ioffe.ru [Ioffe Institute, Politekhnicheskaya 26, 194021 St. Petersburg (Russian Federation); St. Petersburg Polytechnic University, Politekhnicheskaya 29, St. Petersburg 195251 (Russian Federation); Smolin, Andrey G. [Ioffe Institute, Politekhnicheskaya 26, 194021 St. Petersburg (Russian Federation)

    2015-01-14

    We present a detailed study of two-color two-photon excited fluorescence in indole dissolved in propylene glycol. Femtosecond excitation pulses at effective wavelengths from 268 to 293.33 nm were used to populate the two lowest indole excited states {sup 1}L{sub a} and {sup 1}L{sub b} and polarized fluorescence was then detected. All seven molecular parameters and the two-photon polarization ratio Ω containing information on two-photon absorption dynamics, molecular lifetime τ{sub f}, and rotation correlation time τ{sub rot} have been determined from experiment and analyzed as a function of the excitation wavelength. The analysis of the experimental data has shown that {sup 1}L{sub b}–{sup 1}L{sub a} inversion occurred under the conditions of our experiment. The two-photon absorption predominantly populated the {sup 1}L{sub a} state at all excitation wavelengths but in the 287–289 nm area which contained an absorption hump of the {sup 1}L{sub b} state 0-0 origin. The components of the two-photon excitation tensor S were analyzed giving important information on the principal tensor axes and absorption symmetry. The results obtained are in a good agreement with the results reported by other groups. The lifetime τ{sub f} and the rotation correlation time τ{sub rot} showed no explicit dependence on the effective excitation wavelength. Their calculated weighted average values were found to be τ{sub f} = 3.83 ± 0.14 ns and τ{sub rot} = 0.74 ± 0.06 ns.

  15. Laser-induced periodic surface structures on fused silica upon cross-polarized two-color double-fs-pulse irradiation

    Science.gov (United States)

    Höhm, S.; Herzlieb, M.; Rosenfeld, A.; Krüger, J.; Bonse, J.

    2015-05-01

    The dynamics of the formation of laser-induced periodic surface structures (LIPSS) on fused silica upon irradiation with linearly polarized fs-laser pulses (50 fs pulse duration) is studied by cross-polarized two-color double-fs-pulse experiments. In order to analyze the relevance of temporally distributed energy deposition in the early stage of LIPSS formation, a Mach-Zehnder interferometer was used for generating multiple double-pulse sequences at two different wavelengths (400 and 800 nm). The inter-pulse delay between the individual cross-polarized pulses of each sequence was systematically varied in the sub-ps range and the resulting LIPSS morphologies were characterized by scanning electron microscopy. It is found that the polarization of the first laser pulse arriving to the surface determines the orientation and the periodicity of the LIPSS. These two-color experiments further confirm the importance of the ultrafast energy deposition to the silica surface for LIPSS formation, particularly by the first laser pulse of each sequence. The second laser pulse subsequently reinforces the previously seeded spatial LIPSS characteristics (period, orientation).

  16. Frequency modulation of high-order harmonic generation in an orthogonally polarized two-color laser field.

    Science.gov (United States)

    Li, Guicun; Zheng, Yinghui; Ge, Xiaochun; Zeng, Zhinan; Li, Ruxin

    2016-08-08

    We have experimentally investigated the frequency modulation of high-order harmonics in an orthogonally polarized two-color laser field consisting of a mid-infrared 1800nm fundamental pulse and its second harmonic pulse. It is demonstrated that the high harmonic spectra can be fine-tuned as we slightly change the relative delay of the two-color laser pulses. By analyzing the relative frequency shift of each harmonic at different two-color delays, the nonadiabatic spectral shift induced by the rapid variation of the intensity-dependent intrinsic dipole phase can be distinguished from the blueshift induced by the change of the refractive index during self-phase modulation (SPM). Our comprehensive analysis shows that the frequency modulation pattern is a reflection of the average emission time of high-order harmonic generation (HHG), thus offering a simple method to fine-tune the spectra of the harmonics on a sub-cycle time scale.

  17. Two-color infrared FEL facility employing a 250-MeV linac injector of Saga synchrotron light source

    CERN Document Server

    Tomimasu, T; Koga, N; Hashiguchi, Y; Ochiai, Y; Ishibashi, M

    2001-01-01

    A two-color infrared free electron laser (FEL) facility is proposed. This FEL facility will employ a new 250-MeV linac injector of the Saga synchrotron light source (SLS). The linac has two operation modes: short macropulse mode of 1 mu s at 250 MeV is for injection to a 1.4-GeV storage ring and long macropulse mode of 13 mu s at 40 MeV is for the two-color FEL facility. The two-color FEL uses a single electron beam and simultaneously provides both infrared (IR) and far-IR laser pulses for pump-probe studies of quantum-well structures and studying vibrational relaxation of molecules. The Saga SLS will be operated in 2004 to promote material science, bio-medical and industrial applications in Kyushu.

  18. Two-color temporal focusing multiphoton excitation imaging with tunable-wavelength excitation

    Science.gov (United States)

    Lien, Chi-Hsiang; Abrigo, Gerald; Chen, Pei-Hsuan; Chien, Fan-Ching

    2017-02-01

    Wavelength tunable temporal focusing multiphoton excitation microscopy (TFMPEM) is conducted to visualize optical sectioning images of multiple fluorophore-labeled specimens through the optimal two-photon excitation (TPE) of each type of fluorophore. The tunable range of excitation wavelength was determined by the groove density of the grating, the diffraction angle, the focal length of lenses, and the shifting distance of the first lens in the beam expander. Based on a consideration of the trade-off between the tunable-wavelength range and axial resolution of temporal focusing multiphoton excitation imaging, the presented system demonstrated a tunable-wavelength range from 770 to 920 nm using a diffraction grating with groove density of 830 lines/mm. TPE fluorescence imaging examination of a fluorescent thin film indicated that the width of the axial confined excitation was 3.0±0.7 μm and the shifting distance of the temporal focal plane was less than 0.95 μm within the presented wavelength tunable range. Fast different wavelength excitation and three-dimensionally rendered imaging of Hela cell mitochondria and cytoskeletons and mouse muscle fibers were demonstrated. Significantly, the proposed system can improve the quality of two-color TFMPEM images through different excitation wavelengths to obtain higher-quality fluorescent signals in multiple-fluorophore measurements.

  19. Enhanced sensitivity in H photofragment detection by two-color reduced-Doppler ion imaging

    Energy Technology Data Exchange (ETDEWEB)

    Epshtein, Michael; Portnov, Alexander; Kupfer, Rotem; Rosenwaks, Salman; Bar, Ilana, E-mail: ibar@bgu.ac.il [Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel)

    2013-11-14

    Two-color reduced-Doppler (TCRD) and one-color velocity map imaging (VMI) were used for probing H atom photofragments resulting from the ∼243.1 nm photodissociation of pyrrole. The velocity components of the H photofragments were probed by employing two counterpropagating beams at close and fixed wavelengths of 243.15 and 243.12 nm in TCRD and a single beam at ∼243.1 nm, scanned across the Doppler profile in VMI. The TCRD imaging enabled probing of the entire velocity distribution in a single pulse, resulting in enhanced ionization efficiency, as well as improved sensitivity and signal-to-noise ratio. These advantages were utilized for studying the pyrrole photodissociation at ∼243.1 and 225 nm, where the latter wavelength provided only a slight increase in the H yield over the self-signal from the probe beams. The TCRD imaging enabled obtaining high quality H{sup +} images, even for the low H photofragment yields formed in the 225 nm photolysis process, and allowed determining the velocity distributions and anisotropy parameters and getting insight into pyrrole photodissociation.

  20. Phase diagram of dense two-color QCD within lattice simulations

    Science.gov (United States)

    Braguta, V. V.; Ilgenfritz, E.-M.; Kotov, A. Yu.; Molochkov, A. V.; Nikolaev, A. A.

    2017-03-01

    We present the results of a low-temperature scan of the phase diagram of dense two-color QCD with Nf = 2 quarks. The study is conducted using lattice simulation with rooted staggered quarks. At small chemical potential we observe the hadronic phase, where the theory is in a confining state, chiral symmetry is broken, the baryon density is zero and there is no diquark condensate. At the critical point μ = mπ/2 we observe the expected second order transition to Bose-Einstein condensation of scalar diquarks. In this phase the system is still in confinement in conjunction with nonzero baryon density, but the chiral symmetry is restored in the chiral limit. We have also found that in the first two phases the system is well described by chiral perturbation theory. For larger values of the chemical potential the system turns into another phase, where the relevant degrees of freedom are fermions residing inside the Fermi sphere, and the diquark condensation takes place on the Fermi surface. In this phase the system is still in confinement, chiral symmetry is restored and the system is very similar to the quarkyonic state predicted by SU(Nc) theory at large Nc.

  1. Two-color detector: Mercury-cadmium-telluride as a terahertz and infrared detector

    Energy Technology Data Exchange (ETDEWEB)

    Sizov, F.; Zabudsky, V.; Petryakov, V.; Golenkov, A.; Andreyeva, K.; Tsybrii, Z. [Institute of Semiconductor Physics, 03028 Kiev (Ukraine); Dvoretskii, S. [Institute of Semiconductor Physics of SB RAS, 630090 Novosibirsk (Russian Federation)

    2015-02-23

    In this paper, issues associated with the development of infrared (IR) and terahertz (THz) radiation detectors based on HgCdTe are discussed. Two-color un-cooled and cooled to 78 K narrow-gap mercury-cadmium-telluride semiconductor thin layers with antennas were considered both as sub-THz (sub-THz) direct detection bolometers and 3–10 μm IR photoconductors. The noise equivalent power (NEP) for one of the detectors studied at ν ≈ 140 GHz reaches NEP{sub 300 K} ≈ 4.5 × 10{sup −10} W/Hz{sup 1/2} and NEP{sub 78 K} ≈ 5 × 10{sup −9} W/Hz{sup 1/2}. The same detector used as an IR photoconductor showed the responsivity at temperatures T = 78 K and 300 K with signal-to-noise ratio S/N ≈ 750 and 50, respectively, under illumination by using IR monochromator and globar as a thermal source.

  2. Study of the phase diagram of dense two-color QCD within lattice simulation

    CERN Document Server

    Braguta, V V; Kotov, A Yu; Molochkov, A V; Nikolaev, A A

    2016-01-01

    In this paper we carry out a low-temperature scan of the phase diagram of dense two-color QCD with $N_f=2$ quarks. The study is conducted using lattice simulation with rooted staggered quarks. At small chemical potential we observe the hadronic phase, where the theory is in a confining state, chiral symmetry is broken, the baryon density is zero and there is no diquark condensate. At the critical point $\\mu = m_{\\pi}/2$ we observe the expected second order transition to Bose-Einstein condensation of scalar diquarks. In this phase the system is still in confinement in conjunction with nonzero baryon density, but the chiral symmetry is restored in the chiral limit. We have also found that in the first two phases the system is well described by chiral perturbation theory. For larger values of the chemical potential the system turns into another phase, where the relevant degrees of freedom are fermions residing inside the Fermi sphere, and the diquark condensation takes place on the Fermi surface. In this phase t...

  3. Radiation damage free two-color X-ray ghost diffraction with atomic resolution

    CERN Document Server

    Li, Zheng; Chapman, Henry; Shih, Yanhua

    2015-01-01

    The X-ray free electron lasers (XFEL) can enable diffractive structural determination of protein crystals or single molecules that are too small and radiation-sensitive for conventional X-ray analysis. However the electronic form factor could have been modified during the ultrashort X-ray pulse due to photoionization and electron cascade caused by the intense X-ray pulse. For general X-ray imaging techniques, to minimize radiation damage effect is of major concern to ensure faithful reconstruction of the structure. Here we show that a radiation damage free diffraction can be achieved with an atomic spatial resolution, by using X-ray parametric down-conversion (PDC), and two-color biphoton ghost imaging. We illustrate that formation of the diffractive patterns satisfies a condition analogous to the Bragg equation, with a resolution that could be as fine as the lattice length scale of several Angstrom. Because the samples are illuminated by the optical photons of low energy, they can be free of radiation damage...

  4. 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

  5. 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

  6. The Impact of Photobleaching on Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Marcel von der Haar

    2015-09-01

    Full Text Available DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner’s laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube’s voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results.

  7. A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments

    Directory of Open Access Journals (Sweden)

    Umbach David M

    2009-12-01

    Full Text Available Abstract Background For gene expression data obtained from a time-course microarray experiment, Liu et al. 1 developed a new algorithm for clustering genes with similar expression profiles over time. Performance of their proposal was compared with three other methods including the order-restricted inference based methodology of Peddada et al. 23. In this note we point out several inaccuracies in Liu et al. 1 and conclude that the order-restricted inference based methodology of Peddada et al. (programmed in the software ORIOGEN indeed operates at the desired nominal Type 1 error level, an important feature of a statistical decision rule, while being computationally substantially faster than indicated by Liu et al. 1. Results Application of ORIOGEN to the well-known breast cancer cell line data of Lobenhofer et al. 4 revealed that ORIOGEN software took only 21 minutes to run (using 100,000 bootstraps with p = 0.0025, substantially faster than the 72 hours found by Liu et al. 1 using Matlab. Also, based on a data simulated according to the model and parameters of simulation 1 (σ2 = 1, M = 5 in 1 we found that ORIOGEN took less than 30 seconds to run in stark contrast to Liu et al. who reported that their implementation of the same algorithm in R took 2979.29 seconds. Furthermore, for the simulation studies reported in 1, unlike the claims made by Liu et al. 1, ORIOGEN always maintained the desired false positive rate. According to Figure three in Liu et al. 1 their algorithm had a false positive rate ranging approximately from 0.20 to 0.70 for the scenarios that they simulated. Conclusions Our comparisons of run times indicate that the implementations of ORIOGEN's algorithm in Matlab and R by Liu et al. 1 is inefficient compared to the publicly available JAVA implementation. Our results on the false positive rate of ORIOGEN suggest some error in Figure three of Liu et al. 1, perhaps due to a programming error.

  8. Phase diagram of two-color QCD in a Dyson-Schwinger approach

    Energy Technology Data Exchange (ETDEWEB)

    Buescher, Pascal Joachim

    2014-04-28

    We investigate two-color QCD with N{sub f}=2 at finite temperatures and chemical potentials using a Dyson-Schwinger approach. We employ two different truncations for the quark loop in the gluon DSE: one based on the Hard-Dense/Hard-Thermal Loop (HDTL) approximation of the quark loop and one based on the back-coupling of the full, self-consistent quark propagator (SCQL). We compare results for the different truncations with each other as well as with other approaches. As expected, we find a phase dominated by the condensation of quark-quark pairs. This diquark condensation phase overshadows the critical end point and first-order phase transition which one finds if diquark condensation is neglected. The phase transition from the phase without diquark condensation to the diquark-condensation phase is of second order. We observe that the dressing with massless quarks in the HDTL approximation leads to a significant violation of the Silver Blaze property and to a too small diquark condensate. The SCQL truncation, on the other hand, is found to reproduce all expected features of the μ-dependent quark condensates. Moreover, with parameters adapted to the situation in other approaches, we also find good to very good agreement with model and lattice calculations in all quark quantities. We find indictions that the physics in recent lattice calculations is likely to be driven solely by the explicit chiral symmetry breaking. Discrepancies w.r.t. the lattice are, however, observed in two quantities that are very sensitive to the screening of the gluon propagator, the dressed gluon propagator itself and the phase-transition line at high temperatures.

  9. MarC-V: a spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments.

    Science.gov (United States)

    Schageman, J J; Basit, M; Gallardo, T D; Garner, H R; Shohet, R V

    2002-02-01

    The comprehensive analysis and visualization of data extracted from cDNA microarrays can be a time-consuming and error-prone process that becomes increasingly tedious with increased number of gene elements on a particular microarray. With the increasingly large number of gene elements on today's microarrays, analysis tools must be developed to meet this challenge. Here, we present MarC-V, a Microsoft Excel spreadsheet tool with Visual Basic macros to automate much of the visualization and calculation involved in the analysis process while providing the familiarity and flexibility of Excel. Automated features of this tool include (i) lower-bound thresholding, (ii) data normalization, (iii) generation of ratio frequency distribution plots, (iv) generation of scatter plots color-coded by expression level, (v) ratio scoring based on intensity measurements, (vi) filtering of data based on expression level or specific gene interests, and (vii) exporting data for subsequent multi-array analysis. MarC-V also has an importing function included for GenePix results (GPR) raw data files.

  10. Pseudo-rephasing and pseudo-free-induction-decay mechanism in two-color three-pulse photon echo of a binary system.

    Science.gov (United States)

    Dong, Hui; Ryu, Ian Seungwan; Fleming, Graham R

    2013-12-27

    We investigate the two-color three-pulse photon echo peak shift in a (left-right) binary system, where each component consists of a heterodimer. On the basis of the model, we find that the effect of the excitonic asymmetry between two components leads to an additional factor in the peak shift. A pseudo-rephasing and pseudo-free-induction-decay mechanism is proposed to explain the resultant negative peak shift, when the differences between the two left/right components have the opposite sign. In such a case, estimates of the electronic coupling strength via two- and one-color peak shift experiments lead to an underestimate of the coupling magnitude.

  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. Ionization in Orthogonal Two-Color Laser Fields - Origin and Phase Dependence of Trajectory-Resolved Coulomb Effects

    CERN Document Server

    Richter, Martin; Schöffler, Markus; Jahnke, Till; Schmidt, Lothar Ph H; Dörner, Reinhard

    2016-01-01

    We report on electron momentum distributions from single ionization of Ar in strong orthogonally polarized two-color (OTC) laser fields measured with the COLTRIMS technique. We study the effect of Coulomb focusing whose signature is a cusp like feature in the center of the electron momentum spectrum. While the direct electrons show the expected strong dependence on the phase between the two colors, surprisingly the Coulomb focused structure is almost not influenced by the weak second harmonic streaking field. This effect is explained by the use of a CTMC simulation which describes the tunneled electron wave packet in terms of classical trajectories under the influence of the combined Coulomb- and OTC laser field. We find a subtle interplay between the initial momentum of the electron upon tunneling, the ionization phase and the action of the Coulomb field that makes the Coulomb focused part of the momentum spectrum apparently insensitive to the weaker streaking field.

  13. Matching-based fresh-slice method for generating two-color x-ray free-electron lasers

    Directory of Open Access Journals (Sweden)

    Weilun Qin

    2017-09-01

    Full Text Available Two-color high intensity x-ray free-electron lasers (FELs provide powerful tools for probing ultrafast dynamic systems. A novel concept of realizing fresh-slice two-color lasing through slice-dependent transverse mismatch has been proposed by one of the authors [Y. Chao, SLAC Report No. SLAC-PUB-16935, 2016]. In this paper we present a feasible example following this concept based on the Linac Coherent Light Source parameters. Time-dependent mismatch along the bunch is generated by a passive dechirper module and controlled by downstream matching sections, enabling FEL lasing at different wavelength with a split undulator configuration. Simulations for soft x-ray FELs show that tens of gigawatts pulses with femtosecond duration can be generated.

  14. Channel-resolved subcycle interferences of electron wave packets emitted from H$_2$ in two-color laser fields

    CERN Document Server

    Xie, Xinhua; Kartashov, Daniil; Zhang, Li; Baltuška, Andrius; Kitzler, Markus

    2016-01-01

    We report on the observation of subcycle interferences of electron wave packets released during the strong field ionization of H$_2$ with cycle-shaped two-color laser fields. With a reaction microscope, channel-resolved photoelectron momentum distribution are obtained for different final products originating from single ionization of H$_2$. Our results show that the subcycle interference structures of electron wave packet are very sensitive to the cycle-shape of the two-color laser field. The reason is that the ionization time within an optical cycle is determined by the cycle-shape of the laser field. The subcycle interference structures can be further used to get the subcycle dynamics of molecules during strong field interaction.

  15. Density profiles of small Dirac operator eigenvalues for two color QCD at nonzero chemical potential compared to matrix models

    Energy Technology Data Exchange (ETDEWEB)

    Akemann, Gernot [Service de Physique Theorique, CEA/DSM/SPhT Saclay, Unite associee CNRS/SPM/URA 2306, F-91191 Gif-sur-Yvette Cedex (France); Department of Mathematical Sciences, Brunel University West London, Uxbridge, UB8 3PH (United Kingdom); Bittner, Elmar [Institut fuer Theoretische Physik, Universitaet Leipzig, Augustplatz 10/11, D-04109 Leipzig (Germany); Lombardo, Maria-Paola [INFN-Laboratori Nazionali di Frascati, I-00044 Frascati (Italy); Markum, Harald [Atominstitut, Technische Universitaet Wien, A-1040 Vienna (Austria); Pullirsch, Rainer [Atominstitut, Technische Universitaet Wien, A-1040 Vienna (Austria)

    2005-03-15

    We investigate the eigenvalue spectrum of the staggered Dirac matrix in two color QCD at finite chemical potential. The profiles of complex eigenvalues close to the origin are compared to a complex generalization of the chiral Gaussian Symplectic Ensemble, confirming its predictions for weak and strong non-Hermiticity. They differ from the QCD symmetry class with three colors by a level repulsion from both the real and imaginary axis.

  16. Improved treatment of the turning point in tunnel ionization of atoms in a low-frequency two color laser field

    Science.gov (United States)

    Petrović, V. M.; Miladinović, T. B.

    2016-12-01

    The tunneling photoionization rate for a two color (bichromatic) field consisting of coherent superposition of the fundamental laser field frequency ω and its second harmonic with frequency 2ω , was studied theoretically within the framework of the adiabatic Landau-Dykhne approach. Analytical expressions were derived for the case of fixed specified values of relative phase shift, \\varphi =0 between the harmonics of the incident bichromatic field.

  17. Generation of an isolated sub-30 attosecond pulse in a two-color laser field and a static electric field

    Institute of Scientific and Technical Information of China (English)

    Zhang Gang-Tai; Bai Ting-Ting; Zhang Mei-Guang

    2012-01-01

    We theoretically investigate high-order harmonic generation(HHG)from a helium ion model in a two-color laser field,which is synthesized by a fundamental pulse and its second harmonic pulse.It is shown that a supercontinuum spectrum can be generated in the two-color field.However,the spectral intensity is very low,limiting the application of the generated attosecond(as)pulse.By adding a static electric field to the synthesized two-color field,not only is the ionization yield of electrons contributing to the harmonic emission remarkably increased,but also the quantum paths of the HHG can be significantly modulated.As a result,the extension and enhancement of the supercontinuum spectrum are achieved,producing an intense isolated 26-as pulse with a bandwidth of about 170.5 eV.In particular,we also analyse the influence of the laser parameters on the ultrabroad supercontinuum spectrum and isolated sub-30-as pulse generation.

  18. Microarray Inspector: tissue cross contamination detection tool for microarray data.

    Science.gov (United States)

    Stępniak, Piotr; Maycock, Matthew; Wojdan, Konrad; Markowska, Monika; Perun, Serhiy; Srivastava, Aashish; Wyrwicz, Lucjan S; Świrski, Konrad

    2013-01-01

    Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.

  19. 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.

  20. 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

  1. Prominent feature selection of microarray data

    Institute of Scientific and Technical Information of China (English)

    Yihui Liu

    2009-01-01

    For wavelet transform, a set of orthogonal wavelet basis aims to detect the localized changing features contained in microarray data. In this research, we investigate the performance of the selected wavelet features based on wavelet detail coefficients at the second level and the third level. The genetic algorithm is performed to optimize wavelet detail coefficients to select the best discriminant features. Exper-iments are carried out on four microarray datasets to evaluate the performance of classification. Experimental results prove that wavelet features optimized from detail coefficients efficiently characterize the differences between normal tissues and cancer tissues.

  2. Two-color ghost interference with photon pairs generated in hot atoms

    Directory of Open Access Journals (Sweden)

    Dong-Sheng Ding

    2012-09-01

    Full Text Available We report on an experimental observation of a two-photon ghost interference experiment. A distinguishing feature of our experiment is that the photons are generated via a non-degenerated spontaneous four-wave mixing process in a hot atomic ensemble; therefore the photon has narrow bandwidth. Besides, there is a large difference in frequency between two photons in a pair. Our works may be important to achieve more secure, large transmission capacity long-distance quantum communication.

  3. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  4. 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.

  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. Development of a novel two color tracer perfusion technique for the hydrodynamic study of aqueous outflow in bovine eyes

    Institute of Scientific and Technical Information of China (English)

    ZHU Jing-yin; YE Wen; GONG Hai-yan

    2010-01-01

    Background Elevation of intraocular pressure is usually associated with primary open angle glaucoma and caused by increased outflow resistance. A two-color fluorescent tracer technique was developed to investigate the hydrodynamics of aqueous humor outflow with changing intraocular pressure within the same eye, to better understand the relationship between outflow facility and effective filtration area. Methods Eighteen enucleated bovine eyes were first perfused at 30 mmHg with Dulbecco's phosphate-buffered saline containing 5.5 mmol/L D-glucose. After a stable baseline facility, red fluorescent microspheres (0.5 μm, 0.002% v/v) were exchanged and perfused. Eyes in the one-color control group (n=6) were immediately perfused with fixative. In the experimental group (n=6), eyes were perfused with green tracer after intraocular pressure reduced to 7 mmHg, while in the two-color control group (n=6), eyes were perfused with green tracer with intraocular pressure remaining at 30 mmHg. All 12 eyes were then perfusion-fixed. Outflow facility was continuously recorded in all eyes. Confocal images were taken along the inner wall of the aqueous plexus and the percent of the effective filtration length (PEFL; length of inner wall exhibiting tracer labeling/total length of inner wall) was measured. The relationships between outflow facility and PEFL were analyzed statistically. Results No significant differences were found in baseline facilities (ulmin~(-1)·mmHg~(-1)) among the three groups (the experimental group: 0.93 0.12; the two-color control group: 0.90 0.19; the one-color control group: 0.98 0.13). In the experimental group, the outflow facility was significantly higher at 7 mmHg (4.29±1.01) than that at 30 mmHg (1.90±0.67, P <0.001), which corresponded to a significant increase in the PEFL at 7 mmHg (54.70±8.42) from that at 30 mmHg ((11.76±4.56)%, P<0.001). The PEFL labeled by red fluorescent microspheres in the experimental group ((11.76±4.56)%) showed no

  7. 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.

  8. Stimulated emission pumping of NH in flames by using two-color resonant four-wave mixing

    Energy Technology Data Exchange (ETDEWEB)

    Radi, P.P.; Frey, H.M.; Mischler, B.; Tzannis, A.P.; Beaud, P.; Gerber, T. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    In this work we examine the analytical potential of two-color resonant four-wave mixing for the determination and characterization of trace elements in a combustion environment. Experimental results for NH in flames at atmospheric pressure are presented. The selectivity of the technique is used to simplify the Q-branch region of the (0-0)A{sup 3}{Pi}-X{sup 3}{Sigma} vibronic transition of NH. In addition, we demonstrate that the technique is sensitive to state changing collisions. (author) 2 figs., 5 refs.

  9. Enhanced harmonic generation and wave-mixing via two-color multiphoton excitation of atoms/molecules

    CERN Document Server

    Avetissian, H K; Mkrtchian, G F

    2016-01-01

    We consider harmonics generation and wave-mixing by two-color multi photon resonant excitation of three-level atoms/molecules in strong laser fields. The coherent part of the spectra corresponding to multicolor harmonics generation is investigated. The obtained analytical results on the basis of generalized rotating wave approximation are in a good agreement with numerical calculations. The results applied to the hydrogen atom and homonuclear diatomic molecular ion show that one can achieve efficient generation of moderately high multicolor harmonics via multiphoton resonant excitation by appropriate laser pulses.

  10. Efficient generation of isolated attosecond pulses with high beam-quality by two-color Bessel-Gauss beams

    CERN Document Server

    Wang, Zhe; Zhang, Qingbin; Wang, Shaoyi; Lu, Peixiang

    2011-01-01

    The generation of isolated attosecond pulses with high efficiency and high beam quality is essential for attosec- ond spectroscopy. We numerically investigate the supercontinuum generation in a neutral rare-gas medium driven by a two-color Bessel-Gauss beam. The results show that an efficient smooth supercontinuum in the plateau is obtained after propagation, and the spatial profile of the generated attosecond pulse is Gaussian-like with the divergence angle of 0.1 degree in the far field. This bright source with high beam quality is beneficial for detecting and controlling the microscopic processes on attosecond time scale.

  11. Terahertz radiation driven by two-color laser pulses at near-relativistic intensities: Competition between photoionization and wakefield effects.

    Science.gov (United States)

    González de Alaiza Martínez, P; Davoine, X; Debayle, A; Gremillet, L; Bergé, L

    2016-06-03

    We numerically investigate terahertz (THz) pulse generation by linearly-polarized, two-color femtosecond laser pulses in highly-ionized argon. Major processes consist of tunneling photoionization and ponderomotive forces associated with transverse and longitudinal field excitations. By means of two-dimensional particle-in-cell (PIC) simulations, we reveal the importance of photocurrent mechanisms besides transverse and longitudinal plasma waves for laser intensities >10(15) W/cm(2). We demonstrate the following. (i) With two-color pulses, photoionization prevails in the generation of GV/m THz fields up to 10(17) W/cm(2) laser intensities and suddenly loses efficiency near the relativistic threshold, as the outermost electron shell of ionized Ar atoms has been fully depleted. (ii) PIC results can be explained by a one-dimensional Maxwell-fluid model and its semi-analytical solutions, offering the first unified description of the main THz sources created in plasmas. (iii) The THz power emitted outside the plasma channel mostly originates from the transverse currents.

  12. Simulation of Far-Field Superresolution Fluorescence Imaging with Two-Color One-Photon Excitation of Reversible Photoactivatable Protein

    Institute of Scientific and Technical Information of China (English)

    WANG Chen; QIAO Ling-Ling; MAO Zheng-Le

    2011-01-01

    We propose to achieve far-field super-resolution imaging by using offset two-color one-photon (2C1P) excitation of reversible photoactivatable fluorescence proteins. Due to the distinctive photoswitching performance of the proteins, such as dronpa, the fluorescence emission will only come from the overlapped region of activation beam and excitation beam. The analysis solution of rate equation shows that the resolution of offset 2C1P microscope is "engineered" by laser power of excitation and activation beams and the power ratio between them. Superior lateral and transverse resolution is theoretically demonstrated compared with conventional fluorescence scanning microscopy.%@@ We propose to achieve far-field super-resolution imaging by using offset two-color one-photon(2C1P) excitation of reversible photoactivatable fluorescence proteins.Due to the distinctive photoswitching performance of the proteins,such as dronpa,the fluorescence emission will only come from the overlapped region of activation beam and excitation beam.The analysis solution of rate equation shows that the resolution of offset 2C1P microscope is "engineered" by laser power of excitation and activation beams and the power ratio between them.Superior lateral and transverse resolution is theoretically demonstrated compared with conventional fluorescence scanning microscopy.

  13. Power dependence of terahertz carrier frequency in a plasma-based two-color generation process

    Science.gov (United States)

    Zhao, Ji; Zhang, Liang-Liang; Luo, Yi-Man; Wu, Tong; Zhang, Cun-Lin; Zhao, Yue-Jin

    2014-12-01

    We conduct a frequency spectrum experiment to investigate terahertz (THz) emissions from laser-induced air plasma under different laser incident powers. The frequency spectra are measured using both air-biased-coherent detection and a Michelson interferometer. The red-shift of the THz pulse carrier frequency is observed as a response to increased pump power. These phenomena are related to plasma collisions and can be explained by the plasma collision model. Based on these findings, it is apparent that the tuning of the THz carrier frequency can be achieved through regulation of the pump beam.

  14. Superluminal two-color light in a multiple Raman gain medium

    KAUST Repository

    Kudriašov, V.

    2014-09-17

    We investigate theoretically the formation of two-component light with superluminal group velocity in a medium controlled by four Raman pump fields. In such an optical scheme only a particular combination of the probe fields is coupled to the matter and exhibits superluminal propagation; the orthogonal combination is uncoupled. The individual probe fields do not have a definite group velocity in the medium. Calculations demonstrate that this superluminal component experiences an envelope advancement in the medium with respect to the propagation in vacuum.

  15. MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs

    Directory of Open Access Journals (Sweden)

    Ferhatosmanoglu Nilgun

    2009-09-01

    Full Text Available Abstract Background Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided. Conclusion A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.

  16. Spatially resolved two-color diffusion measurements in human skin applied to transdermal liposome penetration.

    Science.gov (United States)

    Brewer, Jonathan; Bloksgaard, Maria; Kubiak, Jakub; Sørensen, Jens Ahm; Bagatolli, Luis A

    2013-05-01

    A multiphoton excitation-based fluorescence fluctuation spectroscopy method, Raster image correlation spectroscopy (RICS), was used to measure the local diffusion coefficients of distinct model fluorescent substances in excised human skin. In combination with structural information obtained by multiphoton excitation fluorescence microscopy imaging, the acquired diffusion information was processed to construct spatially resolved diffusion maps at different depths of the stratum corneum (SC). Experiments using amphiphilic and hydrophilic fluorescently labeled molecules show that their diffusion in SC is very heterogeneous on a microscopic scale. This diffusion-based strategy was further exploited to investigate the integrity of liposomes during transdermal penetration. Specifically, the diffusion of dual-color fluorescently labeled liposomes--containing an amphiphilic fluorophore in the lipid bilayer and a hydrophilic fluorophore encapsulated in the liposome lumen--was measured using cross-correlation RICS. This type of experiment allows discrimination between separate (uncorrelated) and joint (correlated) diffusion of the two different fluorescent probes, giving information about liposome integrity. Independent of the liposome composition (phospholipids or transfersomes), our results show a clear lack of cross-correlation below the skin surface, indicating that the penetration of intact liposomes is highly compromised by the skin barrier.

  17. Collinear, two-color optical Kerr effect shutter for ultrafast time-resolved imaging

    CERN Document Server

    Purwar, Harsh; Rozé, Claude; Sedarsky, David; Blaisot, Jean-Bernard

    2015-01-01

    Imaging with ultrashort exposure times is generally achieved with a crossed-beam geometry. In the usual arrangement, an off-axis gating pulse induces birefringence in a medium exhibiting a strong Kerr response (commonly carbon disulfide) which is followed by a polarizer aligned to fully attenuate the on-axis imaging beam. By properly timing the gate pulse, imaging light experiences a polarization change allowing time-dependent transmission through the polarizer to form an ultrashort image. The crossed-beam system is effective in generating short gate times, however, signal transmission through the system is complicated by the crossing angle of the gate and imaging beams. This work presents a robust ultrafast time-gated imaging scheme based on a combination of type-I frequency doubling and a collinear optical arrangement in carbon disulfide. We discuss spatial effects arising from crossed-beam Kerr gating, and examine the imaging spatial resolution and transmission timing affected by collinear activation of th...

  18. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    Nanosatellites offer frequent, low-cost space access as secondary payloads on launches of larger conventional satellites. We summarize the payload science and technology of the Microsatellite in-situ Space Technologies (MisST) nanosatellite for conducting automated biological experiments. The payload (two fused 10-cm cubes) includes 1) an integrated fluidics system that maintains organism viability and supports growth and 2) a fixed-focus imager with fluorescence and scattered-light imaging capabilities. The payload monitors temperature, pressure and relative humidity, and actively controls temperature. C. elegans (nematode, 50 m diameter x 1 mm long) was selected as a model organism due to previous space science experience, its completely sequenced genome, size, hardiness, and the variety of strains available. Three strains were chosen: two green GFP-tagged strains and one red tdTomato-tagged strain that label intestinal, nerve, and pharyngeal cells, respectively. The integrated fluidics system includes bioanalytical and reservoir modules. The former consists of four 150 L culture wells and a 4x5 mm imaging zone the latter includes two 8 mL fluid reservoirs for reagent and waste storage. The fluidic system is fabricated using multilayer polymer rapid prototyping: laser cutting, precision machining, die cutting, and pressure-sensitive adhesives it also includes eight solenoid-operated valves and one mini peristaltic pump. Young larval-state (L2) nematodes are loaded in C. elegans Maintenance Media (CeMM) in the bioanalytical module during pre-launch assembly. By the time orbit is established, the worms have grown to sufficient density to be imaged and are fed fresh CeMM. The strains are pumped sequentially into the imaging area, imaged, then pumped into waste. Reagent storage utilizes polymer bags under slight pressure to prevent bubble formation in wells or channels. The optical system images green and red fluorescence bands by excitation with blue (473 nm peak

  19. SIMAGE: simulation of DNA-microarray gene expression data

    Directory of Open Access Journals (Sweden)

    Kuipers Oscar P

    2006-04-01

    Full Text Available Abstract Background Simulation of DNA-microarray data serves at least three purposes: (i optimizing the design of an intended DNA microarray experiment, (ii comparing existing pre-processing and processing methods for best analysis of a given DNA microarray experiment, (iii educating students, lab-workers and other researchers by making them aware of the many factors influencing DNA microarray experiments. Results Our model has multiple layers of factors influencing the experiment. The relative influence of such factors can differ significantly between labs, experiments within labs, etc. Therefore, we have added a module to roughly estimate their parameters from a given data set. This guarantees that our simulated data mimics real data as closely as possible. Conclusion We introduce a model for the simulation of dual-dye cDNA-microarray data closely resembling real data and coin the model and its software implementation "SIMAGE" which stands for simulation of microarray gene expression data. The software is freely accessible at: http://bioinformatics.biol.rug.nl/websoftware/simage.

  20. Two-color light-emitting diodes with polarization-sensitive high extraction efficiency based on graphene

    Science.gov (United States)

    H, Sattarian; S, Shojaei; E, Darabi

    2016-05-01

    In the present study, graphene photonic crystals are employed to enhance the light extraction efficiency (LEE) of two-color, red and blue, light-emitting diode (LED). The transmission characteristics of one-dimensional (1D) Fibonacci graphene photonic crystal LED (FGPC-LED) are investigated by using the transfer matrix method and the scaling study is presented. We analyzed the influence of period, thickness, and permittivity in the structure to enhance the LEE. The transmission spectrum of 1D FGPC has been optimized in detail. In addition, the effects of the angle of incidence and the state of polarization are investigated. As the main result, we found the optimum values of relevant parameters to enhance the extraction of red and blue light from an LED as well as provide perfect omnidirectional and high peak transmission filters for the TE and TM modes.

  1. The research on two-color photon sources in infrared and X-ray ranges by compton scattering

    CERN Document Server

    Yu Zhao

    2001-01-01

    The generation of a two-color source of FEL light in both the infrared and soft X-ray ranges by intracavity Compton backscattering is demonstrated by the Beijing FEL facility. 1.20-1.35 keV soft X-rays are successfully extracted from the optical cavity of the FEL through a porous metallic mirror, while a 9-10 mu m FEL laser is output in the other dielectric mirror simultaneously. The average output flux of X-ray is 10 sup 2 -10 sup 3 photons/s when the average output FEL laser power is 6-20 mW. The experimental result allows us to envision a convenient way to expand the application areas of IR FEL facilities into X-ray or gamma-ray ranges.

  2. Ultrafast molecular photoionization by two-color orthogonally polarized ultraviolet laser pulses: Effects of relative pulse phases

    Science.gov (United States)

    Yuan, Kai-Jun; Chelkowski, Szczepan; Bandrauk, André D.

    2017-09-01

    We present molecular photoionization by two-color 2ω1 =ω2 orthogonally polarized ultraviolet laser pulses. Simulations are performed on aligned H+ by numerically solving time-dependent Schrödinger equations. Two ionization processes with one ω2 photon interfering with two ω1 photon absorption are studied at different molecular alignments. Molecular frame photoelectron momentum and angular distributions exhibit asymmetries which are functions of the relative pulse phase. For resonant excitation processes by the ω1 pulse, symmetric distributions are obtained. An attosecond ionization model is adopted to describe the ultrafast ionization dynamics. The dependence of the ionization asymmetry on the molecular alignment allows to further monitor interference effects on orbital symmetry.

  3. Flow cytometric quantification of all phases of the cell cycle and apoptosis in a two-color fluorescence plot.

    Directory of Open Access Journals (Sweden)

    Christine Vignon

    Full Text Available An optimal technology for cell cycle analysis would allow the concomitant measurement of apoptosis, G0, G1, S, G2 and M phases in combination with cell surface phenotyping. We have developed an easy method in flow cytometry allowing this discrimination in an only two-color fluorescent plot. It is based on the concomitant use of 7-amino-actinomycin D and the antibodies anti-Ki67 and anti-phospho(Ser10-histone H3, both conjugated to Alexa Fluor®488 to discriminate G0 and M phases, respectively. The method is particularly valuable in a clinical setting as verified in our laboratory by analyzing human leukemic cells from marrow samples or after exposure to cell cycle modifiers.

  4. 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.

  5. Element Selective Probe of the Ultra-Fast Magnetic Response to an Element Selective Excitation in Fe-Ni Compounds Using a Two-Color FEL Source

    Directory of Open Access Journals (Sweden)

    Eugenio Ferrari

    2017-01-01

    Full Text Available The potential of the two-color mode implemented at the FERMI free-electron laser (FEL source for pumping and probing selectively different atomic species has been demonstrated by time-resolved scattering experiments with permalloy (FeNi alloy and NiFe2O4 samples. We monitored the ultra-fast demagnetization of Ni induced by the pump FEL pulse, by tuning the linearly-polarized FEL probe pulse to the Ni-3p resonance and measuring the scattered intensity in the transverse magneto-optical Kerr effect geometry. The measurements were performed by varying the intensity of the FEL pump pulse, tuning its wavelength to and off of the Fe-3p resonance, and by spanning the FEL probe pulse delays across the 300–900 fs range. The obtained results have evidenced that for the case of NiFe2O4, there is a sensible difference in the magnetic response at the Ni site when the pump pulse causes electronic excitations at the Fe site.

  6. Normalization of one-channel microarrays for identification of organisms

    Directory of Open Access Journals (Sweden)

    Zierer, Astrid

    2007-03-01

    Full Text Available Microarrays are widely used in gene expression analysis, but there are further areas they can be applied to, like e.g. the identification of organisms. To interpret and compare the results of microarray experiments it is necessary to standardize the data. In this context standardization is referred to as normalization. We present data derived from a microarray experiment aiming to identify different subtypes of the hepatitis C virus. Most of the methods developed to normalize microarray data are focused on gene expression analysis. Their use for the identification of organisms is restricted and needs adaption for the special requirements. Based on our data setting, we present several possibilities how to modify the existing methods and deal with the specific conditions.

  7. Cluster stability scores for microarray data in cancer studies

    OpenAIRE

    Ghosh Debashis; Smolkin Mark

    2003-01-01

    Abstract Background A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical tool used to define disease subtypes from microarray experiments in cancer settings. Assessing cluster reliability poses a major complication in analyzing output from clustering procedures. While most work has focused on estimating the number of clusters in a dataset, t...

  8. Two Color Entanglement

    CERN Document Server

    Samblowski, Aiko; Grosse, Nicolai; Lam, Ping Koy; Schnabel, Roman

    2010-01-01

    We report on the generation of entangled states of light between the wavelengths 810 and 1550 nm in the continuous variable regime. The fields were produced by type I optical parametric oscillation in a standing-wave cavity build around a periodically poled potassium titanyl phosphate crystal, operated above threshold. Balanced homodyne detection was used to detect the non-classical noise properties, while filter cavities provided the local oscillators by separating carrier fields from the entangled sidebands. We were able to obtain an inseparability of I=0.82, corresponding to about -0.86 dB of non-classical quadrature correlation.

  9. Rapid and quantitative quality control of microarrays using cationic nanoparticles.

    Science.gov (United States)

    Sun, Ye; Fan, Wenhua; McCann, Michael P; Golovlev, Val

    2009-02-15

    The fabrication quality of microarrays significantly influences the accuracy and reproducibility of microarray experiments. In this report, we present a simple and fast quality control (QC) method for spotted oligonucleotide and cDNA microarrays. It employs a nonspecific electrostatic interaction of colloidal gold nanoparticles with the chemical groups of DNA molecules and other biomolecules immobilized on the microarray surface that bear positive or negative charges. An inexpensive flatbed scanner is used to visualize and quantify the binding of cationic gold particles to the anionic DNA probes on the microarray surface. An image analysis software was designed to assess the various parameters of the array spots including spot intensity, shape and array homogeneity, calculate the overall array quality score, and save the detailed array quality report in an Excel file. The gold staining technique is fast and sensitive. It can be completed in 10 min and detect less than 1% of the probe amount commonly recommended for microarrays. Compared to the current microarray QC method that utilizes the hybridization of probes with short random sequence oligonucleotides labeled with fluorophore, our gold staining method requires less time for the analysis, reduces the reagent cost, and eliminates the need for the expensive laser scanner.

  10. 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.

  11. 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

  12. 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....

  13. 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.

  14. Signal stability of Cy3 and Cy5 on antibody microarrays

    Directory of Open Access Journals (Sweden)

    Kim Caroline

    2006-10-01

    Full Text Available Abstract Background The antibody microarray technique is a newly emerging proteomics tool for differential protein expression analyses that uses fluorescent dyes Cy 3 and Cy 5. Environmental factors, such as light exposure, can affect the signal intensity of fluorescent dyes on microarray slides thus, it is logical to scan microarray slides immediately after the final wash and drying processes. However, no research data are available concerning time-dependent changes of fluorescent signals on antibody microarray slides to this date. In the present study, microarray slides were preserved at -20°C after regular microarray experiments and were rescanned at day 10, 20 and 30 to evaluate change in signal intensity. Results Fluorescent intensities of microarray spots were detected using a confocal laser scanner after the experiment at day 0, and re-examined at day 10, 20 and 30, respectively. Fluorescent intensities of rescanned microarray spots did not show significant changes when compared with those scanned immediately after standard microarray experiments. Conclusion Microarray slides can be preserved and rescanned multiple times using a confocal laser scanner over a period of days or weeks.

  15. 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.

  16. 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.

  17. 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.

  18. Tunable Two-color Luminescence and Host–guest Energy Transfer of Fluorescent Chromophores Encapsulated in Metal-Organic Frameworks

    Science.gov (United States)

    Yan, Dongpeng; Tang, Yanqun; Lin, Heyang; Wang, Dan

    2014-01-01

    Co-assembly of chromophore guests with host matrices can afford materials which have photofunctionalities different from those of individual components. Compared with clay and zeolite materials, the use of metal–organic frameworks (MOFs) as a host structure for fabricating luminescent host–guest materials is still at an early stage. Herein, we report the incorporation of a laser dye, 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM), into stilbene-based and naphthalene-based MOF systems. The resulting materials exhibit blue/red two-color emission, and the intensity ratio of blue to red fluorescence varies in different planes within the MOF crystal as detected by 3D confocal fluorescence microscopy. The observed changes in ratiometric fluorescence suggest the occurrence of energy transfer from MOF host to DCM molecules, which can be further confirmed by periodic density functional theoretical (DFT) calculations. Moreover, selective changes in luminescence behavior are observed on treating the guest@MOF samples with volatile organic compounds (methanol, acetone and toluene), indicating that these host–guest systems have potential applications as fluorescence sensors. It can be expected that by rational selection of MOF hosts and guest chromophores with suitable emissive colors and energy levels, a wide variety of multi-color luminescent and energy-transfer systems can readily be prepared in a similar manner. PMID:24614015

  19. Intramolecular triplet energy transfer via higher triplet excited state during stepwise two-color two-laser irradiation.

    Science.gov (United States)

    Oseki, Yosuke; Fujitsuka, Mamoru; Sakamoto, Masanori; Majima, Tetsuro

    2007-10-01

    We studied the energy transfer processes in the molecular array consisting of pyrene (Py), biphenyl (Ph2), and bisphthalimidethiophene (ImT), (Py-Ph2)2-ImT, during two-color two-laser flash photolysis (2-LFP). The first laser irradiation predominantly generates ImT in the lowest triplet excited state (ImT(T1)) because of the efficient singlet energy transfer from Py in the lowest singlet excited state to ImT and, then, intersystem crossing of ImT. ImT(T1) was excited to the higher triplet excited state (Tn) with the second laser irradiation. Then, the triplet energy was rapidly transferred to Py via a two-step triplet energy transfer (TET) process through Ph2. The efficient generation of Py(T1) was suggested from the nanosecond-picosecond 2-LFP. The back-TET from Py(T1) to ImT was observed for several tens of microseconds after the second laser irradiation. The estimated intramolecular TET rate from Py(T1) to ImT was as slow as 3.1 x 104 s-1. Hence, long-lived Py(T1) was selectively and efficiently produced during the 2-LFP.

  20. Ultrafast energy redistribution in C(60) fullerenes: a real time study by two-color femtosecond spectroscopy.

    Science.gov (United States)

    Shchatsinin, Ihar; Laarmann, Tim; Zhavoronkov, Nick; Schulz, Claus Peter; Hertel, Ingolf V

    2008-11-28

    Strong-field excitation and energy redistribution dynamics of C(60) fullerenes are studied by means of time-resolved mass spectrometry in a two-color femtosecond pump-probe setup. Resonant pre-excitation of the electronic system via the first dipole-allowed HOMO-->LUMO+1(t(1g)) (HOMO denotes highest occupied molecular orbital and LUMO denotes lowest unoccupied molecular orbital) transition with ultrashort 25 fs pulses at 399 nm of some 10(12) W cm(-2) results in a highly nonequilibrium distribution of excited electrons and vibrational modes in the neutral species. The subsequent coupling among the electronic and nuclear degrees of freedom is monitored by probing the system with time-delayed 27 fs pulses at 797 nm of some 10(13) W cm(-2). Direct information on the characteristic relaxation time is derived from the analysis of transient singly and multiply charged parent and fragment ion signals as a function of pump-probe delay and laser pulse intensity. The observed relaxation times tau(el) approximately 60-400 fs are attributed to different microcanonical ensembles prepared in the pre-excitation process and correspond to different total energy contents and energy sharing between electronic and vibrational degrees. The characteristic differences and trends allow one to extract a consistent picture for the formation dynamics of ions in different charge states and their fullerenelike fragments and give evidence to collective effects in multiple ionization such as plasmon-enhanced energy deposition.

  1. Stimulated Emission Pumping by Two-Color Resonant Four-Wave Mixing: Rotational Characterization of Vibrationally Excited HCO

    Energy Technology Data Exchange (ETDEWEB)

    Radi, P.P.; Tulej, M.; Knopp, G.; Beaud, P.; Gerber, T.

    2004-03-01

    Stimulated emission pumping by applying two-color resonant four-wave mixing is used to measure rotationally resolved spectra of the HCO (0,0,0) B {sup 2}A' - (0,3,1) X {sup 2}A' transition. The formyl radical is produced by photodissociation of formaldehyde at 31710.8 cm{sup -1} under thermalized conditions in a low pressure cell. In contrast to the highly congested one-color spectrum of HCO at room temperature, the doubleresonance method yields well isolated transitions which are assigned unambiguously due to intermediate level labeling. 89 rotational transitions have been assigned and yield accurate rotational constants for the vibrationally excited (0,3,1) band of the electronic ground state X {sup 2}A' of HCO. The determined rotational constant A = 25.84{+-}0.01 cm-1 is considerably higher than that for the vibrationless ground state and reflects the structural change due to excitation of the bending mode of the formyl radical. (author)

  2. Two-color widefield fluorescence microendoscopy enables multiplexed molecular imaging in the alveolar space of human lung tissue

    Science.gov (United States)

    Krstajić, Nikola; Akram, Ahsan R.; Choudhary, Tushar R.; McDonald, Neil; Tanner, Michael G.; Pedretti, Ettore; Dalgarno, Paul A.; Scholefield, Emma; Girkin, John M.; Moore, Anne; Bradley, Mark; Dhaliwal, Kevin

    2016-04-01

    We demonstrate a fast two-color widefield fluorescence microendoscopy system capable of simultaneously detecting several disease targets in intact human ex vivo lung tissue. We characterize the system for light throughput from the excitation light emitting diodes, fluorescence collection efficiency, and chromatic focal shifts. We demonstrate the effectiveness of the instrument by imaging bacteria (Pseudomonas aeruginosa) in ex vivo human lung tissue. We describe a mechanism of bacterial detection through the fiber bundle that uses blinking effects of bacteria as they move in front of the fiber core providing detection of objects smaller than the fiber core and cladding (˜3 μm). This effectively increases the measured spatial resolution of 4 μm. We show simultaneous imaging of neutrophils, monocytes, and fungus (Aspergillus fumigatus) in ex vivo human lung tissue. The instrument has 10 nM and 50 nM sensitivity for fluorescein and Cy5 solutions, respectively. Lung tissue autofluorescence remains visible at up to 200 fps camera acquisition rate. The optical system lends itself to clinical translation due to high-fluorescence sensitivity, simplicity, and the ability to multiplex several pathological molecular imaging targets simultaneously.

  3. Generation of attosecond x-ray pulses with a multi-cycle two-color ESASE scheme

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Y.; Huang, Z.; Ratner, D.; Bucksbaum, P.; /SLAC; Merdji, H.; /Saclay /SLAC

    2009-03-04

    Generation of attosecond x-ray pulses is attracting much attention within the x-ray free-electron laser (FEL) user community. Several schemes using extremely short laser pulses to manipulate the electron bunches have been proposed. In this paper, we extend the attosecond two-color ESASE scheme proposed by Zholents et al. to the long optical cycle regime using a second detuned laser and a tapered undulator. Both lasers can be about ten-optical-cycles long, with the second laser frequency detuned from the first to optimize the contrast between the central and side current spikes. A tapered undulator mitigates the degradation effect of the longitudinal space charge (LSC) force in the undulator and suppresses the FEL gain of all side current peaks. Simulations using the LCLS parameters show a single attosecond x-ray spike of {approx} 110 attoseconds can be produced. The second laser can also be detuned to coherently control the number of the side x-ray spikes and the length of the radiation pulse.

  4. Two-color vibrational, femtosecond, fully resonant electronically enhanced CARS (FREE-CARS) of gas-phase nitric oxide

    Science.gov (United States)

    Stauffer, Hans U.; Roy, Sukesh; Schmidt, Jacob B.; Wrzesinski, Paul J.; Gord, James R.

    2016-09-01

    A resonantly enhanced, two-color, femtosecond time-resolved coherent anti-Stokes Raman scattering (CARS) approach is demonstrated and used to explore the nature of the frequency- and time-dependent signals produced by gas-phase nitric oxide (NO). Through careful selection of the input pulse wavelengths, this fully resonant electronically enhanced CARS (FREE-CARS) scheme allows rovibronic-state-resolved observation of time-dependent rovibrational wavepackets propagating on the vibrationally excited ground-state potential energy surface of this diatomic species. Despite the use of broadband, ultrafast time-resolved input pulses, high spectral resolution of gas-phase rovibronic transitions is observed in the FREE-CARS signal, dictated by the electronic dephasing timescales of these states. Analysis and computational simulation of the time-dependent spectra observed as a function of pump-Stokes and Stokes-probe delays provide insight into the rotationally resolved wavepacket motion observed on the excited-state and vibrationally excited ground-state potential energy surfaces of NO, respectively.

  5. 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.

  6. A novel scheme to assess factors involved in the reproducibility of DNA-microarray data

    NARCIS (Netherlands)

    Hijum, Sacha A.F.T. van; Jong, Anne de; Baerends, Richard J.S.; Karsens, Harma A.; Kramer, Naomi E.; Larsen, Rasmus; Hengst, Chris D. den; Albers, Casper J.; Kok, Jan; Kuipers, Oscar P.

    2005-01-01

    Background: In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel a

  7. An experimental evaluation of a loop versus a reference design for two-channel microarrays

    NARCIS (Netherlands)

    Vinciotti, V.; Khanin, R.; Alimonte, D. D’; Liu, X.; Cattini, N.; Hotchkiss, G.; Bucca, G.; Jesus, O. de; Rasaiyaah, J.; Kellam, P.; Wit, Ernst

    2005-01-01

    Motivation: Despite theoretical arguments that so-called ‘loop designs’ for two-channel DNA microarray experiments are more efficient, biologists continue to use ‘reference designs’. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammali

  8. Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

    Institute of Scientific and Technical Information of China (English)

    PeterJ.vanderSpek; AndreasKremer; LynnMurry; MichaelG.Walker

    2003-01-01

    Microarray analyses of gene expression are widely used,but reports of the same analyses by different groups give widely divergent results,and raise questions regarding reproducibility and reliability.We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes.These reports show substantial differences in their results.In this article,we review the methodology,results,and potential causes of differences in these applications of microarrays.Finally,we suggest practices to improve the reliability and reproducibility of microarray experiments.

  9. Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

    Institute of Scientific and Technical Information of China (English)

    Peter J. van der Spek; Andreas Kremer; Lynn Murry; Michael G. Walker

    2003-01-01

    Microarray analyses of gene expression are widely used, but reports of the same analyses by different groups give widely divergent results, and raise questions regarding reproducibility and reliability. We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes. These reports show substantial differences in their results. In this article, we review the methodology, results, and potential causes of differences in these applications of microarrays. Finally, we suggest practices to improve the reliability and reproducibility of microarray experiments.

  10. Characterization and simulation of cDNA microarray spots using a novel mathematical model

    OpenAIRE

    2007-01-01

    Abstract Background The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of s...

  11. Linking microarray reporters with protein functions

    Directory of Open Access Journals (Sweden)

    Gaj Stan

    2007-09-01

    Full Text Available Abstract Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.

  12. 35. Detection of numerical chromosome aberrations in sperm of workers exposed to benzene series by two-color fluorescence in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To study the frequency of numerical chromosome aberrations in sperm of workers exposed to benzene series, the aneuploidy frequencies of 9 and 18 chromosomes were detected in sperm of workers by two color fluorescence in situ hybridization with digoxingenin labeled 9 chromosome probe (D9zl) and biotin labeled 18 chromosome probe (D18zl). The timeweight average air concentration (TWA ) of benzene in the workplace was 86.49 mg/m3, it was two fold higher than the national maximum allowable concentration. The concentration of urinary trans,trans-muconic acid (ttMA) in exposed group was significantly higher than that of control group. The sperms counted in 14 exposed workers and 16 control workers were 136 401 and 156 955 respectively. The results showed that the disomy frequencies of sperm for chromosome 9, 18 in (0.168%±0.063% and 0.055%±0.031% respectively) and the frequency of diploidy sperm (0.073%±0.045%) were statistically increased over that of the control group(0.050%±0.030%; 0.033%±0.025% and 0.040%±0.036%, respectively). The nullisomic frequencies of 9,18 chromosome in the exposed group (0.206%±0.047%, 0.068%±0.044%) were statistically increased over that of the control group too (0.067%±0.037%, 0.048%±0.034%). The frequency of overall numerical chromosome aberrations in the exposed group was 0.570%±0.144%, when this value was compared with that of control (0.218%±0.071%), a statistically significance was presented. Our experiments showed that exposed to benzene at higher concentration may induce increase in aneuploidy frequency of sperm autosomal chromosome in exposed workers.

  13. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays.

    Science.gov (United States)

    von der Haar, Marcel; Heuer, Christopher; Pähler, Martin; von der Haar, Kathrin; Lindner, Patrick; Scheper, Thomas; Stahl, Frank

    2016-11-30

    The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

  14. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Marcel von der Haar

    2016-11-01

    Full Text Available The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS. Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.

  15. Fabrication of two-color annular hybrid wave plate for three-dimensional super-resolution microscopy

    Science.gov (United States)

    Kumagai, Hiroshi; Iketaki, Yoshinori; Jahn, Kornel; Bokor, Nador

    2016-03-01

    In super-resolution microscopy, we use fluorescence depletion, where an erase beam quenches a molecule in the S1 state generated by a pump beam, and then prevents fluorescence from the S1 state. When a tight doughnut shaped erase beam with is focused on the dyed sample together with a Gaussian pump beam, the remaining fluorescence spot in the focal plane becomes smaller than the diffraction-limited size. Applying destructive interference to the erase beam, erase beam has a minute three-dimensional dark spot surrounded by the light near the focal region. Since this spot introduces fluorescence depletion along the optical axis as in the focal plane, we can achieve three-dimensional super-resolution microscopy. However, to overcome the diffraction limit, an extremely precise optical alignment is required for projecting the focused pump beam into the dark spot of the erase beam. To resolve this technical issue, we fabricated a two-color annular hybrid wave plate (TAHWP) by combining two multi-order wave quartz plates. Although the pump and erase beams co-axially pass through the plate; the pump beam retains its original Gaussian shape, while the erase beam undergoes destructive interference. Inserting the TAHWP into a commercial scanning laser microscope, a three-dimensional spherical fluorescence spot with a volume of (~100 nm)3 can be created. Beside eliminating alignment problems and yielding a compact setup, the TAHWP makes our proposed method very suitable for commercial microscope systems. In this study, we report about detailed fabrication procedure and three-dimensional image properties given by the TAHWP.

  16. The effect of frequency chirping on electron-positron pair production in the one- and two-color laser pulse fields

    CERN Document Server

    Abdukerim, Nuriman; Xie, Bai-Song

    2016-01-01

    The effect of the frequency chirping on momentum spectrum and pair production rate in one- and two-color laser pulse fields is investigated by solving the quantum Vlasov equation. A small frequency chirp shifts the momentum spectrum along the momentum axis. The positive and negative frequency chirp parameters play the same role in increasing the pair number density. The sign change of frequency chirp parameter at the moment $t=0$ leads pulse shape and momentum spectrum to be symmetric, and the number density to be increased. The number density of produced pairs in the two-color pulse field is much higher than that in the one-color pulse field and the larger frequency chirp pulse field dominates more strongly. In the two-color pulse fields, the relation between the frequency ratio of two colors and the number density is not sensitive to the parameters of small frequency chirp added in either low frequency strong field or high frequency weak field but sensitive to the parameters of large frequency chirp added i...

  17. The 2 1Ag state of isolated cis-trans-1,3,5,7-octatetraene: two-color resonance enhanced two-photon ionization studies

    NARCIS (Netherlands)

    B.E. Kohler; T. Shaler; W.J. Buma

    1992-01-01

    Vibrationally resolved 1 1Ag2 1Ag excitation spectra and decay times for cis,trans-1,3,5,7-octatetraene seeded in a supersonic He expansion have been measured by two-color resonance enhanced two-photon ionization spectroscopy. The excitation energy of the 1 1Ag2 1Ag 0-0 band (29 035 cm-1 ) is ~6500

  18. 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.

  19. 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.

  20. Plant-pathogen interactions: what microarray tells about it?

    Science.gov (United States)

    Lodha, T D; Basak, J

    2012-01-01

    Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

  1. Microarray Technologies in Fungal Diagnostics.

    Science.gov (United States)

    Rupp, Steffen

    2017-01-01

    Microarray technologies have been a major research tool in the last decades. In addition they have been introduced into several fields of diagnostics including diagnostics of infectious diseases. Microarrays are highly parallelized assay systems that initially were developed for multiparametric nucleic acid detection. From there on they rapidly developed towards a tool for the detection of all kind of biological compounds (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.). The combination of closed-tube systems and lab on chip devices with microarrays further enabled a higher automation degree with a reduced contamination risk. Microarray-based diagnostic applications currently complement and may in the future replace classical methods in clinical microbiology like blood cultures, resistance determination, microscopic and metabolic analyses as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel nucleic acid based biomarkers. Here I focus an microarray technologies in diagnostics and as research tools, based on nucleic acid-based arrays.

  2. Carbohydrate microarrays in plant science.

    Science.gov (United States)

    Fangel, Jonatan U; Pedersen, Henriette L; Vidal-Melgosa, Silvia; Ahl, Louise I; Salmean, Armando Asuncion; Egelund, Jack; Rydahl, Maja Gro; Clausen, Mads H; Willats, William G T

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important 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.

  3. 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.

  4. Robust protein microarray image segmentation using improved seeded region growing algorithm

    Institute of Scientific and Technical Information of China (English)

    Liqiang Wang(王立强); Xuxiang Ni(倪旭翔); Zukang Lu(陆祖康)

    2003-01-01

    Protein microarray technology has recently emerged as a powerful tool for biomedical research. Before automatic analysis the protein microarray images, protein spots in the images must be determined appropriately by spot segmentation algorithm. In this paper, an improved seeded region growing (ISRG)algorithm for protein microarray segmentation is presented, the seeds are obtained by finding the positions of the printed spots, and the protein spot regions are grown through these seeds. The experiment results show that the presented algorithm is accurate for adaptive shape segmentation and robust for protein microarray images contaminated by noise.

  5. 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

  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 st

  7. 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...

  8. Spectral dynamics of THz pulses generated by two-color laser filaments in air: The role of Kerr nonlinearities and pump wavelength

    CERN Document Server

    Nguyen, A; Dechard, J; Thiele, I; Babushkin, I; Skupin, S; Berge, L

    2016-01-01

    We theoretically and numerically study the influence of both instantaneous and Raman-delayed Kerr nonlinearities as well as a long-wavelength pump in the terahertz (THz) emissions produced by two-color femtosecond filaments in air. Although the Raman-delayed nonlinearity induced by air molecules weakens THz generation, four-wave mixing is found to impact the THz spectra accumulated upon propagation via self-, cross-phase modulations and self-steepening. Besides, using the local current theory, we show that the scaling of laser-to-THz conversion efficiency with the fundamental laser wavelength strongly depends on the relative phase between the two colors, the pulse duration and shape, rendering a universal scaling law impossible. Scaling laws in powers of the pump wavelength may only provide a rough estimate of the increase in the THz yield. We confront these results with comprehensive numerical simulations of strongly focused pulses and of filaments propagating over meter-range distances.

  9. High harmonic generation in a two-color field composed of a pump field and a weak subsidiary high frequency field

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    “Coherent control of high-harmonic generation in a two-color field” has been widely concerned. Using split-operator algorithm, we have calculated the high-harmonic generation for helium ion He+ in a two-color field which is composed of a driving field and a weak subsidiary high frequency field (Is=I0/100, (ω,13ω), …(ω, 120ω)) and found that such a field can produce much higher harmonic intensity, typically increasing the harmonics corresponding to the incident frequency of the subsidiary field. The different effects coming from the different subsidiary fields are calculated and analyzed. It is indicated that one of the important underlying mechanisms is high frequency photon induced radiation.

  10. Silicon isotope separation utilizing infrared multiphoton dissociation of Si{sub 2}F{sub 6} irradiated with two-color CO{sub 2} laser light

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Atsushi; Ohba, Hironori; Hashimoto, Masashi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Ishii, Takeshi; Ohya, Akio [Nuclear Development Corp., Tokai, Ibaraki (Japan); Arai, Shigeyoshi [Hill Research Co. Ltd., Tokyo (Japan)

    2002-08-01

    Silicon isotope separation has been done by utilizing the Infrared Multiphoton Dissociation (IRMPD) of Si{sub 2}F{sub 6} irradiated with two-color CO{sub 2} laser lights. The two-color excitation method improved the separation efficiency keeping the high enrichment factors. For example, 99.74% of {sup 28}Si was obtained at 49.63% dissociation of Si{sub 2}F{sub 6} after the simultaneous irradiation of 200 pulses with 966.23 cm{sup -1} photons (0.084 J/cm{sup 2}) and 954.55 cm{sup -1} photons (0.658 J/cm{sup 2}), while 2000 pulses were needed to obtain 99.35% of {sup 28}Si at 35.6% dissociation in the case of only one-color irradiation at 954.55 cm{sup -1} (0.97 J/cm{sup 2}). (author)

  11. Identification of the origin of marker chromosomes by two-color fluorescence in situ hybridization and polymerase chain reaction in azoospermic patients.

    Science.gov (United States)

    Wei, C L; Cheng, J L; Yang, W C; Li, L Y; Cheng, H C; Fu, J J

    2015-11-19

    Y chromosomal microdeletions at the azoospermia factor locus and chromosome abnormalities have been implicated as the major causes of idiopathic male infertility. A marker chromosome is a structurally abnormal chromosome in which no part can be identified by cytogenetics. In this study, to identify the origin of the marker chromosomes and to perform a genetic diagnosis of patients with azoospermia, two-color fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques were carried out. The marker chromosomes for the two patients with azoospermia originated in the Y chromosome; it was ascertained that the karyotype of both patients was 46,X, ish del(Y)(q11)(DYZ3+, DXZ1-). The combination of two-color FISH and PCR techniques is an important method for the identification of the origin of marker chromosomes. Thus, genetic counseling and a clear genetic diagnosis of patients with azoospermia before intracytoplasmic sperm injection or other clinical managements are important.

  12. Two-color injection mould for the handle of egg mixer%鸡蛋搅拌机手柄双色注射模设计

    Institute of Scientific and Technical Information of China (English)

    陈罡; 陈乐平; 毛金明

    2012-01-01

    The structure layout, design points and working process of a two-color injection mould for the handle of an egg mixer were analyzed; and the design of gating system was presented in detail. The application of composite half-mechanism and mechanism of core-pulling by inclined ejector pin achieves sequential parting of the two-color mould.%分析了鸡蛋搅拌机手柄双色注射模的结构、设计要点和工作过程,详细介绍了模具浇注系统设计,采用复合哈夫机构和斜推杆内抽芯机构,实现了双色模具顺序分型动作.实践表明,模具结构可靠,运动平稳顺畅,制品精度和外观质量均符合要求.

  13. Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Gregory Stephanopoulos

    2004-07-31

    Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

  14. How do we select multiple features? Transient costs for selecting two colors rather than one, persistent costs for color-location conjunctions.

    Science.gov (United States)

    Lo, Shih-Yu; Holcombe, Alex O

    2014-02-01

    In a previous study Lo, Howard, & Holcombe (Vision Research 63:20-33, 2012), selecting two colors did not induce a performance cost, relative to selecting one color. For example, requiring possible report of both a green and a red target did not yield a worse performance than when both targets were green. Yet a cost of selecting multiple colors was observed when selection needed be contingent on both color and location. When selecting a red target to the left and a green target to the right, superimposing a green distractor to the left and a red distractor to the right impeded performance. Possibly, participants cannot confine attention to a color at a particular location. As a result, distractors that share the target colors disrupt attentional selection of the targets. The attempt to select the targets must then be repeated, which increases the likelihood that the trial terminates when selection is not effective, even for long trials. Consistent with this, here we find a persistent cost of selecting two colors when the conjunction of color and location is needed, but the cost is confined to short exposure durations when the observer just has to monitor red and green stimuli without the need to use the location information. These results suggest that selecting two colors is time-consuming but effective, whereas selection of simultaneous conjunctions is never entirely successful.

  15. The Three-Color and Two-Color Tantrix(TM) Rotation Puzzle Problems are NP-Complete via Parsimonious Reductions

    CERN Document Server

    Baumeister, Dorothea

    2007-01-01

    Holzer and Holzer (Discrete Applied Mathematics 144(3):345--358, 2004) proved the Tantrix(TM) rotation puzzle problem with four colors NP-complete. Baumeister and Rothe (MCU 2007) modified their construction to achieve a parsimonious reduction from satisfiability to this problem. Since parsimonious reductions preserve the number of solutions, it follows that the unique version of the four-color Tantrix(TM) rotation puzzle problem is DP-complete under randomized reductions. In this paper, we study the three-color and the two-color Tantrix(TM) rotation puzzle problem. Restricting the number of allowed colors to three (respectively, to two) reduces the set of available Tantrix(TM) tiles from 56 to 14 (respectively, to 8). We prove that both the three-color and the two-color Tantrix(TM) rotation puzzle problem is NP-complete, which answers a question raised by Holzer and Holzer in the affirmative. Since both these reductions are parsimonious, it follows that both the unique three-color and the unique two-color Ta...

  16. 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.

  17. Biclustering of time series microarray data.

    Science.gov (United States)

    Meng, Jia; Huang, Yufei

    2012-01-01

    Clustering is a popular data exploration technique widely used in microarray data analysis. In this chapter, we review ideas and algorithms of bicluster and its applications in time series microarray analysis. We introduce first the concept and importance of biclustering and its different variations. We then focus our discussion on the popular iterative signature algorithm (ISA) for searching biclusters in microarray dataset. Next, we discuss in detail the enrichment constraint time-dependent ISA (ECTDISA) for identifying biologically meaningful temporal transcription modules from time series microarray dataset. In the end, we provide an example of ECTDISA application to time series microarray data of Kaposi's Sarcoma-associated Herpesvirus (KSHV) infection.

  18. A folded-sandwich polarization-entangled two-color photon pair source with large tuning capability for applications in hybrid quantum architectures

    CERN Document Server

    Dietz, Otto; Kreißl, Thomas; Herzog, Ulrike; Kroh, Tim; Ahlrichs, Andreas; Benson, Oliver

    2015-01-01

    We demonstrate a two-color entangled pho ton pair source which can be adapted easily to a wide range of wavelengths combinations. A Fresnel rhomb as a geometrical quarter-wave plate and a versatile combination of compensation crystals are key components of the source. Entanglement of two photons at the Cs D1 line (894.3 nm) and at the telecom O-band (1313.1 nm) with a fidelity of $F = 0.753 \\pm 0.021$ is demonstrated and improvements of the setup are discussed.

  19. An experimental evaluation of a loop versus a reference design for two-channel microarrays

    OpenAIRE

    2005-01-01

    http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/4/492 Motivation: Despite theoretical arguments that socalled \\loop designs" of two-channel DNA microarray experiments are more e cient, biologists keep on using \\reference designs". We describe two sets of microarray experiments with RNA from two di erent biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparatio...

  20. Interpreting microarray data to build models of microbial genetic regulation networks

    Science.gov (United States)

    Sokhansanj, Bahrad A.; Garnham, Janine B.; Fitch, J. Patrick

    2002-06-01

    Microarrays and DNA chips are an efficient, high-throughput technology for measuring temporal changes in the expression of message RNA (mRNA) from thousands of genes (often the entire genome of an organism) in a single experiment. A crucial drawback of microarray experiments is that results are inherently qualitative: data are generally neither quantitatively repeatable, nor may microarray spot intensities be calibrated to in vivo mRNA concentrations. Nevertheless, microarrays represent by the far the cheapest and fastest way to obtain information about a cell's global genetic regulatory networks. Besides poor signal characteristics, the massive number of data produced by microarray experiments pose challenges for visualization, interpretation and model building. Towards initial model development, we have developed a Java tool for visualizing the spatial organization of gene expression in bacteria. We are also developing an approach to inferring and testing qualitative fuzzy logic models of gene regulation using microarray data. Because we are developing and testing qualitative hypotheses that do not require quantitative precision, our statistical evaluation of experimental data is limited to checking for validity and consistency. Our goals are to maximize the impact of inexpensive microarray technology, bearing in mind that biological models and hypotheses are typically qualitative.

  1. Interpreting Microarray Data to Build Models of Microbial Genetic Regulation Networks

    Energy Technology Data Exchange (ETDEWEB)

    Sokhansanj, B; Garnham, J B; Fitch, J P

    2002-01-23

    Microarrays and DNA chips are an efficient, high-throughput technology for measuring temporal changes in the expression of message RNA (mRNA) from thousands of genes (often the entire genome of an organism) in a single experiment. A crucial drawback of microarray experiments is that results are inherently qualitative: data are generally neither quantitatively repeatable, nor may microarray spot intensities be calibrated to in vivo mRNA concentrations. Nevertheless, microarrays represent by the far the cheapest and fastest way to obtain information about a cells global genetic regulatory networks. Besides poor signal characteristics, the massive number of data produced by microarray experiments poses challenges for visualization, interpretation and model building. Towards initial model development, we have developed a Java tool for visualizing the spatial organization of gene expression in bacteria. We are also developing an approach to inferring and testing qualitative fuzzy logic models of gene regulation using microarray data. Because we are developing and testing qualitative hypotheses that do not require quantitative precision, our statistical evaluation of experimental data is limited to checking for validity and consistency. Our goals are to maximize the impact of inexpensive microarray technology, bearing in mind that biological models and hypotheses are typically qualitative.

  2. Surface characterization of carbohydrate microarrays.

    Science.gov (United States)

    Scurr, David J; Horlacher, Tim; Oberli, Matthias A; Werz, Daniel B; Kroeck, Lenz; Bufali, Simone; Seeberger, Peter H; Shard, Alexander G; Alexander, Morgan R

    2010-11-16

    Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

  3. 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.

  4. Living Cell Microarrays: An Overview of Concepts

    Directory of Open Access Journals (Sweden)

    Rebecca Jonczyk

    2016-05-01

    Full Text Available Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

  5. The spatial distribution in high-order harmonic generation of H2+ with different time delays of the two-color laser fields

    Science.gov (United States)

    Zhang, Jun; Pan, Xue-Fei; Du, Hui; Xu, Tong-Tong; Guo, Jing; Liu, Xue-Shen

    2017-01-01

    We theoretically investigate the high-order harmonic generation (HHG) and the spatial distribution in HHG of the H2+ molecule by introducing a time-delayed two-color laser field which consists of the mid-infrared and near-infrared laser field. For the different time delays of the two-color laser fields, the pulse shapes are changed which result in the variation of the electron recombined with the nuclei along the positive- or negative-z direction. When the time delay is 0 fs (1.34 fs), a smooth harmonic plateau from the electron recombined with the nuclei along the negative (positive)-z direction can be achieved. An isolated attosecond pulse with a duration of about 99 as is generated when the time delay is 1.34 fs. We perform the classical analysis which is consistent with the numerical results from the one-dimensional non-Born-Oppenheimer time dependent Schrödinger equation (TDSE). We also investigate emission time of harmonics in terms of a time-frequency analysis to further understand the underlying physical mechanism.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Gene expression profiling of mouse embryos with microarrays

    Science.gov (United States)

    Sharov, Alexei A.; Piao, Yulan; Ko, Minoru S. H.

    2011-01-01

    Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and becomes an essential tool in biological and medical sciences. Typical questions that can be addressed by microarray analysis in developmental biology include: (1) to find a set of genes expressed in a specific cell type; (2) to identify genes expressed commonly in multiple cell types; (3) to follow the time-course changes of gene expression patterns; (4) to demonstrate cell’s identity by showing similarities or differences among two or multiple cell types; (5) to find regulatory pathways and/or networks affected by gene manipulations, such as overexpression or repression of gene expression; (6) to find downstream target genes of transcription factors; (7) to find downstream target genes of cell signaling; (8) to examine the effects of environmental manipulation of cells on gene expression patterns; and (9) to find the effects of genetic manipulation in embryos and adults. Here we describe strategies for executing these experiments and monitoring changes of cell state with gene expression microarrays in application to mouse embryology. Both statistical assessment and interpretation of data are discussed. We also present a protocol for performing microarray analysis on a small amount of embryonic materials. PMID:20699157

  8. From single gene to integrative molecular concept MAPS: pitfalls and potentials of microarray technology.

    Science.gov (United States)

    Chiorino, G; Mello Grand, M; Scatolini, M; Ostano, P

    2008-01-01

    Microarray experiments have a large variety of applications and several important achievements have been obtained by means of this technology, especially within the field of whole genome expression profiling, which undoubtedly is the most diffused world-wide. Nevertheless, care must be taken in unconditionally applying such high-throughput techniques and in extracting/interpreting their results. Both the validity and the reproducibility of microarray-based clinical research have recently been challenged. Pitfalls and potentials of the microarray technology for gene expression profiling are critically reviewed in this paper.

  9. Pineal function: impact of microarray analysis

    DEFF Research Database (Denmark)

    Klein, David C; Bailey, Michael J; Carter, David A

    2009-01-01

    Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity...... foundation that microarray analysis has provided will broadly support future research on pineal function....

  10. 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

  11. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  12. Chaotic mixer improves microarray hybridization.

    Science.gov (United States)

    McQuain, Mark K; Seale, Kevin; Peek, Joel; Fisher, Timothy S; Levy, Shawn; Stremler, Mark A; Haselton, Frederick R

    2004-02-15

    Hybridization is an important aspect of microarray experimental design which influences array signal levels and the repeatability of data within an array and across different arrays. Current methods typically require 24h and use target inefficiently. In these studies, we compare hybridization signals obtained in conventional static hybridization, which depends on diffusional target delivery, with signals obtained in a dynamic hybridization chamber, which employs a fluid mixer based on chaotic advection theory to deliver targets across a conventional glass slide array. Microarrays were printed with a pattern of 102 identical probe spots containing a 65-mer oligonucleotide capture probe. Hybridization of a 725-bp fluorescently labeled target was used to measure average target hybridization levels, local signal-to-noise ratios, and array hybridization uniformity. Dynamic hybridization for 1h with 1 or 10ng of target DNA increased hybridization signal intensities approximately threefold over a 24-h static hybridization. Similarly, a 10- or 60-min dynamic hybridization of 10ng of target DNA increased hybridization signal intensities fourfold over a 24h static hybridization. In time course studies, static hybridization reached a maximum within 8 to 12h using either 1 or 10ng of target. In time course studies using the dynamic hybridization chamber, hybridization using 1ng of target increased to a maximum at 4h and that using 10ng of target did not vary over the time points tested. In comparison to static hybridization, dynamic hybridization reduced the signal-to-noise ratios threefold and reduced spot-to-spot variation twofold. Therefore, we conclude that dynamic hybridization based on a chaotic mixer design improves both the speed of hybridization and the maximum level of hybridization while increasing signal-to-noise ratios and reducing spot-to-spot variation.

  13. Atom waveguide and 1D optical lattice using a two-color evanescent light field around an optical micro/nano-fiber

    Institute of Scientific and Technical Information of China (English)

    Jian Fu; Xiang Yin; Ningyuan Li; Limin Tong

    2008-01-01

    We propose a two-color scheme of atom waveguides and one-dimensional(1D)optical lattices using evanescent wave fields of different transverse modes around an optical micro/nano-fiber.The atom guide potential can be produced when the optical fiber carries a red-detuned light with TE01 mode and a blue-detuned light with HE11 mode,and the 1D optical lattice potential can be produced when the red-detuned light is transformed to the superposition of the TE01 mode and HE11 mode.The two trapping potentials can be transformed to each other for accurately controlling mode transformation for the red-detuned light.This might provide a new approach to realize flexible transition between the guiding and trapping states of atoms.

  14. Hierarchical information representation and efficient classification of gene expression microarray data

    OpenAIRE

    Bosio, Mattia

    2014-01-01

    In the field of computational biology, microarryas are used to measure the activity of thousands of genes at once and create a global picture of cellular function. Microarrays allow scientists to analyze expression of many genes in a single experiment quickly and eficiently. Even if microarrays are a consolidated research technology nowadays and the trends in high-throughput data analysis are shifting towards new technologies like Next Generation Sequencing (NGS), an optimum method for sample...

  15. Comparison of soot formation for diesel and jet-a in a constant volume combustion chamber using two-color pyrometry

    KAUST Repository

    Jing, Wei

    2014-04-01

    The measurement of the two-color line of sight soot and KL factor for NO.2 diesel and jet-A fuels was conducted in an optical constant volume combustion chamber by using a high speed camera under 1000 K ambient temperature and varied oxygen concentration conditions. The ambient conditions were set as follows: four oxygen cases including 10%, 15%, 18% and 21% at 1000 K ambient temperature. KL factor and soot temperature were determined based on the two-color pyrometry technique using two band-pass filters with wavelengths of 650 nm and 550 nm. The results show that low soot temperature is observed in the upstream inner flame along the centerline, which is surrounded by high soot temperature regions, and a high KL factor is found in the same region with a low soot temperature. The results under different times suggest that soot temperature is higher for high O2 conditions during the entire flame development; meanwhile, both integrated KL factor and soot area decrease with the increase of O2 concentration. The two fuels share a similar trend of soot temperature and KL factor, however, diesel flame has a higher soot temperature and a larger high soot temperature area compared to jet-A flame. On the other hand, diesel flame shows a lower soot level during the quasi-steady state with a higher total soot level at the end of the combustion under low O2 conditions. A lower O2 concentration range from 10% to 15% is expected to have the possibility to achieve a simultaneous reduction of soot and NOx in sooting flames under the 1000 K ambient temperature condition. Copyright © 2014 SAE International.

  16. A python module to normalize microarray data by the quantile adjustment method.

    Science.gov (United States)

    Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C; Sangaré, Djibril; Doumbia, Seydou; Traoré, Sekou F; Maiga, Mohamed S; Dembélé, Doulaye

    2011-06-01

    Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools.

  17. Laser radiation frequency conversion in carbon- and cluster-containing plasma plumes under conditions of single and two-color pumping by pulses with a 10-Hz repetition rate

    Science.gov (United States)

    Ganeev, R. A.

    2013-07-01

    This work reviews a series of investigations of different plasma plumes using single- and two-color laser systems that emit femtosecond pulses with a 10-Hz repetition rate. Results of investigation of the resonant enhancement of harmonics in tin plasma with the use of two types of pumps are analyzed, and it is shown that the tuning of the wavelengths of harmonics to ion-resonance levels plays an important role in increasing the conversion efficiency to high-order harmonics of the radiation to be converted. Investigations of different carbon-containing plasma media (carbon nanotubes, graphite, carbon aerogel, etc.) exhibit attractive properties of the nonlinear medium of this type for efficient generation of high-order harmonics. The results of the first experiments on the use of nanoparticles produced directly in the course of laser ablation of metals for increasing the efficiency of harmonics generated in this cluster-containing medium are analyzed. It is shown that new approaches realized in these investigations give hope that the nonlinear optical response of plasma media in the far-ultraviolet range can be further increased.

  18. 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.

  19. Using pre-existing microarray datasets to increase experimental power: application to insulin resistance.

    Directory of Open Access Journals (Sweden)

    Bernie J Daigle

    2010-03-01

    Full Text Available Although they have become a widely used experimental technique for identifying differentially expressed (DE genes, DNA microarrays are notorious for generating noisy data. A common strategy for mitigating the effects of noise is to perform many experimental replicates. This approach is often costly and sometimes impossible given limited resources; thus, analytical methods are needed which increase accuracy at no additional cost. One inexpensive source of microarray replicates comes from prior work: to date, data from hundreds of thousands of microarray experiments are in the public domain. Although these data assay a wide range of conditions, they cannot be used directly to inform any particular experiment and are thus ignored by most DE gene methods. We present the SVD Augmented Gene expression Analysis Tool (SAGAT, a mathematically principled, data-driven approach for identifying DE genes. SAGAT increases the power of a microarray experiment by using observed coexpression relationships from publicly available microarray datasets to reduce uncertainty in individual genes' expression measurements. We tested the method on three well-replicated human microarray datasets and demonstrate that use of SAGAT increased effective sample sizes by as many as 2.72 arrays. We applied SAGAT to unpublished data from a microarray study investigating transcriptional responses to insulin resistance, resulting in a 50% increase in the number of significant genes detected. We evaluated 11 (58% of these genes experimentally using qPCR, confirming the directions of expression change for all 11 and statistical significance for three. Use of SAGAT revealed coherent biological changes in three pathways: inflammation, differentiation, and fatty acid synthesis, furthering our molecular understanding of a type 2 diabetes risk factor. We envision SAGAT as a means to maximize the potential for biological discovery from subtle transcriptional responses, and we provide it as a

  20. 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....

  1. Microarrays--analysis of signaling pathways.

    Science.gov (United States)

    Ramachandran, Anassuya; Black, Michael A; Shelling, Andrew N; Love, Donald R

    2008-01-01

    Microarrays provide a powerful means of analyzing the expression level of multiple transcripts in two sample populations. In this study, we have used microarray technology to identify genes that are differentially regulated in response to activin-treated ovarian cancer cells. We find a number of biologically relevant genes that are involved in regulating activin signaling and genes potentially contributing to activin-mediated growth arrest appear to be differentially regulated. Thus, microarrays are an important tool for dissecting gene expression changes in normal physiological processes and disease.

  2. DNA Microarrays in Herbal Drug Research

    Directory of Open Access Journals (Sweden)

    Preeti Chavan

    2006-01-01

    Full Text Available Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts.

  3. 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.

  4. Assessing the reliability of amplified RNA used in microarrays: a DUMB table approach.

    Science.gov (United States)

    Bearden, Edward D; Simpson, Pippa M; Peterson, Charlotte A; Beggs, Marjorie L

    2006-01-01

    A certain minimal amount of RNA from biological samples is necessary to perform a microarray experiment with suitable replication. In some cases, the amount of RNA available is insufficient, necessitating RNA amplification prior to target synthesis. However, there is some uncertainty about the reliability of targets that have been generated from amplified RNA, because of nonlinearity and preferential amplification. This current work develops a straightforward strategy to assess the reliability of microarray data obtained from amplified RNA. The tabular method we developed, which utilises a Down-Up-Missing-Below (DUMB) classification scheme, shows that microarrays generated with amplified RNA targets are reliable within constraints. There was an increase in false negatives because of the need for increased filtering. Furthermore, this analysis method is generic and can be broadly applied to evaluate all microarray data. A copy of the Microsoft Excel spreadsheet is available upon request from Edward Bearden.

  5. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays.

    Science.gov (United States)

    Polen, Tino; Wendisch, Volker F

    2004-01-01

    DNA microarray technology has become an important research tool for biotechnology and microbiology. It is now possible to characterize genetic diversity and gene expression in a genomewide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Escherichia coli, but only recently have they been developed for the Gram-positive Corynebacterium glutamicum. Both bacteria are widely used for biotechnological amino acid production. In this article, in addition to the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, we describe recent applications of DNA microarray technology regarding amino acid production in C. glutamicum and E. coli. We also discuss the impact of functional genomics studies on fundamental as well as applied aspects of amino acid production with C. glutamicum and E. coli.

  6. Relationship between gene co-expression and probe localization on microarray slides

    Directory of Open Access Journals (Sweden)

    Qian Jiang

    2003-12-01

    Full Text Available Abstract Background Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. Results In this work we studied the association between the co-expression of genes, their location on the chromosome and their location on the microarray slides by analyzing a number of eukaryotic expression datasets, derived from the S. cerevisiae, C. elegans, and D. melanogaster. We find that in several different yeast microarray experiments the distribution of the number of gene pairs with correlated expression profiles as a function of chromosomal spacing is peaked at short separations and has two superimposed periodicities. The longer periodicity has a spacing of 22 genes (~42 Kb, and the shorter periodicity is 2 genes (~4 Kb. Conclusion The relative positioning of DNA probes on microarray slides and source plates introduces subtle but significant correlations between pairs of genes. Careful consideration of this spatial artifact is important for analysis of microarray expression data. It is particularly relevant to recent microarray analyses that suggest that co-expressed genes cluster along chromosomes or are spaced by multiples of a fixed number of genes along the chromosome.

  7. SAMMD: Staphylococcus aureus Microarray Meta-Database

    Directory of Open Access Journals (Sweden)

    Elasri Mohamed O

    2007-10-01

    Full Text Available Abstract Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL. Conclusion SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9500 entries for regulated genes, from 67 microarray

  8. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars;

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...

  9. 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.

  10. Goober: a fully integrated and user-friendly microarray data management and analysis solution for core labs and bench biologists.

    Science.gov (United States)

    Luo, Wen; Gudipati, Murali; Jung, Kevin; Chen, Mao; Marschke, Keith B

    2009-08-23

    Despite the large number of software tools developed to address different areas of microarray data analysis, very few offer an all-in-one solution with little learning curve. For microarray core labs, there are even fewer software packages available to help with their routine but critical tasks, such as data quality control (QC) and inventory management. We have developed a simple-to-use web portal to allow bench biologists to analyze and query complicated microarray data and related biological pathways without prior training. Both experiment-based and gene-based analysis can be easily performed, even for the first-time user, through the intuitive multi-layer design and interactive graphic links. While being friendly to inexperienced users, most parameters in Goober can be easily adjusted via drop-down menus to allow advanced users to tailor their needs and perform more complicated analysis. Moreover, we have integrated graphic pathway analysis into the website to help users examine microarray data within the relevant biological content. Goober also contains features that cover most of the common tasks in microarray core labs, such as real time array QC, data loading, array usage and inventory tracking. Overall, Goober is a complete microarray solution to help biologists instantly discover valuable information from a microarray experiment and enhance the quality and productivity of microarray core labs. The whole package is freely available at http://sourceforge.net/projects/goober. A demo web server is available at http://www.goober-array.org.

  11. Use of a Novel Two Color PALM Method to Examine Structural Properties of Drp1 Helical Rings during Mammalian Mitochondrial Fission In Situ

    Science.gov (United States)

    Rosenbloom, Alyssa Blair

    In this thesis, we accomplish two goals: 1) we develop a novel two color photoactivatable light microscopy (PALM) method for imaging in mammalian cells and 2) we explore our original biological question and discern the structural properties of the Drp1 helical ring during fission. We established that mitochondrial membranes can be distinguished with the available photoactivatable fluorescent protein mEos2. However, we were not able to use any of the published photoactivatable and photoswitchable green fluorescent proteins, predominantly because of an inability to identify individual fluorescent events due to rapidity of the photoswitiching. Based on published crystal structures, we created novel Dronpa variants with increasing steric hindrance around the chromophore, likely partially inhibiting the isomerization. We replaced Val157 with isoleucine, leucine, or phenyalanine. DronpaV157F showed no fluorescence and was discarded. DronpaV157I and DronpaV157L showed photoswitchable green fluorescence, with individual fluorescent events that were more easily discerned. DronpaV157L in particular had bright fluorescent events that were well separated when imaged in mammalian cells at 20 Hz. We named this new variant rsKame. Using PALM we successfully imaged rsKame expressed and localized to the mammalian mitochondrial inner membrane. With the novel photoswitchable fluorescent protein, rsKame, available, we returned to the development of a novel two color PALM method. We chose PAmCherry1 as the partner for rsKame since PAmCherry1 has distinct and well separated excitation/emission spectra from rsKame and is not activated by low 405 nm laser power density. We first imaged rsKame with 405 nm activation at (0.61 mW/mm2) and 488 nm activation/excitation (5.87 W/mm 2) to completion. We then imaged PAmCherry1 with increasing 405 nm activation (0.6-6.0 W/mm2) and 561 nm excitation (22 W/mm 2). With the novel PALM imaging method, we labeled the inner and outer mitochondrial

  12. Terahertz Emission Dependence on the Fundamental Optical Intensity in Generating Terahertz Waves from Two-Color Laser-Induced Gas Plasma

    Institute of Scientific and Technical Information of China (English)

    DAI Hou-Mei; LIU Jin-Song

    2011-01-01

    A transient photocurrent model is used to explain terahertz ermission from gas plasma irritated by two-color laser pulses,with one the second harmonic of the other.Taking multiple degrees of ionization into account,the gas ionization process at different laser intensities from 1014 W/cm2 to 1015 W/cm2 is discussed.The results show that when Iω ≥ 6 × 1014 W/cm2,double ionization plays an important role in producing electrons.The corresponding terahertz spectra and waveforms are calculated,showing that increasing laser intensity can broaden the spectra to high frequencies and enhance the terahertz field.A promising method for generating terahertz (THz) waves involves emission from laser induced gas plasmas,which was first introduced hy Hamster et al.[1,2] By focusing laser femtosecond pulses with intensity greater than the thresholl for ionization of the gas molecules,one can obtain significant plasma formation.The ionized electrons will then accelerate by the lapser ponderomotive force,thus an electromagnetic pulse at THz frcqucncies can be produced.Since then,other plasma-based THz generation scheines have been proposed.L(o)ffler et al.,[3,4] applied an external dc bias to the plasma region,leading to an approximately one order of magnitude increase in the THz field strength.%A transient photocurrent model is used to explain terahertz emission from gas plasma irritated by two-color laser pulses, with one the second harmonic of the other. Taking multiple degrees of iom'xntion into account, the gas ionizntion process at different laser intensities from 1014 W/cm2 to 1015 W/cm2 is discussed. The results show that when /w > 6 X 1014 W/cin2, double ionization plays an important role in producing electrons. The corresponding terahertz spectra and waveforms are calculated, showing that increasing laser intensity can broaden the spectra to high frequencies and enhance the terahertz Geld.

  13. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  14. PATMA: parser of archival tissue microarray.

    Science.gov (United States)

    Roszkowiak, Lukasz; Lopez, Carlos

    2016-01-01

    Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  15. Subtype Identification of Avian Influenza Virus on DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    WANG Xiu-rong; YU Kang-zhen; DENG Guo-hua; SHI Rui; LIU Li-ling; QIAO Chuan-ling; BAO Hong-mei; KONG Xian-gang; CHEN Hua-lan

    2005-01-01

    We have developed a rapid microarray-based assay for the reliable detection of H5, H7 and H9 subtypes of avian influenza virus (AIV). The strains used in the experiment were A/Goose/Guangdong/1/96 (H5N1), A/African starling/983/79 (H7N1) and A/Turkey/Wiscosin/1/66 (H9N2). The capture DNAs clones which encoding approximate 500-bp avian influenza virus gene fragments obtained by RT-PCR, were spotted on a slide-bound microarray. Cy5-1abeled fluorescent cDNAs,which generated from virus RNA during reverse transcription were hybridized to these capture DNAs. These capture DNAs contained multiple fragments of the hemagglutinin and matrix protein genes of AIV respectively, for subtyping and typing AIV. The arrays were scanned to determine the probe binding sites. The hybridization pattern agreed approximately with the known grid location of each target. The results show that DNA microarray technology provides a useful diagnostic method for AIV.

  16. DNA Microarray Technologies: A Novel Approach to Geonomic Research

    Energy Technology Data Exchange (ETDEWEB)

    Hinman, R.; Thrall, B.; Wong, K,

    2002-01-01

    A cDNA microarray allows biologists to examine the expression of thousands of genes simultaneously. Researchers may analyze the complete transcriptional program of an organism in response to specific physiological or developmental conditions. By design, a cDNA microarray is an experiment with many variables and few controls. One question that inevitably arises when working with a cDNA microarray is data reproducibility. How easy is it to confirm mRNA expression patterns? In this paper, a case study involving the treatment of a murine macrophage RAW 264.7 cell line with tumor necrosis factor alpha (TNF) was used to obtain a rough estimate of data reproducibility. Two trials were examined and a list of genes displaying either a > 2-fold or > 4-fold increase in gene expression was compiled. Variations in signal mean ratios between the two slides were observed. We can assume that erring in reproducibility may be compensated by greater inductive levels of similar genes. Steps taken to obtain results included serum starvation of cells before treatment, tests of mRNA for quality/consistency, and data normalization.

  17. Sequence-dependent fluorescence of cyanine dyes on microarrays.

    Science.gov (United States)

    Agbavwe, Christy; Somoza, Mark M

    2011-01-01

    Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5'-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5' guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5'-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.

  18. Sequence-dependent fluorescence of cyanine dyes on microarrays.

    Directory of Open Access Journals (Sweden)

    Christy Agbavwe

    Full Text Available Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5'-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5' guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5'-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.

  19. THEME: a web tool for loop-design microarray data analysis.

    Science.gov (United States)

    Chen, Chaang-Ray; Shu, Wun-Yi; Tsai, Min-Lung; Cheng, Wei-Chung; Hsu, Ian C

    2012-02-01

    A number of recent studies have shown that loop-design is more efficient than reference control design. Data analysis for loop-design microarray experiments is commonly undertaken using linear models and statistical tests. These techniques require specialized knowledge in statistical programming. However, limited loop-design web-based tools are available. We have developed the THEME (Tsing Hua Engine of Microarray Experiment) that exploits all necessary data analysis tools for loop-design microarray studies. THEME allows users to construct linear models and to apply multiple user-defined statistical tests of hypotheses for detection of DEG (differentially expressed genes). Users can modify entries of design matrix for experimental design as well as that of contrast matrix for statistical tests of hypotheses. The output of multiple user-defined statistical tests of hypotheses, DEG lists, can be cross-validated. The web platform provides data assessment and visualization tools that significantly assist users when evaluating the performance of microarray experimental procedures. THEME is also a MIAME (Minimal Information About a Microarray Experiment) compliant system, which enables users to export formatted files for GEO (Gene Expression Omnibus) submission. THEME offers comprehensive web services to biologists for data analysis of loop-design microarray experiments. This web-based resource is especially useful for core facility service as well as collaboration projects when researchers are not at the same site. Data analysis procedures, starting from uploading raw data files to retrieving DEG lists, can be flexibly operated with natural workflows. These features make THEME a reliable and powerful on-line system for data analysis of loop-design microarrays. The THEME server is available at http://metadb.bmes.nthu.edu.tw/theme/.

  20. BASE--2nd generation software for microarray data management and analysis.

    Science.gov (United States)

    Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari

    2009-10-12

    Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.

  1. BASE - 2nd generation software for microarray data management and analysis

    Directory of Open Access Journals (Sweden)

    Nordborg Nicklas

    2009-10-01

    Full Text Available Abstract Background Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. Results The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. Conclusion BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.

  2. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements

    Directory of Open Access Journals (Sweden)

    Scully Adam T

    2007-02-01

    Full Text Available Abstract Background Environmental ozone can rapidly degrade cyanine 5 (Cy5, a fluorescent dye commonly used in microarray gene expression studies. Cyanine 3 (Cy3 is much less affected by atmospheric ozone. Degradation of the Cy5 signal relative to the Cy3 signal in 2-color microarrays will adversely reduce the Cy5/Cy3 ratio resulting in unreliable microarray data. Results Ozone in central Arkansas typically ranges between ~22 ppb to ~46 ppb and can be as high as 60–100 ppb depending upon season, meteorological conditions, and time of day. These levels of ozone are common in many areas of the country during the summer. A carbon filter was installed in the laboratory air handling system to reduce ozone levels in the microarray laboratory. In addition, the airflow was balanced to prevent non-filtered air from entering the laboratory. These modifications reduced the ozone within the microarray laboratory to ~2–4 ppb. Data presented here document reductions in Cy5 signal on both in-house produced microarrays and commercial microarrays as a result of exposure to unfiltered air. Comparisons of identically hybridized microarrays exposed to either carbon-filtered or unfiltered air demonstrated the protective effect of carbon-filtration on microarray data as indicated by Cy5 and Cy3 intensities. LOWESS normalization of the data was not able to completely overcome the effect of ozone-induced reduction of Cy5 signal. Experiments were also conducted to examine the effects of high humidity on microarray quality. Modest, but significant, increases in Cy5 and Cy3 signal intensities were observed after 2 or 4 hours at 98–99% humidity compared to 42% humidity. Conclusion Simple installation of carbon filters in the laboratory air handling system resulted in low and consistent ozone levels. This allowed the accurate determination of gene expression by microarray using Cy5 and Cy3 fluorescent dyes.

  3. Chromosomal microarray versus karyotyping for prenatal diagnosis.

    Science.gov (United States)

    Wapner, Ronald J; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C; Eng, Christine M; Zachary, Julia M; Savage, Melissa; Platt, Lawrence D; Saltzman, Daniel; Grobman, William A; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N; Thom, Elizabeth A; Beaudet, Arthur L; Ledbetter, David H; Shaffer, Lisa G; Jackson, Laird

    2012-12-06

    Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down's syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.).

  4. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets.

    Science.gov (United States)

    Yang, Jianji; Cohen, Aaron; Hersh, William

    2009-02-05

    Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS) is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html.

  5. Development of a DNA-based microarray for the detection of zoonotic pathogens in rodent species.

    Science.gov (United States)

    Giles, Timothy; Yon, Lisa; Hannant, Duncan; Barrow, Paul; Abu-Median, Abu-Bakr

    2015-12-01

    The demand for diagnostic tools that allow simultaneous screening of samples for multiple pathogens is increasing because they overcome the limitations of other methods, which can only screen for a single or a few pathogens at a time. Microarrays offer the advantages of being capable to test a large number of samples simultaneously, screening for multiple pathogen types per sample and having comparable sensitivity to existing methods such as PCR. Array design is often considered the most important process in any microarray experiment and can be the deciding factor in the success of a study. There are currently no microarrays for simultaneous detection of rodent-borne pathogens. The aim of this report is to explicate the design, development and evaluation of a microarray platform for use as a screening tool that combines ease of use and rapid identification of a number of rodent-borne pathogens of zoonotic importance. Nucleic acid was amplified by multiplex biotinylation PCR prior to hybridisation onto microarrays. The array sensitivity was comparable to standard PCR, though less sensitive than real-time PCR. The array presented here is a prototype microarray identification system for zoonotic pathogens that can infect rodent species.

  6. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  7. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  8. The PowerAtlas: a power and sample size atlas for microarray experimental design and research

    Directory of Open Access Journals (Sweden)

    Wang Jelai

    2006-02-01

    Full Text Available Abstract Background Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. Results To address this challenge, we have developed a Microrarray PowerAtlas 1. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO. The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC. Conclusion This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes.

  9. Review: DNA Microarray Technology and Drug Development

    Directory of Open Access Journals (Sweden)

    Sushma Drabu

    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 control
    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 microarray
    promises to be the next generation sequencer which could explain how organisms evolve and adapt looking
    at the whole

  10. GenePublisher: automated analysis of DNA microarray data

    DEFF Research Database (Denmark)

    Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, T.

    2003-01-01

    GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with aspecification of the data. The server performs normalization......, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user....

  11. High throughput production of mouse monoclonal antibodies using antigen microarrays

    DEFF Research Database (Denmark)

    De Masi, Federico; Chiarella, P.; Wilhelm, H.;

    2005-01-01

    Recent advances in proteomics research underscore the increasing need for high-affinity monoclonal antibodies, which are still generated with lengthy, low-throughput antibody production techniques. Here we present a semi-automated, high-throughput method of hybridoma generation and identification....... Monoclonal antibodies were raised to different targets in single batch runs of 6-10 wk using multiplexed immunisations, automated fusion and cell-culture, and a novel antigen-coated microarray-screening assay. In a large-scale experiment, where eight mice were immunized with ten antigens each, we generated...

  12. Posttranslational Modification Assays on Functional Protein Microarrays.

    Science.gov (United States)

    Neiswinger, Johnathan; Uzoma, Ijeoma; Cox, Eric; Rho, HeeSool; Jeong, Jun Seop; Zhu, Heng

    2016-10-03

    Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs-phosphorylation, acetylation, ubiquitylation, and SUMOylation-have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.

  13. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  14. Hybridization and Selective Release of DNA Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy

  15. Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots

    Directory of Open Access Journals (Sweden)

    Song Yang

    2006-01-01

    Full Text Available We developed a quality assurance (QA tool, namely microarray outlier filter (MOF, and have applied it to our microarray datasets for the identification of problematic arrays. Our approach is based on the comparison of the arrays using the correlation coefficient and the number of outlier spots generated on each array to reveal outlier arrays. For a human universal reference (HUR dataset, which is used as a technical control in our standard hybridization procedure, 3 outlier arrays were identified out of 35 experiments. For a human blood dataset, 12 outlier arrays were identified from 185 experiments. In general, arrays from human blood samples displayed greater variation in their gene expression profiles than arrays from HUR samples. As a result, MOF identified two distinct patterns in the occurrence of outlier arrays. These results demonstrate that this methodology is a valuable QA practice to identify questionable microarray data prior to downstream analysis.

  16. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data.

    Science.gov (United States)

    Lewin, Alex; Grieve, Ian C

    2006-10-03

    Gene Ontology (GO) terms are often used to assess the results of microarray experiments. The most common way to do this is to perform Fisher's exact tests to find GO terms which are over-represented amongst the genes declared to be differentially expressed in the analysis of the microarray experiment. However, due to the high degree of dependence between GO terms, statistical testing is conservative, and interpretation is difficult. We propose testing groups of GO terms rather than individual terms, to increase statistical power, reduce dependence between tests and improve the interpretation of results. We use the publicly available package POSOC to group the terms. Our method finds groups of GO terms significantly over-represented amongst differentially expressed genes which are not found by Fisher's tests on individual GO terms. Grouping Gene Ontology terms improves the interpretation of gene set enrichment for microarray data.

  17. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data

    Directory of Open Access Journals (Sweden)

    Grieve Ian C

    2006-10-01

    Full Text Available Abstract Background Gene Ontology (GO terms are often used to assess the results of microarray experiments. The most common way to do this is to perform Fisher's exact tests to find GO terms which are over-represented amongst the genes declared to be differentially expressed in the analysis of the microarray experiment. However, due to the high degree of dependence between GO terms, statistical testing is conservative, and interpretation is difficult. Results We propose testing groups of GO terms rather than individual terms, to increase statistical power, reduce dependence between tests and improve the interpretation of results. We use the publicly available package POSOC to group the terms. Our method finds groups of GO terms significantly over-represented amongst differentially expressed genes which are not found by Fisher's tests on individual GO terms. Conclusion Grouping Gene Ontology terms improves the interpretation of gene set enrichment for microarray data.

  18. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  19. 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...

  20. Microarrays - A Key Technology for Glycobiology

    Science.gov (United States)

    Liu, Yan; Feizi, Ten

    Carbohydrate chains of glycoproteins , glycolipids , and proteoglycans can mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is a priority therefore in biomedical sciences. Carbohydrate microarray technology is a new development at the frontiers of glycomics that has revolutionized the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, immune defense mechanisms, and microbe-host interactions. In this chapter we briefly touch upon the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept, and have provided new biological information.

  1. Fabrication of DNA Microarrays on Polydopamine-Modified Gold Thin Films for SPR Imaging Measurements

    Science.gov (United States)

    Wood, Jennifer B.; Szyndler, Megan W.; Halpern, Aaron R.; Cho, Kyunghee

    2013-01-01

    Polydopamine (PDA) films were fabricated on thin film gold substrates in a single-step polymerization-deposition process from dopamine solutions and then employed in the construction of robust DNA microarrays for the ultra-sensitive detection of biomolecules with nanoparticle-enhanced surface plasmon resonance (SPR) imaging. PDA multilayers with thicknesses varying from 1 to 5 nm were characterized with a combination of scanning angle SPR and AFM experiments, and 1.3 ± 0.2 nm PDA multilayers were chosen as an optimal thickness for the SPR imaging measurements. DNA microarrays were then fabricated by the reaction of amine-functionalized single-stranded DNA (ssDNA) oligonucleotides with PDA-modified gold thin film microarray elements, and were subsequently employed in SPR imaging measurements of DNA hybridization adsorption and protein-DNA binding. Concurrent control experiments with noncomplementary ssDNA sequences demonstrated that the adhesive PDA multilayer was also able to provide good resistance to the nonspecific binding of biomolecules. Finally, a series of SPR imaging measurements of the hybridization adsorption of DNA-modified gold nanoparticles onto mixed sequence DNA microarrays were used to confirm that the use of PDA multilayer films is a simple, rapid and versatile method for fabricating DNA microarrays for ultrasensitive nanoparticle-enhanced SPR imaging biosensing. PMID:23902428

  2. Fabrication of DNA microarrays on polydopamine-modified gold thin films for SPR imaging measurements.

    Science.gov (United States)

    Wood, Jennifer B; Szyndler, Megan W; Halpern, Aaron R; Cho, Kyunghee; Corn, Robert M

    2013-08-27

    Polydopamine (PDA) films were fabricated on thin film gold substrates in a single-step polymerization-deposition process from dopamine solutions and then employed in the construction of robust DNA microarrays for the ultrasensitive detection of biomolecules with nanoparticle-enhanced surface plasmon resonance (SPR) imaging. PDA multilayers with thicknesses varying from 1 to 5 nm were characterized with a combination of scanning angle SPR and AFM experiments, and 1.3 ± 0.2 nm PDA multilayers were chosen as an optimal thickness for the SPR imaging measurements. DNA microarrays were then fabricated by the reaction of amine-functionalized single-stranded DNA (ssDNA) oligonucleotides with PDA-modified gold thin film microarray elements, and were subsequently employed in SPR imaging measurements of DNA hybridization adsorption and protein-DNA binding. Concurrent control experiments with non-complementary ssDNA sequences demonstrated that the adhesive PDA multilayer was also able to provide good resistance to the nonspecific binding of biomolecules. Finally, a series of SPR imaging measurements of the hybridization adsorption of DNA-modified gold nanoparticles onto mixed sequence DNA microarrays were used to confirm that the use of PDA multilayer films is a simple, rapid, and versatile method for fabricating DNA microarrays for ultrasensitive nanoparticle-enhanced SPR imaging biosensing.

  3. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results

    Directory of Open Access Journals (Sweden)

    Dai Yilin

    2012-06-01

    Full Text Available Abstract Background Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. Findings We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Conclusion Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  4. 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.

  5. Microarray Assisted Gene Discovery in Ulcerative Colitis

    DEFF Research Database (Denmark)

    Brusgaard, Klaus

    ), and microarray based expression studies. In IBD the increased production of chemo attractants from the inflamed microenvironment results in recruitment of activated CD4+ T lymphocytes which results in tissue damage. Where Th1 cell-derived cytokines has been reported to be essential mediators in CD with high (IFN...

  6. Shrinkage covariance matrix approach for microarray data

    Science.gov (United States)

    Karjanto, Suryaefiza; Aripin, Rasimah

    2013-04-01

    Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

  7. Pineal function : Impact of microarray analysis

    NARCIS (Netherlands)

    Klein, David C.; Bailey, Michael J.; Carter, David A.; Kim, Jong-so; Shi, Qiong; Ho, Anthony K.; Chik, Constance L.; Gaildrat, Pascaline; Morin, Fabrice; Ganguly, Surajit; Rath, Martin F.; Moller, Morten; Sugden, David; Rangel, Zoila G.; Munson, Peter J.; Weller, Joan L.; Coon, Steven L.

    2010-01-01

    Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity to the retin

  8. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    -mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin...

  9. Characterization of the 1 ^5Πu - 1 ^5Πg Band of C_2 by Two-Color Resonant Four-Wave Mixing and Lif

    Science.gov (United States)

    Radi, Peter

    2015-06-01

    The application of two-color resonant four-wave mixing (TC-RFWM) in combination with a discharge slit-source in a molecular beam environment is advantageous for the study of perturbations in C_2. Initial investigations have shown the potential of the method by a detailed deperturbation of the d3Π_g, v=4 state. The deperturbation of the d3Π_g, v=6 state unveiled the presence of the energetically lowest high-spin state of C_2. This dark state gains transition strength through the perturbation process with the d3Π_g, v=6 state yielding weak spectral features that are observable by the high sensitivity of the TC-RFWM technique. The successful deperturbation study of the d3Π_g, v=6 state resulted in the spectroscopic characterization of the quintet (15Πg) and an additional triplet state (d3Π_g, v=19). More recently, investigations have been performed by applying unfolded TC-RFWM to obtain further information on the quintet manifold. The first high-spin transition (15Πu) - 15Πg)) has been observed via an intermediate ``gateway'' state exhibiting both substantial triplet and quintet character owing to the perturbation between the 15Πg), v=0 and the d3Π_g, v=6 states. The high-lying quintet state is found to be predissociative and displays a shallow potential that accommodates three vibrational levels only. Further studies of the high-spin system will be presented in this contribution. By applying TC-RFWM and laser-induced fluorescence, data on the vibrational structure of the 15Πu - 15Πg system is obtained. The results are combined with high-level ab initio computations at the multi-reference configuration interaction (MRCI) level of theory and the largest possible basis currently implemented in the 2012 version of MOLPRO. P. Bornhauser, G. Knopp, T. Gerber, and P.P. Radi, Journal of Molecular Spectroscopy 262, 69 (2010) P. Bornhauser, Y. Sych, G. Knopp, T. Gerber, and P.P. Radi, Journal of Chemical Physics 134, 044302 (2011) Bornhauser, P., Marquardt, R

  10. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Hyunseok P Kang

    2010-01-01

    Full Text Available Background: Tissue microarrays (TMAs are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs, which are global in scope. We present an OWL (Web Ontology Language schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

  11. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.

    Energy Technology Data Exchange (ETDEWEB)

    Rohde, Rachel M.; Timlin, Jerilyn Ann

    2005-11-01

    This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.

  12. 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

  13. Design of a covalently bonded glycosphingolipid microarray.

    Science.gov (United States)

    Arigi, Emma; Blixt, Ola; Buschard, Karsten; Clausen, Henrik; Levery, Steven B

    2012-01-01

    Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform for in vitro study of their functional interactions. However, with few exceptions, the most widely used microarray platforms display only the glycan moiety of GSLs, which not only ignores potential modulating effects of the lipid aglycone, but inherently limits the scope of application, excluding, for example, the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2-mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin, a monoclonal antibody to sulfatide, Sulph 1; and a polyclonal antiserum reactive to asialo-G(M2)). Preliminary evaluation of the method indicated successful immobilization of the GSLs, and selective binding of test probes. The potential utility of this methodology for designing covalent microarrays that incorporate GSLs for serodiagnosis is discussed.

  14. Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.

    Science.gov (United States)

    Griffith, Obi L; Pleasance, Erin D; Fulton, Debra L; Oveisi, Mehrdad; Ester, Martin; Siddiqui, Asim S; Jones, Steven J M

    2005-10-01

    Large amounts of gene expression data from several different technologies are becoming available to the scientific community. A common practice is to use these data to calculate global gene coexpression for validation or integration of other "omic" data. To assess the utility of publicly available datasets for this purpose we have analyzed Homo sapiens data from 1202 cDNA microarray experiments, 242 SAGE libraries, and 667 Affymetrix oligonucleotide microarray experiments. The three datasets compared demonstrate significant but low levels of global concordance (rc<0.11). Assessment against Gene Ontology (GO) revealed that all three platforms identify more coexpressed gene pairs with common biological processes than expected by chance. As the Pearson correlation for a gene pair increased it was more likely to be confirmed by GO. The Affymetrix dataset performed best individually with gene pairs of correlation 0.9-1.0 confirmed by GO in 74% of cases. However, in all cases, gene pairs confirmed by multiple platforms were more likely to be confirmed by GO. We show that combining results from different expression platforms increases reliability of coexpression. A comparison with other recently published coexpression studies found similar results in terms of performance against GO but with each method producing distinctly different gene pair lists.

  15. Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

    NARCIS (Netherlands)

    Neerincx, P.B.T.; Casel, P.; Prickett, D.; Nie, H.; Watson, M.; Leunissen, J.A.M.; Groenen, M.A.M.; Klopp, C.

    2009-01-01

    Background - Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/

  16. Pathways analysis: combining microarray data and physiological data to study myogenesis

    NARCIS (Netherlands)

    Pas, te M.F.W.; Hulsegge, B.; Pool, M.H.

    2007-01-01

    Microarray experiments investigate the changes in the expression of the transcriptome of a tissue during biological processes such as development of the tissue. Analysis usually produces a list of up and down regulated genes. While this in itself mayhighlight important biological processes taking

  17. Detection of protein microarrays by oblique-incidence reflectivity difference technique

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Biological microarrays with different proteins and different protein concentrations are detected without external labeling by an oblique-incidence reflectivity difference (OIRD) technique. The initial experiment results reveal that the intensities of OIRD signals can distinguish the different proteins and concentrations of protein. The OIRD technique promises feasible applications to life sciences for label-free and high-throughput detection.

  18. Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

    NARCIS (Netherlands)

    Neerincx, P.B.T.; Casel, P.; Prickett, D.; Nie, H.; Watson, M.; Leunissen, J.A.M.; Groenen, M.A.M.; Klopp, C.

    2009-01-01

    Background - Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/

  19. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  20. 基于彩色CCD的双色与三色比色测温法比较研究%Comparative Study on Two-Color and Three-Color Colorimetric Temperature Measurement Based on Colored CCD

    Institute of Scientific and Technical Information of China (English)

    孙元; 彭小奇

    2015-01-01

    双色与三色比色测温是彩色CCD辐射测温常用方法。通过理论分析和实验研究,分别从测温动态范围和测温精度两方面对双色法和三色法进行了比较研究。研究发现,在光圈快门组合保持不变的条件下,选取红、绿双色进行比色测温具有较宽的测温动态范围;在对辐射体做灰体假设的情况下,三色测温方法具有更高的测温精度。提出了构建一种可切换测温方法的统一测温硬件平台,统一测温平台综合了双色法和三色法两者的优点,可同时满足更宽的测温动态范围和更高的测温精度的要求,应用灵活。%The two-color and three-color colorimetric temperature measurements are major methods of the colored CCD-based radiation thermometry. The dynamic range and temperature measurement accuracy of the two-color and three-color thermometry are analyzed and compared respectively. The theory analysis and experimental results show that the two-color thermometry using red-green colors has much wider dynamic range than the three-color thermome⁃try in the combination of an aperture and shutter. In the other hand,the three-color thermometry has higher accura⁃cy than the two-color method when the radiator is assumed as a gray-body. Finally,the general temperature measure⁃ment platform flexibly switching the two-color and the three-color thermometry is proposed. The measurement plat⁃form combines the advantages of the two-color and three-color thermometry,which meets the requirements of wide dynamic range and high measurement accuracy.

  1. Post-normalization quality assessment visualization of microarray data

    NARCIS (Netherlands)

    McClure, John; Wit, Ernst

    2003-01-01

    Post-normalization checking of microarrays rarely occurs, despite the problems that using unreliable data for inference can cause. This paper considers a number of different ways to check microarrays after normalization for a variety of potential problems. Four types of problem with microarray data

  2. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data.

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Burton, Mark; Mose, Kristian Fredløv; Andersen, Klaus Ejner; Hjelmborg, Jacob; Kruse, Torben

    2017-06-06

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

  3. Ontology-based retrieval of bio-medical information based on microarray text corpora

    DEFF Research Database (Denmark)

    Hansen, Kim Allan; Zambach, Sine; Have, Christian Theil

    Microarray technology is often used in gene expression exper- iments. Information retrieval in the context of microarrays has mainly been concerned with the analysis of the numeric data produced; how- ever, the experiments are often annotated with textual metadata. Al- though biomedical resources...... are exponentially growing, the text corpora are sparse and inconsistent in spite of attempts to standardize the format. Ordinary keyword search may in some cases be insucient to nd rele- vant information and the potential benet of using a semantic approach in this context has only been investigated to a limited...

  4. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Burton, Mark

    2017-01-01

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering...... the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray...... time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health....

  5. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Burton, Mark

    2017-01-01

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering...... the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray...

  6. FiRe and microarrays: a fast answer to burning questions.

    Science.gov (United States)

    Garcion, Christophe; Baltensperger, Richard; Fournier, Thomas; Pasquier, Jérôme; Schnetzer, Marc-Adrien; Gabriel, Jean-Pierre; Métraux, Jean-Pierre

    2006-07-01

    FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .

  7. Bioinformatics/biostatistics: microarray analysis.

    Science.gov (United States)

    Eichler, Gabriel S

    2012-01-01

    The quantity and complexity of the molecular-level data generated in both research and clinical settings require the use of sophisticated, powerful computational interpretation techniques. It is for this reason that bioinformatic analysis of complex molecular profiling data has become a fundamental technology in the development of personalized medicine. This chapter provides a high-level overview of the field of bioinformatics and outlines several, classic bioinformatic approaches. The highlighted approaches can be aptly applied to nearly any sort of high-dimensional genomic, proteomic, or metabolomic experiments. Reviewed technologies in this chapter include traditional clustering analysis, the Gene Expression Dynamics Inspector (GEDI), GoMiner (GoMiner), Gene Set Enrichment Analysis (GSEA), and the Learner of Functional Enrichment (LeFE).

  8. Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines.

    Science.gov (United States)

    Tra, Yolande V; Evans, Irene M

    2010-01-01

    BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course.

  9. Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

    Science.gov (United States)

    Evans, Irene M.

    2010-01-01

    BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course. PMID:20810954

  10. Evaluation criteria of rat hepatocytes transcriptome analysis under the influence of interferon alpha by DNA microarray

    Directory of Open Access Journals (Sweden)

    Kuklin A. V.

    2013-10-01

    Full Text Available The changes induced in transcriptome of rat hepatocytes treated with interferon alpha (IFN during three and six hours were analyzed by DNA microarray. Aim. To conduct a stepwise analysis of the results of microarray experiment and to determine whether they meet/fail to the conventional requirements. Methods. The files obtained after scanning microarrays were subjected to the analysis in statistical environment R by Bioconductor’s packages «affy», «simpleaffy», «affyPLM» and BRB Array Tools software for paired T-test. Results. All microarrays had quality metrics lying within recommended ranges, passed quality control, were normalized and are comparable with each other. The T-test revealed 28 and 124 differentially expressed genes after three and six hours of cells cultivation with IFNα , respectively. Conclusions. The obtained data meet the conventional criteria of quality and are applicable for further evaluation of their biological significance. The R-codes used in this study can be used for the analysis of the microarrays data.

  11. Generation of a non-small cell lung cancer transcriptome microarray

    Directory of Open Access Journals (Sweden)

    Johnston Patrick G

    2008-05-01

    Full Text Available Abstract Background Non-small cell lung cancer (NSCLC is the leading cause of cancer mortality worldwide. At present no reliable biomarkers are available to guide the management of this condition. Microarray technology may allow appropriate biomarkers to be identified but present platforms are lacking disease focus and are thus likely to miss potentially vital information contained in patient tissue samples. Methods A combination of large-scale in-house sequencing, gene expression profiling and public sequence and gene expression data mining were used to characterise the transcriptome of NSCLC and the data used to generate a disease-focused microarray – the Lung Cancer DSA research tool. Results Built on the Affymetrix GeneChip platform, the Lung Cancer DSA research tool allows for interrogation of ~60,000 transcripts relevant to Lung Cancer, tens of thousands of which are unavailable on leading commercial microarrays. Conclusion We have developed the first high-density disease specific transcriptome microarray. We present the array design process and the results of experiments carried out to demonstrate the array's utility. This approach serves as a template for the development of other disease transcriptome microarrays, including non-neoplastic diseases.

  12. Signal oscillation is another reason for variability in microarray-based gene expression quantification.

    Directory of Open Access Journals (Sweden)

    Raghvendra Singh

    Full Text Available Microarrays have been widely used for various biological applications, such as, gene expression profiling, determination of SNPs, and disease profiling. However, quantification and analysis of microarray data have been a challenge. Previously, by taking into account translational and rotational diffusion of the target DNA, we have shown that the rate of hybridization depends on its size. Here, by mathematical modeling of surface diffusion of transcript, we show that the dynamics of hybridization on DNA microarray surface is inherently oscillatory and the amplitude of oscillation depends on fluid velocity. We found that high fluid velocity enhances the signal without affecting the background, and reduces the oscillation, thereby reducing likelihood of inter- and intra-experiment variability. We further show that a strong probe reduces dependence of signal-to-noise ratio on probe strength, decreasing inter-microarray variability. On the other hand, weaker probes are required for SNP detection. Therefore, we recommend high fluid velocity and strong probes for all microarray applications except determination of SNPs. For SNP detection, we recommend high fluid velocity with weak probe on the spot. We also recommend a surface with high adsorption and desorption rates of transcripts.

  13. A Hybrid Reduction Approach for Enhancing Cancer Classification of Microarray Data

    Directory of Open Access Journals (Sweden)

    Abeer M. Mahmoud

    2014-10-01

    Full Text Available This paper presents a novel hybrid machine learning (MLreduction approach to enhance cancer classification accuracy of microarray data based on two ML gene ranking techniques (T-test and Class Separability (CS. The proposed approach is integrated with two ML classifiers; K-nearest neighbor (KNN and support vector machine (SVM; for mining microarray gene expression profiles. Four public cancer microarray databases are used for evaluating the proposed approach and successfully accomplish the mining process. These are Lymphoma, Leukemia SRBCT, and Lung Cancer. The strategy to select genes only from the training samples and totally excluding the testing samples from the classifier building process is utilized for more accurate and validated results. Also, the computational experiments are illustrated in details and comprehensively presented with literature related results. The results showed that the proposed reduction approach reached promising results of the number of genes supplemented to the classifiers as well as the classification accuracy.

  14. Exhaustive Search for Fuzzy Gene Networks from Microarray Data

    Energy Technology Data Exchange (ETDEWEB)

    Sokhansanj, B A; Fitch, J P; Quong, J N; Quong, A A

    2003-07-07

    Recent technological advances in high-throughput data collection allow for the study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are required to interpret large and complex data sets. Rationally designed system perturbations (e.g. gene knock-outs, metabolite removal, etc) can be used to iteratively refine hypothetical models, leading to a modeling-experiment cycle for high-throughput biological system analysis. We use fuzzy logic gene network models because they have greater resolution than Boolean logic models and do not require the precise parameter measurement needed for chemical kinetics-based modeling. The fuzzy gene network approach is tested by exhaustive search for network models describing cyclin gene interactions in yeast cell cycle microarray data, with preliminary success in recovering interactions predicted by previous biological knowledge and other analysis techniques. Our goal is to further develop this method in combination with experiments we are performing on bacterial regulatory networks.

  15. Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

    A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

  16. Two color morphs of the pelagic yellow-bellied sea snake, Pelamis platura, from different locations of Costa Rica: snake venomics, toxicity, and neutralization by antivenom.

    Science.gov (United States)

    Lomonte, Bruno; Pla, Davinia; Sasa, Mahmood; Tsai, Wan-Chih; Solórzano, Alejandro; Ureña-Díaz, Juan Manuel; Fernández-Montes, María Laura; Mora-Obando, Diana; Sanz, Libia; Gutiérrez, José María; Calvete, Juan J

    2014-05-30

    the treatment of envenomations by this species. Integrative analyses of animal venoms that combine the power of proteomics (venomics) with the characterization of their functional and immunological properties are significantly expanding knowledge on these remarkable bioweapons, both from a basic and a medical perspective. Costa Rica harbors a unique population of the yellow-bellied sea snake, Pelamis platura, that is restricted to a fjord-like gulf (Golfo Dulce). This population differs markedly from oceanic populations found elsewhere along the Pacific coast of this country, by presenting a patternless bright yellow coloration, instead of the typical bicolored or tricolored pattern of this species. It has been suggested that the dominance of this yellow-morph in Golfo Dulce might reflect gene flow restrictions, caused by the oceanographic conditions at this location. The present study demonstrates that the remarkable phenotypic variation between the two color morphs inhabiting Golfo Dulce and Golfo de Papagayo, respectively, is not associated with differences in the expression of venom components, as shown by their conserved RP-HPLC profiles. Proteomic analysis revealed the relatively simple toxin composition of P. platura venom, which contains three predominant types of proteins: three-finger toxins (protein abundance: 49.9%), phospholipases A2 (32.9%), and cysteine-rich secretory proteins (9.1%), together with few minor components. Further, the involvement of these most abundant proteins in the toxic effects of the venom, and their cross-recognition and neutralization by a sea snake antivenom produced against the venom of Enhydrina schistosa, were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Comparison of Alexa Fluor and CyDye for practical DNA microarray use.

    Science.gov (United States)

    Ballard, Joanne L; Peeva, Violet K; deSilva, Christopher J S; Lynch, Jessica L; Swanson, Nigel R

    2007-07-01

    Microarrays are a powerful tool for comparison and understanding of gene expression levels in healthy and diseased states. The method relies upon the assumption that signals from microarray features are a reflection of relative gene expression levels of the cell types under investigation. It has previously been reported that the classical fluorescent dyes used for microarray technology, Cy3 and Cy5, are not ideal due to the decreased stability and fluorescence intensity of the Cy5 dye relative to the Cy3, such that dye bias is an accepted phenomena necessitating dye swap experimental protocols and analysis of differential dye affects. The incentive to find new fluorophores is based on alleviating the problem of dye bias through synonymous performance between counterpart dyes. Alexa Fluor 555 and Alexa Fluor 647 are increasingly promoted as replacements for CyDye in microarray experiments. Performance relates to the molecular and steric similarities, which will vary for each new pair of dyes as well as the spectral integrity for the specific application required. Comparative analysis of the performance of these two competitive dye pairs in practical microarray applications is warranted towards this end. The findings of our study showed that both dye pairs were comparable but that conventional CyDye resulted in significantly higher signal intensities (P 0.05). This translated to greater levels of differential gene expression with CyDye than with the Alexa Fluor counterparts. However, CyDye fluorophores and in particular Cy5, were found to be less photostable over time and following repeated scans in microarray experiments. These results suggest that precautions against potential dye affects will continue to be necessary and that no one dye pair negates this need.

  18. 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.

  19. Optimization of cDNA microarrays procedures using criteria that do not rely on external standards

    Directory of Open Access Journals (Sweden)

    Beisvag Vidar

    2007-10-01

    Full Text Available Abstract Background The measurement of gene expression using microarray technology is a complicated process in which a large number of factors can be varied. Due to the lack of standard calibration samples such as are used in traditional chemical analysis it may be a problem to evaluate whether changes done to the microarray procedure actually improve the identification of truly differentially expressed genes. The purpose of the present work is to report the optimization of several steps in the microarray process both in laboratory practices and in data processing using criteria that do not rely on external standards. Results We performed a cDNA microarry experiment including RNA from samples with high expected differential gene expression termed "high contrasts" (rat cell lines AR42J and NRK52E compared to self-self hybridization, and optimized a pipeline to maximize the number of genes found to be differentially expressed in the "high contrasts" RNA samples by estimating the false discovery rate (FDR using a null distribution obtained from the self-self experiment. The proposed high-contrast versus self-self method (HCSSM requires only four microarrays per evaluation. The effects of blocking reagent dose, filtering, and background corrections methodologies were investigated. In our experiments a dose of 250 ng LNA (locked nucleic acid dT blocker, no background correction and weight based filtering gave the largest number of differentially expressed genes. The choice of background correction method had a stronger impact on the estimated number of differentially expressed genes than the choice of filtering method. Cross platform microarray (Illumina analysis was used to validate that the increase in the number of differentially expressed genes found by HCSSM was real. Conclusion The results show that HCSSM can be a useful and simple approach to optimize microarray procedures without including external standards. Our optimizing method is highly

  20. Viral diagnosis in Indian livestock using customized microarray chips.

    Science.gov (United States)

    Yadav, Brijesh S; Pokhriyal, Mayank; Ratta, Barkha; Kumar, Ajay; Saxena, Meeta; Sharma, Bhaskar

    2015-01-01

    Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable. It should be noted that customized application requires a detailed cost efficiency calculation.

  1. 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.

  2. Harshlight: a "corrective make-up" program for microarray chips

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    Wittkowski Knut M

    2005-12-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs, few tools are available to help with the detection of those defects. Results We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. Conclusion We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.

  3. Cluster stability scores for microarray data in cancer studies

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    Ghosh Debashis

    2003-09-01

    Full Text Available Abstract Background A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical tool used to define disease subtypes from microarray experiments in cancer settings. Assessing cluster reliability poses a major complication in analyzing output from clustering procedures. While most work has focused on estimating the number of clusters in a dataset, the question of stability of individual-level clusters has not been addressed. Results We address this problem by developing cluster stability scores using subsampling techniques. These scores exploit the redundancy in biologically discriminatory information on the chip. Our approach is generic and can be used with any clustering method. We propose procedures for calculating cluster stability scores for situations involving both known and unknown numbers of clusters. We also develop cluster-size adjusted stability scores. The method is illustrated by application to data three cancer studies; one involving childhood cancers, the second involving B-cell lymphoma, and the final is from a malignant melanoma study. Availability Code implementing the proposed analytic method can be obtained at the second author's website.

  4. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  5. Protein microarrays: applications and future challenges.

    Science.gov (United States)

    Stoll, Dieter; Templin, Markus F; Bachmann, Jutta; Joos, Thomas O

    2005-03-01

    Within the last decade protein microarray technology has been successfully applied for the simultaneous identification, quantification and functional analysis of proteins in basic and applied proteome research. These miniaturized and parallelized assay systems have the potential to replace state-of-the-art singleplex analysis systems. However, prior to their general application in robust, reliable, routine and high-throughput applications it is mandatory that they demonstrate robustness, sensitivity, automation and appropriate pricing. In this review, the current state of protein microarray technology will be summarized. Recent applications for the simultaneous determination of a variety of parameters using only minute amounts of sample will be described and future challenges of this cutting-edge technology will be discussed.

  6. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  7. PMD: A Resource for Archiving and Analyzing Protein Microarray data.

    Science.gov (United States)

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-Hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-Ce

    2016-01-27

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

  8. Microarray for serotyping of Bartonella species

    OpenAIRE

    Raoult Didier; Nappez Claude; Bonhomme Cyrille J

    2007-01-01

    Abstract Background Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies. Results We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarra...

  9. Undetected sex chromosome aneuploidy by chromosomal microarray.

    Science.gov (United States)

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay

    2012-11-01

    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  10. Hybridization thermodynamics of NimbleGen Microarrays

    Directory of Open Access Journals (Sweden)

    Posekany Alexandra

    2010-01-01

    Full Text Available Abstract Background While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. Results We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex. Conclusions This analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals.

  11. A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

    Directory of Open Access Journals (Sweden)

    Albers Casper J

    2005-05-01

    Full Text Available Abstract Background In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed. Results A number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance. Conclusion Even in cases where 90 % of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days, the CV was at an acceptable 25 %. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.

  12. Microarray for serotyping of Bartonella species

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2007-06-01

    Full Text Available Abstract Background Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies. Results We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarray for serotyping of Bartonella strains and defining the profile of monoclonal antibodies. Bartonella strains gave a strong positive signal and all were correctly identified. Screening of monoclonal antibodies towards the Gro EL protein of B. clarridgeiae identified 3 groups of antibodies, which were observed with variable affinities against Bartonella strains. Conclusion We demonstrated that microarray of spotted bacteria can be a practical tool for serotyping of unidentified strains or species (and also for affinity determination by polyclonal and monoclonal antibodies. This could be used in research and for identification of bacterial strains.

  13. Chicken sperm transcriptome profiling by microarray analysis.

    Science.gov (United States)

    Singh, R P; Shafeeque, C M; Sharma, S K; Singh, R; Mohan, J; Sastry, K V H; Saxena, V K; Azeez, P A

    2016-03-01

    It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21,639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

  14. Microarrays for rapid identification of plant viruses.

    Science.gov (United States)

    Boonham, Neil; Tomlinson, Jenny; Mumford, Rick

    2007-01-01

    Many factors affect the development and application of diagnostic techniques. Plant viruses are an inherently diverse group that, unlike cellular pathogens, possess no nucleotide sequence type (e.g., ribosomal RNA sequences) in common. Detection of plant viruses is becoming more challenging as globalization of trade, particularly in ornamentals, and the potential effects of climate change enhance the movement of viruses and their vectors, transforming the diagnostic landscape. Techniques for assessing seed, other propagation materials and field samples for the presence of specific viruses include biological indexing, electron microscopy, antibody-based detection, including enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and microarray detection. Of these, microarray detection provides the greatest capability for parallel yet specific testing, and can be used to detect individual, or combinations of viruses and, using current approaches, to do so with a sensitivity comparable to ELISA. Methods based on PCR provide the greatest sensitivity among the listed techniques but are limited in parallel detection capability even in "multiplexed" applications. Various aspects of microarray technology, including probe development, array fabrication, assay target preparation, hybridization, washing, scanning, and interpretation are presented and discussed, for both current and developing technology.

  15. An imputation approach for oligonucleotide microarrays.

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    Ming Li

    Full Text Available Oligonucleotide microarrays are commonly adopted for detecting and qualifying the abundance of molecules in biological samples. Analysis of microarray data starts with recording and interpreting hybridization signals from CEL images. However, many CEL images may be blemished by noises from various sources, observed as "bright spots", "dark clouds", and "shadowy circles", etc. It is crucial that these image defects are correctly identified and properly processed. Existing approaches mainly focus on detecting defect areas and removing affected intensities. In this article, we propose to use a mixed effect model for imputing the affected intensities. The proposed imputation procedure is a single-array-based approach which does not require any biological replicate or between-array normalization. We further examine its performance by using Affymetrix high-density SNP arrays. The results show that this imputation procedure significantly reduces genotyping error rates. We also discuss the necessary adjustments for its potential extension to other oligonucleotide microarrays, such as gene expression profiling. The R source code for the implementation of approach is freely available upon request.

  16. A New Distribution Family for Microarray Data

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    Diana Mabel Kelmansky

    2017-02-01

    Full Text Available The traditional approach with microarray data has been to apply transformations that approximately normalize them, with the drawback of losing the original scale. The alternative stand point taken here is to search for models that fit the data, characterized by the presence of negative values, preserving their scale; one advantage of this strategy is that it facilitates a direct interpretation of the results. A new family of distributions named gpower-normal indexed by p∈R is introduced and it is proven that these variables become normal or truncated normal when a suitable gpower transformation is applied. Expressions are given for moments and quantiles, in terms of the truncated normal density. This new family can be used to model asymmetric data that include non-positive values, as required for microarray analysis. Moreover, it has been proven that the gpower-normal family is a special case of pseudo-dispersion models, inheriting all the good properties of these models, such as asymptotic normality for small variances. A combined maximum likelihood method is proposed to estimate the model parameters, and it is applied to microarray and contamination data. Rcodes are available from the authors upon request.

  17. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.

    Science.gov (United States)

    Stokes, Todd H; Torrance, J T; Li, Henry; Wang, May D

    2008-05-28

    A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (Semantic Agents

  18. Classification, Dose-response Modelling and the Evaluation of Biomarkers in a Micro-array Setting

    OpenAIRE

    Lin, Dan

    2008-01-01

    Dose-response microarray experiments consist of monitoring expression levels of thousands of genes with respect to increasing dose of the treatment under investigation. The primary goal of such an experiment is to establish a dose-response relationship, while the secondary goals are to determine the minimum effective dose level and to identify the shape of the dose-response curve. Recently, Lin et al.[1] discussed several testing procedures to test for monotone trend based on isotonic regress...

  19. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy

    Directory of Open Access Journals (Sweden)

    Archer Kellie J

    2008-02-01

    Full Text Available Abstract Background With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the results from various microarray studies, though most of them rely on distributional assumptions, such as the t-statistic based, mixed-effects model, or Bayesian model methods. However, often the sample size for each individual microarray experiment is small. Therefore, in this paper we present a non-parametric meta-analysis approach for combining data from independent microarray studies, and illustrate its application on two independent Affymetrix GeneChip studies that compared the gene expression of biopsies from kidney transplant recipients with chronic allograft nephropathy (CAN to those with normal functioning allograft. Results The simulation study comparing the non-parametric meta-analysis approach to a commonly used t-statistic based approach shows that the non-parametric approach has better sensitivity and specificity. For the application on the two CAN studies, we identified 309 distinct genes that expressed differently in CAN. By applying Fisher's exact test to identify enriched KEGG pathways among those genes called differentially expressed, we found 6 KEGG pathways to be over-represented among the identified genes. We used the expression measurements of the identified genes as predictors to predict the class labels for 6 additional biopsy samples, and the predicted results all conformed to their pathologist diagnosed class labels. Conclusion We present a new approach for combining data from multiple independent microarray studies. This approach is non-parametric and does not rely on any distributional assumptions. The rationale behind the approach is logically intuitive and can be easily understood by researchers not having advanced training in statistics. Some of the identified genes and pathways have been

  20. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

    Science.gov (United States)

    Kong, Xiangrong; Mas, Valeria; Archer, Kellie J

    2008-02-26

    With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the results from various microarray studies, though most of them rely on distributional assumptions, such as the t-statistic based, mixed-effects model, or Bayesian model methods. However, often the sample size for each individual microarray experiment is small. Therefore, in this paper we present a non-parametric meta-analysis approach for combining data from independent microarray studies, and illustrate its application on two independent Affymetrix GeneChip studies that compared the gene expression of biopsies from kidney transplant recipients with chronic allograft nephropathy (CAN) to those with normal functioning allograft. The simulation study comparing the non-parametric meta-analysis approach to a commonly used t-statistic based approach shows that the non-parametric approach has better sensitivity and specificity. For the application on the two CAN studies, we identified 309 distinct genes that expressed differently in CAN. By applying Fisher's exact test to identify enriched KEGG pathways among those genes called differentially expressed, we found 6 KEGG pathways to be over-represented among the identified genes. We used the expression measurements of the identified genes as predictors to predict the class labels for 6 additional biopsy samples, and the predicted results all conformed to their pathologist diagnosed class labels. We present a new approach for combining data from multiple independent microarray studies. This approach is non-parametric and does not rely on any distributional assumptions. The rationale behind the approach is logically intuitive and can be easily understood by researchers not having advanced training in statistics. Some of the identified genes and pathways have been reported to be relevant to renal diseases. Further study on the

  1. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates.

    Science.gov (United States)

    Boopathi, Pon Arunachalam; Subudhi, Amit Kumar; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-12-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n=14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n=85) present in the arrays showed perfect correlation (r(2)=0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r≥0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates.

  2. Accurate detection of carcinoma cells by use of a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shohei Yamamura

    Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.

  3. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  4. Exploring the use of internal and externalcontrols for assessing microarray technical performance

    Directory of Open Access Journals (Sweden)

    Game Laurence

    2010-12-01

    Full Text Available Abstract Background The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. Results A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes" was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification. External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC metrics. Conclusions These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray

  5. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

    Directory of Open Access Journals (Sweden)

    Cohen Aaron

    2009-02-01

    Full Text Available Abstract Background Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. Results The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. Conclusion The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. Availability GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html

  6. Graph-driven features extraction from microarray data

    CERN Document Server

    Vert, J P; Vert, Jean-Philippe; Kanehisa, Minoru

    2002-01-01

    Gene function prediction from microarray data is a first step toward better understanding the machinery of the cell from relatively cheap and easy-to-produce data. In this paper we investigate whether the knowledge of many metabolic pathways and their catalyzing enzymes accumulated over the years can help improve the performance of classifiers for this problem. The complex network of known biochemical reactions in the cell results in a representation where genes are nodes of a graph. Formulating the problem as a graph-driven features extraction problem, based on the simple idea that relevant features are likely to exhibit correlation with respect to the topology of the graph, we end up with an algorithm which involves encoding the network and the set of expression profiles into kernel functions, and performing a regularized form of canonical correlation analysis in the corresponding reproducible kernel Hilbert spaces. Function prediction experiments for the genes of the yeast S. Cerevisiae validate this appro...

  7. 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.

  8. 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.

  9. Formation and characterization of DNA microarrays at silicon nitride substrates.

    Science.gov (United States)

    Manning, Mary; Redmond, Gareth

    2005-01-01

    A versatile method for direct, covalent attachment of DNA microarrays at silicon nitride layers, previously deposited by chemical vapor deposition at silicon wafer substrates, is reported. Each microarray fabrication process step, from silicon nitride substrate deposition, surface cleaning, amino-silanation, and attachment of a homobifunctional cross-linking molecule to covalent immobilization of probe oligonucleotides, is defined, characterized, and optimized to yield consistent probe microarray quality, homogeneity, and probe-target hybridization performance. The developed microarray fabrication methodology provides excellent (high signal-to-background ratio) and reproducible responsivity to target oligonucleotide hybridization with a rugged chemical stability that permits exposure of arrays to stringent pre- and posthybridization wash conditions through many sustained cycles of reuse. Overall, the achieved performance features compare very favorably with those of more mature glass based microarrays. It is proposed that this DNA microarray fabrication strategy has the potential to provide a viable route toward the successful realization of future integrated DNA biochips.

  10. 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.

  11. Miniaturised Spotter-Compatible Multicapillary Stamping Tool for Microarray Printing

    OpenAIRE

    Drobyshev, Alexei L.; Verkhodanov, Nikolai N; Zasedatelev, Alexander S.

    2007-01-01

    Novel microstamping tool for microarray printing is proposed. The tool is capable to spot up to 127 droplets of different solutions in single touch. It is easily compatible with commercially available microarray spotters. The tool is based on multichannel funnel with polypropylene capillaries inserted into its channels. Superior flexibility is achieved by ability to replace any printing capillary of the tool. As a practical implementation, hydrogel-based microarrays were stamped and successfu...

  12. Miniaturised Spotter-Compatible Multicapillary Stamping Tool for Microarray Printing

    CERN Document Server

    Drobyshev, A L; Zasedatelev, A S; Drobyshev, Alexei L; Verkhodanov, Nikolai N; Zasedatelev, Alexander S

    2007-01-01

    Novel microstamping tool for microarray printing is proposed. The tool is capable to spot up to 127 droplets of different solutions in single touch. It is easily compatible with commercially available microarray spotters. The tool is based on multichannel funnel with polypropylene capillaries inserted into its channels. Superior flexibility is achieved by ability to replace any printing capillary of the tool. As a practical implementation, hydrogel-based microarrays were stamped and successfully applied to identify the Mycobacterium tuberculosis drug resistance.

  13. Identification of candidate genes in osteoporosis by integrated microarray analysis

    OpenAIRE

    Li, J J; Wang, B. Q.; Fei, Q.; Yang, Y; Li, D.

    2017-01-01

    Objectives In order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis. Methods We searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed...

  14. Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data

    OpenAIRE

    Vehkala, Minna; Shubin, Mikhail; Connor, Thomas Richard; Thomson, Nicholas R.; Corander, Jukka

    2015-01-01

    Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, resp...

  15. 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...

  16. Chemiluminescence microarrays in analytical chemistry: a critical review.

    Science.gov (United States)

    Seidel, Michael; Niessner, Reinhard

    2014-09-01

    Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review.

  17. An algorithm for finding biologically significant features in microarray data based on a priori manifold learning.

    Science.gov (United States)

    Hira, Zena M; Trigeorgis, George; Gillies, Duncan F

    2014-01-01

    Microarray databases are a large source of genetic data, which, upon proper analysis, could enhance our understanding of biology and medicine. Many microarray experiments have been designed to investigate the genetic mechanisms of cancer, and analytical approaches have been applied in order to classify different types of cancer or distinguish between cancerous and non-cancerous tissue. However, microarrays are high-dimensional datasets with high levels of noise and this causes problems when using machine learning methods. A popular approach to this problem is to search for a set of features that will simplify the structure and to some degree remove the noise from the data. The most widely used approach to feature extraction is principal component analysis (PCA) which assumes a multivariate Gaussian model of the data. More recently, non-linear methods have been investigated. Among these, manifold learning algorithms, for example Isomap, aim to project the data from a higher dimensional space onto a lower dimension one. We have proposed a priori manifold learning for finding a manifold in which a representative set of microarray data is fused with relevant data taken from the KEGG pathway database. Once the manifold has been constructed the raw microarray data is projected onto it and clustering and classification can take place. In contrast to earlier fusion based methods, the prior knowledge from the KEGG databases is not used in, and does not bias the classification process--it merely acts as an aid to find the best space in which to search the data. In our experiments we have found that using our new manifold method gives better classification results than using either PCA or conventional Isomap.

  18. Tissue microarrays: Potential in the Indian subcontinent

    Directory of Open Access Journals (Sweden)

    Venkataraman Girish

    2005-01-01

    Full Text Available Tissue microarrays (TMAs are a means of combining hundreds of specimens of tissue on to a single slide for analysis simultaneously. The evolution of this technology to validate the results of cDNA microarrays has impacted tremendously in accurately identifying prognostic indicators significant in determining survival demographics for patients. TMAs can be generated from archival paraffin blocks, combined with sophisticated image analysis software for reading TMA immunohistochemistry, and a staggering amount of useful information can be generated in terms of the biomarkers useful in predicting patient outcome. There is a wide range of uses for the TMA technology including profiling of specific proteins in cancerous tissues and non-cancerous tissues. Given the wide variety of tissue resources available in India, investment in a dedicated TMA facility will be of immense use in the research arena in India. This review article discusses the basics of TMA construction, design, the software available for the analysis of this technology and its relevance to Indian scientists. A potential workflow structure for setting up a TMA facility is also included.

  19. Microarray analysis of the developing cortex.

    Science.gov (United States)

    Semeralul, Mawahib O; Boutros, Paul C; Likhodi, Olga; Okey, Allan B; Van Tol, Hubert H M; Wong, Albert H C

    2006-12-01

    Abnormal development of the prefrontal cortex (PFC) is associated with a number of neuropsychiatric disorders that have an onset in childhood or adolescence. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. To map the overall pattern of changes in cortical gene transcripts during postnatal development, we made serial measurements of mRNA levels in mouse PFC using oligonucleotide microarrays. We observed changes in mRNA transcripts consistent with known postnatal morphological and biochemical events. Overall, most transcripts that changed significantly showed a progressive decrease in abundance after birth, with the majority of change between postnatal weeks 2 and 4. Genes with cell proliferative, cytoskeletal, extracellular matrix, plasma membrane lipid/transport, protein folding, and regulatory functions had decreases in mRNA levels. Quantitative PCR verified the microarray results for six selected genes: DNA methyltransferase 3A (Dnmt3a), procollagen, type III, alpha 1 (Col3a1), solute carrier family 16 (monocarboxylic acid transporters), member 1 (Slc16a1), MARCKS-like 1 (Marcksl1), nidogen 1 (Nid1) and 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) (Bdh).

  20. Stochastic models for inferring genetic regulation from microarray gene expression data.

    Science.gov (United States)

    Tian, Tianhai

    2010-03-01

    Microarray expression profiles are inherently noisy and many different sources of variation exist in microarray experiments. It is still a significant challenge to develop stochastic models to realize noise in microarray expression profiles, which has profound influence on the reverse engineering of genetic regulation. Using the target genes of the tumour suppressor gene p53 as the test problem, we developed stochastic differential equation models and established the relationship between the noise strength of stochastic models and parameters of an error model for describing the distribution of the microarray measurements. Numerical results indicate that the simulated variance from stochastic models with a stochastic degradation process can be represented by a monomial in terms of the hybridization intensity and the order of the monomial depends on the type of stochastic process. The developed stochastic models with multiple stochastic processes generated simulations whose variance is consistent with the prediction of the error model. This work also established a general method to develop stochastic models from experimental information.

  1. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies

    Directory of Open Access Journals (Sweden)

    Guillermo Lay-Son

    2015-04-01

    Full Text Available OBJECTIVES: Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS: Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan(tm HD Array, Affymetrix, Inc., Santa Clara, CA, USA. Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS: This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION: Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting.

  2. A robust measure of correlation between two genes on a microarray

    Directory of Open Access Journals (Sweden)

    Hicks Leanne

    2007-06-01

    Full Text Available Abstract Background The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to experimental conditions could be co-expressed and show similar patterns of expression on a microarray. Using any of a variety of clustering methods or gene network analyses we can partition genes of interest into groups, clusters, or modules based on measures of similarity. Typically, Pearson correlation is used to measure distance (or similarity before implementing a clustering algorithm. Pearson correlation is quite susceptible to outliers, however, an unfortunate characteristic when dealing with microarray data (well known to be typically quite noisy. Results We propose a resistant similarity metric based on Tukey's biweight estimate of multivariate scale and location. The resistant metric is simply the correlation obtained from a resistant covariance matrix of scale. We give results which demonstrate that our correlation metric is much more resistant than the Pearson correlation while being more efficient than other nonparametric measures of correlation (e.g., Spearman correlation. Additionally, our method gives a systematic gene flagging procedure which is useful when dealing with large amounts of noisy data. Conclusion When dealing with microarray data, which are known to be quite noisy, robust methods should be used. Specifically, robust distances, including the biweight correlation, should be used in clustering and gene network analysis.

  3. Ontology-based, Tissue MicroArray oriented, image centered tissue bank

    Directory of Open Access Journals (Sweden)

    Viti Federica

    2008-04-01

    Full Text Available Abstract Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. Results In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. Conclusions Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.

  4. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data.

    Science.gov (United States)

    Watson, Christopher M; Crinnion, Laura A; Gurgel-Gianetti, Juliana; Harrison, Sally M; Daly, Catherine; Antanavicuite, Agne; Lascelles, Carolina; Markham, Alexander F; Pena, Sergio D J; Bonthron, David T; Carr, Ian M

    2015-09-01

    Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease-causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome-wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.

  5. Development and validation of a flax (Linum usitatissimum L. gene expression oligo microarray

    Directory of Open Access Journals (Sweden)

    Gutierrez Laurent

    2010-10-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars and its cellulose-rich fibres (fibre-flax cultivars used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well

  6. Generation of EST and cDNA Microarray Resources for the Study of Bovine Immunobiology*

    Directory of Open Access Journals (Sweden)

    Coussens PM

    2003-03-01

    unstimulated cells. A second experiment with PBMCs from a different group of animals was performed to test reproducibility of microarray results. There was a high correlation between the 2 experiments (r = 0.72, P

  7. Two-color facility based on a broadly tunable infrared free-electron laser and a subpicosecond-synchronized 10-fs-Ti : Sapphire laser

    NARCIS (Netherlands)

    Knippels, G.M.H.; van de Pol, M.J.; Pellemans, H. P. M.; Planken, P. C. M.; van der Meer, A. F. G.

    1998-01-01

    Subpicosecond synchronization between a mirror-dispersion-controlled 10-fs Ti:sapphire laser and the Free-Electron Laser for Infrared Experiments has been achieved. The measured intensity cross correlation between the two lasers is consistent with a jitter of only 400 fs rms. The wide and continuous

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

    Directory of Open Access Journals (Sweden)

    Gravelat Fabrice

    2010-09-01

    Full Text Available Abstract Background Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality can be used to study a complex environment efficiently. Conclusions We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments

  9. Bulk segregant analysis using single nucleotide polymorphism microarrays.

    Directory of Open Access Journals (Sweden)

    Anthony Becker

    Full Text Available Bulk segregant analysis (BSA using microarrays, and extreme array mapping (XAM have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files.

  10. Obtaining reliable information from minute amounts of RNA using cDNA microarrays

    OpenAIRE

    2002-01-01

    Abstract Background High density cDNA microarray technology provides a powerful tool to survey the activity of thousands of genes in normal and diseased cells, which helps us both to understand the molecular basis of the disease and to identify potential targets for therapeutic intervention. The promise of this technology has been hampered by the large amount of biological material required for the experiments (more than 50 μg of total RNA per array). We have modified an amplification procedu...

  11. Fabrication of DNA Microarrays on Polydopamine-Modified Gold Thin Films for SPR Imaging Measurements

    OpenAIRE

    Wood, Jennifer B.; Szyndler, Megan W.; Halpern, Aaron R.; Cho, Kyunghee; Corn, Robert M.

    2013-01-01

    Polydopamine (PDA) films were fabricated on thin film gold substrates in a single-step polymerization-deposition process from dopamine solutions and then employed in the construction of robust DNA microarrays for the ultra-sensitive detection of biomolecules with nanoparticle-enhanced surface plasmon resonance (SPR) imaging. PDA multilayers with thicknesses varying from 1 to 5 nm were characterized with a combination of scanning angle SPR and AFM experiments, and 1.3 ± 0.2 nm PDA multilayers ...

  12. 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...

  13. Experimental Approaches to Microarray Analysis of Tumor Samples

    Science.gov (United States)

    Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

    2008-01-01

    Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

  14. Defining best practice for microarray analyses in nutrigenomic studies

    NARCIS (Netherlands)

    Garosi, P.; Filippo, C. de; Erk, M. van; Rocca-Serra, P.; Sansone, S.A.; Elliott, R.

    2005-01-01

    Microarrays represent a powerful tool for studies of diet-gene interactions. Their use is, however, associated with a number of technical challenges and potential pitfalls. The cost of microarrays continues to drop but is still comparatively high. This, coupled with the complex logistical issues

  15. 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

  16. 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

  17. Automatic Spot Identification for High Throughput Microarray Analysis

    Science.gov (United States)

    Wu, Eunice; Su, Yan A.; Billings, Eric; Brooks, Bernard R.; Wu, Xiongwu

    2013-01-01

    High throughput microarray analysis has great potential in scientific research, disease diagnosis, and drug discovery. A major hurdle toward high throughput microarray analysis is the time and effort needed to accurately locate gene spots in microarray images. An automatic microarray image processor will allow accurate and efficient determination of spot locations and sizes so that gene expression information can be reliably extracted in a high throughput manner. Current microarray image processing tools require intensive manual operations in addition to the input of grid parameters to correctly and accurately identify gene spots. This work developed a method, herein called auto-spot, to automate the spot identification process. Through a series of correlation and convolution operations, as well as pixel manipulations, this method makes spot identification an automatic and accurate process. Testing with real microarray images has demonstrated that this method is capable of automatically extracting subgrids from microarray images and determining spot locations and sizes within each subgrid, regardless of variations in array patterns and background noises. With this method, we are one step closer to the goal of high throughput microarray analysis. PMID:24298393

  18. Uses of Dendrimers for DNA Microarrays

    Science.gov (United States)

    Caminade, Anne-Marie; Padié, Clément; Laurent, Régis; Maraval, Alexandrine; Majoral, Jean-Pierre

    2006-01-01

    Biosensors such as DNA microarrays and microchips are gaining an increasing importance in medicinal, forensic, and environmental analyses. Such devices are based on the detection of supramolecular interactions called hybridizations that occur between complementary oligonucleotides, one linked to a solid surface (the probe), and the other one to be analyzed (the target). This paper focuses on the improvements that hyperbranched and perfectly defined nanomolecules called dendrimers can provide to this methodology. Two main uses of dendrimers for such purpose have been described up to now; either the dendrimer is used as linker between the solid surface and the probe oligonucleotide, or the dendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the first case the dendrimer generally induces a higher loading of probes and an easier hybridization, due to moving away the solid phase. In the second case the high number of localized labels (generally fluorescent) induces an increased sensitivity, allowing the detection of small quantities of biological entities.

  19. Uses of Dendrimers for DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Majoral

    2006-08-01

    Full Text Available Biosensors such as DNA microarrays and microchips are gaining an increasingimportance in medicinal, forensic, and environmental analyses. Such devices are based onthe detection of supramolecular interactions called hybridizations that occur betweencomplementary oligonucleotides, one linked to a solid surface (the probe, and the other oneto be analyzed (the target. This paper focuses on the improvements that hyperbranched andperfectly defined nanomolecules called dendrimers can provide to this methodology. Twomain uses of dendrimers for such purpose have been described up to now; either thedendrimer is used as linker between the solid surface and the probe oligonucleotide, or thedendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the firstcase the dendrimer generally induces a higher loading of probes and an easier hybridization,due to moving away the solid phase. In the second case the high number of localized labels(generally fluorescent induces an increased sensitivity, allowing the detection of smallquantities of biological entities.

  20. Normalization strategy of microarray gene expression data

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To discuss strategies and methods of normalization on how to deal with and analyze data for different chips with the combination of statistics, mathematics and bioinformatics in order to find significant difference genes. Methods: With Excel and SPSS software, high or low density chips were analyzed through total intensity normalization (TIN) and locally weighted linear regression normalization (LWLRN). Results: These methods effectively reduced systemic errors and made data more comparable and reliable. Conclusion: These methods can search the genes of significant difference, although normalization methods are being developed and need to be improved further. Great breakthrough will be obtained in microarray data normalization analysis and transformation with the development of non-linear technology, software and hardware of computer.

  1. 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.

  2. GEPAS, a web-based tool for microarray data analysis and interpretation

    Science.gov (United States)

    Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Huerta-Cepas, Jaime; Minguez, Pablo; Alloza, Eva; Al-Shahrour, Fátima; Vegas-Azcárate, Susana; Goetz, Stefan; Escobar, Pablo; Garcia-Garcia, Francisco; Conesa, Ana; Montaner, David; Dopazo, Joaquín

    2008-01-01

    Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org. PMID:18508806

  3. 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.

  4. DNA microarray-based mutation discovery and genotyping.

    Science.gov (United States)

    Gresham, David

    2011-01-01

    DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (T (m)) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the T (m) of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

  5. Differential splicing using whole-transcript microarrays

    Directory of Open Access Journals (Sweden)

    Robinson Mark D

    2009-05-01

    Full Text Available Abstract Background The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events. Results We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis. RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of differential splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms. Conclusion We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data. Software implementing our methods is freely available as an R package.

  6. Lipid Microarray Biosensor for Biotoxin Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  7. Polymer microarray technology for stem cell engineering.

    Science.gov (United States)

    Coyle, Robert; Jia, Jia; Mei, Ying

    2016-04-01

    Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. During the past decade, significant progress has been made in developing soluble factors (e.g., small molecules and growth factors) to direct stem cells into a desired phenotype. However, the current lack of suitable synthetic materials to regulate stem cell activity has limited the realization of the enormous potential of stem cells. This can be attributed to a large number of materials properties (e.g., chemical structures and physical properties of materials) that can affect stem cell fate. This makes it challenging to design biomaterials to direct stem cell behavior. To address this, polymer microarray technology has been developed to rapidly identify materials for a variety of stem cell applications. In this article, we summarize recent developments in polymer array technology and their applications in stem cell engineering. Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. In the last decade, significant progress has been made in developing chemically defined media to direct stem cells into a desired phenotype. However, the current lack of the suitable synthetic materials to regulate stem cell activities has been limiting the realization of the potential of stem cells. This can be attributed to the number of variables in material properties (e.g., chemical structures and physical properties) that can affect stem cells. Polymer microarray technology has shown to be a powerful tool to rapidly identify materials for a variety of stem cell applications. Here we summarize recent developments in polymer array technology and their applications in stem cell engineering. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  8. A cell spot microarray method for production of high density siRNA transfection microarrays

    Directory of Open Access Journals (Sweden)

    Mpindi John-Patrick

    2011-03-01

    Full Text Available Abstract Background High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. Results Here, we describe the optimization of a miniaturized cell spot microarray (CSMA method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. Conclusions The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.

  9. Metabolic cytometry: capillary electrophoresis with two-color fluorescence detection for the simultaneous study of two glycosphingolipid metabolic pathways in single primary neurons.

    Science.gov (United States)

    Essaka, David C; Prendergast, Jillian; Keithley, Richard B; Palcic, Monica M; Hindsgaul, Ole; Schnaar, Ronald L; Dovichi, Norman J

    2012-03-20

    Metabolic cytometry is a form of chemical cytometry wherein metabolic cascades are monitored in single cells. We report the first example of metabolic cytometry where two different metabolic pathways are simultaneously monitored. Glycolipid catabolism in primary rat cerebella neurons was probed by incubation with tetramethylrhodamine-labeled GM1 (GM1-TMR). Simultaneously, both catabolism and anabolism were probed by coincubation with BODIPY-FL labeled LacCer (LacCer-BODIPY-FL). In a metabolic cytometry experiment, single cells were incubated with substrate, washed, aspirated into a capillary, and lysed. The components were separated by capillary electrophoresis equipped with a two-spectral channel laser-induced fluorescence detector. One channel monitored fluorescence generated by the metabolic products produced from GM1-TMR and the other monitored the metabolic products produced from LacCer-BODIPY-FL. The metabolic products were identified by comparison with the mobility of a set of standards. The detection system produced at least 6 orders of magnitude dynamic range in each spectral channel with negligible spectral crosstalk. Detection limits were 1 zmol for BODIPY-FL and 500 ymol for tetramethylrhodamine standard solutions.

  10. Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differntial expression

    NARCIS (Netherlands)

    Watson, M.; Perez-Alegre, M.; Denis Baron, M.; Delmas, C.; Dovc, P.; Duval, M.; Foulley, J.L.; Garrido-Pavon, J.J.; Hulsegge, B.; Jafrezic, F.; Jiménez-Marín, A.; Lavric, M.; Lê Cao, K.A.; Marot, G.; Mouzaki, D.; Pool, M.H.; Robert-Granié, C.; San Cristobal, M.; Tosser-Klop, G.; Waddington, D.; Koning, de D.J.

    2007-01-01

    Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised

  11. Development of a cDNA microarray of zebra mussel (Dreissena polymorpha) foot and its use in understanding the early stage of underwater adhesion.

    Science.gov (United States)

    Xu, Wei; Faisal, Mohamed

    2009-05-01

    The underwater adhesion of the zebra mussel (Dreissena polymorpha) to substrates is a complex process that is controlled by a delicate apparatus, the byssus. As a critical activity of the byssus glands embedded in the zebra mussel feet, byssogenesis is highly active to produce numerous byssal threads from the settled juvenile stage through the adult stage in its life cycle. This lifelong activity helps the zebra mussel to firmly attach to substrata underwater, thereby causing severe economic and ecologic impacts. In an attempt to better understand the zebra mussel's byssus activity, a cDNA microarray (ZMB) including 716 genes, generated from a Suppression Subtractive Hybridization (SSH) cDNA library, was printed and used for the comparison of gene expression during zebra mussel adhesion and non-adhesion. To better understand the byssogenesis mechanism, RNA samples from the zebra mussel feet with byssogenesis and without byssogenesis were used in a two-color hybridization to reveal the gene differential expression in the two states. Based on the P values (Pbyssus cDNA microarray is an efficient tool for the studies of differential gene expression in different byssogenesis states, thereby revealing important details of the underwater adhesion.

  12. A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food

    Directory of Open Access Journals (Sweden)

    Noriko Goji

    2012-01-01

    Full Text Available The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.

  13. Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

    Directory of Open Access Journals (Sweden)

    Manish Biyani

    2015-07-01

    Full Text Available Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density, ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era.

  14. Microintaglio Printing for Soft Lithography-Based in Situ Microarrays.

    Science.gov (United States)

    Biyani, Manish; Ichiki, Takanori

    2015-07-14

    Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called "microintaglio printing technology", for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era.

  15. The application of protein microarray assays in psychoneuroimmunology.

    Science.gov (United States)

    Ayling, K; Bowden, T; Tighe, P; Todd, I; Dilnot, E M; Negm, O H; Fairclough, L; Vedhara, K

    2017-01-01

    Protein microarrays are miniaturized multiplex assays that exhibit many advantages over the commonly used enzyme-linked immunosorbent assay (ELISA). This article aims to introduce protein microarrays to readers of Brain, Behavior, and Immunity and demonstrate its utility and validity for use in psychoneuroimmunological research. As part of an ongoing investigation of psychological and behavioral influences on influenza vaccination responses, we optimized a novel protein microarray to quantify influenza-specific antibody levels in human sera. Reproducibility was assessed by calculating intra- and inter-assay coefficients of variance on serially diluted human IgG concentrations. A random selection of samples was analyzed by microarray and ELISA to establish validity of the assay. For IgG concentrations, intra-assay and inter-assay precision profiles demonstrated a mean coefficient of variance of 6.7% and 11.5% respectively. Significant correlations were observed between microarray and ELISA for all antigens, demonstrating the microarray is a valid alternative to ELISA. Protein microarrays are a highly robust, novel assay method that could be of significant benefit for researchers working in psychoneuroimmunology. They offer high throughput, fewer resources per analyte and can examine concurrent neuro-immune-endocrine mechanisms.

  16. An overview of innovations and industrial solutions in Protein Microarray Technology.

    Science.gov (United States)

    Gupta, Shabarni; Manubhai, K P; Kulkarni, Vishwesh; Srivastava, Sanjeeva

    2016-04-01

    The complexity involving protein array technology reflects in the fact that instrumentation and data analysis are subject to change depending on the biological question, technical compatibility of instruments and software used in each experiment. Industry has played a pivotal role in establishing standards for future deliberations in sustenance of these technologies in the form of protein array chips, arrayers, scanning devices, and data analysis software. This has enhanced the outreach of protein microarray technology to researchers across the globe. These have encouraged a surge in the adaptation of "nonclassical" approaches such as DNA-based protein arrays, micro-contact printing, label-free protein detection, and algorithms for data analysis. This review provides a unique overview of these industrial solutions available for protein microarray based studies. It aims at assessing the developments in various commercial platforms, thus providing a holistic overview of various modalities, options, and compatibility; summarizing the journey of this powerful high-throughput technology.

  17. [Development of single base extension-tags microarray for the detection of food-borne pathogens].

    Science.gov (United States)

    Lu, Changyong; Shi, Chunlei; Zhang, Chunxiu; Chen, Jing; Shi, Xianming

    2009-04-01

    We developed single base extension-tags (SBE-tags) microarray to detect eight common food-borne pathogens, including Staphylococcus aureus, Vibrio parahaemolyticus, Listeria monocytogenes, Salmonella, Enterobacter sakazaki, Shigella, Escherichia coli O157:H7 and Campylobacter jejuni. With specific PCR primers identified and integrated for eight food-borne pathogens, target sequences were amplified and purified as template DNA of single base extension-tags reaction. The products were hybridized to microarrays and scanned for fluorescence intensity. The experiment showed a specific and simultaneous detection of eight food-borne pathogens. The system limits is 0.1 pg for a genomic DNA and 5x10(2) CFU/mL for Salmonella typhimurium cultures. The single base extension-tags assay can be used to detect food-borne pathogens rapidly and accurately with a high sensitivity, and provide an efficient way for diagnosis and control of disease caused by food-borne pathogens.

  18. Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Alfred O. Hero

    2004-01-01

    Full Text Available This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery rate (FDR, variance-normalized differential expression levels (paired t statistics, and minimum acceptable difference (MAD. The methodology also provides a set of simultaneous FDR confidence intervals on the true expression differences. The analysis can be implemented as a two-stage algorithm in which there is an initial screen that controls only FDR, which is then followed by a second screen which controls both FDR and MAD. It can also be implemented by computing and thresholding the set of FDR P values for each gene that satisfies the MAD criterion. We illustrate the procedure to identify differentially expressed genes from a wild type versus knockout comparison of microarray data.

  19. An Archived Multi Objective Simulated Annealing Method to Discover Biclusters in Microarray Data

    Directory of Open Access Journals (Sweden)

    Mohsen Lashkargir

    2011-01-01

    Full Text Available With the advent of microarray technology it has been possible to measure thousands of expression values of genes in a single experiment. Analysis of large scale geonomics data, notably gene expression, has initially focused on clustering methods. Recently, biclustering techniques were proposed for revealing submatrices showing unique patterns. Biclustering or simultaneous clustering of both genes and conditions is challenging particularly for the analysis of high-dimensional gene expression data in information retrieval, knowledge discovery, and data mining. In biclustering of microarray data, several objectives have to be optimized simultaneously and often these objectives are in conflict with each other. A multi objective model is very suitable for solving this problem. Our method proposes a algorithm which is based on multi objective Simulated Annealing for discovering biclusters in gene expression data. Experimental result in bench mark data base present a significant improvement in overlap among biclusters and coverage of elements in gene expression and quality of biclusters.

  20. Imaging combined autoimmune and infectious disease microarrays

    Science.gov (United States)

    Ewart, Tom; Raha, Sandeep; Kus, Dorothy; Tarnopolsky, Mark

    2006-09-01

    Bacterial and viral pathogens are implicated in many severe autoimmune diseases, acting through such mechanisms as molecular mimicry, and superantigen activation of T-cells. For example, Helicobacter pylori, well known cause of stomach ulcers and cancers, is also identified in ischaemic heart disease (mimicry of heat shock protein 65), autoimmune pancreatitis, systemic sclerosis, autoimmune thyroiditis (HLA DRB1*0301 allele susceptibility), and Crohn's disease. Successful antibiotic eradication of H.pylori often accompanies their remission. Yet current diagnostic devices, and test-limiting cost containment, impede recognition of the linkage, delaying both diagnosis and therapeutic intervention until the chronic debilitating stage. We designed a 15 minute low cost 39 antigen microarray assay, combining autoimmune, viral and bacterial antigens1. This enables point-of-care serodiagnosis and cost-effective narrowly targeted concurrent antibiotic and monoclonal anti-T-cell and anti-cytokine immunotherapy. Arrays of 26 pathogen and 13 autoimmune antigens with IgG and IgM dilution series were printed in triplicate on epoxysilane covalent binding slides with Teflon well masks. Sera diluted 1:20 were incubated 10 minutes, washed off, anti-IgG-Cy3 (green) and anti-IgM-Dy647 (red) were incubated for 5 minutes, washed off and the slide was read in an ArrayWoRx(e) scanning CCD imager (Applied Precision, Issaquah, WA). As a preliminary model for the combined infectious disease-autoimmune diagnostic microarray we surveyed 98 unidentified, outdated sera that were discarded after Hepatitis B antibody testing. In these, significant IgG or IgM autoantibody levels were found: dsDNA 5, ssDNA 11, Ro 2, RNP 7, SSB 4, gliadin 2, thyroglobulin 13 cases. Since control sera showed no autoantibodies, the high frequency of anti-DNA and anti-thyroglobulin antibodies found in infected sera lend increased support for linkage of infection to subsequent autoimmune disease. Expansion of the antigen

  1. Optimality criteria for the design of 2-color microarray studies.

    Science.gov (United States)

    Kerr, Kathleen F

    2012-01-13

    We discuss the definition and application of design criteria for evaluating the efficiency of 2-color microarray designs. First, we point out that design optimality criteria are defined differently for the regression and block design settings. This has caused some confusion in the literature and warrants clarification. Linear models for microarray data analysis have equivalent formulations as ANOVA or regression models. However, this equivalence does not extend to design criteria. We discuss optimality criterion, and argue against applying regression-style D-optimality to the microarray design problem. We further disfavor E- and D-optimality (as defined in block design) because they are not attuned to scientific questions of interest.

  2. 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....

  3. Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

    Directory of Open Access Journals (Sweden)

    Regiane de Fátima Travensolo

    2009-06-01

    Full Text Available DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized, spotted onto glass slides and the array was hybridized against fluorescently labeled cDNAs. The emitted signals were quantified, normalized and the data were statistically analyzed to verify the differentially expressed genes. According to the data, 104 genes were differentially expressed in XDM2 and 30 genes in BCYE media. The present study showed that DNA microarray technique efficiently differentiate the expressed genes under different conditions.DNA Microarray foi desenvolvida para monitorar a expressão de muitos genes de Xylella fastidiosa, permitindo a comparação de duas situações distintas em um único experimento. Os experimentos foram feitos utilizando células de X. fastidiosa cultivada em dois meios de cultura: BCYE e XDM2. Pares de oligonucleotídeos iniciadores foram sintetizados, depositados em lâminas de vidro e o arranjo foi hibridizado contra cDNAs marcados fluorescentemente. Os sinais emitidos foram quantificados, normalizados e os dados foram estatisticamente analisados para verificar os genes diferencialmente expressos. De acordo com nossos dados, 104 genes foram diferencialmente expressos para o meio de cultura XDM2 e 30 genes para o BCYE. No presente estudo, nós demonstramos que a técnica de DNA microarrays eficientemente diferencia genes expressos sob diferentes condições de cultivo.

  4. Consistent Differential Expression Pattern (CDEP on microarray to identify genes related to metastatic behavior

    Directory of Open Access Journals (Sweden)

    Tsoi Lam C

    2011-11-01

    Full Text Available Abstract Background To utilize the large volume of gene expression information generated from different microarray experiments, several meta-analysis techniques have been developed. Despite these efforts, there remain significant challenges to effectively increasing the statistical power and decreasing the Type I error rate while pooling the heterogeneous datasets from public resources. The objective of this study is to develop a novel meta-analysis approach, Consistent Differential Expression Pattern (CDEP, to identify genes with common differential expression patterns across different datasets. Results We combined False Discovery Rate (FDR estimation and the non-parametric RankProd approach to estimate the Type I error rate in each microarray dataset of the meta-analysis. These Type I error rates from all datasets were then used to identify genes with common differential expression patterns. Our simulation study showed that CDEP achieved higher statistical power and maintained low Type I error rate when compared with two recently proposed meta-analysis approaches. We applied CDEP to analyze microarray data from different laboratories that compared transcription profiles between metastatic and primary cancer of different types. Many genes identified as differentially expressed consistently across different cancer types are in pathways related to metastatic behavior, such as ECM-receptor interaction, focal adhesion, and blood vessel development. We also identified novel genes such as AMIGO2, Gem, and CXCL11 that have not been shown to associate with, but may play roles in, metastasis. Conclusions CDEP is a flexible approach that borrows information from each dataset in a meta-analysis in order to identify genes being differentially expressed consistently. We have shown that CDEP can gain higher statistical power than other existing approaches under a variety of settings considered in the simulation study, suggesting its robustness and

  5. Roger S. Mitchell lecture. Uses of expression microarrays in studies of pulmonary fibrosis, asthma, acute lung injury, and emphysema.

    Science.gov (United States)

    Sheppard, Dean

    2002-03-01

    Expression microarrays are a powerful tool that could provide new information about the molecular pathways regulating common lung diseases. To exemplify how this tool can be useful, selected examples of informative experiments are reviewed. In studies relevant to asthma, the cytokine interleukin-13 has been shown to produce many of the phenotypic features of this disease, but the cellular targets in the airways and the molecular pathways activated are largely unknown. We have used microarrays to begin to dissect the different transcriptional responses of primary lung cells to this cytokine. In experiments designed to identify global transcriptional programs responsible for regulating lung inflammation and pulmonary fibrosis, we performed microarray experiments on lung tissue from wild-type mice and mice lacking a member of the integrin family know to be involved in activation of latent transforming growth factor (TGF)-beta. In addition to identifying distinct cluster of genes involved in each of these processes, these studies led to the identification of novel pathways by which TGF-beta can regulate acute lung injury and emphysema. Together, these examples demonstrate how careful application and thorough analysis of expression microarrays can facilitate the discovery of novel molecular targets for intervening in common lung diseases.

  6. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  7. Ontology-Based Analysis of Microarray Data.

    Science.gov (United States)

    Giuseppe, Agapito; Milano, Marianna

    2016-01-01

    The importance of semantic-based methods and algorithms for the analysis and management of biological data is growing for two main reasons. From a biological side, knowledge contained in ontologies is more and more accurate and complete, from a computational side, recent algorithms are using in a valuable way such knowledge. Here we focus on semantic-based management and analysis of protein interaction networks referring to all the approaches of analysis of protein-protein interaction data that uses knowledge encoded into biological ontologies. Semantic approaches for studying high-throughput data have been largely used in the past to mine genomic and expression data. Recently, the emergence of network approaches for investigating molecular machineries has stimulated in a parallel way the introduction of semantic-based techniques for analysis and management of network data. The application of these computational approaches to the study of microarray data can broad the application scenario of them and simultaneously can help the understanding of disease development and progress.

  8. Tissue microarray profiling in human heart failure.

    Science.gov (United States)

    Lal, Sean; Nguyen, Lisa; Tezone, Rhenan; Ponten, Fredrik; Odeberg, Jacob; Li, Amy; Dos Remedios, Cristobal

    2016-09-01

    Tissue MicroArrays (TMAs) are a versatile tool for high-throughput protein screening, allowing qualitative analysis of a large number of samples on a single slide. We have developed a customizable TMA system that uniquely utilizes cryopreserved human cardiac samples from both heart failure and donor patients to produce formalin-fixed paraffin-embedded sections. Confirmatory upstream or downstream molecular studies can then be performed on the same (biobanked) cryopreserved tissue. In a pilot study, we applied our TMAs to screen for the expression of four-and-a-half LIM-domain 2 (FHL2), a member of the four-and-a-half LIM family. This protein has been implicated in the pathogenesis of heart failure in a variety of animal models. While FHL2 is abundant in the heart, not much is known about its expression in human heart failure. For this purpose, we generated an affinity-purified rabbit polyclonal anti-human FHL2 antibody. Our TMAs allowed high-throughput profiling of FHL2 protein using qualitative and semiquantitative immunohistochemistry that proved complementary to Western blot analysis. We demonstrated a significant relative reduction in FHL2 protein expression across different forms of human heart failure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. The use of microarray technology for cytogenetics.

    Science.gov (United States)

    Bejjani, Bassem A; Shaffer, Lisa G; Ballif, Blake C

    2010-01-01

    The use of microarray technology is revolutionizing the field of clinical cytogenetics. This new technology has transformed the cytogenetics laboratory by adapting techniques that have heretofore been the province of molecular geneticists. Intimate knowledge and comfortable familiarity with these techniques are now a must for the modern cytogeneticist, rather than a stimulating but discretionary intellectual exercise or an elective luxury. The cytogenetic laboratory of the future will likely have more scanners than microscopes, more software packages than darkrooms, and more technologists, supervisors, and directors with molecular training than ever before. This technical convergence between molecular diagnostics and clinical cytogenetics is exciting and has already resulted in many stimulating discoveries. However, the traditional skills of the cytogeneticist are needed now more than ever before. As our ability to inspect the genome increases, so does the variety of abnormalities that we uncover. Understanding the mechanisms of these aberrations to guide additional testing of the parents and genetic counseling of the patients and their families requires the expertise of individuals who are well-versed in meiotic mechanisms and chromosomal structures that may lead to these abnormalities. Cytogeneticists are uniquely positioned to understand these mechanisms and assist genetic counselors and clinicians in their daily interactions with patients and families.

  10. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  11. Antibody microarrays for native toxin detection.

    Science.gov (United States)

    Rucker, Victor C; Havenstrite, Karen L; Herr, Amy E

    2005-04-15

    We have developed antibody-based microarray techniques for the multiplexed detection of cholera toxin beta-subunit, diphtheria toxin, anthrax lethal factor and protective antigen, Staphylococcus aureus enterotoxin B, and tetanus toxin C fragment in spiked samples. Two detection schemes were investigated: (i) a direct assay in which fluorescently labeled toxins were captured directly by the antibody array and (ii) a competition assay that employed unlabeled toxins as reporters for the quantification of native toxin in solution. In the direct assay, fluorescence measured at each array element is correlated with labeled toxin concentration to yield baseline binding information (Langmuir isotherms and affinity constants). Extending from the direct assay, the competition assay yields information on the presence, identity, and concentration of toxins. A significant advantage of the competition assay over reported profiling assays is the minimal sample preparation required prior to analysis because the competition assay obviates the need to fluorescently label native proteins in the sample of interest. Sigmoidal calibration curves and detection limits were established for both assay formats. Although the sensitivity of the direct assay is superior to that of the competition assay, detection limits for unmodified toxins in the competition assay are comparable to values reported previously for sandwich-format immunoassays of antibodies arrayed on planar substrates. As a demonstration of the potential of the competition assay for unlabeled toxin detection, we conclude with a straightforward multiplexed assay for the differentiation and identification of both native S. aureus enterotoxin B and tetanus toxin C fragment in spiked dilute serum samples.

  12. 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.

  13. ADVANTAGES AND APPLICATIONS OF TISSUE MICROARRAY TECHNOLOGY ON CANCER RESEARCH

    Institute of Scientific and Technical Information of China (English)

    张喜平; 苏丹; 程琪辉

    2003-01-01

    S To provide evidences for exploiting tissue microarray (TMA) technology, we reviewed advantages and applications of TMA on tumor research. TMA has many advantages, including (1) section from TMA blocks can be utilized for the simultaneous analysis of up to 1,000 different tumors at DNA, RNA or protein level; (2) TMA is highly representative of their donor tissues; (3) TMA can improve conservation of tissue resources and experimental reagents, improve internal experimental control, and increase sample numbers per experiment, and can be used for large-scale, massively parallel in situ analysis; (4) TMA facilitates rapid translation of molecular discoveries to clinical applications. TMA has been applied to tumor research, such as glioma, breast tumor, lung cancer and so on. The development of novel biochip technologies has opened up new possibilities for the high-throughput molecular profiling of human tumors. Novel molecular markers emerging from high-throughput expression surveys could be analyzed on tumor TMA. It is anticipated that TMA, a new member of biochip, will soon become a widely used tool for all types of tissue-based research. TMA will lead to a significant acceleration of the transition of basic research findings into clinical applications.

  14. Application of Phenotype Microarray technology to soil microbiology

    Science.gov (United States)

    Mocali, Stefano

    2016-04-01

    It is well established that soil microorganisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Furthermore, addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. High-throughput culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. Thus, over the last years, Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are still missing. Here potential applications of phenotype arrays to soil microorganisms, use of the plates in stress response studies and for assessment of phenotype of environmental communities are described. Considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting are also discussed. In particular, here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns.

  15. Microarray analysis of human epithelial cell responses to bacterial interaction.

    Science.gov (United States)

    Mans, Jeffrey J; Lamont, Richard J; Handfield, Martin

    2006-09-01

    Host-pathogen interactions are inherently complex and dynamic. The recent use of human microarrays has been invaluable to monitor the effects of various bacterial and viral pathogens upon host cell gene expression programs. This methodology has allowed the host response transcriptome of several cell lines to be studied on a global scale. To this point, the great majority of reports have focused on the response of immune cells, including macrophages and dendritic cells. These studies revealed that the immune response to microbial pathogens is tailored to different microbial challenges. Conversely, the paradigm for epithelial cells has--until recently--held that the epithelium mostly served as a relatively passive physical barrier to infection. It is now generally accepted that the epithelial barrier contributes more actively to signaling events in the immune response. In light of this shift, this review will compare transcriptional profiling data from studies that involved host-pathogen interactions occurring with epithelial cells. Experiments that defined both a common core response, as well as pathogen-specific host responses will be discussed. This review will also summarize the contributions that transcriptional profiling analysis has made to our understanding of bacterial physio-pathogensis of infection. This will include a discussion of how host transcriptional responses can be used to infer the function of virulence determinants from bacterial pathogens interacting with epithelial mucosa. In particular, we will expand upon the lessons that have been learned from gastro-intestinal and oral pathogens, as well as from members of the commensal flora.

  16. On the Statics for Micro-Array Data Analysis

    Science.gov (United States)

    Urushibara, Tomoko; Akasaka, Shizu; Ito, Makiko; Suzuki, Tomonori; Miyazaki, Satoru

    2010-01-01

    Recently after human genome sequence has been determined almost perfectly, more and more researchers have been studying genes in detail. Therefore, we are sure that accumulated gene information for human will be getting more important in the near future to develop customized medicine and to make gene interactions clear. Among plenty of information, micro array might be one of the most important analysis method for genes because it is the technique that can get big amount of the gene expressions data from one time experiment and also can be used for DNA isolation. To get the novel knowledge from micro array data, we need to enrich statistical tools for its data analysis. So far, many mathematical theories and definition have been proposing. However, many of those proposals are tested with strict conditions or customized to data for specific species. In this paper, we reviewed existing typical statistical methods for micro array analysis and discussed the repeatability of the analysis, construction the guideline with more general procedure. First we analyzed the micro array data for TG rats, with statistical methods of family-wise error rate (FWER) control approach and False Discovery Rate (FDR) control approach. As existing report, no significantly different gene could be detected with FWER control approach. On the other hand, we could find several genes significantly with FDR control approach even q=0.5. To find out the reliability of FDR control approach with micro array conditions, we have analyzed 2 more pieces of data from Gene Expression Omnibus (GEO) public database on the web site with SAM in addition to FWER and FDR control approaches. We could find a certain number of significantly different genes with BH method and SAM in the case of q=0.05. However, we have to note that the number and kinds of detected genes are different when we compare our result with the one from the published paper. Even if the same approach is used to analyze the same micro array

  17. Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

    Science.gov (United States)

    Liu, Robin H.; Lodes, Mike; Fuji, H. Sho; Danley, David; McShea, Andrew

    Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed

  18. Cell-Based Microarrays for In Vitro Toxicology.

    Science.gov (United States)

    Wegener, Joachim

    2015-01-01

    DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by which molecular recognition assays can be performed and analyzed. Cell microarrays (CMAs) make use of similar construction principles. They are applied to profile a given cell population with respect to the expression of specific molecular markers and also to measure functional cell responses to drugs and chemicals. This review focuses on the use of cell-based microarrays for assessing the cytotoxicity of drugs, toxins, or chemicals in general. It also summarizes CMA construction principles with respect to the cell types that are used for such microarrays, the readout parameters to assess toxicity, and the various formats that have been established and applied. The review ends with a critical comparison of CMAs and well-established microtiter plate (MTP) approaches.

  19. Glycan microarray analysis of Candida glabrata adhesin ligand specificity

    National Research Council Canada - National Science Library

    Zupancic, Margaret L; Frieman, Matthew; Smith, David; Alvarez, Richard A; Cummings, Richard D; Cormack, Brendan P

    2008-01-01

    ...) family responsible for mediating adherence to host cells. To better understand the mechanism by which the Epa proteins contribute to pathogenesis, we have used glycan microarray analysis to characterize their carbohydrate...

  20. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    黄承志; 李原芳; 黄新华; 范美坤

    2000-01-01

    The microarray of DNA probes with 5’ -NH2 and 5’ -Tex/3’ -NH2 modified terminus on 10 um carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) is characterized in the preseni paper. it was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentra-tion of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  1. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The microarray of DNA probes with 5′-NH2 and 5′-Tex/3′-NH2 modified terminus on 10 m m carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)- carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  2. Cell-Based Microarrays for In Vitro Toxicology

    Science.gov (United States)

    Wegener, Joachim

    2015-07-01

    DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by which molecular recognition assays can be performed and analyzed. Cell microarrays (CMAs) make use of similar construction principles. They are applied to profile a given cell population with respect to the expression of specific molecular markers and also to measure functional cell responses to drugs and chemicals. This review focuses on the use of cell-based microarrays for assessing the cytotoxicity of drugs, toxins, or chemicals in general. It also summarizes CMA construction principles with respect to the cell types that are used for such microarrays, the readout parameters to assess toxicity, and the various formats that have been established and applied. The review ends with a critical comparison of CMAs and well-established microtiter plate (MTP) approaches.

  3. Development of a spot reliability evaluation score for DNA microarrays.

    Science.gov (United States)

    Matsumura, Yonehiro; Shimokawa, Kazuro; Hayashizaki, Yoshihide; Ikeo, Kazuho; Tateno, Yoshio; Kawai, Jun

    2005-05-09

    We developed a reliability index named SRED (Spot Reliability Evaluation Score for DNA microarrays) that represents the probability that the calibrated gene expression level from a DNA microarray would be less than a factor of 2 different from that of quantitative real-time polymerase chain reaction assays whose dynamic quantification range is treated statistically to be similar to that of the DNA microarray. To define the SRED score, two parameters, the reproducibility of measurement value and the relative expression value were selected from nine candidate parameters. The SRED score supplies the probability that the expression level in each spot of a microarray is less than a certain-fold different compared to other expression profiling data, such as QRT-PCR. This score was applied to approximately 1,500,000 points of the expression profile in the RIKEN Expression Array Database.

  4. Rapid Diagnosis of Bacterial Meningitis Using a Microarray

    Directory of Open Access Journals (Sweden)

    Ren-Jy Ben

    2008-06-01

    Conclusion: The microarray method provides a more accurate and rapid diagnostic tool for bacterial meningitis compared to traditional culture methods. Clinical application of this new technique may reduce the potential risk of delay in treatment.

  5. 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...

  6. Gene expression profiling of mouse embryos with microarrays

    OpenAIRE

    Sharov, Alexei A; Piao, Yulan; Minoru S.H. Ko

    2010-01-01

    Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and becomes an essential tool in biological and medical sciences. Typical questions that can be addressed by microarray analysis in developmental biology include: (1) to find a set of genes expressed in a specific cell type; (2) to identify genes expressed commonly in multiple cell types; (3) to follow the time-course changes of gene expression patterns; (4) to demonstrate cell’s identity by showing s...

  7. Identification of differentially expressed genes in mouse kidney after irradiation using microarray analysis.

    Science.gov (United States)

    Kruse, Jacqueline J C M; te Poele, Johannes A M; Velds, Arno; Kerkhoven, Ron M; Boersma, Liesbeth J; Russell, Nicola S; Stewart, Fiona A

    2004-01-01

    Irradiation of the kidney induces dose-dependent, progressive renal functional impairment, which is partly mediated by vascular damage. The molecular mechanisms underlying the development of radiation-induced nephropathy are unclear. Given the complexity of radiation-induced responses, microarrays may offer new opportunities to identify a wider range of genes involved in the development of radiation injury. The aim of the present study was to determine whether microarrays are a useful tool for identifying time-related changes in gene expression and potential mechanisms of radiation-induced nephropathy. Microarray experiments were performed using amplified RNA from irradiated mouse kidneys (1 x 16 Gy) and from sham-irradiated control tissue at different intervals (1-30 weeks) after irradiation. After normalization procedures (using information from straight-color, color-reverse and self-self experiments), the differentially expressed genes were identified. Control and repeat experiments were done to confirm that the observations were not artifacts of the array procedure (RNA amplification, probe synthesis, hybridizations and data analysis). To provide independent confirmation of microarray data, semi-quantitative PCR was performed on a selection of genes. At 1 week after irradiation (before the onset of vascular and functional damage), 16 genes were significantly up-regulated and 9 genes were down-regulated. During the period of developing nephropathy (10 to 20 weeks), 31 and 42 genes were up-regulated and 9 and 4 genes were down-regulated. At the later time of 30 weeks, the vast majority of differentially expressed genes (191 out of 203) were down-regulated. Potential genes of interest included TSA-1 (also known as Ly6e) and Jagged 1 (Jag1). Increased expression of TSA-1, a member of the Ly-6 family, has previously been reported in response to proteinuria. Jagged 1, a ligand for the Notch receptor, is known to play a role in angiogenesis, and is particularly

  8. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  9. 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.

  10. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

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    Andrea Flannery

    2015-12-01

    Full Text Available Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i conventional carbohydrate or glycan microarrays; (ii whole mucin microarrays; and (iii microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.

  11. DNA Microarray Characterization of Pathogens Associated with Sexually Transmitted Diseases.

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    Cao, Boyang; Wang, Suwei; Tian, Zhenyang; Hu, Pinliang; Feng, Lu; Wang, Lei

    2015-01-01

    This study established a multiplex PCR-based microarray to detect simultaneously a diverse panel of 17 sexually transmitted diseases (STDs)-associated pathogens including Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma, Herpes simplex virus (HSV) types 1 and 2, and Human papillomavirus (HPV) types 6, 11, 16, 18, 31, 33, 35, 39, 54 and 58. The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. A total of 34 probes were selected for the microarray including 31 specific probes, one as positive control, one as negative control, and one as positional control probe for printing reference. The microarray is specific as the commensal and pathogenic microbes (and closely related organisms) in the genitourinary tract did not cross-react with the microarray probes. The microarray is 10 times more sensitive than that of the multiplex PCR. Among the 158 suspected HPV specimens examined, the microarray showed that 49 samples contained HPV, 21 samples contained Ureaplasma, 15 contained M. hominis, four contained C. trachomatis, and one contained N. gonorrhoeae. This work reports the development of the first high through-put detection system that identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool for STDs.

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

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    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.

  13. Design and analysis of mismatch probes for long oligonucleotide microarrays

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    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  14. Pipeline for macro- and microarray analyses

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    R. Vicentini

    2007-05-01

    Full Text Available The pipeline for macro- and microarray analyses (PMmA is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps. It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

  15. Photopatterning of Hydrogel Microarrays in Closed Microchips.

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    Gumuscu, Burcu; Bomer, Johan G; van den Berg, Albert; Eijkel, Jan C T

    2015-12-14

    To date, optical lithography has been extensively used for in situ patterning of hydrogel structures in a scale range from hundreds of microns to a few millimeters. The two main limitations which prevent smaller feature sizes of hydrogel structures are (1) the upper glass layer of a microchip maintains a large spacing (typically 525 μm) between the photomask and hydrogel precursor, leading to diffraction of UV light at the edges of mask patterns, (2) diffusion of free radicals and monomers results in irregular polymerization near the illumination interface. In this work, we present a simple approach to enable the use of optical lithography to fabricate hydrogel arrays with a minimum feature size of 4 μm inside closed microchips. To achieve this, we combined two different techniques. First, the upper glass layer of the microchip was thinned by mechanical polishing to reduce the spacing between the photomask and hydrogel precursor, and thereby the diffraction of UV light at the edges of mask patterns. The polishing process reduces the upper layer thickness from ∼525 to ∼100 μm, and the mean surface roughness from 20 to 3 nm. Second, we developed an intermittent illumination technique consisting of short illumination periods followed by relatively longer dark periods, which decrease the diffusion of monomers. Combination of these two methods allows for fabrication of 0.4 × 10(6) sub-10 μm sized hydrogel patterns over large areas (cm(2)) with high reproducibility (∼98.5% patterning success). The patterning method is tested with two different types of photopolymerizing hydrogels: polyacrylamide and polyethylene glycol diacrylate. This method enables in situ fabrication of well-defined hydrogel patterns and presents a simple approach to fabricate 3-D hydrogel matrices for biomolecule separation, biosensing, tissue engineering, and immobilized protein microarray applications.

  16. The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

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    Edgerton Mary E

    2003-05-01

    Full Text Available Abstract Background Tissue Microarrays (TMAs allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1 Header, containing the specification Dublin Core identifiers, 2 Block, describing the paraffin-embedded array of tissues, 3Slide, describing the glass slides produced from the Block, and 4 Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange

  17. An antibody microarray analysis of serum cytokines in neurodegenerative Parkinsonian syndromes

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    Mahlknecht Philipp

    2012-11-01

    Full Text Available Abstract Background Microarray technology may offer a new opportunity to gain insight into disease-specific global protein expression profiles. The present study was performed to apply a serum antibody microarray to screen for differentially regulated cytokines in Parkinson's disease (PD, multiple system atrophy (MSA, progressive supranuclear palsy (PSP and corticobasal syndrome (CBS. Results Serum samples were obtained from patients with clinical diagnoses of PD (n = 117, MSA (n = 31 and PSP/CBS (n = 38 and 99 controls. Cytokine profiles of sera from patients and controls were analyzed with a semiquantitative human antibody array for 174 cytokines and the expression of 12 cytokines was found to be significantly altered. In a next step, results from the microarray experiment were individually validated by different immunoassays. Immunoassay validation confirmed a significant increase of median PDGF-BB levels in patients with PSP/CBS, MSA and PD and a decrease of median prolactin levels in PD. However, neither PDGF-BB nor prolactin were specific biomarkers to discriminate PSP/CBS, MSA, PD and controls. Conclusions In our unbiased cytokine array based screening approach and validation by a different immunoassay only two of 174 cytokines were significantly altered between patients and controls.

  18. Clinical Presentation and Microarray Analysis of Peruvian Children with Atypical Development and/or Aberrant Behavior

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    Merlin G. Butler

    2014-01-01

    Full Text Available We report our experience with high resolution microarray analysis in infants and young children with developmental disability and/or aberrant behavior enrolled at the Centro Ann Sullivan del Peru in Lima, Peru, a low income country. Buccal cells were collected with cotton swabs from 233 participants for later DNA isolation and identification of copy number variation (deletions/duplications and regions of homozygosity (ROH for estimating consanguinity status in 15 infants and young children (12 males, 3 females; mean age ± SD = 28.1 m ±   7.9 m; age range 14 m–41 m randomly selected for microarray analysis. An adequate DNA yield was found in about one-half of the enrolled participants. Ten participants showed deletions or duplications containing candidate genes reported to impact behavior or cognitive development. Five children had ROHs which could have harbored recessive gene alleles contributing to their clinical presentation. The coefficient of inbreeding was calculated and three participants showed first-second cousin relationships, indicating consanguinity. Our preliminary study showed that DNA isolated from buccal cells using cotton swabs was suboptimal, but yet in a subset of participants the yield was adequate for high resolution microarray analysis and several genes were found that impact development and behavior and ROHs identified to determine consanguinity status.

  19. Identification of Escherichia coli O157 by using a novel colorimetric detection method with DNA microarrays.

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    Quiñones, Beatriz; Swimley, Michelle S; Taylor, Amber W; Dawson, Erica D

    2011-06-01

    Shiga toxin-producing Escherichia coli O157 is a leading cause of foodborne illness worldwide. To evaluate better methods to rapidly detect and genotype E. coli O157 strains, the present study evaluated the use of ampliPHOX, a novel colorimetric detection method based on photopolymerization, for pathogen identification with DNA microarrays. A low-density DNA oligonucleotide microarray was designed to target stx1 and stx2 genes encoding Shiga toxin production, the eae gene coding for adherence membrane protein, and the per gene encoding the O157-antigen perosamine synthetase. Results from the validation experiments demonstrated that the use of ampliPHOX allowed the accurate genotyping of the tested E. coli strains, and positive hybridization signals were observed for only probes targeting virulence genes present in the reference strains. Quantification showed that the average signal-to-noise ratio values ranged from 47.73 ± 7.12 to 76.71 ± 8.33, whereas average signal-to-noise ratio values below 2.5 were determined for probes where no polymer was formed due to lack of specific hybridization. Sensitivity tests demonstrated that the sensitivity threshold for E. coli O157 detection was 100-1000 CFU/mL. Thus, the use of DNA microarrays in combination with photopolymerization allowed the rapid and accurate genotyping of E. coli O157 strains.

  20. A study of inter-lab and inter-platform agreement of DNA microarray data

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    Wilson Carole

    2005-05-01

    Full Text Available Abstract As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degree of agreement we can expect from different labs and different platforms. To address this question, we conducted a study of inter-lab and inter-platform agreement of microarray data across three platforms and three labs. The statistical measures of consistency and agreement used in this paper are the Pearson correlation, intraclass correlation, kappa coefficients, and a measure of intra-transcript correlation. The three platforms used in the present paper were Affymetrix GeneChip, custom cDNA arrays, and custom oligo arrays. Using the within-platform variability as a benchmark, we found that these technology platforms exhibited an acceptable level of agreement, but the agreement between two technologies within the same lab was greater than that between two labs using the same technology. The consistency of replicates in each experiment varies from lab to lab. When there is high consistency among replicates, different technologies show good agreement within and across labs using the same RNA samples. On the other hand, the lab effect, especially when confounded with the RNA sample effect, plays a bigger role than the platform effect on data agreement.